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 composition-based statistics:
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



>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 =  431 bits (1109), Expect = e-119,   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   MIERNWQELIRPEKPQV-EGGSDPQHKARLIAEPLERGFGVTLGNALRRVLLSSLQGAAV 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|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 =  431 bits (1109), Expect = e-119,   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|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 =  430 bits (1107), Expect = e-118,   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|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 =  429 bits (1102), Expect = e-118,   Method: Composition-based stats.
 Identities = 225/339 (66%), Positives = 278/339 (82%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++I           ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFIT--NGSRTHATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 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|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 =  429 bits (1102), Expect = e-118,   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   MIQKNWQELIKPNKVDFITHGSRT--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+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 =  428 bits (1101), Expect = e-118,   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   MIQKNWQELIKPNKVDFITHGSRT--HATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 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|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 =  428 bits (1101), Expect = e-118,   Method: Composition-based stats.
 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|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 =  428 bits (1100), Expect = e-118,   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   MIQKNWQELIKPNKVDFITHGSRT--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+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|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 =  428 bits (1100), Expect = e-118,   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   MIQKNWQELIKPNKVDFITHGSRT--HATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 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|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 =  428 bits (1100), Expect = e-118,   Method: Composition-based stats.
 Identities = 210/339 (61%), Positives = 268/339 (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
              D     LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 240 TA-DEAKPELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++P+WPPE+IE+LAKK+ED+
Sbjct: 299 KSLNEIKEVLAGMGLHLGMDVPNWPPENIEDLAKKFEDQ 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 =  427 bits (1099), Expect = e-118,   Method: Composition-based stats.
 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|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 =  427 bits (1098), Expect = e-117,   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   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 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 =  427 bits (1097), Expect = e-117,   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   MIQKNWQELIKPNKVDFITHGSRT--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+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|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 =  426 bits (1096), Expect = e-117,   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   MIQKNWQELIKPNKVDFITHGSRT--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+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|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 =  426 bits (1096), Expect = e-117,   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   MIQKNWQELIKPNKVDFITHGSRT--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+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|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 =  425 bits (1093), Expect = e-117,   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   MIQKNWQELIKPNKVDFITHGSRT--HATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 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|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 =  424 bits (1091), Expect = e-117,   Method: Composition-based stats.
 Identities = 233/339 (68%), Positives = 280/339 (82%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+         +  ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVEF---SSSGRTKATLVAEPLERGFGLTLGNALRRVLLSSLRGAAV 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|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 =  424 bits (1090), Expect = e-116,   Method: Composition-based stats.
 Identities = 212/338 (62%), Positives = 270/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN ++    G + +    ++AEPL RGF  TLGN+LRRVL+SSL+GAA+
Sbjct: 28  VIQKNWQELIKPNKLQV-TAGDDPKRVATVVAEPLERGFGTTLGNSLRRVLLSSLQGAAV 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|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 =  424 bits (1090), Expect = e-116,   Method: Composition-based stats.
 Identities = 238/339 (70%), Positives = 282/339 (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 TEE-EAVTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 297 KSLNEIKEVLASMGLHLGMEVPAWPPENIEDLAKRYEDQ 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 =  424 bits (1090), Expect = e-116,   Method: Composition-based stats.
 Identities = 233/339 (68%), Positives = 282/339 (83%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+         +  ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVEF---ASSGRTKATLVAEPLERGFGLTLGNALRRVLLSSLRGAAV 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 =  424 bits (1089), Expect = e-116,   Method: Composition-based stats.
 Identities = 232/339 (68%), Positives = 282/339 (83%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +++         +  ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVDFT---SSGRTKATLVAEPLERGFGLTLGNALRRVLLSSLRGAAV 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 AEE-EAVTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM +P WPPE+IE+LAK+YED+
Sbjct: 297 KSLNEIKEVLASMGLHLGMEVPSWPPENIEDLAKRYEDQ 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 =  424 bits (1089), Expect = e-116,   Method: Composition-based stats.
 Identities = 236/339 (69%), Positives = 283/339 (83%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKP+ IE+     +   +T ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPSKIEFT---SKGRTQTNLVAEPLERGFGLTLGNALRRVLLSSLRGAAV 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|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 =  423 bits (1088), Expect = e-116,   Method: Composition-based stats.
 Identities = 237/339 (69%), Positives = 283/339 (83%), Gaps = 4/339 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+         +  ++AEPL RGF  TLGNALRRVL+SSLRGAA+
Sbjct: 1   MIQKNWQELIKPNKVEFT---SSGRTKATLVAEPLERGFGLTLGNALRRVLLSSLRGAAV 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|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 =  423 bits (1087), Expect = e-116,   Method: Composition-based stats.
 Identities = 234/339 (69%), Positives = 281/339 (82%), 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 AEE-ESVTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

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


>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 =  423 bits (1087), Expect = e-116,   Method: Composition-based stats.
 Identities = 208/338 (61%), Positives = 266/338 (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 VSEEKHE-EVPFNKNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKTEAEMLRTPNFGR 298

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


>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 =  422 bits (1086), Expect = e-116,   Method: Composition-based stats.
 Identities = 211/338 (62%), Positives = 269/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN ++    G + +    ++AEPL RGF  TLGN+LRRVL+SSL+GAA+
Sbjct: 2   VIQKNWQELIKPNKLQV-SAGDDPKRVATVVAEPLERGFGTTLGNSLRRVLLSSLQGAAV 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|23010819|ref|ZP_00051380.1| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Magnetospirillum magnetotacticum MS-1]
          Length = 339

 Score =  422 bits (1085), Expect = e-116,   Method: Composition-based stats.
 Identities = 212/338 (62%), Positives = 270/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN ++    G + +    ++AEPL RGF  TLGN+LRRVL+SSL+GAA+
Sbjct: 2   VIQKNWQELIKPNKLQV-TAGDDPKRVATVVAEPLERGFGTTLGNSLRRVLLSSLQGAAV 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|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 =  422 bits (1084), Expect = e-116,   Method: Composition-based stats.
 Identities = 207/339 (61%), Positives = 265/339 (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 VE-GEAKPELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++P+WPPE+IEELAKK+ED+
Sbjct: 299 KSLNEIKEVLAGMGLHLGMDVPNWPPENIEELAKKFEDQ 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 =  421 bits (1083), Expect = e-116,   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   VIQKNWQELIKPNKLEVVP-GHDPKRVATVVAEPLERGFGTTLGNALRRVLLSSLQGAAV 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|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 =  421 bits (1083), Expect = e-116,   Method: Composition-based stats.
 Identities = 211/338 (62%), Positives = 272/338 (80%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN ++    G + +    ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 2   VIQKNWQELIKPNKLQV-TTGDDPKRVATVVAEPLERGFGTTLGNALRRVLLSSLQGAAV 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|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 =  421 bits (1082), Expect = e-116,   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  IQKNWQELIKPTKLDV-KPGEDPRFVATVVAEPLERGYGLTLGNALRRILLSSLQGAAVT 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|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 =  421 bits (1082), Expect = e-115,   Method: Composition-based stats.
 Identities = 237/339 (69%), Positives = 280/339 (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 VA-AEAVTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

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


>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 =  420 bits (1081), Expect = e-115,   Method: Composition-based stats.
 Identities = 226/339 (66%), Positives = 279/339 (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  +  V  L FNP+LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 238 V-HEETVAELAFNPSLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

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


>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 =  420 bits (1080), Expect = e-115,   Method: Composition-based stats.
 Identities = 217/339 (64%), Positives = 272/339 (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
              + +   L FN ALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE++MLR  NFGR
Sbjct: 240 -HVEESRPELEFNAALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P+WPPE+IEELAK+YED+
Sbjct: 299 KSLNEIKEVLAQMGLHLGMEVPNWPPENIEELAKRYEDQ 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 =  420 bits (1080), Expect = e-115,   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 DQGGADEELL-FNAALLRKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL T+GL LGM++PDWPP++IEELA+K+ED+
Sbjct: 299 KSLNEIKEVLATLGLHLGMDVPDWPPDNIEELARKFEDQ 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 =  420 bits (1080), Expect = e-115,   Method: Composition-based stats.
 Identities = 212/338 (62%), Positives = 270/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN ++    G + +    ++AEPL RGF  TLGN+LRRVL+SSL+GAA+
Sbjct: 2   VIQKNWQELIKPNKLQV-TAGDDPKRVATVVAEPLERGFGTTLGNSLRRVLLSSLQGAAV 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|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 =  420 bits (1080), Expect = e-115,   Method: Composition-based stats.
 Identities = 212/337 (62%), Positives = 269/337 (79%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELIKP+ +E    G +     + +AEPL RGF  TLGNALRR+L+SSL+G+AIT
Sbjct: 3   IQKNWQELIKPSKLEV-TAGDDPRRVAVAVAEPLERGFGVTLGNALRRILLSSLQGSAIT 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|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 =  420 bits (1079), Expect = e-115,   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|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 =  420 bits (1079), Expect = e-115,   Method: Composition-based stats.
 Identities = 208/339 (61%), Positives = 262/339 (77%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI++NWQ+LI+P   +    GQ+ + +  ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIERNWQQLIRPEKPQIES-GQDSQRKMRLVAEPLERGFGVTLGNALRRVLLSSLQGAAV 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
           +  +     LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE++MLR  NFGR
Sbjct: 240 I-VEEGKPELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +MGL LGM++P+WPPE++E+LAKK+ED+
Sbjct: 299 KSLNEIKEVLQSMGLSLGMDVPNWPPENVEDLAKKFEDQ 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 =  420 bits (1079), Expect = e-115,   Method: Composition-based stats.
 Identities = 219/338 (64%), Positives = 277/338 (81%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKP  +E   +G + +    ++AEPL RGF  TLGNALRR+L+SSL+GAA+
Sbjct: 1   MIQKNWQELIKPEKLEV-AVGSDPKRLATVVAEPLERGFGQTLGNALRRILLSSLQGAAV 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 TE-SPAMQELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

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


>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 =  420 bits (1079), Expect = e-115,   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|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 =  420 bits (1079), Expect = e-115,   Method: Composition-based stats.
 Identities = 236/339 (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 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 VA-AEAVTELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 296

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


>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 =  420 bits (1079), Expect = e-115,   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|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 =  420 bits (1079), Expect = e-115,   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   VIQKNWQELIKPNKLQV-TAGDDPKRVATVVAEPLERGFGTTLGNSLRRVLLSSLQGAAV 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|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 =  419 bits (1078), Expect = e-115,   Method: Composition-based stats.
 Identities = 207/338 (61%), Positives = 266/338 (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 VEE-EKKDELPFNKNLLRKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM + +WPPE+IEELAKK E+
Sbjct: 299 KSLNEIKEVLAQMGLHLGMEIANWPPENIEELAKKLEE 336


>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 =  419 bits (1078), Expect = e-115,   Method: Composition-based stats.
 Identities = 213/338 (63%), Positives = 272/338 (80%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKPN +E    G + +    ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 2   VIQKNWQELIKPNKLEV-APGHDPKRIATVVAEPLERGFGTTLGNALRRVLLSSLQGAAV 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|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 =  419 bits (1077), Expect = e-115,   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   VLQKNWQSLIKPEKLEV-EPGPVASRIATVVAEPLERGFGMTLGNALRRILLSSLQGAAV 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|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 =  418 bits (1076), Expect = e-115,   Method: Composition-based stats.
 Identities = 216/339 (63%), Positives = 272/339 (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
              + +   L FN ALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TE++MLR  NFGR
Sbjct: 259 -HVEESRPELEFNAALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 317

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


>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 =  418 bits (1076), Expect = e-115,   Method: Composition-based stats.
 Identities = 196/338 (57%), Positives = 258/338 (76%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M+++NW+ LI+P  ++    G +     +++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MLERNWRSLIRPEKLDV-EPGADPSRVAVVVAEPLERGFGMTLGNALRRVLLSSLQGAAV 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+ E
Sbjct: 180 RRVAYQVQPTRVGQRTDYDKLVLTVETDGTVAPEDAVALAARILQDQLQLFINFDEPR-E 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            K +     LPFN  LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q+TE +MLR  NFGR
Sbjct: 239 RKVEEVQDDLPFNRNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKTEQEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL +MGL LGM +P WPPE+IE+LAKK E+
Sbjct: 299 KSLNEIKEVLASMGLSLGMTVPGWPPENIEDLAKKIEE 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 =  418 bits (1076), Expect = e-115,   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|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 =  418 bits (1075), Expect = e-115,   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   IQKNWQELIKPTKLEV-KPGDDPRFLATVVAEPLERGYGLTLGNALRRILLSSLQGAAVT 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|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 =  418 bits (1074), Expect = e-115,   Method: Composition-based stats.
 Identities = 215/337 (63%), Positives = 269/337 (79%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELIKPN +E    G +       +AEPL RGF  TLGNALRR+L+SSL+GAAIT
Sbjct: 3   IQKNWQELIKPNKLEV-TAGDDPRRVATAVAEPLERGFGVTLGNALRRILLSSLQGAAIT 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|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 =  417 bits (1073), Expect = e-115,   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|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 =  417 bits (1073), Expect = e-114,   Method: Composition-based stats.
 Identities = 205/338 (60%), 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   VLQKNWQSLIKPEKLEV-EPGAEPSRTATVVAEPLERGFGMTLGNAIRRVLLSSLQGAAV 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 RRVSYKVEQTRVGQVTDYDRLLLTVETNGAVTPEDSVALAARILQDQLQLFINFDEPR-A 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|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 =  417 bits (1073), Expect = e-114,   Method: Composition-based stats.
 Identities = 202/338 (59%), 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   VLQKNWQSLIKPEKLEV-EPGGEPLRTATVVAEPLERGFGMTLGNAIRRVLLSSLQGAAV 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|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 =  417 bits (1073), Expect = e-114,   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   VIQRNWQSLIKPEKLDV-EPGNEPSRIATIVAEPLERGFGMTLGNAIRRILLSSLQGAAV 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|144900908|emb|CAM77772.1| DNA-directed RNA polymerase alpha chain (RNAP alpha subunit)
           [Magnetospirillum gryphiswaldense MSR-1]
          Length = 338

 Score =  417 bits (1072), Expect = e-114,   Method: Composition-based stats.
 Identities = 204/338 (60%), Positives = 263/338 (77%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKP+ ++    G +      +IAEPL RGF  TLGN+LRR+L+SSL+GAA+
Sbjct: 1   MIQKNWQELIKPSKLQV-EPGADAARVATVIAEPLERGFGMTLGNSLRRILLSSLQGAAV 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 VEE-EKKDELPFNKNLLRKVDELELSVRSANCLKNDNIIYIGDLVQKTEAEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL  MGL LGM +P+WPPE+IE+LAKK E+
Sbjct: 299 KSLNEIKEVLSHMGLHLGMEIPNWPPENIEDLAKKLEE 336


>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 =  417 bits (1072), Expect = e-114,   Method: Composition-based stats.
 Identities = 216/337 (64%), Positives = 272/337 (80%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++    G +      ++AEPL RGF  TLGNALRRVL+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLQV-TPGSDSGRFATLVAEPLERGFGQTLGNALRRVLLSSLQGAAVQ 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|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 =  417 bits (1072), Expect = e-114,   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   MIHKNWAELIKPTQLDV-KPGNDPLRQATVVAEPLERGFGLTLGNALRRVLLSSLQGAAI 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|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 =  417 bits (1072), Expect = e-114,   Method: Composition-based stats.
 Identities = 205/339 (60%), Positives = 257/339 (75%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI++NWQ+LI+P   +    G +   +  ++AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIERNWQQLIRPEKPQV-EAGTDASRKMRLVAEPLERGFGVTLGNALRRVLLSSLQGAAV 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  +     LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLI +TE++MLR  NFGR
Sbjct: 240 V-VEEGKPELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLILKTESEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL +M L LGM++P+WPPE++E+LAKK+ED+
Sbjct: 299 KSLNEIKEVLASMNLSLGMDIPNWPPENVEDLAKKFEDQ 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 =  417 bits (1071), Expect = e-114,   Method: Composition-based stats.
 Identities = 210/338 (62%), Positives = 269/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKP  ++    G + +    +IAEPL RGF  TLGNALRR+L+SSL+GAA+
Sbjct: 1   MIQKNWQELIKPEKLQV-NPGHDPKRFATVIAEPLERGFGMTLGNALRRILLSSLQGAAV 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
            +    +++LPF+PALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++E +MLR  NFGR
Sbjct: 240 SET-TAIQTLPFSPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSETEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL ++GL LGM +P WPPE+IEELAK++E+
Sbjct: 299 KSLNEIKEVLASLGLHLGMEVPGWPPENIEELAKRFEE 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 =  417 bits (1071), Expect = e-114,   Method: Composition-based stats.
 Identities = 203/338 (60%), 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   VLQKNWQSLIKPEKLEV-EPGAEPSRIATVVAEPLERGFGMTLGNAIRRVLLSSLQGAAV 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 RRVSYKVEQTRVGQVTDYDRLLLTVETNGAVTPEDAVALAARILQDQLQLFINFDEPR-T 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|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 =  416 bits (1070), Expect = e-114,   Method: Composition-based stats.
 Identities = 209/339 (61%), Positives = 265/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E    G +      ++AEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLEV-RPGADPSRVATVVAEPLERGFGLTLGNALRRVLLSSLQGAAI 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|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 =  416 bits (1069), Expect = e-114,   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  TLGNALRR+L+SSL+GAA+ 
Sbjct: 7   IQKNWQELIRPNKLQV-TPGSDPARFATIVAEPLERGFGQTLGNALRRILLSSLQGAAVQ 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 =  416 bits (1069), Expect = e-114,   Method: Composition-based stats.
 Identities = 219/337 (64%), Positives = 272/337 (80%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++    G +      ++AEPL RGF  TLGNALRRVL+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLQV-TAGSDATRFATLVAEPLERGFGQTLGNALRRVLLSSLQGAAVQ 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|163796895|ref|ZP_02190852.1| lipoyltransferase [alpha proteobacterium BAL199]
 gi|159177884|gb|EDP62433.1| lipoyltransferase [alpha proteobacterium BAL199]
          Length = 338

 Score =  416 bits (1069), Expect = e-114,   Method: Composition-based stats.
 Identities = 206/338 (60%), Positives = 263/338 (77%), 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 AE-AEEAHDLPFNKNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKTEPEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK VL +MGL LGM + +WPPE+IEELAK+ E+
Sbjct: 299 KSLNEIKEVLASMGLSLGMEITNWPPENIEELAKRLEE 336


>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 =  416 bits (1069), Expect = e-114,   Method: Composition-based stats.
 Identities = 218/337 (64%), Positives = 274/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++    G +      ++AEPL RGF  TLGNALRRVL+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLQV-SPGSDATRFATLVAEPLERGFGQTLGNALRRVLLSSLQGAAVQ 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|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 =  415 bits (1068), Expect = e-114,   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  MIHKNWAELIKPTQLD-GKPGNDPARQATIVAEPLERGFGLTLGNALRRVLMSSLQGAAI 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|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 =  415 bits (1067), Expect = e-114,   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|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 =  415 bits (1067), Expect = e-114,   Method: Composition-based stats.
 Identities = 213/337 (63%), Positives = 271/337 (80%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++    G +      ++AEPL RGF  TLGNALRRVL+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLQV-TPGSDPSRFATLVAEPLERGFGQTLGNALRRVLLSSLQGAAVQ 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|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 =  415 bits (1066), Expect = e-114,   Method: Composition-based stats.
 Identities = 217/337 (64%), Positives = 273/337 (81%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++    G +      ++AEPL RGF  TLGNALRRVL+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLQV-TAGSDATRFATLVAEPLERGFGQTLGNALRRVLLSSLQGAAVQ 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|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 =  414 bits (1065), Expect = e-114,   Method: Composition-based stats.
 Identities = 212/338 (62%), Positives = 269/338 (79%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKP+ ++    G + +    +IAEPL RGF  TLGNALRR+L+SSL+GAAI
Sbjct: 1   MIQKNWQELIKPSKLDV-TPGDDSKRFATIIAEPLERGFGLTLGNALRRILLSSLQGAAI 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|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 =  414 bits (1064), Expect = e-113,   Method: Composition-based stats.
 Identities = 211/337 (62%), Positives = 272/337 (80%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++    G +      ++AEPL RGF  TLGNALRRVL+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLQV-TPGADATRFATVVAEPLERGFGQTLGNALRRVLLSSLQGAAVQ 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 =  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  TLGNALRR+L+SSL+GAA+ 
Sbjct: 7   IQKNWQELIRPNKLQV-TPGSDATRFATVVAEPLERGFGQTLGNALRRILLSSLQGAAVQ 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|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 =  413 bits (1063), Expect = e-113,   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|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 =  413 bits (1063), Expect = e-113,   Method: Composition-based stats.
 Identities = 209/339 (61%), Positives = 267/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  +E    G +      ++AEPL RGF  T+GNALRR+L+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLEV-RPGADPSRVATVVAEPLERGFGLTMGNALRRILLSSLQGAAI 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|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 =  413 bits (1063), Expect = e-113,   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|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 =  413 bits (1063), Expect = e-113,   Method: Composition-based stats.
 Identities = 216/337 (64%), Positives = 272/337 (80%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN ++    G +      ++AEPL RGF  TLGNALRRVL+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLQV-TPGSDATRFATLVAEPLERGFGQTLGNALRRVLLSSLQGAAVQ 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|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 =  413 bits (1063), Expect = e-113,   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|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 =  413 bits (1062), Expect = e-113,   Method: Composition-based stats.
 Identities = 217/338 (64%), Positives = 271/338 (80%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           +IQKNWQELIKP  ++    G + +    ++AEPL RGF  TLGN+LRR+L+SSL+GAA+
Sbjct: 4   VIQKNWQELIKPEKLQV-TAGADPKRLATVVAEPLERGFGMTLGNSLRRILLSSLQGAAV 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
            +    ++ LPFNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ++E +MLR  NFGR
Sbjct: 243 SET-AAIQELPFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKSETEMLRTPNFGR 301

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


>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 =  413 bits (1062), 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   IQKNWQELIRPNKLQVVP-GSDPSRFATLIAEPLERGFGQTLGNALRRILLSSLQGAAVQ 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|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 =  413 bits (1061), Expect = e-113,   Method: Composition-based stats.
 Identities = 212/339 (62%), Positives = 266/339 (78%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI KNW ELIKP  ++    G +   +  +IAEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIHKNWAELIKPTQLDV-KPGNDPMRQATVIAEPLERGFGLTLGNALRRVLLSSLQGAAI 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 GRESEDE-GLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 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 =  413 bits (1061), Expect = e-113,   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   MIHKNWAELIKPTQLEV-KPGNDPMRQATVIAEPLERGFGLTLGNALRRVLLSSLQGAAI 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|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 =  412 bits (1060), Expect = e-113,   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|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 =  412 bits (1060), Expect = e-113,   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   MIHKNWAELIKPTQLEV-KPGNDPLRQAVLIAEPLERGFGLTLGNALRRVLLSSLQGAAI 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|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 =  412 bits (1059), Expect = e-113,   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|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 =  412 bits (1059), Expect = e-113,   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 EQEP-DLGFNPVLLKKVDELELSVRSANCLRNDNIVYIGDLIQKSEAEMLRTPNFGRKSL 306

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
            EIK VL TMGL LGM++P WPPE+IE+LAKKYED
Sbjct: 307 NEIKEVLATMGLHLGMDVPSWPPENIEDLAKKYED 341


>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 =  412 bits (1059), Expect = e-113,   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|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 =  412 bits (1058), Expect = e-113,   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|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 =  412 bits (1058), Expect = e-113,   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|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 =  412 bits (1058), Expect = e-113,   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   MIHKNWAELIKPTQLDV-KPGNDPLRQAVLIAEPLERGFGLTLGNALRRVLLSSLQGAAI 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|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 =  411 bits (1057), Expect = e-113,   Method: Composition-based stats.
 Identities = 214/339 (63%), Positives = 269/339 (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 KKVSYKVENTREGQILDYDKLTMVVETDGSVRPEDAVALAARILQDQLAVFINFEEPKKA 241

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +E      L FN ALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 242 QEE-QRHPELAFNAALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 300

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


>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 =  411 bits (1057), Expect = e-113,   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 TRQDDD-DGLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

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


>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 =  411 bits (1057), 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 +      ++AEPL RGF  TLGNALRR+L+SSL+GAA+ 
Sbjct: 7   IQKNWQELIRPNKLQVVP-GSDPSRFATLVAEPLERGFGQTLGNALRRILLSSLQGAAVQ 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|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 =  411 bits (1057), Expect = e-113,   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|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 =  411 bits (1057), Expect = e-113,   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   MIHKNWAELIKPTQLDV-KPGNDPSRQATVIAEPLERGFGLTLGNALRRVLMSSLQGAAI 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|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 =  411 bits (1057), Expect = e-113,   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|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 =  411 bits (1056), Expect = e-113,   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   MIHKNWQELIKPTQLEV-KPGNEPARQATVVAEPLERGFGLTLGNALRRVLMSSLQGAAI 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 KKVSYDVQPTREGQVLDYDKLTLKLETDGSVTPDDAVAYAARILQDQLSVFVNFDEPEAA 244

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             +      L FNP LLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 245 RSQSEE-DDLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 303

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM++ DWPPE+IE+LAKK+ED+
Sbjct: 304 KSLNEIKEVLSGMGLHLGMDILDWPPENIEDLAKKFEDQ 342


>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 =  410 bits (1055), Expect = e-112,   Method: Composition-based stats.
 Identities = 210/339 (61%), Positives = 264/339 (77%), Gaps = 2/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI +NW ELIKP  ++    G +   +  ++AEPL RGF  TLGNALRR+L+SSL+GAAI
Sbjct: 1   MIHRNWSELIKPTQLDV-RPGADAARQATIVAEPLERGFGLTLGNALRRILLSSLQGAAI 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|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 =  410 bits (1055), Expect = e-112,   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   MIHKNWAELIKPAQLEV-KPGNDPARQATVVAEPLERGFGLTLGNALRRVLMSSLQGAAI 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|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 =  410 bits (1055), Expect = e-112,   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|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 =  410 bits (1055), Expect = e-112,   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   MIHKNWAELIKPTQLEV-KPGNDPARQATVIAEPLERGFGLTLGNALRRILMSSLQGAAI 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|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 =  410 bits (1054), Expect = e-112,   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   MIHKNWAELIKPTQLDV-KPGNDPARQATVVAEPLERGFGLTLGNALRRVLMSSLQGAAI 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|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 =  410 bits (1054), Expect = e-112,   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   MIHKNWAELIKPQQLDV-KPGNDPARQATVVAEPLERGFGLTMGNALRRVLMSSLQGAAI 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|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 =  410 bits (1054), Expect = e-112,   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   MIHKNWAELIKPTQLDV-KPGFDPSRQATVVAEPLERGFGLTLGNALRRVLMSSLQGAAI 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|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 =  410 bits (1054), Expect = e-112,   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|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 =  410 bits (1054), Expect = e-112,   Method: Composition-based stats.
 Identities = 215/337 (63%), Positives = 268/337 (79%), Gaps = 2/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           IQKNWQELI+PN +  +  G +      +IAEPL RGF  TLGNALRR+L+SSL+GAA+ 
Sbjct: 3   IQKNWQELIRPNKLHVVP-GSDPSRFATLIAEPLERGFGQTLGNALRRILLSSLQGAAVQ 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|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 =  410 bits (1054), Expect = e-112,   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   MIHKNWAELIKPTQLDV-KPGNDPARQATVVAEPLERGFGLTLGNALRRVLMSSLQGAAI 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|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 =  410 bits (1054), Expect = e-112,   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   MIHKNWAELIKPMQLDV-KPGNDPMRQATMVAEPLERGFGLTLGNALRRILMSSLQGAAI 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|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 =  410 bits (1054), Expect = e-112,   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  MIHKNWAELIKPTQLD-GKPGNDPARQATLVAEPLERGFGLTLGNALRRVLMSSLQGAAI 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 =  410 bits (1053), Expect = e-112,   Method: Composition-based stats.
 Identities = 204/337 (60%), Positives = 260/337 (77%), 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 RVSYRVEPTRVGQVTDYDRLILNIETNGAVTPEDAVALAARILQDQLGMFINFEEPQR-L 246

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           + +     LPFNP LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q++E +MLR  NFGRK
Sbjct: 247 RAEEPRPELPFNPNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKSEQEMLRTPNFGRK 306

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM + DWPPE+IEEL K+ ++
Sbjct: 307 SLNEIKEVLSAMGLGLGMVVQDWPPENIEELVKRSDN 343


>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 =  410 bits (1053), Expect = e-112,   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   MIHKNWAELIKPTQLEA-KPGNDPARQATIIAEPLERGFGLTLGNALRRVLMSSLQGAAI 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|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 =  409 bits (1052), Expect = e-112,   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|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 =  409 bits (1052), Expect = e-112,   Method: Composition-based stats.
 Identities = 228/339 (67%), Positives = 272/339 (80%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E         N   +IAEPL RGF  TLGNALRRVL+SSLRGAAI
Sbjct: 1   MIQKNWQELIKPNKVESCAHDN--PNVISVIAEPLERGFGLTLGNALRRVLLSSLRGAAI 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 PVEEADS-ELSFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPPE+I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEIPAWPPENIDDLAKRYEDQ 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 =  409 bits (1052), Expect = e-112,   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   MIHKNWAELIKPTQLDV-KPGNDAGRQATVVAEPLERGFGLTLGNALRRVLMSSLQGAAI 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|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 =  409 bits (1051), Expect = e-112,   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   MIHKNWAELIKPTQLEV-KPGNDPARQATVIAEPLERGFGLTLGNALRRILMSSLQGAAI 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|319408741|emb|CBI82398.1| DNA-directed RNA polymerase alpha subunit [Bartonella
           schoenbuchensis R1]
          Length = 337

 Score =  409 bits (1051), Expect = e-112,   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   MIQKNWQELIKPNKVEFHADGN--SNVVSVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 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 LVEEPAS-ELSFNLALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 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 =  408 bits (1050), Expect = e-112,   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   MIHKNWAELIKPTQLEV-KPGNDPARQATLVAEPLERGFGLTLGNALRRILMSSLQGAAI 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|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 =  408 bits (1050), Expect = e-112,   Method: Composition-based stats.
 Identities = 164/328 (50%), Positives = 224/328 (68%), Gaps = 1/328 (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 KSLVEIKGVLGTMGLFLGMNLPDWPPES 328
           KSL EIK +L  MGL LGM L +WPP+ 
Sbjct: 304 KSLKEIKEILAEMGLSLGMKLENWPPKQ 331


>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 =  408 bits (1050), Expect = e-112,   Method: Composition-based stats.
 Identities = 203/337 (60%), Positives = 260/337 (77%), 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 RVSYRVEPTRVGQVTDYDRLILNIETNGAVTPEDAVALAARILQDQLGMFINFEEPQR-L 240

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           + +     LPFNP LL+KV+ELELSVRS NCL+ +NIVY+GDL+Q++E +MLR  NFGRK
Sbjct: 241 RAEEPRPELPFNPNLLRKVDELELSVRSANCLKNDNIVYIGDLVQKSEQEMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK VL  MGL LGM + DWPPE+IEEL K+ ++
Sbjct: 301 SLNEIKEVLSAMGLGLGMVVQDWPPENIEELVKRSDN 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 =  408 bits (1050), Expect = e-112,   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   MIHKNWAELIKPQQLDV-KPGNDPARQATVMAEPLERGFGLTLGNALRRVLMSSLQGAAI 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|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 =  408 bits (1049), Expect = e-112,   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   MIHKNWAELIKPTQLEV-KPGNDPARQATLVAEPLERGFGLTLGNALRRILMSSLQGAAI 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|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 =  408 bits (1049), Expect = e-112,   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   MIHKNWAELIKPQQLDV-KPGNDPARQATVIAEPLERGFGLTMGNALRRVLMSSLQGAAI 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|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 =  408 bits (1049), Expect = e-112,   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   MIHKNWAELIKPTQLEA-KPGNDPARQATIIAEPLERGFGLTLGNALRRVLMSSLQGAAI 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|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 =  408 bits (1048), Expect = e-112,   Method: Composition-based stats.
 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   MIQKNWQELIKPNKVEFCTHDN--PNISSVIVEPLERGFGLTLGNALRRVLLSSLRGAAI 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 IVDESDS-ELTFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPPE+I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEIPTWPPENIDDLAKRYEDQ 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 =  407 bits (1047), Expect = e-111,   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|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 =  407 bits (1047), Expect = e-111,   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   MIHKNWAELIKPQQLDV-KPGNDPARQATVTAEPLERGFGLTMGNALRRVLMSSLQGAAI 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|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 =  407 bits (1046), Expect = e-111,   Method: Composition-based stats.
 Identities = 217/343 (63%), Positives = 270/343 (78%), Gaps = 6/343 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI  NWQ+L KPN + +   G   +    + AEPL RGF  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MIASNWQDLTKPNQVVFKNGGSRSK--ASLTAEPLERGFGLTLGNALRRVLLSSLQGAAI 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 ----VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 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|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 =  407 bits (1045), Expect = e-111,   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   MIHKNWAELIKPQQLDV-KPGNDPARQATVTAEPLERGFGLTMGNALRRVLMSSLQGAAI 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 =  406 bits (1044), Expect = e-111,   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   MIHKNWAELIKPQQLDV-KPGNDPARQATVTAEPLERGFGLTMGNALRRVLMSSLQGAAI 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|319407401|emb|CBI81052.1| DNA-directed RNA polymerase alpha subunit [Bartonella sp. 1-1C]
          Length = 337

 Score =  406 bits (1043), Expect = e-111,   Method: Composition-based stats.
 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   MIQKNWQELIKPSKVEFHA--HNDPNIVSVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 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 LVEEPDS-ELSFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 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 =  406 bits (1043), Expect = e-111,   Method: Composition-based stats.
 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   MIQKNWQELIKPSKVEFHA--HNDPNIVSVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 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 LVEEPDS-ELSFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

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


>gi|296282607|ref|ZP_06860605.1| DNA-directed RNA polymerase subunit alpha [Citromicrobium
           bathyomarinum JL354]
          Length = 352

 Score =  405 bits (1042), Expect = e-111,   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|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 =  405 bits (1042), Expect = e-111,   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   MIHKNWAELIKPTQLDV-KPGNDPSRQATVVAEPLERGFGLTMGNALRRVLMSSLQGAAI 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 KKVSYDVQPTREGQVLDYDKLTMKVETDGSITPDDAVAFAARILQDQLSIFVNFDEPES- 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|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 =  405 bits (1042), Expect = e-111,   Method: Composition-based stats.
 Identities = 221/339 (65%), Positives = 271/339 (79%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPN +E+        N + +I EPL RGF  TLGNALRRVL+SSLRGAAI
Sbjct: 1   MIQKNWQELIKPNKVEFSKHDN--PNISSVIVEPLERGFGLTLGNALRRVLLSSLRGAAI 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 TVEESNS-ELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPPE+I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEVPTWPPENIDDLAKRYEDQ 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 =  405 bits (1042), Expect = e-111,   Method: Composition-based stats.
 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   MIQKNWQELIKPNKVE--SFTHDNSNIISVIAEPLERGFGLTLGNALRRVLLSSLRGAAI 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 PVEEADS-ELSFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 297

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


>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 =  405 bits (1041), Expect = e-111,   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   MIHKNWAELIKPTQLDV-QPGNDPSRQATVIAEPLERGFGLTLGNALRRILMSSLQGAAI 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|319405874|emb|CBI79506.1| DNA-directed RNA polymerase alpha subunit [Bartonella sp. AR 15-3]
          Length = 337

 Score =  405 bits (1041), Expect = e-111,   Method: Composition-based stats.
 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   MIQKNWQELIKPNKVEFHA--HNDPNIVSVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 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 LIEEPDP-ELSFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 297

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


>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 =  405 bits (1041), Expect = e-111,   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 QRQDEE-DDLEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

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


>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 =  405 bits (1040), Expect = e-111,   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|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 =  404 bits (1039), Expect = e-111,   Method: Composition-based stats.
 Identities = 204/338 (60%), Positives = 265/338 (78%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++ KNWQ+LIKP  I  +  G   +    ++AEPL RGF  TLGNALRRVL+SSL+G A+
Sbjct: 9   VLNKNWQDLIKPGKINVVP-GANPKYVASIVAEPLERGFGLTLGNALRRVLLSSLQGGAV 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 VAE-ERIPQLEFNAALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 306

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


>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 =  404 bits (1038), Expect = e-110,   Method: Composition-based stats.
 Identities = 218/339 (64%), Positives = 274/339 (80%), 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
           +  +     L FNPALLKKV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGR
Sbjct: 239 L-IEEPASELTFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 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 =  403 bits (1037), Expect = e-110,   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   MIHKNWQELIKPNQLKV-QPGNDPSRQATVIAEPLERGFGLTMGNALRRILMSSLQGAAI 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 SRADEE-DELEFNPLLLKKVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGR 298

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


>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 =  403 bits (1036), Expect = e-110,   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 KVNYRVTNARVGHRTDYDRLILQVWTDGSVKPDDALAYAAKIVKEQLSIFINHEEIE-ET 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|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 =  403 bits (1035), Expect = e-110,   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   KNWQELKKPNSLEV-KPGNDPQRRATFIAEPLERGFGLTLGNALRRVLLSSLQGAAVTSI 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|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 =  402 bits (1034), Expect = e-110,   Method: Composition-based stats.
 Identities = 196/347 (56%), Positives = 255/347 (73%), Gaps = 12/347 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPN++E I +  +   +   +AEPL RGF  TLGNALRRVL+SSL+GAA+T++
Sbjct: 6   KNWQELKKPNSLE-IKVSGDGRRKATFVAEPLERGFGLTLGNALRRVLLSSLQGAAVTSI 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 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE------- 236
           +Y V++ R GQ LDYDKLS+T++TDG++T ED+VA A+RILQDQL +F++FE+       
Sbjct: 185 AYKVDNTRVGQELDYDKLSLTVETDGTVTPEDAVAYAARILQDQLQLFVHFEDALPAAAP 244

Query: 237 ----PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 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|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 =  402 bits (1033), Expect = e-110,   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   KNWQELKKPNSLEIKVAGD-GRRKATFVAEPLERGFGLTLGNALRRVLLSSLQGAAVTSI 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 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE------- 236
           +Y V++ R GQ LDYDKLS+T++TDG++T ED+VA A+RILQDQL +F++FE+       
Sbjct: 185 AYKVDNTRVGQELDYDKLSLTVETDGTVTPEDAVAYAARILQDQLQLFVHFEDALPAAAP 244

Query: 237 ----PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 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|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 =  402 bits (1032), Expect = e-110,   Method: Composition-based stats.
 Identities = 193/345 (55%), Positives = 254/345 (73%), Gaps = 10/345 (2%)

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 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE--- 240
           +Y V++AR GQ LDYDKL++T++TDG++T ED+VA A+RILQDQL +F++FEE   +   
Sbjct: 185 AYKVDNARIGQELDYDKLNLTVETDGTVTPEDAVAYAARILQDQLQVFVHFEEAMSDSGL 244

Query: 241 ------VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 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|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 =  401 bits (1030), Expect = e-110,   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|9837272|gb|AAG00506.1|AF285111_1 RNA polymerase alpha subunit [Bartonella henselae]
          Length = 337

 Score =  400 bits (1029), Expect = e-109,   Method: Composition-based stats.
 Identities = 219/339 (64%), Positives = 269/339 (79%), Gaps = 3/339 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELI PN +E+        N + +I EPL RGF  TLGNALRRVL+S LRGAAI
Sbjct: 1   MIQKNWQELINPNKVEFSKHDN--PNISSVIVEPLERGFGLTLGNALRRVLLSYLRGAAI 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 TVEESNS-ELAFNPALLKKVDELELSVRSANCLKNDNIVYIGDLIQKTESEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM +P WPPE+I++LAK+YED+
Sbjct: 298 KSLNEIKEVLACMGLHLGMEVPTWPPENIDDLAKRYEDQ 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 =  400 bits (1028), Expect = e-109,   Method: Composition-based stats.
 Identities = 219/352 (62%), Positives = 269/352 (76%), Gaps = 16/352 (4%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI  NWQ+L KPN +   V       +  + AEPL RGF  TLGNALRRVL+SSL+GAA+
Sbjct: 1   MIASNWQDLSKPNQV---VFKGSGRTKASLTAEPLERGFGLTLGNALRRVLLSSLQGAAV 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|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 =  400 bits (1027), Expect = e-109,   Method: Composition-based stats.
 Identities = 196/347 (56%), Positives = 255/347 (73%), Gaps = 12/347 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPN++E I    + + +   +AEPL RGF  TLGNALRRVL+SSL+GAA+T++
Sbjct: 2   KNWQELKKPNSLE-IKASGDGKRKATFVAEPLERGFGLTLGNALRRVLLSSLQGAAVTSI 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|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 =  398 bits (1024), Expect = e-109,   Method: Composition-based stats.
 Identities = 197/344 (57%), Positives = 253/344 (73%), Gaps = 9/344 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPN +E    G + + +T  +AEPL RGF  TLGNALRRVL+SSL+GAAIT++
Sbjct: 6   KNWQELKKPNALEIKEGGDK-QRKTTFVAEPLERGFGLTLGNALRRVLLSSLQGAAITSI 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 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK---- 239
           SY VE+AR GQ LDYDKLS+TI+TDG++T ED+VA A+RILQDQL +F++FE+       
Sbjct: 185 SYKVENARVGQELDYDKLSLTIETDGTVTPEDAVAYAARILQDQLTLFVHFEDGIPQPQS 244

Query: 240 ----EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 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 =  398 bits (1024), Expect = e-109,   Method: Composition-based stats.
 Identities = 163/327 (49%), Positives = 222/327 (67%), Gaps = 1/327 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++ KNW++LIKP  +  +            +AEPL RGF  TLGN+LRRVL+SSL+GAAI
Sbjct: 5   IVTKNWRDLIKPRGL-VVDQESLSNTYGKFVAEPLERGFGITLGNSLRRVLLSSLQGAAI 63

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+V+I+GV HE  +I  V ED+TDIILN+K + L++  +  K + I   GP  + AGDI 
Sbjct: 64  TSVKIEGVEHEFMTIPEVAEDVTDIILNLKEVLLQIHTNEVKTLRIEADGPREIKAGDII 123

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               +E+LNP H I  +     VRME+T  +G GYVPA  ++    PIG I IDAL+SPI
Sbjct: 124 ADGQVEILNPGHHILTISEGGRVRMEMTARRGRGYVPADKNKVPGQPIGTIPIDALFSPI 183

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KV+Y V +AR GQ  DYDKLS+ + TDGS+   D+VA A++I+++QL +FINF+E ++ 
Sbjct: 184 RKVNYQVTNARVGQQTDYDKLSLEVWTDGSVAPNDAVAYAAKIVKEQLSIFINFDEAEEP 243

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +E   V+    N  L + V+ELELSVRS NCL+  NI  +GDL+Q+TEA+ML+  NFGR
Sbjct: 244 AEEVKPVEEQKLNENLFRSVDELELSVRSANCLQNANIKTIGDLVQKTEAEMLKTKNFGR 303

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           KSL EIK +L  MGL LGM L +WPP+
Sbjct: 304 KSLKEIKEILAEMGLSLGMKLENWPPK 330


>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 =  398 bits (1023), Expect = e-109,   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   KNWQELKKPNALEKKASGN-GKCKATFVAEPLERGFGLTLGNALRRVLLSSLQGAAITAI 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|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 =  398 bits (1023), Expect = e-109,   Method: Composition-based stats.
 Identities = 197/344 (57%), Positives = 252/344 (73%), Gaps = 9/344 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KNWQEL KPN ++    G +   +   +AEPL RGF  TLGNALRRVL+SSL+GAAIT++
Sbjct: 6   KNWQELKKPNTLDIKDGGDKG-RKATFVAEPLERGFGLTLGNALRRVLLSSLQGAAITSI 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|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 =  398 bits (1023), Expect = e-109,   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|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 =  398 bits (1022), Expect = e-109,   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|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 =  398 bits (1022), Expect = e-109,   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   MIQKNWQELIKPNKIEFHA--HSNPNVLSVVAEPLERGFGLTLGNALRRILLSSLRGAAI 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|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 =  397 bits (1021), Expect = e-109,   Method: Composition-based stats.
 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|239787588|emb|CAX84056.1| DNA-directed RNA polymerase subunit alpha [uncultured bacterium]
          Length = 339

 Score =  397 bits (1019), Expect = e-108,   Method: Composition-based stats.
 Identities = 169/339 (49%), Positives = 242/339 (71%), Gaps = 3/339 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +NW ELIKP  +E +    + + +  ++AEPL RGF  TLGNALRRVL+SSL+GAA++
Sbjct: 1   MYRNWTELIKPRKVELVG-EGDSQYKATLVAEPLERGFGTTLGNALRRVLLSSLQGAAVS 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           AV+I+GVLHE SSI GV ED+TDIILN+KG+ ++M     + +T+     GVVTAGDI  
Sbjct: 60  AVRIEGVLHEFSSIPGVLEDVTDIILNLKGVAIRMRSGVTRTMTLVADKEGVVTAGDIDC 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI-GLITIDALYSPI 180
            +DIE+LNP H I  L+    + M +TV+ G GYV A     +     G 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
            +   +  +  +NP L +KV+ELELSVRS NCL+ ++IVY+GDL+Q+TE++ML+  NFGR
Sbjct: 240 -EGRDDNATPKWNPNLFRKVDELELSVRSANCLKNDDIVYIGDLVQKTESEMLKTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  M L LGM+L  WPPE++E+LA++++++
Sbjct: 299 KSLNEIKEVLEEMDLSLGMHLDGWPPENLEDLARQFDEE 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 =  395 bits (1016), Expect = e-108,   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   KNWQELKKPNGLE-KKSGGDGKRKATFVAEPLERGFGLTLGNSLRRVLLSSLQGAAVTSI 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|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 =  394 bits (1013), Expect = e-108,   Method: Composition-based stats.
 Identities = 181/337 (53%), Positives = 237/337 (70%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q+NW+ELIKP  +E    G           EPL RGF  TLGNALRRVL+SSL+GAAIT
Sbjct: 1   MQRNWRELIKPKRLEVETKG-LPNTYGKFECEPLERGFGITLGNALRRVLLSSLQGAAIT 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 EEEV-RAEPVFNDHLFRSVDELELSVRSANCLKNADIRYIGELVQKTEAEMLKTKNFGRK 298

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP-PESIEELAKKYE 337
           SL EIK +L  MGL LGM L ++P  + IE   K+ E
Sbjct: 299 SLNEIKEILTEMGLSLGMKLENFPSRDDIENRRKEQE 335


>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 =  394 bits (1013), Expect = e-108,   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|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 =  393 bits (1009), Expect = e-107,   Method: Composition-based stats.
 Identities = 177/339 (52%), Positives = 241/339 (71%), Gaps = 2/339 (0%)

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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK-HHRTENDPIGLITIDALYSPI 180
              IE+LNPDH I  L+    + + +TV+ G GYV A+ +   E+  IG I IDA Y+P+
Sbjct: 121 ETGIEILNPDHHIATLNKSGTLDITMTVTTGKGYVRAQLNREDESYAIGDIPIDASYNPV 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKV+Y VE+AR GQ  DYDKL M I+T+G +T ED++ALA++ILQDQL  FINF++    
Sbjct: 181 KKVAYRVENARVGQQTDYDKLIMDIETNGVVTPEDALALAAKILQDQLNPFINFDDV-PT 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             +        +NP L +KV+ELELSVRS NCL+ ++IVY+GDL+Q++E++ML+  NFGR
Sbjct: 240 AHDHEMEDRPQWNPNLFRKVDELELSVRSANCLKNDDIVYIGDLVQKSESEMLKTPNFGR 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK VL  MGL LGM L  WPPE+I++L+K++E++
Sbjct: 300 KSLNEIKEVLDEMGLSLGMTLDTWPPENIDDLSKQFEEE 338


>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 =  391 bits (1004), Expect = e-107,   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|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 =  391 bits (1004), Expect = e-106,   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|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 =  390 bits (1003), Expect = e-106,   Method: Composition-based stats.
 Identities = 189/339 (55%), Positives = 255/339 (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 E
Sbjct: 179 KRVSYNVSNTREGLSIDYDKLTMEIETNGSVASDDCLAFAARILQDQLSLFVNFDEPK-E 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V          FN  LL++V+ELELSVRS NCL+ +NI+Y+GDL+Q+TE +MLR  NFGR
Sbjct: 238 VVVQPTQSEPEFNKNLLRRVDELELSVRSMNCLKNDNIIYIGDLVQKTEGEMLRTPNFGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           KSL EIK V+  M L+LG+ +P+WPPE+I EL+KK ED+
Sbjct: 298 KSLNEIKEVISGMSLYLGIEIPNWPPENISELSKKLEDE 336


>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 =  389 bits (999), Expect = e-106,   Method: Composition-based stats.
 Identities = 164/325 (50%), Positives = 224/325 (68%), Gaps = 1/325 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MI +NW++LI+P  I         +       EPL RGF  T+GN+LRRVL+SSL+GAA 
Sbjct: 10  MIARNWRDLIRPKGISIDA-ESGTQFYAKFTCEPLERGFGITIGNSLRRVLLSSLQGAAA 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 KSLVEIKGVLGTMGLFLGMNLPDWP 325
           KSL EIK +L  MGL LGM + +WP
Sbjct: 309 KSLKEIKEILANMGLSLGMKIDNWP 333


>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 =  388 bits (996), Expect = e-106,   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   MYKNWRDLIKPKRLQVDS-RSLTANYGKFFAEPFERGFGTTIGNSLRRILLSSLQGAAIT 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|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 =  385 bits (988), Expect = e-105,   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|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 =  385 bits (988), Expect = e-105,   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|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 =  384 bits (987), Expect = e-105,   Method: Composition-based stats.
 Identities = 164/328 (50%), Positives = 226/328 (68%), Gaps = 4/328 (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 KSLVEIKGVLGTMGLFLGMNLPDWPPES 328
           KSL EIK +L  MGL LGM L +WP  +
Sbjct: 313 KSLKEIKEILAEMGLSLGMKLDNWPGTN 340


>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 =  384 bits (986), Expect = e-104,   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|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 =  383 bits (984), Expect = e-104,   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|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 =  382 bits (982), Expect = e-104,   Method: Composition-based stats.
 Identities = 156/340 (45%), Positives = 226/340 (66%), Gaps = 3/340 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW++LIKP  ++              +AEP  RGF  TLGN+LRRVL+SSL+GAAIT
Sbjct: 1   MYKNWRDLIKPKQLQIEK-ETLTTTYGKFVAEPFERGFGTTLGNSLRRVLLSSLQGAAIT 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|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 =  382 bits (980), Expect = e-104,   Method: Composition-based stats.
 Identities = 197/320 (61%), Positives = 252/320 (78%), Gaps = 1/320 (0%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
             G +   +  ++AEPL RGF  TLGNALRR+LMSSL+GAAITAVQID VLHE SSI GV
Sbjct: 2   KPGNDPSRQATVVAEPLERGFGLTLGNALRRILMSSLQGAAITAVQIDNVLHEFSSISGV 61

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+TD++LN+KG+ ++M  +  KR+ +  +GPGVVTAGDI     IE+LN DHV+C+LD
Sbjct: 62  REDVTDVVLNLKGVAIRMEVEGPKRLQVQAKGPGVVTAGDISESAGIEILNKDHVLCHLD 121

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
             A + MELTV+ G GYV A+ ++ E+ PIG++ IDA+YSP+KKVSY V+  REGQVLDY
Sbjct: 122 EGAELYMELTVNTGKGYVAAEKNKPEDAPIGMMAIDAIYSPVKKVSYDVQPTREGQVLDY 181

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DKL+M ++TDGSIT +D+VA A+RILQDQL +F+NF+EP+     + +   L FNP LLK
Sbjct: 182 DKLTMKVETDGSITPDDAVAFAARILQDQLSIFVNFDEPESAQAANDD-DGLEFNPLLLK 240

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           KV+ELELSVRS NCL+ +NIVY+GDLIQ+TEA+MLR  NFGRKSL EIK VL  MGL LG
Sbjct: 241 KVDELELSVRSANCLKNDNIVYIGDLIQKTEAEMLRTPNFGRKSLNEIKEVLSGMGLHLG 300

Query: 319 MNLPDWPPESIEELAKKYED 338
           M++ DWPP++IE+LAKK+ED
Sbjct: 301 MDVEDWPPDNIEDLAKKFED 320


>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 =  381 bits (979), Expect = e-104,   Method: Composition-based stats.
 Identities = 161/327 (49%), Positives = 223/327 (68%), Gaps = 1/327 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++ KNW++LIKP  +  +            +AEPL RGF  TLGN+LRRVL+SSL+GAAI
Sbjct: 5   IVTKNWRDLIKPRGL-VVDQDSLSNTYGKFVAEPLERGFGITLGNSLRRVLLSSLQGAAI 63

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+V+++GV HE  +I  V ED+TDIILN+K + L++  +  K + I   GP  + AGD+ 
Sbjct: 64  TSVKVEGVEHEFMTIPEVAEDVTDIILNLKEVLLQIHTNDVKTIRIEADGPKEIKAGDLI 123

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T   +EVLNP H I  +     VR E+T  +G GYVPA+ ++    PIG I IDAL+SPI
Sbjct: 124 TDAQVEVLNPGHHILTISEGGRVRAEMTARRGRGYVPAERNKIPGSPIGTIPIDALFSPI 183

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KV+Y V +AR GQ  DYDKL++ + TDGS+   D+VA A++I+++QL +FINF+E ++ 
Sbjct: 184 RKVNYQVTNARVGQQTDYDKLTLEVWTDGSVAPADAVAFAAKIVKEQLSIFINFDEAEEP 243

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +E   V+    N  L + V+ELELSVRS NCL+  NI  +GDL+Q+TEA+ML+  NFGR
Sbjct: 244 AEEIKPVEEQKLNENLFRSVDELELSVRSANCLQNANIKTIGDLVQKTEAEMLKTKNFGR 303

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           KSL EIK +L  MGL LGM L +WPP+
Sbjct: 304 KSLKEIKEILAEMGLSLGMKLENWPPK 330


>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 =  381 bits (979), Expect = e-104,   Method: Composition-based stats.
 Identities = 161/327 (49%), Positives = 223/327 (68%), Gaps = 1/327 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++ KNW++LIKP  +  +            +AEPL RGF  TLGN+LRRVL+SSL+GAAI
Sbjct: 5   IVTKNWRDLIKPRGL-VVDQDSLSNTYGKFVAEPLERGFGITLGNSLRRVLLSSLQGAAI 63

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+V+++GV HE  +I  V ED+TDIILN+K + L++  +  K + I   GP  + AGD+ 
Sbjct: 64  TSVKVEGVEHEFMTIPEVAEDVTDIILNLKEVLLQIHTNDVKTIRIEADGPKEIKAGDLI 123

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T   +EVLNP H I  +     VR E+T  +G GYVPA+ ++    PIG I IDAL+SPI
Sbjct: 124 TDAQVEVLNPGHHILTISEGGRVRAEMTARRGRGYVPAERNKVPGSPIGTIPIDALFSPI 183

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           +KV+Y V +AR GQ  DYDKL++ + TDGS+   D+VA A++I+++QL +FINF+E ++ 
Sbjct: 184 RKVNYQVTNARVGQQTDYDKLTLEVWTDGSVAPADAVAFAAKIVKEQLSIFINFDEAEEP 243

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +E   V+    N  L + V+ELELSVRS NCL+  NI  +GDL+Q+TEA+ML+  NFGR
Sbjct: 244 AEEIKPVEEQKLNENLFRSVDELELSVRSANCLQNANIKTIGDLVQKTEAEMLKTKNFGR 303

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           KSL EIK +L  MGL LGM L +WPP+
Sbjct: 304 KSLKEIKEILAEMGLSLGMKLENWPPK 330


>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 =  381 bits (979), Expect = e-104,   Method: Composition-based stats.
 Identities = 186/336 (55%), Positives = 255/336 (75%), 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  EV  
Sbjct: 187 SYSISTAREGKALDYDKLIMEVETNGSISAEDAVAYSARIFQDQLNMFVNFDEP-VEVPV 245

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                   FN  LL+KV+ELELSVRS NCL+ +NI+Y+GDL+Q++E +MLR  NFGRKSL
Sbjct: 246 KEVSSEPEFNKNLLRKVDELELSVRSMNCLKNDNIIYIGDLVQKSEGEMLRTPNFGRKSL 305

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            EIK VL  M L+LGM +P+WPPE+I E++KK E++
Sbjct: 306 NEIKEVLTGMSLYLGMEIPNWPPENIAEMSKKLEEQ 341


>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 =  380 bits (977), Expect = e-103,   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|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 =  380 bits (977), Expect = e-103,   Method: Composition-based stats.
 Identities = 184/337 (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   LSKNWNALIKPNKVAYENV-SETNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 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  +E 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDLLPEMAVGLAARILQEQLQLFISFEE--QEE 240

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            + +   +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTEADMLR  NFGRK
Sbjct: 241 DKQVKTDALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTEADMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L  + L  GM++PDWPPE+I+EL+K+YED
Sbjct: 301 SLNEIKEILAKLNLRFGMDVPDWPPENIQELSKRYED 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 =  380 bits (976), Expect = e-103,   Method: Composition-based stats.
 Identities = 183/337 (54%), Positives = 249/337 (73%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y  + +   N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNKVAYENVPE-TNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 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  +E 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDVLPEMAVGLAARILQEQLQLFISFEE--QEE 240

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            + +   +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFGRK
Sbjct: 241 DKQVKTDALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 301 SLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>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 =  380 bits (976), Expect = e-103,   Method: Composition-based stats.
 Identities = 150/336 (44%), 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   MQISVNEFLTPRHIDVQVV---SPTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+E++NPDHVI NL  +  + M+LTV++G GY PA   +T+ D    I    +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 EPVVVEQE---DEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>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 =  380 bits (975), Expect = e-103,   Method: Composition-based stats.
 Identities = 183/337 (54%), Positives = 250/337 (74%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y    +   N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNKVAYENFPE-TNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 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  +E 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGAVLPEMAVGLAARILQEQLQLFISFEE--QEE 240

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            + +   +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTEADMLR  NFGRK
Sbjct: 241 DKQVKTDALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTEADMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L    L  GM++PDWPPE+++EL+K+YED
Sbjct: 301 SLNEIKEILAKFNLRFGMDVPDWPPENMQELSKRYED 337


>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 =  379 bits (974), Expect = e-103,   Method: Composition-based stats.
 Identities = 147/336 (43%), Positives = 224/336 (66%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+      R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQSSVNEFLTPRHIDVQVV---SPTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+E++NPDHVI NL  +  + M+L V++G GY PA   +++ D    I    +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 EPVVVEQE---DEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>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 =  379 bits (974), Expect = e-103,   Method: Composition-based stats.
 Identities = 152/338 (44%), Positives = 216/338 (63%), Gaps = 9/338 (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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+EV NPDHVIC L  D  + + L   +G GY PA       D    I    +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 QTTATEQE---DEVDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKY 336
           G+KSL EIK VL + GL LGM L +WPP S++   +  
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLKNDERLL 332


>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 =  379 bits (973), Expect = e-103,   Method: Composition-based stats.
 Identities = 148/336 (44%), 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   MQISVNEFLTPRHIDVQVV---SPTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+E++NPDHVI NL  +  + M+LTV++G GY PA   +++ D    I    +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 EPVVVEQE---DEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 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 =  379 bits (973), Expect = e-103,   Method: Composition-based stats.
 Identities = 148/336 (44%), 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   MQISVNEFLTPRHIDVQVV---SPTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+E++NPDHVI NL  +  + M+LTV++G GY PA   +++ D    I    +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 EPVVIEQE---DEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>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 =  379 bits (973), Expect = e-103,   Method: Composition-based stats.
 Identities = 180/335 (53%), Positives = 257/335 (76%), 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 EVST-EPEFNKNLLRKVDELELSVRSMNCLKNDNIIYIGDLVQKSEGEMLRTPNFGRKSL 305

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
            EIK VL  M L+LGM +P+WPP++I E++KK E+
Sbjct: 306 NEIKEVLTGMSLYLGMEIPNWPPDNIAEMSKKLEE 340


>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 =  379 bits (973), Expect = e-103,   Method: Composition-based stats.
 Identities = 183/337 (54%), Positives = 248/337 (73%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y    +   N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNKVAYENFPE-TNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 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  +E 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDVLPEMAVGLAARILQEQLQLFISFEE--QEE 240

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            + +   +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFGRK
Sbjct: 241 DKQVKTDTLPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 301 SLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>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 =  378 bits (972), Expect = e-103,   Method: Composition-based stats.
 Identities = 147/336 (43%), Positives = 224/336 (66%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+      R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVV---SPTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+E++NPDHVI NL  +  + M+L V++G GY PA   +++ D    I    +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 EPVVVEQE---DEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>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 =  378 bits (972), Expect = e-103,   Method: Composition-based stats.
 Identities = 181/337 (53%), Positives = 247/337 (73%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y    +   N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNKVAYENFPE-TNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 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  +E 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDLLPEMAVGLAARILQEQLRLFISFEE--QEE 240

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            + +   +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFGRK
Sbjct: 241 DKQVKTDALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 301 SLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>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 =  378 bits (972), Expect = e-103,   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|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 =  378 bits (972), Expect = e-103,   Method: Composition-based stats.
 Identities = 149/336 (44%), Positives = 226/336 (67%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+      R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVV---SPTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+E++NPDHVI NL  + V+ M+LTV++G GY PA   +++ D    I    +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 EPVVIEQE---DEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>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 =  378 bits (971), Expect = e-103,   Method: Composition-based stats.
 Identities = 185/337 (54%), Positives = 246/337 (72%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y    +   N+  +I EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNRVTYENFPE-TNNKAKIIVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 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  +E 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDVLPEMAVGLAARILQEQLQLFIAFEE--QEE 240

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            + +   SLPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFGRK
Sbjct: 241 DKQVKTDSLPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 301 SLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>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 =  378 bits (971), Expect = e-103,   Method: Composition-based stats.
 Identities = 149/336 (44%), Positives = 226/336 (67%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+      R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVV---SPTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+E++NPDHVI NL  + V+ M+LTV++G GY PA   +++ D    I    +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 EPVVIEQE---DEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 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 =  378 bits (971), Expect = e-103,   Method: Composition-based stats.
 Identities = 187/338 (55%), Positives = 247/338 (73%), Gaps = 2/338 (0%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++Q NW+ LIKPN ++    G  +     +I EPL RG+  TLGNALRR+L+SSL+GAA 
Sbjct: 1   VLQNNWEALIKPNKLDV-RYGTPDLRHADIIVEPLERGYGLTLGNALRRILLSSLQGAAF 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 KRVSYKIEQTRVGQRTDFDKLIMSISTDGSLKPDDAVALAARIMQDQLYSFINFDEPK-T 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           + +  +   LPFNP LL+KV+ELELSVRS NCL+ ENI+Y+GDL+Q++E +MLR  NFGR
Sbjct: 239 IDKKESKIELPFNPNLLRKVDELELSVRSANCLKNENIIYIGDLVQKSEHEMLRTPNFGR 298

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EI+ VL TMGL LGM +P+WPPE+IEEL KK ED
Sbjct: 299 KSLNEIREVLETMGLTLGMIIPNWPPENIEELTKKLED 336


>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 =  378 bits (971), Expect = e-103,   Method: Composition-based stats.
 Identities = 155/331 (46%), 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+E+ NP+HVIC+L  +  V M L V++G GY PA     + D    I    +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 EPERVEEEEEIDP---ILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASL 325


>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 =  378 bits (970), Expect = e-103,   Method: Composition-based stats.
 Identities = 182/337 (54%), Positives = 246/337 (72%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y    +   N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNALIKPNKVAYENFPE-TNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 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  +E 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDLLPEMAVGLAARILQEQLQLFISFEE--QEE 240

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            + +   +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFGRK
Sbjct: 241 DKQVKTDALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 301 SLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>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 =  378 bits (970), Expect = e-103,   Method: Composition-based stats.
 Identities = 183/337 (54%), Positives = 246/337 (72%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y    +   N+  +I EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNRVTYENFPE-TNNKAKIIVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 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  +E 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIIFVETNGDVLPEMAVGLAARILQEQLQLFIAFEE--QEE 240

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            + +   SLPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFGRK
Sbjct: 241 DKQVKTDSLPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 301 SLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 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 =  377 bits (969), Expect = e-102,   Method: Composition-based stats.
 Identities = 182/337 (54%), Positives = 246/337 (72%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y    +   N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNKVAYENFPE-TNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 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  +E 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDVLPEMAVGLAARILQEQLQLFISFEE--QEE 240

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            + +   +LPF P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFGRK
Sbjct: 241 DKQVKTDALPFAPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 301 SLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>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 =  377 bits (969), Expect = e-102,   Method: Composition-based stats.
 Identities = 155/333 (46%), Positives = 224/333 (67%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    E + P +I+   +      R  ++ EPL RGF HTLGNALRR+L+SS+ G AI 
Sbjct: 1   MQTAVNEFLTPRHIDVSEI---TPTRARVVLEPLERGFGHTLGNALRRILLSSMAGCAIV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGVLHE S+I+GV ED+ +I+LN+KG+ + M G     +T+ K+GPGVVTAGDIQ 
Sbjct: 58  EAEIDGVLHEYSAIEGVREDVIEILLNLKGVAVVMHGKDSTVLTLSKKGPGVVTAGDIQV 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+E+ NPDHVI N+  +  ++M LT+++G GY PA   R ++D    I    +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         +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 QSAPEQKE---EAIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S++ 
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLKN 327


>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 =  377 bits (969), Expect = e-102,   Method: Composition-based stats.
 Identities = 149/336 (44%), Positives = 224/336 (66%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+   +      R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQEV---SPTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+E++N DHVI NL  +  + M+LTV++G GY PA   +++ D    I    +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 EPVVVEQE---DEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>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 =  377 bits (968), Expect = e-102,   Method: Composition-based stats.
 Identities = 182/337 (54%), Positives = 247/337 (73%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y    +   N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNKVAYENFPE-TNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 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  +E 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDVLPEMAVGLAARILQEQLQLFISFEE--QEE 240

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            + +   +L F+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFGRK
Sbjct: 241 DKQVKTDALLFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 301 SLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>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 =  377 bits (968), Expect = e-102,   Method: Composition-based stats.
 Identities = 180/337 (53%), Positives = 246/337 (72%), 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   E 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGGLLPEMAVGLAARILQEQLQLFISFEEH--EE 240

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            + +   +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFGRK
Sbjct: 241 DKQVKTDTLPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L    L  GM++PDWPPE+I+EL+K+YED
Sbjct: 301 SLNEIKEILAKFNLRFGMDVPDWPPENIQELSKRYED 337


>gi|330969796|gb|EGH69862.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           aceris str. M302273PT]
          Length = 333

 Score =  377 bits (968), Expect = e-102,   Method: Composition-based stats.
 Identities = 149/336 (44%), Positives = 226/336 (67%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+      R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVV---SPTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+E++NPDHVI NL  + V+ M+LTV++G GY PA   +++ D    I    +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 EPVVIEQE---DEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLVSRGLSLGMRLDNWPPASLKKDDK 330


>gi|49087442|gb|AAT51459.1| PA4238 [synthetic construct]
          Length = 334

 Score =  377 bits (967), Expect = e-102,   Method: Composition-based stats.
 Identities = 149/336 (44%), 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   MQSSVNEFLTPRHIDVQVV---SQTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+E++N DHVI NL  +  + M+L V++G GY PA   +++ D    I    +DA +S
Sbjct: 118 DHDVEIINGDHVIANLADNGALNMKLKVARGRGYEPADARQSDEDESRSIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F+   + K
Sbjct: 178 PVRRVSYVVENARVEQRTNLDKLVLDLETNGTLDPEEAIRRAATILQQQLAAFV---DLK 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            + +  +  +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 235 GDSEPVVEEQEDEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>gi|330891907|gb|EGH24568.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           mori str. 301020]
          Length = 333

 Score =  377 bits (967), Expect = e-102,   Method: Composition-based stats.
 Identities = 148/336 (44%), 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   MQISVNEFLTPRHIDVQVV---SPTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+E++NPDHVI NL  + V+ M+LTV++G GY PA   +++ D    I    +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 EPVVIEQE---DEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>gi|2896137|gb|AAC03116.1| DNA-directed RNA polymerase alpha chain [Pseudomonas aeruginosa]
          Length = 358

 Score =  377 bits (967), Expect = e-102,   Method: Composition-based stats.
 Identities = 149/336 (44%), Positives = 224/336 (66%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+    + R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQSSVNEFLTPRHIDVQVV---SQTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+E++N DHVI NL  +  + M+L V++G GY PA   +++ D    I    +DA +S
Sbjct: 118 DHDVEIINGDHVIANLADNGALNMKLKVARGRGYEPADARQSDEDESRSIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F+   + K
Sbjct: 178 PVRRVSYVVENARVEQRTNLDKLVLDLETNGTLDPEEAIRRAATILQQQLAAFV---DLK 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            + +  +  +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 235 GDSEPVVEEQEDEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+ E  +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLTERRQ 330


>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 =  377 bits (967), Expect = e-102,   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   MQNSASEFLKPRLIDVQPV---SATQARVAMEPFERGYAYTLGNALRRILLSSMPGFAPT 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|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 =  377 bits (967), Expect = e-102,   Method: Composition-based stats.
 Identities = 149/336 (44%), 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   MQSSVNEFLTPRHIDVQVV---SQTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+E++N DHVI NL  +  + M+L V++G GY PA   +++ D    I    +DA +S
Sbjct: 118 DHDVEIINGDHVIANLADNGALNMKLKVARGRGYEPADARQSDEDESRSIGRLQLDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSY VE+AR  Q  + DKL + ++T+G++  E+++  A+ ILQ QL  F+   + K
Sbjct: 178 PVRRVSYVVENARVEQRTNLDKLVLDLETNGTLDPEEAIRRAATILQQQLAAFV---DLK 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            + +  +  +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 235 GDSEPVVEEQEDEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>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 =  376 bits (965), Expect = e-102,   Method: Composition-based stats.
 Identities = 153/333 (45%), Positives = 221/333 (66%), Gaps = 9/333 (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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +DIE+ NP+ VI N+  D  + M LTVS+G GY P     T+ D    I    +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 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK +L + GL LGM L +WPP S++ 
Sbjct: 295 GKKSLTEIKDILASRGLSLGMRLENWPPASLKN 327


>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 =  376 bits (965), Expect = e-102,   Method: Composition-based stats.
 Identities = 150/336 (44%), Positives = 220/336 (65%), 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +DIE+ NPDH+I  L+    + M LT+ +G GYVPA   +++++    I    +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 PVHRVAYVVESARVEQRTDLDKLVLDLETNGTIDPEEAIRRAATILQQQLSVFV---DLE 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|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 =  376 bits (965), Expect = e-102,   Method: Composition-based stats.
 Identities = 153/337 (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   MQTKVNELLKPRHIEVTSV---SDRQAKVVLEPLERGFGHTLGNALRRILLSSIPGAAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +I+GVLHE +SI+GV ED+ DI+LN+KGI L+M       +T+ K+GPGVVTAGDI  
Sbjct: 58  EAEIEGVLHEYTSIEGVQEDVVDILLNLKGIALRMHNRDEATLTLKKKGPGVVTAGDITL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALYS 178
            +D+E++NP+HVI +L  +  + M L + +G GY P    +   +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+   E +
Sbjct: 178 PIRRVAYKVESARVEQRTDMDRLVIELETNGTVEADDAIRQAAGILQSQLAAFV---ELQ 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            +       K +  +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 235 GDESTVTESKQMEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
           G+KSL EIK VL + GL +GM L +WPP  +++  KK
Sbjct: 295 GKKSLTEIKDVLASHGLSMGMRLENWPPPGLKDQDKK 331


>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 =  375 bits (964), Expect = e-102,   Method: Composition-based stats.
 Identities = 144/333 (43%), Positives = 216/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +      R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVNS---TRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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+   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 DVTEQAVVEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 327


>gi|330430070|gb|AEC21404.1| DNA-directed RNA polymerase alpha chain [Pusillimonas sp. T7-7]
          Length = 329

 Score =  375 bits (964), Expect = e-102,   Method: Composition-based stats.
 Identities = 148/328 (45%), Positives = 211/328 (64%), Gaps = 6/328 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           Q  +KP +IE   +G   +N   ++ EP  RG+ HTLGNALRR+L+SS+ G A T VQ+ 
Sbjct: 4   QGFLKPRSIEVEPVG---KNHARVVMEPFERGYGHTLGNALRRILLSSMTGYAPTEVQMT 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 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKV 183
           ++NPDHVI NL     + M++ V +G GYVP       +D    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 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL   GL LGM L +WPP  +E 
Sbjct: 301 NEIKEVLAARGLTLGMKLENWPPLGLER 328


>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 =  375 bits (964), Expect = e-102,   Method: Composition-based stats.
 Identities = 181/337 (53%), Positives = 247/337 (73%), Gaps = 3/337 (0%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIKPN + Y    +   N+  ++ EPL RGF  TLGNA+RRVL+SSL+GAAIT
Sbjct: 4   LSKNWNTLIKPNKVAYENFPE-TNNKAKIVVEPLERGFGLTLGNAMRRVLLSSLQGAAIT 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  +E 
Sbjct: 183 SVTYKVENTRVGQVTDYDKLIMFVETNGDLLPEMAVGLAARILQEQLQLFISFEE--QEE 240

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            + +   +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTE+DMLR  NFGRK
Sbjct: 241 DKQVKTDALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTESDMLRTPNFGRK 300

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EIK +L    L  GM++PDWPPE+I+EL+ +YED
Sbjct: 301 SLNEIKEILAKFNLRFGMDVPDWPPENIQELSNRYED 337


>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 =  375 bits (963), Expect = e-102,   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---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 ETAPVEEK---PEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 327


>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 =  375 bits (962), Expect = e-102,   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|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 =  375 bits (962), Expect = e-102,   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---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 VPEQKEEK---PEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 327


>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 =  375 bits (962), Expect = e-102,   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|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 =  375 bits (962), Expect = e-102,   Method: Composition-based stats.
 Identities = 144/336 (42%), Positives = 219/336 (65%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+   +      R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQSSVNEFLTPRHIDVQAV---SPTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+E++N  HVI NL  +  + M+L V++G GY PA   +++ D    I    +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 APVVVEQE---DEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>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 =  375 bits (962), Expect = e-102,   Method: Composition-based stats.
 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 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 FGRKSLVEIKGVLGTMGLFLGMNLPDW-PPESIEE 331
           FGRKSL EIK VL  MGL  GM L  + PPE  +E
Sbjct: 302 FGRKSLNEIKEVLSEMGLSFGMKLEGFQPPEESDE 336


>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 =  375 bits (962), Expect = e-102,   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   MQNSASEFLKPRLIDVQPV---SATHARVSMEPFERGYAHTLGNALRRILLSSMPGFAPT 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 VRRVSFGVESARVEQRTDLDRLVLDIETNGVIEPEQAVRNAARILMDQLSIFA---DLQG 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|332040527|gb|EGI76903.1| DNA-directed RNA polymerase subunit alpha [Hylemonella gracilis
           ATCC 19624]
          Length = 328

 Score =  374 bits (961), Expect = e-102,   Method: Composition-based stats.
 Identities = 159/328 (48%), Positives = 214/328 (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 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG---LITIDALYSPIKKV 183
           ++NP+HVI  L     + M++ V KG GYVP    R  ++       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|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 =  374 bits (961), Expect = e-102,   Method: Composition-based stats.
 Identities = 162/340 (47%), Positives = 228/340 (67%), 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 KEDINVKSLPFNPALL-KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 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|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 =  374 bits (961), Expect = e-102,   Method: Composition-based stats.
 Identities = 145/333 (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---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 EAAPVEEK---PEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 327


>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 =  374 bits (961), Expect = e-102,   Method: Composition-based stats.
 Identities = 150/334 (44%), Positives = 223/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ +    +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPHLVNIEQISS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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 RQPVVKEEK---PEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|330879400|gb|EGH13549.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           glycinea str. race 4]
          Length = 333

 Score =  374 bits (961), Expect = e-102,   Method: Composition-based stats.
 Identities = 148/336 (44%), 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   MQISVNEFLTPRHIDVQVV---SPTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+E++NPDHVI NL  + V+ M+LTV++G GY PA   +++ D    I    +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 EPVVIEQE---DEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>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 =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 152/331 (45%), 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---ESGSTRAKVTLEPLERGFGHTLGSALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             QIDGVLHE S+I+GV ED+ +I+LN+KG+ +KM G     + + K+GPGVVTAGDI+ 
Sbjct: 58  EAQIDGVLHEYSAIEGVQEDVIEILLNLKGVAVKMHGRDDAELMLSKKGPGVVTAGDIKL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+E+ NP+HVIC+L  +  V M L++++G GY PA     + D    I    +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 E---PERVEEEEEIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASL 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 =  374 bits (960), Expect = e-101,   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---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 ETAPVEEK---PEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 327


>gi|331018185|gb|EGH98241.1| DNA-directed RNA polymerase subunit alpha [Pseudomonas syringae pv.
           lachrymans str. M302278PT]
          Length = 333

 Score =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 148/336 (44%), Positives = 224/336 (66%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+      R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQISVNEFLTPRHIDVQVV---SPTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+E++NPDHVI NL  + V+ M+LTV++G GY PA   +++ D    I    +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 EPVVIEQE---DEIDPILLRPVYDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL +  L LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRSLSLGMRLDNWPPASLKKDDK 330


>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 =  374 bits (960), Expect = e-101,   Method: Composition-based stats.
 Identities = 145/338 (42%), Positives = 216/338 (63%), Gaps = 9/338 (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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+++ NPDHVIC+L  D  + M + V +G GY PA       +    I    +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 QATAQEAD---DEVDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKY 336
           G+KSL EIK VL + GL LGM L +WPP S+    +  
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLRNDERLL 332


>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 =  374 bits (960), Expect = e-101,   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   MQSN--TFLTPRIIDVQNI---SPLHARITMEPFERGYGHTLGNALRRILLSSMPGFAPT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP--AKHHRTENDPIGLITIDALYSP 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 PVEQ---PKLPQIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTETELLKTPNLG 292

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           RKSL EIK VL + GL LGM L  WPP ++++  K
Sbjct: 293 RKSLNEIKEVLASRGLTLGMKLESWPPSNLDKGKK 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 =  374 bits (960), Expect = e-101,   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   MQNSASEFLKPRLIDVQPV---SATHARVSMEPFERGYAHTLGNSLRRILLSSMPGYAPT 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 VRRVSFAVESARVEQRTDLDRLVLDIETNGVIEPEQAVRNAARILMDQLSIFA---DLQG 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|149675708|dbj|BAF64734.1| DNA-directed RNA polymerase alpha subunit [Shewanella
           livingstonensis]
          Length = 329

 Score =  373 bits (959), Expect = e-101,   Method: Composition-based stats.
 Identities = 143/333 (42%), Positives = 216/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +      R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVNS---TRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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+   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 DVTEQAVVEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL +IK VL + GL LGM L +WPP S+ +
Sbjct: 295 GKKSLTDIKDVLASRGLSLGMRLENWPPASLAD 327


>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 =  373 bits (959), Expect = e-101,   Method: Composition-based stats.
 Identities = 156/336 (46%), Positives = 227/336 (67%), 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 PVRRVAYSVDNARVEQRTDLDKLVLDIESNGTIDPEEAIRRAATILQQQIAVFVALESES 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +    +        +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 238 EAPVVEEE---DEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL   GL LGM L +WPP S+++ +K
Sbjct: 295 GKKSLTEIKDVLAQRGLSLGMRLENWPPASLKDDSK 330


>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 =  373 bits (959), Expect = e-101,   Method: Composition-based stats.
 Identities = 151/333 (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   MQSN--SLLKPRIIDVQSV---SPVQARVTMEPFERGFGHTLGNALRRILLSSLPGYAPT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP--AKHHRTENDPIGLITIDALYSP 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 VVEQSAAQTIDP---VLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTETELLKTPNLG 292

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEEL 332
           RKSL EIK VL + GL LGM L +WPP  +E+L
Sbjct: 293 RKSLNEIKEVLASRGLTLGMKLENWPPAGLEKL 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 =  373 bits (959), Expect = e-101,   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---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+   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|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 =  373 bits (959), Expect = e-101,   Method: Composition-based stats.
 Identities = 146/336 (43%), Positives = 222/336 (66%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P +I+  V+      R  +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQSSVNEFLTPRHIDVQVV---SPTRAKITLEPLERGFGHTLGNALRRILLSSMPGCAVV 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+E++N DH+I NL  +  + M+L V++G GY PA   +++ D    I    +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 EPVVVEQE---DEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S+++  K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKKDDK 330


>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 =  373 bits (959), Expect = e-101,   Method: Composition-based stats.
 Identities = 128/311 (41%), Positives = 204/311 (65%), Gaps = 2/311 (0%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E+ KP  I+ + L  ++      + EPL RG+  TLGNALRRVL+SSL GAA+T+V+I+
Sbjct: 2   SEMEKPT-IQTVEL-SDDGTYGRFVVEPLERGYGITLGNALRRVLLSSLPGAAVTSVRIE 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE S++ GV ED T+IILN+K + +KM  D  + + I  +G G V A DI T  D+E
Sbjct: 60  GVLHEFSTLPGVVEDTTEIILNLKELAIKMYTDEPQVLRIEAQGEGEVRAADIITPPDVE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           ++N DH+I  L+ D  + ME+TV +G GYVPA  ++  +  IG+I +D++++PI+KV++ 
Sbjct: 120 IVNGDHLIATLEPDGRLFMEMTVQRGRGYVPADRNKDPDRSIGVIPVDSIFTPIRKVNFQ 179

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+ R G+V DYD+L++ + T+G+I  +++ + A++IL D L +F+   +  +     + 
Sbjct: 180 VENTRVGKVTDYDRLTLEVWTNGTIAPDEAASQAAQILTDHLALFLTLTDQARGTGTAVE 239

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L   ++EL+LSVRS NCL+   I  +G+L+++T  DM+R+ N G+KSL E+
Sbjct: 240 KEDDARAKLLEMSIDELDLSVRSYNCLKRAGINTIGELVEKTPEDMMRVRNLGKKSLEEV 299

Query: 307 KGVLGTMGLFL 317
           +  L  +GL L
Sbjct: 300 EEKLAALGLSL 310


>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 =  373 bits (958), Expect = e-101,   Method: Composition-based stats.
 Identities = 141/335 (42%), Positives = 224/335 (66%), Gaps = 9/335 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  E ++P +I+   +     +   ++ EP  RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQRSVTEFLRPRDIKVEEI---SAHHAKIVLEPFERGFGHTLGNALRRILLSSMPGCAVV 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+EV+NP+HVI +++  A ++M+L +++G GY PA      +D    I    +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 E---QEVEEEEDHIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELA 333
           G+KSL EIK VL   GL LGM L +WPP S+++  
Sbjct: 295 GKKSLNEIKDVLAARGLSLGMRLENWPPASLKDDK 329


>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 =  373 bits (958), Expect = e-101,   Method: Composition-based stats.
 Identities = 149/334 (44%), Positives = 223/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ +    +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPHLVNIEQISS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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 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|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 =  373 bits (957), Expect = e-101,   Method: Composition-based stats.
 Identities = 144/333 (43%), Positives = 216/333 (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+   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|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 =  373 bits (957), Expect = e-101,   Method: Composition-based stats.
 Identities = 145/331 (43%), Positives = 215/331 (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+   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|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 =  373 bits (957), Expect = e-101,   Method: Composition-based stats.
 Identities = 161/340 (47%), Positives = 228/340 (67%), 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 KEDINVKSLPFNPALL-KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 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|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 =  372 bits (956), Expect = e-101,   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|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 =  372 bits (956), Expect = e-101,   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   MQSN--ALLKPRIIDVQSI---SPVQARVTMEPFERGFGHTLGNALRRILLSSLPGHAPT 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|110812362|gb|ABG91718.1| DNA-directed RNA polymerase, alpha subunit [Shewanella putrefaciens
           200]
          Length = 336

 Score =  372 bits (956), Expect = e-101,   Method: Composition-based stats.
 Identities = 143/333 (42%), Positives = 215/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +      R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 8   MQGSVTEFLKPRLVDIEQVNS---TRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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+   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 =  372 bits (955), Expect = e-101,   Method: Composition-based stats.
 Identities = 144/333 (43%), Positives = 216/333 (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+   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|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 =  372 bits (955), Expect = e-101,   Method: Composition-based stats.
 Identities = 148/336 (44%), Positives = 227/336 (67%), Gaps = 10/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  E ++P +I+   +     N   ++ EP  RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQRSVTEFLRPRDIKVEEI---NANHAKIVLEPFERGFGHTLGNALRRILLSSMPGCAVV 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT-IFKRGPGVVTAGDIQ 120
             +I+GVLHE S+I+GV ED+ +I+LN+K + +KM G+  + V  + K+GP VVTAGDI 
Sbjct: 58  EAEIEGVLHEYSAIEGVQEDVIEILLNLKDVAVKMHGNRDEVVLALSKQGPSVVTAGDIA 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALY 177
             +D+E++NPDHVI +L+    ++M+L V +G GY PA    +E D    I    +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 KE---QEVEEEEDQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELA 333
            G+KSL EIK VL   GL LGM L +WPP S+++  
Sbjct: 295 LGKKSLNEIKDVLAARGLSLGMRLENWPPASLKDDK 330


>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 =  372 bits (955), Expect = e-101,   Method: Composition-based stats.
 Identities = 148/334 (44%), Positives = 222/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +   +     ++ EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISSTQ---AKVVLEPLERGFGHTLGNALRRILLSSMPGCAVT 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
           ++   ++       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQPEIKEEK---PEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>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 =  372 bits (955), Expect = e-101,   Method: Composition-based stats.
 Identities = 143/333 (42%), Positives = 215/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +      R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVNS---TRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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+   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 =  372 bits (955), Expect = e-101,   Method: Composition-based stats.
 Identities = 143/333 (42%), Positives = 215/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +      R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVNS---TRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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+   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|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 =  372 bits (955), Expect = e-101,   Method: Composition-based stats.
 Identities = 149/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISS---THAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 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 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|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 =  372 bits (955), Expect = e-101,   Method: Composition-based stats.
 Identities = 148/333 (44%), Positives = 220/333 (66%), Gaps = 9/333 (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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+E+ NP+ VI N+  D  + M+LT+++G GY P    +++ D    I    +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 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK +L + GL LGM L +WPP S++ 
Sbjct: 295 GKKSLTEIKDILASRGLSLGMRLENWPPASLKN 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 =  372 bits (954), Expect = e-101,   Method: Composition-based stats.
 Identities = 149/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISS---THAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 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 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|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 =  372 bits (954), Expect = e-101,   Method: Composition-based stats.
 Identities = 157/333 (47%), Positives = 214/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++  V+      R  +  EP+ RGF +TLGNALRRVL+SS+ G AIT
Sbjct: 1   MQNSPTEYLKPRVVDVDVI---SPVRARVTLEPMERGFGYTLGNALRRVLLSSIPGFAIT 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 SEVEVKQA---PQVDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKAPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL + GL LGM L +WPP  +E+
Sbjct: 295 GRKSLNEIKDVLASKGLTLGMKLENWPPAGLEK 327


>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 =  372 bits (954), Expect = e-101,   Method: Composition-based stats.
 Identities = 152/336 (45%), Positives = 224/336 (66%), Gaps = 8/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  E + P +I+   +    + R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQRSVNEFLSPRHIDVQEI---SKTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+I+GV ED+ +I+LN+KGI + +  +    +T+ K   G VTAGDIQ 
Sbjct: 58  EVEIDGVLHEYSTIEGVQEDVIEILLNLKGIAVLLHNNDEAVLTLSKSEAGPVTAGDIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
             D+E+ NPDHVI +L+  A + M+LT+ +G GYVPA    ++ +    I    +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 DQAKDEPEE--PEIDPILLRPVDDLELTVRSANCLKAEQIYYIGDLIQRTEVELLKTPNL 295

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S++   K
Sbjct: 296 GKKSLTEIKDVLASKGLSLGMRLENWPPASLKNDDK 331


>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 =  371 bits (953), Expect = e-101,   Method: Composition-based stats.
 Identities = 154/340 (45%), Positives = 227/340 (66%), 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 KEDINVKS-LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 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|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 =  371 bits (953), Expect = e-101,   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|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 =  371 bits (953), Expect = e-101,   Method: Composition-based stats.
 Identities = 161/340 (47%), Positives = 228/340 (67%), 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 KEDINVKSLPFNPALL-KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 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|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 =  371 bits (953), Expect = e-101,   Method: Composition-based stats.
 Identities = 155/335 (46%), Positives = 222/335 (66%), Gaps = 9/335 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  N  E +KP  ++   L    + R  ++ EPL RGF HTLGNALRR+L+SS+ GAA+T
Sbjct: 1   MSGNVNEFLKPRLVDVQQL---SDTRAKVVLEPLERGFGHTLGNALRRILLSSMPGAAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            VQIDGVLHE ++I+GV ED+ +I+LN+K + + ++  +   +++ K+G G V AGDIQ 
Sbjct: 58  EVQIDGVLHEYTTIEGVQEDVLEILLNLKNLAIVLNAKNEAVLSLSKKGKGPVKAGDIQA 117

Query: 122 VNDIEVLNPDHVICNLDVDAV-VRMELTVSKGHGYVPAKHHRT--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 VSEEEDDASDIDP---VLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELA 333
           G+KSL EIK VL   GL LGM L +WPP SI + A
Sbjct: 295 GKKSLTEIKDVLAQHGLSLGMRLENWPPASIAKEA 329


>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 =  371 bits (953), Expect = e-101,   Method: Composition-based stats.
 Identities = 149/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISS---THAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  371 bits (952), Expect = e-100,   Method: Composition-based stats.
 Identities = 141/331 (42%), Positives = 217/331 (65%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF +TLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQI---SPTHAKVTLEPLERGFGYTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE SS +GV ED+ +++LN+KG+ + + G     +T+ K G G VTAGD   
Sbjct: 58  EVEIDGVLHEYSSKEGVQEDVIEVLLNLKGLAVSVEGKDEATLTLNKSGAGPVTAGDFTH 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYS 178
             D+E++NP+HVIC+L  D  + M + V +G GYVPA   +    +  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+   E +
Sbjct: 178 PVERIAYSVDAARVEQRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLDAFV---ELR 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              + +   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 235 DISEPEEKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIQYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASL 325


>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 =  370 bits (951), Expect = e-100,   Method: Composition-based stats.
 Identities = 142/333 (42%), Positives = 215/333 (64%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +      R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVNS---TRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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+   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|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 =  370 bits (951), Expect = e-100,   Method: Composition-based stats.
 Identities = 150/334 (44%), Positives = 223/334 (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-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 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|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 =  370 bits (951), Expect = e-100,   Method: Composition-based stats.
 Identities = 127/322 (39%), Positives = 191/322 (59%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +      E R+  I EPL  GF +T+GN+LRR L+SS+ GAA+T+++I+GVLHE S++ G
Sbjct: 9   LQEEPLSEYRSRFILEPLEPGFGYTIGNSLRRTLLSSIPGAAVTSIRIEGVLHEFSTVPG 68

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+TDIILN+K + +    D    + + K+GPG VTA DI     +EV NP+  I  L
Sbjct: 69  VKEDVTDIILNLKQLVVSSEHDEPVVMYLRKQGPGEVTAADIAPPAGVEVHNPELHIATL 128

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           +  A + MELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+ R  Q  D
Sbjct: 129 NGKAKLEMELTVERGRGYVSAAQNKQPGQEIGRIPIDSIYSPVLKVTYKVEATRVEQRTD 188

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +D+L + ++T  SI   D+VA A + L +  G+        + ++   +         L 
Sbjct: 189 FDRLILDVETKPSIKPRDAVASAGKTLVELFGLARELNVEAEGIEIGPSPTDAALAADLA 248

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +EEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  MGL L
Sbjct: 249 LPIEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLDIRNFGAKSIEEVKQKLAEMGLTL 308

Query: 318 GMNLPDWPPESIEELAKKYEDK 339
             + P + P ++     + +D+
Sbjct: 309 KDSPPGFDPATVAGGGGRLDDE 330


>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 =  370 bits (951), Expect = e-100,   Method: Composition-based stats.
 Identities = 155/332 (46%), Positives = 216/332 (65%), Gaps = 9/332 (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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP--AKHHRTENDPIGLITIDALYSP 179
            +DIEVLNPDHVI +L     + ME+ +  G GY P  A+    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 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           RKSL EIK VL + GL LGM L +WPP  +E 
Sbjct: 294 RKSLNEIKDVLASKGLSLGMKLENWPPAGLER 325


>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 =  370 bits (950), Expect = e-100,   Method: Composition-based stats.
 Identities = 142/331 (42%), Positives = 215/331 (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+   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|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 =  370 bits (950), Expect = e-100,   Method: Composition-based stats.
 Identities = 149/328 (45%), Positives = 207/328 (63%), Gaps = 7/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           Q  +KP +IE   +G    +   ++ EP  RG+ HTLGNALRR+L+SS+ G A T VQ+ 
Sbjct: 4   QGFLKPRSIEVEPVG---AHHAKIVMEPFERGYGHTLGNALRRILLSSMTGYAPTEVQMT 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 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKV 183
           ++NPDH+ICNL     + M++ V KG GYVP        D       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 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +   +   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 241 PV-RGTPQIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 299

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL   GL LGM L +WPP  +E 
Sbjct: 300 NEIKEVLAARGLTLGMKLENWPPLGLER 327


>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 =  370 bits (950), Expect = e-100,   Method: Composition-based stats.
 Identities = 164/338 (48%), Positives = 230/338 (68%), Gaps = 4/338 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +++NW+ELIKP+ ++                EPL RGF HT+GNALRR+L+SSL+GAA+T
Sbjct: 1   MERNWRELIKPSRLQIDE-EIHTSRYGKFSCEPLERGFGHTIGNALRRILISSLQGAAVT 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 KVSYVVTQARVGQITDYDKLTLEVHTNGAVRPEDAVAYAAKILKEQLQIFINF-PEEPEP 238

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
             +   +    N  L + V+ELELSVRS NCL+  +I Y+G+L+QR+EA+ML+  NFGRK
Sbjct: 239 THEEEREEPRLNENLFRTVDELELSVRSANCLKNADIKYIGELVQRSEAEMLKTKNFGRK 298

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           SL EIK +L  MGL LGM L  +P    ++L  +  +K
Sbjct: 299 SLNEIKEMLTDMGLSLGMKLDGFPAR--DDLENRDREK 334


>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 =  370 bits (950), Expect = e-100,   Method: Composition-based stats.
 Identities = 148/334 (44%), Positives = 222/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  +E   +      R+ ++ EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVEIDAV---SPTRSKVVLEPLERGFGHTLGNALRRILLSSMPGCAVT 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-DAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALY 177
             D+ + NPDHVIC+L   ++ + M + V +G GYVPA +      +  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 TEPVAKEEK---PEFDPILLRPVDDLELTVRSANCLKAEQIQYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP S+ E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASLAE 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 =  370 bits (950), Expect = e-100,   Method: Composition-based stats.
 Identities = 154/336 (45%), Positives = 219/336 (65%), 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+E+ NPDHVICN+   + V ++L VS+G GY PA     E D    I    +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 EAEAVVEEDEVDP---ILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S++   +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKNDDR 330


>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 =  370 bits (950), Expect = e-100,   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|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 =  370 bits (949), Expect = e-100,   Method: Composition-based stats.
 Identities = 151/326 (46%), Positives = 215/326 (65%), Gaps = 9/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  +E   +     N   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 6   LLKPRIVEVETV---APNSAKVVMEPFERGYGHTLGNALRRVLLSSMIGYAPTEVSIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE S++ GV ED+ D++LN+KGI  K+       VT+ +   GVVTAGDI+  +D+E++
Sbjct: 63  VHEYSTLDGVQEDVVDLLLNLKGIVFKLESRDVVTVTLKREVEGVVTAGDIELPHDVEII 122

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG---LITIDALYSPIKKVSY 185
           NPDHVI +L     + M++ V KG GYVP    R  ++P      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 AVESARVEQRTDLDRLVMSIETNGVLSPEESIRLAARILVEQLSVFAALEN---TAEPEV 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|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 =  370 bits (949), Expect = e-100,   Method: Composition-based stats.
 Identities = 160/334 (47%), Positives = 218/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N   L+KP +I    + Q   NR  +  EP  RG+ HTLGNALRRVL+SS+ G A T
Sbjct: 1   MQNN---LLKPKSI---SVEQLGPNRAKVALEPFERGYGHTLGNALRRVLLSSMPGFAAT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GVLHE SSI GV ED+ +I+LN+KG+  K+       +++ K   GVVTA DIQT
Sbjct: 55  EVTIAGVLHEYSSIDGVQEDVVNILLNLKGVVFKLHNREEVTLSLRKDTEGVVTAADIQT 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG---LITIDALYS 178
            +D+E++NP+HVI NL     + M++ V KG GYVP    R  ++P      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|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 =  370 bits (949), Expect = e-100,   Method: Composition-based stats.
 Identities = 143/331 (43%), Positives = 215/331 (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+   E +
Sbjct: 178 PVARIAYTVEAARVEQRTDLDKLVIDMTTNGTLDPEEAIRRAATILAEQLDAFV---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|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 =  370 bits (949), Expect = e-100,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 222/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ +    +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPHLVNIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  370 bits (949), Expect = e-100,   Method: Composition-based stats.
 Identities = 148/334 (44%), Positives = 222/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ +    +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPHLVNIEQISS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  370 bits (949), Expect = e-100,   Method: Composition-based stats.
 Identities = 162/337 (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---LLKPKTINVEQLGH---NRAKVVLEPFERGYGHTLGNALRRVLLSSMVGYAAT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG---LITIDALYS 178
            +D+E++NPDHVI +L     + M++ V KG GYVP    R  ++       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 KEVKEDINV----KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 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|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 =  370 bits (949), Expect = e-100,   Method: Composition-based stats.
 Identities = 157/336 (46%), Positives = 232/336 (69%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  EL+ P NIE   + +  + R+ +  +PL RGF HTLGNALRR+L+SS+ G AI 
Sbjct: 1   MQRSVSELLTPRNIE---VQEAGKTRSKVTLQPLERGFGHTLGNALRRILLSSMPGCAIV 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|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 =  369 bits (948), Expect = e-100,   Method: Composition-based stats.
 Identities = 149/328 (45%), Positives = 207/328 (63%), Gaps = 7/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           Q  +KP +IE   +G    +   ++ EP  RG+ HTLGNALRR+L+SS+ G A T VQ+ 
Sbjct: 4   QGFLKPRSIEVEPVGT---HHAKIVMEPFERGYGHTLGNALRRILLSSMTGYAPTEVQMT 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 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKV 183
           ++NPDH+ICNL     V M++ V KG GYVP        D       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 SYAVESARVEQRTDLDKLVLDIETNGVISPEEAVRQSARILMDQISVFAALEGAGDSYEA 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +   +   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 241 PV-RGTPQIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 299

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL   GL LGM L +WPP  +E 
Sbjct: 300 NEIKEVLAARGLTLGMKLENWPPLGLER 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 =  369 bits (948), Expect = e-100,   Method: Composition-based stats.
 Identities = 148/328 (45%), Positives = 207/328 (63%), Gaps = 7/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           Q  +KP +IE   +G    N   ++ EP  RG+ HTLGNALRR+L+SS+ G A T VQ+ 
Sbjct: 4   QGFLKPRSIEVEPVG---PNHAKIVMEPFERGYGHTLGNALRRILLSSMTGYAPTEVQMT 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 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKV 183
           ++NP+H ICNL     + M++ V KG GYVP        D       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 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +   +   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 241 PV-RGTPQIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 299

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL   GL LGM L +WPP  +E 
Sbjct: 300 NEIKEVLAARGLTLGMKLENWPPLGLER 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 =  369 bits (948), Expect = e-100,   Method: Composition-based stats.
 Identities = 148/334 (44%), Positives = 223/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ ++   +         +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPHLVDIEQISS---THAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  369 bits (948), Expect = e-100,   Method: Composition-based stats.
 Identities = 149/334 (44%), Positives = 223/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +   +     +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISSTQ---AKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  369 bits (948), Expect = e-100,   Method: Composition-based stats.
 Identities = 151/334 (45%), Positives = 223/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ +    +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPHLVNIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  369 bits (948), Expect = e-100,   Method: Composition-based stats.
 Identities = 155/333 (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---LLKPKAINVDPLG---GHRAKVTLEPFERGFGHTLGNALRRVLLSSMVGYAPT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG---LITIDALYS 178
            +D+E++NPDHVI +L     + M++ V KG GYVP    R  ++P      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|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 =  369 bits (948), Expect = e-100,   Method: Composition-based stats.
 Identities = 160/326 (49%), Positives = 217/326 (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   YKFWREMIKPKGFEVDR-DSLRDDYAKFIIRPLERGFGVTLGNSLRRILLSSMMGSAITA 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 DKIEVLNPDLPIATLGANANFNAEIVVSFGRGYVPV-ENRETDLPVGFIGVDALYSPIRK 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|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 =  369 bits (948), Expect = e-100,   Method: Composition-based stats.
 Identities = 149/334 (44%), Positives = 223/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ +    +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPHLVNIEQISS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  369 bits (948), Expect = e-100,   Method: Composition-based stats.
 Identities = 154/336 (45%), Positives = 215/336 (63%), Gaps = 1/336 (0%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
            +NW +L++P  I        +        EPL RG+  T+GNALRRVL+SSL+GAA  A
Sbjct: 12  SRNWAKLVRPEQI-VCDSDPNDTMYGKFTYEPLERGYGVTIGNALRRVLLSSLQGAAFVA 70

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
           V+I GV HE ++I GV ED+TD+ILNIK + L M+ D  + +T+     G VTA DI T 
Sbjct: 71  VKISGVQHEFTTIPGVLEDITDVILNIKQVRLGMTTDEPQHLTLSVSKKGPVTAADIMTN 130

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
            ++EVLNP+  I  L  D  + ME  V  G GYVPA  H    D IGLI +DA +SP++K
Sbjct: 131 ANVEVLNPELHIATLTEDMELSMEFEVRMGKGYVPADMHEGLPDTIGLIKLDASFSPVRK 190

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V+YTVE AR GQ+ +YDKL + + TDGS+  ED++A +++I++DQ+ +FI+F+E      
Sbjct: 191 VAYTVEQARVGQMTNYDKLILEVWTDGSVLPEDAIAYSAKIIKDQISVFISFDERISGES 250

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                 S   N  L K ++ELELSVR+TNCLR  NI  +G+L+QR EA+ML+  NFG+KS
Sbjct: 251 GGEGGGSADINDNLFKGIDELELSVRATNCLRSANIATVGELVQRPEAEMLKTKNFGKKS 310

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           L EIK VL +MGL  GM + ++  +  E   K++ +
Sbjct: 311 LDEIKAVLESMGLDFGMKIDNFEKKYQEWKRKQHHE 346


>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 =  369 bits (947), Expect = e-100,   Method: Composition-based stats.
 Identities = 127/318 (39%), Positives = 190/318 (59%), Gaps = 4/318 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLSE----ETVNETRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+T+IILN+K + +    D    + + K+GPG VTA DI   + + V N
Sbjct: 61  HEFSTVPGVKEDVTEIILNLKELVVSSEEDEPVTMYLRKQGPGEVTAADIVPPSGVTVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I +L+    + +EL V +G GYVPA  ++     IG I ID++YSP+ KV+Y VE+
Sbjct: 121 PDLHIASLNGKGKLEIELVVERGRGYVPALQNKQAGAEIGRIPIDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SIT  D+VA A + L +  G+        + ++   + + 
Sbjct: 181 TRVEQRTDFDKLVLDVETKPSITPRDAVASAGKTLVELFGLARELNVDAEGIEIGPSPQE 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                A    +E+L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 ADTIAAYAMPIEDLDLTVRSYNCLKREGIHTVGELVSRSEADLLDIRNFGAKSIDEVKMK 300

Query: 310 LGTMGLFLGMNLPDWPPE 327
           L  +GL L  + P + P 
Sbjct: 301 LAGLGLTLKDSPPGFDPT 318


>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 =  369 bits (947), Expect = e-100,   Method: Composition-based stats.
 Identities = 147/331 (44%), Positives = 218/331 (65%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  E + P  IE   +         +  EPL RGF HTLG+ALRR+L+SS+ G A+ 
Sbjct: 1   MQRSLNEFLTPRTIEVNQI---NATHAKVTLEPLERGFGHTLGSALRRILLSSMPGCAVV 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +D+E+ NPD VICNL+ +  V+M+L V++G GY PA    + +D    I    +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 EPEKVEEQEEIDP---ILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL + GL LGM L +WPP SI
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASI 325


>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 =  369 bits (947), Expect = e-100,   Method: Composition-based stats.
 Identities = 149/334 (44%), Positives = 221/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISS---THAKVILEPLERGFGHTLGNALRRILLSSMPGYAVT 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|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 =  369 bits (947), Expect = e-100,   Method: Composition-based stats.
 Identities = 152/336 (45%), Positives = 221/336 (65%), Gaps = 9/336 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  + + P +I+   +     NR  +  EPL RGF HTLGNALRR+L+SS+ GAAIT
Sbjct: 1   MQRSANDFLTPRHIDVQEV---NANRAKITLEPLERGFGHTLGNALRRILLSSMPGAAIT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            + +EV NPDHVI +L   A V M L V+ G GYVPA+   +E D    I    +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 EAVQEKEE---DKIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L  WPP S++   K
Sbjct: 295 GKKSLTEIKDVLASKGLSLGMVLEAWPPASLKNDDK 330


>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 =  368 bits (946), Expect = e-100,   Method: Composition-based stats.
 Identities = 147/328 (44%), Positives = 205/328 (62%), Gaps = 7/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           Q  +KP +IE   +G    +   ++ EP  RG+ HTLGNALRR+L+SS+ G A T VQ+ 
Sbjct: 4   QGFLKPRSIEVEPVGT---HHAKIVMEPFERGYGHTLGNALRRILLSSMTGYAPTEVQMT 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 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKV 183
           ++NP H ICNL     + M++ V KG GYVP        D       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 SYAVESARVEQRTDLDKLVLDIETNGVISPEEAVRQSARILMDQISVFAALEGAGDSYEA 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +   +   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 241 PV-RGTPQIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 299

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL   GL LGM L +WPP  +E 
Sbjct: 300 NEIKEVLAARGLTLGMKLENWPPLGLER 327


>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 =  368 bits (946), Expect = e-100,   Method: Composition-based stats.
 Identities = 142/310 (45%), Positives = 206/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDG
Sbjct: 3   EIEKP-KIETVEL-SEDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 AKLAELGLSL 310


>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 =  368 bits (946), Expect = e-100,   Method: Composition-based stats.
 Identities = 156/336 (46%), Positives = 221/336 (65%), 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +DIE+ NPDH+IC L+  + V M+LTV++G GY PA       +    I    +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 QAVTSDAE---DEVDPVLLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L  WPP S+    K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLESWPPASLRNDEK 330


>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 =  368 bits (946), Expect = e-100,   Method: Composition-based stats.
 Identities = 143/338 (42%), Positives = 219/338 (64%), Gaps = 8/338 (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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--RTENDPIGLITIDALYSP 179
              ++++N  H+I NL     + M + V +G GY PA+      E+  IG + +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 PEPVEE---REEIDPILLRPVDDLELTVRSANCLKAENVYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337
           +KSL EIK VL + GL LGM L +WPP S+++  +  +
Sbjct: 295 KKSLTEIKDVLASKGLSLGMRLENWPPASLKDDDRVLK 332


>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 =  368 bits (946), Expect = e-100,   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   MQNSPTEYLKPRVVDVEVL---SPLRARVTLEPMERGFGYTLGNALRRVLLSSIPGFAIT 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|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 = 208/313 (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-KIETVELTDNG-TYGRFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 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|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 =  368 bits (945), Expect = e-100,   Method: Composition-based stats.
 Identities = 127/318 (39%), Positives = 190/318 (59%), Gaps = 4/318 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLTE----DSVTETRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TDIILN+K + +    D    + + K+GPG VTAGDI     + V N
Sbjct: 61  HEFTTVPGVKEDVTDIILNLKELVVSSEEDEPVTMYLRKQGPGPVTAGDIVPPAGVTVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLHIATLNDKGRLEVELVVERGRGYVPAMQNKATGAEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SIT  D++A A + L +  G+        + ++   + + 
Sbjct: 181 TRVEQRTDFDKLVLDVETKPSITPRDALASAGKTLVELFGLARELNVDAEGIEIGPSPQE 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                A    +EEL+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 ADTIAAFAMPIEELDLTVRSYNCLKREGIHTVGELVGRSEADLLDIRNFGAKSIDEVKMK 300

Query: 310 LGTMGLFLGMNLPDWPPE 327
           L  +GL L  + P + P 
Sbjct: 301 LVGLGLALKDSPPGFDPS 318


>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 =  368 bits (945), Expect = e-100,   Method: Composition-based stats.
 Identities = 181/338 (53%), Positives = 247/338 (73%), Gaps = 4/338 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + KNW  LIK + + Y    +   N++ +I EPL RGF  TLGNA+RRVL+SSL+GAA+T
Sbjct: 4   LSKNWNALIKTDKVSYESFPE-TNNKSKIIVEPLERGFGLTLGNAMRRVLLSSLQGAAVT 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  +E
Sbjct: 183 KSVTYKVENTRIGQVTDYDKLIMFVETNGDILPEMAVGLAARILQEQLQLFISFEE--QE 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             + +   +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTEADMLR  NFGR
Sbjct: 241 EDKQVKTDALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTEADMLRTPNFGR 300

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK +L    L  GM++PDWPPE+I EL+K+YED
Sbjct: 301 KSLNEIKEILAKFSLRFGMDVPDWPPENIHELSKRYED 338


>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 =  368 bits (945), Expect = e-100,   Method: Composition-based stats.
 Identities = 129/311 (41%), Positives = 202/311 (64%), Gaps = 2/311 (0%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E+ KP  IE + +  E+      + EPL RG+  TLGNALRRVL+SSL GAA+T+V+I+
Sbjct: 2   NEMEKPT-IETVEI-SEDGTYGRFVVEPLERGYGITLGNALRRVLLSSLPGAAVTSVRIE 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE S+I GV ED T+IILN+K + +KM  D  + + +  +G G V A DI    ++E
Sbjct: 60  GVLHEFSTIPGVVEDTTEIILNLKELAIKMHTDEPQILRVEAQGEGEVRAADIIAPPEVE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           ++N DH+I  L+ D  + ME+TV +G GYVPA  ++  +  IGLI +D++++PI+KV++ 
Sbjct: 120 IVNGDHLIATLEHDGRLFMEMTVQRGRGYVPADRNKGPDRSIGLIPVDSIFTPIRKVNFQ 179

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+ R G+V DYD+L++ I T+G++  +++ + A+RIL D L +F+   +  +       
Sbjct: 180 VENTRVGKVTDYDRLTLEIWTNGTVAPDEAASQAARILTDHLALFLTLTDQTRGAGTAAE 239

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L   ++EL+LSVRS NCL+   I  +G+L+++T  DM+R+ N G+KSL E+
Sbjct: 240 KEDDARAKLLEMSIDELDLSVRSYNCLKRAGINTIGELVEKTPEDMMRVRNLGKKSLEEV 299

Query: 307 KGVLGTMGLFL 317
           +  L  +GL L
Sbjct: 300 EEKLAALGLSL 310


>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 =  368 bits (945), Expect = e-100,   Method: Composition-based stats.
 Identities = 153/333 (45%), Positives = 219/333 (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--ALLKPRIID---VQSTSPVQARVTMEPFERGFGHTLGNALRRILLSSLPGHAPT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP--AKHHRTENDPIGLITIDALYSP 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 E---RVEAASPTIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTETELLKTPNLG 292

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEEL 332
           RKSL EIK VL + GL LGM L +WPP  +E+L
Sbjct: 293 RKSLNEIKEVLASRGLTLGMKLENWPPAGLEKL 325


>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 =  368 bits (945), Expect = e-100,   Method: Composition-based stats.
 Identities = 146/326 (44%), Positives = 212/326 (65%), Gaps = 7/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP     I +    ++   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPK---IIAVEPLGDHHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 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 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKVSY 185
           NP+HVI +L     + M++ V +G GYVP    +  ++   +   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  +   +   
Sbjct: 182 AVESARVEQRTDLDKLVMNIETDGVISPEEAIRQSARILVDQLSVFAALEGTESAAEAAS 241

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           +  +   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL E
Sbjct: 242 SR-TPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSLNE 300

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL + GL LGM L +WPP  +E+
Sbjct: 301 IKEVLASRGLTLGMKLENWPPAGLEK 326


>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 =  368 bits (944), Expect = e-100,   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   MQNSPTEYLKPRVVDVEVL---SPLRARVTLEPMERGFGYTLGNALRRVLLSSIPGFAIT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALYS 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|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 =  368 bits (944), Expect = e-100,   Method: Composition-based stats.
 Identities = 142/317 (44%), Positives = 205/317 (64%), Gaps = 1/317 (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 IKGVLGTMGLFLGMNLP 322
           IK +L  MGL LGM + 
Sbjct: 301 IKEILANMGLSLGMRID 317


>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 =  368 bits (944), Expect = e-100,   Method: Composition-based stats.
 Identities = 182/338 (53%), Positives = 247/338 (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  +E
Sbjct: 183 KSVTYKVENTRIGQVTDYDKLIMFVETNGDILPEMAVGLAARILQEQLQLFISFEE--QE 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             + +   +LPF+P LLK+V+ELELSVRS NCL+ +NI+Y+GDL++RTEADMLR  NFGR
Sbjct: 241 EDKQVKTDALPFSPYLLKRVDELELSVRSANCLKNDNIIYIGDLVKRTEADMLRTPNFGR 300

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK +L    L  GM++PDWPPE+I EL+K+YED
Sbjct: 301 KSLNEIKEILAKFSLRFGMDVPDWPPENIHELSKRYED 338


>gi|330432099|gb|AEC17158.1| DNA-directed RNA polymerase subunit alpha [Gallibacterium anatis
           UMN179]
          Length = 327

 Score =  368 bits (944), Expect = e-100,   Method: Composition-based stats.
 Identities = 145/332 (43%), Positives = 219/332 (65%), Gaps = 8/332 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPHLVDIEQI---SPTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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-DVDAVVRMELTVSKGHGYVPA-KHHRTENDPIGLITIDALYSP 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|332107893|gb|EGJ09117.1| DNA-directed RNA polymerase subunit alpha [Rubrivivax
           benzoatilyticus JA2]
          Length = 328

 Score =  368 bits (944), Expect = e-100,   Method: Composition-based stats.
 Identities = 150/326 (46%), Positives = 210/326 (64%), Gaps = 6/326 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP  I    +      R   + EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPKAI---HVEPLGGYRAKAVLEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 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 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG---LITIDALYSPIKKVSY 185
           NPDHVI +L     + M++ V KG GYVP    R  ++       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|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 =  368 bits (944), Expect = e-99,   Method: Composition-based stats.
 Identities = 142/310 (45%), Positives = 206/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDG
Sbjct: 3   EIEKPR-IETVEI-SEDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 AKLAELGLSL 310


>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 =  368 bits (944), Expect = e-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-KIETVDL-NEDGTYGRFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 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|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 =  368 bits (944), Expect = e-99,   Method: Composition-based stats.
 Identities = 156/337 (46%), Positives = 224/337 (66%), Gaps = 2/337 (0%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
            +NW EL+KP  ++        E     + EPL RGF  TLGNALRRVL+SSL+GAAI A
Sbjct: 12  SRNWTELVKPEVLD--KDPSSTETFGRFVCEPLERGFGTTLGNALRRVLLSSLQGAAIVA 69

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
            +I+GV HE S+I GV ED+T+IILN+K + L M+ D  +R+T+  +  G V A  IQ  
Sbjct: 70  ARIEGVQHEFSTIPGVIEDVTEIILNLKQVRLAMATDEPQRLTLLAKEKGEVRASAIQGN 129

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           +++ VL+ D +I  L  D   R++L V  G GYVPA  H      IGLI +DA +SP+KK
Sbjct: 130 HNVSVLSEDVLIATLSEDRDFRIDLEVRMGKGYVPADMHEGLESEIGLILLDASFSPVKK 189

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V+YT+E AR GQ+ +YDKL + + TDGSI  ED+++ +++IL+DQL +FINF+E + E +
Sbjct: 190 VAYTIEQARVGQMTNYDKLVLEVTTDGSIAPEDAISYSAKILKDQLTVFINFDEKESEAE 249

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           ++     +  NP+L K ++ELELSVR+TNCL+  NI  +G+L+Q+TE +ML+  NFG+KS
Sbjct: 250 KNRRRDDIELNPSLFKSIDELELSVRATNCLKSANIQTVGELMQKTEHEMLKTKNFGKKS 309

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             EI+ VL  MGL  GM + ++  +  E L +K  D+
Sbjct: 310 FEEIRRVLEDMGLEFGMRIENFDQKYQEWLKRKQTDE 346


>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 =  367 bits (943), Expect = e-99,   Method: Composition-based stats.
 Identities = 154/335 (45%), Positives = 216/335 (64%), Gaps = 8/335 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQ-EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 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 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG---LITIDALY 177
           T +D+E++NPDHVI +L     + M++ V KG GYVP    R  ++P      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 KKEV-KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 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|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 =  367 bits (943), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 148/336 (44%), Positives = 217/336 (64%), Gaps = 1/336 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW EL+KP+ I        +      + EPL RG+  T+GNA+RRVL++SL+GAA  AV
Sbjct: 13  RNWSELVKPDQISRAS-ESADTMYGKFVCEPLERGYGTTIGNAMRRVLLASLQGAAFVAV 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 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            EI+ VLG M L  GM +  +  +  E L +K +++
Sbjct: 312 DEIRRVLGEMSLDFGMKVDGFEKKYQEWLKRKQQNE 347


>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 =  367 bits (943), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 160/336 (47%), Positives = 220/336 (65%), Gaps = 1/336 (0%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
            +NW+ELIKP  IE              + EPL RGF  T+GNALRR+L+SSL+GAAI +
Sbjct: 6   SRNWRELIKPKRIEIDQ-ETNTSTYGKFVCEPLERGFGITIGNALRRILLSSLQGAAIVS 64

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
           V+ + V+HE SS+ GV ED+TDIILN+K I LK        + + + G G+VTAGDI+T 
Sbjct: 65  VKFEDVVHEFSSMPGVLEDVTDIILNLKEIKLKTLDVEEAVIKVNREGEGIVTAGDIETD 124

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
             +EVL P   I  L+ +  + ME+ V  G GYVPA+  + EN PIG+I IDA +S +KK
Sbjct: 125 GSVEVLEPVQHIATLNKEGKLNMEMVVKMGKGYVPAERLKEENTPIGVIAIDATFSCVKK 184

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V+Y V ++R GQV DYDKL++ + TDGS+  ED+VA A++IL++Q+  FINFEE  + V+
Sbjct: 185 VNYVVTNSRVGQVTDYDKLTLEVWTDGSVFPEDAVAFAAKILKEQMNPFINFEEEIEPVE 244

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           E+   +    N  L + V +LELSVRS NCL+   I  +G+L+Q+T+A+ML+  NFGRKS
Sbjct: 245 EEEVREDQEVNENLFRPVSDLELSVRSANCLQNAKINLIGELVQKTDAEMLKTKNFGRKS 304

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           L EIK +L  MGL LGM L  +PP    +   +  D
Sbjct: 305 LNEIKAILSDMGLSLGMKLDFFPPSQESDDEGEKTD 340


>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 =  367 bits (943), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 162/337 (48%), Positives = 216/337 (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---LLKPKTINVEQLGH---NRAKVVLEPFERGYGHTLGNALRRVLLSSMVGYAAT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG---LITIDALYS 178
            +D+E++NPDHVI NL     + M++ V KG GYVP    R  ++       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 KEVKEDINV----KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 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|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 =  367 bits (943), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 148/333 (44%), Positives = 218/333 (65%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E ++P  ++   +      R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLRPRLVDIEQISS---TRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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 PVSRIAYNVEAARVEQRTNLDKLVIDMETDGTLDPEEAIRRAATILAEQLDAFVDLRDV- 236

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              + +   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 237 --TEPEQKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 327


>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 =  367 bits (943), Expect = 1e-99,   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    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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG---LITIDALYS 178
            +D+E++NP+HVI  L     + M++ V KG GYVP    R  ++       I +DA +S
Sbjct: 115 PHDVEIVNPEHVIATLSAGGKLDMQIKVEKGRGYVPGNLRRYADEATKSIGRIVLDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+K+VSYTVESAR  Q  D DKL + I+T+G+IT ED+V  +++IL +QL +F   E  +
Sbjct: 175 PVKRVSYTVESARVEQRTDLDKLVVEIETNGAITAEDAVRASAKILVEQLAVFAQLEGGE 234

Query: 239 KEVKEDI--NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 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|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 =  367 bits (942), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 143/323 (44%), Positives = 214/323 (66%), Gaps = 9/323 (2%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++P   +   L     NR  ++ EPL RG+ HTLGNALRRVL+SS+ G AIT V+IDGVL
Sbjct: 9   LRPRGPQIERL---NGNRAKIVIEPLERGYGHTLGNALRRVLLSSIPGFAITEVEIDGVL 65

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE ++++G+ ED+ +++LN+K + ++M       +++ K+GPGVVTAGDI+T + +E+LN
Sbjct: 66  HEYTTVEGLQEDVLEVLLNLKDVAIRMHTGESATLSLAKQGPGVVTAGDIKTDHSVEILN 125

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYT 186
           P+HVIC+L  D  + M L + +G GY PA   R  ++    I    +DA +SP+++V+Y+
Sbjct: 126 PEHVICHLTKDTALNMRLKIERGFGYQPATSRRRPDEETRAIGRLMLDASFSPVRRVAYS 185

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+AR  Q  D DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +   
Sbjct: 186 VEAARVEQRTDLDKLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPAQ 245

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
               P    LL+ +++LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N G+KSL EI
Sbjct: 246 AGVDP---VLLRPIDDLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKSLTEI 302

Query: 307 KGVLGTMGLFLGMNLPDWPPESI 329
           K VL   GL LGM L +WPP  +
Sbjct: 303 KEVLAQRGLSLGMKLENWPPAGV 325


>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 =  367 bits (942), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 150/333 (45%), Positives = 221/333 (66%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISS---THAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 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-DVDAVVRMELTVSKGHGYVPAKH--HRTENDPIGLITIDALYS 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|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 =  367 bits (942), Expect = 1e-99,   Method: Composition-based stats.
 Identities = 150/333 (45%), Positives = 221/333 (66%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISS---THAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 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-DVDAVVRMELTVSKGHGYVPAKH--HRTENDPIGLITIDALYS 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|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 =  367 bits (942), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 149/333 (44%), 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYS 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+++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 EPVEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIQYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPPESI E
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPESIAE 327


>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 =  367 bits (942), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 149/333 (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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYS 178
            +D+E++NP+HVIC+L  +A + M + +  G GYVPA    H   +  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 EPVAKEEK---PEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP S+ E
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASLSE 327


>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 =  367 bits (942), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 143/310 (46%), Positives = 205/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDG
Sbjct: 3   EIEKP-KIETVEL-SEDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 AKLAELGLSL 310


>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 =  366 bits (941), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 143/310 (46%), Positives = 206/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDG
Sbjct: 3   EIEKPR-IETVEI-SEDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 AKLAELGLSL 310


>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 =  366 bits (941), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 141/325 (43%), Positives = 213/325 (65%), Gaps = 9/325 (2%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++P   +   L    +NR  ++ EPL RG+ HTLGNALRRVL+SS+ G AIT V+IDGVL
Sbjct: 9   LRPRGPQIERL---TDNRAKVVIEPLERGYGHTLGNALRRVLLSSIPGFAITEVEIDGVL 65

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE ++++G+ ED+ D++LN+K + ++M       +++ K+GPG VTA DI+T +++E++N
Sbjct: 66  HEYTTVEGLQEDVLDVLLNLKDVAIRMHSGDSATLSLSKQGPGTVTAADIRTDHNVEIIN 125

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYT 186
            DHVIC+L  D  + M L + +G GY PA   R  ++    I    +DA +SP+++V+Y 
Sbjct: 126 GDHVICHLTKDTALNMRLKIERGFGYQPAAARRRPDEETRTIGRLMLDASFSPVRRVAYA 185

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+AR  Q  D DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +   
Sbjct: 186 VEAARVEQRTDLDKLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPAA 245

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
               P    LL+ +++LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N G+KSL EI
Sbjct: 246 SGVDP---VLLRPIDDLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKSLTEI 302

Query: 307 KGVLGTMGLFLGMNLPDWPPESIEE 331
           K VL   GL LGM L +WPP  + +
Sbjct: 303 KEVLAQRGLALGMKLENWPPAGVAQ 327


>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 =  366 bits (941), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 147/333 (44%), Positives = 210/333 (63%), Gaps = 9/333 (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 TEVEVQQA---PQIDPVLLRPVDDLELTVRSANCLKAESIYYIGDLIQRNESDLLKAPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK +L T GL LGM + +WPP  +E+
Sbjct: 295 GRKSLNEIKDILATKGLSLGMKVENWPPAGVEK 327


>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 =  366 bits (941), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  366 bits (941), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 144/334 (43%), Positives = 216/334 (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-DAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 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
            +  +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 SEPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 328


>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 =  366 bits (941), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 141/318 (44%), Positives = 206/318 (64%), Gaps = 1/318 (0%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           W+   KP  +         E      A+P  RGF  T+GN LRR L+SS+ GAA+TAV++
Sbjct: 3   WRGFQKPKRLAV-EGETLTEKYGKFSAQPFERGFGTTIGNGLRRTLLSSIEGAAVTAVRL 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|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 =  366 bits (941), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 150/333 (45%), Positives = 220/333 (66%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISS---THAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 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-DVDAVVRMELTVSKGHGYVPAKH--HRTENDPIGLITIDALYS 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|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 =  366 bits (941), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 153/333 (45%), Positives = 212/333 (63%), Gaps = 11/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +   L+KP  IE  VLG        ++ EP  RG+ HTLGNALRRVL+SS+ G A T
Sbjct: 1   MQNS---LLKPRIIEVEVLGAG---HAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYS 178
            +D+E++NPDHVI +L     + M++ V KG GYVP    R   D       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|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 =  366 bits (941), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 125/307 (40%), Positives = 185/307 (60%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
               E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I GV E
Sbjct: 12  EAVAETRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSLRIDGVLHEFTTIPGVKE 71

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+TD+ILN+K + +    D    + + K+GPG VTA DI     + V NPD  I  L+  
Sbjct: 72  DVTDVILNLKELVVSSEEDEPVTMYLRKQGPGEVTAADIVPPAGVTVHNPDLHIATLNGK 131

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+DK
Sbjct: 132 GKLEIELVVERGRGYVPAVQNKQTGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDK 191

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L + ++T  SIT  D+VA A R L +  G+        + ++   +        A    +
Sbjct: 192 LILDVETKPSITPRDAVASAGRTLVELFGLARELNVDAEGIEIGPSPAEADTIAAYAMPI 251

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           E+L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L  +GL L  +
Sbjct: 252 EDLDLTVRSYNCLKREGIHTVGELVSRSEADLLDIRNFGAKSIDEVKLKLVGLGLSLKDS 311

Query: 321 LPDWPPE 327
            P + P 
Sbjct: 312 PPGFDPS 318


>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 =  366 bits (940), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 161/335 (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---LLKPKAINVEQLGH---NRAKVALEPFERGYGHTLGNAIRRVLLSSMVGYAAT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG---LITIDALYS 178
            +D+E++NPDHVI NL     + M++ V KG GYVP    R  ++       I +DA +S
Sbjct: 115 PHDVEIVNPDHVIANLSAGGKLDMQIKVEKGRGYVPGNLRRYADESTKSIGRIVLDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+K+VSYTVESAR  Q  D DKL + I+T+G+IT ED+V  +++IL +QL +F   E  +
Sbjct: 175 PVKRVSYTVESARVEQRTDLDKLVVEIETNGAITAEDAVRASAKILVEQLAVFAQLEGGE 234

Query: 239 KEVKEDI--NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 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|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 =  366 bits (940), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 124/308 (40%), Positives = 186/308 (60%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
               E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVLHE S++ GV E
Sbjct: 38  DPISEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVLHEFSTVPGVKE 97

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+TD+ILN+K + +    D    + + K+GPG VTA DI     +EV NPD  +  L+  
Sbjct: 98  DVTDLILNLKELVVSSDNDEPTVMYLRKQGPGEVTAADIAPPAGVEVHNPDLHLATLNDK 157

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             + +ELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+ R  Q  D+D+
Sbjct: 158 GKLEIELTVERGRGYVSAAQNKQPGQEIGRIPIDSIYSPVLKVTYKVEATRVEQRTDFDR 217

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L + ++T  SI+  D++A A + L    G+        + V    +         L   +
Sbjct: 218 LIVDVETKQSISPRDAMASAGKTLVGLFGLAQELNAEAEGVDIGPSAADAALAADLALPI 277

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           EE++L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  LG MGL L  +
Sbjct: 278 EEMDLTVRSYNCLKREGIHTIGELVSRSEADLLDIRNFGQKSIDEVKTKLGAMGLQLKDS 337

Query: 321 LPDWPPES 328
            P + P  
Sbjct: 338 PPGFDPRQ 345


>gi|221133740|ref|ZP_03560045.1| DNA-directed RNA polymerase subunit alpha [Glaciecola sp. HTCC2999]
          Length = 326

 Score =  366 bits (940), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 145/330 (43%), Positives = 222/330 (67%), Gaps = 9/330 (2%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           +  E +KP  ++   +      R  ++ EPL RGF HTLGNALRR+L+SS+ G A+T V+
Sbjct: 3   SVTEFLKPRLVD---IENVSPTRAKVVLEPLERGFGHTLGNALRRILLSSMPGVAVTEVE 59

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G +   +T+ K G G V AGDIQ   D
Sbjct: 60  IDGVLHEYSTKEGVQEDVIEILLNLKGLAVRLEGKTEATLTLVKSGAGAVVAGDIQHDGD 119

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALYSPIK 181
           +E++NP+HVIC L  +A V M + V  G GYVPA   +    ++ PIG + +DA +SP++
Sbjct: 120 VEIINPEHVICTLTGEAEVSMRIKVETGRGYVPASVRRSSEEDDRPIGRLLVDASFSPVE 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +++Y+VESAR  Q  D DKL + ++T+G++  E+++  ++ IL +QL  F++  +  +  
Sbjct: 180 RIAYSVESARVEQRTDLDKLIIDMETNGTLDPEEAIRRSATILAEQLDAFVDLRDVSQPE 239

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++       F+P LL+ V++LEL+VRS NCL+ E + Y+GDL+QRTE ++L+  N G+K
Sbjct: 240 AKEEK---PEFDPILLRPVDDLELTVRSANCLKAEAVQYIGDLVQRTEVELLKTPNLGKK 296

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           SL EIK VL + GL LGM L +WPPESI +
Sbjct: 297 SLTEIKDVLASRGLSLGMRLENWPPESIAD 326


>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 =  366 bits (940), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 159/334 (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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG---LITIDALYS 178
            +D+E++NPDHVI +L     + M++ V KG GYVP    R  ++P      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 KEVKEDINVK-SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 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|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 =  366 bits (940), Expect = 2e-99,   Method: Composition-based stats.
 Identities = 153/336 (45%), Positives = 221/336 (65%), 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +DIE+ NP+H+IC L+  + V M+LT+++G GY PA       +    I    +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 QAVTSDAE---DEVDPVLLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L  WPP S+    K
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLESWPPASLRNDEK 330


>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 =  366 bits (940), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  366 bits (940), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 150/333 (45%), Positives = 221/333 (66%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISS---THAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 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-DVDAVVRMELTVSKGHGYVPAKH--HRTENDPIGLITIDALYS 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|332175074|gb|AEE24328.1| DNA-directed RNA polymerase, alpha subunit [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 329

 Score =  366 bits (940), Expect = 3e-99,   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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYS 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+++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 EPVEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIQYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPPESI E
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPESIAE 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 =  366 bits (940), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 161/335 (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---LLKPKTINVEQLGH---NRAKVALEPFERGYGHTLGNAIRRVLLSSMVGYAAT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG---LITIDALYS 178
            +D+E++NPDHVI +L     + M++ V KG GYVP    R  ++       I +DA +S
Sbjct: 115 PHDVEIVNPDHVIAHLSQGGKLDMQIKVEKGRGYVPGNLRRYADESTKSIGRIVLDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+K+VSYTVESAR  Q  D DKL + I+T+G+IT ED+V  +++IL +QL +F   E  +
Sbjct: 175 PVKRVSYTVESARVEQRTDLDKLVVEIETNGAITAEDAVRASAKILVEQLAVFAQLEGGE 234

Query: 239 KEVKEDI--NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 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|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 =  366 bits (939), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 148/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  366 bits (939), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 150/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    E +KP  ++   +   +     +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGAVTEFLKPRLVDIEQISSTQ---AKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  366 bits (939), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 149/333 (44%), Positives = 221/333 (66%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISS---THAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 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-DVDAVVRMELTVSKGHGYVPAKH--HRTENDPIGLITIDALYS 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|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 =  366 bits (939), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 146/334 (43%), 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   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  366 bits (939), Expect = 3e-99,   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---IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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
           +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>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 =  366 bits (939), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 153/334 (45%), Positives = 221/334 (66%), 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 LFGED---GPQFDPLLLHPVDDLELTVRSANCLKAENIFYIGDLIQRSEADLLKTPNLGK 294

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           KSL EIK VL T GL LGM L +WPPE +++L +
Sbjct: 295 KSLTEIKDVLATKGLSLGMRLENWPPEGLKKLNQ 328


>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 =  366 bits (939), Expect = 3e-99,   Method: Composition-based stats.
 Identities = 149/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    E +KP  ++   +   +     +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGAVTEFLKPRLVDIEQVSSTQ---AKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  366 bits (939), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 123/328 (37%), Positives = 192/328 (58%), Gaps = 4/328 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++I+G L
Sbjct: 5   QRPTLTE----ETISEQRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIEGTL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+IILN+KG+ +    D    + + K+GPG VTA DI     +EV N
Sbjct: 61  HEFTTVPGVKEDVTEIILNLKGLVVSSDSDEPVTMYLRKQGPGEVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  I  L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PELHIATLNGKGRLEIELVVERGRGYVPAPQNKQPGQEIGRIPVDSIYSPVLKVTYAVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  SI   D++A A   L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDRLVVDVETKPSIAPRDAIASAGSTLVELFGLLRELNIDAEGIEVGPSPAE 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                     +E+++L+VRS NCL+ E +  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 AADIANFSMPIEDMDLTVRSYNCLKREGVHTVGELVTRSEADLLDIRNFGAKSIDEVKMK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYE 337
           L  MGL L  + P + P S+E   + YE
Sbjct: 301 LAAMGLALKDSPPGFIPTSVESYDEGYE 328


>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 =  366 bits (939), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 151/334 (45%), Positives = 222/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ +    +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPHLVNIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  365 bits (938), Expect = 4e-99,   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   MQNSPTEYLKPRVVDVEVI---SPVRARVTLEPMERGFGYTLGNALRRVLLSSIPGFAIT 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|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 =  365 bits (938), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 126/320 (39%), Positives = 197/320 (61%), Gaps = 4/320 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V     ENR+  + EPL  GF +T+GN+LRR L+SS+ GAA+T+++I+GVL
Sbjct: 5   QRPTLTEEVV----SENRSRFVLEPLEPGFGYTIGNSLRRTLLSSIPGAAVTSIRIEGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TDIILN+KG+ +    D    + + K+GPG VTAGDI     +EV N
Sbjct: 61  HEFTTVPGVKEDVTDIILNLKGLVVSSVEDEPVTMYLKKQGPGAVTAGDIVPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLHIATLNEKGRLEIELVVERGRGYVPAGLNKDAGHEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  S+T  D++A A + L +  G+     E  + ++   +   
Sbjct: 181 TRVHQRTDFDRLVLDVETKNSMTARDALASAGKTLVELFGLARELNEEAEGIEIGPSPAE 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                A    +++L+LSVRS NCL+ E +  +G+L+ R+E+D+L + NFG+KS+ E+K  
Sbjct: 241 ADHIAAYGMPIDDLDLSVRSYNCLKREGVHTVGELVARSESDLLDIRNFGQKSIDEVKVK 300

Query: 310 LGTMGLFLGMNLPDWPPESI 329
           L  +GL L    P + P S+
Sbjct: 301 LVELGLSLKDAPPGFDPASV 320


>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 =  365 bits (938), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 146/334 (43%), 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   MQGSVTEFLKPRLVDIEQVNS---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 +
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
           +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>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 =  365 bits (938), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 151/326 (46%), Positives = 214/326 (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 NPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALYSPIKKVSY 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|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 =  365 bits (938), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 152/333 (45%), Positives = 212/333 (63%), Gaps = 11/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +   L+KP  IE  VLG        ++ EP  RG+ HTLGNALRRVL+SS+ G A T
Sbjct: 1   MQNS---LLKPRIIEVEVLGAG---HAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYS 178
            +D+E++NPDHVI +L     + M++ V KG GYVP    R   D       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|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 =  365 bits (938), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 153/336 (45%), Positives = 220/336 (65%), 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +DIE+ NPDHVIC+L+  + + M+LTV++G GY PA       +    I    +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 ESESVEEEDEVDP---ILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           G+KSL EIK VL + GL LGM L +WPP S++   +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLDNWPPASLKNDDR 330


>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 =  365 bits (938), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  365 bits (938), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 148/334 (44%), 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   MQGSVTEFLKPRLVD---IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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
           +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 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 =  365 bits (938), Expect = 4e-99,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  365 bits (938), Expect = 5e-99,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  365 bits (937), Expect = 5e-99,   Method: Composition-based stats.
 Identities = 149/330 (45%), Positives = 219/330 (66%), Gaps = 9/330 (2%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           +  E +KP  +E   +      R  +  EPL RGF HTLGNALRR+L+SS+ G A+T V+
Sbjct: 3   SVTEFLKPRLVE---IENVSPTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVE 59

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G +   +T+ K G G V AGDIQ   D
Sbjct: 60  IDGVLHEYSTKEGVQEDVIEILLNLKGLAVRLEGKTEATLTLVKSGAGPVVAGDIQHDGD 119

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYSPIK 181
           +E+ NPDHVIC L  +A + M + V  G GYVPA   R    ++ PIG + +DA YSP++
Sbjct: 120 VEITNPDHVICTLTGEAEISMRIKVEMGRGYVPASTRRSSEEDDRPIGRLLVDASYSPVE 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +++Y+VESAR  Q  D DKL + ++T+G++  E+++  ++ IL +QL  F++  +  +  
Sbjct: 180 RIAYSVESARVEQRTDLDKLIIDMETNGTLDPEEAIRRSATILAEQLDAFVDLRDVSEPE 239

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+K
Sbjct: 240 AKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIQYIGDLVQRTEVELLKTPNLGKK 296

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           SL EIK VL + GL LGM L +WPPESI E
Sbjct: 297 SLTEIKDVLASRGLSLGMRLENWPPESIAE 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 =  365 bits (937), Expect = 5e-99,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  365 bits (937), Expect = 5e-99,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  365 bits (937), Expect = 5e-99,   Method: Composition-based stats.
 Identities = 147/334 (44%), 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   MQGSVTEFLKPRLVD---IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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
           +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>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 =  365 bits (937), Expect = 5e-99,   Method: Composition-based stats.
 Identities = 141/328 (42%), Positives = 214/328 (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 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKV 183
           +LN DHVIC+L  D  + M L + +G GY PA   R  ++    I    +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 PANNGVDP---VLLRPIDDLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKSL 299

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL   GL LGM L +WPP  +  
Sbjct: 300 TEIKEVLAQRGLSLGMKLENWPPAGVAS 327


>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 =  365 bits (937), Expect = 5e-99,   Method: Composition-based stats.
 Identities = 144/331 (43%), Positives = 219/331 (66%), 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 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
Sbjct: 178 KRVAYTVESARVEQRTNLDKLVLDVETNGVLEPEEAVRFAAGLLRDQLSVFV--DLEGGE 235

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            + +   +    +P LL+ ++ELEL+VRS NCL+ E+I Y+GDL+QRTE ++L+  N G+
Sbjct: 236 FEAEQEEQEPDVDPILLRPIDELELTVRSANCLKAESIHYVGDLVQRTEVELLKTPNLGK 295

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           KSL EIK  L + GL LGM L +WPP  + E
Sbjct: 296 KSLTEIKETLASHGLSLGMRLENWPPAGLGE 326


>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 =  365 bits (937), Expect = 5e-99,   Method: Composition-based stats.
 Identities = 156/337 (46%), Positives = 224/337 (66%), Gaps = 2/337 (0%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
            +NW EL+KP  +E        +     + EPL RGF  TLGNALRRVL+SSL+GAAI A
Sbjct: 12  SRNWTELVKPETLE--RDSASTDTHGRFVCEPLERGFGTTLGNALRRVLLSSLQGAAIVA 69

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
            +I+GV HE S+I GV ED+T++ILN+K + L M+ +  +R+T+F    G V A  IQ  
Sbjct: 70  ARIEGVQHEFSTIPGVIEDVTEVILNLKQVRLAMATEDPQRLTLFANKKGEVLASAIQGN 129

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
            ++ VL+ D +I  L  D   R+EL V  G GYV A  H   +  IGLI +D+ +SP+KK
Sbjct: 130 QNVTVLSEDVLIATLSEDRDFRIELEVRMGKGYVTADMHEGLDSEIGLILLDSSFSPVKK 189

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V+YT+E AR GQ+ +YDKL + +DTDGSI+ ED+++ +++IL+DQL +FINF+E + E  
Sbjct: 190 VAYTIEQARVGQMTNYDKLVLEVDTDGSISPEDAISYSAKILKDQLTVFINFDEKESEAD 249

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           +      +  NP+L K ++ELELSVR+TNCL+  NI  +G+L+Q+TE +ML+  NFG+KS
Sbjct: 250 KARRRDDIELNPSLFKSIDELELSVRATNCLKSANIQTVGELMQKTENEMLKTKNFGKKS 309

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           L EI+ VL  MGL  GM + ++  +  E L +K  D+
Sbjct: 310 LEEIRRVLEDMGLEFGMRIENFEQKYQEWLKRKQVDE 346


>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 =  365 bits (937), Expect = 5e-99,   Method: Composition-based stats.
 Identities = 149/333 (44%), Positives = 220/333 (66%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISS---THAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 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-DVDAVVRMELTVSKGHGYVPAKH--HRTENDPIGLITIDALYS 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|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 =  365 bits (937), Expect = 6e-99,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|258591343|emb|CBE67642.1| DNA-directed RNA polymerase alpha chain [NC10 bacterium 'Dutch
           sediment']
          Length = 342

 Score =  365 bits (937), Expect = 6e-99,   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-FKGIQKPKRLEC-ELESLTSTYGKFFAEPFERGFGLTIGNALRRTLLSAIEGAAV 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|254776830|ref|ZP_05218346.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium avium
           subsp. avium ATCC 25291]
          Length = 347

 Score =  365 bits (937), Expect = 6e-99,   Method: Composition-based stats.
 Identities = 121/320 (37%), Positives = 193/320 (60%), Gaps = 4/320 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E ++     +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLSEEVL----TDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T IILN+K + +    D    + + K+GPG VTAGDI     + V N
Sbjct: 61  HEFTTVPGVKEDVTAIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  I  L+    + +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++
Sbjct: 121 PELHIATLNDKGKLEVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SIT  D++A A + L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDKLILDVETKSSITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPPE 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                +    +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  
Sbjct: 241 ADHIASFALPIDDLDLTVRSYNCLKREGVHTVGELVSRTESDLLDIRNFGQKSIDEVKVK 300

Query: 310 LGTMGLFLGMNLPDWPPESI 329
           L  +GL L  + P + P  +
Sbjct: 301 LHQLGLSLKDSPPSFDPSQV 320


>gi|289669368|ref|ZP_06490443.1| DNA-directed RNA polymerase subunit alpha [Xanthomonas campestris
           pv. musacearum NCPPB4381]
          Length = 332

 Score =  365 bits (937), Expect = 6e-99,   Method: Composition-based stats.
 Identities = 141/325 (43%), Positives = 213/325 (65%), Gaps = 9/325 (2%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++P   +   L    +NR  ++ EPL RG+ HTLGNALRRVL+SS+ G AIT V+IDGVL
Sbjct: 9   LRPRGPQIERL---TDNRAKVVIEPLKRGYGHTLGNALRRVLLSSIPGFAITEVEIDGVL 65

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE ++++G+ ED+ D++LN+K + ++M       +++ K+GPG VTA DI+T +++E++N
Sbjct: 66  HEYTTVEGLQEDVLDVLLNLKDVAIRMHSGDSATLSLSKQGPGTVTAADIRTDHNVEIIN 125

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYT 186
            DHVIC+L  D  + M L + +G GY PA   R  ++    I    +DA +SP+++V+Y 
Sbjct: 126 GDHVICHLTKDTALNMRLKIERGFGYQPAAARRRPDEETRTIGRLMLDASFSPVRRVAYA 185

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+AR  Q  D DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +   
Sbjct: 186 VEAARVEQRTDLDKLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPAA 245

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
               P    LL+ +++LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N G+KSL EI
Sbjct: 246 SGVDP---VLLRPIDDLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKSLTEI 302

Query: 307 KGVLGTMGLFLGMNLPDWPPESIEE 331
           K VL   GL LGM L +WPP  + +
Sbjct: 303 KEVLAQRGLALGMKLENWPPAGVAQ 327


>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 =  365 bits (936), Expect = 7e-99,   Method: Composition-based stats.
 Identities = 149/328 (45%), Positives = 211/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP     I +    E+   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPK---IIAVESLGESHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIA 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 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKV 183
           V+NPDHVI +L     + +++ V KG GYVP    R   +   +   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  +   + 
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAALEGTEAAAE- 238

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 239 -APSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>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 =  365 bits (936), Expect = 7e-99,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  365 bits (936), Expect = 7e-99,   Method: Composition-based stats.
 Identities = 152/328 (46%), Positives = 210/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP     I +    EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPK---IIAVESLGENHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIA 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 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKV 183
           V+NPDHVI +L     + +++ V KG GYVP    R   D   +   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  +   + 
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETTGVITPEEAIRQSARILVDQLSVFAALEGTETAAE- 238

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 239 -APSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 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 =  365 bits (936), Expect = 7e-99,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  365 bits (936), Expect = 7e-99,   Method: Composition-based stats.
 Identities = 158/335 (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---LLKPKAINVEQLGH---HHAKVALEPFERGYGHTLGNAIRRVLLSSMVGYAAT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN---DPIGLITIDALYS 178
            +D+E++NPDHVI NL     + M++ V KG GY+P    R  +     IG I +DA +S
Sbjct: 115 PHDVEIVNPDHVIANLSQGGKLDMQIKVEKGRGYMPGNLRRYADEVTKSIGRIVLDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++VSYTVESAR  Q  D DKL + I+T+G+IT ED+V  +++IL +QL +F   E  +
Sbjct: 175 PVRRVSYTVESARVEQRTDLDKLVVEIETNGAITAEDAVRASAKILVEQLAVFAQLEGGE 234

Query: 239 KEVKEDI--NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 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|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 =  365 bits (936), Expect = 7e-99,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  365 bits (936), Expect = 7e-99,   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---IEQLSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  365 bits (936), Expect = 7e-99,   Method: Composition-based stats.
 Identities = 150/333 (45%), Positives = 220/333 (66%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISS---THAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 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-DVDAVVRMELTVSKGHGYVPAKH--HRTENDPIGLITIDALYS 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|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 =  365 bits (936), Expect = 7e-99,   Method: Composition-based stats.
 Identities = 142/328 (43%), Positives = 214/328 (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 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKV 183
           +LN DHVIC+L  D  V M L + +G GY PA   R  ++    I    +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 PANNGVDP---VLLRPIDDLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKSL 299

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL   GL LGM L +WPP  +  
Sbjct: 300 TEIKEVLAQRGLSLGMKLENWPPAGVAS 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 =  365 bits (936), Expect = 7e-99,   Method: Composition-based stats.
 Identities = 162/345 (46%), Positives = 220/345 (63%), Gaps = 9/345 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +NW  LI+P  IE              + +PL RGF  TLGNALRRVL+SS++GAAI 
Sbjct: 1   MVRNWCSLIRPRRIEIDE-STHTRFYGEFVCQPLERGFGITLGNALRRVLLSSIQGAAIV 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 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE----- 236
           KV+YTV  AR GQ+ DYDKLS+ + TDG++  ED+VA A++IL+ QL +F+         
Sbjct: 180 KVNYTVTHARVGQIADYDKLSLEVWTDGNVLPEDAVAFAAKILKKQLQVFVGLHTVIGTE 239

Query: 237 -PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
             ++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|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 =  365 bits (936), Expect = 7e-99,   Method: Composition-based stats.
 Identities = 121/320 (37%), Positives = 193/320 (60%), Gaps = 4/320 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E ++     +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLSEEVL----TDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T IILN+K + +    D    + + K+GPG VTAGDI     + V N
Sbjct: 61  HEFTTVPGVKEDVTAIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  I  L+    + +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++
Sbjct: 121 PELHIATLNDKGKLEVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SIT  D++A A + L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDKLILDVETKSSITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAE 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                +    +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  
Sbjct: 241 ADHIASFALPIDDLDLTVRSYNCLKREGVHTVGELVSRTESDLLDIRNFGQKSIDEVKVK 300

Query: 310 LGTMGLFLGMNLPDWPPESI 329
           L  +GL L  + P + P  +
Sbjct: 301 LHQLGLSLKDSPPSFDPSQV 320


>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 =  365 bits (936), Expect = 7e-99,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +      R+ ++ EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIDAI---NPTRSKVVLEPLERGFGHTLGNALRRILLSSMPGCAVT 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-DVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALY 177
             D+ + NPDHVICNL   ++ + M + V +G GYVPA        +  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 ---TEPEEKEEKPEFDPILLRPVDDLELTVRSANCLKAEQIQYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP S+ E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASLAE 328


>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 =  365 bits (936), Expect = 8e-99,   Method: Composition-based stats.
 Identities = 151/326 (46%), Positives = 214/326 (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 NPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALYSPIKKVSY 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|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 =  365 bits (936), Expect = 8e-99,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  365 bits (936), Expect = 8e-99,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  365 bits (936), Expect = 8e-99,   Method: Composition-based stats.
 Identities = 155/337 (45%), Positives = 224/337 (66%), Gaps = 2/337 (0%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
            +NW EL+KP  +E        +     + EPL RGF  TLGNALRRVL+SSL+GAAI A
Sbjct: 12  SRNWTELVKPEKLE--KDPGATDTFGRFVCEPLERGFGTTLGNALRRVLLSSLQGAAIVA 69

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
            +I+GV HE S+I GV ED+T+IILN+K + L M+ +  +R+T+F    G V A  IQ  
Sbjct: 70  ARIEGVQHEFSTIPGVIEDVTEIILNLKQVRLAMTTEDPQRLTLFANQKGEVLASAIQGN 129

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
            ++ VL+ D +I  L  D   R++L V  G GYVPA  H   +  IGLI +D+ +SP+KK
Sbjct: 130 QNVTVLSDDVLIATLSEDRDFRIDLEVRMGKGYVPADMHEGLDSEIGLILLDSSFSPVKK 189

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V+YT+E AR GQ+ +YDKL + + TDGSI+ +D+++ +++IL+DQL +FINF+E + E  
Sbjct: 190 VAYTIEQARVGQMTNYDKLVLEVGTDGSISPDDAISYSAKILKDQLTVFINFDEKESEAD 249

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           +      +  NP+L K ++ELELSVR+TNCL+  NI  +G+L+Q+TE +ML+  NFG+KS
Sbjct: 250 KARRRDDIELNPSLFKSIDELELSVRATNCLKSANIQTVGELMQKTENEMLKTKNFGKKS 309

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           L EI+ VL  MGL  GM + ++  +  E L +K  D+
Sbjct: 310 LEEIRRVLEDMGLEFGMRIENFEQKYQEWLKRKQVDE 346


>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 =  365 bits (936), Expect = 8e-99,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  365 bits (936), Expect = 8e-99,   Method: Composition-based stats.
 Identities = 158/336 (47%), Positives = 215/336 (63%), 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---LLKPKAINVEQLGH---NRAKVELEPFERGYGHTLGNAIRRVLLSSMVGYAAT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG---LITIDALYS 178
            +D+E++NPDHVI  L     + M++ V KG GYVP    R  ++       I +DA +S
Sbjct: 115 PHDVEIVNPDHVIATLSAGGKLDMQIKVEKGRGYVPGNLRRFADESTKSIGRIVLDASFS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN---FE 235
           P+K+VSYTVESAR  Q  D DKL + I+T+G+I+ E++V  +++IL +QL +F      E
Sbjct: 175 PVKRVSYTVESARVEQRTDLDKLVLEIETNGAISAEEAVRASAKILVEQLAVFAQLDGGE 234

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 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|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 =  365 bits (936), Expect = 8e-99,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|332037268|gb|EGI73723.1| DNA-directed RNA polymerase alpha subunit [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 328

 Score =  364 bits (935), Expect = 8e-99,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +      R+ ++ EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIDAI---NPTRSKIVLEPLERGFGHTLGNALRRILLSSMPGCAVT 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-DVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALY 177
             D+ + NPDHVICNL   ++ + M + V +G GYVPA        +  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 ---TEPEEKEEKPEFDPILLRPVDDLELTVRSANCLKAEQIQYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP S+ E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASLAE 328


>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 =  364 bits (935), Expect = 8e-99,   Method: Composition-based stats.
 Identities = 149/333 (44%), Positives = 220/333 (66%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISS---THAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 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-DVDAVVRMELTVSKGHGYVPAKH--HRTENDPIGLITIDALYS 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|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 =  364 bits (935), Expect = 8e-99,   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-KIETVSV-NEDGSYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 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|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 =  364 bits (935), Expect = 9e-99,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  364 bits (935), Expect = 9e-99,   Method: Composition-based stats.
 Identities = 147/328 (44%), Positives = 211/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP     I +    +N   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPK---IIAVDSLGDNHAKVVMEPFERGYGHTLGNALRRVLLSSMIGYAPTEVTIA 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 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKV 183
           V+NP+HVI +L     + +++ V KG GYVP    R  ++   +   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  +   + 
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAALEGTETTAE- 238

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 239 -APSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>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 =  364 bits (935), Expect = 9e-99,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  364 bits (935), Expect = 9e-99,   Method: Composition-based stats.
 Identities = 150/336 (44%), Positives = 218/336 (64%), Gaps = 1/336 (0%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
            +NW +L++P  +    +            EPL RG+  T+GNALRRVL+SSL+GAA  +
Sbjct: 12  SRNWAKLVRPEAV-INNMESNTTTYGRFEYEPLERGYGITIGNALRRVLLSSLQGAAFVS 70

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
           V+I GV HE ++I G+ ED+TDIILN+K + L M  D  + +++F    G+VTA DIQT 
Sbjct: 71  VKILGVQHEFTTIPGILEDVTDIILNLKQVRLAMDTDEPQHLSLFVSKKGIVTAADIQTN 130

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
             +EVLNP+  I  L  D  +RME  V  G GYVPA+ H   ++ IGLI +D+ +SPI+ 
Sbjct: 131 QHVEVLNPEQHIATLTEDIELRMEFEVRMGKGYVPAEMHEDLHEEIGLIKLDSSFSPIRN 190

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V+Y VE AR GQ+ +YDKL + + TDGS++ ED++A +++I++DQ+ +FINF+E      
Sbjct: 191 VTYVVEQARVGQMTNYDKLVLEVWTDGSVSPEDAIAYSAKIIKDQISVFINFDERISGSG 250

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
            +    S   N  L K ++ELELSVR+TNCLR  NI  +G+L+Q+ EADML+  NFG+KS
Sbjct: 251 GNEGSGSSDLNDNLFKGIDELELSVRATNCLRSANISTVGELVQKAEADMLKTKNFGKKS 310

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           L EIK +L +MGL  GM +  +  +  E   K++ +
Sbjct: 311 LDEIKALLTSMGLDFGMKIDGFEKKYQEWKRKQHHE 346


>gi|205372042|ref|ZP_03224859.1| DNA-directed RNA polymerase subunit alpha [Bacillus coahuilensis
           m4-4]
          Length = 314

 Score =  364 bits (935), Expect = 9e-99,   Method: Composition-based stats.
 Identities = 136/310 (43%), Positives = 204/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  ++      + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETVEV-SDDATYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 AKLDELGLGL 310


>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 =  364 bits (935), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 149/334 (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---IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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
           +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 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 =  364 bits (935), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  364 bits (935), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 148/333 (44%), Positives = 220/333 (66%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISS---THAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 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-DVDAVVRMELTVSKGHGYVPAKH--HRTENDPIGLITIDALYS 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|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 =  364 bits (935), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +      R+ ++ EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIDAI---NPTRSKIVLEPLERGFGHTLGNALRRILLSSMPGCAVT 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 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALY 177
             D+ + NPDHVICNL   ++ + M + V +G GYVPA        +  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 ---TEPEEKEEKPEFDPILLRPVDDLELTVRSANCLKAEQIQYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP S+ E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASLAE 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 =  364 bits (935), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 145/334 (43%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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
           ++   ++   + +P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQPEVKEEKPEFVP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|301628933|ref|XP_002943603.1| PREDICTED: DNA-directed RNA polymerase subunit alpha-like [Xenopus
           (Silurana) tropicalis]
          Length = 332

 Score =  364 bits (934), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 162/337 (48%), Positives = 219/337 (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---LLKPKTIQVEQLGH---NRAKVELEPFERGYGHTLGNALRRVLLSSMVGYAAT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYS 178
            +D+E++NPDHVI +L   A + M++ V KG GYVP    R  ++P      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|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 =  364 bits (934), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  364 bits (934), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 145/334 (43%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  364 bits (934), Expect = 1e-98,   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|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 =  364 bits (934), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 149/328 (45%), Positives = 211/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP     I +    E+   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPK---IIAVESLGESHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIA 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 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKV 183
           V+NPDHVI +L     + +++ V KG GYVP    R   +   +   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  +   + 
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAALEGTEAAAET 239

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 240 P--SRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>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 =  364 bits (934), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  364 bits (934), Expect = 1e-98,   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 SVPEKKEDK---PEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP S+ +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASLAD 328


>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 =  364 bits (934), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 160/333 (48%), Positives = 217/333 (65%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  I+          R  +  +P  RGF HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQNSTAEFLKPRQIDVNTF---SATRAKVSMQPFERGFGHTLGNALRRILLSSMNGFAPT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALYS 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 PISRVSFEVEPARVEQRTDLDKLVLDIETDGSIDPEEAVRSAARILIDQMSIFANLQGTP 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            E   ++  K+ P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N 
Sbjct: 238 VE---EVEEKAPPIDPVLLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 295 GRKSLNEIKEVLASKGLTLGSKLEAWPPAGLEK 327


>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 =  364 bits (934), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 149/333 (44%), Positives = 211/333 (63%), Gaps = 11/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +   L+KP  IE   LG        ++ EP  RG+ HTLGNALRRVL+SS+ G A T
Sbjct: 1   MQNS---LLKPRIIEVETLGAG---HAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYS 178
            +D+E++NPDHVI +L     + M++ V KG GYVP    R   D       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
              +     ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N 
Sbjct: 235 AAAE--APSRAPSVDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRSENELLKTPNL 292

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL + GL LGM L +WPP  +E+
Sbjct: 293 GRKSLNEIKEVLASRGLTLGMKLENWPPAGLEK 325


>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 =  364 bits (934), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 150/335 (44%), Positives = 217/335 (64%), Gaps = 8/335 (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 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 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           +KSL EIK VL + GL LGM L +WPP S++   +
Sbjct: 295 KKSLTEIKDVLASRGLSLGMRLENWPPASLKSERE 329


>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 =  364 bits (934), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 129/317 (40%), Positives = 188/317 (59%), Gaps = 4/317 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E     Q +E R+  I EPL  GF +T+GN+LRR L+SS+ GAA+T+++I+GVL
Sbjct: 5   QRPTLTE----EQIDEYRSRFIIEPLEPGFGYTIGNSLRRTLLSSIPGAAVTSIRIEGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I GV ED+TDIILN+K + +    D    + + K+GPG VTA DI     +EV N
Sbjct: 61  HEFSTIPGVKEDVTDIILNLKELVVSSEHDEPVVMYLRKQGPGQVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+  A + MELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+
Sbjct: 121 PDLHIATLNSKAKLEMELTVERGRGYVSAAQNKQPGQEIGRIPIDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  ++   D+VA A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDRLILDVETKPAMLPRDAVASAGKTLVELFGLARELNVEAEGIDMGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  
Sbjct: 241 AALAADLALPIEELNLTVRSYNCLKREGIHTVGELVARSEQDLLDIRNFGAKSIEEVKQK 300

Query: 310 LGTMGLFLGMNLPDWPP 326
           L  MGL L  + P + P
Sbjct: 301 LADMGLSLKDSPPGFDP 317


>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 =  364 bits (934), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 150/328 (45%), Positives = 210/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP     I +    EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPK---IIAVESLGENHARVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIA 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 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKV 183
           V+NP+HVI +L     + +++ + KG GYVP    R   D   +   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  +   + 
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETSGVITPEEAIRQSARILVDQLSVFAALEGTETAAE- 238

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 239 -APSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>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 =  364 bits (934), Expect = 1e-98,   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|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 =  364 bits (934), Expect = 1e-98,   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|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 =  364 bits (934), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 151/328 (46%), Positives = 212/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP     I +    EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPK---IIAVESLGENHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIA 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 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKV 183
           V+NP+HVI +L     + +++ V KG GYVP    R  ++   +   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  +   + 
Sbjct: 180 SYTVESARVEQRTDLDKLVMNIETSGVITPEEAIRQSARILVDQLSVFAALEGTETAAE- 238

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 239 -APSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>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 =  363 bits (933), Expect = 1e-98,   Method: Composition-based stats.
 Identities = 148/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  363 bits (933), Expect = 1e-98,   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---IEQLSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|329298509|ref|ZP_08255845.1| DNA-directed RNA polymerase subunit alpha [Plautia stali symbiont]
          Length = 329

 Score =  363 bits (933), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 148/334 (44%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  363 bits (933), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 150/328 (45%), Positives = 211/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP     I +    EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPK---IIAVESLGENHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIA 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 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKV 183
           V+NP+HVI +L     + +++ V KG GYVP    R  ++   +   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  +   + 
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETSGVITPEEAIRQSARILVDQLSVFAALEGTETAAE- 238

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 239 -APSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 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 =  363 bits (933), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  363 bits (933), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 124/307 (40%), Positives = 186/307 (60%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
               E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV E
Sbjct: 12  ETVNETRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKE 71

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+TDIILN+K + +    D    + + K+GPG VTA DI     + V NPD  I +L+  
Sbjct: 72  DVTDIILNLKELVVSSEEDEPVTMYLRKQGPGEVTAADIVPPAGVTVHNPDLHIASLNGK 131

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+DK
Sbjct: 132 GKLEIELVVERGRGYVPALQNKQAGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDK 191

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L + ++T  SIT  D+VA A + L +  G+        + ++   + +      A    +
Sbjct: 192 LILDVETKPSITPRDAVASAGKTLVELFGLARELNVDAEGIEIGPSPQEADTIAAYAMPI 251

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           E+L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L  +GL L  +
Sbjct: 252 EDLDLTVRSYNCLKREGIHTVGELVSRSEADLLDIRNFGAKSIDEVKLKLVGLGLALKDS 311

Query: 321 LPDWPPE 327
            P + P 
Sbjct: 312 PPGFDPT 318


>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 =  363 bits (933), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 149/328 (45%), Positives = 211/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP     I +    E+   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPK---IIAVESLGESHAKVVMEPFERGYGHTLGNALRRVLLSSMIGYAPTEVTIA 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 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKV 183
           V+NPDHVI +L     + +++ V KG GYVP    R   +   +   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  +   + 
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAALEGTEATAE- 238

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 239 -APSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>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 = 130/310 (41%), Positives = 205/310 (66%), Gaps = 4/310 (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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 EKLHALGLSL 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 =  363 bits (933), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 145/334 (43%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  363 bits (933), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 145/334 (43%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  363 bits (933), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 147/326 (45%), Positives = 212/326 (65%), Gaps = 7/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP     I +    ++   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPK---IIAVEPLGDHHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 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 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKVSY 185
           NP HVI +L     + M++ V +G GYVP    +  ++   +   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 AVESARVEQRTDLDKLVMNIETDGVISPEEAIRQSARILVDQLSVFAAL-EGTESAAEAA 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|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 =  363 bits (933), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 140/324 (43%), Positives = 205/324 (63%), Gaps = 3/324 (0%)

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  +    P E  EE
Sbjct: 301 QKLHSLGLSLKKS-DSTPKEEEEE 323


>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 =  363 bits (932), Expect = 2e-98,   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-LETVEI-NESGTYGKFVIEPLERGYGTTLGNALRRILLSSLPGAACTSVKIDG 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|322659535|gb|EFY55779.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Montevideo str. 19N]
          Length = 329

 Score =  363 bits (932), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  363 bits (932), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 150/328 (45%), Positives = 210/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP     I +    EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPK---IIAVESLGENHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIA 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 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKV 183
           V+NP+HVI +L     + +++ + KG GYVP    R   D   +   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  +   + 
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETSGVITPEEAIRQSARILVDQLSVFAALEGTETAAE- 238

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 239 -APSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>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 =  363 bits (932), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 141/324 (43%), Positives = 205/324 (63%), Gaps = 3/324 (0%)

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  +    P E  EE
Sbjct: 301 QKLHSLGLSLKKS-DSTPKEEEEE 323


>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 =  363 bits (932), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 142/325 (43%), Positives = 214/325 (65%), Gaps = 9/325 (2%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++P   +   L    +NR  ++ EPL RG+ HTLGNALRRVL+SS+ G AIT V+ID VL
Sbjct: 9   LRPRGPQIERL---TDNRAKVVIEPLERGYGHTLGNALRRVLLSSIPGFAITEVEIDNVL 65

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE ++++G+ ED+ +++LN+K + ++M       +++ K+GPG VTA DI+T +++E+LN
Sbjct: 66  HEYTTVEGLQEDVLEVLLNLKDVAIRMHTGDSATLSLSKQGPGTVTATDIKTDHNVEILN 125

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYT 186
            DHVIC+L  D  + M L + +G GY PA   R  ++    I    +DA +SP+++V+Y 
Sbjct: 126 SDHVICHLTKDTALNMRLKIERGFGYQPAAARRRPDEETRTIGRLVLDASFSPVRRVAYA 185

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VESAR  Q  D DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +     + 
Sbjct: 186 VESARVEQRTDLDKLVLDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGA---VK 242

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
             S   +P LL+ +++LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N G+KSL EI
Sbjct: 243 PASNGVDPVLLRPIDDLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNLGKKSLTEI 302

Query: 307 KGVLGTMGLFLGMNLPDWPPESIEE 331
           K VL   GL LGM L +WPP  + +
Sbjct: 303 KEVLAQRGLSLGMKLENWPPAGVAQ 327


>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 =  363 bits (932), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 124/320 (38%), Positives = 192/320 (60%), Gaps = 4/320 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        ENR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLSE----ETVAENRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TDIILN+KG+ +    D    + + K+GPGVVTAGDI     + V N
Sbjct: 61  HEFTTVPGVKEDVTDIILNLKGLVVSSDDDEPVTMYLRKQGPGVVTAGDIVPPAGVTVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDMHIATLNDKGKLEVELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SI+  D++A A   L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDKLIIDVETKNSISPRDALASAGGTLVELFGLARELNADSEHIEIGPSPAE 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                +    +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  
Sbjct: 241 ADHIASFALPIDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIK 300

Query: 310 LGTMGLFLGMNLPDWPPESI 329
           L  +GL L  +   + P  +
Sbjct: 301 LHQLGLSLKDSPATFDPSEV 320


>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 =  363 bits (932), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 124/307 (40%), Positives = 186/307 (60%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
               E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV E
Sbjct: 12  ETVNETRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKE 71

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+TDIILN+K + +    D    + + K+GPG VTA DI     + V NPD  I +L+  
Sbjct: 72  DVTDIILNLKELVVSSEEDEPVTMYLRKQGPGEVTAADIVPPAGVTVHNPDLHIASLNGK 131

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+DK
Sbjct: 132 GKLEIELVVERGRGYVPALQNKQAGAEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDK 191

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L + ++T  SIT  D+VA A + L +  G+        + ++   + +      A    +
Sbjct: 192 LILDVETKPSITARDAVASAGKTLVELFGLARELNVDAEGIEIGPSPQEADTIAAYAMPI 251

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           E+L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L  +GL L  +
Sbjct: 252 EDLDLTVRSYNCLKREGIHTVGELVSRSEADLLDIRNFGAKSIDEVKLKLVGLGLALKDS 311

Query: 321 LPDWPPE 327
            P + P 
Sbjct: 312 PPGFDPS 318


>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 =  363 bits (932), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 148/334 (44%), Positives = 219/334 (65%), Gaps = 7/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q    EL+KP  ++  VL      R  ++ EPL RGF +TLGNALRR+L+SS+ G A+T
Sbjct: 1   MQLGSTELLKPRLVDVQVLD---ATRARVVLEPLERGFGYTLGNALRRILLSSIPGVAVT 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 RRVSYSVERARVEQRTDLDSLVLDIETNGSISAEDAIRQAAGILVDQLSVFVDLKAEKVE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
              +        +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G+
Sbjct: 238 PVVEQA---PAVDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEIELLKTPNLGK 294

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           KSL EIK VL   GL LG  L +WPP  +  LA+
Sbjct: 295 KSLTEIKDVLAKQGLSLGQRLENWPPAELLNLAE 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 =  363 bits (932), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 147/331 (44%), Positives = 210/331 (63%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +   L+KP  I+   +      +  ++ EP  RG+ HTLGNALRR+L+SS+ G A T
Sbjct: 1   MQSS--GLLKPRIIDVQSV---SPVQAKVVMEPFERGYGHTLGNALRRILLSSMVGYAPT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN-DPIGLITIDALYSPI 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|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 =  363 bits (931), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  363 bits (931), Expect = 2e-98,   Method: Composition-based stats.
 Identities = 138/310 (44%), Positives = 205/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + + +E       + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETVDVNEEG-TYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 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|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 =  363 bits (931), Expect = 3e-98,   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|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 =  363 bits (931), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  363 bits (931), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 150/329 (45%), Positives = 220/329 (66%), Gaps = 10/329 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E +KP+ +    +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+ID
Sbjct: 2   TEFLKPHLVNIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEID 58

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE SS +GV ED+ +++LN+KG+ +K+SG     +T+ K G G VTA DI    D+E
Sbjct: 59  GVLHEYSSKEGVQEDILEVLLNLKGLAVKVSGKDDIILTLNKSGIGPVTAADITHDGDVE 118

Query: 127 VLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKK 182
           ++NP HVIC+L D DA + M + V +G GYVPA    H + E+ PIG + +DA +SP+ +
Sbjct: 119 IVNPHHVICHLTDKDASISMRIRVQRGRGYVPASARVHSQDEDRPIGRLLVDARFSPVDR 178

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           ++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++   
Sbjct: 179 IAYNVEAARVEQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP-- 236

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
            ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KS
Sbjct: 237 -EVKEEKPEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKS 295

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           L EIK VL + GL LGM L +WPP SI E
Sbjct: 296 LTEIKDVLASRGLSLGMRLENWPPASIAE 324


>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 =  363 bits (931), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 151/333 (45%), Positives = 209/333 (62%), 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYS 178
            +D+E++NPDHVI NL     + M++ V KG GYVP    R   D       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 PVRRVSYAVESARVEQRTDLDKLVMNIETNGVITPEEAIRQSARVLVDQLNVFAALEGTE 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              +     ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQR+E ++L+  N 
Sbjct: 235 ATAE--APSRAPQVDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRSENELLKTPNL 292

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL + GL LGM L +WPP  +E+
Sbjct: 293 GRKSLNEIKEVLASRGLTLGMKLENWPPAGLEK 325


>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 (931), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 142/310 (45%), Positives = 206/310 (66%), Gaps = 2/310 (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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 AKLEELGLGL 310


>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 =  363 bits (931), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 131/315 (41%), Positives = 197/315 (62%), Gaps = 6/315 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            ++ KP  IE   +  E+      I EPL  G+  T GN+LRR+L+SSL GAA+T++QID
Sbjct: 2   TDIEKP-KIEIAEI-SEDGRYGRFICEPLEPGYGTTFGNSLRRMLLSSLDGAAVTSIQID 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE S+I GV +D+T I+L +K + ++M     + + I   G   VTA DI+  +DIE
Sbjct: 60  GVLHEFSTIPGVRDDVTSIVLALKQLCIRMQDSEPRTIRIDAAGACEVTAADIECGSDIE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +LNPD  I  L     +++++TV +G GYVPA  ++  +D IG+I ID+++SP+++V+YT
Sbjct: 120 ILNPDLHIATLGDTGKLKIDMTVERGRGYVPADRNKKPDDVIGVIPIDSIFSPVQRVNYT 179

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE----EPKKEVK 242
           VE  R G V DYD+L + + T+GSI  E++V+ A+ IL   L +F N +    E ++EV 
Sbjct: 180 VEDTRVGNVTDYDRLILDVWTNGSIRPEEAVSKAAAILVMHLRLFQNMDGSAAEEEEEVP 239

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                +       L   +++L+LSVRS NCL+   I  + DL Q+TE DM+++ N GRKS
Sbjct: 240 NFPPEEVDDSAKVLEMTIDDLDLSVRSFNCLKRAGINTVADLAQKTEDDMMKVRNLGRKS 299

Query: 303 LVEIKGVLGTMGLFL 317
           L E+K  L  +GL L
Sbjct: 300 LDEVKKKLEELGLSL 314


>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 =  363 bits (931), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 149/328 (45%), Positives = 210/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP     I +    EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPK---IIAVESLGENHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIA 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 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKV 183
           V+NPDHVI +L     + +++ + KG GYVP    R   +   +   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  +   + 
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETSGVITPEEAIRQSARILVDQLSVFAALEGTETAAE- 238

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 239 -APSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>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 =  363 bits (931), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 135/310 (43%), Positives = 201/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  ++      + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETVEI-SDDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 HKLEELGLGL 310


>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 =  363 bits (931), Expect = 3e-98,   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|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 =  362 bits (930), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 139/324 (42%), Positives = 204/324 (62%), Gaps = 3/324 (0%)

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  +    P E  EE
Sbjct: 301 QKLHSLGLSLKKS-DSTPKEEEEE 323


>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 =  362 bits (930), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 145/326 (44%), Positives = 211/326 (64%), Gaps = 7/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP     I +    ++   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPK---IIAVEPLGDHHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 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 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSY 185
           NP HVI +L     + M++ V +G GYVP    +  ++   +I    +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 AVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAAL-EGTESAAEAA 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|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 =  362 bits (930), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 142/324 (43%), Positives = 208/324 (64%), Gaps = 3/324 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP  I    L  + +     + EPL RG+  T+GNALRR L+SSL GAA+TAV+IDG
Sbjct: 3   EFQKP-AIRCEELSPDNK-YGRYVIEPLERGYGITVGNALRRTLLSSLPGAAVTAVKIDG 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  +    P E  EE
Sbjct: 301 QKLHSLGLSLKKS-DSTPKEEEEE 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 =  362 bits (930), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 143/336 (42%), Positives = 218/336 (64%), Gaps = 2/336 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW EL++P  +E     +  +     + EPL RGF  T+GNALRRVL+SSL+GAA  +V
Sbjct: 14  RNWAELVRPEQLE--KDPKCNDMYGRFVCEPLERGFGTTIGNALRRVLLSSLQGAAPVSV 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 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +I+ VL +MGL  G+ + ++     + L +  ED+
Sbjct: 312 EDIRRVLESMGLDFGIRVDNFDELYQDWLKRNEEDE 347


>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 =  362 bits (930), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 152/325 (46%), Positives = 203/325 (62%), Gaps = 10/325 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  N   L+KP  I+          +  ++ EP  RG+ HTLGNALRRVL+SS+ G A+T
Sbjct: 1   MSNN--NLLKPRIIDVQR---SSATQARVVMEPFERGYGHTLGNALRRVLLSSMPGYAVT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSP 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++    K  P    LL+ V++LEL+ RS+NCL+ ++I Y+GDLIQ TEAD+LR  N G
Sbjct: 236 PVEKPQTPKVDPM---LLRPVDDLELTPRSSNCLKAQSIHYIGDLIQNTEADLLRTPNLG 292

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDW 324
           RKSL EIK VL   GL LGM L +W
Sbjct: 293 RKSLNEIKQVLAEHGLSLGMKLENW 317


>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 =  362 bits (930), Expect = 3e-98,   Method: Composition-based stats.
 Identities = 125/319 (39%), Positives = 190/319 (59%), Gaps = 4/319 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        E R+  + EPL  GF +TLGN+LRR L+SS+ GA++T+++IDGVL
Sbjct: 5   QRPTLAE----EPIAEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+TD+ILN+K + +    D    + + K+GPG VTA DI     +EV N
Sbjct: 61  HEFSTVPGVKEDVTDVILNLKELVVSSDNDEPTVMYLRKQGPGEVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  +  ++    + +ELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+
Sbjct: 121 PELHLATINDKGKLEIELTVERGRGYVSAAQNKQPGQEIGRIPIDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SI+  D++A A + L    G+        + V    + + 
Sbjct: 181 TRVEQRTDFDKLIVDVETKPSISPRDAMASAGKTLVGLFGLAQELNAEAEGVDIGPSAQD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EE++L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  
Sbjct: 241 AQLAADLALPIEEMDLTVRSYNCLKREGIHTIGELVSRSEADLLDIRNFGQKSIDEVKTK 300

Query: 310 LGTMGLFLGMNLPDWPPES 328
           LG MGL L  + P + P  
Sbjct: 301 LGAMGLQLKDSPPGFDPRQ 319


>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 =  362 bits (930), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 149/333 (44%), Positives = 211/333 (63%), Gaps = 10/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N   L+KP     I +     N+  ++ EP  RG+ HTLGNALRRVL+SS+ G A T
Sbjct: 1   MQTN---LLKPK---IISVEALTANQAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GV+HE S++ GV ED+ +++LN+KGI  K+       + + K GPGVVTA DI  
Sbjct: 55  EVAIAGVVHEYSTLDGVQEDVVNLLLNLKGIVFKLQSRDEVTINLRKEGPGVVTAKDIDL 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYS 178
            +D+E++NPDHVI +L     + M++ V KG GYVP    +  ++   +   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 PVSRVSYAVESARVEQRTDLDRLVMTIETNGVLSPEEAIRQAASILVDQLVVFAALESSE 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                  +  S   +P L++ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 235 VSGDLAPSR-SSMVDPMLMRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNL 293

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL   GL LGM L  WPP ++E+
Sbjct: 294 GRKSLNEIKDVLAARGLSLGMKLESWPPANLEK 326


>gi|167587746|ref|ZP_02380134.1| DNA-directed RNA polymerase subunit alpha [Burkholderia ubonensis
           Bu]
          Length = 325

 Score =  362 bits (930), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 149/328 (45%), Positives = 209/328 (63%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP     I +    EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPK---IIAVESLGENHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIA 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 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKV 183
           V+NP+HVI +L     + +++ + KG GYVP    R   D   +   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  +   + 
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETSGVITPEEAIRQSARILVDQLSVFAALEGTETAAE- 238

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 239 -APSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>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 =  362 bits (930), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 149/333 (44%), Positives = 210/333 (63%), Gaps = 10/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N   L+KP     I +     N+  ++ EP  RG+ HTLGNALRRVL+SS+ G A T
Sbjct: 1   MQTN---LLKPK---IISVEALTANQAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V I GV+HE S++ GV ED+ +++LN+KGI  K+       + + K GPGVVTA DI  
Sbjct: 55  EVAIAGVVHEYSTLDGVQEDVVNLLLNLKGIVFKLQSRDEVIINLRKEGPGVVTAKDIDL 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG---LITIDALYS 178
            +D+E++NPDHVI +L     + M++ V KG GYVP    +  ++       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 PVSRVSYAVESARVEQRTDLDRLVMTIETNGVLSPEEAIRQAASILVDQLVVFAALESSE 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                  +  S   +P L++ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 235 VSGDLAPSR-SSMVDPMLMRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNL 293

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GRKSL EIK VL   GL LGM L  WPP ++E+
Sbjct: 294 GRKSLNEIKDVLAARGLSLGMKLESWPPANLEK 326


>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 =  362 bits (930), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 137/310 (44%), Positives = 204/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+TA+QIDG
Sbjct: 3   EIEKP-KIETVEL-NEDAKYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDG 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|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 =  362 bits (930), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 150/334 (44%), Positives = 223/334 (66%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP+ +    +         +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQGSVIEFLKPHLVNIEQISS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVA 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|311029077|ref|ZP_07707167.1| DNA-directed RNA polymerase subunit alpha [Bacillus sp. m3-13]
          Length = 314

 Score =  362 bits (930), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 137/310 (44%), Positives = 203/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  ++ N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETVEI-SDDANYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 HKLEELGLGL 310


>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 =  362 bits (930), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 148/333 (44%), Positives = 218/333 (65%), Gaps = 9/333 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E ++P  ++   +      R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLRPRLVDIEQISS---TRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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 PVSRIAYNVESARVEQRTNLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDV- 236

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
              + +   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 237 --TEPEQKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 327


>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 =  362 bits (930), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 139/337 (41%), Positives = 214/337 (63%), Gaps = 7/337 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q  +++ ++P  +    +    +   ++  EPL RGF HTLGNALRRVL+SS+ G A+ 
Sbjct: 1   MQGQFKDFLRPRLV---GVEALSDRHAMITLEPLERGFGHTLGNALRRVLLSSMPGYAVV 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+  +    
Sbjct: 178 VRRVAYNVESARVEQRTDLDKLVMDIETNGVLEPEEAVRFAAGLLRDQLSVFV--DLEGG 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|42799|emb|CAA26395.1| unnamed protein product [Escherichia coli]
          Length = 329

 Score =  362 bits (929), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|311693295|gb|ADP96168.1| DNA-directed RNA polymerase subunit alpha [marine bacterium HP15]
          Length = 319

 Score =  362 bits (929), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 150/313 (47%), Positives = 216/313 (69%), Gaps = 6/313 (1%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           + +    R  +  EPL RGF HTLG+ALRR+L+SS+ G A+T  QIDGVLHE S+I+GV 
Sbjct: 1   MKESSATRAKVTLEPLERGFGHTLGSALRRILLSSMPGCAVTEAQIDGVLHEYSAIEGVQ 60

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+ +I+LN+KG+ +KM+G     +T+ K+GPGVVTAGDI+  +D+E+ NP+HVIC+L  
Sbjct: 61  EDVIEILLNLKGVAVKMNGRDDAELTLSKKGPGVVTAGDIKLDHDVEIANPEHVICHLSE 120

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVL 196
           +  V M L V++G GY PA     + D    I    +DA +SP+++V+Y VESAR  Q  
Sbjct: 121 NGEVNMRLRVARGRGYEPADQRGLDEDETRAIGRLQLDATFSPVRRVAYAVESARVEQRT 180

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           D DKL + ++T+G+I  E+++  A+ ILQ QL +F++F+  K+  + +   +  P    L
Sbjct: 181 DLDKLVIDLETNGTIDPEEAIRRAATILQQQLAVFVDFDHEKEPERVEEEEEIDP---IL 237

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
           L+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G+KSL EIK VL + GL 
Sbjct: 238 LRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNLGKKSLTEIKDVLASRGLS 297

Query: 317 LGMNLPDWPPESI 329
           LGM L +WPP S+
Sbjct: 298 LGMRLDNWPPASL 310


>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 =  362 bits (929), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 145/326 (44%), Positives = 211/326 (64%), Gaps = 7/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP     I +    ++   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPK---IIAVEPLGDHHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 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 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKVSY 185
           NP HVI +L     + M++ V +G GYVP    +  ++   +   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 AVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAAL-EGTESAAEAA 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|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 =  362 bits (929), Expect = 4e-98,   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-VIETIEI-SEDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 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|237747390|ref|ZP_04577870.1| RNA polymerase [Oxalobacter formigenes HOxBLS]
 gi|229378741|gb|EEO28832.1| RNA polymerase [Oxalobacter formigenes HOxBLS]
          Length = 325

 Score =  362 bits (929), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 152/333 (45%), Positives = 212/333 (63%), Gaps = 11/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q N    +KP     I +      R+++  EP  RG+ HTLGNALRRVL+SS+ G A T
Sbjct: 1   MQNN---FLKPR---IINVESLGGGRSIVEMEPFERGYGHTLGNALRRVLLSSMTGYAPT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYS 178
            +D+E++NPDHVI NL  +  + M++ V KG GYVP    R   D       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|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 =  362 bits (929), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 125/319 (39%), Positives = 190/319 (59%), Gaps = 4/319 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P  +E        E R+  + EPL  GF +TLGN+LRR L+SS+ GA++T++++DGVL
Sbjct: 5   QRPTLVE----DPITEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIRVDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+TD+ILN+K + +    D    + + K+GPG VTA DI     +EV N
Sbjct: 61  HEFSTVPGVKEDVTDLILNLKELVVSSDNDEPTVMYLRKQGPGDVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  +  L+    + +ELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+
Sbjct: 121 PDLHLATLNDKGKLEIELTVERGRGYVSAAQNKQPGQEIGRIPIDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  SI+  D++A A + L    G+        + V    +   
Sbjct: 181 TRVEQRTDFDRLIVDVETKQSISPRDAMASAGKTLVGLFGLAQELNAEAEGVDIGPSAAD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EE++L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  
Sbjct: 241 AALAADLALPIEEMDLTVRSYNCLKREGIHTIGELVSRSEADLLDIRNFGQKSIDEVKTK 300

Query: 310 LGTMGLFLGMNLPDWPPES 328
           LG MGL L  + P + P  
Sbjct: 301 LGAMGLQLKDSPPGFDPRQ 319


>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 =  362 bits (929), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 147/329 (44%), Positives = 216/329 (65%), 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 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPI 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
             E         +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N G+
Sbjct: 238 EPEKEE---PEIDPILLRPVDDLELTVRSANCLKTENIHYIGDLVQRTEVELLKTPNLGK 294

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           KSL EIK VL + GL LGM L +WPP SI
Sbjct: 295 KSLTEIKDVLASRGLSLGMRLENWPPSSI 323


>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 =  362 bits (929), Expect = 4e-98,   Method: Composition-based stats.
 Identities = 159/334 (47%), Positives = 213/334 (63%), 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG---LITIDALYS 178
            +D+E++NP+HVI NL     + M++ V  G GYVP    R  ++       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|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 =  362 bits (929), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 145/326 (44%), Positives = 213/326 (65%), Gaps = 7/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP     I +    ++   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPK---IIAVEPLGDHHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 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 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKVSY 185
           NP+HVI +L     + M++ V +G GYVP    +  ++   +   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 AVESARVEQRTDLDKLVMNIETDGVISPEEAIRQSARILVDQLSVFAAL-EGTESAAEAA 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|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 =  362 bits (929), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 148/334 (44%), 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   MQGSVTEFLKPRLVD---IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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
           +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>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 =  362 bits (929), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 122/320 (38%), Positives = 194/320 (60%), Gaps = 4/320 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E ++     +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLSEEVL----TDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T IILN+KG+ +    D    + + K+GPG VTAGDI     + V N
Sbjct: 61  HEFTTVAGVKEDVTAIILNLKGLVVSSEEDEPVTMYLRKQGPGAVTAGDIVPPAGVTVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  I  L+    + +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++
Sbjct: 121 PEMHIATLNDKGKLEVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SIT  D++A A + L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDKLILDVETKSSITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAE 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                +    +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  
Sbjct: 241 ADHIASFALPIDDLDLTVRSYNCLKREGVHTVGELVSRTESDLLDIRNFGQKSIDEVKVK 300

Query: 310 LGTMGLFLGMNLPDWPPESI 329
           L  +GL L  + P + P  +
Sbjct: 301 LHQLGLSLKDSPPSFDPSQV 320


>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 =  362 bits (929), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 137/311 (44%), Positives = 200/311 (64%), Gaps = 2/311 (0%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E+ KP  IE + +  E+     ++ EPL RG+  TLGN+LRRVL+SSL GAAIT+V+ID
Sbjct: 2   TEIEKPR-IELVEI-SEDNTYGKIVIEPLERGYGTTLGNSLRRVLLSSLPGAAITSVKID 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV HE S+I GV ED  +II+NIKG+ +KM  D  K + I  +G G VTA DI    D+E
Sbjct: 60  GVQHEFSTIPGVLEDTVEIIMNIKGLAIKMHSDEPKLLRIEAQGEGEVTAKDIICDADVE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           ++N DH I  LD D  +  ELT+ KG GYV A+ ++    PIG+I ID++++P+ K +YT
Sbjct: 120 IINKDHHIATLDKDGRLFAELTLEKGKGYVTAEKNKKPGQPIGIIPIDSIFTPVIKANYT 179

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE  R GQV DYDKL++ + T+G+I  +++V+ A++IL D   +F       K+V+  + 
Sbjct: 180 VEHTRVGQVTDYDKLTLEVWTNGTIKPDEAVSAAAKILIDYFNLFTGLTTAVKKVEAPVE 239

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L   +EEL+LSVRS NCL+   I  +G+LIQ+T  +M+++ N G+KSL E+
Sbjct: 240 KEKDERERILEMPIEELDLSVRSYNCLKRAGINTIGELIQKTPEEMMKVRNLGKKSLEEV 299

Query: 307 KGVLGTMGLFL 317
           +  L  + L L
Sbjct: 300 EEKLAALNLSL 310


>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 =  362 bits (929), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 136/310 (43%), Positives = 208/310 (67%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  ++ +    + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDG
Sbjct: 3   EIEKP-KIEVVEV-SDDNSYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVRTVQIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 EKLAELGLSL 310


>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 =  362 bits (929), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 142/310 (45%), 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-KIETVEI-SEDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 AKLEELGLSL 310


>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 =  362 bits (929), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 123/310 (39%), Positives = 187/310 (60%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +      E R+  + EPL  GF +TLGN++RR L+SS+ GAA+T+++IDGVLHE +++ G
Sbjct: 9   LSEEAVSETRSRFVIEPLEPGFGYTLGNSIRRTLLSSIPGAAVTSIRIDGVLHEFTTVPG 68

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+TDIILN+K + +    D    + + K+GPG VTAGDI     + V NPD  I  L
Sbjct: 69  VKEDVTDIILNLKELVVSSEEDEPVTMYLRKQGPGAVTAGDIVPPAGVTVHNPDLHIATL 128

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           +    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D
Sbjct: 129 NGKGKLEIELVVERGRGYVPAVQNKQAGAEIGRIPVDSIYSPVMKVTYKVEATRVEQRTD 188

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL + +++  SIT  D+VA A + L +  G+        + ++   +        A  
Sbjct: 189 FDKLILDVESKPSITPRDAVASAGKTLVELFGLARELNVDAEGIEIGPSPAEADTIAAFA 248

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +E+L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  L  +GL L
Sbjct: 249 MPIEDLDLTVRSYNCLKREGIHTVGELVSRSEADLLDIRNFGAKSIDEVKMKLVGLGLAL 308

Query: 318 GMNLPDWPPE 327
             + P + P 
Sbjct: 309 KDSPPGFDPS 318


>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 =  362 bits (929), Expect = 5e-98,   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|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 =  362 bits (929), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 149/328 (45%), Positives = 210/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP     I +    EN   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPK---IIAVESLGENHAKVVMEPFERGYGHTLGNALRRVLLSSMIGYAPTEVTIA 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 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKV 183
           V+NPDHVI +L     + +++ + KG GYVP    R   +   +   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  +   + 
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETSGVITPEEAIRQSARILVDQLSVFAALEGTETAAE- 238

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 239 -APSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>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 =  362 bits (929), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 123/320 (38%), Positives = 192/320 (60%), Gaps = 4/320 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V      NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLSEEVVAE----NRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TDIILN+KG+ +    D    + + K+GPG VTAGDI     + V N
Sbjct: 61  HEFTTVPGVKEDVTDIILNLKGLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDMHIATLNDKGKLEVELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SI+  D++A A + L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDKLILDVETKNSISPRDALASAGKTLVELFGLARELNIEAEGIEIGPSPAE 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                     +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  
Sbjct: 241 ADQAAHFALPIDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIK 300

Query: 310 LGTMGLFLGMNLPDWPPESI 329
           L  +GL L  +   + P  +
Sbjct: 301 LHQLGLSLKDSPASFDPSEV 320


>gi|326905303|gb|EGE52236.1| DNA-directed RNA polymerase subunit alpha rpoA [Mycobacterium
           tuberculosis W-148]
          Length = 348

 Score =  362 bits (929), Expect = 5e-98,   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|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 =  362 bits (929), Expect = 5e-98,   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|327438303|dbj|BAK14668.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Solibacillus silvestris StLB046]
          Length = 314

 Score =  362 bits (929), Expect = 5e-98,   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-KIETVEI-SEDAKYGKFVVEPLERGYGNTLGNSLRRILLSSLPGAAVTSIQIDG 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|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 =  362 bits (929), Expect = 5e-98,   Method: Composition-based stats.
 Identities = 138/311 (44%), Positives = 204/311 (65%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  E+      + EPL RG+  TLGN+LRR+L+SSL G A+T+++IDG
Sbjct: 3   EIEKP-KIECV-ISSEDNTYGKFVVEPLERGYGITLGNSLRRILLSSLPGIAVTSIKIDG 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|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 =  362 bits (929), Expect = 5e-98,   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-KIEIVEI-SEDNRYGKIVWEPLERGFGITLGNSLRRVLLSSLPGAAVTSVKIDG 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 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI-- 245
              R G V DYDKL++ + TDGS+  E++V+ A+ IL   L +F N      E +     
Sbjct: 181 TDTRVGNVTDYDKLTLEVWTDGSMRPEEAVSKAAGILVAHLKLFQNITGTPAEDEAGDGP 240

Query: 246 --NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 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|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 =  361 bits (928), Expect = 6e-98,   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   VNDFLTPRSIAVNAI---NQTHAKVVLEPLERGFGHTLGTALRRILISSMPGCAITEVEI 60

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGV HE SSI+GV ED+ +I+LN+KG+ LKM       + + K+GPGVVTA DIQ  + +
Sbjct: 61  DGVQHEYSSIEGVQEDVINILLNLKGVALKMEDSEETTLELVKKGPGVVTANDIQRDHSV 120

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKK 182
           E++NPDH+IC +  D  +R++L V KG GYV A   ++E+D    I    +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 VAYVVEAARVEQRTDLDKLVIDLETDGTIEPEEAIRRAATILQQQIAVFVDLE---QDAK 237

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
            +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N G+KS
Sbjct: 238 PEPKQEREEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLGKKS 297

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           L EIK VL + GL LGM L +WPP S+ +  +
Sbjct: 298 LTEIKDVLASKGLSLGMRLENWPPVSLRDDDR 329


>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 =  361 bits (928), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 137/310 (44%), 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-KIETVEI-SDDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 HKLEDLGLGL 310


>gi|284006138|emb|CBA71380.1| DNA-directed RNA polymerase alpha chain [Arsenophonus nasoniae]
          Length = 329

 Score =  361 bits (928), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 148/334 (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   MQGSVTEFLKPRLVDIEQISS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  361 bits (928), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 139/324 (42%), Positives = 205/324 (63%), Gaps = 3/324 (0%)

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  +    P E  EE
Sbjct: 301 QKLHSLGLSLKKS-DSTPKEEEEE 323


>gi|254819221|ref|ZP_05224222.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           intracellulare ATCC 13950]
          Length = 347

 Score =  361 bits (928), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 120/320 (37%), Positives = 191/320 (59%), Gaps = 4/320 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E ++     +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLSEEVL----TDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T IILN+K + +    D    + + K+GPG VTAGDI     + V N
Sbjct: 61  HEFTTVPGVKEDVTAIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+    + +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++
Sbjct: 121 PDLHIATLNDKGKLEVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SI   D++A A + L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDKLILDVETKSSINPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAE 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                +    +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  
Sbjct: 241 ADHIASFALPIDDLDLTVRSYNCLKREGVHTVGELVSRTESDLLDIRNFGQKSIDEVKVK 300

Query: 310 LGTMGLFLGMNLPDWPPESI 329
           L  +GL L  +   + P  +
Sbjct: 301 LHQLGLSLKDSPASFDPSQV 320


>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 =  361 bits (928), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 148/328 (45%), Positives = 211/328 (64%), Gaps = 8/328 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+KP     I +    E+   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I 
Sbjct: 3   TSLLKPK---IIAVESLGESHAKVVMEPFERGYGHTLGNALRRVLLSSMIGYAPTEVTIA 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 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKV 183
           V+NPDHVI +L     + +++ V KG GYVP    R   +   +   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  +   + 
Sbjct: 180 SYAVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAALEGTEATAE- 238

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N GRKSL
Sbjct: 239 -APSRAPQIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTENELLKTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            EIK VL + GL LGM L +WPP  +++
Sbjct: 298 NEIKEVLASRGLTLGMKLENWPPAGLDK 325


>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 =  361 bits (928), Expect = 6e-98,   Method: Composition-based stats.
 Identities = 148/334 (44%), 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   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
           +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 328


>gi|240167783|ref|ZP_04746442.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium kansasii
           ATCC 12478]
          Length = 347

 Score =  361 bits (928), Expect = 6e-98,   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|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 =  361 bits (928), Expect = 7e-98,   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 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EPKKEVKE 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|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 =  361 bits (928), Expect = 7e-98,   Method: Composition-based stats.
 Identities = 155/327 (47%), Positives = 211/327 (64%), 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 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG---LITIDALYSPIKKVSY 185
           NPDHVI +L     + M++ V KG GYVP    R  ++P      I +DA +SP+K+VSY
Sbjct: 122 NPDHVIAHLSQGGKLDMQIKVEKGRGYVPGTMRRYADEPTKSIGRIVLDASFSPVKRVSY 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EPKKEVKED 244
           TVESAR  Q  D DKL + I+T+G+IT ED+V  +++IL +QL +F   E          
Sbjct: 182 TVESARVEQRTDLDKLLVEIETNGAITAEDAVRASAKILVEQLAVFAQLEGGELAAFDAP 241

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
               +  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|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 =  361 bits (928), Expect = 7e-98,   Method: Composition-based stats.
 Identities = 145/334 (43%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVI 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|42810|emb|CAA37839.1| unnamed protein product [Escherichia coli]
          Length = 329

 Score =  361 bits (928), Expect = 7e-98,   Method: Composition-based stats.
 Identities = 145/334 (43%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  361 bits (927), Expect = 8e-98,   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-KIETVDV-NDDGTYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 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|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 =  361 bits (927), Expect = 8e-98,   Method: Composition-based stats.
 Identities = 136/310 (43%), Positives = 204/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+TA+QIDG
Sbjct: 3   EIEKP-KIETVEL-NEDAKYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDG 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|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 =  361 bits (927), Expect = 8e-98,   Method: Composition-based stats.
 Identities = 137/310 (44%), Positives = 200/310 (64%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +      E  N    + EPL RG+  TLGN+LRR+L+SSL GAAI+++QIDG
Sbjct: 3   EFEKPNITKV----DESTNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAISSIQIDG 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|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 =  361 bits (927), Expect = 8e-98,   Method: Composition-based stats.
 Identities = 132/315 (41%), Positives = 207/315 (65%), Gaps = 2/315 (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 GVLGTMGLFLGMNLP 322
             L  +GL L  +  
Sbjct: 301 NKLTELGLSLKDSKE 315


>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 =  361 bits (927), Expect = 9e-98,   Method: Composition-based stats.
 Identities = 139/326 (42%), Positives = 208/326 (63%), Gaps = 4/326 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP          +++     + EPL RG+  T+GNALRR L+SSL GAA+TAV+IDG
Sbjct: 3   EIQKPTI--RCEELSQDQKYGRYVIEPLERGYGITIGNALRRTLLSSLPGAAVTAVKIDG 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 GVLGTMGLFLGMNLPDWPPESIEELA 333
             L ++GL L     D  P+  EE  
Sbjct: 301 QKLHSLGLSL--KKSDSTPKGEEEEK 324


>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 =  361 bits (927), Expect = 9e-98,   Method: Composition-based stats.
 Identities = 146/326 (44%), Positives = 211/326 (64%), Gaps = 7/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP     I +    ++   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPK---IIAVEPLGDHHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 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 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKVSY 185
           NP HVI NL     + ++L V +G GYVP    +  ++   +   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 AVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAAL-EGTESAAEAA 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|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 =  361 bits (927), Expect = 9e-98,   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|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 =  361 bits (926), Expect = 9e-98,   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|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 =  361 bits (926), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 136/310 (43%), Positives = 200/310 (64%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +      E  N    + EPL RG+  TLGN+LRR+L+SSL GAA++++QIDG
Sbjct: 3   EFEKPNITKV----DESTNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVSSIQIDG 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|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 (926), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 137/310 (44%), Positives = 204/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+TA+QIDG
Sbjct: 3   EIEKP-KIETVEL-NEDAKYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDG 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|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 =  361 bits (926), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 138/310 (44%), Positives = 204/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+TA+QIDG
Sbjct: 3   EIEKP-KIETVEL-NEDAKYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDG 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|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 =  361 bits (926), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 123/320 (38%), Positives = 191/320 (59%), Gaps = 4/320 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        ENR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLSE----ETLAENRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TDIILN+K + +    D    + + K+GPG VTAGDI     + V N
Sbjct: 61  HEFTTVPGVKEDVTDIILNLKSLVVSSEEDEPVTMYLRKQGPGAVTAGDIVPPAGVTVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDMHIATLNDKGKLEIELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYNVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SI+  D++A A + L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDKLVLDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAE 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                +    +E+L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  
Sbjct: 241 ADHIASFALPIEDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIK 300

Query: 310 LGTMGLFLGMNLPDWPPESI 329
           L  +GL L  +   + P  +
Sbjct: 301 LHQLGLSLKDSPTSFDPSEV 320


>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 =  361 bits (926), Expect = 1e-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-KIETVDV-NDDGTYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 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|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 =  361 bits (926), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 148/330 (44%), Positives = 212/330 (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   MQNSTYEFLKPRQIDVDAL---SATRAKVFMEPFERGFGYTLGNALRRILLSSMNGFAPT 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    E 
Sbjct: 178 RVSFEVQAARVEQRTDLDCLVLDIETNGAIDPEEAVRRAARILIDQMSVFADLEGTPVEE 237

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            ++      P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N GRK
Sbjct: 238 SKEEA---PPIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPNLGRK 294

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           SL EIK VL + GL LG  L  WPP  +++
Sbjct: 295 SLNEIKEVLASKGLTLGSKLDVWPPVGLDK 324


>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 =  361 bits (926), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 121/320 (37%), Positives = 191/320 (59%), Gaps = 4/320 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLSE----ETVADNRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TDIILN+K + +    D    + + K+GPG VTAGDI     + V N
Sbjct: 61  HEFTTVPGVKEDVTDIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  I  L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PEMHIATLNDKGKLEVELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SIT  D++A A + L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDKLILDVETKNSITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAE 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                +    +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  
Sbjct: 241 ADHIASFALPIDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIK 300

Query: 310 LGTMGLFLGMNLPDWPPESI 329
           L  +GL L  +   + P  +
Sbjct: 301 LHQLGLSLKDSPATFDPSEV 320


>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 =  361 bits (926), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 126/319 (39%), Positives = 190/319 (59%), Gaps = 4/319 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P  IE        E R+  + EPL  GF +TLGN+LRR L+SS+ GA++T+++IDGVL
Sbjct: 5   QRPTLIE----DPISEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+TD+ILN+K + +    D    + + K+GPG VTA DI     +EV N
Sbjct: 61  HEFSTVPGVKEDVTDLILNLKELVVSSDNDEPTVMYLRKQGPGEVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  +  L+    + +ELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+
Sbjct: 121 PELRLATLNDKGKLEIELTVERGRGYVSAAQNKQAGQEIGRIPIDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  SI+  D++A A + L    G+        + V    +   
Sbjct: 181 TRVEQRTDFDRLIVDVETKPSISPRDAMASAGKTLVGLFGLAQELNAEAEGVDIGPSAAD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EE++L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  
Sbjct: 241 AALAADLALPIEEMDLTVRSYNCLKREGIHTIGELVSRSEADLLDIRNFGQKSIDEVKTK 300

Query: 310 LGTMGLFLGMNLPDWPPES 328
           LG MGL L  + P + P  
Sbjct: 301 LGAMGLQLKDSPPGFDPRQ 319


>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 =  361 bits (926), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 124/330 (37%), Positives = 191/330 (57%), Gaps = 4/330 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        + R+  + EPL  GF +T+GN+LRR L+SS+ GAA+T+++I+GV 
Sbjct: 5   QRPTLTE----EASSDLRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGAAVTSIRIEGVE 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T++ILN+KG+ +    D    + + K+GPGVVTA DI     +EV N
Sbjct: 61  HEFTTVPGVKEDVTEMILNLKGLVVSSEHDEPVLMYLRKQGPGVVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+    + MELTV +G GYV A  ++     IG I ID++YSP+ +V+Y VE+
Sbjct: 121 PDLHIATLNGKGKLEMELTVERGRGYVSATQNKQAGQEIGRIPIDSIYSPVLRVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + I+T  +I   D+VA A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDRLIVDIETKPAIRPRDAVASAGKTLVELFGLARELNVDAEGIDMGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +E+L L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  
Sbjct: 241 AALAADLALPIEDLNLTVRSYNCLKREGIHSVGELVARSEQDLLDIRNFGAKSIDEVKQK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           L  MGL L  + P + P S  +     +D+
Sbjct: 301 LVDMGLSLKDSPPGFDPSSAADSYSSEDDE 330


>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 =  361 bits (926), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 144/335 (42%), Positives = 220/335 (65%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQIST---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 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
            +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>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 =  361 bits (926), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 156/333 (46%), 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   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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALYS 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 PISRVSFEVEPARVEQRTDLDKLVLDIETNGSIDPEEAVRSAARILIDQMSIFA---DLQ 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|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 =  361 bits (926), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 155/333 (46%), 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   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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALYS 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 PISRVSFEVEPARVEQRTDLDKLVLDIETNGSIDPEEAVRSAARILIDQMSIFA---DLQ 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|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 =  360 bits (925), Expect = 1e-97,   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-IETVEV-SEDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDS 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|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 =  360 bits (925), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 144/335 (42%), Positives = 219/335 (65%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQIST---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 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
            +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>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 =  360 bits (925), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 123/320 (38%), Positives = 193/320 (60%), Gaps = 4/320 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E ++      NR+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLTEEVIAE----NRSKFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TDIILN+KG+ +    D    + + K+GPG VTAGDI     + V N
Sbjct: 61  HEFTTVPGVKEDVTDIILNLKGLVVSSEEDEPVTMYVRKQGPGTVTAGDIVPPAGVVVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDMHIATLNDKGKLEIELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  SI+  D++A A + L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDRLILDVETKNSISARDALASAGKTLVELFGLARELNVEAEGIEIGPSPAE 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                +    +E+L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  
Sbjct: 241 ADHIASFGLPIEDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKVK 300

Query: 310 LGTMGLFLGMNLPDWPPESI 329
           L  +GL L  +   + P S+
Sbjct: 301 LHALGLSLKDSPASFDPSSV 320


>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 =  360 bits (925), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 144/335 (42%), Positives = 219/335 (65%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQIST---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 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
            +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>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 =  360 bits (925), Expect = 1e-97,   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   VNDFLTPRSIAVNAI---NQTHAKVVLEPLERGFGHTLGTALRRILISSMPGCAITEVEI 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 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKK 182
           E++NPDH+IC +  D  +R++L V KG GYV A   ++E+D    I    +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 VAYVVEAARVEQRTDLDKLVIDLETDGTIDPEEAIRRAATILQQQIAVFVDLE---QDAK 237

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
            +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+  N G+KS
Sbjct: 238 PEPKQEREEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLGKKS 297

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           L EIK VL + GL LGM L +WPP S+ +  +
Sbjct: 298 LTEIKDVLASKGLSLGMRLENWPPVSLRDDDR 329


>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 =  360 bits (925), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 160/335 (47%), Positives = 215/335 (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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG---LITIDALYS 178
            +D+E++NPDHVI NL     + M++ V  G GYVP    R  ++       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|324999252|ref|ZP_08120364.1| DNA-directed RNA polymerase subunit alpha [Pseudonocardia sp. P1]
          Length = 350

 Score =  360 bits (925), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 126/318 (39%), Positives = 194/318 (61%), Gaps = 4/318 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P+  E +V     E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPSLTEDVV----TETRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TDIILN+K + +    D    + + K+GPG VTAGDI     + V N
Sbjct: 61  HEFTTVPGVKEDVTDIILNLKELVVSSEEDEPVTMYLRKQGPGAVTAGDIVPPAGVTVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I +L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLHIASLNDKGRLEVELVVERGRGYVPAMQNKATGAEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + +++  SIT  D++A + + L +  G+        + ++   + + 
Sbjct: 181 TRVEQRTDFDKLVLDVESKPSITPRDALASSGKTLVELFGLARELNVDAEGIEIGPSPQE 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                A    +EEL+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 ADTIAAFAMPIEELDLTVRSYNCLKREGIHTVGELVGRSEADLLDIRNFGAKSIDEVKMK 300

Query: 310 LGTMGLFLGMNLPDWPPE 327
           L  +GL L  + P + P 
Sbjct: 301 LVGLGLALKDSPPGFDPS 318


>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 =  360 bits (925), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 157/320 (49%), Positives = 213/320 (66%), Gaps = 2/320 (0%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           +IKP   E        ++    I  PL RGF  TLGN+LRR+L+SS+ G+AITAV+ +GV
Sbjct: 1   MIKPKGFEVDR-DSLRDDYAKFIIRPLERGFGVTLGNSLRRILLSSMMGSAITAVKFEGV 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 NPDLPIATLGANANFNAEIVVSFGRGYVPV-ENRETDLPVGFIGVDALYSPIRKVNYNVS 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|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 =  360 bits (925), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 132/314 (42%), Positives = 197/314 (62%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  E+      + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDG
Sbjct: 3   EIEKP-KIEIVEI-SEDNRYGKFVCEPLERGYGTTLGNSLRRILLSSLPGAAITSIRIDG 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 VEIKGVLGTMGLFL 317
            E+K  L    L L
Sbjct: 301 EEVKKKLEEYDLTL 314


>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 =  360 bits (925), Expect = 1e-97,   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|260907114|ref|ZP_05915436.1| DNA-directed RNA polymerase subunit alpha [Brevibacterium linens
           BL2]
          Length = 332

 Score =  360 bits (925), Expect = 1e-97,   Method: Composition-based stats.
 Identities = 122/330 (36%), Positives = 195/330 (59%), Gaps = 4/330 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V     ENR+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLTEEVV----SENRSRFAIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+T+ ILN+K + +    D      + K+GPG VTA D+     +E+ N
Sbjct: 61  HEFSTVPGVKEDVTEFILNLKSLVVSSEFDEPVVAYLRKQGPGTVTAADVSAPAGVEIHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+ +  + MELT+ +G GYV +  ++  +  IG + +D++YSP+ KV+Y VE+
Sbjct: 121 PDLHIATLNGEGRLDMELTIERGRGYVSSAQNKNADAEIGRVPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + I+T  S+T  D++A A + L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDRLVLDIETKPSMTPRDAIASAGKTLVELFGLARELNVEAEGIEIGPSPVD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +E+L+L+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  
Sbjct: 241 AALAADLALAIEDLDLTVRSYNCLKREGIHTVGELVARSEADLMDIRNFGSKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           L  +GL L  +   +    ++E     ED+
Sbjct: 301 LNELGLSLKDSPAGFEAGLVDEDQSYVEDE 330


>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 (925), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 133/310 (42%), Positives = 206/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  ++      + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETVEV-SDDATYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 AKLEDLGLGL 310


>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 =  360 bits (925), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 137/310 (44%), Positives = 204/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+TA+QIDG
Sbjct: 3   EIEKP-KIETVEL-NEDAKYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDG 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|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 =  360 bits (925), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 147/355 (41%), Positives = 210/355 (59%), Gaps = 34/355 (9%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           ++KP  +E   +     +   ++ EP  RG+ HTLGNALRRVL+SS+ G A T VQI GV
Sbjct: 5   MLKPRLVEVQEIS--GPSHARVVMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVQIAGV 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 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR-TENDPIGLITIDALYSPIKKVSYTV 187
           NPDHVI  L     + M++ V +G GYVP       ++  IG 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 NIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           NI Y+GDLIQRTE ++L+  N GRKSL EIK VL + GL LGM L DWPP  +E 
Sbjct: 303 NIYYIGDLIQRTENELLKTPNLGRKSLNEIKEVLASRGLTLGMRLDDWPPAGLER 357


>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 =  360 bits (924), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 137/334 (41%), Positives = 220/334 (65%), Gaps = 6/334 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++   ++ +KP ++E   +    +NR  ++ EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MKGYLKDFLKPRSVE---IEPLSDNRAKVVLEPLERGFGHTLGNALRRLLLSSMPGTAVT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND-PIGLITIDALYSPI 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 GGDEQEE--PEIDPVLLRPIDDLELTVRSANCLKAESIHFVGDLVQRTEVELLKTPNLGK 295

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           KSL EIK  L   GL LGM L +WPP S+ + A+
Sbjct: 296 KSLNEIKDTLAEHGLSLGMQLDNWPPPSLGDRAR 329


>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 =  360 bits (924), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 158/333 (47%), Positives = 217/333 (65%), 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALYS 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 PISRVSFEVEPARVEQRTDLDKLVLDIETDGSLDPEEAVRSAARILIDQMSIFA---DLQ 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|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 =  360 bits (924), Expect = 2e-97,   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--DFLKPRIIEVQKI---SETQAKVVMEPFERGFGHTLGNALRRILLSSMAGAAPT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSP 179
             ++EVLNP+HVI +L     + M++ V +G GYV A  +    E   +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|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 =  360 bits (924), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 149/331 (45%), Positives = 211/331 (63%), Gaps = 8/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  +E  ++     NR  ++ EP+ RGF  TLGNALRRVL+SS+ G AIT
Sbjct: 1   MQNSPTEYLKPRIVEVDLI---NPNRAKVVLEPMERGFGFTLGNALRRVLLSSIPGFAIT 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 EVEVQQA---PQIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLIQRHENDLLKAPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           RKSL EIK +L T GL LGM + +WPP+ +E
Sbjct: 295 RKSLNEIKDILATKGLSLGMKVDNWPPQGVE 325


>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 =  360 bits (924), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 147/335 (43%), Positives = 215/335 (64%), Gaps = 9/335 (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 RRVTYEVDSARVEQRTDLDKLIIEIETNGTIASDEAVRKAATILQDQLTAFV---ELEGK 234

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +     K+   +P LL+ +++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N G+
Sbjct: 235 TETAKEKKTAEIDPVLLQPIDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNLGK 294

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
           KSL EIK VL + GL LGM L +WPP  + E   K
Sbjct: 295 KSLTEIKDVLASRGLSLGMRLENWPPAGLHEEETK 329


>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 =  360 bits (924), Expect = 2e-97,   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|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 =  360 bits (924), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 137/310 (44%), Positives = 204/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+TA+QIDG
Sbjct: 3   EIEKP-KIETVEL-NEDAKYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDG 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|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 =  360 bits (924), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 156/333 (46%), 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   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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALYS 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 PISRVSFEVEPARVEQRTDLDKLVLDIETNGSIDPEEAVRSAARILIDQMSIFA---DLQ 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|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 =  360 bits (924), Expect = 2e-97,   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|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 (924), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 134/310 (43%), Positives = 204/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  E       + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDG
Sbjct: 3   EIEKP-KIETVEVNDEG-TYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 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|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 =  360 bits (924), Expect = 2e-97,   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|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 =  360 bits (923), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 154/333 (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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALYS 178
            +D+EV+NP+HVI  +  +  + M LT   G GY P    +    +   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|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 =  360 bits (923), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 150/336 (44%), Positives = 223/336 (66%), Gaps = 6/336 (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 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE--P 237
           I++V+Y V ++R  Q  D+DKL++ + TDGS+  ED+VA A++I+++Q+ +FINF+E   
Sbjct: 182 IRRVNYVVGNSRVKQKTDFDKLTLEVWTDGSVLPEDAVAFAAKIMKEQMNVFINFDESAE 241

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            +      +     FN  L + V ELELSVRS+NCL+   I  +  L+Q+TE++ML+  N
Sbjct: 242 PEHAGRKDDSGGKVFNENLYRSVNELELSVRSSNCLKNAEIDKLYQLVQKTESEMLKTKN 301

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELA 333
           FGRKSL EIK +L  MGL LGM+L  + P + +   
Sbjct: 302 FGRKSLNEIKELLAEMGLSLGMDLEGFVPPAEDNKE 337


>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 =  360 bits (923), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 157/333 (47%), 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   MQNSTTEFLKPRQIDVNTF---SATRAKVSMQPFERGFGHTLGNALRRILLSSMNGFAPT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALYS 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 PISRVSFEVEPARVEQRTDLDKLVLDIETDGSIDPEEAVRSAARILIDQMSIFA---DLQ 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|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 =  360 bits (923), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 144/335 (42%), Positives = 219/335 (65%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQIST---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 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
            +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>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 =  360 bits (923), Expect = 2e-97,   Method: Composition-based stats.
 Identities = 145/326 (44%), Positives = 211/326 (64%), Gaps = 7/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP     I +    ++   ++ EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   LLKPK---IIAVEPLGDHHAKVVMEPFERGYGHTLGNALRRVLLSSMVGYASTEVTIAGV 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 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKVSY 185
           NP HVI +L     + M++ V +G GYVP    +  ++   +   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 AVESARVEQRTDLDKLVMNIETNGVISPEEAIRQSARILVDQLSVFAAL-EGTESAAEAA 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|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 =  360 bits (923), Expect = 2e-97,   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---IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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
            +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>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 =  360 bits (923), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 159/333 (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   MQNSTTEFLKPRQIDVNTF---SATRAKVSMQPFERGFGHTLGNALRRILLSSMNGFAPT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALYS 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 PISRVSFEVEPARVEQRTDLDKLVLDIETDGSIDPEEAVRSAARILIDQMSIFA---DLQ 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|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 =  359 bits (922), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 146/331 (44%), Positives = 211/331 (63%), Gaps = 9/331 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E ++P  +    +      R  +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLRPRLV---GIETVSPRRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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
           +  + +      P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QR E ++L+  N 
Sbjct: 238 EVEQVEEKPLFDP---ILLRPVDDLELTVRSANCLKAEAIQYIGDLVQRAEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           G+KSL EIK VL + GL LGM L +WPPESI
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMRLENWPPESI 325


>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 =  359 bits (922), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 144/334 (43%), 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   MQGSVTEFLKPRLVDIEQISS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  359 bits (922), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 147/332 (44%), Positives = 219/332 (65%), Gaps = 9/332 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            +L+ P  I+   +         ++ EP  RG+ HTLGNALRR+L+SS+ G A T ++I 
Sbjct: 4   TDLLTPRIIDVQNI---SPLHAKVVMEPFERGYGHTLGNALRRILLSSMTGYAPTEIKIA 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 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYSPIKKV 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 PQA---PQIDPILLRPVDDLELTVRSANCLKVENIYYIGDLIQRTEAELLRTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
            EIK VL +  L LGM L +WPP +++ ++K+
Sbjct: 298 NEIKEVLASRELTLGMKLDNWPPANLDSVSKE 329


>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 =  359 bits (922), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 145/338 (42%), Positives = 219/338 (64%), Gaps = 9/338 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q++  E + P +I+   +   +     +  EPL RGF HTLG ALRR+L+SS+ GAAI 
Sbjct: 1   MQRSVNEFLTPRHIQVEQVSNTQ---AKVTLEPLERGFGHTLGAALRRILLSSMPGAAIV 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALYS 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 PVKRVAYGVENARVEQRTDLDKLVIDLETNGTIEPEEAIRRSATILQQQLAVFV---DLE 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            E + +   +    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  N 
Sbjct: 235 NEAEPEPEEQEDEIDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKY 336
           G+KSL EIK VL + GL LGM+L +WPP S+++  K  
Sbjct: 295 GKKSLTEIKDVLASRGLSLGMHLENWPPASLKKDDKAL 332


>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 =  359 bits (922), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 144/335 (42%), 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---IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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
            +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>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 =  359 bits (922), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 152/306 (49%), 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 LTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
           L V++G GY PA     + D    I    +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 DLETNGTIDPEEAIRRAATILQQQLAVFVDFDHEKEPERVEEEEEIDP---ILLRPVDDL 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|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 =  359 bits (922), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 121/320 (37%), Positives = 194/320 (60%), Gaps = 4/320 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E ++     ++R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLSEEVL----TDSRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TDIILN+K + +    D    + + K+GPG VTAGDI     + V N
Sbjct: 61  HEFTTVPGVKEDVTDIILNLKALVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  I  L+    + +EL V +G GYVPA  +R     IG I +D++YSP+ KV+Y V++
Sbjct: 121 PNMRIATLNDKGKLEVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SIT  D++A A + L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDKLILDVETKNSITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAE 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                +    +++L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  
Sbjct: 241 ADHIASFALPIDDLDLTVRSYNCLKREGVHTVGELVSRTESDLLDIRNFGQKSIDEVKVK 300

Query: 310 LGTMGLFLGMNLPDWPPESI 329
           L  +GL L  + P + P  +
Sbjct: 301 LHQLGLSLKDSPPSFDPSEV 320


>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 =  359 bits (922), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 147/334 (44%), Positives = 221/334 (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 SVPEKKEEK---PEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 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 =  359 bits (922), Expect = 3e-97,   Method: Composition-based stats.
 Identities = 145/334 (43%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|42812|emb|CAA37838.1| unnamed protein product [Escherichia coli]
          Length = 329

 Score =  359 bits (921), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 145/334 (43%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALR +L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRCILLSSMPGCAVT 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|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 =  359 bits (921), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 147/335 (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---IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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
            +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>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 =  359 bits (921), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 148/332 (44%), Positives = 214/332 (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   MQNSTSEFLKPRQIDVDTL---SATRAKVSMQPFERGFGHTLGNALRRILLSSMNGFAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV-TIFKRGPGVVTAGDIQ 120
            + I GVLHE S++ GV ED+ DI+LN+K +  K+ G+  + V ++ K G G V A D +
Sbjct: 58  EITIAGVLHEYSTLDGVQEDVVDILLNVKSVVFKLHGNRTEAVLSLKKTGAGPVYASDFE 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP-AKHHRTENDPIGLITIDALYSP 179
             +D+E++NP  VIC+L  +  + ME+ V +G GY   +    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+      P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N G
Sbjct: 238 EVEEEKA---PPIDPVLLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           RKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 295 RKSLNEIKEVLASKGLTLGSRLESWPPAGLEK 326


>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 =  359 bits (921), Expect = 4e-97,   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|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 =  359 bits (921), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 122/321 (38%), Positives = 194/321 (60%), Gaps = 4/321 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E ++     + R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLSEEVI----SDARSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TDIILN+KG+ +    D    + + K+GPG VTAGDI     + V N
Sbjct: 61  HEFTTVPGVKEDVTDIILNLKGLVVSSEDDEPVTMYVRKQGPGAVTAGDIVPPASVTVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLHIATLNDKGKLEIELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  S+T  D++A A + L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDRLILDVETKNSMTARDALASAGKTLVELFGLARELNVEAEGIEIGPSPAE 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                A    +E+L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  
Sbjct: 241 ADHIAAFSLPIEDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKVK 300

Query: 310 LGTMGLFLGMNLPDWPPESIE 330
           L  +GL L  +   + P  ++
Sbjct: 301 LHALGLALKDSPASFDPSQVD 321


>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 =  359 bits (921), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 151/336 (44%), Positives = 214/336 (63%), Gaps = 2/336 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW  L+ P  +E        EN      EPL RGF  TLGNALRRVL+SSL+GAAI AV
Sbjct: 13  RNWSTLVHPETLE--RDEDSTENYGKFSCEPLERGFGTTLGNALRRVLLSSLQGAAIVAV 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  +  +  +   +  +D+
Sbjct: 311 EDIRKVIHELGLDFGMKLDGFEEQYKKWRERNQQDE 346


>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 =  359 bits (921), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 144/333 (43%), Positives = 208/333 (62%), Gaps = 10/333 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
              + P  +E   +         ++ EP   GF +TLGNALRRVL+SS+ G A T V I 
Sbjct: 4   NSFLTPRIVEVHNI---SPLHAKVVMEPFEHGFGYTLGNALRRVLLSSIPGCAPTKVSIS 60

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV-TIFKRGPGVVTAGDIQTVNDI 125
           GV+HE S+I G+ ED+ D+ILN+KG+ LK+  +  + V T+ K   G+VTAGDI+  +D+
Sbjct: 61  GVVHEYSTIDGLQEDVVDLILNLKGVVLKLHNNKTQSVLTLKKSSEGIVTAGDIEATHDV 120

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKK 182
           E++NPDHVI ++     +  ++TV KG GY P+ +   E+        I +DA +SPI++
Sbjct: 121 EIVNPDHVIAHITSGGKIEAQITVEKGRGYWPSANRSKEDKSSSSIGDILLDASFSPIRR 180

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           VSY VESAR  Q  D DKL + I+T+GS+  E+++  A+++L +Q   F + E      +
Sbjct: 181 VSYAVESARVEQRTDLDKLIIDIETNGSVDPEEAIRYAAKVLVEQFSFFADLESTPLPTE 240

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           +       P    LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTEA++LR  N GRKS
Sbjct: 241 QPKAPVIDP---ILLRPVDDLELTVRSANCLKVENIFYIGDLIQRTEAELLRTPNLGRKS 297

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
           L EIK VL +  L LGM L +WPP ++E   K+
Sbjct: 298 LNEIKEVLASRDLSLGMKLENWPPANLENYIKE 330


>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 =  359 bits (921), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 124/320 (38%), Positives = 196/320 (61%), Gaps = 4/320 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E ++      NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLTEEVIAE----NRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TDIILN+KG+ +    D    + + K+GPGVVTAGDI     + V N
Sbjct: 61  HEFTTVPGVKEDVTDIILNLKGLVVSSEEDEPVTMYVRKQGPGVVTAGDIVPPAGVTVNN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLHIATLNDKGKLEIELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  SIT  D++A A + L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDRLILDVETKNSITARDALASAGKTLVELFGLARELNVEAEGIEIGPSPAE 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                +    +E+L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  
Sbjct: 241 ADHIASFGLPIEDLDLTVRSYNCLKREGVHTVGELVGRTESDLLDIRNFGQKSIDEVKVK 300

Query: 310 LGTMGLFLGMNLPDWPPESI 329
           L ++GL L  +   + P ++
Sbjct: 301 LHSLGLALKDSPASFDPTTV 320


>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 =  359 bits (921), Expect = 4e-97,   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-IETVEV-SEDAKYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSVQIDG 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|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 =  359 bits (921), Expect = 4e-97,   Method: Composition-based stats.
 Identities = 123/320 (38%), Positives = 192/320 (60%), Gaps = 4/320 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E I+     +NR+  + EPL  GF +TLGN+LRR L+SS+ GAAIT+++IDGVL
Sbjct: 5   QRPTLTEEIL----ADNRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAITSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TDIILN+KG+ +    D    + + K+GPG VT  DI     + V N
Sbjct: 61  HEFTTVPGVKEDVTDIILNLKGLVVSSEEDEPVTMYVRKQGPGTVTGADIVPPAGVTVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLHIATLNDKGKLEIELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  SI+  D++A A + L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDRLVLDVETKNSISARDALASAGKTLVELFGLARELNVEAEGIEIGPSPAE 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                +    +E+LEL+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  
Sbjct: 241 ADHIASFSLPIEDLELTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKVK 300

Query: 310 LGTMGLFLGMNLPDWPPESI 329
           L  +GL L  +   + P  +
Sbjct: 301 LHALGLSLKDSPASFDPSQV 320


>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 =  358 bits (920), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 126/321 (39%), Positives = 187/321 (58%), Gaps = 4/321 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E          R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G L
Sbjct: 5   QRPTLTE----ESINPQRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGAL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+I+LNIKGI L    D    + + K G G VTAGDI     + + N
Sbjct: 61  HEFTTLPGVVEDVTEILLNIKGIVLTSEYDEPVVMYLRKSGNGEVTAGDITPPAGVTIAN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L  D  + +E TV +G GYVPA+ ++ + D IG I +D++YSP+ KVSY VE+
Sbjct: 121 PDQHIATLADDGELEIEFTVERGRGYVPAQMNKQDTDEIGRIPVDSIYSPVLKVSYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  +I+  D+VA A   L +  G+        + V+      +
Sbjct: 181 TRVEQRTDFDKLILDVETKPAISPRDAVASAGSTLVELFGLCRELNVQAEGVEVGPAPVA 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              NP +   +E+L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  
Sbjct: 241 EETNPEMAVPIEDLNLTQRSYNCLKREGIHTIGELVAHTEQDLLDIRNFGMKSIDEVKDK 300

Query: 310 LGTMGLFLGMNLPDWPPESIE 330
           L +MGL L  +   +   ++E
Sbjct: 301 LQSMGLSLKSSPLGFDTNNLE 321


>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 =  358 bits (920), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 147/332 (44%), Positives = 218/332 (65%), 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL--ITIDALYSP 179
            + ++++NPDHVI ++  D  + M L  + G GY P+    T +    +  + +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 IRRVTYSVENARVEKRTDLDKLIIDLETDGTLDPEEAIRFAAAVLQHQLAAFV---DLKQ 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|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 =  358 bits (920), Expect = 5e-97,   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-KIEIAEI-SEDNRYGKFICEPLERGYGTTFGNSLRRMLLSSLEGAAITSIRIDG 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|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 =  358 bits (920), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 137/311 (44%), Positives = 203/311 (65%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  E+      + EPL RG+  TLGN+LRR+L+SSL G A+T+++IDG
Sbjct: 3   EIEKP-KIECV-VCSEDNRYGKFVVEPLERGYGITLGNSLRRILLSSLPGVAVTSIKIDG 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|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 =  358 bits (920), Expect = 5e-97,   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 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV- 241
           V      AR GQ  DYDKL++ I TDGSI  ED++A A++IL++Q+ +FINF+E      
Sbjct: 188 VRVITSQARVGQQTDYDKLTLEITTDGSILPEDALAYAAKILKEQMQVFINFDESAVVPV 247

Query: 242 -KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 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|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 =  358 bits (920), Expect = 5e-97,   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  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDI 119
             +I+GV HE S+++GV ED+ +I+LN+KG+ + M     SH  +++ K+GPGVVTA DI
Sbjct: 58  EAEIEGVEHEYSALEGVQEDIIEILLNLKGVAVVMHDQEKSHAMLSLKKKGPGVVTAADI 117

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDAL 176
              +++E+ NPDHVI  +  D  + M L++++G GY PA   R+++D    I    +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 FSPVKRLAYSVESARVEQRTDLDKLVLDLETNGTIDPEEAIRRSATILQQQLAVFV---D 234

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            + E   +   K    +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTE ++L+  
Sbjct: 235 LESEKSSEPEEKEEDVDPILLRPVDDLELTVRSANCLKAENIYYIGDLIQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LG+ L +WPP S+
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGLRLENWPPASL 327


>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 =  358 bits (920), Expect = 5e-97,   Method: Composition-based stats.
 Identities = 134/310 (43%), Positives = 202/310 (65%), 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-KIEIVE-QSEDNTYGKFVVEPLERGYGITLGNSLRRILLSSLPGAAVTSVKIEG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 NKLAELGLSL 310


>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 =  358 bits (920), Expect = 6e-97,   Method: Composition-based stats.
 Identities = 134/310 (43%), Positives = 207/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE +     ++     + EPL RG+  TLGN+LRR+L+SSL GAA   ++IDG
Sbjct: 4   EIEKP-KIEIVE-QSNDDTYAKFVIEPLERGYGITLGNSLRRMLLSSLPGAAAKTIKIDG 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|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 (920), Expect = 6e-97,   Method: Composition-based stats.
 Identities = 123/320 (38%), Positives = 196/320 (61%), Gaps = 4/320 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E ++     +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLTEEVI----ADNRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TDIILN+KG+ +    D    + + K+GPG VTAGDI     + V N
Sbjct: 61  HEFTTVPGVKEDVTDIILNLKGLVVNSEEDEPVTMYVRKQGPGAVTAGDIVPPAGVTVNN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLHIATLNDKGKLEIELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  SIT  D++A A + L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDRLVLDVETKNSITARDALASAGKTLVELFGLARELNVEAEGIEIGPSPAE 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                +    +E+L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  
Sbjct: 241 ADHIASFGLPIEDLDLTVRSYNCLKREGVHTVGELVGRTESDLLDIRNFGQKSIDEVKVK 300

Query: 310 LGTMGLFLGMNLPDWPPESI 329
           L ++GL L  +   + P ++
Sbjct: 301 LHSLGLSLKDSPASFDPTTV 320


>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 =  358 bits (920), Expect = 6e-97,   Method: Composition-based stats.
 Identities = 135/310 (43%), Positives = 203/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  + +     + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETVEISDDAK-YGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 AKLEELGLGL 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 =  358 bits (919), Expect = 6e-97,   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   MQGSVTEFLKPRLVDIEQISS---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 YSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>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 =  358 bits (919), Expect = 6e-97,   Method: Composition-based stats.
 Identities = 122/316 (38%), Positives = 187/316 (59%), Gaps = 4/316 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 32  QRPTLTE----ENISEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 87

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+T+IILNIKG+ +    D      + K G G VTA DI     +E+ N
Sbjct: 88  HEFSTVPGVKEDVTEIILNIKGLVVSSEHDEPITAYLRKTGAGQVTAADISAPAGVEIHN 147

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+ VI  L+  A   +ELT+ +G GYV A+ +R E    G I ID++YSP+ KV+Y VE+
Sbjct: 148 PELVIATLNDKAKFEVELTIERGRGYVSAQQNRNEYSEAGQIPIDSIYSPVLKVTYRVEA 207

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R G+  D+D+L + ++T  +I+  D++A A R L +  G+        + ++       
Sbjct: 208 TRAGERTDFDRLVVDVETKPAISPRDAIASAGRTLVELFGLARELNSAAEGIEIGPAPVD 267

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              +  L   +E+L+LSVRS NCL+ E I  + +L+  +E  ++ + NFG+KS+ E+K  
Sbjct: 268 QVLSSELSMPIEDLDLSVRSYNCLKREGINTVSELVSLSETQLMNIRNFGQKSVDEVKDK 327

Query: 310 LGTMGLFLGMNLPDWP 325
           L  MGL L  ++P + 
Sbjct: 328 LTEMGLSLKDSVPGFD 343


>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 =  358 bits (919), Expect = 7e-97,   Method: Composition-based stats.
 Identities = 146/335 (43%), Positives = 218/335 (65%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISS---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 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
            +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>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 =  358 bits (919), Expect = 7e-97,   Method: Composition-based stats.
 Identities = 124/319 (38%), Positives = 190/319 (59%), Gaps = 4/319 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P  +E        E R+  + EPL  GF +TLGN+LRR L+SS+ GA++T+++IDGVL
Sbjct: 5   QRPTLVE----DPISEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+TD+ILN+K + +    D    + + K+GPG VTA DI     +EV +
Sbjct: 61  HEFSTVPGVKEDVTDLILNLKELVVSSDNDEPTVMYLRKQGPGEVTAADIAPPAGVEVHS 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  +  L+    + +ELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+
Sbjct: 121 PELRLATLNDKGKLEIELTVERGRGYVSAAQNKQAGQEIGRIPIDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  SI+  D++A A + L    G+        + V    +   
Sbjct: 181 TRVEQRTDFDRLIVDVETKPSISPRDAMASAGKTLVGLFGLAQELNAEAEGVDIGPSAAD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EE++L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  
Sbjct: 241 AALAADLALPIEEMDLTVRSYNCLKREGIHTIGELVSRSEADLLDIRNFGQKSIDEVKTK 300

Query: 310 LGTMGLFLGMNLPDWPPES 328
           LG MGL L  + P + P  
Sbjct: 301 LGAMGLQLKDSPPGFDPRQ 319


>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 =  358 bits (919), Expect = 7e-97,   Method: Composition-based stats.
 Identities = 140/310 (45%), Positives = 209/310 (67%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + L  E+      + EPL RG+  TLGN+LRR+L+SSL GAA+T+V+IDG
Sbjct: 3   EIEKP-KIECVEL-SEDNTYGKFVVEPLERGYGITLGNSLRRILLSSLPGAAVTSVKIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 NKLAELGLSL 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 =  358 bits (919), Expect = 7e-97,   Method: Composition-based stats.
 Identities = 135/310 (43%), Positives = 206/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE +     ++     + EPL RG+  TLGN+LRR+L+SSL GAA   ++IDG
Sbjct: 4   EIEKP-KIEIVE-QSNDDTYAKFVIEPLERGYGITLGNSLRRMLLSSLPGAAAKTIKIDG 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|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 =  358 bits (918), Expect = 8e-97,   Method: Composition-based stats.
 Identities = 145/329 (44%), Positives = 217/329 (65%), Gaps = 10/329 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+ID
Sbjct: 2   TEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEID 58

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI    D+E
Sbjct: 59  GVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVE 118

Query: 127 VLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKK 182
           ++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA YSP+++
Sbjct: 119 IVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVER 178

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           ++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++   
Sbjct: 179 IAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP-- 236

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
            ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KS
Sbjct: 237 -EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKS 295

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           L EIK VL + GL LGM L +WPP SI +
Sbjct: 296 LTEIKDVLASRGLSLGMRLENWPPASIAD 324


>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 =  358 bits (918), Expect = 8e-97,   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|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 =  358 bits (918), Expect = 9e-97,   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 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSY 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|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 =  358 bits (918), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 123/320 (38%), Positives = 196/320 (61%), Gaps = 4/320 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E ++     +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLTEEVI----ADNRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TDIILN+KG+ +    D    + + K+GPG VTAGDI     + V N
Sbjct: 61  HEFTTVPGVKEDVTDIILNLKGLVVSSEEDEPVTMYVRKQGPGAVTAGDIVPPAGVTVNN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLHIATLNDKGKLEIELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  SIT  D++A A + L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDRLVLDVETKNSITARDALASAGKTLVELFGLARELNVEAEGIEIGPSPAE 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                +    +E+L+L+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  
Sbjct: 241 ADHIASFGLPIEDLDLTVRSYNCLKREGVHTVGELVGRTESDLLDIRNFGQKSIDEVKVK 300

Query: 310 LGTMGLFLGMNLPDWPPESI 329
           L ++GL L  +   + P ++
Sbjct: 301 LHSLGLALKDSPASFDPTTV 320


>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 =  357 bits (917), Expect = 1e-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 DLTVRSYNCLKREGVHIVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPPS 314

Query: 324 WPPESI 329
           + P  +
Sbjct: 315 FDPSEV 320


>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 =  357 bits (917), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 138/311 (44%), Positives = 204/311 (65%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE +    ++      I EPL RG+  TLGN+LRR+L+SSL GAA+ +++IDG
Sbjct: 3   EIEKPR-IECVS-NSDDNTYGKFIVEPLERGYGITLGNSLRRILLSSLPGAAVNSIKIDG 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|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 =  357 bits (917), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 122/317 (38%), Positives = 183/317 (57%), Gaps = 4/317 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        E R+  I EPL  GF +T+GN+LRR L+SS+ GAA+T+++I+GV 
Sbjct: 5   QRPTLTE----EPISEFRSKFILEPLEPGFGYTIGNSLRRTLLSSIPGAAVTSIRIEGVE 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+IILN+KG+ +    D    + + K+GPGVVTA DI     +EV N
Sbjct: 61  HEFTTVPGVKEDVTEIILNLKGLVVSSEHDEPVLMYLRKQGPGVVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  I  L+    + ME+TV +G GYV A  ++     IG I ID++YSP+ +V+Y VE+
Sbjct: 121 PEMHIATLNSKGKLEMEMTVERGRGYVSAAQNKQPGQEIGRIPIDSIYSPVMRVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + + T  +I   D+VA A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDRLILDVWTKPAIRPRDAVASAGKTLVELFGLARELNVDAEGIDMGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +E+L L+VRS NCL+ E I  +G+L+ RTE D+L + NFG KS+ E+K  
Sbjct: 241 AALAADLALPIEDLNLTVRSYNCLKREGIHTVGELVARTEQDLLDIRNFGAKSIEEVKQK 300

Query: 310 LGTMGLFLGMNLPDWPP 326
           L  MGL L      + P
Sbjct: 301 LSDMGLALKDAQGGFDP 317


>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 =  357 bits (917), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 138/311 (44%), Positives = 204/311 (65%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE +    ++      I EPL RG+  TLGN+LRR+L+SSL G+A+ +++IDG
Sbjct: 3   EIEKPR-IECVS-NSDDNTYGKFIVEPLERGYGITLGNSLRRILLSSLPGSAVNSIKIDG 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|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 =  357 bits (916), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 125/322 (38%), Positives = 197/322 (61%), Gaps = 4/322 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V     +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLTEEVV----ADNRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+IILNIK I +    D    + + K+GPGVVTA DI     +EV N
Sbjct: 61  HEFTTVPGVKEDVTEIILNIKNIVVSSENDEPVVMYLRKQGPGVVTAADITPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  ++    + +ELTV +G GYV A+ ++  +  IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLHIATVNGKGKLEVELTVERGRGYVSAQQNKAYDTEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + +++  +I+  D+VA A + L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDKLIVDVESKPAISPRDAVASAGKTLVELFGLARELNTAAEGIEIGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +E+L+L++RS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 AALAADLALPIEDLDLTIRSYNCLKREGIHQVGELVARSEADLLDIRNFGAKSITEVKEK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEE 331
           L  +GL L  +  D+ P  + +
Sbjct: 301 LAALGLSLKDSPADFDPSLVTD 322


>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 =  357 bits (916), Expect = 1e-96,   Method: Composition-based stats.
 Identities = 157/334 (47%), Positives = 226/334 (67%), Gaps = 2/334 (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 KED-INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           ++  +  +    NP L K VE+LELSVRS NCL+  +I ++GDL+QRT+ +ML+  NFGR
Sbjct: 250 EKKAVETEEKQENPYLDKPVEDLELSVRSANCLKNADINFIGDLVQRTDQEMLKTKNFGR 309

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           KSL EIK +L  M L LG+ L  W   S  E  +
Sbjct: 310 KSLNEIKTLLQDMDLTLGVKLEGWNAPSDAETEE 343


>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 =  357 bits (916), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 135/315 (42%), Positives = 198/315 (62%), Gaps = 6/315 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            ++ KP  IE   +  E+      + EPL  G+  T GN+LRR+L+SSL GAA+T++QID
Sbjct: 2   TDIEKP-KIEITEI-SEDGRYGRFVCEPLEPGYGTTFGNSLRRMLLSSLEGAAVTSIQID 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE S+I GV +D+T I+LNIK + LKM G     + I   G   VTA DI+  +DIE
Sbjct: 60  GVLHEFSTIPGVRDDVTSIVLNIKQLCLKMQGSDPHTIRIDVAGEREVTAADIECGSDIE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +LNP+  I  L+    +++E+TV +G GYVPA  ++  +D IG+I ID+++SP+ +V+YT
Sbjct: 120 ILNPELHIATLNATGKLKIEMTVERGRGYVPADKNKKPDDSIGVIPIDSIFSPVHRVNYT 179

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE----EPKKEVK 242
           VE  R G V DYD+L + + T+GSI  E++V+ A+ IL   L +F N +    E ++EV 
Sbjct: 180 VEDTRVGNVTDYDRLILDVWTNGSIRPEEAVSKAAAILVMHLRLFQNMDGNVVEEEEEVA 239

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                +       L   +++L+LSVRS NCL+   I  + DL Q+TE DM+++ N GRKS
Sbjct: 240 NFPPEEVDDSAKVLEMTIDDLDLSVRSFNCLKRAGINSVADLTQKTEEDMMKVRNLGRKS 299

Query: 303 LVEIKGVLGTMGLFL 317
           L E+K  L  +GL L
Sbjct: 300 LDEVKKKLEELGLSL 314


>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 =  357 bits (916), Expect = 2e-96,   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   MQGSVTEFLKPRLVDIEQINT---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 YSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
            +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>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 =  357 bits (916), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 121/316 (38%), Positives = 190/316 (60%), Gaps = 4/316 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V     +NR+  I EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLSEEVV----SDNRSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+IILNIK +++    D      + K+GPGVVTA DI     +E  N
Sbjct: 61  HEFTTVPGVKEDVTEIILNIKNLSVSSEHDEPVVAYLRKQGPGVVTAADIAPPAGVEFHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+      +ELT+ +G GYV A  +++ +  IG I +D++YSP+ KV++ VE+
Sbjct: 121 PDLHIATLNSKGKFELELTIERGRGYVSAAQNKSGDAEIGRIPVDSIYSPVLKVTFRVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  +I   D+VA A   L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDRLIVDVETKQAIAPRDAVASAGTTLVELFGLARELNTAAEGIEIGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 +   +E+L+L+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  
Sbjct: 241 AALAADMALPIEDLDLTVRSYNCLKREGIHTVGELVARSEADLMDIRNFGAKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWP 325
           L  +GL L  + P + 
Sbjct: 301 LVELGLSLKDSPPGFD 316


>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 =  357 bits (916), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 149/323 (46%), Positives = 209/323 (64%), Gaps = 3/323 (0%)

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 322
           +KSL+EIK +L  M L LGM+L 
Sbjct: 300 KKSLLEIKEILKEMNLTLGMDLD 322


>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 =  357 bits (916), Expect = 2e-96,   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-KIETIEISDDAK-YGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 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|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 =  357 bits (916), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 136/311 (43%), Positives = 203/311 (65%), Gaps = 2/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  E+      + EPL RG+  TLGN+LRR+L+SSL G A+T+++IDG
Sbjct: 3   EIEKP-KIECV-VCSEDNRYGKFVVEPLERGYGITLGNSLRRILLSSLPGVAVTSIKIDG 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|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 =  356 bits (915), Expect = 2e-96,   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 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR--TENDPIGLITIDALYSPIKKVSY 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|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 =  356 bits (915), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 147/326 (45%), Positives = 207/326 (63%), Gaps = 8/326 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP     I +      R+++  EP  RG+ HTLGNALRRVL+SS+ G A T V I GV
Sbjct: 5   FLKPR---IINVESLGAGRSVVEMEPFERGYGHTLGNALRRVLLSSMVGYAPTEVTIAGV 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 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKVSY 185
           NP+HVI NL  +  + M++ V KG GYVP    R   D       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|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 =  356 bits (915), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 151/326 (46%), Positives = 209/326 (64%), Gaps = 7/326 (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 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKH---HRTENDPIGLITIDALYSPIKKVSY 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 EVENARVGQRTDQDKLILDIETNGVLTPEDAVRQAARILMDQISVFASL-EGSPNMYEAP 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 IKGVLGTMGLFLGMNLPDWPPESIEE 331
           IK VL   GL LGM L +WPP  ++ 
Sbjct: 301 IKDVLTARGLSLGMKLENWPPIGLDR 326


>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 =  356 bits (915), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 152/332 (45%), Positives = 214/332 (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   MQNSTTEFLKPRQIDVDTL---SATRAKVSMQPFERGFGHTLGNALRRILLSSMNGFAPT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSP 179
            +D+E++NPDHV+C+L  +  + ME+ V +G GY     +    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+      P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE ++L+  N G
Sbjct: 238 EVEEEKA---PPIDPVLLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           RKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 295 RKSLNEIKEVLASKGLTLGSKLEAWPPAGLEK 326


>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 =  356 bits (914), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 157/336 (46%), Positives = 223/336 (66%), Gaps = 3/336 (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 SKES-DLDLNPNLFKSIDELELSVRATNCLKAANIRIVGELVQRTEQTMLKTKNFGRKSL 309

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            EI+ VL +M L  GM L D+  +  E L +K +++
Sbjct: 310 DEIRRVLDSMELKFGMVLEDFDKKHQEWLKRKEKNE 345


>gi|330722390|gb|EGH00238.1| DNA-directed RNA polymerase alpha subunit [gamma proteobacterium
           IMCC2047]
          Length = 335

 Score =  356 bits (914), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 151/335 (45%), Positives = 214/335 (63%), Gaps = 8/335 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +   E + P +I+   +G    N   ++ EP  RGF HTLGN+LRR+L+SS+ GAAI 
Sbjct: 1   MSRPVTEFLTPKHIQVEEVG---VNHAKVVLEPFERGFGHTLGNSLRRILLSSMPGAAIV 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 PEQQEDEDEVDP---ILLRPVDDLELTVRSANCLKAENLYYIGDLIQRTEVDLLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           +KSL EIK VL + GL LGM L  WPP S++   +
Sbjct: 295 KKSLTEIKDVLASKGLSLGMRLEKWPPASLKNDDR 329


>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 =  356 bits (914), Expect = 2e-96,   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-KIEAVEV-SEDGSYGKFVVEPLERGYGTTLGNSLRRILLSSLPGSAVTSVQFDG 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|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 =  356 bits (914), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 126/320 (39%), Positives = 188/320 (58%), Gaps = 4/320 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P  +E       EE R+  I EPL  GF +T+GN+LRR L+SS+ GAA+T+++I+GVL
Sbjct: 11  QRPTLLE----ESLEETRSKFIIEPLEPGFGYTIGNSLRRTLLSSIPGAAVTSIRIEGVL 66

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+TDIILN+K + +    D    + + K+GPG VTA DI     +EV N
Sbjct: 67  HEFSTVPGVKEDVTDIILNLKELVVSSEHDEPVVMYLRKQGPGEVTAADIAPPAGVEVHN 126

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  I  L+  A + MELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+
Sbjct: 127 PELRIATLNGKAKLEMELTVERGRGYVSAAQNKQPGQEIGRIPIDSIYSPVLKVTYKVEA 186

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T   +   D+VA A + L +  G+        + +    +   
Sbjct: 187 TRVEQRTDFDRLILDVETKPCMKPRDAVASAGKTLVELFGLARELNVEAEGIDIGPSPTD 246

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  
Sbjct: 247 AALAADLALPIEELNLTVRSYNCLKREGIHTVGELVARSEQDLLDIRNFGAKSIEEVKQK 306

Query: 310 LGTMGLFLGMNLPDWPPESI 329
           L  M L L  + P + P ++
Sbjct: 307 LHEMTLALKDSPPGFDPSAV 326


>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 =  356 bits (914), Expect = 2e-96,   Method: Composition-based stats.
 Identities = 122/316 (38%), Positives = 187/316 (59%), Gaps = 4/316 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLTE----ENISEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+T+IILNIKG+ +    D      + K G G VTA DI     +E+ N
Sbjct: 61  HEFSTVPGVKEDVTEIILNIKGLVVSSEHDEPITAYLRKTGAGQVTAADISAPAGVEIHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+ VI  L+  A   +ELT+ +G GYV A+ +R E    G I ID++YSP+ KV+Y VE+
Sbjct: 121 PELVIATLNDKAKFEVELTIERGRGYVSAQQNRNEYSEAGQIPIDSIYSPVLKVTYRVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R G+  D+D+L + ++T  +I+  D++A A R L +  G+        + ++       
Sbjct: 181 TRAGERTDFDRLVVDVETKPAISPRDAIASAGRTLVELFGLARELNSAAEGIEIGPAPVD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              +  L   +E+L+LSVRS NCL+ E I  + +L+  +E  ++ + NFG+KS+ E+K  
Sbjct: 241 QVLSSELSMPIEDLDLSVRSYNCLKREGINTVSELVSLSETQLMNIRNFGQKSVDEVKDK 300

Query: 310 LGTMGLFLGMNLPDWP 325
           L  MGL L  ++P + 
Sbjct: 301 LTEMGLSLKDSVPGFD 316


>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 =  356 bits (914), Expect = 3e-96,   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-KIETIEISDDAK-YGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 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|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 (913), Expect = 3e-96,   Method: Composition-based stats.
 Identities = 133/310 (42%), Positives = 198/310 (63%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+I+P  IE +    E+      + EPL RG+  TLGN+LRRVL+SS+ GAA  +V+IDG
Sbjct: 3   EIIEP-KIEIVE-QSEDGRYGKFVVEPLERGYGITLGNSLRRVLLSSIPGAAPKSVKIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 QKLAALGLSL 310


>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 =  356 bits (913), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 142/332 (42%), Positives = 215/332 (64%), Gaps = 9/332 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
              + P  IE          R  ++ EP  RGF +TLGNALRRVL+SS+ G A T + I 
Sbjct: 4   NSFLTPRIIEVH---NLSPLRAKVVMEPFERGFGYTLGNALRRVLLSSIPGCAPTKISIS 60

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S+I G+ ED+ D+ILN+KG+ LK+   +   +++ K   G+VTAGDI++ +D+E
Sbjct: 61  GVVHEYSTIDGLQEDIVDLILNLKGVVLKLHSKNSTVLSLKKDTEGIVTAGDIESSHDVE 120

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---ITIDALYSPIKKV 183
           ++NP+HVI ++     +  ++TV KG GY+P+ +   E+  +     I +DA +SP+++V
Sbjct: 121 IVNPEHVIAHITSGGRIEAQITVEKGRGYLPSVNRSREDKSLSSIGDILLDASFSPVRRV 180

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           SYT+E+AR  Q  D DKL + I+T+GS+  E+++  A+R+L +Q   F + E      ++
Sbjct: 181 SYTIENARVEQRTDLDKLIIDIETNGSVDPEEAIRYAARVLVEQFSFFADLESTLLPTEQ 240

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               ++   +P LL+ V++LEL+VRS NCL+ ENI Y+GDLIQRTEA++LR  N GRKSL
Sbjct: 241 ---PRAPAIDPILLRPVDDLELTVRSANCLKVENIFYIGDLIQRTEAELLRTPNLGRKSL 297

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
            EIK VL +  L LGM L +WPP ++E   K+
Sbjct: 298 NEIKEVLASRDLSLGMKLENWPPANLENYVKE 329


>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 =  356 bits (913), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 121/320 (37%), Positives = 192/320 (60%), Gaps = 4/320 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E ++      NR+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLSEEVIAE----NRSKFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+IILN+KG+ +    D    + + K+GPG VT  DI     + V N
Sbjct: 61  HEFTTVPGVKEDVTNIILNLKGLVVSSEEDEPVTMYVRKQGPGAVTGADIVPPAGVTVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+    + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLHIATLNDKGKLEIELVVERGRGYVPAVQNKATGAEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  S+T  D++A A + L +  G+        + ++   + + 
Sbjct: 181 TRVEQRTDFDRLVLDVETKNSMTARDALASAGKTLVELFGLARELNVEAEGIEIGPSPQE 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                A    +E+LEL+VRS NCL+ E +  +G+L+ RTE+D+L + NFG+KS+ E+K  
Sbjct: 241 ADHIAAFSLPIEDLELTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKVK 300

Query: 310 LGTMGLFLGMNLPDWPPESI 329
           L ++GL L  +   + P  +
Sbjct: 301 LHSLGLALKDSPASFDPSQV 320


>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 =  356 bits (913), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 126/318 (39%), Positives = 191/318 (60%), Gaps = 4/318 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E ++     ENRT    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLTEEVI----SENRTRFAIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+IILNIK + +    D    + + K+G G VTA DI     +EV N
Sbjct: 61  HEFTTVPGVKEDVTEIILNIKNLVVSSENDEPVVMYLRKQGAGAVTAADIVPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+    + +ELTV +G GYV A  +++ +  IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLHIATLNDKGKLEIELTVERGRGYVSAAQNKSLDAEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  +IT  D++A A + L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDKLIVDVETKPAITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EEL L++RS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 SALAADLALPIEELNLTIRSYNCLKREGIHQVGELVARSEADLLDIRNFGAKSINEVKEK 300

Query: 310 LGTMGLFLGMNLPDWPPE 327
           L  +GL L  +  D+ P 
Sbjct: 301 LAELGLALKDSPLDFDPS 318


>gi|308272953|emb|CBX29557.1| DNA-directed RNA polymerase subunit alpha [uncultured
           Desulfobacterium sp.]
          Length = 340

 Score =  355 bits (912), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 148/327 (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 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE--P 237
           +K+V+Y V +AR GQ  DYDKL++ + TDGS++  ++++ +++I+++Q+ +FINF+E   
Sbjct: 183 VKRVNYVVGNARVGQRTDYDKLTIEVWTDGSLSPVEALSYSAKIIKEQMSIFINFDEKLE 242

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            +  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|307694123|ref|ZP_07636360.1| DNA-directed RNA polymerase subunit alpha [Ruminococcaceae
           bacterium D16]
          Length = 316

 Score =  355 bits (912), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 131/314 (41%), Positives = 194/314 (61%), Gaps = 4/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEE-NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           E+ KP       +    + +    + EPL RG+  TLGN+LRR+L+SSL G A+T+++I 
Sbjct: 3   EIEKPR---IDCVENPGDASYGKYVVEPLERGYGTTLGNSLRRILLSSLPGTAVTSIKIA 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV HE S+I G+ ED+T+I+LNIK I  K+  + +K V I   G   VTAGDI+   D+E
Sbjct: 60  GVQHEFSTIPGIKEDVTEIVLNIKSIIAKLHCEENKTVHIEASGECEVTAGDIKCDADVE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +LNP+  I  L  DA + MELT+S G GYVPA  ++     IGLI +D++Y+P++KV+YT
Sbjct: 120 ILNPELHIATLGPDATLSMELTLSHGRGYVPADRNKPAQTIIGLIPVDSIYTPVRKVNYT 179

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+ R G   DYDKL++ + TDG+I   D+V+L +RIL D   +F +  E        + 
Sbjct: 180 VENTRVGDATDYDKLTLEVWTDGTIDARDAVSLGARILCDHFALFTDLSETMGSRSTVVE 239

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
                 +  +   +++++LSVRS NCL+  NI  + DLI +TE +M+++ N GRKSL E+
Sbjct: 240 KAETQRDKVMEMTIDDMDLSVRSYNCLKRANINTVEDLISKTEEEMMKVRNLGRKSLEEV 299

Query: 307 KGVLGTMGLFLGMN 320
              L  MGL L  +
Sbjct: 300 INKLAMMGLSLASD 313


>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 =  355 bits (912), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 130/322 (40%), Positives = 195/322 (60%), Gaps = 4/322 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TD+ILNIK + +    D    + + K+GPGVVTA DI     +EV N
Sbjct: 61  HEFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGVVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLVLATLNAKGKLEMELTVERGRGYVSAVQNKQAGQEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNVDAEGIDMGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 AALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEE 331
           L  MGL L  + P + P S  +
Sbjct: 301 LAGMGLALKDSPPGFDPTSAAD 322


>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 =  355 bits (912), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 123/316 (38%), Positives = 190/316 (60%), Gaps = 4/316 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V     ENR+  I EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLSEEVV----SENRSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+IILNIK +++    D      + K+GPGVVTA DI     +E  N
Sbjct: 61  HEFTTVPGVKEDVTEIILNIKSLSVSSEHDEPVVAYLRKQGPGVVTAADIAPPAGVEFHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+      +ELT+ +G GYV A  +++ +  IG I +D++YSP+ KV++ VE+
Sbjct: 121 PDLHIATLNSKGKFELELTIERGRGYVSAAQNKSGDAEIGRIPVDSIYSPVLKVTFRVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  +I   D+VA A   L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDKLIVDVETKQAIAPRDAVASAGTTLVELFGLARELNTAAEGIEIGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 +   +E+L+L+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  
Sbjct: 241 AALAADMALPIEDLDLTVRSYNCLKREGIHTVGELVARSEADLMDIRNFGAKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWP 325
           L  +GL L  + P + 
Sbjct: 301 LVELGLSLKDSPPGFD 316


>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 =  355 bits (912), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 136/313 (43%), Positives = 195/313 (62%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE +     + +    + EPL RG+  TLGN+LRR+L+SSL G A+T+++I G
Sbjct: 3   EIEKPR-IECVE-NPGDGSYGKYVVEPLERGYGTTLGNSLRRILLSSLPGTAVTSIKIAG 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|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 =  355 bits (912), Expect = 4e-96,   Method: Composition-based stats.
 Identities = 123/316 (38%), Positives = 190/316 (60%), Gaps = 4/316 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V     ENR+  I EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLSEEVV----SENRSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+IILNIK +++    D      + K+GPGVVTA DI     +E  N
Sbjct: 61  HEFTTVPGVKEDVTEIILNIKNLSVSSEHDEPVVAYLRKQGPGVVTAADIAPPAGVEFHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+      +ELT+ +G GYV A  +++ +  IG I +D++YSP+ KV++ VE+
Sbjct: 121 PDLHIATLNSKGKFELELTIERGRGYVSAAQNKSGDSEIGRIPVDSIYSPVLKVTFRVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  +I   D+VA A   L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDKLIVDVETKQAIAPRDAVASAGTTLVELFGLARELNTAAEGIEIGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 +   +E+L+L+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  
Sbjct: 241 AALAADMALPIEDLDLTVRSYNCLKREGIHTVGELVARSEADLMDIRNFGAKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWP 325
           L  +GL L  + P + 
Sbjct: 301 LVELGLSLKDSPPGFD 316


>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 =  355 bits (912), Expect = 5e-96,   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-KIETIEISDDAK-YGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 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|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 =  355 bits (912), Expect = 5e-96,   Method: Composition-based stats.
 Identities = 148/332 (44%), Positives = 208/332 (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--GLFKPRIIDVQSL---SPVHARVVMEPFERGYGHTLGNALRRILLSSMPGYAPT 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY--VPAKHHRTENDPIGLITIDALYSP 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|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 =  355 bits (911), Expect = 5e-96,   Method: Composition-based stats.
 Identities = 123/316 (38%), Positives = 190/316 (60%), Gaps = 4/316 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V     ENR+  I EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLSEEVV----SENRSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+IILNIK +++    D      + K+GPGVVTA DI     +E  N
Sbjct: 61  HEFTTVPGVKEDVTEIILNIKNLSVSSEHDEPVVAYLRKQGPGVVTAADIAPPAGVEFHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+      +ELT+ +G GYV A  +++ +  IG I +D++YSP+ KV++ VE+
Sbjct: 121 PDLHIATLNSKGKFELELTIERGRGYVSAAQNKSGDSEIGRIPVDSIYSPVMKVTFRVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  +I   D+VA A   L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDKLIVDVETKQAIAPRDAVASAGTTLVELFGLARELNTAAEGIEIGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 +   +E+L+L+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  
Sbjct: 241 AALAADMALPIEDLDLTVRSYNCLKREGIHTVGELVARSEADLMDIRNFGAKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWP 325
           L  +GL L  + P + 
Sbjct: 301 LVELGLSLKDSPPGFD 316


>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 = 134/310 (43%), Positives = 196/310 (63%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+I+P  IE +    E+      + EPL RG+  TLGN+LRRVL+SSL GAA  +V+IDG
Sbjct: 3   EMIEP-KIEIVE-QSEDGTYGKFVVEPLERGYGITLGNSLRRVLLSSLPGAAPKSVKIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 QKLEALGLSL 310


>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 =  355 bits (911), Expect = 5e-96,   Method: Composition-based stats.
 Identities = 145/335 (43%), Positives = 217/335 (64%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+ 
Sbjct: 1   MQGSVTEFLKPRLVDIEQISS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVI 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
            +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 329


>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 =  355 bits (911), Expect = 5e-96,   Method: Composition-based stats.
 Identities = 137/310 (44%), Positives = 207/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  ++      + EPL RG+  TLGN+LRR+L+SSL GAA+T+V+IDG
Sbjct: 3   EIEKP-KIEIVEM-SDDNTYGKFVVEPLERGYGITLGNSLRRILLSSLPGAAVTSVKIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 NKLHELGLSL 310


>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 =  355 bits (911), Expect = 5e-96,   Method: Composition-based stats.
 Identities = 124/317 (39%), Positives = 188/317 (59%), Gaps = 4/317 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P  IE        E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLIE----ESISEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+TD+ILN+K + +    D    + + K+GPGVVTA DI     +EV +
Sbjct: 61  HEFSTVPGVKEDVTDLILNLKELVVSSENDEPTVMYLRKQGPGVVTAADIAPPAGVEVHS 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
            D  +  L+    + +ELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 LDLALATLNDKGKLEIELTVERGRGYVSAAQNKQPGQEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  SI+  D++A A + L    G+        + V    +   
Sbjct: 181 TRVEQRTDFDRLIVDVETKQSISPRDAMASAGKTLVGLFGLAQELNAEAEGVDIGPSAAD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EE++L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  
Sbjct: 241 AALAADLALPIEEMDLTVRSYNCLKREGIHTIGELVSRSEADLLDIRNFGQKSIDEVKTK 300

Query: 310 LGTMGLFLGMNLPDWPP 326
           L  M L L  + P + P
Sbjct: 301 LAAMALQLKDSPPGFDP 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 =  355 bits (911), Expect = 6e-96,   Method: Composition-based stats.
 Identities = 131/310 (42%), Positives = 203/310 (65%), 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-KIEIVE-QSEDNTYGKFVVEPLERGYGITLGNSLRRILLSSLPGAAVTSVKIEG 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|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 =  355 bits (911), Expect = 6e-96,   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-KVEVVEINAEN-TYGKFTVEPLERGYGTTLGNSLRRIMLSSLPGAAVTSVKIDG 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|313606573|gb|EFR83374.1| DNA-directed RNA polymerase, alpha subunit [Listeria monocytogenes
           FSL F2-208]
          Length = 314

 Score =  355 bits (911), Expect = 7e-96,   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-KIETIEISDDAK-YGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 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|27262232|gb|AAN87397.1| DNA-directed RNA polymerase alpha chain [Heliobacillus mobilis]
          Length = 315

 Score =  355 bits (910), Expect = 7e-96,   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-KIECVD-RSEDATYGKFVVEPLERGYGVTLGNSLRRILLSSLPGAAVTSVKIEG 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|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 =  355 bits (910), Expect = 7e-96,   Method: Composition-based stats.
 Identities = 131/315 (41%), Positives = 196/315 (62%), Gaps = 6/315 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            ++ KP  IE   +  E+      + EPL  G+  T GN+LRR+L+SSL GAA+T++QID
Sbjct: 2   TDIEKP-KIEIAEI-SEDGRYGRFVCEPLEPGYGTTFGNSLRRMLLSSLDGAAVTSIQID 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE S+I GV +D+T I+L +K + ++M G     + I   G   VTA DI+  +DIE
Sbjct: 60  GVLHEFSTIPGVRDDVTSIVLALKQLCIRMQGSELHTLRIEAEGEREVTAADIECGSDIE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +LNP+  I  L     +++E+TV +G GYVPA  ++   D IG+I ID+++SP+++V+YT
Sbjct: 120 ILNPELHIATLGATGKLKIEMTVERGRGYVPADKNKKSEDSIGVIPIDSIFSPVQRVNYT 179

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE----EPKKEVK 242
           VE  R G V DYD+L + + T+GSI  E++V+ A+ IL   L +F N +    E ++EV 
Sbjct: 180 VEDTRVGNVTDYDRLILDVWTNGSIRPEEAVSKAAAILVMHLRLFQNMDGTMLEEEEEVP 239

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                +       L   +++L+LSVRS NCL+   I  + DL Q+TE DM+++ N GRKS
Sbjct: 240 NFPPEEVDDSAKVLEMTIDDLDLSVRSFNCLKRAGINTVADLAQKTEDDMMKVRNLGRKS 299

Query: 303 LVEIKGVLGTMGLFL 317
           L E+K  L  +GL L
Sbjct: 300 LDEVKKKLEELGLSL 314


>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 =  355 bits (910), Expect = 8e-96,   Method: Composition-based stats.
 Identities = 144/312 (46%), Positives = 202/312 (64%), 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 LNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSY 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|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 =  355 bits (910), Expect = 8e-96,   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|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 =  354 bits (909), Expect = 9e-96,   Method: Composition-based stats.
 Identities = 136/310 (43%), Positives = 196/310 (63%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+I+P  IE +    E+      + EPL RG+  TLGN+LRRVL+SSL GAA  +V+IDG
Sbjct: 3   EIIEP-KIEIVE-QAEDGTYGKFVVEPLERGYGITLGNSLRRVLLSSLPGAAPKSVKIDG 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|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 =  354 bits (909), Expect = 9e-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-KIETVEL-SDNATFGKFVVEPLERGFGTTLGNSLRRILLSSLPGAAVTAVQIDG 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|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 =  354 bits (909), Expect = 9e-96,   Method: Composition-based stats.
 Identities = 134/310 (43%), 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-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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 AKLEELGLGL 310


>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 (909), Expect = 9e-96,   Method: Composition-based stats.
 Identities = 134/310 (43%), Positives = 196/310 (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   EMIEP-KIEIIE-QSEDGTYGKFVVEPLERGYGITLGNSLRRVLLSSLPGAAPKSVKIDG 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|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 =  354 bits (909), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 139/330 (42%), Positives = 215/330 (65%), Gaps = 8/330 (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-VDAVVRMELTVSKGHGYVPAK-HHRTENDPIGLITIDALYSP 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 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP   
Sbjct: 295 KKSLTEIKDVLASRGLSLGMRLENWPPLGF 324


>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 =  354 bits (909), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 149/336 (44%), Positives = 217/336 (64%), Gaps = 5/336 (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 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV- 241
           V      AR GQ  DYDKL + I TDGSI  ED++A  ++IL++QL +FINF+E +    
Sbjct: 210 VKVITSQARVGQQTDYDKLILEITTDGSIRPEDALAYGAKILKEQLQVFINFDEERVVPV 269

Query: 242 -KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             +    +    N  L + VE+LELSVRS NCLR   I ++G+L+Q++EA+ML+  NFGR
Sbjct: 270 KSDSEPGEKPKLNENLYRSVEDLELSVRSANCLRNAEINHIGELVQKSEAEMLKTKNFGR 329

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDW-PPESIEELAKK 335
           KSL EIK +L  M L+LGM +  W PP + E+  ++
Sbjct: 330 KSLNEIKQLLAEMDLYLGMKIDGWEPPPAAEQETEE 365


>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 =  354 bits (909), Expect = 1e-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|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 =  354 bits (909), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 129/322 (40%), Positives = 195/322 (60%), Gaps = 4/322 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TD+ILNIK + +    D    + + K+GPGVVTA DI     +EV N
Sbjct: 61  HEFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGVVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD V+  L+    + +ELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLVLATLNAKGKLELELTVERGRGYVSAVQNKQAGQEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNVDAEGIDMGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 AALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEE 331
           L  MGL L  + P + P S  +
Sbjct: 301 LAGMGLALKDSPPGFDPTSAAD 322


>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 =  354 bits (909), Expect = 1e-95,   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   MSVNALLKPRSIEVETAEG-NPYSATVTMEPFETGYAHTLGNALRRVLLSSMVGFAPTEA 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|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 =  354 bits (908), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 127/323 (39%), Positives = 193/323 (59%), Gaps = 6/323 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E       + +R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLTE----DYIDSSRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE ++I GV ED++DIILNIKG+ L    D    V + + G G VTA DI+    +E+ N
Sbjct: 61  HEFTTIPGVKEDVSDIILNIKGLVLSSEFDEPATVYLRREGAGAVTAADIECPAGVEIHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PDH I  L+    + +E+ V +G GYVPA  +      IG I +D +YSP+ KVSY VE+
Sbjct: 121 PDHHIATLNESGRLEIEMIVERGRGYVPATPNS--GGEIGRIPMDQIYSPVLKVSYKVEA 178

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SIT  D++A A + L +  G+     E  + ++   + + 
Sbjct: 179 TRVEQRTDFDKLIIDVETKNSITARDAMASAGKTLVELFGLARELNEAAEGIEIGPSPRE 238

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                A    +E+L+ S+RS NCL+ E I  +G+L  RTE+D+L + NFG KS+ E+K  
Sbjct: 239 AEDVAAYQTPIEDLDFSMRSYNCLKREEIHTVGELAARTESDLLDIRNFGDKSINEVKEK 298

Query: 310 LGTMGLFLGMNLPDWPPESIEEL 332
           L  +GL L  +  ++ P ++ +L
Sbjct: 299 LAELGLALKDSPNNFDPAAVADL 321


>gi|325560586|gb|ADZ31263.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus sp.
           SL1108]
          Length = 298

 Score =  354 bits (908), Expect = 1e-95,   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|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 =  354 bits (908), Expect = 1e-95,   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|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 =  354 bits (908), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 136/310 (43%), 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-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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 AKLEELGLGL 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 =  354 bits (908), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 151/336 (44%), Positives = 224/336 (66%), Gaps = 3/336 (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 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            EI+ VL  M L  GM++ D+  +  E L +K +++
Sbjct: 310 DEIRRVLDGMALKFGMSVEDFDKKYQEWLKRKEKNE 345


>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 =  354 bits (908), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 152/347 (43%), Positives = 205/347 (59%), Gaps = 22/347 (6%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            +   L+KP +IE             +  EP   G+AHTLGNALRRVL+SS+ G A T  
Sbjct: 1   MSVNALLKPRSIEVETAEG-NPYSATVTMEPFETGYAHTLGNALRRVLLSSMVGFAPTEA 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|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 = 140/310 (45%), Positives = 200/310 (64%), Gaps = 4/310 (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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLAELGLSL 308


>gi|311896536|dbj|BAJ28944.1| putative DNA-directed RNA polymerase subunit alpha [Kitasatospora
           setae KM-6054]
          Length = 340

 Score =  353 bits (907), Expect = 1e-95,   Method: Composition-based stats.
 Identities = 127/318 (39%), Positives = 193/318 (60%), Gaps = 4/318 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVL
Sbjct: 5   QRPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TD+ILNIK + +    D    + + K+GPGVVTA DI     +EV N
Sbjct: 61  HEFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGVVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+ V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PELVLATLNGKGKLEMELTVERGRGYVSAVQNKASGQEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDKLIVDVETKPAMRPRDAMASAGKTLVELFGLARELNVDAEGIDMGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 AALAADLALPIEELELTVRSYNCLKREGIHTVGELVARSEADLLDIRNFGAKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWPPE 327
           L  MGL L  + P + P 
Sbjct: 301 LAGMGLALKDSPPGFDPT 318


>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 =  353 bits (907), Expect = 2e-95,   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|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 =  353 bits (907), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 136/312 (43%), Positives = 204/312 (65%), 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 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV--KEDINVKSLPF 252
            ++Y++L + I TDGS++ E+++  A+ IL+D + +FI  E   +    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|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 =  353 bits (907), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 127/322 (39%), Positives = 185/322 (57%), Gaps = 5/322 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E          R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G L
Sbjct: 5   QRPTLTE----ESLNPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGAL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+I+LNIKGI L    D    + + K G G  TAGDI     + + N
Sbjct: 61  HEFTTLPGVQEDVTEILLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGVTIAN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L  D  + +E TV +G GYVPA  ++ + D IG I +D++YSP+ KVSY VE+
Sbjct: 121 PDKHIATLAEDGELEIEFTVERGRGYVPASMNKQDADEIGRIPVDSIYSPVLKVSYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  +I+  D+VA A   L +  G+        + V+       
Sbjct: 181 TRVEQRTDFDKLILDVETKPAISPRDAVASAGSTLVELFGLCRELNVQAEGVEVGSAPVV 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              NP     +E+L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  
Sbjct: 241 EEANPEHAVPIEDLNLTQRSYNCLKREGIHTIGELVSHTEQDLLDIRNFGMKSIDEVKEK 300

Query: 310 LGTMGLFLGMN-LPDWPPESIE 330
           L ++GL L  + L D+ P ++E
Sbjct: 301 LQSLGLSLKASPLGDFDPNNLE 322


>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 =  353 bits (907), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 135/310 (43%), 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-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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 AKLEELGLGL 310


>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 =  353 bits (906), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 142/334 (42%), Positives = 220/334 (65%), Gaps = 9/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +     ++++P   +   L    ENR  ++ EPL RG+AHTLGNALRRVL+SS+ G AIT
Sbjct: 1   MTVTVSQVLRPRGPQIERL---TENRAKVVLEPLGRGYAHTLGNALRRVLLSSIPGFAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE ++++G+ ED+ +++LN+K + +++       +++FK+G GVVTA DI+T
Sbjct: 58  EVEIDGVLHEYTTVEGLQEDVLEVLLNLKDVAIRIHSGDTATLSLFKQGAGVVTAADIKT 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +++E++N  HVIC+L  D  + M L + +G GY PA   R  +D    I    +DA +S
Sbjct: 118 DHNVEIINDGHVICHLTKDTTINMRLKIERGFGYQPAVVRRRPDDENRTIGRLILDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++V+Y VE+AR  Q  D DKL + I+T+G+I  E+++  A+ IL DQL +F +F    
Sbjct: 178 PVRRVAYVVEAARVEQRTDLDKLIIDIETNGTIDAEEALRTAADILTDQLSVFGDFTHRD 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +     +   S   +P LL+ +++LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N 
Sbjct: 238 RGT---VKPASSGVDPVLLRPIDDLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEEL 332
           G+KSL EIK VLG  GL LG+ L +WPP  + + 
Sbjct: 295 GKKSLTEIKEVLGQRGLGLGVKLENWPPPGVSQY 328


>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 =  353 bits (906), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 130/315 (41%), Positives = 197/315 (62%), Gaps = 6/315 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            ++ KP  IE   +  E+      I EPL  G+  T GN+LRR+L+SSL GAA+T++QID
Sbjct: 2   TDIEKP-KIEIAEI-SEDGRYGRFICEPLEPGYGTTFGNSLRRMLLSSLDGAAVTSIQID 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE S+I GV +D+T I+L +K + ++M     + + I   G   VTA DI+  +DIE
Sbjct: 60  GVLHEFSTIPGVRDDVTSIVLALKQLCIRMQDSEPRTIRIEAAGAREVTAADIECGSDIE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +LNP+  I  +     +++E+TV +G GYVPA  ++  +D IG+I ID+++SP+++V+YT
Sbjct: 120 ILNPELHIATMGETGKLKIEMTVERGRGYVPADRNKKPDDVIGVIPIDSIFSPVQRVNYT 179

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE----EPKKEVK 242
           VE  R G V DYD+L + + T+GSI  E++V+ A+ IL   L +F N +    E ++EV 
Sbjct: 180 VEDTRVGNVTDYDRLILEVWTNGSIRPEEAVSKAAAILVMHLRLFQNMDGSVVEEEEEVP 239

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                +       L   +++L+LSVRS NCL+   I  + DL Q+TE DM+++ N GRKS
Sbjct: 240 NFPPEEVDDSAKVLEMTIDDLDLSVRSFNCLKRAGINTVADLAQKTEDDMMKVRNLGRKS 299

Query: 303 LVEIKGVLGTMGLFL 317
           L E+K  L  +GL L
Sbjct: 300 LDEVKKKLEELGLSL 314


>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 =  353 bits (906), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 124/321 (38%), Positives = 185/321 (57%), Gaps = 4/321 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E          R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I GV 
Sbjct: 5   QRPTLTE----ESLNPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGVP 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+I+LNIKGI L    D    + + K G G  TAGDI     + + N
Sbjct: 61  HEFTTLPGVEEDVTEILLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGVTIAN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I +L  D  + +E TV +G GYVPA+ ++ +N  IG I +D++YSP+ KVSY VE+
Sbjct: 121 PDMHIASLADDGELEIEFTVERGRGYVPAQMNKQDNAEIGRIPVDSIYSPVLKVSYRVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  +I+  D+VA A   L +  G+        + V+      +
Sbjct: 181 TRVEQRTDFDKLILDVETKPAISPRDAVASAGSTLVELFGLCRELNTQAEGVEVGPAPVA 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              NP +   +E+L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  
Sbjct: 241 EETNPEMAVPIEDLNLTQRSYNCLKREGIHTIGELVAHTEQDLLDIRNFGMKSIDEVKEK 300

Query: 310 LGTMGLFLGMNLPDWPPESIE 330
           L  +GL L  +   +   ++E
Sbjct: 301 LQALGLALKASPLGFDANNLE 321


>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 =  353 bits (906), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 143/334 (42%), Positives = 220/334 (65%), Gaps = 9/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +     ++++P   +   L    ENR  ++ EPL RG+AHTLGNALRRVL+SS+ G AIT
Sbjct: 1   MTVTVSQVLRPRGPQIERL---TENRAKVVLEPLGRGYAHTLGNALRRVLLSSIPGFAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE ++++G+ ED+ +++LN+K + +++       +++FK+G GVVTA DI+T
Sbjct: 58  EVEIDGVLHEYTTVEGLQEDVLEVLLNLKDVAIRIHSGDTATLSLFKQGAGVVTAADIKT 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYS 178
            +++E++N  HVIC+L  D  + M L + +G GY PA   R  +D    I    +DA +S
Sbjct: 118 DHNVEIINDGHVICHLTKDTTINMRLKIERGFGYQPAVVRRRPDDENRTIGRLILDASFS 177

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+++V+Y VE+AR  Q  D DKL + I+T+G+I  E+++  A+ IL DQL +F NF    
Sbjct: 178 PVRRVAYVVEAARVEQRTDLDKLIIDIETNGTIDAEEALRTAADILTDQLSVFGNFTHRD 237

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +     +   S   +P LL+ +++LEL+VRS NCL+ E+I Y+GDLIQ+TE ++L+  N 
Sbjct: 238 RGT---VKPASSGVDPVLLRPIDDLELTVRSANCLKAESIYYIGDLIQKTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEEL 332
           G+KSL EIK VLG  GL LG+ L +WPP  + + 
Sbjct: 295 GKKSLTEIKEVLGQRGLGLGVKLENWPPPGVSQY 328


>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 =  353 bits (906), Expect = 2e-95,   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|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 =  353 bits (906), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 134/310 (43%), Positives = 201/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  + +     + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDG
Sbjct: 3   EIEKP-KIETVEISDDAK-YGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 AKLEELGLGL 310


>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 =  353 bits (906), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 141/310 (45%), Positives = 200/310 (64%), Gaps = 4/310 (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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLAELGLSL 308


>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 =  353 bits (906), Expect = 2e-95,   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-KIECVEMDPEG-TYGKFVVDPLERGYGITLGNSLRRVLLASLPGAAVTAVKIDG 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|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 =  353 bits (906), Expect = 2e-95,   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|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 =  353 bits (906), Expect = 2e-95,   Method: Composition-based stats.
 Identities = 150/336 (44%), Positives = 216/336 (64%), Gaps = 2/336 (0%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +NW  L+KP+ ++     +  E       EPL RGF +T GNALRR+L+SSL+GAAI A+
Sbjct: 13  RNWSSLVKPDQVQ--RDEKSTEQYGKFSCEPLERGFGNTFGNALRRILLSSLQGAAIVAI 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 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +I+ V+  MG      + ++  +  E L +K +D+
Sbjct: 311 EDIRRVIEQMGYDFNTQIDNFDQKYQEWLKRKEDDE 346


>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 =  353 bits (905), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 124/321 (38%), Positives = 181/321 (56%), Gaps = 4/321 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E          R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G L
Sbjct: 5   QRPTLTE----ESLNPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGAL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+I+LNIKGI L    D    + + K G G  TAGDI     + + N
Sbjct: 61  HEFTTLPGVEEDVTEILLNIKGIVLTSEYDEPVVMYLRKNGKGEATAGDITPPAGVTIAN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L  D  + +E TV +G GYVPA+ ++ EN  IG I +D++YSP+ KVSY VE+
Sbjct: 121 PDLHIATLAEDGELEIEFTVERGRGYVPAQMNKQENSEIGRIPVDSIYSPVLKVSYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  +IT  D+VA A   L +  G+        + V+       
Sbjct: 181 TRVEQRTDFDKLILDVETKPAITPRDAVASAGSTLVELFGLCRELNVDAEGVEVGPAPTH 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              +  L   +E++  + RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  
Sbjct: 241 DEADSQLAIPIEDMNFTQRSYNCLKREGIHTVGELVVHTEQDLLDIRNFGMKSIDEVKEK 300

Query: 310 LGTMGLFLGMNLPDWPPESIE 330
           L  MGL L  +   +   ++E
Sbjct: 301 LQAMGLSLKASPIGFDANNLE 321


>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 =  353 bits (905), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 143/326 (43%), Positives = 218/326 (66%), 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 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYT 186
             HVIC+L  D  + M L V +G GY PA   R  +D    I    +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 =  353 bits (905), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 139/324 (42%), Positives = 210/324 (64%), 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 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK--KEV 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|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 =  353 bits (905), Expect = 3e-95,   Method: Composition-based stats.
 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  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 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|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 =  353 bits (905), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 125/313 (39%), Positives = 193/313 (61%)

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 LGMNLPDWPPESI 329
           L  + P + P ++
Sbjct: 308 LKDSPPGFDPSAL 320


>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 =  353 bits (905), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 126/320 (39%), Positives = 195/320 (60%), Gaps = 4/320 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLTEDVV----DEYRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSLRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +S+ GV ED+T+I+LN+K + +    D    + + K+GPG VTA DI     +EV N
Sbjct: 61  HEFTSVPGVKEDVTEIVLNVKNLVVSSEHDEPVVMYLRKQGPGAVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+    + +ELTV +G GYV A  ++T    IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLHIATLNAKGKLELELTVERGRGYVSAAQNKTGEQEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  +I+  D+VA A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDRLVVDVETKHAISPRDAVASAGKTLTELFGLARELNVEAEGIDMGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L  ++E L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG+KS+ E+K  
Sbjct: 241 AALAADLALEIEALDLTVRSYNCLKREGIHSVGELVSRSEADLLDIRNFGQKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWPPESI 329
           L  MGL L  + P + P ++
Sbjct: 301 LVGMGLHLKDSPPGFDPSAV 320


>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 =  353 bits (905), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 125/322 (38%), Positives = 187/322 (58%), Gaps = 5/322 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E          R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I GV 
Sbjct: 5   QRPTLTE----ESLNPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGVP 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+I+LNIKGI L    D    + + K G G  TAGDI     + + N
Sbjct: 61  HEFTTLPGVEEDVTEILLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGVTIAN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L  D  + +E TV +G GYVPA+ ++ +N  IG I +D++YSP+ KVSY VE+
Sbjct: 121 PDMHIATLAEDGELEIEFTVERGRGYVPAQMNKQDNAEIGRIPVDSIYSPVLKVSYRVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  +I+  D+VA A   L +  G+        + V+      +
Sbjct: 181 TRVEQRTDFDKLILDVETKPAISPRDAVASAGSTLVELFGLCRELNTQAEGVEVGPAPVA 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              NP +   +E+L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  
Sbjct: 241 EETNPEMNIPIEDLNLTQRSYNCLKREGIHTIGELVAHTEQDLLDIRNFGMKSIDEVKEK 300

Query: 310 LGTMGLFLGMN-LPDWPPESIE 330
           L ++GL L  + L ++   ++E
Sbjct: 301 LQSLGLALKASPLGNFDANNLE 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 =  353 bits (905), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 141/310 (45%), Positives = 200/310 (64%), Gaps = 4/310 (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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLADLGLSL 308


>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 =  353 bits (905), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 125/321 (38%), Positives = 182/321 (56%), Gaps = 4/321 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E          R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G L
Sbjct: 5   QRPTLTE----ESLNPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGAL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+I+LNIKGI L    D    + + K G G  TAGDI     + + N
Sbjct: 61  HEFTTLPGVEEDVTEILLNIKGIVLTSEYDEPVVMYLRKNGKGEATAGDITPPAGVTIAN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L  D  + +E TV +G GYVPA+ ++ EN  IG I +D++YSP+ KVSY VE+
Sbjct: 121 PDLHIATLAEDGELEIEFTVERGRGYVPAQMNKQENSEIGRIPVDSIYSPVLKVSYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  +IT  D+VA A   L +  G+        + V+       
Sbjct: 181 TRVEQRTDFDKLILDVETKPAITPRDAVASAGSTLVELFGLCRELNVDAEGVEVGPAPTH 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              +  L   +E++  + RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  
Sbjct: 241 DEADSQLAIPIEDMNFTQRSYNCLKREGIHTVGELVVHTEQDLLDIRNFGMKSIDEVKEK 300

Query: 310 LGTMGLFLGMNLPDWPPESIE 330
           L TMGL L  +   +   ++E
Sbjct: 301 LQTMGLSLKASPIGFDANNLE 321


>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 =  352 bits (904), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 170/341 (49%), Positives = 228/341 (66%), 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   +
Sbjct: 183 PVRRVSYKVENSMVGQMTNYDKLIITVETNGVVNPDAALGLAARILLDQLQVFINF--QE 240

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            E ++   ++    NP LLKKV ELELSVRS NCL+ ENIVY+GDL+ RTE  ML+ ANF
Sbjct: 241 VEEEKPEKLELQTINPVLLKKVYELELSVRSQNCLKNENIVYVGDLVARTETQMLKTANF 300

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           GRKSL E+K VL    L  GM    WPPE++E LAKK+ED+
Sbjct: 301 GRKSLNELKKVLANFNLEFGMKDIGWPPENLESLAKKHEDQ 341


>gi|206602703|gb|EDZ39184.1| DNA-directed RNA polymerase, alpha subunit [Leptospirillum sp.
           Group II '5-way CG']
          Length = 324

 Score =  352 bits (904), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 138/324 (42%), Positives = 210/324 (64%), 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 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK--KEV 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|327332743|gb|EGE74477.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL097PA1]
          Length = 338

 Score =  352 bits (904), Expect = 3e-95,   Method: Composition-based stats.
 Identities = 122/322 (37%), Positives = 185/322 (57%), Gaps = 4/322 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV 
Sbjct: 5   QRPTLTE----ESISEFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQ 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I+G  ED+T+IILN+KG+ L    D    + + K G G VTA DI     + + N
Sbjct: 61  HEFSTIEGCVEDVTEIILNLKGLVLSSEEDEPVAMYLRKTGAGEVTAADINPPAGVTIHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  I  L+ D    MEL V +G GYV +  +   N  IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PELHIATLNDDGRFEMELIVERGRGYVSSALNDDPNAEIGRIAVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SI   D++A A + L +  G+        + ++       
Sbjct: 181 TRVEQRTDFDKLVVDVETKPSILPRDAIASAGKTLVELFGLTRELNAEAEGIEIGSGPVD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
             +  +L   VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  
Sbjct: 241 EEYAESLGTPVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEE 331
           L  +GL L  + P + P +  E
Sbjct: 301 LTELGLALKDSAPGFDPLAAAE 322


>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 =  352 bits (904), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 169/341 (49%), Positives = 228/341 (66%), 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   +
Sbjct: 183 PVRRVSYKVENSMVGQMTNYDKLIITVETNGVVNPDAALGLAARILLDQLQVFINF--QE 240

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
            E ++   ++    NP LLKKV ELELSVRS NCL+ ENIVY+GDL+ RTE  ML+ ANF
Sbjct: 241 VEEEKPEKLELQTINPVLLKKVYELELSVRSQNCLKNENIVYVGDLVARTETQMLKTANF 300

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           GRKSL E+K VL    L  GM    WPP+++E LAKK+ED+
Sbjct: 301 GRKSLNELKKVLANFNLEFGMKDIGWPPDNLESLAKKHEDQ 341


>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 =  352 bits (904), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 121/330 (36%), Positives = 193/330 (58%), Gaps = 4/330 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V     + R+  I EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVL
Sbjct: 5   QRPTLNEEVV----SDYRSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+T+ ILN+K + +    D      + K+GPG VTA DI     +EV N
Sbjct: 61  HEFSTVPGVKEDVTEFILNLKSLVVSSEFDEPVVAYLRKQGPGEVTAADISAPGGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I +L+ +  + +ELT+ +G GYV A  ++  +  IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLHIASLNDEGQLDIELTIERGRGYVSAAQNKNADAEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  SI   D+VA A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDRLIIDVETKPSILPRDAVASAGKTLVELFGLARELNVEAEGIDIGPSPVD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +E+L+L+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  
Sbjct: 241 AALAADLALAIEDLDLTVRSYNCLKREGIHTVGELVARSEADLMDIRNFGSKSIDEVKQK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           L  + L L  +   +   +++      ED+
Sbjct: 301 LNELNLSLKDSPNGFGEANLDSDESFVEDE 330


>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 =  352 bits (904), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 121/316 (38%), Positives = 187/316 (59%), Gaps = 4/316 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLTE----ESISEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+T+IILNIKG+ +    D      + K+G G VTA DI     +E+ N
Sbjct: 61  HEFSTVPGVKEDVTEIILNIKGLVVSSEHDEPITAYLRKQGAGQVTAADISAPAGVEIHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+ VI  L+  A   +ELT+ +G GYV A  +R+E    G I +D++YSP+ KV+Y VE+
Sbjct: 121 PELVIATLNEKAKFELELTIERGRGYVSATQNRSEFSEAGQIPVDSIYSPVLKVTYRVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R G+  D+D+L + ++T  +IT  D++A A R L +  G+        + ++       
Sbjct: 181 TRAGERTDFDRLVVDVETKSAITPRDAIASAGRTLTELFGLARELNSAAEGIEIGPAPVD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              +  L   +E+L+LSVRS NCL+ E I  + +L+  +E  ++ + NFG+KS+ E+K  
Sbjct: 241 AVLSSELSMPIEDLDLSVRSYNCLKREGIHNVSELVALSETQLMNIRNFGQKSVDEVKDK 300

Query: 310 LGTMGLFLGMNLPDWP 325
           L  +GL L   +P + 
Sbjct: 301 LVELGLSLKDAVPGFD 316


>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 =  352 bits (904), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 125/322 (38%), Positives = 187/322 (58%), Gaps = 5/322 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E          R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I GV 
Sbjct: 17  QRPTLTE----ESLNPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGVP 72

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+I+LNIKGI L    D    + + K G G  TAGDI     + + N
Sbjct: 73  HEFTTLPGVEEDVTEILLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGVTIAN 132

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L  D  + +E TV +G GYVPA+ ++ +N  IG I +D++YSP+ KVSY VE+
Sbjct: 133 PDMHIATLAEDGELEIEFTVERGRGYVPAQMNKQDNAEIGRIPVDSIYSPVLKVSYRVEA 192

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  +I+  D+VA A   L +  G+        + V+      +
Sbjct: 193 TRVEQRTDFDKLILDVETKPAISPRDAVASAGSTLVELFGLCRELNTQAEGVEVGPAPVA 252

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              NP +   +E+L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  
Sbjct: 253 EETNPEMNIPIEDLNLTQRSYNCLKREGIHTIGELVAHTEQDLLDIRNFGMKSIDEVKEK 312

Query: 310 LGTMGLFLGMN-LPDWPPESIE 330
           L ++GL L  + L ++   ++E
Sbjct: 313 LQSLGLALKASPLGNFDANNLE 334


>gi|313808805|gb|EFS47259.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL087PA2]
          Length = 338

 Score =  352 bits (904), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 123/329 (37%), Positives = 187/329 (56%), Gaps = 4/329 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV 
Sbjct: 5   QRPTLTE----ESISEFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQ 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I+G  ED+T+IILN+KG+ L    D    + + K G G VTA DI     + + N
Sbjct: 61  HEFSTIEGCVEDVTEIILNLKGLVLSSEEDEPVAMYLRKSGAGEVTAADITPPAGVTIHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  I  L+ D    MEL V +G GYV +  +   N  IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PELHIATLNDDGRFEMELIVERGRGYVSSALNDDPNAEIGRIAVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SI   D++A A + L +  G+        + ++       
Sbjct: 181 TRVEQRTDFDKLVVDVETKPSILPRDAIASAGKTLVELFGLTRELNAEAEGIEIGSGPVD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
             +  +L   VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  
Sbjct: 241 EEYAESLGTPVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYED 338
           L  +GL L  + P + P +  E   +  D
Sbjct: 301 LTELGLALKDSAPGFDPLAAAEAYDEAND 329


>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 =  352 bits (904), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 152/336 (45%), Positives = 222/336 (66%), Gaps = 3/336 (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
           +++      NP L K ++ELELSVR+TNCL+  NI  +G+L+QRTE  ML+  NFGRKSL
Sbjct: 251 EVDSSID-LNPNLFKSIDELELSVRATNCLKAANIQLVGELVQRTEQAMLKTKNFGRKSL 309

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            EI+ VL +M L  GM + D+  +  E L +K +++
Sbjct: 310 DEIRRVLDSMSLKFGMGVEDFDKKYQEWLKRKEKNE 345


>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 =  352 bits (904), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 121/312 (38%), Positives = 189/312 (60%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +      E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I G
Sbjct: 23  LSEESINETRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTIPG 82

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ ++++NIK + +    D    + + K+GPG VTAGDIQ    + V NPD  +  L
Sbjct: 83  VKEDVVELVMNIKELCVSSEHDEPVSMYLRKQGPGDVTAGDIQPPAGVSVHNPDLKLATL 142

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           +    + MELTV +G GYV A  ++     IG I +D++YSP+ +V+Y VE+ R  Q  D
Sbjct: 143 NGKGRLDMELTVERGRGYVTAAQNKQAGAEIGRIPVDSIYSPVLRVTYRVEATRVEQRTD 202

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +D+L + +++  S+    ++A A   L +  G+    +E  + +    + +       L 
Sbjct: 203 FDRLIIDVESKPSMGPRTALASAGSTLVELFGLARELDETAEGIDIGPSPQDAQLAADLA 262

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +EEL+L+VRS NCL+ E I  +G+LI RTEAD+L + NFG+KS+ E+K  L  MGL L
Sbjct: 263 LPIEELDLTVRSYNCLKREGINTVGELIGRTEADLLDIRNFGQKSIDEVKMKLAGMGLGL 322

Query: 318 GMNLPDWPPESI 329
             + P++ P ++
Sbjct: 323 KDSAPNFDPANV 334


>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 =  352 bits (904), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 125/322 (38%), Positives = 187/322 (58%), Gaps = 5/322 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E          R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I GV 
Sbjct: 5   QRPTLTE----ESLNPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGVP 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+I+LNIKGI L    D    + + K G G  TAGDI     + + N
Sbjct: 61  HEFTTLPGVEEDVTEILLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGVTIAN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L  D  + +E TV +G GYVPA+ ++ +N  IG I +D++YSP+ KVSY VE+
Sbjct: 121 PDMHIATLAEDGELEIEFTVERGRGYVPAQMNKQDNAEIGRIPVDSIYSPVLKVSYRVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  +I+  D+VA A   L +  G+        + V+      +
Sbjct: 181 TRVEQRTDFDKLILDVETKPAISPRDAVASAGSTLVELFGLCRELNTQAEGVEVGPAPVA 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              NP +   +E+L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  
Sbjct: 241 EETNPEMAVPIEDLNLTQRSYNCLKREGIHTIGELVAHTEQDLLDIRNFGMKSIDEVKEK 300

Query: 310 LGTMGLFLGMN-LPDWPPESIE 330
           L ++GL L  + L ++   ++E
Sbjct: 301 LQSLGLALKASPLGNFDTNNLE 322


>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 =  352 bits (904), Expect = 4e-95,   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|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 =  352 bits (904), Expect = 4e-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-KIECVET-SEDGNYGKFVVEPLERGYGITLGNALRRILLSSLPGVAANHIKIDG 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|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 =  352 bits (904), Expect = 4e-95,   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|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 =  352 bits (904), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 145/333 (43%), Positives = 213/333 (63%), Gaps = 9/333 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
               +KP  ++   +    +  T +  EPL RGF HTLGNALRR+L+SS+ G AI   QI
Sbjct: 3   VSNFLKPRIVDVQRI---NDYATKVTLEPLERGFGHTLGNALRRILLSSMPGCAIIEAQI 59

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGVLHE ++ +GV ED+T+I+LN+KG+ +K+ G     + +  +GP  VTAGDIQ  +D+
Sbjct: 60  DGVLHEYTTKEGVQEDMTEILLNLKGVAVKLHGRDEVTLNLSSKGPVTVTAGDIQLEHDV 119

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH---RTENDPIGLITIDALYSPIKK 182
           EV+NP+HVI +L     + + + V +G GY  A        +   IG + +DA +SPI++
Sbjct: 120 EVINPEHVIAHLTKSGELNLTMKVVRGRGYQSASMRIPKEEDERSIGHLILDASFSPIRR 179

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V+Y V+SAR  Q  D DKL + I+T+G+I  +++V  A+ ILQDQL  F+   E + +++
Sbjct: 180 VTYEVDSARVEQRTDLDKLIIEIETNGTIAPDEAVRKAATILQDQLTAFV---ELEGKIE 236

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                K+   +P LL+ +++LEL+VRS NCL+ ENI Y+GDLIQ+TE ++L+  N G+KS
Sbjct: 237 TAKEKKAAEIDPVLLQPIDDLELTVRSANCLKAENIYYIGDLIQKTEVELLKTPNLGKKS 296

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
           L EIK VL   GL LGM L +WPP  + E   K
Sbjct: 297 LTEIKDVLTLRGLSLGMRLENWPPAGLREEETK 329


>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 =  352 bits (903), Expect = 4e-95,   Method: Composition-based stats.
 Identities = 123/329 (37%), Positives = 187/329 (56%), Gaps = 4/329 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV 
Sbjct: 5   QRPTLTE----ESISEFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQ 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I+G  ED+T+IILN+KG+ L    D    + + K G G VTA DI     + + N
Sbjct: 61  HEFSTIEGCVEDVTEIILNLKGLVLSSEEDEPVAMYLRKSGAGEVTAADINPPAGVTIHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  I  L+ D    MEL V +G GYV +  +   N  IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PELHIATLNDDGRFEMELIVERGRGYVSSALNDDPNAEIGRIAVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SI   D++A A + L +  G+        + ++       
Sbjct: 181 TRVEQRTDFDKLVVDVETKPSILPRDAIASAGKTLVELFGLTRELNAEAEGIEIGSGPVD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
             +  +L   VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  
Sbjct: 241 EEYAESLGTPVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYED 338
           L  +GL L  + P + P +  E   +  D
Sbjct: 301 LTELGLALKDSAPGFDPLAAAEAYDEAND 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 =  352 bits (903), Expect = 4e-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-KIECVET-SEDGNYGKFVVEPLERGYGTTLGNALRRILLSSLPGVAASHVKIDG 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|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 =  352 bits (903), Expect = 4e-95,   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|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 =  352 bits (903), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 119/330 (36%), Positives = 193/330 (58%), Gaps = 4/330 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V     ENR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLTEEVV----SENRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+T++ILNIK + +    D    + + +   G VTA DI     +E+ N
Sbjct: 61  HEFSTVPGVKEDITEVILNIKNLVVSSENDEPVVMYLRREEAGRVTAADITPPAGVEIHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+    + +EL V +G GYV A  ++  +  IG + +D++YSP+ KV+Y VE+
Sbjct: 121 PDLHIATLNEKGRLEIELIVERGRGYVSAAQNKGVDGEIGRVPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  +I+  D+VA A + L +  G+     +  + ++   +   
Sbjct: 181 TRVEQRTDFDKLIVDVETKPAISPRDAVASAGKTLVELFGLAHELNQEAEGIEIGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   + +L L+VRS NCL  E +  +G+L  R+EAD+L + NFG+KS+ E+K  
Sbjct: 241 QALAADLALPINDLNLTVRSYNCLMREGVHTVGELTARSEADLLDIRNFGQKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           L  +GL L  +   + P +++  +  + D+
Sbjct: 301 LADLGLSLKDSPAGFDPSALDSYSDDFGDQ 330


>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 = 140/310 (45%), Positives = 200/310 (64%), Gaps = 4/310 (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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 NKLTDLGLSL 308


>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 =  352 bits (903), Expect = 5e-95,   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|323465848|gb|ADX69535.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus helveticus
           H10]
          Length = 312

 Score =  352 bits (903), Expect = 5e-95,   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|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 =  352 bits (903), Expect = 5e-95,   Method: Composition-based stats.
 Identities = 123/321 (38%), Positives = 186/321 (57%), Gaps = 4/321 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E          R+  I EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G L
Sbjct: 5   QRPTLTE----ESLNPQRSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGAL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ G+ ED+T+I+LNIKGI L    D    + + K G G  TAGDI     + + N
Sbjct: 61  HEFTTLPGIEEDVTEILLNIKGIVLTSEYDEPVVMYLRKAGSGEATAGDITPPAGVTIAN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L  D  + +E TV +G GYVPA+ ++ + D IG I +D++YSP+ KVSY VE+
Sbjct: 121 PDLHIATLAEDGELEIEFTVERGRGYVPAQMNKQDGDEIGRIPVDSIYSPVLKVSYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  +I+  D+VA A   L +  G+        + V+      +
Sbjct: 181 TRVEQRTDFDKLILDVETKPAISPRDAVASAGSTLVELFGLCRELNTQAEGVEIGPAPVA 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              +P +   +E+L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  
Sbjct: 241 EQADPGMSVPIEDLNLTQRSYNCLKREGIHTVGELVNHTEQDLLDIRNFGMKSIDEVKEK 300

Query: 310 LGTMGLFLGMNLPDWPPESIE 330
           L ++GL L  +   +   ++E
Sbjct: 301 LQSLGLSLKSSPLGFDTNNLE 321


>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 =  352 bits (903), Expect = 5e-95,   Method: Composition-based stats.
 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   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 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|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 =  352 bits (903), Expect = 5e-95,   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|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 =  351 bits (902), Expect = 6e-95,   Method: Composition-based stats.
 Identities = 125/322 (38%), Positives = 187/322 (58%), Gaps = 5/322 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E          R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I GV 
Sbjct: 5   QRPTLTE----ESLNPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGVP 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+I+LNIKGI L    D    + + K G G  TAGDI     + + N
Sbjct: 61  HEFTTLPGVEEDVTEILLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGVTIAN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L  D  + +E TV +G GYVPA+ ++ +N  IG I +D++YSP+ KVSY VE+
Sbjct: 121 PDMHIATLAEDGELEIEFTVERGRGYVPAQMNKQDNAEIGRIPVDSIYSPVLKVSYRVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  +I+  D+VA A   L +  G+        + V+      +
Sbjct: 181 TRVEQRTDFDKLILDVETKPAISPRDAVASAGSTLVELFGLCRELNTQAEGVEVGPAPVA 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              NP +   +E+L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  
Sbjct: 241 EETNPEMNIPIEDLNLTQRSYNCLKREGIHTIGELVAHTEQDLLDIRNFGMKSIDEVKEK 300

Query: 310 LGTMGLFLGMN-LPDWPPESIE 330
           L ++GL L  + L ++   ++E
Sbjct: 301 LQSLGLALKASPLGNFDTNNLE 322


>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 =  351 bits (902), Expect = 7e-95,   Method: Composition-based stats.
 Identities = 121/323 (37%), Positives = 196/323 (60%), Gaps = 4/323 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E ++     E+R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLTEEVI----SESRSRFSIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+IILN+K + +    D    + + K+G GVVTA DI     +EV N
Sbjct: 61  HEFTTVPGVKEDVTEIILNVKNLVVSSENDEPVVMYLRKQGSGVVTAADIVPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+    + +ELTV +G GYV A+ +++ +  IG + +D++YSP+ KV+Y VE+
Sbjct: 121 PDLHIATLNDKGKLEIELTVERGRGYVSAQQNKSFDAEIGRVPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  +I+  D++A A + L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDKLIVDVETKQAISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +E+L+L++RS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 AALAADLALPIEDLQLTIRSYNCLKREGIHAVGELVARSEADLLDIRNFGAKSINEVKDK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEEL 332
           L  +GL L  +  D+ P + +  
Sbjct: 301 LAELGLSLKDSPLDFDPTTADYY 323


>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 =  351 bits (902), Expect = 7e-95,   Method: Composition-based stats.
 Identities = 118/316 (37%), Positives = 187/316 (59%), Gaps = 4/316 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        E R+  + EPL  GF +TLGN++RR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLAE----ENISEFRSRFVIEPLEPGFGYTLGNSIRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+T++ILNIK + +    D      + K+G G VTA DI     +E+ N
Sbjct: 61  HEFSTVAGVKEDVTEVILNIKNLVVSSEHDEPITAYLRKQGAGEVTAADISAPAGVEIHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+ VI  L+  A   +ELT+ +G GYV A  +R+E    G I +D++YSP+ KV+Y VE+
Sbjct: 121 PELVIATLNDKAKFELELTIERGRGYVTATQNRSEFSEAGQIPVDSIYSPVLKVTYRVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R G+  D+D+L + ++T  +IT  D++A A R L +  G+        + ++       
Sbjct: 181 TRAGERTDFDRLVVDVETKSAITPRDAIASAGRTLTELFGLARELNTAAEGIEIGPAPVD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              +  L   +E+L+LSVRS NCL+ E I  + +L+  +E  ++ + NFG+KS+ E++  
Sbjct: 241 AVLSTELSMPIEDLDLSVRSYNCLKREGINTVSELVALSETQLMNIRNFGQKSVDEVRDK 300

Query: 310 LGTMGLFLGMNLPDWP 325
           L  MGL L  ++P + 
Sbjct: 301 LVEMGLSLKDSVPGFD 316


>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 (902), Expect = 7e-95,   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-KIETVEI-SEDATFGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTAVQIDG 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|281415637|ref|ZP_06247379.1| DNA-directed RNA polymerase subunit alpha [Micrococcus luteus NCTC
           2665]
          Length = 334

 Score =  351 bits (902), Expect = 7e-95,   Method: Composition-based stats.
 Identities = 121/318 (38%), Positives = 194/318 (61%), Gaps = 4/318 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V     ++R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVL
Sbjct: 7   QRPTLTEEVV----SDHRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL 62

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+T+IILNIK +++    D      + K+G GVVTA DI     +E+ N
Sbjct: 63  HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEIHN 122

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+      MELT+ +G GYV A  +++ +  IG I +D++YSP+ KV++ VE+
Sbjct: 123 PDLHIATLNAKGKFDMELTIERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEA 182

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  ++   D+VA A   L +  G+  +     + +      + 
Sbjct: 183 TRVEQRTDFDRLILDVETKENMLPRDAVASAGSTLVELFGLARSLNVEAEGIDLGDEPEV 242

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           +  +  L + +EELEL+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  
Sbjct: 243 VEGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEK 302

Query: 310 LGTMGLFLGMNLPDWPPE 327
           L  +GL L  +   + P+
Sbjct: 303 LQELGLSLKDSPAGYDPQ 320


>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 =  351 bits (901), Expect = 8e-95,   Method: Composition-based stats.
 Identities = 121/318 (38%), Positives = 194/318 (61%), Gaps = 4/318 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V     ++R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVL
Sbjct: 5   QRPTLTEEVV----SDHRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+T+IILNIK +++    D      + K+G GVVTA DI     +E+ N
Sbjct: 61  HEFSTVNGVKEDVTEIILNIKKLSVSSENDEPVVAYLRKQGAGVVTAADITAPAGVEIHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+      MELT+ +G GYV A  +++ +  IG I +D++YSP+ KV++ VE+
Sbjct: 121 PDLHIATLNAKGKFDMELTIERGRGYVTAAQNKSADAEIGRIPVDSIYSPVLKVTFKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  ++   D+VA A   L +  G+  +     + +      + 
Sbjct: 181 TRVEQRTDFDRLILDVETKENMLPRDAVASAGSTLVELFGLARSLNVEAEGIDLGDEPEV 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           +  +  L + +EELEL+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  
Sbjct: 241 VEGSADLAQPIEELELTVRSYNCLKREGIHTVGELVGRSEADLMDIRNFGAKSIDEVKEK 300

Query: 310 LGTMGLFLGMNLPDWPPE 327
           L  +GL L  +   + P+
Sbjct: 301 LQELGLSLKDSPAGYDPQ 318


>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 =  351 bits (901), Expect = 8e-95,   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-KIETVEI-SENATFGKFVVEPLERGYGATLGNSLRRILLSSLPGAAVTTVQIDG 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|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 =  351 bits (901), Expect = 8e-95,   Method: Composition-based stats.
 Identities = 124/321 (38%), Positives = 185/321 (57%), Gaps = 4/321 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E          R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G L
Sbjct: 5   QRPTLTE----ESLNPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGAL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+I+LNIKGI L    D    + + K G G   AGDI     + + N
Sbjct: 61  HEFTTLPGVQEDVTEILLNIKGIVLTSEYDEPVVMYLRKSGKGEAVAGDITPPAGVTIAN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  I  L  D  + +E TV +G GYVPA+ ++ +ND IG I +D++YSP+ KVSY VE+
Sbjct: 121 PEQHIATLADDGELEIEFTVERGRGYVPAQMNKQDNDEIGRIPVDSIYSPVLKVSYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  +I+  D+VA A   L +  G+        + V+      +
Sbjct: 181 TRVEQRTDFDKLILDVETKPAISPRDAVASAGSTLVELFGLCRELNAQAEGVEVGPAPVA 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              NP +   +E+L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  
Sbjct: 241 EETNPEMAVPIEDLNLTQRSYNCLKREGIHTIGELVSHTEQDLLDIRNFGMKSIDEVKEK 300

Query: 310 LGTMGLFLGMNLPDWPPESIE 330
           L T+GL L  +   +   ++E
Sbjct: 301 LQTLGLSLKSSPMAFDTNNLE 321


>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 =  351 bits (901), Expect = 8e-95,   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|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 =  351 bits (901), Expect = 8e-95,   Method: Composition-based stats.
 Identities = 121/316 (38%), Positives = 187/316 (59%), Gaps = 4/316 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLTE----ESISEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+T+IILNIKG+ +    D      + K+G G VTA DI     +E+ N
Sbjct: 61  HEFSTVPGVKEDVTEIILNIKGLVVSSEHDEPITAYLRKQGAGQVTAADISAPAGVEIHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+ VI  L+  A   +ELT+ +G GYV A  +R+E    G I +D++YSP+ KV+Y VE+
Sbjct: 121 PELVIATLNEKAKFELELTIERGRGYVSATQNRSEFSEAGQIPVDSIYSPVLKVTYRVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R G+  D+D+L + ++T  +IT  D++A A R L +  G+        + ++       
Sbjct: 181 TRAGERTDFDRLVVDVETKSAITPRDAIASAGRTLTELFGLARELNSAAEGIEIGPAPVD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              +  L   +E+L+LSVRS NCL+ E I  + +L+  +E  ++ + NFG+KS+ E+K  
Sbjct: 241 AVLSSELSMPIEDLDLSVRSYNCLKREGINNVSELVALSETQLMNIRNFGQKSVDEVKDK 300

Query: 310 LGTMGLFLGMNLPDWP 325
           L  +GL L   +P + 
Sbjct: 301 LVELGLSLKDAVPGFD 316


>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 =  351 bits (901), Expect = 8e-95,   Method: Composition-based stats.
 Identities = 125/320 (39%), Positives = 190/320 (59%), Gaps = 4/320 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLSE----ESINETRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE ++I GV ED+ ++++NIK + +    D    + + K+GPG VTAGDIQ    + V N
Sbjct: 61  HEFTTIPGVKEDVVELVMNIKELCVSSEHDEPVSMYLRKQGPGDVTAGDIQPPAGVSVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  +  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLKLATLNGKGRLDMELTVERGRGYVTAAQNKQAGAEIGRIPVDSIYSPVLKVTYRVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  S+    ++A A   L +  G+    +E  + +    + + 
Sbjct: 181 TRVEQRTDFDRLIIDVETKPSMGPRTALASAGSTLVELFGLARELDETAEGIDIGPSPQD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EEL+L+VRS NCL+ E I  +G+LI RTEAD+L + NFG+KS+ E+K  
Sbjct: 241 AQLAADLALPIEELDLTVRSYNCLKREGINSVGELIGRTEADLLDIRNFGQKSIDEVKMK 300

Query: 310 LGTMGLFLGMNLPDWPPESI 329
           L  MGL L  + P++ P  +
Sbjct: 301 LAGMGLGLKDSAPNFDPAHV 320


>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 =  351 bits (901), Expect = 9e-95,   Method: Composition-based stats.
 Identities = 123/312 (39%), Positives = 188/312 (60%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +      E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I G
Sbjct: 9   LSEESINETRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTIPG 68

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ ++++NIK + +    D    + + K+GPG VTAGDIQ    + V NPD  +  L
Sbjct: 69  VKEDVVELVMNIKELCVSSEHDEPVSMYLRKQGPGDVTAGDIQPPAGVSVHNPDLKLATL 128

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           +    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+ R  Q  D
Sbjct: 129 NGKGRLDMELTVERGRGYVTAAQNKQAGAEIGRIPVDSIYSPVLKVTYRVEATRVEQRTD 188

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +D+L + ++T  S+    ++A A   L +  G+    +E  + +    + +       L 
Sbjct: 189 FDRLIIDVETKPSMGPRTALASAGSTLVELFGLARELDETAEGIDIGPSPQDAQLAADLA 248

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +EEL+L+VRS NCL+ E I  +G+LI RTEAD+L + NFG+KS+ E+K  L  MGL L
Sbjct: 249 LPIEELDLTVRSYNCLKREGINSVGELIGRTEADLLDIRNFGQKSIDEVKMKLAGMGLGL 308

Query: 318 GMNLPDWPPESI 329
             + P++ P  +
Sbjct: 309 KDSAPNFDPAHV 320


>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 =  351 bits (901), Expect = 9e-95,   Method: Composition-based stats.
 Identities = 131/310 (42%), Positives = 199/310 (64%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +      E  N    + EPL RG+  TLGN+LRR+L++SL G A+T +QIDG
Sbjct: 3   EFEKPNITKV----DESTNYGKFVVEPLERGYGTTLGNSLRRILLASLPGTAVTDIQIDG 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|308171338|gb|ADO15988.1| RpoA [Vibrio caribbenthicus]
          Length = 323

 Score =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 141/329 (42%), Positives = 215/329 (65%), Gaps = 11/329 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++ +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MRGSVTEFLKPRLVD---IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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
            +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           N G+KSL EIK VL + GL LGM L +WP
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWP 323


>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 =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 127/323 (39%), Positives = 189/323 (58%), Gaps = 8/323 (2%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +   Q    R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ G
Sbjct: 9   LTEEQVTPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTTLPG 68

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+T+I+LNIK + L    D    + + K G G  TA DI     + + NPD  I  L
Sbjct: 69  VKEDVTEILLNIKELVLTSEYDEPVVMYLRKSGEGEATAADITPPAGVVIANPDLHIATL 128

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D  + +E TV +G GYVPA+ ++ E D IG I +D++YSP+ KVSY VE+ R  Q  D
Sbjct: 129 AEDGELEIEFTVERGRGYVPAQMNKQEGDEIGRIPVDSIYSPVVKVSYKVEATRVEQRTD 188

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL + ++T  +IT  D+VA A   L +  G+F       + V+      +   +P + 
Sbjct: 189 FDKLIVDVETKPAITPRDAVASAGSTLVELFGLFHELNNQAEGVEVGPAPVTEEVDPQME 248

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +E+L L+ RS NCL+ E I  +G+L++R+E D+L + NFG+KS+ E+K  L +MGL L
Sbjct: 249 IPIEDLNLTQRSYNCLKREGIHTIGELVKRSEQDLLDIRNFGQKSIDEVKDKLASMGLSL 308

Query: 318 G--------MNLPDWPPESIEEL 332
                    ++L D    S E+L
Sbjct: 309 KQSPLGLGQIDLDDSNFFSPEDL 331


>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 =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 124/321 (38%), Positives = 183/321 (57%), Gaps = 4/321 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E          R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G L
Sbjct: 5   QRPTLTE----ESLNPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGAL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+I+LNIKGI L    D    + + K G G  TAGDI     + + N
Sbjct: 61  HEFTTLPGVEEDVTEILLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGVTIAN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  I  L  D  + +E TV +G GYVPA+ ++ EN  IG I +D++YSP+ KVSY VE+
Sbjct: 121 PEMHIATLAEDGELEIEFTVERGRGYVPAQMNKQENSEIGRIPVDSIYSPVLKVSYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  +IT  D+VA A   L +  G+        + V+       
Sbjct: 181 TRVEQRTDFDKLILDVETKPAITPRDAVASAGSTLVELFGLCRELNVDAEGVEVGPAPVM 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              +  +   +E+L L+ RS NCL+ E I  +G+L+  TE D+L + NFG KS+ E+K  
Sbjct: 241 GEVDSQMATPIEDLNLTQRSYNCLKREGIHTVGELVVHTEQDLLDIRNFGMKSIDEVKEK 300

Query: 310 LGTMGLFLGMNLPDWPPESIE 330
           L +MGL L  +   +   ++E
Sbjct: 301 LQSMGLSLKASPLGFDANNLE 321


>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 =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 121/318 (38%), Positives = 187/318 (58%), Gaps = 4/318 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P+  E        +NR+  I EPL  GF +TLGN+LRR L+SS+ GA++T++++DGVL
Sbjct: 5   QRPSLTE----EPVADNRSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIRVDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T++ILN+K + +    D    + + K+GPG VTA DI     + V N
Sbjct: 61  HEFTTVPGVKEDITELILNLKELVVSSEDDEPVTMYLRKQGPGDVTAADIAPPAGVTVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
            D  +  L     + +EL V +G GYVPA  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 SDLKLATLTKKGKLEIELVVERGRGYVPASPNKVVGAEIGRIPVDSIYSPVLKVTYRVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SIT  D++A A   L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDKLVLDVETKPSITPRDALASAGTTLVELFGLARELNVDAEGIEIGPSPAE 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                A    +EE++L+VRS NCL+ E I  +G+L+ RTEAD+L + NFG+KS+ E+K  
Sbjct: 241 ADHIAAFGLPIEEMDLTVRSYNCLKREGIHTVGELVSRTEADLLDIRNFGQKSIDEVKIK 300

Query: 310 LGTMGLFLGMNLPDWPPE 327
           L  MGL L  +   + P 
Sbjct: 301 LAGMGLALKDSPAGFDPA 318


>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 =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 134/311 (43%), Positives = 204/311 (65%), Gaps = 5/311 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP   +        +N       PL RG+  TLGN+LRRVL+SSL GAAIT+V+I+G
Sbjct: 3   EIEKPKIEKVEC----TDNYGKFEVAPLERGYGITLGNSLRRVLLSSLPGAAITSVKIEG 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 KGVLGTMGLFL 317
           K  L  + L L
Sbjct: 299 KEKLNELDLKL 309


>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 =  351 bits (900), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 154/338 (45%), Positives = 214/338 (63%), Gaps = 5/338 (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 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK +L    L LGM    W     E+  +K E+
Sbjct: 311 KSLNEIKALLAEHNLTLGMKYEGWVAP--EKREEKLEE 346


>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 =  350 bits (899), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 145/333 (43%), Positives = 213/333 (63%), Gaps = 9/333 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
               +KP  ++   +    +  T +  EPL RGF HTLGNALRR+L+SS+ G AI   QI
Sbjct: 3   VSNFLKPRIVDVQRI---NDYATKVTLEPLERGFGHTLGNALRRILLSSMPGCAIIEAQI 59

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGVLHE ++ +GV ED+T+I+LN+KG+ +K+ G     +++  +GP  VTAGDIQ  +D+
Sbjct: 60  DGVLHEYTTKEGVQEDMTEILLNLKGVAIKLHGRDEVTLSLSSKGPVTVTAGDIQLEHDV 119

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKK 182
           EV+NP HVI +L     + + + V +G GY PA        +   IG + +DA +SPI++
Sbjct: 120 EVINPKHVIAHLTKSGELNLTMKVVRGRGYQPASVRIPKEEDERSIGHLILDASFSPIRR 179

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V+Y V+SAR  Q  D DKL + I+T+G+I  +++V  A+ ILQDQL  F+   E +  ++
Sbjct: 180 VTYEVDSARVEQRTDLDKLIIEIETNGTIAPDEAVRKAATILQDQLTAFV---ELEGRIE 236

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                K+   +P LL+ +++LEL+VRS NCL+ ENI Y+GDLIQ+TE ++L+  N G+KS
Sbjct: 237 TAKEKKAAEIDPVLLQPIDDLELTVRSANCLKAENIYYIGDLIQKTEVELLKTPNLGKKS 296

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
           L EIK VL   GL LG+ L +WPP  + E   K
Sbjct: 297 LTEIKDVLTLRGLSLGIRLENWPPAGLREEETK 329


>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 =  350 bits (899), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 121/312 (38%), Positives = 189/312 (60%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +      E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I G
Sbjct: 9   LSEESINETRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTIPG 68

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ ++++NIK + +    D    + + K+GPG VTAGDIQ    + V NPD  +  L
Sbjct: 69  VKEDVVELVMNIKELCVSSEHDEPVSMYLRKQGPGDVTAGDIQPPAGVSVHNPDLKLATL 128

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           +    + MELTV +G GYV A  ++     IG I +D++YSP+ +V+Y VE+ R  Q  D
Sbjct: 129 NGKGRLDMELTVERGRGYVTAAQNKQAGAEIGRIPVDSIYSPVLRVTYRVEATRVEQRTD 188

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +D+L + +++  S+    ++A A   L +  G+    +E  + +    + +       L 
Sbjct: 189 FDRLIIDVESKPSMGPRTALASAGSTLVELFGLARELDETAEGIDIGPSPQDAQLAADLA 248

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +EEL+L+VRS NCL+ E I  +G+LI RTEAD+L + NFG+KS+ E+K  L  MGL L
Sbjct: 249 LPIEELDLTVRSYNCLKREGINSVGELIGRTEADLLDIRNFGQKSIDEVKMKLAGMGLGL 308

Query: 318 GMNLPDWPPESI 329
             + P++ P ++
Sbjct: 309 KDSAPNFDPANV 320


>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 =  350 bits (899), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 121/322 (37%), Positives = 185/322 (57%), Gaps = 4/322 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV 
Sbjct: 5   QRPTLTE----ESISEFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQ 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I+G  ED+T+IILN+KG+ L    D    + + K G G +TA DI     + + N
Sbjct: 61  HEFSTIEGCVEDVTEIILNLKGLVLSSEEDEPVAMYLRKTGAGEITAADINPPAGVTIHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  I  L+ D    MEL V +G GYV +  +   N  IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PELHIATLNDDGRFEMELIVERGRGYVSSALNDDPNAEIGRIAVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SI   D++A A + L +  G+        + ++       
Sbjct: 181 TRVEQRTDFDKLVVDVETKPSILPRDAIASAGKTLVELFGLTRELNVEAEGIEIGSGPVD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
             +  +L   VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  
Sbjct: 241 EEYAESLGTPVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEE 331
           L  +GL L  + P + P +  E
Sbjct: 301 LTELGLALKDSAPGFDPLAAAE 322


>gi|315109197|gb|EFT81173.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL030PA2]
          Length = 338

 Score =  350 bits (899), Expect = 1e-94,   Method: Composition-based stats.
 Identities = 121/322 (37%), Positives = 185/322 (57%), Gaps = 4/322 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV 
Sbjct: 5   QRPTLTE----ESISEFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQ 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I+G  ED+T+IILN+KG+ L    D    + + K G G +TA DI     + + N
Sbjct: 61  HEFSTIEGCVEDVTEIILNLKGLVLSSEEDEPVAMYLRKTGAGEITAADINPPAGVTIHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  I  L+ D    MEL V +G GYV +  +   N  IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PELHIATLNDDGRFEMELIVERGRGYVSSALNDDPNAEIGRIAVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SI   D++A A + L +  G+        + ++       
Sbjct: 181 TRVEQRTDFDKLVVDVETKPSILPRDAIASAGKTLVELFGLTRELNVEAEGIEIGSGPVD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
             +  +L   VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  
Sbjct: 241 EEYAESLGTPVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEE 331
           L  +GL L  + P + P +  E
Sbjct: 301 LTELGLALKDSAPGFDPLAAAE 322


>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 =  350 bits (899), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 127/315 (40%), Positives = 188/315 (59%), Gaps = 3/315 (0%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V+    + R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+IDGV 
Sbjct: 25  QRPTLTEEVVVE---DRRSRFVLEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRIDGVP 81

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE  +I GV ED+  IILNIK I L    D    + + K GP  VTAGDI     +E+ N
Sbjct: 82  HEFRTIPGVKEDVAQIILNIKEIVLSSENDEPVVMYLRKSGPSEVTAGDITPPAGVEIHN 141

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+ VI  L+    + +ELTV +G GYV A  ++  N  I  I +D++YSP+KKVSY+VE+
Sbjct: 142 PELVIATLNEKGKLEIELTVERGRGYVSANQNKDPNAEISRIPVDSIYSPVKKVSYSVEA 201

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  SIT  D++A A + L +  G+        + ++   +   
Sbjct: 202 TRVEQRTDFDRLIVDVETKSSITPRDALASAGKTLVELFGLARELNVEAEGIEVGPSPID 261

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
             F   L   ++EL+L  RS+N L+ E I  +G+L+ R+EAD+L + NFG KS+ EIK  
Sbjct: 262 EAFQQDLALMIDELDLQARSSNALKREGIHTVGELVSRSEADLLDIRNFGAKSISEIKDK 321

Query: 310 LGTMGLFLGMNLPDW 324
           L  +GL L  +  D+
Sbjct: 322 LAELGLSLKGSPVDY 336


>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 =  350 bits (899), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 128/315 (40%), Positives = 188/315 (59%), Gaps = 3/315 (0%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V+    + R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+IDGV 
Sbjct: 5   QRPTLTEEVVVE---DRRSRFVLEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRIDGVP 61

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE  +I GV ED+  IILNIK I L    D    + + K GP  VTAGDI     +E+ N
Sbjct: 62  HEFRTIPGVKEDVAQIILNIKEIVLSSENDEPVVMYLRKSGPSEVTAGDITPPAGVEIHN 121

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD VI  L+    + +ELTV +G GYV A  ++  N  I  I +D++YSP+KKVSY+VE+
Sbjct: 122 PDLVIATLNEKGKLEIELTVERGRGYVSANQNKDPNAEISRIPVDSIYSPVKKVSYSVEA 181

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  SIT  D++A A + L +  G+        + ++   +   
Sbjct: 182 TRVEQRTDFDRLIVDVETKSSITPRDALASAGKTLVELFGLARELNVEAEGIEVGPSPID 241

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
             F   L   ++EL+L  RS+N L+ E I  +G+L+ R+EAD+L + NFG KS+ EIK  
Sbjct: 242 EAFQQDLALMIDELDLQARSSNALKREGIHTVGELVSRSEADLLDIRNFGAKSISEIKDK 301

Query: 310 LGTMGLFLGMNLPDW 324
           L  +GL L  +  D+
Sbjct: 302 LAELGLSLKGSPVDY 316


>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 =  350 bits (899), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 123/321 (38%), Positives = 186/321 (57%), Gaps = 4/321 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E          R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G L
Sbjct: 5   QRPTLTE----ESLNPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGAL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+I+LNIKGI L    D    + + K G G  TAGDI   + + + N
Sbjct: 61  HEFTTLPGVQEDVTEILLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPSGVTIAN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  I  L  D  + +E TV +G GYVPA+ ++ + D IG I +D++YSP+ KVSY VE+
Sbjct: 121 PEQHIATLAEDGELEIEFTVERGRGYVPAQMNKQDTDEIGRIPVDSIYSPVLKVSYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  +I+  D+VA A   L +  G+        + V+      +
Sbjct: 181 TRVEQRTDFDKLILDVETKPAISPRDAVASAGSTLVELFGLCRELNAQAEGVEVGPAPVA 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              NP +   +E+L L+ RS NCL+ E +  +G+L+  TE D+L + NFG KS+ E+K  
Sbjct: 241 EETNPEMAVPIEDLNLTQRSYNCLKREGVHTIGELVSHTEQDLLDIRNFGMKSIDEVKEK 300

Query: 310 LGTMGLFLGMNLPDWPPESIE 330
           L T+GL L  +   +   ++E
Sbjct: 301 LQTLGLSLKSSPMAFDTNNLE 321


>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 =  350 bits (898), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 125/316 (39%), Positives = 186/316 (58%), Gaps = 4/316 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E     +  E R+  + EPL  GF +T+GNALRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLTE----EKVGEFRSRFVIEPLEPGFGYTIGNALRRSLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I GV ED+T+IILNIK + +    D      + K G G VTA DI     +EV N
Sbjct: 61  HEFSTIPGVKEDVTEIILNIKQLVVSSERDEPITAYLRKTGSGEVTAADISAPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD VI  L+  A   +ELT+ +G GYV A  +R E    G I ID++YSP+ KVSY VE+
Sbjct: 121 PDLVIATLNDTAKFELELTIERGRGYVSATQNRNEYAEAGQIPIDSIYSPVLKVSYRVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R G+  D+DKL + +++  SI   D+VA A R L +  G+        + ++       
Sbjct: 181 TRAGERTDFDKLVLDVESKPSIAPRDAVASAGRTLTELFGLARELNVEAEGIEIGPAPVE 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              +  L   +E+L+LSVRS NCL+ E I  + +L+  +E  ++ + NFG+KS+ E++  
Sbjct: 241 TVLSNELSMPIEDLDLSVRSYNCLKREGINTVSELVALSETQLMNIRNFGQKSVDEVRDK 300

Query: 310 LGTMGLFLGMNLPDWP 325
           L ++GL L  ++P + 
Sbjct: 301 LVSLGLSLKDSVPGFD 316


>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 =  350 bits (898), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 136/310 (43%), Positives = 201/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE +    ++ +    + EPL RG+  TLGN+LRR+L+SSL G A+T+V+I+G
Sbjct: 3   EIEKP-KIECVE-RTDDNSYAKFVVEPLERGYGITLGNSLRRILLSSLPGTAVTSVKIEG 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|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 =  350 bits (898), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 130/310 (41%), Positives = 190/310 (61%), Gaps = 4/310 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           + KP  +    L    +     + EPL RG+  TLGNALRRVL+SS+ GAA+T V+I+GV
Sbjct: 4   IEKPR-VSVDSLAPTGD-YGRFVIEPLVRGYGITLGNALRRVLLSSIPGAAVTMVKIEGV 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 NPDHYIASLAPEGRLFMEMTVRRGRGYVPADRQRH-DHVIGAIPVDADFSPVKKVNYRVE 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 QKLAELGLSL 310


>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 =  350 bits (898), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 130/330 (39%), Positives = 198/330 (60%), Gaps = 6/330 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E I+    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLTEEII----DEYRSRFLIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE ++I GV ED+TD+ILNIK + +    D    + + K+GPG VTA DI     +EV N
Sbjct: 61  HEFTTIPGVKEDVTDLILNIKQLVVSSEIDEPVTMYLRKQGPGTVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+ +I  L+    + MELTV +G GYV A  ++     IG I ID++YSP+ KV Y VE+
Sbjct: 121 PELIIATLNGKGKLEMELTVERGRGYVSAVQNKQAGQEIGRIPIDSIYSPVLKVKYDVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  S+   D+VA A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDRLVLDVETKQSMRPRDAVASAGKTLVELFGLARELNIEAEGIDMGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +E+LEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 AALAADLALPIEDLELTVRSYNCLKREGIHTVGELVARSEADLLDIRNFGAKSIDEVKVK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           L +MGL L  + P + P  + +   +Y+++
Sbjct: 301 LMSMGLALKDSPPGFDPSLVVDN--QYDEE 328


>gi|157100343|emb|CAP03337.1| RpoA protein [Vibrio aestuarianus]
          Length = 323

 Score =  350 bits (898), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 141/329 (42%), Positives = 214/329 (65%), Gaps = 11/329 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQIST---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 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
            +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           N G+KSL EIK VL + GL LGM L +WP
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWP 323


>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 =  350 bits (898), Expect = 2e-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-KIECVEV-NEDGSYGKFVVEPLERGYGITLGNALRRILLSSLPGVAANHIKIDG 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|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 =  350 bits (897), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 128/318 (40%), Positives = 193/318 (60%), Gaps = 4/318 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV N
Sbjct: 61  HEFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLVLATLNGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNVDAEGIDMGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 AALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWPPE 327
           L  MGL L  + P + P 
Sbjct: 301 LAGMGLALKDSPPGFDPT 318


>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 =  350 bits (897), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 131/323 (40%), Positives = 193/323 (59%), Gaps = 7/323 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
            P  +         E     +AEP   G+ HT+GN+LRRVL+SSL GAAI++++IDG +H
Sbjct: 1   MPKRLTKDETTS-TETYAKFVAEPFETGYGHTIGNSLRRVLLSSLEGAAISSIKIDGAMH 59

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E +++ GV ED+TDI+LN+K +  K      + + +     G VTA DIQ   +IE++NP
Sbjct: 60  EFTTVDGVVEDVTDIVLNLKKVLFKAHNREPQTLLLSANKDGEVTAADIQVNQNIELVNP 119

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
              IC LD      +EL V  G G+ P   ++  N  IG+I ID+L+SP+ +V Y VESA
Sbjct: 120 KQHICTLDKKKKFEIELEVKVGRGFCPGDENKKPNQAIGVIAIDSLFSPVTRVRYAVESA 179

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R GQ  DYD+L + + TDG I+ +D++  AS ILQ  L +F+ +++   E +E ++ +  
Sbjct: 180 RVGQRTDYDRLILEVWTDGRISPDDALTQASAILQHHLDVFVGYDKNAVEFEEVVDKQDE 239

Query: 251 PFNPALL---KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                       V E+ELSVR+ NCL   NI  +G L  +TEA+ML+  NFG+KSL EIK
Sbjct: 240 EKTKLKKLLGMSVNEIELSVRAANCLNNANITTVGQLAMKTEAEMLKYRNFGKKSLNEIK 299

Query: 308 GVLGTMGLFLGMNLPDWPPESIE 330
             L  +GL LGM+   + PE+++
Sbjct: 300 EKLTALGLSLGMS---FDPEALD 319


>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 =  350 bits (897), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 136/311 (43%), Positives = 199/311 (63%), 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-IETAELKS-DGTYGRFILEPLERGFGTTLGNSLRRVLLSSLPGVAVTSIKIDG 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|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 =  350 bits (897), Expect = 2e-94,   Method: Composition-based stats.
 Identities = 135/320 (42%), Positives = 204/320 (63%), Gaps = 5/320 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E+ +P  IE   L   +      +AEPL RGF  TLGN+LRRVL+SSL G A+T+V+ID
Sbjct: 16  MEIERP-KIETASL-SPDGRYGKFVAEPLERGFGITLGNSLRRVLLSSLPGVAVTSVKID 73

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S+I+GV ED+T+I+LN+KGI  K+  D  K V +   GP  VTA +I+  +DIE
Sbjct: 74  GVVHEFSTIEGVKEDVTEIVLNLKGIAAKLYTDGPKTVRVEAVGPCEVTADNIKQGDDIE 133

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKV 183
           +LNP+  I  L     + MELT  KG GYVPA+ ++    E + I  + +D++Y+P+ KV
Sbjct: 134 ILNPEWHIATLGEGGKLVMELTFDKGRGYVPAERNKQAIIEKNDINTLPVDSIYTPVLKV 193

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VES R GQ +DYDKL++ + TDG+I  +++V+LA+R+L + L +F+N  +     + 
Sbjct: 194 NYNVESTRVGQAIDYDKLTIEVWTDGTINAQEAVSLAARVLTEHLNLFVNLSDEAAGAEI 253

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +   +     AL   +EEL+LSVRS NCL+   I  + DL+ ++E +M+++ N GRKSL
Sbjct: 254 MVEKTNDDKEKALEMTIEELDLSVRSFNCLKRAGINTVEDLVSKSEDEMMKVRNLGRKSL 313

Query: 304 VEIKGVLGTMGLFLGMNLPD 323
            E+   L ++G  L  +  +
Sbjct: 314 EEVMAKLDSLGFKLNTDDDN 333


>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 =  349 bits (896), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 131/328 (39%), Positives = 192/328 (58%), Gaps = 5/328 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +   W+ L  P+ +          N    IAEP  RGF  T+GN+LRR+L+SSL GAA+T
Sbjct: 1   MHIRWRGLELPSVVNC-EAESLSPNYGKFIAEPFERGFGVTIGNSLRRILLSSLEGAAVT 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 KEDINVKSLPFNPA----LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
                 +S   +P     L   + 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|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 =  349 bits (896), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 140/314 (44%), Positives = 201/314 (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 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKV 183
           ++LNPD  I  +   A   M +T  KG GYV A     R  + 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|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 =  349 bits (896), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 121/330 (36%), Positives = 194/330 (58%), Gaps = 9/330 (2%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V      NR+    EPL  GF +T+GN+LRR L+SS+ GAA+T+V+IDGVL
Sbjct: 5   QRPTLTEEVV----APNRSRFTIEPLEPGFGYTMGNSLRRTLLSSIPGAAVTSVRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+T+IILN+K +++    D      + K+G G +TA DI+    +E+ N
Sbjct: 61  HEFSTVPGVTEDVTEIILNVKKLSISSENDEPVVAYLRKQGEGELTAADIEVPAGVEIHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  I  L+  A    EL + +G GYV A  ++T +  IG I +D++YSP+ KV+++V +
Sbjct: 121 PELHIATLNAKANFNAELIIERGRGYVSAAQNKTGDAEIGRIPVDSIYSPVLKVTFSVNA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D L++ ++T  +I   D+VA A   L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDSLTLDVETKEAIAPRDAVASAGSTLVELFGLARELNVAAEGIEVGPSPAD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +E+L +SVRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  
Sbjct: 241 ESMAADLALPIEDLNMSVRSYNCLKREGIHTVGELVTRSEADLMDIRNFGAKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           L  +GL L  + P + P     +A+ Y+D+
Sbjct: 301 LHELGLALKDSPPGFEP-----VARAYDDE 325


>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 =  349 bits (896), Expect = 3e-94,   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|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 =  349 bits (896), Expect = 3e-94,   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-IETAELTS-DGSYGRFVVEPLERGYGTTLGNSLRRVLLSSLPGVAVTQVKIDG 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|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 =  349 bits (896), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 125/330 (37%), Positives = 197/330 (59%), Gaps = 7/330 (2%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        ENR+  + EPL  GF +TLGN+LRR L+SS+ GA++T+++IDGVL
Sbjct: 5   QRPTLTE----EAVAENRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+++GV ED+T++ILNIK ++L    D      + K+GPG VTA DI     +EV N
Sbjct: 61  HEFSTVEGVKEDVTELILNIKKLSLSSEEDEPVTAWLRKQGPGEVTAADISAPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  I  L+    + +ELT+ +G GYV A  +++ +  +G I +D++YSP+ KV++ VE+
Sbjct: 121 PELHIATLNSKGQLEIELTIERGRGYVSASQNKSGDAEVGRIPVDSIYSPVLKVTFRVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  +I+  D+VA A   L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDKLILDVETKEAISPRDAVASAGTTLVELFGLARELNSSAEGIEIGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 +   +E+LELSVRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  
Sbjct: 241 AAAAADMALPIEDLELSVRSYNCLKREGIHSVGELVGRSEADLMDIRNFGAKSIDEVKDK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           LG +GL L  + P +    +   A   ED+
Sbjct: 301 LGELGLALKDSPPGYD---LAAHAASLEDE 327


>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 =  349 bits (896), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 135/317 (42%), Positives = 203/317 (64%), Gaps = 5/317 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E+ +P  IE   L   +      +AEPL RGF  TLGN+LRRVL+SSL G A+T+V+ID
Sbjct: 16  MEIERP-KIETASL-SPDGRYGRFVAEPLERGFGITLGNSLRRVLLSSLPGVAVTSVKID 73

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S+I+GV ED+T+I+LN+KGI  K+  D  K V +   GP  VTA +I+  +DIE
Sbjct: 74  GVVHEFSTIEGVKEDVTEIVLNLKGIAAKLYTDGPKTVRVEAVGPCEVTADNIKQGDDIE 133

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKV 183
           +LNP+  I  L     + MELT  KG GYVPA+ ++    E + I  + +D++Y+P+ KV
Sbjct: 134 ILNPEWHIATLGEGGKLVMELTFDKGRGYVPAERNKQAIVEKNDINTLPVDSIYTPVLKV 193

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VES R GQ +DYDKL++ + TDG+I  +++V+LA+R+L + L +F+N  +     + 
Sbjct: 194 NYNVESTRVGQAIDYDKLTIEVWTDGTINAQEAVSLAARVLTEHLNLFVNLSDEAAGTEI 253

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +   +     AL   +EEL+LSVRS NCL+   I  + DL+ ++E +M+++ N GRKSL
Sbjct: 254 MVEKTNDDKEKALEMTIEELDLSVRSFNCLKRAGINTVEDLVSKSEDEMMKVRNLGRKSL 313

Query: 304 VEIKGVLGTMGLFLGMN 320
            E+   L ++G  L  +
Sbjct: 314 EEVMAKLDSLGFKLNTD 330


>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 =  349 bits (896), Expect = 3e-94,   Method: Composition-based stats.
 Identities = 131/313 (41%), Positives = 208/313 (66%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I    E+      + EPL RG+  TLGNALRR+L+SSL G A T+V+IDG
Sbjct: 3   EIEKP-IIECIE-SNEDGTYGKYVVEPLERGYGITLGNALRRILLSSLPGVAPTSVKIDG 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|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 =  349 bits (895), Expect = 4e-94,   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  MSDHWNKLTKPSSIKVVNHGN-ALNKADLIIEPLESGFALTLGNALRRVMMSSLRGFAVY 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|308171332|gb|ADO15985.1| RpoA [Vibrio ichthyoenteri ATCC 700023]
          Length = 323

 Score =  349 bits (895), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 140/329 (42%), Positives = 214/329 (65%), Gaps = 11/329 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++ +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MRGSVTEFLKPRLVDIEQIST---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 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
            +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           N G+KSL EIK VL + GL LGM L +WP
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWP 323


>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 =  349 bits (895), Expect = 4e-94,   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|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 =  349 bits (895), Expect = 4e-94,   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|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 =  349 bits (895), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 127/330 (38%), Positives = 191/330 (57%), Gaps = 7/330 (2%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V     + R+  + EPL  GF +TLGN+LRR L+SS+ GA+IT+++I+G  
Sbjct: 5   QRPTLSEEVV----NDFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASITSIKIEGNQ 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+T+IILN+KG+ L    D    + + K G G VTA DI     +E+ N
Sbjct: 61  HEFSTLPGVVEDVTEIILNLKGLVLSSEEDEPVAMYLRKSGAGEVTAADIAVPTGVEIYN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L  D  + MEL V +G GYV +  +   +  IG I +D+LYSP+  VSY VE+
Sbjct: 121 PDLHIATLADDGSIEMELVVERGRGYVSSTLNNNPDAEIGRIAVDSLYSPVLTVSYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R     D+D+L + ++T  SI   D+VA A + L +  G+F       + V+   +   
Sbjct: 181 TRVETRTDFDRLIVDVETKPSIRPHDAVASAGKTLVELFGLFRELNVEAEGVEMGPSPVD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 +   VE+L LSVRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  
Sbjct: 241 EQLAADMALPVEDLNLSVRSYNCLKREGIHTVGELVSRSEQDLLDIRNFGSKSIDEVKEK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           LG +GL L  + P + P +  +   ++ED+
Sbjct: 301 LGDLGLTLKDSTPGFDPLAAAD---RFEDE 327


>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 =  349 bits (895), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 135/312 (43%), Positives = 204/312 (65%), Gaps = 3/312 (0%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            ++ KP  IE +    E+      I EPL RG+  TLGN+LRR+L+SSL G A+T+V+ID
Sbjct: 1   MQIEKPR-IECVET-NEDNTYGKFIVEPLERGYGITLGNSLRRILLSSLPGVAVTSVKID 58

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVNDI 125
           GVLHE S++ GV ED+TDIILN+K + LKM G+   K + I  +G G V AGDI   +D+
Sbjct: 59  GVLHEFSTVPGVREDVTDIILNLKSLRLKMHGEADEKILRIEAQGEGEVRAGDIVPDSDV 118

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E+LNPD  I  L  +  + M++T+++G GY  A+ ++     IG+I ID++++P+ KV+Y
Sbjct: 119 EILNPDMYIATLAANGRLSMDITIARGRGYFSAERNKKGEPIIGVIPIDSIFTPVYKVNY 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           +VE+ R GQ  DYDKLS+ I TDGSI  +++ +LA++I+ + L +FI   E  K+V+  +
Sbjct: 179 SVENTRVGQRTDYDKLSIEIWTDGSIHPDEAASLAAKIMSEHLQLFIGLTEETKDVEIMV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +    +  +   +EEL+LSVRS NCL+   I  + +LIQR E DM+++ N G+KSL E
Sbjct: 239 EKEEEKKDKIMEMTIEELDLSVRSYNCLKRACINTVEELIQRNEEDMMKVRNLGKKSLEE 298

Query: 306 IKGVLGTMGLFL 317
           +   L  +G+ L
Sbjct: 299 VIQKLNELGVSL 310


>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 =  349 bits (895), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 128/318 (40%), Positives = 193/318 (60%), Gaps = 4/318 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV N
Sbjct: 61  HEFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLVLATLNGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNIDAEGIDMGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 AALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWPPE 327
           L  MGL L  + P + P 
Sbjct: 301 LAGMGLALKDSPPGFDPT 318


>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 =  349 bits (895), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 121/330 (36%), Positives = 194/330 (58%), Gaps = 9/330 (2%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V      NR+    EPL  GF +T+GN+LRR L+SS+ GAA+T+V+IDGVL
Sbjct: 5   QRPTLTEEVV----APNRSRFTIEPLEPGFGYTMGNSLRRTLLSSIPGAAVTSVRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+T+IILN+K +++    D      + K+G G +TA DI+    +E+ N
Sbjct: 61  HEFSTVPGVTEDVTEIILNVKKLSISSENDEPVVAYLRKQGEGELTAADIEVPAGVEIHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  I  L+  A    EL + +G GYV A  ++T +  IG I +D++YSP+ KV+++V +
Sbjct: 121 PELHIATLNAKANFNAELIIERGRGYVSAAQNKTGDAEIGRIPVDSIYSPVLKVTFSVNA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D L++ ++T  +I   D+VA A   L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDSLTLDVETKEAIAPRDAVASAGSTLVELFGLARELNVAAEGIEVGPSPAD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +E+L +SVRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  
Sbjct: 241 ESMAADLALPIEDLSMSVRSYNCLKREGIHTVGELVTRSEADLMDIRNFGAKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           L  +GL L  + P + P     +A+ Y+D+
Sbjct: 301 LHELGLALKDSPPGFEP-----VARAYDDE 325


>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 =  349 bits (895), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 128/318 (40%), Positives = 193/318 (60%), Gaps = 4/318 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV N
Sbjct: 61  HEFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLVLATLNAKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNIDAEGIDMGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 AALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWPPE 327
           L  MGL L  + P + P 
Sbjct: 301 LAGMGLALKDSPPGFDPT 318


>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 =  349 bits (895), Expect = 4e-94,   Method: Composition-based stats.
 Identities = 124/321 (38%), Positives = 186/321 (57%), Gaps = 4/321 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E          R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G L
Sbjct: 25  QRPTLTE----ESITPQRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGAL 80

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+I+LNIKGI L    D    + + K G G  TAGDI     I + N
Sbjct: 81  HEFTALPGVEEDVTEILLNIKGIVLTSEYDEPVVMYLRKSGKGEATAGDITPPAGITIAN 140

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  I +L  D  + +E TV +G GYVPA+ ++ ++D IG I +D++YSP+ KVSY VE+
Sbjct: 141 PEMHIASLAEDGELEIEFTVERGRGYVPAQMNKQDSDEIGRIPVDSIYSPVLKVSYKVEA 200

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  +I+  D+VA A   L +  G+        + V+       
Sbjct: 201 TRVEQRTDFDKLILDVETKPAISPRDAVASAGSTLVELFGLCRELNMQAEGVEVGPAPVV 260

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              NP L   +E+L L+ RS NCL+ E I  +G+L+   E D+L + NFG KS+ E+K  
Sbjct: 261 EETNPELAVPIEDLNLTQRSYNCLKREGIHTVGELVAHNEQDLLDIRNFGMKSIDEVKEK 320

Query: 310 LGTMGLFLGMNLPDWPPESIE 330
           L ++GL L  +   +   ++E
Sbjct: 321 LQSLGLSLKASPLGFDTTNLE 341


>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 =  349 bits (895), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 134/333 (40%), Positives = 193/333 (57%), 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 KEDINVKSLPFNPAL---LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +   +  S   N         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|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 =  349 bits (895), Expect = 5e-94,   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  MSDHWNKLTKPSSIKVVNHGN-ALNKADLIIEPLESGFALTLGNALRRVMMSSLRGFAVY 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|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 =  348 bits (894), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 128/318 (40%), Positives = 193/318 (60%), Gaps = 4/318 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPSLTEEVV----DEYRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV N
Sbjct: 61  HEFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLVLATLNGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNIDAEGIDMGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 AALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWPPE 327
           L  MGL L  + P + P 
Sbjct: 301 LAGMGLALKDSPPGFDPT 318


>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 =  348 bits (894), Expect = 5e-94,   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  MSDHWNKLTKPSSIKVVNHGN-ALNKADLIIEPLESGFALTLGNALRRVMMSSLRGFAVY 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 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|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 =  348 bits (894), Expect = 5e-94,   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-KIECVA-RSDDATYGKFVVEPLERGYGVTLGNSLRRILLTSLFGAAVTSVKIEG 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|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 =  348 bits (894), Expect = 5e-94,   Method: Composition-based stats.
 Identities = 125/323 (38%), Positives = 193/323 (59%), Gaps = 4/323 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E ++     + R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLSEEVI----SDARSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I GV ED+T+IILN+K + L    D    + + K+G GVVTA DI     +EV N
Sbjct: 61  HEFSTITGVKEDVTEIILNVKNLVLSSENDEPVVMYLRKQGAGVVTAADIVPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+    + +ELTV +G GYV A+ +++ +  IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLHIATLNDKGKLEIELTVERGRGYVSAQQNKSMDAEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  SI   D++A A + L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDRLIVDVETKSSIVPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +E+L L++RS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 AALAADLALPIEDLNLTIRSYNCLKREGIHQVGELVARSEADLLDIRNFGAKSINEVKEK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEEL 332
           L  +GL L  +  D+ P S  + 
Sbjct: 301 LHELGLSLKDSPLDFQPSSESDY 323


>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 =  348 bits (893), Expect = 6e-94,   Method: Composition-based stats.
 Identities = 144/332 (43%), Positives = 217/332 (65%), Gaps = 10/332 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  + ++P  ++   +       T +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQNSIMDFLRPRLVDIEQI---SATHTKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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
           ++    +   +   F P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RE---PEFKEEKPEFEPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            G+KSL EIK VL +  L LGM L +WPP SI
Sbjct: 295 LGKKSLTEIKDVLASRSLSLGMRLENWPPSSI 326


>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 =  348 bits (893), Expect = 7e-94,   Method: Composition-based stats.
 Identities = 120/330 (36%), Positives = 192/330 (58%), Gaps = 9/330 (2%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V      NR+    EPL  GF +T+GN+LRR L+SS+ GAA+T+V+IDGVL
Sbjct: 5   QRPTLTEEVV----APNRSRFTIEPLEPGFGYTMGNSLRRTLLSSIPGAAVTSVRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+T+IILNIK +++    D      + K+G G +TAGDI+    +E+ N
Sbjct: 61  HEFSTVPGVTEDVTEIILNIKKLSISSENDEPVVAYLRKQGEGELTAGDIEVPAGVEIHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  +  L+  A    EL + +G GYV A  ++  +  IG I +D++YSP+ KV+++V +
Sbjct: 121 PELHLATLNASANFNAELVIERGRGYVTAAQNKAGDSEIGRIPVDSIYSPVLKVTFSVNA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D L++ ++T  +I   D+VA A   L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDSLTLDVETKEAIAPRDAVASAGSTLVELFGLARELNIAAEGIEVGPSPAD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +E+L +SVRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  
Sbjct: 241 ESMAADLALPIEDLNMSVRSYNCLKREGIHTVGELVTRSEADLMDIRNFGAKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           L  +GL L  + P + P      A+  +D+
Sbjct: 301 LTELGLSLKDSPPGFEPA-----ARPLDDE 325


>gi|295101439|emb|CBK98984.1| DNA-directed RNA polymerase subunit alpha [Faecalibacterium
           prausnitzii L2-6]
          Length = 318

 Score =  348 bits (893), Expect = 7e-94,   Method: Composition-based stats.
 Identities = 135/317 (42%), Positives = 203/317 (64%), Gaps = 5/317 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E+ +P  IE   L   +      +AEPL RGF  TLGN+LRRVL+SSL G A+T+V+ID
Sbjct: 2   MEIERP-KIETASL-SPDGRYGKFVAEPLERGFGITLGNSLRRVLLSSLPGVAVTSVKID 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S+I+GV ED+T+I+LN+KGI  K+  D  K V +   GP  VTA +I+  +DIE
Sbjct: 60  GVVHEFSTIEGVKEDVTEIVLNLKGIAAKLYTDGPKTVRVEAVGPCEVTADNIKQGDDIE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKV 183
           +LNP+  I  L     + MELT  KG GYVPA+ ++    E + I  + +D++Y+P+ KV
Sbjct: 120 ILNPEWHIATLGEGGKLVMELTFDKGRGYVPAERNKQAIIEKNDINTLPVDSIYTPVLKV 179

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VES R GQ +DYDKL++ + TDG+I  +++V+LA+R+L + L +F+N  +     + 
Sbjct: 180 NYNVESTRVGQAIDYDKLTIEVWTDGTINAQEAVSLAARVLTEHLNLFVNLSDEAAGAEI 239

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +   +     AL   +EEL+LSVRS NCL+   I  + DL+ ++E +M+++ N GRKSL
Sbjct: 240 MVEKTNDDKEKALEMTIEELDLSVRSFNCLKRAGINTVEDLVSKSEDEMMKVRNLGRKSL 299

Query: 304 VEIKGVLGTMGLFLGMN 320
            E+   L ++G  L  +
Sbjct: 300 EEVMAKLDSLGFKLNTD 316


>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 =  348 bits (893), Expect = 7e-94,   Method: Composition-based stats.
 Identities = 125/323 (38%), Positives = 186/323 (57%), Gaps = 11/323 (3%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +   Q    R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I G LHE +++ G
Sbjct: 9   LTEEQINPQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRISGALHEFTALPG 68

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+ +I+LNIK + L    D    + + K G G  TA DI     + V NPD  I  L
Sbjct: 69  VKEDVAEILLNIKELVLTSEYDEPVVMYLRKSGEGEATAADITPPAGVVVANPDLHIATL 128

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D  + +E TV +G GYVPA+ ++ E D IG I +D++YSP+ KVSY V+  R  Q  D
Sbjct: 129 AEDGELEIEFTVERGRGYVPAQMNKQEGDEIGRIPVDSIYSPVLKVSYKVDPTRVEQRTD 188

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL++ ++T  SI+  D+VA A   L +  G+F       + V+          +P + 
Sbjct: 189 FDKLTVDVETKPSISPRDAVASAGSTLVELFGLFHELNNQAEGVEVGPAPVVEEVDPQME 248

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +E+L L+ RS NCL+ E I  +G+L++R+E D+L + NFG+KS+ E+K  L +MGL L
Sbjct: 249 IPIEDLNLTQRSYNCLKREGIHTIGELVKRSEQDLLDIRNFGQKSIDEVKEKLDSMGLSL 308

Query: 318 G--------MNLPD---WPPESI 329
                    ++L     + PE I
Sbjct: 309 KQSPLGLGQIDLEGDNFFSPEDI 331


>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 =  348 bits (893), Expect = 7e-94,   Method: Composition-based stats.
 Identities = 124/318 (38%), Positives = 186/318 (58%), Gaps = 4/318 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E       +E R+  + EPL  GF +TLGN+LRR L+SS+ GA++T+++ID VL
Sbjct: 5   QRPTLSE----ETVDEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIKIDNVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I+GV ED+T++ILN+KG+ +    D    + + K G G VTA DI     +EV N
Sbjct: 61  HEFSTIEGVKEDVTEVILNLKGLVVSSEHDEPVTMYLRKSGAGDVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L     + MEL V +G GYV A  ++  ++ IG + +D++YSP+ KV+Y VE+
Sbjct: 121 PDLKIATLSDKGKLEMELVVERGRGYVSAVQNKGADNEIGRMPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SI   D++A A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDKLVIDVETKPSIRPRDAIASAGKTLVELFGLARELNVEAEGIDIGPSPVD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   VE+L+L+VRS NCL+ E I  +G+LI R+E D+L + NFG KS+ E+K  
Sbjct: 241 EQLAADLALPVEDLQLTVRSYNCLKREGIHTVGELISRSEQDLLDIRNFGAKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWPPE 327
           L  MGL L  + P + P 
Sbjct: 301 LVEMGLSLKDSAPGFDPH 318


>gi|295103950|emb|CBL01494.1| DNA-directed RNA polymerase subunit alpha [Faecalibacterium
           prausnitzii SL3/3]
          Length = 318

 Score =  348 bits (893), Expect = 7e-94,   Method: Composition-based stats.
 Identities = 136/317 (42%), Positives = 204/317 (64%), Gaps = 5/317 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E+ +P  IE   L   +      +AEPL RGF  TLGN+LRRVL+SSL G A+T+V+ID
Sbjct: 2   MEIERP-KIETASL-SPDGRYGKFVAEPLERGFGITLGNSLRRVLLSSLPGVAVTSVKID 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S+I+GV ED+T+I+LN+KGI  K+  D  K V +   GP  VTA +I+  +DIE
Sbjct: 60  GVVHEFSTIEGVKEDVTEIVLNLKGIAAKLYTDGPKTVRVEAVGPCEVTADNIKQGDDIE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKV 183
           +LNP+  I  L   A + MELT  KG GYVPA+ ++    E + I  + +D++Y+P+ KV
Sbjct: 120 ILNPEWHIATLGEGAKLVMELTFDKGRGYVPAERNKQAIIEKNDINTLPVDSIYTPVLKV 179

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VES R GQ +DYDKL++ + TDG+I  +++V+LA+R+L + L +F+N  +     + 
Sbjct: 180 NYNVESTRVGQAIDYDKLTIEVWTDGTINAQEAVSLAARVLTEHLNLFVNLSDEAAGAEI 239

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +   +     AL   +EEL+LSVRS NCL+   I  + DL+ ++E +M+++ N GRKSL
Sbjct: 240 MVEKTNDDKEKALEMTIEELDLSVRSFNCLKRAGINTVEDLVSKSEDEMMKVRNLGRKSL 299

Query: 304 VEIKGVLGTMGLFLGMN 320
            E+   L ++G  L  +
Sbjct: 300 EEVMAKLDSLGFKLNTD 316


>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 =  348 bits (893), Expect = 7e-94,   Method: Composition-based stats.
 Identities = 137/328 (41%), Positives = 210/328 (64%), Gaps = 5/328 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M+   W+ L  P + + +  G+ +      + E L RG+  TLGNALRRVL+SSL+GAAI
Sbjct: 1   MM---WKSLQMPRSFQKVETGE-DGRYAKFVVEALERGWGITLGNALRRVLLSSLQGAAI 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 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EPKK 239
           +KV+  +   R GQ  DY++L + I TDGSI  ED++A A+++L D L +FINFE + + 
Sbjct: 177 QKVAMHISDTRVGQKTDYNRLELEITTDGSIDPEDALAYAAKLLVDHLEIFINFEGDLES 236

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
             + +++ +       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|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 =  348 bits (893), Expect = 7e-94,   Method: Composition-based stats.
 Identities = 136/317 (42%), Positives = 204/317 (64%), Gaps = 5/317 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E+ +P  IE   L   +      +AEPL RGF  TLGN+LRRVL+SSL G A+T+V+ID
Sbjct: 16  MEIERP-KIETASL-SPDGRYGKFVAEPLERGFGITLGNSLRRVLLSSLPGVAVTSVKID 73

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S+I+GV ED+T+I+LN+KGI  K+  D  K V +   GP  VTA +I+  +DIE
Sbjct: 74  GVVHEFSTIEGVKEDVTEIVLNLKGIAAKLYTDGPKTVRVEAVGPCEVTADNIKQGDDIE 133

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDPIGLITIDALYSPIKKV 183
           +LNP+  I  L   A + MELT  KG GYVPA+ ++    E + I  + +D++Y+P+ KV
Sbjct: 134 ILNPEWHIATLGEGAKLVMELTFDKGRGYVPAERNKQAIIEKNDINTLPVDSIYTPVLKV 193

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VES R GQ +DYDKL++ + TDG+I  +++V+LA+R+L + L +F+N  +     + 
Sbjct: 194 NYNVESTRVGQAIDYDKLTIEVWTDGTINAQEAVSLAARVLTEHLNLFVNLSDEAAGAEI 253

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +   +     AL   +EEL+LSVRS NCL+   I  + DL+ ++E +M+++ N GRKSL
Sbjct: 254 MVEKTNDDKEKALEMTIEELDLSVRSFNCLKRAGINTVEDLVSKSEDEMMKVRNLGRKSL 313

Query: 304 VEIKGVLGTMGLFLGMN 320
            E+   L ++G  L  +
Sbjct: 314 EEVMAKLDSLGFKLNTD 330


>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 =  348 bits (893), Expect = 7e-94,   Method: Composition-based stats.
 Identities = 127/318 (39%), Positives = 193/318 (60%), Gaps = 4/318 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVL
Sbjct: 5   QRPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV N
Sbjct: 61  HEFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLVLATLNGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNVDAEGIDMGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 AALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWPPE 327
           L  MGL L  + P + P 
Sbjct: 301 LAGMGLALKDSPPGFDPT 318


>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 =  348 bits (893), Expect = 7e-94,   Method: Composition-based stats.
 Identities = 127/318 (39%), Positives = 190/318 (59%), Gaps = 5/318 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
              P+ +E I     + N    +AEP   G+ HTLGN+LRRVL+ SL GAAIT+V+I G 
Sbjct: 20  FEVPSRLEKIE-DPNDANHLTFVAEPFENGYGHTLGNSLRRVLLGSLEGAAITSVRIAGA 78

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE SS+ GV ED+T+I+LN+K +  K +G   + +++     GVVTA DI      +V+
Sbjct: 79  QHEFSSLPGVVEDVTEIVLNLKKVKFKHNGKEPRLLSLRVHKQGVVTAADIADDTVYQVV 138

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NPD +IC LD D +   E  V  G G+     ++  + PIG+I ID+++SP+ +V Y+V+
Sbjct: 139 NPDQIICTLDQDTMFECEFQVRVGRGFATGDENKVPDMPIGVIPIDSIFSPVTRVKYSVQ 198

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           + R GQ+ DYDKL + + TDG I   D++  AS IL+  L +F+N+++ +   +E  +  
Sbjct: 199 NTRVGQMTDYDKLILEVWTDGRIAPADAMLQASAILRHHLDVFVNYDDKQVNFEEAPSAV 258

Query: 249 SLPF----NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
                      L   V E+ELSVR+ NCL   NI  +G L  ++E++ML+  NFG+KSL 
Sbjct: 259 QDEETARLRKLLNMSVNEIELSVRAANCLNNANITTVGQLAMKSESEMLKYRNFGKKSLN 318

Query: 305 EIKGVLGTMGLFLGMNLP 322
           EIK  L  +GL LG+ + 
Sbjct: 319 EIKDKLLELGLSLGVQVD 336


>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 =  348 bits (893), Expect = 8e-94,   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|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 =  348 bits (892), Expect = 8e-94,   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|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 =  348 bits (892), Expect = 9e-94,   Method: Composition-based stats.
 Identities = 121/316 (38%), Positives = 192/316 (60%), Gaps = 4/316 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V      NR+  + EPL  GF +TLGN+LRR L+SS+ GA++T+++IDGVL
Sbjct: 5   QRPTLTEEVVAE----NRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+T+++LNIK +++    D      + K+GPG+VTA DI     +E  N
Sbjct: 61  HEFTTVAGVKEDVTELVLNIKNLSVSSEHDEPVVAYLRKQGPGIVTAADITPPAGVEFHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+ +    MELT+ +G GYV A  +++ +  IG I +D++YSP+ KV++ VE+
Sbjct: 121 PDLHIATLNANGKFDMELTIERGRGYVSAAQNKSADGEIGRIPVDSIYSPVLKVTFRVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  SIT  D+VA A   L +  G+F       + ++   +   
Sbjct: 181 TRVEQRTDFDRLIVDVETKESITPRDAVASAGTTLVELFGLFRELNTQAEGIEIGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 +   +E+LEL+VRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  
Sbjct: 241 AAMAADMALPIEDLELTVRSYNCLKREGIHSVGELVTRSEADLMDIRNFGAKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWP 325
           L  +GL L  + P + 
Sbjct: 301 LVELGLALKDSPPGFD 316


>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 =  348 bits (892), Expect = 9e-94,   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 GHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVP    +  ++   +I    +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 GVISPEEAIRQSARILVDQLSVFAAL-EGTESAAEAAAARAPQIDPILLRPVDDLELTVR 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|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 =  348 bits (892), Expect = 9e-94,   Method: Composition-based stats.
 Identities = 144/332 (43%), Positives = 216/332 (65%), Gaps = 10/332 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  + ++P  ++   +       T +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQNSIMDFLRPRLVDIEQI---SATHTKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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
           ++    +   +   F P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RE---PEFKEEKPEFEPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            G+KSL EIK VL +  L LGM L +WPP SI
Sbjct: 295 LGKKSLTEIKDVLASRSLSLGMRLENWPPSSI 326


>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 = 129/310 (41%), Positives = 201/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE +    E+      + EPL RG+  TLGN+LRR+L+SSL G A  +++IDG
Sbjct: 3   EIEKP-KIECVEA-SEDGTYGKFVIEPLERGYGITLGNSLRRILLSSLPGGAANSIKIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 EKLAALGLGL 310


>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 =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 145/332 (43%), Positives = 214/332 (64%), Gaps = 10/332 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +    +KP  +E   +       T +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQNSIIGFLKPRLVEIEQI---TATHTKVTLEPLERGFGHTLGNALRRILLSSMPGYAVT 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+   ++   +  P    LL+ V++LEL+VRS NCL+ E+I Y+GDL+QRTE ++L+  N
Sbjct: 238 KEPEIKEEKPEFEP---ILLRPVDDLELTVRSANCLKAESIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            G+KSL EIK +L    L LGM L  WPP SI
Sbjct: 295 LGKKSLTEIKDILAARNLSLGMKLEKWPPSSI 326


>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 = 130/310 (41%), Positives = 202/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE +    E+      + EPL RG+  TLGN+LRR+L+SSL G A  +++IDG
Sbjct: 3   EIEKP-KIECVEA-SEDGTYGKFVIEPLERGYGITLGNSLRRILLSSLPGVAANSIKIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 EKLAALGLGL 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 =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 129/310 (41%), Positives = 202/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE +    E+      + EPL RG+  TLGN+LRR+L+SSL G A  +++IDG
Sbjct: 3   EIEKP-KIECVEA-SEDGTYGKFVIEPLERGYGITLGNSLRRILLSSLPGVAANSIKIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 EKLAALGLGL 310


>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 =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 136/312 (43%), Positives = 201/312 (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 LNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSY 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|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 =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 135/311 (43%), Positives = 201/311 (64%), Gaps = 4/311 (1%)

Query: 8   ELIKPNNIEYIVLGQEEEN-RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           E+ +P       + +  +N     + EPL RGF  TLGN+LRRVL+SSL GAAI+ ++ID
Sbjct: 3   EIERPR---IECVERTPDNRYGKFVIEPLERGFGITLGNSLRRVLLSSLPGAAISTIKID 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE S+I GV ED T+IILN+K + L+   D  K V + +RGP  V AGDI    +IE
Sbjct: 60  GVLHEFSTIPGVVEDTTEIILNLKQVVLRYDYDQPKTVFVEQRGPKEVKAGDIIRDAEIE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +LNP+  I  L+ D  + ME+TV +G GYV A   + + + IGLI ID++++PI KV++T
Sbjct: 120 ILNPELHIATLNEDGRLAMEMTVERGRGYVSADQKKKDENVIGLIPIDSIFTPINKVNFT 179

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+AR G+V DYD+L + + T+GSI+ E++V+L++ IL D L +F    +    V+  + 
Sbjct: 180 VENARVGRVTDYDRLMLEVWTNGSISPEEAVSLSAHILIDHLKLFTEINDSYSPVEILVE 239

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +    +  L   +EELELSVR++N L+  NI  +GDL+++T  +M ++ N G+KSL EI
Sbjct: 240 KEEDQKDKILDMSIEELELSVRASNGLKRANINTVGDLVEKTREEMSKIRNLGQKSLDEI 299

Query: 307 KGVLGTMGLFL 317
           +  L  +GL  
Sbjct: 300 ERKLKELGLSF 310


>gi|327451569|gb|EGE98223.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL092PA1]
          Length = 338

 Score =  347 bits (891), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 121/329 (36%), Positives = 186/329 (56%), Gaps = 4/329 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV 
Sbjct: 5   QRPTLTE----ESISEFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQ 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I+G  ED+T+IILN+KG+ L    D    + + K G G + A DI     + + N
Sbjct: 61  HEFSTIEGCVEDVTEIILNLKGLVLSSEEDEPVAMYLRKTGAGEIPAADINPPAGVTIHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  I  L+ D    MEL V +G GYV +  +   N  IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PELHIATLNDDGRFEMELIVERGRGYVSSALNDDPNAEIGRIAVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SI   D++A A + L +  G+        + ++       
Sbjct: 181 TRVEQRTDFDKLVVDVETKPSILPRDAIASAGKTLVELFGLTRELNVEAEGIEIGSGPVD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
             +  +L   VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  
Sbjct: 241 EEYAESLGTPVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYED 338
           L  +GL L  + P + P +  E   +  D
Sbjct: 301 LTELGLALKDSAPGFDPLAAAEAYDEAND 329


>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 =  347 bits (891), Expect = 1e-93,   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   SDLLRPEHYDLEVL---SPRRARISLGPLERGFGHTLGNALRRVLLSSLKGAAVTEVEIE 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|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 =  347 bits (890), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 126/313 (40%), Positives = 183/313 (58%), Gaps = 3/313 (0%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +     + +R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+I+GVLHE +++ G
Sbjct: 9   LTEEYIDSSRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRIEGVLHEFTTVPG 68

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED++DIILNIKG+ L    D    + I K GPG VTAGDI     +E+ NPD  I  L
Sbjct: 69  VTEDVSDIILNIKGLVLSSDSDDPVTMYIRKEGPGEVTAGDIMPPAGVEIHNPDMHIATL 128

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           +    + +EL V +G GYVPA     E    G I +D +YSP+ KVSY VE+ R  Q  D
Sbjct: 129 NEQGKLDIELVVERGRGYVPAAQATGEI---GRIPVDQIYSPVLKVSYKVEATRVEQRTD 185

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +D+L + ++T  SIT  D++A A   L +  G+        + ++   + +      A  
Sbjct: 186 FDRLVIDVETKNSITARDAMASAGGTLVELFGLARELNTAAEGIEIGPSPQESEHIQAYG 245

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +E+L  SVRS NCL+ E I  +G+L  RTE+D+L + NFG+KS+ E+K  L  +GL L
Sbjct: 246 MPIEDLNFSVRSYNCLKREEIHTVGELASRTESDLLDIRNFGQKSINEVKVKLAGLGLAL 305

Query: 318 GMNLPDWPPESIE 330
                 +    IE
Sbjct: 306 KDAPEGYDVSEIE 318


>gi|314924147|gb|EFS87978.1| DNA-directed RNA polymerase, alpha subunit [Propionibacterium acnes
           HL001PA1]
          Length = 338

 Score =  347 bits (890), Expect = 1e-93,   Method: Composition-based stats.
 Identities = 121/329 (36%), Positives = 185/329 (56%), Gaps = 4/329 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV 
Sbjct: 5   QRPTLTE----ESISEFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQ 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I+G  ED+T+IIL ++G  L    D    + + K G G VTA DI     + + N
Sbjct: 61  HEFSTIEGCVEDVTEIILTLRGFVLPSEEDEPVAMYLRKSGAGEVTAADINPPAGVTIHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  I  L+ D    MEL V +G GYV +  +   N  IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PELHIATLNDDGRFEMELIVERGRGYVSSALNDDPNAEIGRIAVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SI   D++A A + L +  G+        + ++       
Sbjct: 181 TRVEQRTDFDKLVVDVETKPSILPRDAIASAGKTLVELFGLTRELNAEAEGIEIGSGPVD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
             +  +L   VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  
Sbjct: 241 EEYAESLGTPVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYED 338
           L  +GL L  + P + P +  E   +  D
Sbjct: 301 LTELGLALKDSAPGFDPLAAAEAYDEAND 329


>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 =  347 bits (890), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 118/314 (37%), Positives = 181/314 (57%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +      E R+  + EPL  GF +T+GN+LRR L+SS+ GA++T+++I+GV HE S+I+G
Sbjct: 9   LTEETISEFRSKFVIEPLEPGFGYTIGNSLRRTLLSSIPGASVTSIKIEGVQHEFSTIEG 68

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
             ED+T+IILN+KG+ L    D    + + K G G + A DI     + + NP   I  L
Sbjct: 69  CVEDVTEIILNLKGLVLSSEEDEPVAMYLRKSGTGEIIAADINPPAGVTIHNPGLHIATL 128

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           + D    MEL V +G GYV +  +   +  IG I +D++YSP+ KV+Y VE+ R  Q  D
Sbjct: 129 NDDGRFEMELVVERGRGYVSSALNDDPSAEIGRIAVDSIYSPVLKVTYKVEATRVEQRTD 188

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL + ++T  SI   D+VA A + L +  G+        + ++         +  +L 
Sbjct: 189 FDKLVVDVETKPSILPRDAVASAGKTLVELFGLTRELNAEAEGIEIGAGPVDEEYAESLS 248

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             VEEL L+VRS NCL+ E I  +G+L+ R+E D+L + NFG KS+ E+K  L  +GL L
Sbjct: 249 TPVEELNLTVRSYNCLKREGIHTVGELVSRSEQDLLAIRNFGSKSIDEVKEKLTELGLAL 308

Query: 318 GMNLPDWPPESIEE 331
             + P + P +  E
Sbjct: 309 KDSAPGFDPLAAAE 322


>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 =  347 bits (890), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 133/320 (41%), Positives = 204/320 (63%), Gaps = 5/320 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E+ +P  IE   L   +      + EPL RGF  TLGN+LRRVL+SSL G A+T+V+ID
Sbjct: 2   MEIERP-KIETASL-SPDGRYGKFVVEPLERGFGTTLGNSLRRVLLSSLPGVAVTSVKID 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV+HE S+I+GV ED+T+I+LN+KGI  K+ G+S K V +   GP  + AG I+  +D+E
Sbjct: 60  GVVHEFSTIEGVREDVTEIVLNLKGIAAKIYGESPKTVRVEAVGPCELIAGSIKGGDDLE 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYSPIKKV 183
           +LNP+  I  L   A + MELT  KG GYVPA+ ++    E + I  + +D++Y+P+ K 
Sbjct: 120 ILNPEWHIATLGEGAKLVMELTFDKGRGYVPAERNKLALIEKNDISTLPVDSIYTPVLKA 179

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +YTV+  R GQ+ DYDKL + + TDG+   +++++LA+R+L + L +F+N  +   E + 
Sbjct: 180 NYTVDHTRVGQITDYDKLIIEVWTDGTCNAQEALSLAARVLTEHLNLFVNLCDETGETEI 239

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            ++        AL   +EEL+LSVRS NCL+   I  +GDLI ++E +M+++ N GRKSL
Sbjct: 240 MVDNDDQGREKALEMTIEELDLSVRSFNCLKRAGINTVGDLINKSEDEMMKVRNLGRKSL 299

Query: 304 VEIKGVLGTMGLFLGMNLPD 323
            E+   L ++G  L  +  +
Sbjct: 300 EEVMAKLDSLGFSLTKDDEN 319


>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 =  347 bits (890), Expect = 2e-93,   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|157100341|emb|CAP03336.1| RpoA protein [Vibrio aestuarianus]
          Length = 323

 Score =  347 bits (890), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 141/329 (42%), Positives = 214/329 (65%), Gaps = 11/329 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQIST---THAKVTLEPLERGFGHTLGNALRRILLSSMAGCAVT 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
            +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           N G+KSL EIK VL + GL LGM L +WP
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWP 323


>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 =  347 bits (890), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 128/318 (40%), Positives = 193/318 (60%), Gaps = 4/318 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVL
Sbjct: 5   QRPSLTEEVV----DEYRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TDIILNIK + +    D    + + K+GPG+VTA DI     +EV N
Sbjct: 61  HEFTTVPGVKEDVTDIILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLVLATLNGKGKLEMELTVERGRGYVSAVQNKQLGQEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNIDAEGIDMGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 AALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWPPE 327
           L  MGL L  + P + P 
Sbjct: 301 LAGMGLALKDSPPGFDPT 318


>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 =  347 bits (890), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 127/329 (38%), Positives = 193/329 (58%), Gaps = 7/329 (2%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V     E+R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGV 
Sbjct: 5   QRPTLSEDVV----SESRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVQ 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I GV ED+T++ILNIKG+ +    D    + + K+G GVVTA DI     +EV N
Sbjct: 61  HEFSTIPGVKEDVTEVILNIKGLVVSSEHDEPVVMYLRKQGAGVVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+    + MELTV +G GYV A  +++    IG I +D++YSP+  V+Y VE+
Sbjct: 121 PDLEIATLNDKGSIEMELTVERGRGYVSAALNKSAEQEIGRIPVDSIYSPVLAVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  S+   D++A A   L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDKLIVDVETKNSMAPRDAMASAGSTLVELFGLARELNVEAEGIDMGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +E+L+L+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+   
Sbjct: 241 AALAEDLALPIEDLDLTVRSYNCLKREGIHTVGELVSRSEADLLDIRNFGSKSIHEVADK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYED 338
           L  MGL L  + P +    I +   +Y++
Sbjct: 301 LRDMGLQLKDSPPGFDASVIAD---RYDE 326


>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 =  347 bits (890), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 125/331 (37%), Positives = 192/331 (58%), Gaps = 5/331 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V     E+R+  + EPL  GF +TLGN++RR L+SS+ GAA+T++++DGVL
Sbjct: 5   QRPTLTEEVV----GEHRSRFVIEPLEPGFGYTLGNSIRRTLLSSIPGAAVTSIKVDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED T +ILN+K + +    D    + + K+GPG VTA DI     +EV N
Sbjct: 61  HEFSTVAGVKEDATQLILNLKDLVVSSEHDEPVTMYLRKQGPGDVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+    + MEL V +G GYV A  +++ +  IG + +D++YSP+ KV+Y VE+
Sbjct: 121 PDLKIATLNEKGRLEMELVVERGRGYVSAIQNKSADAEIGRMPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  S+   D+VA A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDRLVVDVETKPSMLPRDAVASAGKTLVELFGLARELNVEAEGIDIGPSPVD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   VE+L+L+VRS NCL+ E I  +G+LI R+E D+L + NFG KS+ E+K  
Sbjct: 241 EQMAADLALPVEDLQLTVRSYNCLKREGIHTVGELISRSEQDLLDIRNFGSKSIDEVKLK 300

Query: 310 LGTMGLFLGMNLPDWP-PESIEELAKKYEDK 339
           L  MGL L  + P +    + E      ED+
Sbjct: 301 LAEMGLSLKDSPPGFDLRAAAEAYGDDAEDE 331


>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 =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 132/324 (40%), Positives = 208/324 (64%), Gaps = 7/324 (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 RKSLVEIKGVLGTMGLFLGMNLPD 323
           +KS  E++  L ++G  L  +  +
Sbjct: 295 KKSFEEVRAKLQSLGFDLASDDDN 318


>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 =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 123/334 (36%), Positives = 192/334 (57%), Gaps = 8/334 (2%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+T+IILN+K + +    D    + +     GVVT  +I+    +EV N
Sbjct: 61  HEFSTVPGVTEDVTEIILNLKNLVVSSENDEPVVMYLRADTAGVVTGANIEPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  +  L+    + +EL V +G GYV A  ++T ++ IG + ID++YSP+ KV+Y VE+
Sbjct: 121 PDLHVATLNDKGRLEIELVVERGRGYVSAVQNKTGDEEIGRMPIDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  SI   D++A A   L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDRLVVDVETKKSILPRDAIASAGSTLVELFGLARELNVEAEGIDIGPSPVD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +E+L  +VRS NCL+ E I  +G+LI R+E D+L + NFG KS+ E+K  
Sbjct: 241 EQLAADLALPIEDLNFTVRSYNCLKREGIHTVGELITRSEQDLLDIRNFGSKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWPPESI----EELAKKYEDK 339
           L  MGL L  +   + P ++    +E A   ED+
Sbjct: 301 LAEMGLALKDSPAGFDPSAVIADYDEDASFAEDE 334


>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 =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 122/318 (38%), Positives = 191/318 (60%), Gaps = 4/318 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E ++     E+R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLTEEVI----SEHRSRFSIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I GV ED+T+IILNIK + +    D    + + K+G G VT  DI     +EV N
Sbjct: 61  HEFSTIPGVKEDVTEIILNIKNLVVSSENDEPVVMYLRKQGAGEVTGADIVPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  +  L+    + +ELTV +G GYV A  +++ +  IG I ID++YSP+ KV+Y VE+
Sbjct: 121 PELHLATLNEKGKLEIELTVERGRGYVSANQNKSFDAEIGRIPIDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + +++  +I+  D++A A R L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDKLIVDVESKPAISPRDALASAGRTLVELFGLARELNVEAEGIEIGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +E+L+L++RS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 AALAADLALPIEDLQLTIRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSITEVKEK 300

Query: 310 LGTMGLFLGMNLPDWPPE 327
           L  +GL L  +  D+ P 
Sbjct: 301 LAELGLTLKDSPLDFDPS 318


>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 =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 129/318 (40%), Positives = 193/318 (60%), Gaps = 4/318 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVL
Sbjct: 5   QRPSLTEEVV----DEYRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TDIILNIK + +    D    + + K+GPG+VTA DI     +EV N
Sbjct: 61  HEFTTVPGVKEDVTDIILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD V+  L+    + MELTV +G GYV A  ++     IG I ID++YSP+ KV+Y VE+
Sbjct: 121 PDLVLATLNGKGKLEMELTVERGRGYVSAVQNKQLGQEIGRIPIDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNIDAEGIDMGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 AALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWPPE 327
           L  MGL L  + P + P 
Sbjct: 301 LAGMGLALKDSPPGFDPT 318


>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 =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 132/313 (42%), Positives = 203/313 (64%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE +    E+ +    + EPL RG+  TLGN+LRR+L+SSL G A  +V+I+G
Sbjct: 3   EIEKP-KIECVE-STEDGSYGRFVVEPLERGYGITLGNSLRRILLSSLPGVAANSVRIEG 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|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 =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 133/324 (41%), Positives = 208/324 (64%), Gaps = 7/324 (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 RKSLVEIKGVLGTMGLFLGMNLPD 323
           +KS  E++  L ++G  L  +  +
Sbjct: 295 KKSFEEVRAKLQSLGFDLASDDDN 318


>gi|308171334|gb|ADO15986.1| RpoA [Vibrio scophthalmi LMG 19158]
          Length = 321

 Score =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 140/326 (42%), Positives = 212/326 (65%), Gaps = 11/326 (3%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+
Sbjct: 2   SVTEFLKPRLVDIEQIST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVE 58

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    
Sbjct: 59  IEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDG 118

Query: 124 DIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSP 179
           D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP
Sbjct: 119 DVEITNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSP 178

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           + K++Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + + 
Sbjct: 179 VDKIAYSVDAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRV 238

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
             +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G
Sbjct: 239 PEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLG 295

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWP 325
           +KSL EIK VL + GL LGM L +WP
Sbjct: 296 KKSLTEIKDVLASRGLSLGMRLENWP 321


>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 =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 126/318 (39%), Positives = 194/318 (61%), Gaps = 4/318 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T++++DGVL
Sbjct: 5   QRPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRVDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV N
Sbjct: 61  HEFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLVLATLNGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNIDAEGIDMGPSPVD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L+  +EELEL+VRS NCL+ E +  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 AALAADLVMPIEELELTVRSYNCLKREGVHSVGELVARSEADLLDIRNFGAKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWPPE 327
           L  MGL L  + P + P 
Sbjct: 301 LAGMGLGLKDSPPGFDPT 318


>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 =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 125/325 (38%), Positives = 193/325 (59%), Gaps = 5/325 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +   W+    P+ +               +AEP  RGF  T+GN+LRR+L+SSL G+AIT
Sbjct: 1   MHIRWRGFELPSIVNCDAT-TLTSTYGKFVAEPFERGFGTTIGNSLRRILLSSLEGSAIT 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 KEDINVKSLPFNPALL----KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
                  S   + AL       + 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|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 =  346 bits (889), Expect = 2e-93,   Method: Composition-based stats.
 Identities = 132/308 (42%), Positives = 188/308 (61%), Gaps = 3/308 (0%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V   EE+ R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+IDGV 
Sbjct: 5   QRPTLSEEVV---EEDRRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVRIDGVP 61

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE  +I GV ED+T IILNIK I L    D    + + K GPGVVTAGDI     +E+ N
Sbjct: 62  HEFRTIAGVKEDVTQIILNIKEIVLSSENDEPVVMYLRKSGPGVVTAGDITPPAGVEIHN 121

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD VI NL+    + +ELTV +G GYV A  ++  N  I  I +D++YSP+KKVSY VE+
Sbjct: 122 PDLVIANLNEKGKLEIELTVERGRGYVSANQNKDPNGEISRIPVDSIYSPVKKVSYAVEA 181

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  SIT  D++A A + L +  G+        + ++   +   
Sbjct: 182 TRVEQRTDFDRLVVDVETKASITPRDALASAGKTLVELFGLARELNVEAEGIEVGPSPMD 241

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   ++EL+L  RS+N L+ E I  +G+L+ R+EAD+L + NFG KS+ EIK  
Sbjct: 242 QALQQDLALMIDELDLQARSSNALKREGIHTVGELVARSEADLLDIRNFGAKSISEIKEK 301

Query: 310 LGTMGLFL 317
           L  +GL L
Sbjct: 302 LAELGLSL 309


>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 =  346 bits (888), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 126/318 (39%), Positives = 192/318 (60%), Gaps = 4/318 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV N
Sbjct: 61  HEFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD V+  L+    + MELTV +G GYV A  ++     IG + +D++YSP+ KV+Y VE+
Sbjct: 121 PDLVLATLNAKGKLEMELTVERGRGYVSAVQNKQAGQEIGRVPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNVDAEGIDMGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 AALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWPPE 327
           L  M L L  + P + P 
Sbjct: 301 LAGMSLALKDSPPGFDPT 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 =  346 bits (888), Expect = 3e-93,   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-IEIAEI-SADRTYGKFVVEPLERGYGTTIGNSLRRIMLSSLPGAAVTNVKIEN 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|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 =  346 bits (888), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 128/310 (41%), Positives = 202/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  ++ I L  E+      + EPL RG+  T+GNALRR+L+SSL G A+ AV+I+G
Sbjct: 3   EIEKP-KVDIIEL-SEDFRYGKFVVEPLERGYGITIGNALRRILLSSLPGVAVNAVKIEG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 QKLDELGLGL 310


>gi|308171330|gb|ADO15984.1| RpoA [Vibrio brasiliensis LMG 20546]
          Length = 318

 Score =  346 bits (888), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 142/324 (43%), Positives = 212/324 (65%), Gaps = 11/324 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+
Sbjct: 1   TEFLKPRLVD---IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIE 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
           +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+K
Sbjct: 238 EKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKK 294

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWP 325
           SL EIK VL + GL LGM L +WP
Sbjct: 295 SLTEIKDVLASRGLSLGMRLENWP 318


>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 =  346 bits (888), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 164/348 (47%), Positives = 233/348 (66%), Gaps = 12/348 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           I  +W  L +P++I+ +  G    +   +I EPL  GFA TLGNALRRV+MSSLRG A+ 
Sbjct: 21  ISDHWDRLTRPSSIKVVGDGDVSRS-AELIVEPLESGFALTLGNALRRVMMSSLRGFAVY 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|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 =  346 bits (888), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 134/310 (43%), Positives = 208/310 (67%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I    E       + EPL RG+  TLGNALRR+L+SSL GAA T+V+IDG
Sbjct: 3   EIEKP-IIECIEA-NENGTYGKYVIEPLERGYGITLGNALRRILLSSLPGAAPTSVKIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 RKLKELGLGL 310


>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 =  346 bits (888), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 128/318 (40%), Positives = 186/318 (58%), Gaps = 4/318 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E       EE R+  + EPL  GF +TLGN+LRR L+SS+ GA++T+++IDGVL
Sbjct: 5   QRPTLSE----ESVEEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGASVTSIKIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I+GV ED+T+IILN+KG+ +    D    + + K G G VTA DI     +EV N
Sbjct: 61  HEFSTIEGVKEDVTEIILNLKGLVVSSEHDEPVTMYLRKSGAGDVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L     + +EL V +G GYV A  ++   + IG I +D++YSP+ KVSY VE+
Sbjct: 121 PDLKIATLSDKGKIELELVVERGRGYVSAVQNKGAENEIGRIPVDSIYSPVLKVSYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SI   D++A A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDKLVIDVETKPSIAPRDAIASAGKTLVELFGLARELNVDAEGIDIGPSPVD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   VE+L+L+VRS NCL+ E I  +G+LI R+E D+L + NFG KS+ E+K  
Sbjct: 241 EQLAADLALPVEDLQLTVRSYNCLKREGIHTVGELISRSEQDLLDIRNFGAKSIDEVKLK 300

Query: 310 LGTMGLFLGMNLPDWPPE 327
           L  MGL L  + P + P 
Sbjct: 301 LHEMGLSLKDSAPGFDPS 318


>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 =  346 bits (888), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 137/310 (44%), Positives = 198/310 (63%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP   +      EE++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDG
Sbjct: 3   EFEKPRIAKI----DEEKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 AKLHDLGLGL 308


>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 =  346 bits (887), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 138/312 (44%), Positives = 205/312 (65%), Gaps = 6/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +     +E ++    + EPL RG+  TLGN+LRRVL++SL GAAIT++QIDG
Sbjct: 3   EFEKPNIHKV----EETDSYGKFVVEPLERGYGTTLGNSLRRVLLASLPGAAITSIQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K ++LK+  +  K + I  +GP  VTAGDIQ   ++EV
Sbjct: 59  VLHEFSTVEGVTEDVTQIILNLKKVSLKLDSEEQKDLEIDVKGPAEVTAGDIQGDGEVEV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSY 185
           LNPD  I  +   A + +++T  KG GY+ A     R ++  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 IKGVLGTMGLFL 317
           IK  L  +G+  
Sbjct: 299 IKLKLNDLGVSF 310


>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 =  346 bits (887), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 123/315 (39%), Positives = 193/315 (61%), Gaps = 4/315 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV N
Sbjct: 61  HEFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLVLATLNGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNIDAEGIDMGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L+  +E+L+L+VRS NCL+ E +  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 AALAADLVMPIEDLDLTVRSYNCLKREGVHSVGELVARSEADLLDIRNFGAKSIDEVKEK 300

Query: 310 LGTMGLFLGMNLPDW 324
           L  +GL L  + P +
Sbjct: 301 LAGLGLGLKDSPPGF 315


>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 =  346 bits (887), Expect = 3e-93,   Method: Composition-based stats.
 Identities = 146/335 (43%), Positives = 215/335 (64%), Gaps = 11/335 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q + +E +KP+ I      +  +    +I EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVKEFLKPSLIS----EKISQTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVT 56

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG-DSHKRVTIFKRGPGVVTAGDIQ 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 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           N G+KSL EIK VL   GL LGM L +WPP SI +
Sbjct: 295 NLGKKSLTEIKDVLAVHGLSLGMRLENWPPASIAD 329


>gi|224713514|gb|ACN62064.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus minor]
          Length = 309

 Score =  346 bits (887), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 140/312 (44%), Positives = 209/312 (66%), Gaps = 7/312 (2%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
               + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S
Sbjct: 1   KPHLVNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYS 60

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           S +GV ED+ +++LN+KG+ +K+       +T+ K G G VTAGDI    D+E++NPDHV
Sbjct: 61  SKEGVQEDILEVLLNLKGLAVKVQSKDDVVLTLNKSGIGPVTAGDITHDGDVEIVNPDHV 120

Query: 134 ICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVES 189
           IC+L D +A + M + V +G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+
Sbjct: 121 ICHLTDKNASINMRIRVQRGRGYVPASARIHAQDDDRPIGRLLVDARFSPVDRIAYNVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  + 
Sbjct: 181 ARVEQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEK 237

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
             F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK V
Sbjct: 238 PEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDV 297

Query: 310 LGTMGLFLGMNL 321
           L + GL LGM L
Sbjct: 298 LASRGLSLGMRL 309


>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 =  345 bits (886), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 141/334 (42%), 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   MQGSEIEFLKPRLVNIEQI---SPSHAKITLEPLERGFGHTLGNALRRILLSSMQGYAVT 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-DVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALY 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 RQPELKEEK---PEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL +  L LGM L +WPP ++ +
Sbjct: 295 LGKKSLTEIKDVLASRALSLGMRLENWPPANLSD 328


>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 =  345 bits (886), Expect = 4e-93,   Method: Composition-based stats.
 Identities = 135/310 (43%), Positives = 197/310 (63%), Gaps = 2/310 (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 GVLGTMGLFL 317
             L  MGL L
Sbjct: 301 HKLAEMGLSL 310


>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 =  345 bits (886), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 135/311 (43%), Positives = 205/311 (65%), Gaps = 5/311 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +     +E +N    + EPL RG+  TLGN+LRRV+++SL GAAIT++ IDG
Sbjct: 3   EFEKPNIHKV----EETDNYGKFVVEPLERGYGTTLGNSLRRVMLASLPGAAITSINIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K ++L++  +  K + +  +GP  VTAGDIQ   D+ V
Sbjct: 59  VLHEFSTVEGVTEDVTQIILNLKKVSLRIDSEDQKNLELDVKGPAEVTAGDIQGDGDVTV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT-ENDPIGLITIDALYSPIKKVSYT 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|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 =  345 bits (886), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 126/318 (39%), Positives = 193/318 (60%), Gaps = 4/318 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 4   QRPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 59

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV N
Sbjct: 60  HEFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLRKQGPGLVTAADIAPPAGVEVHN 119

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 120 PDLVLATLNGKGKLEMELTVERGRGYVSAVQNKQVGQEIGRIPVDSIYSPVLKVTYKVEA 179

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +   
Sbjct: 180 TRVEQRTDFDKLIVDVETKQAMRPRDAMASAGKTLVELFGLARELNIGAEGIDMGPSPTD 239

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EELEL+VRS NCL+ E +  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 240 AALAADLALPIEELELTVRSYNCLKREGVHSVGELLARSEADLLDIRNFGAKSIDEVKAK 299

Query: 310 LGTMGLFLGMNLPDWPPE 327
           L  +GL L  + P + P 
Sbjct: 300 LAGLGLALKDSPPGFAPT 317


>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 =  345 bits (886), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 147/324 (45%), Positives = 221/324 (68%), 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 EVKEDINV-KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           EVK+D    ++      L 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|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 =  345 bits (886), Expect = 5e-93,   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-IEIAEI-SDDKKYGKFVVEPLERGYGITLGNSLRRIMLSSMPGVAVTQIKIEG 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 EVLNPDHVICNLD--VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 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|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 =  345 bits (886), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 136/310 (43%), Positives = 199/310 (64%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP   +      E+++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDG
Sbjct: 3   EFEKPRIAKI----DEDKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 VKLHDLGLGL 308


>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 =  345 bits (886), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 127/315 (40%), Positives = 191/315 (60%), Gaps = 3/315 (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    G I +D +YSP+ +VSY VE+ R  Q  D+DKL +
Sbjct: 135 DMELVVERGRGYVPAAPTSGEI---GRIPVDQIYSPVLQVSYKVEATRVEQRTDFDKLII 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 WPPESIEELAKKYED 338
           + P  +E    +  D
Sbjct: 312 FDPTQLEGYDAETGD 326


>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 =  345 bits (886), Expect = 5e-93,   Method: Composition-based stats.
 Identities = 138/337 (40%), Positives = 211/337 (62%), Gaps = 7/337 (2%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           ++  NW+E+I P  +               + EPL +G+  T+GN+LRR+++SSL GAAI
Sbjct: 6   LVYMNWREIIMPEKVAV----TTTSTYGKFVCEPLEKGYGITIGNSLRRIILSSLYGAAI 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 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           FGRKSL EIK VL +M L LGM+L  + P   +++ +
Sbjct: 302 FGRKSLNEIKEVLTSMDLSLGMDLEGFEPPEEDQIKE 338


>gi|308171336|gb|ADO15987.1| RpoA [Vibrio sinaloensis DSM 21326]
          Length = 321

 Score =  345 bits (885), Expect = 6e-93,   Method: Composition-based stats.
 Identities = 141/325 (43%), Positives = 212/325 (65%), Gaps = 11/325 (3%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           +  E +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+
Sbjct: 3   SVTEFLKPRLVD---IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVE 59

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    
Sbjct: 60  IEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDG 119

Query: 124 DIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSP 179
           D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP
Sbjct: 120 DVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSP 179

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           + K++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + + 
Sbjct: 180 VDKIAYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRV 239

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
             +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G
Sbjct: 240 PEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLG 296

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDW 324
           +KSL EIK VL + GL LGM L +W
Sbjct: 297 KKSLTEIKDVLASRGLSLGMRLENW 321


>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 =  345 bits (885), Expect = 6e-93,   Method: Composition-based stats.
 Identities = 133/313 (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 ++V+IDG
Sbjct: 3   EIEKP-IIECIEA-SEDGTYGKYVVEPLERGYGITLGNALRRILLSSLPGVATSSVKIDG 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|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 =  345 bits (884), Expect = 7e-93,   Method: Composition-based stats.
 Identities = 131/310 (42%), Positives = 208/310 (67%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  +E   +  ++      + EPL RG+  TLGN+LRR+++SSL GAA+T+V+I+G
Sbjct: 3   EMEKP-KVEVFEI-SDDSTYGKFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVTSVKIEG 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|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 =  345 bits (884), Expect = 8e-93,   Method: Composition-based stats.
 Identities = 120/330 (36%), Positives = 192/330 (58%), Gaps = 9/330 (2%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E +V      NR+    EPL  GF +T+GN+LRR L+SS+ GAA+T+V+IDGVL
Sbjct: 5   QRPTLTEEVV----APNRSRFTIEPLEPGFGYTMGNSLRRTLLSSIPGAAVTSVRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+T+IILNIK +++    D      + K+G G +TAGDI+    +E+ N
Sbjct: 61  HEFSTVPGVTEDVTEIILNIKKLSISSENDEPVVAYLRKQGEGELTAGDIEVPAGVEIHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  +  L+  A    EL + +G GYV A  ++  +  IG I +D++YSP+ KV+++V +
Sbjct: 121 PELHLATLNASANFNAELVIERGRGYVTAAQNKVGDGEIGRIPVDSIYSPVLKVTFSVNA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D L++ ++T  +I   D+VA A   L +  G+        + ++   +   
Sbjct: 181 TRVEQRTDFDSLTLDVETKEAIAPRDAVASAGSTLVELFGLARELNIAAEGIEVGPSPAD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +E+L +SVRS NCL+ E I  +G+L+ R+EAD++ + NFG KS+ E+K  
Sbjct: 241 ESMAADLALPIEDLNMSVRSYNCLKREGIHTVGELVTRSEADLMDIRNFGAKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           L  +GL L  + P + P      A+  +D+
Sbjct: 301 LIELGLALKDSPPGFEPA-----ARPLDDE 325


>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 =  345 bits (884), Expect = 8e-93,   Method: Composition-based stats.
 Identities = 139/310 (44%), Positives = 200/310 (64%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP   +      EE++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDG
Sbjct: 3   EFEKPRIAKI----DEEKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 VKLHDLGLGL 308


>gi|224713516|gb|ACN62065.1| DNA-directed RNA polymerase subunit alpha [Actinobacillus minor]
          Length = 307

 Score =  345 bits (884), Expect = 8e-93,   Method: Composition-based stats.
 Identities = 140/310 (45%), Positives = 208/310 (67%), Gaps = 7/310 (2%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
               + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE S
Sbjct: 1   KPHLVNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYS 60

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           S +GV ED+ +++LN+KG+ +K+       +T+ K G G VTAGDI    D+E++NPDHV
Sbjct: 61  SKEGVQEDILEVLLNLKGLAVKVQSKDDVVLTLNKSGIGPVTAGDITHDGDVEIVNPDHV 120

Query: 134 ICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVES 189
           IC+L D +A + M + V +G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+
Sbjct: 121 ICHLTDKNASINMRIRVQRGRGYVPASARVHTQDDDRPIGRLLVDARFSPVDRIAYNVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++ V ++     
Sbjct: 181 ARVEQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQPVVKEEK--- 237

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
             F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK V
Sbjct: 238 PEFDPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDV 297

Query: 310 LGTMGLFLGM 319
           L + GL LGM
Sbjct: 298 LASRGLSLGM 307


>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 =  344 bits (883), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 136/310 (43%), Positives = 199/310 (64%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E  +    + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDG
Sbjct: 3   EFEKPR----IEKIDENRDYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 LKLHDLGLGL 308


>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 =  344 bits (883), Expect = 1e-92,   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|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 =  344 bits (883), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 130/310 (41%), Positives = 201/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  I+ +    +         EPL RG+  TLGNALRR+L+SSL G A T+V+ID 
Sbjct: 3   EIEKP-VIQCVE-SNDNGTYGKFEIEPLERGYGITLGNALRRILLSSLPGVAPTSVKIDS 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 RKLNELGLNL 310


>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 =  344 bits (883), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 128/310 (41%), Positives = 200/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  ++ + L  E+      + EPL RG+  T+GNALRR+L+SSL G A+ A++IDG
Sbjct: 3   EIEKP-KVDIVEL-SEDYRYGKFVIEPLERGYGITIGNALRRILLSSLPGVAVNAIKIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 QKLEELGLGL 310


>gi|239933876|ref|ZP_04690829.1| DNA-directed RNA polymerase subunit alpha [Streptomyces ghanaensis
           ATCC 14672]
          Length = 329

 Score =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 123/304 (40%), Positives = 187/304 (61%)

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 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            ++T  ++   D++A A + L +  G+        + +    +         L   +EEL
Sbjct: 187 DVETKQAMRPRDAMASAGKTLVELFGLARELNIGAEGIDMGPSPTDAALAADLALPIEEL 246

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           EL+VRS NCL+ E +  +G+L+ R+EAD+L + NFG KS+ E+K  L  +GL L  + P 
Sbjct: 247 ELTVRSYNCLKREGVHSVGELLARSEADLLDIRNFGAKSIDEVKAKLAGLGLALKDSPPG 306

Query: 324 WPPE 327
           + P 
Sbjct: 307 FAPT 310


>gi|157100339|emb|CAP03335.1| RpoA protein [Vibrio aestuarianus]
          Length = 323

 Score =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 140/329 (42%), Positives = 213/329 (64%), Gaps = 11/329 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGN LRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQIST---THAKVTLEPLERGFGHTLGNXLRRILLSSMXGCAVT 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
            +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 VRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           N G+KSL EIK VL + GL LGM L +WP
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGMRLENWP 323


>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 =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 122/321 (38%), Positives = 188/321 (58%), Gaps = 3/321 (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     +    G I ID +YSP+ KVSY VE+ R  Q  D
Sbjct: 129 NDTAKLDMELVVERGRGYVPAAPTSGDI---GRIPIDQIYSPVLKVSYKVEATRVEQRTD 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 GMNLPDWPPESIEELAKKYED 338
                D+ P  +E    +  D
Sbjct: 306 KDTPEDFDPTQLEGYDAETGD 326


>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 =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 135/310 (43%), Positives = 199/310 (64%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP   +      E+++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDG
Sbjct: 3   EFEKPRIAKI----DEDKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 VKLHDLGLGL 308


>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 =  344 bits (882), Expect = 1e-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|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 =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 162/346 (46%), 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  ISDHWDKLTRPSSIKVVGDGDLSRS-AELIVEPLESGFALTLGNALRRVMMSSLRGFAVY 79

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            ++++GV HE++S+ GV ED+ D++LN+  + +K+     + + +  +GPG +TA  I  
Sbjct: 80  GIEVEGVSHELTSLSGVREDVADLVLNLSMLRVKLLTSESRVLRLVAKGPGEITAAAIGD 139

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR-------TENDPIGLITID 174
                VLN D  IC L  D    M++ V+ G GYVPA  +R       T     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 EEPKKEV--KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           EE + E   K D    +LP++  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|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 = 129/310 (41%), Positives = 201/310 (64%), Gaps = 4/310 (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 GVLGTMGLFL 317
             L  +G  L
Sbjct: 299 QKLEELGFSL 308


>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 =  343 bits (881), Expect = 2e-92,   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-KIEAVEL-SEDGTYGKFVVEPLERGYGTTLGNSLRRILLNSLPGSAVTSVQFNN 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|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 =  343 bits (881), Expect = 2e-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  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|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 =  343 bits (880), Expect = 2e-92,   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|73913591|gb|AAZ91712.1| RNA polymerase alpha subunit [Corynebacterium stationis]
          Length = 334

 Score =  343 bits (880), Expect = 2e-92,   Method: Composition-based stats.
 Identities = 122/321 (38%), Positives = 188/321 (58%), Gaps = 3/321 (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     +    G I ID +YSP+ KVSY VE+ R  Q  D
Sbjct: 129 NDTAKLDMELVVERGRGYVPAAPTSGDI---GRIPIDQIYSPVLKVSYKVEATRVEQRTD 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 GMNLPDWPPESIEELAKKYED 338
                D+ P  +E    +  D
Sbjct: 306 KDTPEDFDPTQLEGYDAETGD 326


>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 =  343 bits (879), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 132/310 (42%), Positives = 206/310 (66%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I    E+      + EPL RG+  TLGNALRR+L+SSL G A T+V+IDG
Sbjct: 3   EIEKP-IIECIEA-NEDGTYGKYVVEPLERGYGITLGNALRRILLSSLPGVATTSVKIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 RKLKELGLAL 310


>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 =  343 bits (879), Expect = 3e-92,   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|257471550|ref|ZP_05635549.1| DNA-directed RNA polymerase subunit alpha [Buchnera aphidicola str.
           LSR1 (Acyrthosiphon pisum)]
          Length = 324

 Score =  343 bits (879), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 143/327 (43%), Positives = 213/327 (65%), Gaps = 10/327 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            + ++P  ++   +       T +  EPL RGF HTLGNALRR+L+SS+ G A+T V+ID
Sbjct: 1   MDFLRPRLVDIEQI---SATHTKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEID 57

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GVLHE S+ +GV ED+ +I+LN+K + +K+ G     +T+ K G G +TA DI    D+E
Sbjct: 58  GVLHEYSTKEGVQEDVLEILLNLKALAVKVYGKDETLLTLHKSGIGSITAADIIHDGDVE 117

Query: 127 VLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKK 182
           ++ P HVIC+L D +A ++M + V +G GY+PA    H   +  PIG + +DA YSPI +
Sbjct: 118 IIKPQHVICHLTDENASIKMRIKVQRGRGYIPASSRVHLEEDARPIGCLLVDACYSPINR 177

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           +SY VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++   
Sbjct: 178 ISYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDIRE--- 234

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
            +   +   F P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KS
Sbjct: 235 PEFKEEKPEFEPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKS 294

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESI 329
           L EIK VL +  L LGM L +WPP SI
Sbjct: 295 LTEIKDVLASRSLSLGMRLENWPPSSI 321


>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 =  343 bits (879), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 126/315 (40%), Positives = 190/315 (60%), Gaps = 3/315 (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    G I +D +YSP+ KVSY VE+ R  Q  D+DKL++
Sbjct: 135 DIELVVERGRGYVPAAPTSGEI---GRIPVDQIYSPVLKVSYKVEATRVEQRTDFDKLTI 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 WPPESIEELAKKYED 338
           + P  +E    +  D
Sbjct: 312 FDPTQLEGYDAETGD 326


>gi|297163220|gb|ADI12932.1| DNA-directed RNA polymerase subunit alpha [Streptomyces
           bingchenggensis BCW-1]
          Length = 337

 Score =  343 bits (879), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 121/317 (38%), Positives = 189/317 (59%), Gaps = 4/317 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P+  E +V    +  R+  + EPL  GF +TLGN+LRR L+SS+  AA+T+++IDGVL
Sbjct: 5   QRPSLTEEVV----DAYRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPAAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TD+ILN+K + +    D    + + K+GPG+ TA DI     +EV N
Sbjct: 61  HEFTTVPGVREDITDLILNLKQLVVSSEHDEPVVMYLRKQGPGLATAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD V+  L+    + +ELTV +G GYV A  +  +   IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLVLATLNAKGKLEIELTVERGRGYVSAVQNTQQGQEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  ++   D++A A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDKLIVDVETKPAMHPRDAIASAGKTLVELFGLARGLNIDAEGIDIGPSPTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EELEL+VRS NCL+ E +  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 241 TALASDLALPIEELELTVRSYNCLKREGVHSVGELVARSEADLLDIRNFGAKSIDEVKAK 300

Query: 310 LGTMGLFLGMNLPDWPP 326
           L  MGL    + P + P
Sbjct: 301 LAGMGLAFKDSPPGFDP 317


>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 =  343 bits (879), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 127/315 (40%), Positives = 190/315 (60%), Gaps = 3/315 (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    G I ID +YSP+ KVSY VE+ R  Q  D+DKL++
Sbjct: 135 DIELVVERGRGYVPAAATSGEI---GRIPIDQIYSPVLKVSYKVEATRVEQRTDFDKLTI 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 WPPESIEELAKKYED 338
           + P  +E    +  D
Sbjct: 312 FDPTQLEGYDAETGD 326


>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 =  343 bits (879), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 146/332 (43%), Positives = 219/332 (65%), Gaps = 7/332 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            +LI P +I      +       ++ EPL RG+  T+GN+LRR+L+SSL GAA+T+V +D
Sbjct: 1   MQLINPRHISIE--EKVPGRAAKIVFEPLERGYGTTIGNSLRRMLLSSLPGAAVTSVLMD 58

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           GV HE  SIKGV ED+ DIIL++K ++L+M GD    +++  +G  +VTA DI+    + 
Sbjct: 59  GVAHEYDSIKGVREDVMDIILSLKELDLRMEGDEAATISLEIKGSAIVTAADIKCPAGLS 118

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           VLNP+ ++ +L+ DA +++E  V KG GY PA     +   +G + +DA YSPI++VS  
Sbjct: 119 VLNPELILAHLNDDAHLKIEAVVEKGRGYEPATDREVDERAVGSLLVDASYSPIRRVSTR 178

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+AR GQ  +YDKL M I+T+GS++ E+++  A++IL+ QL +F++FE      +    
Sbjct: 179 VEAARVGQRTNYDKLIMEIETNGSLSPEEALNSAAKILEAQLAVFVDFENVSIVSE--PE 236

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
                 +  L++ +E L+LSVRS NCL+ +++  +GDL+QR+E +MLR  NFGRKSL EI
Sbjct: 237 GPDDTLDNLLIQPIEHLDLSVRSMNCLKSDDVFRVGDLVQRSEQEMLRTPNFGRKSLNEI 296

Query: 307 KGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           K VL  MGL LGM+LP+WPP   +E A+  ED
Sbjct: 297 KEVLENMGLELGMDLPNWPP---QEDAEALED 325


>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 =  343 bits (879), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 133/313 (42%), Positives = 203/313 (64%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP   +      E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T+++IDG
Sbjct: 3   EFEKPTITKI----DENKDYGRFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSIKIDG 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|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 =  342 bits (878), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 136/312 (43%), Positives = 201/312 (64%), Gaps = 6/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +     +E +N    + EPL RG+  TLGN+LRRV+++SL GAAIT++QIDG
Sbjct: 3   EFEKPNIHKV----EETDNYGKFVVEPLERGYGTTLGNSLRRVMLASLPGAAITSIQIDG 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 LNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSY 185
           LN D  I  +   A + +++T  KG GY  A     R 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|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 =  342 bits (878), Expect = 3e-92,   Method: Composition-based stats.
 Identities = 136/310 (43%), Positives = 198/310 (63%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E  +    + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDG
Sbjct: 3   EFEKPR----IEKIDENRDYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 LKLHDLGLGL 308


>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 =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 123/314 (39%), Positives = 185/314 (58%), 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 LNDDGRLNMELVVERGRGYVPAAM-NNDVAEIGRIPVDQIYSPVLKVSYKVEATRVEQRT 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|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 =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 128/328 (39%), Positives = 196/328 (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 ----KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 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|1524340|emb|CAA63080.1| RNA polymerase alpha subunit [Streptomyces coelicolor A3(2)]
          Length = 339

 Score =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 127/318 (39%), Positives = 192/318 (60%), Gaps = 5/318 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P+  E +V    +E R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPSLTEEVV----DEFRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE +++ GV ED+TD+ILNIK + +    D    + + K+GPG+VTA DI     +EV N
Sbjct: 61  HEFTTVPGVKEDVTDLILNIKQLVVSSEHDEPVVMYLSKQGPGLVTAADIAPPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD V+  L+    + MELTV +G GYV A  ++     IG I +D++YSP+ KV+Y VE+
Sbjct: 121 PDLVLATLNGKGKLEMELTVERGRGYVSAVQNKEVGQEIGRIPVDSIYSPVLKVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  ++    ++A A + L +  G+        + +    +   
Sbjct: 181 TRVEQRTDFDKLIVDVETKQAMRPR-AMASAGKTLVELFGLARELNIDAEGIDMGPSPTD 239

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EELEL+VRS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ E+K  
Sbjct: 240 AALAADLALPIEELELTVRSYNCLKREGIHSVGELVARSEADLLDIRNFGAKSIDEVKAK 299

Query: 310 LGTMGLFLGMNLPDWPPE 327
           L  MGL L  + P + P 
Sbjct: 300 LAGMGLALKDSPPGFDPT 317


>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 =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 133/313 (42%), Positives = 203/313 (64%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP   +      E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T+++IDG
Sbjct: 3   EFEKPTITKI----DENKDYGRFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSIKIDG 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|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 =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 140/315 (44%), Positives = 193/315 (61%), Gaps = 7/315 (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 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV-----K 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 LVEIKGVLGTMGLFL 317
           L EIK  L  MGL  
Sbjct: 301 LEEIKKKLEDMGLHF 315


>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 =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 133/313 (42%), Positives = 203/313 (64%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP   +      E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T+++IDG
Sbjct: 3   EFEKPTITKI----DENKDYGRFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSIKIDG 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|319442995|ref|ZP_07992151.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           variabile DSM 44702]
          Length = 337

 Score =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 123/313 (39%), Positives = 180/313 (57%), Gaps = 3/313 (0%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +        R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++I+GVLHE ++I G
Sbjct: 9   LTEEYISPARSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIEGVLHEFTTIPG 68

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED++DIILNIK + +    D    + I K G G VT  D+     +EV NPD  I  L
Sbjct: 69  VKEDVSDIILNIKALVISSDSDEPVTMYIRKEGLGEVTGADVVVPAGVEVHNPDLHIATL 128

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           +    + +EL V +G GYVPA     E    G I +D +YSP+ KVSY VE+ R  Q  D
Sbjct: 129 NEQGKLDIELVVERGRGYVPAAATTGEI---GRIPVDQIYSPVLKVSYKVEATRVEQRTD 185

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL + ++T  SIT  D++A A   L +  G+        + ++   + +      A  
Sbjct: 186 FDKLVLDVETKNSITARDAIASAGGTLVELFGLARELNTEAEGIEIGPSPQETEHIAAYS 245

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +E+L+ SVRS NCL+ E+I  +G+L  RTE+D+L + NFG+KS+ E+K  L  +GL L
Sbjct: 246 LPIEDLDFSVRSYNCLKREDIHTVGELAARTESDLLDIRNFGQKSINEVKVKLAELGLGL 305

Query: 318 GMNLPDWPPESIE 330
                 +   SIE
Sbjct: 306 KDAPEGFDINSIE 318


>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 =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 127/321 (39%), Positives = 204/321 (63%), Gaps = 6/321 (1%)

Query: 9   LIKPNNIEYIVLG----QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           L+    IE   +     +        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 LVEIKGVLGTMGLFLGMNLPD 323
             E+K  L ++G  L     +
Sbjct: 306 FDEVKEKLHSLGYELNSEEDN 326


>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 =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 128/310 (41%), Positives = 200/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  ++ + L  E+      + EPL RG+  T+GNALRR+L+SSL G A+ A++IDG
Sbjct: 3   EIEKP-KVDIVEL-SEDYRYGKFVIEPLERGYGITIGNALRRILLSSLPGVAVNAIKIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 QKLEELGLGL 310


>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 =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 135/310 (43%), Positives = 199/310 (64%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP   +      E+++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDG
Sbjct: 3   EFEKPRIAKI----DEDKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 VKLHDLGLGL 308


>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 =  342 bits (878), Expect = 4e-92,   Method: Composition-based stats.
 Identities = 141/312 (45%), Positives = 192/312 (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 LNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSY 185
           LNPD  IC +         LT   G GY  A     R  + 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|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 =  342 bits (877), Expect = 5e-92,   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+  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 GVLGTMGLFL 317
             L  + L L
Sbjct: 301 HKLEELQLNL 310


>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 =  342 bits (877), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 133/330 (40%), Positives = 207/330 (62%), Gaps = 8/330 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  N  E + PN I    +    E    +  EPL RGF HTLGNALRR+L+SSL GAA+ 
Sbjct: 1   MMLNATEFLTPNAINVDTV---NETIAKVTLEPLERGFGHTLGNALRRILLSSLPGAAVI 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             +IDGV HE S+++G+ ED+ D++LN+KG+ + +   +   +T+ K+GPG +TA DI  
Sbjct: 58  EAEIDGVDHEYSTLEGLQEDVLDLLLNLKGLAITLHDQNEVFLTLDKQGPGTITAADITL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL--ITIDALYSP 179
            ++++++NP+ V+  L     ++M L V  G GY PA   R + D   +  + +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 VLRVAYQVENARVEQRTDLDRLIIELETNGTIDPEEAIRKAATILQQQISIFVDLEAEEA 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
                        +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QR+E ++L+  N G
Sbjct: 238 PEPVKEK---EEVDPVLLRPVDDLELTVRSANCLKAENIYYIGDLVQRSETELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL +  L LGM L +WPP  +
Sbjct: 295 KKSLTEIKDVLASKDLELGMRLDNWPPADL 324


>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 =  342 bits (877), Expect = 5e-92,   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|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 =  342 bits (877), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 143/331 (43%), Positives = 216/331 (65%), Gaps = 9/331 (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 APVEVEEK---PEFDPILLRPVNDLELTVRSANCLKAESIYYIGDLVQRTEVELLKMPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           GRKSL EIK  L + GL+LGM L +WPP S+
Sbjct: 295 GRKSLTEIKDDLVSRGLYLGMRLENWPPASL 325


>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 =  342 bits (877), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 141/312 (45%), 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 LNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSY 185
           LNPD  IC +         LT   G GY  A     R  + 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|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 =  342 bits (877), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 126/315 (40%), Positives = 189/315 (60%), Gaps = 3/315 (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    G I +D +YSP+ KVSY VE+ R  Q  D+DKL +
Sbjct: 135 EMELVVERGRGYVPAAATSGEI---GRIPVDQIYSPVLKVSYKVEATRVEQRTDFDKLII 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 WPPESIEELAKKYED 338
           + P  +E    +  D
Sbjct: 312 FDPTQLEGYDAETGD 326


>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 =  342 bits (877), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 136/310 (43%), Positives = 199/310 (64%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E  +    + EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDG
Sbjct: 3   EFEKPR----IEKIDENRDYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 LNLHDLGLGL 308


>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 =  342 bits (877), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 138/310 (44%), Positives = 199/310 (64%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP   +      EE++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDG
Sbjct: 3   EFEKPRIAKI----DEEKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDG 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|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 =  342 bits (877), Expect = 5e-92,   Method: Composition-based stats.
 Identities = 126/312 (40%), Positives = 197/312 (63%), Gaps = 4/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP       +   +      + EPL RGF  TLGN+LRRVL+SSL G A+T+++IDG
Sbjct: 3   EIEKPRI--DTEVLSADGTYGKFVVEPLERGFGTTLGNSLRRVLLSSLPGVAVTSIKIDG 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 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSY 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 IKGVLGTMGLFL 317
           +   L ++G  L
Sbjct: 301 VVYKLNSLGFSL 312


>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 =  342 bits (877), Expect = 5e-92,   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   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 NETAKIEIELIVERGRGYVPATVTATGG-EIGRIPVDQIYSPVLKVSYKVEATRVEQRTD 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|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 =  341 bits (876), Expect = 6e-92,   Method: Composition-based stats.
 Identities = 133/312 (42%), Positives = 196/312 (62%), Gaps = 6/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E   P     I+L +E+ N    + EPL RG+  TLGN+LRRVL+SSL GAAI +VQIDG
Sbjct: 20  EFENPK----IMLVEEDSNYGKFVVEPLERGYGTTLGNSLRRVLLSSLPGAAINSVQIDG 75

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K +++++  D  K + +   GP  VTAGDI   +D+E+
Sbjct: 76  VLHEFSTVEGVVEDVTQIILNLKKVSMRIDSDDEKTLEVNVTGPADVTAGDIAGDSDVEI 135

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSY 185
           LN D  I  +   A + M LT  +G GYV    ++   +  PIG++ ID++++PI++V+Y
Sbjct: 136 LNGDLHIATVAAGATLHMTLTAVRGRGYVSGDQNKELHDEMPIGVLAIDSIFTPIERVNY 195

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R GQ  D+DKL++ + TDGS+T  ++V+LA+RI+ D L  FI+  E     +   
Sbjct: 196 QVENTRVGQRDDFDKLTLDVWTDGSLTATEAVSLAARIMSDHLNAFIDMSERAITAQVMA 255

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           + +  P        +EEL+LSVRS NCL+   I  + +L +RTE  M+ + N GRKSL E
Sbjct: 256 DKEEEPTTKHADTPIEELDLSVRSYNCLKRAGINSVQELTERTETQMMSVRNLGRKSLDE 315

Query: 306 IKGVLGTMGLFL 317
           I+  L  +GL  
Sbjct: 316 IQDKLKLLGLGF 327


>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 =  341 bits (876), Expect = 7e-92,   Method: Composition-based stats.
 Identities = 131/314 (41%), Positives = 204/314 (64%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP  IE   +  +++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+I+G
Sbjct: 3   DFQKP-KIEIATI-SDDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIEG 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 VEIKGVLGTMGLFL 317
            E+   L  +GL L
Sbjct: 301 EEVLAKLKELGLQL 314


>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 =  341 bits (875), Expect = 8e-92,   Method: Composition-based stats.
 Identities = 133/313 (42%), Positives = 192/313 (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 NETAKIEIELIVERGRGYVPATVTATGG-EIGRIPVDQIYSPVLKVSYKVEATRVEQRTD 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|326692212|ref|ZP_08229217.1| DNA-directed RNA polymerase subunit alpha [Leuconostoc argentinum
           KCTC 3773]
          Length = 314

 Score =  341 bits (875), Expect = 8e-92,   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|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 =  341 bits (875), Expect = 8e-92,   Method: Composition-based stats.
 Identities = 129/321 (40%), Positives = 192/321 (59%), Gaps = 5/321 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E       +  R+  I EPL  GF +TLGN+LRR L+SS+ GAA+T+V+IDGVL
Sbjct: 5   QRPTLTE----EYVDSARSRFIIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVKIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE ++I GV ED++DIILNIKG+ L    D    + + K G GVV+AGDI+    +E+ N
Sbjct: 61  HEFTTINGVKEDVSDIILNIKGLVLSSDSDEPVVMYLRKEGAGVVSAGDIEPPAGVEIHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  I  L+    + +E+ V +G GYVPA  +   N  IG I +D +YSP+ KVSY VE+
Sbjct: 121 PDLHIATLNEQGRLDIEMIVERGRGYVPASLYAGTN-EIGRIPVDQIYSPVLKVSYKVEA 179

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  SI   D++A A + L +  G+        + ++   + + 
Sbjct: 180 TRVEQRTDFDKLIIDVETKNSIAPSDALASAGKTLVELFGLARELNTAAEGIEIGPSPQE 239

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
             +  A    +E+L  SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  
Sbjct: 240 TEYIAAYSMPIEDLNFSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVKIK 299

Query: 310 LGTMGLFLGMNLPDWPPESIE 330
           L  +GLFL  +  D+ P  +E
Sbjct: 300 LAGLGLFLKDSPEDFDPTQLE 320


>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 =  341 bits (875), Expect = 8e-92,   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   MMLNATEFLTPNAIHVDTV---NETHAKVTLEPLERGFGHTLGNALRRILLSSLPGAAVI 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|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 =  341 bits (875), Expect = 9e-92,   Method: Composition-based stats.
 Identities = 132/330 (40%), Positives = 209/330 (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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL--ITIDALYSP 179
            ++++++NP+ V+  L     ++M L V  G GY PA   R + D   +  + +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 VSRVAYQVENARVEQRTDLDRLIIELETNGTIDPEEAIRKAATILQQQISIFVDLEAEEA 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
                        +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QR+E ++L+  N G
Sbjct: 238 PEPVKEK---EEVDPVLLRPVDDLELTVRSANCLKAENIYYIGDLVQRSETELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL L M L +WPP  +
Sbjct: 295 KKSLTEIKDVLASKGLELDMRLENWPPADL 324


>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 =  341 bits (875), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 133/310 (42%), Positives = 201/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE I +  + +     + EPL RG+  TLGN+LRR+L+SSL GAA+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 GVLGTMGLFL 317
             L  + L L
Sbjct: 301 FKLAELDLNL 310


>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 =  341 bits (874), Expect = 1e-91,   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|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 =  341 bits (874), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 138/312 (44%), Positives = 204/312 (65%), Gaps = 6/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +     +E +N    + EPL RG+  TLGN+LRRVL++SL GAAIT +QIDG
Sbjct: 3   EFEKPNIHKV----EETDNYGKFVVEPLERGYGTTLGNSLRRVLIASLPGAAITTMQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++KGV ED+T IILN+K ++LK++ +  K + +  +GP  VTAGDIQ  +++ V
Sbjct: 59  VLHEFSTVKGVTEDVTQIILNLKKVSLKINSEDQKDLELDVKGPAEVTAGDIQGDSEVSV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSY 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 IKGVLGTMGLFL 317
           IK  L  +G+  
Sbjct: 299 IKLKLNDLGVSF 310


>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 =  341 bits (874), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 123/321 (38%), Positives = 191/321 (59%), Gaps = 2/321 (0%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +     + NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE ++I G
Sbjct: 9   LTEEYIDTNRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVLHEFTTING 68

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           + E++++IILN+K I L    D    + + K GPG VTAGDI+   D+ + NPD  I +L
Sbjct: 69  IKENVSEIILNVKNIVLSSDSDEPVVLYLSKEGPGDVTAGDIELTADVAIHNPDLHIASL 128

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           +  A + MEL V +G GYVPA  +       G I +D +YSP+ +V+Y VE+ R  Q  D
Sbjct: 129 NDSARLEMELVVERGRGYVPAMPYA--GGEAGRIPVDQIYSPVTRVAYKVEATRVEQRTD 186

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL + ++T  S+T  D++A A   L +  G+        + ++   + +   +  A  
Sbjct: 187 FDKLIIDVETKNSMTARDALASAGSTLVELFGLARELNTAAEGLEIGPSPQETEYIAAYN 246

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +E+L  SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L ++GL L
Sbjct: 247 LPIEDLNFSVRSYNCLKRQEIHSVGELAEYTESDLLDIRNFGQKSINEVKIKLASLGLTL 306

Query: 318 GMNLPDWPPESIEELAKKYED 338
                D+ P  IE    +  D
Sbjct: 307 KDAPEDFDPTQIEGYDAETGD 327


>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 =  341 bits (874), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 144/336 (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   MYTEINEMLTPK---VLKVQAESPYKARIVLEPLERGFGHTLGNALRRILLSSMPGSAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
              IDGVLHE S+I+GV ED+ D++LN+K + +K++  +  +VT+ K GP  VTAGDIQ 
Sbjct: 58  EASIDGVLHEYSTIEGVQEDVVDLLLNLKSVAIKLTVGNEAQVTLNKEGPCQVTAGDIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA------KHHRTENDPIGLITIDA 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 SFSPVKKVAYFVDSARVENRTDLDKLTIELETNGTIDAEEAIRISASILQRQLHAFVDM- 236

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
             K E     N +   F+P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE+++L+ 
Sbjct: 237 --KFEESRADNKERNDFDPVLLRSVDDLELTVRSANCLKAENIHYIGDLVQRTESELLKT 294

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL +  L LGM L +WPP S+ E
Sbjct: 295 PNLGKKSLTEIKDVLASRSLSLGMKLENWPPASLGE 330


>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 =  341 bits (874), Expect = 1e-91,   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|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 =  341 bits (874), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 144/336 (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   MYTEINEMLTPK---VLKVQAESPYKARIVLEPLERGFGHTLGNALRRILLSSMPGSAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
              IDGVLHE S+I+GV ED+ D++LN+K + +K++  +  +VT+ K GP  VTAGDIQ 
Sbjct: 58  EASIDGVLHEYSTIEGVQEDVVDLLLNLKSVAIKLTVGNEAQVTLNKEGPCQVTAGDIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA------KHHRTENDPIGLITIDA 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 SFSPVKKVAYFVDSARVENRTDLDKLTIELETNGTIDAEEAIRISASILQRQLHAFVDM- 236

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
             K E     N +   F+P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE+++L+ 
Sbjct: 237 --KFEESRADNKERNDFDPVLLRSVDDLELTVRSANCLKAENIHYIGDLVQRTESELLKT 294

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL +  L LGM L +WPP S+ E
Sbjct: 295 PNLGKKSLTEIKDVLASRSLSLGMKLENWPPASLGE 330


>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 =  341 bits (874), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 129/329 (39%), Positives = 196/329 (59%), Gaps = 7/329 (2%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
             P +I               I EP   G+ HTLGN+LRR+L+SSL GAAI++V+I+GV+
Sbjct: 9   EMPRSI-VKDETVSNSTFGKYIIEPFESGYGHTLGNSLRRILLSSLEGAAISSVKIEGVM 67

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE ++++GV ED+ DI+LN+K + +KM     +   +     G VTAGDIQ    +E++N
Sbjct: 68  HEFTTMEGVVEDVVDIVLNLKKVLIKMPDRQTRVFRVDVFKEGAVTAGDIQVDPGVEIVN 127

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+ +IC LD    + MEL V  G G++  ++++ ++  IG+I ID L+SP++ V YTVE+
Sbjct: 128 PEQLICTLDKKQRLLMELEVKVGRGFLLGEYNKKQDQSIGVIPIDCLFSPVRHVKYTVEN 187

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R GQ  DYD+L   I TDG I  ++++  ++ ILQ  L +F+ + +   E ++      
Sbjct: 188 TRVGQRTDYDRLIFEIWTDGRIGPDEALVQSAAILQHHLDIFVQYGKEPVEFEKPKPPIK 247

Query: 250 LPFNP---ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
              N     L   V E+ELSVR+ NCL   NI  +G L  +TEA+ML+  NFG+KSL EI
Sbjct: 248 EEENRLRKILNMSVNEIELSVRAANCLNNANITTVGQLAMKTEAEMLKYRNFGKKSLNEI 307

Query: 307 KGVLGTMGLFLGMNLPDWPPESIEELAKK 335
           K  L ++GL LGM    + P  +++  +K
Sbjct: 308 KEKLASLGLSLGM---KFDPSLLDQTEEK 333


>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 =  340 bits (873), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 146/328 (44%), Positives = 202/328 (61%), Gaps = 9/328 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           L+KP +++   + +   NR ++  EP  RG+ HTLGNALRR+L+SS+ G A T  QI G+
Sbjct: 6   LLKPTSVDV-SVDESNPNRAVITLEPFERGYGHTLGNALRRILLSSMVGFAPTEAQITGI 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 NPDHVICNLDVDAVVRMELTVSKGHGYVP----AKHHRTENDPIGLITIDALYSPIKKVS 184
           NPDHVI +L     + M++ + KG GY P    A         IG I +DA +SPI +V+
Sbjct: 125 NPDHVIAHLS-GGRLEMQVKIEKGRGYQPGDVRAFRDDYSKSSIGRIIMDASFSPILRVA 183

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV--- 241
           Y V +AR  Q  D DKL MTI+T+G+I  E+++  + RILQDQL +F      +      
Sbjct: 184 YQVMAARVAQRTDLDKLEMTIETNGAIGPEEALRESVRILQDQLAVFGAIHPEQGTDGIK 243

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 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|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 =  340 bits (873), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 147/330 (44%), Positives = 217/330 (65%), Gaps = 8/330 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  +  E +KP  ++   +    +    +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MHNSATEFLKPRLVDIEQI---SKTHAKITLEPLERGFGHTLGNALRRILLSSMPGYAVT 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+  + + 
Sbjct: 178 IERISYNVEAARVEQRTDLDKLIIEMETNGTIDPESAIRRAATILSEQLEAFIDLRDIR- 236

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
             K +I  +   F+P LL+ V++LEL+VRS NCL+ E+I Y+GDL+QRTE ++L+  N G
Sbjct: 237 --KPEIKEEKPEFDPVLLRPVDDLELTVRSANCLKAESIHYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL T  L LGM + +WPP SI
Sbjct: 295 KKSLTEIKDVLSTRNLTLGMRIENWPPVSI 324


>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 =  340 bits (873), 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  IE +    E+ +    + EPL RG+  TLGN+LRR+L+SSL G A  +++IDG
Sbjct: 3   EIEKP-KIECVE-STEDGSYGKFVIEPLERGYGITLGNSLRRILLSSLPGVAANSIKIDG 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|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 =  340 bits (873), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 130/333 (39%), Positives = 193/333 (57%), 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 KEDINVKSLPFNPAL---LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +   +  S   N         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|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 =  340 bits (873), Expect = 1e-91,   Method: Composition-based stats.
 Identities = 138/315 (43%), Positives = 208/315 (66%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 28  DFEKPN-IEIAEI-SEDKKYGKFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 85

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDI 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 VEIKGVLGTMGLFLG 318
            E+   L  +GL L 
Sbjct: 326 EEVLAKLKELGLQLN 340


>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 =  340 bits (873), Expect = 2e-91,   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-IECVE-RSEDNTYAKFVIEPLERGYGITLGNSLRRILLSSLPGSAVTSVKIEG 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|171911662|ref|ZP_02927132.1| DNA-directed RNA polymerase subunit alpha [Verrucomicrobium
           spinosum DSM 4136]
          Length = 371

 Score =  340 bits (873), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 132/335 (39%), Positives = 195/335 (58%), Gaps = 8/335 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +         PN +         +     +AEP  RG+ HT+GN+LRRVL+SSL GA+IT
Sbjct: 1   MSIRLARFEMPNRL-VKNEATATDYYAQFVAEPFDRGYGHTIGNSLRRVLLSSLEGASIT 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQ 120
           +V+I G  HE +++ GV ED+T I+LN+K +  +       + + +     GVVTAGDI+
Sbjct: 60  SVRIKGAEHEFTTLPGVLEDVTQIVLNLKKVKFRHFENKETRLLQVSVDKEGVVTAGDIK 119

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
                +V+N D VIC LD       EL V  G G+   + ++  + PIG+I ID+++SP+
Sbjct: 120 DDTSYQVINKDQVICTLDRKGKFEAELEVKVGRGFATNEDNKRPDMPIGVIPIDSIFSPV 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            +V Y VE+ R GQ  DYDKL + + TDG IT +D++  +S IL+  L +F+N+++ + E
Sbjct: 180 TRVKYGVEATRVGQNTDYDKLLIDVWTDGRITPQDALLQSSAILRKHLDVFVNYDDNQVE 239

Query: 241 VK---EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
            +   E  + ++L     L   V E+ELSVR+ NCL   NI  +G L  ++EA+MLR  N
Sbjct: 240 FEVAPEAQSEENLELRKLLNMSVNEIELSVRAANCLNNANITSVGQLAMKSEAEMLRYRN 299

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEEL 332
           FG+KSL EIK  L  +GL LGM L    P  +E L
Sbjct: 300 FGKKSLTEIKEKLSELGLTLGMKL---DPSLLEPL 331


>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 =  340 bits (873), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 123/321 (38%), Positives = 189/321 (58%), Gaps = 2/321 (0%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +     + NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++I+GVLHE ++I G
Sbjct: 9   LTEEYIDTNRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIEGVLHEFTTING 68

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V E++++IILNIK + L    D    + +  +GP  VTA DI    D+ V NPD  I +L
Sbjct: 69  VKENVSEIILNIKNLVLSSDSDEPVVMYLSAQGPTDVTAADIDLPADVTVHNPDLHIASL 128

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           +  A + MEL V +G GYVPA  +      IG I +D +YSP+ KVSY VE+ R  Q  D
Sbjct: 129 NESARLDMELVVERGRGYVPAMTNS--GGEIGRIPVDQIYSPVLKVSYKVEATRVEQRTD 186

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL + ++T  S++  D++A A   L +  G+        + ++   + +   +  A  
Sbjct: 187 FDKLIIDVETKNSMSARDALASAGSTLVELFGLARELNTAAEGIEIGPSPQETEYIAAYN 246

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +E+L  SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L ++GL L
Sbjct: 247 MPIEDLNFSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVKIKLASLGLTL 306

Query: 318 GMNLPDWPPESIEELAKKYED 338
                D+ P  IE    +  D
Sbjct: 307 KDAPEDFDPTQIEGYDAETGD 327


>gi|168701504|ref|ZP_02733781.1| DNA-directed RNA polymerase subunit alpha [Gemmata obscuriglobus
           UQM 2246]
          Length = 336

 Score =  340 bits (872), Expect = 2e-91,   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|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 =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 117/321 (36%), Positives = 184/321 (57%), Gaps = 9/321 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            +      + R+    EPL  GF +TLGN+LRR L+SS+ G+A+T+++I+G LHE +++ 
Sbjct: 15  KLTEEVINDQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGSAVTSIKIEGALHEFTTLP 74

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+T I+LNIK I L    D    + + K G G VT GDI     + + NP+H I  
Sbjct: 75  GVKEDVTQIVLNIKEIVLSSDNDEPVVMYLRKTGEGEVTVGDIMPPAGVVIHNPEHHIAT 134

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           L+ D  + +ELTV +G GYV A  ++     I  I +D++YSP+ KVSY VE+ R  Q  
Sbjct: 135 LNKDGKLEIELTVERGRGYVSASQNKDPEAEISRIPVDSIYSPVLKVSYRVEATRVEQRT 194

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           D+D+L + ++T  +I   D++A A + L +  G+  +     + ++   +         L
Sbjct: 195 DFDRLVVDVETKKAILPRDAMASAGKTLVELFGLARDLNHDAEGIELGPSGNDAALAEDL 254

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              VE+L+L+ R+ NCL  E I  +GDL+ R++AD+L + NFG+KS+ EIK  L  MG+ 
Sbjct: 255 AMSVEDLDLTSRALNCLTREGINTVGDLVARSQADLLDIRNFGQKSIDEIKEKLAGMGMS 314

Query: 317 L---------GMNLPDWPPES 328
           L         G ++P +  E+
Sbjct: 315 LKDTPMPAVEGADIPQFSDEN 335


>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 =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 126/315 (40%), Positives = 179/315 (56%), Gaps = 4/315 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
            P ++         +     +AEP   G+ +T+GN+LRRVL+SSL GAAIT+V+I G  H
Sbjct: 1   MPKSL-VKDDASRTDTYAKFVAEPFEAGYGNTIGNSLRRVLLSSLEGAAITSVKITGAQH 59

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E  ++  V +D+TDI+LN+K +  K +    + +TI     G VTAGDI+  +  EVLN 
Sbjct: 60  EFQTLPHVVDDVTDIVLNLKKVKFKANDHEIRNLTINVNKEGAVTAGDIEDSSQCEVLNK 119

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D +IC LD       EL V  G G+     ++  + PIG+I ID+++SP+ +V YTV + 
Sbjct: 120 DQIICTLDKKTKFEAELEVKVGRGFSTGDENKHPDQPIGVIAIDSIFSPVTRVKYTVGNT 179

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           R GQ  DYDKL + I TDG +T E+++  AS IL+     F  ++E   +  E    +S 
Sbjct: 180 RVGQRTDYDKLELEIWTDGRLTPEEALVQASSILKKHFEPFYAYDENAVQFDETPQAQSQ 239

Query: 251 PFNPAL---LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                       V E+ELSVR+ NCL   NI  +G L  +TEA+ML+  NFG+KSL EIK
Sbjct: 240 ENQKMKKLLNMSVNEIELSVRAANCLNNANITTVGQLAMKTEAEMLKYRNFGKKSLNEIK 299

Query: 308 GVLGTMGLFLGMNLP 322
             L  +GL LGM   
Sbjct: 300 DKLTQLGLSLGMKFE 314


>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 =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 143/336 (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   MYTEINEMLTPK---VLKVQAESPYKARIVLEPLERGFGHTLGNALRRILLSSMPGSAIT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
              IDGVLHE S+I+GV ED+ D++LN+K + +K++  +  ++T+ K GP  VTAGDIQ 
Sbjct: 58  EASIDGVLHEYSTIEGVQEDVVDLLLNLKSVAIKLTVGNEAQITLNKEGPCQVTAGDIQL 117

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA------KHHRTENDPIGLITIDA 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 SFSPVKKVAYFVDSARVENRTDLDKLTIELETNGTIDAEEAIRISASILQRQLHAFVDM- 236

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
             K E     N +   F+P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE+++L+ 
Sbjct: 237 --KFEESRADNKERNDFDPVLLRSVDDLELTVRSANCLKAENIHYIGDLVQRTESELLKT 294

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL +  L LGM L +WPP S+ E
Sbjct: 295 PNLGKKSLTEIKDVLASRSLSLGMKLENWPPASLGE 330


>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 =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 137/314 (43%), Positives = 205/314 (65%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAAI+ V+IDG
Sbjct: 3   DFNKPN-IEITEI-SEDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAISQVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDI 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 VEIKGVLGTMGLFL 317
            E+   L  +GL L
Sbjct: 301 EEVLAKLKELGLEL 314


>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 =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 118/321 (36%), Positives = 184/321 (57%), Gaps = 9/321 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            +      E R+    EPL  GF +TLGN+LRR L+SS+ G+A+T+++I+G LHE +++ 
Sbjct: 15  KLTEEVINEQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGSAVTSIKIEGALHEFTTLP 74

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+T I+LNIK I L    D    + + K G G VT GDI     + + NP+H I  
Sbjct: 75  GVKEDVTQIVLNIKEIVLSSDNDEPVVMYLRKTGEGEVTVGDIMPPAGVVIHNPEHHIAT 134

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           L+ D  + +ELTV +G GYV A  ++     I  I +D++YSP+ KVSY VE+ R  Q  
Sbjct: 135 LNKDGKLEIELTVERGRGYVSASQNKDPEAEISRIPVDSIYSPVLKVSYRVEATRVEQRT 194

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           D+D+L + ++T  +I   D++A A + L +  G+  +     + ++   +         L
Sbjct: 195 DFDRLVVDVETKKAILPRDAMASAGKTLVELFGLARDLNHDAEGIELGPSGNDAALAEDL 254

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              VE+L+L+ R+ NCL  E I  +GDL+ R++AD+L + NFG+KS+ EIK  L  MG+ 
Sbjct: 255 AMSVEDLDLTSRALNCLTREGINTVGDLVARSQADLLDIRNFGQKSIDEIKEKLAGMGMS 314

Query: 317 L---------GMNLPDWPPES 328
           L         G ++P +  E+
Sbjct: 315 LKDTPMPAVEGADIPQFSDEN 335


>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 =  340 bits (871), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 114/313 (36%), Positives = 178/313 (56%), Gaps = 10/313 (3%)

Query: 12  PNNIEYIVLGQEEE--NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           P   E +   QE    +       PL RG   T+GNALRRVL+S+L G A+TAV+I GV 
Sbjct: 21  PYQTECVESHQEANGVHYGKFALGPLERGQGITVGNALRRVLLSNLEGTAVTAVRIAGVT 80

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+ +I+LN+K + L+ +    +   +  +GPG VTA  +Q  +++EV+N
Sbjct: 81  HEFSTVPGVREDVMEILLNMKELVLRSNAPDTQVGRLVAQGPGEVTAEKLQLPSEVEVIN 140

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P H I  L   A++ ME  + +G GY    +  +++  I  + ID+++ P++KV+YTVE+
Sbjct: 141 PRHHIATLAEGAILEMEFMIGRGRGYRAVDYSDSKSMAIDFLQIDSVFMPVRKVNYTVEA 200

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           AR GQ L+ D+L + I T+GS+T +++++ A+RIL             +         + 
Sbjct: 201 ARVGQSLEKDRLILEIWTNGSLTPQEALSQAARILVGLFSPL-----QEVSFDTPPEPRQ 255

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              N      +EEL+LSVR+ NCL+   I  + DL+  TE D+L + NFG+KS  E+   
Sbjct: 256 AEDNQKNQIPIEELQLSVRAYNCLKRAQINTVADLLVYTEEDLLEIKNFGQKSAEEVVQA 315

Query: 310 LGTMGLFLGMNLP 322
           L      LG+ LP
Sbjct: 316 LKNR---LGLTLP 325


>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 =  340 bits (871), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 137/315 (43%), Positives = 207/315 (65%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP  IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 3   DFQKP-KIEIAEI-SEDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 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 VEIKGVLGTMGLFLG 318
            E+   L  +GL L 
Sbjct: 301 EEVLAKLKELGLQLN 315


>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 =  340 bits (871), Expect = 2e-91,   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|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|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 =  340 bits (871), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 122/321 (38%), Positives = 189/321 (58%), Gaps = 5/321 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E       +  R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLTE----EYVDSARSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE ++I GV ED++DIILNIKG+ L    D    + + K G GV+TAGDI+    +E+ N
Sbjct: 61  HEFTTINGVKEDVSDIILNIKGLVLSSDSDEPVVMYLRKEGAGVITAGDIEPPAGVEIHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  +  L+    + +E+ V +G GYVPA  +      IG I +D +YSP+ KVSY VE+
Sbjct: 121 PDLHLATLNEQGRLDIEMIVERGRGYVPATLYSGP-AEIGRIPVDQIYSPVLKVSYKVEA 179

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  S+   D++A A + L +  G+        + ++   + + 
Sbjct: 180 TRVEQRTDFDKLIIDVETKNSMAPRDALASAGKTLVELFGLARELNTAAEGIEIGPSPQE 239

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
             +  A    +E+L  SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  
Sbjct: 240 TEYIAAYGMPIEDLNFSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVKIK 299

Query: 310 LGTMGLFLGMNLPDWPPESIE 330
           L  +GL L     D+ P  ++
Sbjct: 300 LAGLGLTLKDAPEDFDPTQLD 320


>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 =  340 bits (871), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 142/333 (42%), Positives = 219/333 (65%), Gaps = 11/333 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +    E R  +  EPL RGF HTLGNALRR+L+SS+ G AIT
Sbjct: 1   MQNSVIEFLKPRLVDIEQI---TETRAKVTLEPLERGFGHTLGNALRRILLSSMPGYAIT 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 VND-IEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDAL 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 IHQPEHKEEK---PEFDPILLRLVDDLELTVRSANCLKAESIHYIGDLVQRTEIELLKTP 294

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           N G+KSL EIK VL + GL LG  L +WPP +I
Sbjct: 295 NLGKKSLTEIKDVLASRGLSLGTRLENWPPTNI 327


>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 =  340 bits (871), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 144/314 (45%), 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----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 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|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 =  340 bits (871), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 132/315 (41%), Positives = 205/315 (65%), Gaps = 6/315 (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 VEIKGVLGTMGLFLG 318
            E+   L  +GL L 
Sbjct: 301 EEVLAKLKELGLSLN 315


>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 =  340 bits (871), Expect = 3e-91,   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|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 (871), Expect = 3e-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|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 =  340 bits (871), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 144/314 (45%), 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----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 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|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 =  340 bits (871), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 126/310 (40%), Positives = 202/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  ++ + L  E+      + EPL RG+  T+GNALRR+L+SSL G A+ +++IDG
Sbjct: 3   EIEKP-KVDIVEL-SEDYRYGKFVVEPLERGYGITIGNALRRILLSSLPGVAVNSIKIDG 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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 QKLEELGLGL 310


>gi|291544484|emb|CBL17593.1| DNA-directed RNA polymerase subunit alpha [Ruminococcus sp. 18P13]
          Length = 318

 Score =  339 bits (870), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 129/312 (41%), Positives = 196/312 (62%), Gaps = 3/312 (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 IKGVLGTMGLFL 317
           +K  L ++G  L
Sbjct: 302 VKEKLQSLGFDL 313


>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 =  339 bits (870), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 127/333 (38%), Positives = 197/333 (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 KED-----------INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 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|291542059|emb|CBL15169.1| DNA-directed RNA polymerase subunit alpha [Ruminococcus bromii
           L2-63]
          Length = 317

 Score =  339 bits (870), Expect = 3e-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|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 =  339 bits (870), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 134/315 (42%), Positives = 204/315 (64%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP  IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 3   DFEKP-KIEIAEI-SEDKRYGKFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 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 VEIKGVLGTMGLFLG 318
            E+   L  +GL L 
Sbjct: 301 EEVLAKLKELGLQLN 315


>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 =  339 bits (870), Expect = 3e-91,   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|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 =  339 bits (870), Expect = 4e-91,   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-KIEITEL-SEDKKFGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 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|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 =  339 bits (870), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 134/312 (42%), Positives = 203/312 (65%), Gaps = 6/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +     +E +N    + EPL RG+  TLGN+LRRVL++SL GAAIT++QIDG
Sbjct: 3   EFEKPNIHKV----EETDNYGKFVVEPLERGYGTTLGNSLRRVLIASLPGAAITSMQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S+++GV ED+T IILN+K ++LK+  +  K + +  +GP  VTA DIQ  N++ +
Sbjct: 59  VLHEFSTVEGVTEDVTQIILNLKKVSLKLDSEDQKNLELDVKGPAEVTASDIQGDNEVTI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSY 185
           LNPD  I  +   A + ++LT  KG GY+ A     R ++  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 IKGVLGTMGLFL 317
           IK  L  +G+  
Sbjct: 299 IKLKLNDLGVSF 310


>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 =  339 bits (869), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 138/314 (43%), Positives = 204/314 (64%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAAI+ V+IDG
Sbjct: 3   DFNKPN-IEITEI-SEDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAISHVKIDG 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 VEIKGVLGTMGLFL 317
            E+   L  +GL L
Sbjct: 301 EEVLAKLKELGLEL 314


>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 =  339 bits (869), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 133/327 (40%), Positives = 205/327 (62%), 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  +    
Sbjct: 180 VAYDVENARVEQRTDLDKLIIELETNGTIDPEEAIRKAATILQQQIAIFVDLEAEEAPEP 239

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                     +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QR+E ++L+  N G+KS
Sbjct: 240 IKEK---EEIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLVQRSETELLKTPNLGKKS 296

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESI 329
           L EIK VL +  L LGM L +WPP  +
Sbjct: 297 LTEIKDVLASKNLELGMRLDNWPPSDL 323


>gi|330718947|ref|ZP_08313547.1| DNA-directed RNA polymerase subunit alpha [Leuconostoc fallax KCTC
           3537]
          Length = 314

 Score =  339 bits (869), Expect = 4e-91,   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|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 =  339 bits (869), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 130/313 (41%), Positives = 202/313 (64%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP   +      E ++    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDG
Sbjct: 3   EFEKPTITKI----DENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDG 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|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 =  339 bits (869), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 128/333 (38%), Positives = 194/333 (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 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE- 240
           +V Y +E  R GQ  +YD+L + I T+G++T E ++  +++IL+  L  FI + EP  E 
Sbjct: 180 RVRYLIEETRVGQRTNYDRLILEIWTNGTVTPESALVESAKILRKHLNPFITYREPGPEM 239

Query: 241 ----------VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 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|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 =  339 bits (869), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 146/314 (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 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|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 =  339 bits (869), Expect = 4e-91,   Method: Composition-based stats.
 Identities = 141/336 (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   MYTEINEMLTPN---VLKVQAESPFKAKIVLEPLERGFGHTLGNALRRILLSSMPGSVIT 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 SFSPVRKVAYYVDSARVENRTDLDKLTIELETNGTIDSEEAIRISASILQRQLHAFVDM- 236

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
             + E       +   F+P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QRTE ++L+ 
Sbjct: 237 --RFEESRSDQKERNDFDPILLRSVDDLELTVRSANCLKAENIHYIGDLVQRTENELLKT 294

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            N G+KSL EIK VL +  L LGM L +WPP ++ E
Sbjct: 295 PNLGKKSLTEIKDVLASRSLSLGMKLENWPPANLGE 330


>gi|325684745|gb|EGD26899.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 312

 Score =  339 bits (869), Expect = 5e-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|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 =  338 bits (868), Expect = 5e-91,   Method: Composition-based stats.
 Identities = 144/305 (47%), Positives = 210/305 (68%), 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 TNGTLDPEEAIRRSATILAEQLEAFVDLRDVSVPEKKEEK---PEFDPILLRPVDDLELT 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|300932966|ref|ZP_07148222.1| DNA-directed RNA polymerase subunit alpha [Corynebacterium
           resistens DSM 45100]
          Length = 337

 Score =  338 bits (868), Expect = 5e-91,   Method: Composition-based stats.
 Identities = 125/314 (39%), Positives = 182/314 (57%), 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    G I +D +YSP+ KVSY VE+ R  Q  
Sbjct: 128 LNEQGKLDIELVVERGRGYVPAATASSEI---GRIPVDQIYSPVLKVSYKVEATRVEQRT 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|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 =  338 bits (868), Expect = 5e-91,   Method: Composition-based stats.
 Identities = 140/323 (43%), Positives = 205/323 (63%), Gaps = 5/323 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           EL++P  ++  V+      R  +   PL RGF HTLG+ LRRVL+SSL+GAA+T V+I+G
Sbjct: 6   ELLRPQGVDVEVI---SARRARLALGPLERGFGHTLGSGLRRVLLSSLKGAAVTEVEIEG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE SSI+GV ED+ DI+LN+K + ++  G     VT+ KRGPG +T  DI + + IEV
Sbjct: 63  VLHEYSSIEGVQEDVVDILLNLKMLAVRAHGRGDAVVTLRKRGPGQMTGADIVSEHGIEV 122

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYV-PAKHHRTENDPIGLITIDALYSPIKKVSYT 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 VENARVEQRTDLDRLILDVETNGVVDPVWAVQEAARIFRSQLGVLAGAETREIP-EASQV 241

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
             S    P L++ V++LEL+VRS NCL+ E+I Y+GDL+Q++E ++L+  N GRKSL EI
Sbjct: 242 QVSQSLTPLLIRPVDDLELTVRSANCLKAEDIFYIGDLVQKSEQELLKAPNLGRKSLNEI 301

Query: 307 KGVLGTMGLFLGMNLPDWPPESI 329
           K VL   GL LGM L  WPPE++
Sbjct: 302 KEVLVAHGLTLGMRLDSWPPENL 324


>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 =  338 bits (868), Expect = 5e-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----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|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 =  338 bits (868), Expect = 6e-91,   Method: Composition-based stats.
 Identities = 136/315 (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-IEITEI-SEDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAISSVKIDG 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 VEIKGVLGTMGLFLG 318
            E+   L  + L L 
Sbjct: 301 EEVLAKLKELDLELN 315


>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 =  338 bits (868), Expect = 6e-91,   Method: Composition-based stats.
 Identities = 136/314 (43%), Positives = 204/314 (64%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVDIEQVSS---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+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 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKE 237

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 238 EKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>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 =  338 bits (867), Expect = 7e-91,   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|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 =  338 bits (867), Expect = 7e-91,   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|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 =  338 bits (867), Expect = 7e-91,   Method: Composition-based stats.
 Identities = 140/324 (43%), Positives = 204/324 (62%), Gaps = 6/324 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L  P   E + + +  ++    +  PL RG+  T+GNALRRVL+SSLRG AITAV+ID
Sbjct: 4   HGLQMP---EGVHVEEVSDSEGQFVMGPLERGYGVTIGNALRRVLLSSLRGLAITAVKID 60

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
           GV HE S+I GV ED+ D+ILN+K +  K        + +   GPG  TA DI +   + 
Sbjct: 61  GVQHEFSTIPGVTEDVADLILNLKEVRFKADEMQEGHLHLNLEGPGNWTAADIDEATAEY 120

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNPD  +  L  DAVV ++L V  G GYVP++ ++ E+DPIG+I ID++++PIK V+Y
Sbjct: 121 DVLNPDQHVATLAEDAVVNVDLRVGYGRGYVPSEENKREDDPIGVIAIDSIFTPIKNVNY 180

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            V+  R GQ +DY++L + ++TDGS+T E+++   + IL+D +  FI  EE  + V E+ 
Sbjct: 181 EVKPTRVGQKIDYEELLLDVETDGSLTPEEAITQGASILRDHVSFFIQLEEEPEPVVEEQ 240

Query: 246 NVKSLPFNPALL--KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            V         L  + V+EL+LSVRS NCL+  NI  +GDL++R E +ML+  NFGRKSL
Sbjct: 241 EVDEEVKRIRELLAQPVDELDLSVRSHNCLKAANIKTIGDLVRREEDEMLKFRNFGRKSL 300

Query: 304 VEIKGVLGTMGLFLGMNLPDWPPE 327
            E+  VL   GL  GM++ ++  E
Sbjct: 301 QELVEVLDERGLQFGMDVEEYLEE 324


>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 =  338 bits (867), Expect = 7e-91,   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|148793282|gb|ABR12705.1| DNA-directed RNA polymerase alpha subunit [Photobacterium
           kishitanii]
          Length = 308

 Score =  338 bits (867), Expect = 7e-91,   Method: Composition-based stats.
 Identities = 139/314 (44%), Positives = 205/314 (65%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +I EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVDIEQVSS---THAKVILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 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 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRV---PE 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|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 =  338 bits (867), Expect = 8e-91,   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|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 =  338 bits (867), Expect = 8e-91,   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|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 =  338 bits (867), Expect = 8e-91,   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|90194010|gb|ABD92566.1| RpoA [Actinobacillus minor NM305]
          Length = 303

 Score =  338 bits (866), Expect = 8e-91,   Method: Composition-based stats.
 Identities = 138/305 (45%), Positives = 206/305 (67%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+       +T+ K G G VTAGDI    D+E++NPDHVIC+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVQSKDDVVLTLNKSGIGPVTAGDITHDGDVEIVNPDHVICH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D +A + M + V +G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+AR 
Sbjct: 121 LTDKNASINMRIRVQRGRGYVPASARVHTQDDDRPIGRLLVDARFSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++ V ++       F
Sbjct: 181 EQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQPVVKEEK---PEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>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 =  338 bits (866), Expect = 9e-91,   Method: Composition-based stats.
 Identities = 134/327 (40%), Positives = 205/327 (62%), 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  +    
Sbjct: 180 VAYDVENARVEQRTDLDKLIIELETNGTIDPEEAIRKAATILQQQIAIFVDLEAEEAPEP 239

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                     +P LL+ V++LEL+VRS NCL+ ENI Y+GDL+QR+E ++L+  N G+KS
Sbjct: 240 IKEK---EEIDPVLLRPVDDLELTVRSANCLKAENIYYIGDLVQRSETELLKTPNLGKKS 296

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESI 329
           L EIK VL +  L LGM L +WPP  +
Sbjct: 297 LTEIKDVLASKNLELGMRLDNWPPSDL 323


>gi|332086261|gb|EGI91417.1| DNA-directed RNA polymerase, alpha subunit [Shigella dysenteriae
           155-74]
          Length = 304

 Score =  338 bits (866), Expect = 9e-91,   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|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 =  338 bits (866), Expect = 9e-91,   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|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 =  338 bits (866), Expect = 9e-91,   Method: Composition-based stats.
 Identities = 112/302 (37%), Positives = 172/302 (56%), Gaps = 8/302 (2%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
                +       PL RG   T+GNALRRVL+S+L G A+TAV+I GV HE S++ GV E
Sbjct: 34  DDNGVHYGKFALGPLERGQGITVGNALRRVLLSNLEGTAVTAVRIAGVTHEFSTVPGVRE 93

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+ +I+LN+K + L+ S    +   +  +GPG VTA  +Q  +D+EV+NP H I  L   
Sbjct: 94  DVMEILLNMKELVLRSSSPETQVGRLVAQGPGEVTAEKLQLPSDVEVINPRHHIATLAEG 153

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
           A++ ME  + +GHGY    +  ++   I  + ID+++ P++KV+Y VE+AR GQ L+ D+
Sbjct: 154 AILEMEFMIGRGHGYRAVDYSDSKAMAIDFLQIDSVFMPVRKVNYAVEAARVGQFLEKDR 213

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L + I T+GS+T +++++ A+RIL             +      +  K    N      +
Sbjct: 214 LVLEIWTNGSLTPQEALSQAARILVGLFAPL-----QEVSFDAPVPPKPDEDNQKNQIPI 268

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           EEL+LSVR+ NCL+   I  + DL+  TE D+L + NFG+KS  E+   L       G+ 
Sbjct: 269 EELQLSVRAYNCLKRAQINTVADLLLYTEEDLLEIKNFGQKSAEEVVQALKAR---FGLT 325

Query: 321 LP 322
           LP
Sbjct: 326 LP 327


>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 =  338 bits (866), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 137/314 (43%), Positives = 204/314 (64%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVDIEQVSS---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+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 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKE 237

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 238 EKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>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 =  338 bits (866), Expect = 1e-90,   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|295315349|gb|ADF97760.1| RpoA [Vibrio sp. KTW-12]
          Length = 311

 Score =  338 bits (866), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 136/316 (43%), Positives = 206/316 (65%), 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 YAVEAARVEQRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKE 238

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRT+ ++L+  N G+KSL 
Sbjct: 239 EKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTDVELLKTPNLGKKSLT 295

Query: 305 EIKGVLGTMGLFLGMN 320
           EIK VL + GL LGM 
Sbjct: 296 EIKDVLASRGLSLGMR 311


>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 =  338 bits (866), Expect = 1e-90,   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|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 =  338 bits (866), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 136/312 (43%), Positives = 204/312 (65%), Gaps = 6/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +     +E +N    + EPL RG+  TLGN+LRRVL++SL G+AIT +QIDG
Sbjct: 3   EFEKPNIHKV----EETDNYGKFVVEPLERGYGTTLGNSLRRVLIASLPGSAITTMQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE S++KGV ED+T IILN+K ++LK++ +  K + +  +GP  VTAGDIQ  +++ V
Sbjct: 59  VLHEFSTVKGVTEDVTQIILNLKKVSLKINSEDQKDLELDVKGPAKVTAGDIQGDSEVSV 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSY 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 IKGVLGTMGLFL 317
           IK  L  +G+  
Sbjct: 299 IKLKLNDLGVSF 310


>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 =  338 bits (866), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 162/345 (46%), Positives = 238/345 (68%), Gaps = 12/345 (3%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           N  +LIKP++++ +     E+  + ++ EPL  GFA TLGNALRRV++SSL+G+A+  ++
Sbjct: 12  NLDKLIKPSSVKVVSDDSSEK--SDIVLEPLESGFALTLGNALRRVMLSSLKGSAVYGIK 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 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--------ENDPIGLITIDAL 176
             ++N D +IC L  +  + M + V+ G GY+P   ++         E D IG I ++AL
Sbjct: 130 CSIVNKDLLICTLGQNVELNMTIYVASGKGYLPVTKYKENELLKLMSEQDLIGFIPVNAL 189

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE- 235
           YSP+ +VSY VE++R GQV D DKL ++I+TDG+I+   +V  A+RILQ+QL  FI+ + 
Sbjct: 190 YSPVNRVSYRVENSRVGQVTDKDKLILSIETDGTISPSQAVDSAARILQEQLQPFISSDV 249

Query: 236 -EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 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|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 =  338 bits (866), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 163/345 (47%), Positives = 238/345 (68%), Gaps = 12/345 (3%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           N  +LIKP++++ I     E+  + ++ EPL  GFA TLGNALRRV++SSL+G+A+  ++
Sbjct: 12  NLDKLIKPSSVKVISDDSSEK--SDIVLEPLESGFALTLGNALRRVMLSSLKGSAVYGIK 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 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--------ENDPIGLITIDAL 176
             ++N D +IC L  +  + M + V+ G GY+P   ++         E D IG I ++AL
Sbjct: 130 CSIVNKDLLICTLGQNVELNMTIYVASGKGYLPVTKYKENELLKLMSEQDLIGFIPVNAL 189

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE- 235
           YSP+ +VSY VE++R GQV D DKL ++I+TDG+I+   +V  A+RILQ+QL  FI+ + 
Sbjct: 190 YSPVNRVSYRVENSRVGQVTDKDKLILSIETDGTISPSQAVDSAARILQEQLQPFISSDV 249

Query: 236 -EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 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|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 =  337 bits (865), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 134/314 (42%), Positives = 204/314 (64%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAAI+ V+IDG
Sbjct: 6   DFNKPN-IEITEI-SEDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAISQVKIDG 63

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDI 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 VEIKGVLGTMGLFL 317
            E+   L  +GL L
Sbjct: 304 EEVLAKLDELGLSL 317


>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 =  337 bits (865), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 160/345 (46%), Positives = 236/345 (68%), Gaps = 12/345 (3%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           +  +L KPN+++   +  +   +  ++ EPL  GFA TLGNALRRV++SSL G+A+  ++
Sbjct: 12  SLDKLTKPNSMKV--VSSDSSEKGDIVLEPLESGFALTLGNALRRVMLSSLIGSAVYGIK 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|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 =  337 bits (865), Expect = 1e-90,   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-KIEITEI-SEDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 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|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 =  337 bits (865), Expect = 1e-90,   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|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 =  337 bits (865), Expect = 1e-90,   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|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 =  337 bits (865), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 133/315 (42%), Positives = 205/315 (65%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  +++     + EPL RG+  TLGN+LRR+++SSL GAAI++V+IDG
Sbjct: 3   DFNKPN-IEITDV-SDDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAISSVKIDG 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 VEIKGVLGTMGLFLG 318
            E+   L  + L L 
Sbjct: 301 EEVLAKLKELNLELN 315


>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 =  337 bits (865), Expect = 1e-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|90194012|gb|ABD92567.1| RpoA [Actinobacillus porcitonsillarum]
          Length = 303

 Score =  337 bits (865), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 137/305 (44%), Positives = 206/305 (67%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+       +T+ K G G VTAGDI    D+E++NPDHVIC+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVQSKDDVVLTLNKSGIGPVTAGDITHDGDVEIVNPDHVICH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D +A + M + V +G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+AR 
Sbjct: 121 LTDKNASINMRIRVQRGRGYVPASARVHAQDDDRPIGRLLVDARFSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>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 =  337 bits (865), Expect = 1e-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|301168432|emb|CBW28022.1| DNA-directed RNA polymerase alpha chain [Bacteriovorax marinus SJ]
          Length = 337

 Score =  337 bits (864), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 147/325 (45%), Positives = 219/325 (67%), Gaps = 4/325 (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 FGRKSLVEIKGVLGTMGLFLGMNLP 322
           FGRKSL EIK +L  MGL LGM + 
Sbjct: 303 FGRKSLNEIKEILSNMGLGLGMKVD 327


>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 =  337 bits (864), Expect = 1e-90,   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 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
            +DY++L + ++TDGS+T E+++   + IL+D +  FI  EE  + V E+  V       
Sbjct: 183 KIDYEELLLDVETDGSLTPEEAITQGASILRDHVSFFIQLEEEPEPVVEEQEVDEEVKRI 242

Query: 255 ALL--KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 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|58416032|emb|CAH57430.1| RNA polymerase alpha-subunit [Vibrio sp. R-21419]
          Length = 308

 Score =  337 bits (864), Expect = 1e-90,   Method: Composition-based stats.
 Identities = 137/314 (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  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 YAVEAARVEQRTDLDKLVIDMQTNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKE 237

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 238 EKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>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 =  337 bits (864), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 135/314 (42%), Positives = 207/314 (65%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  +++     + EPL RG+  TLGN+LRR+++SSL GAAI+ ++IDG
Sbjct: 3   DFNKPN-IEIAEI-SDDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAISQIKIDG 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 VEIKGVLGTMGLFL 317
            E+   L  +GL L
Sbjct: 301 EEVLAKLKELGLEL 314


>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 =  337 bits (864), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 123/307 (40%), Positives = 183/307 (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    G I +D +YSP+ KVSY VE+ R  Q  D+DKL +
Sbjct: 135 EIEMTVERGRGYVPAATASSEI---GRIPVDQIYSPVLKVSYKVEATRVEQRTDFDKLIL 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|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 =  337 bits (864), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 126/310 (40%), Positives = 204/310 (65%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE +    E+ +    + EPL RG+  TLGNALRR+L+SSL G A   ++ID 
Sbjct: 3   EIEKP-KIECVE-NAEDGSYGKFVIEPLERGYGITLGNALRRILLSSLPGVAADHIKIDS 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|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 (864), Expect = 2e-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|190341325|gb|ACE74739.1| RpoA [Enterobacter cowanii]
          Length = 308

 Score =  337 bits (864), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 137/314 (43%), Positives = 207/314 (65%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 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|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 =  337 bits (864), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 131/322 (40%), Positives = 198/322 (61%), Gaps = 8/322 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             EL+ P  ++   +G      + +  EPL RGF +TLG ALRRVL+SS+ GAAIT  QI
Sbjct: 3   LTELLTPRIVQIKEIGSNT---SRVTLEPLERGFGYTLGTALRRVLLSSIEGAAITECQI 59

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGV HE S+I+GV ED+ D++LN+K I L M       + +     G +TAGD +    +
Sbjct: 60  DGVSHEYSAIEGVKEDVIDVLLNLKNIALLMPDLERAEIRLSVTEKGAITAGDFELPAGV 119

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKV 183
           E++NPD VI +L  D    +   V KG GY  A       E+    ++ +DA +SP++++
Sbjct: 120 EIVNPDCVIAHLTRDIPFSLTAVVEKGRGYRVAPQADDNSESTRSNVLRLDASFSPVRRI 179

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE AR  Q  D DKL + I+++G+I  E ++  A+ IL +Q+ +F++ E  ++E +E
Sbjct: 180 AYRVEQARVEQRTDLDKLIIEIESNGTIDPEQAIRDAATILHNQIKVFVDLESTEEETEE 239

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +  +   P    LL+ V++LEL+VRS NCL+ ENI  +GDL++RTE ++L+  N G+KSL
Sbjct: 240 EEEIYIDP---VLLRPVDDLELTVRSANCLKAENINNIGDLVRRTEVELLKTPNLGKKSL 296

Query: 304 VEIKGVLGTMGLFLGMNLPDWP 325
            EIK VL    L LGM++ +WP
Sbjct: 297 NEIKEVLAAHNLELGMDIENWP 318


>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 =  337 bits (864), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 136/314 (43%), Positives = 202/314 (64%), Gaps = 5/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN IE   +  E+      + EPL RG+  TLGN+LRR+++SSL GAA++AV+I G
Sbjct: 3   EFEKPN-IEISEI-SEDNRFGRFVVEPLVRGYGTTLGNSLRRIMLSSLPGAAVSAVKIKG 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 EIKGVLGTMGLFLG 318
           E+   L  +GL L 
Sbjct: 301 EVLAKLNELGLALN 314


>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 =  337 bits (864), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 131/313 (41%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +      E ++  + + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPNITKI----DENKDYGVFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 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|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 =  337 bits (864), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 115/303 (37%), Positives = 177/303 (58%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +        R+    EPL  GF +TLGN+LRR L+SS+ G+A+T+++I+G LHE +++ G
Sbjct: 9   LTEEVINNQRSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGSAVTSIKIEGALHEFTTLPG 68

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+T ++LNIK I L    D    + + K G G VT GDI     + + NP+H I  L
Sbjct: 69  VKEDVTQVVLNIKEIVLSSDNDEPVVMYLRKTGEGEVTVGDIMPPAGVVIHNPEHHIATL 128

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           + D  + +ELTV +G GYV A  ++     I  I +D++YSP+ KVSY VE+ R  Q  D
Sbjct: 129 NKDGKLEIELTVERGRGYVSAAQNKDPEAEISRIPVDSIYSPVLKVSYHVEATRVEQRTD 188

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +D+L + ++T  +I+  D++A A + L +  G+        + ++   +         L 
Sbjct: 189 FDRLIVDVETKKAISPRDAMASAGKTLVELFGLARALNADAEGIELGSSNTDSALAEDLA 248

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             VE+LEL+ R+ NCL  E I  +GDL+ R++AD+L + NFG KS+ EIK  L TMG+ L
Sbjct: 249 MSVEDLELTSRALNCLNREGIKTVGDLVARSQADLLDIRNFGHKSIDEIKEKLATMGMSL 308

Query: 318 GMN 320
             +
Sbjct: 309 KDS 311


>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 =  337 bits (864), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 135/313 (43%), Positives = 205/313 (65%), Gaps = 5/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  +PN IE   +  +++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+I+G
Sbjct: 3   DFERPN-IEVAEI-SDDKKYGKFVVEPLERGYGITLGNSLRRIMLSSLPGAAVSQVKIEG 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 EIKGVLGTMGLFL 317
           E+   L  +GL L
Sbjct: 301 EVLAKLDELGLSL 313


>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 =  336 bits (863), Expect = 2e-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|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 =  336 bits (863), Expect = 2e-90,   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 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP---- 237
           +V Y VE  R GQ  ++DKL M I T G+I  + ++  A++IL+  L  F+ + EP    
Sbjct: 180 RVEYRVEETRVGQKTNFDKLIMRIWTTGTIRPDMALVEAAKILRKHLNPFVQYFEPGPGL 239

Query: 238 ------KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 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|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 =  336 bits (863), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 130/325 (40%), Positives = 208/325 (64%), Gaps = 8/325 (2%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M++K    + KP  IE   L          I EPL RG+  TLGN+LRRVL+SSL G A+
Sbjct: 1   MLEK----IEKP-KIETPELKSNG-TYGKFILEPLERGYGITLGNSLRRVLLSSLPGVAV 54

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T+V+IDGV HE+S+I GV ED+T+IILN+KG+  K+ G+  K + I   G  VVTAGDI+
Sbjct: 55  TSVKIDGVHHELSTIPGVKEDVTEIILNLKGLTAKLYGEGPKTIYIEAEGECVVTAGDIK 114

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYS 178
             +++++L PD  I  L   A + ME+T+ +G GYV A+ +++  +N PIG+I +D++YS
Sbjct: 115 ADSEVDILVPDMHIATLGAGAKLYMEITIDRGRGYVSAEKNKSLMQNAPIGIIAVDSIYS 174

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+ KV+YTV++ R G + D+DKL++ + TDG+I+ +++V++A+++L + L  F++  E  
Sbjct: 175 PVLKVNYTVDNTRVGHITDFDKLTLEVWTDGTISAKEAVSMAAKLLNEHLNPFVDLSEET 234

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
             V+  +          L   +EEL+LSVRS NCL+   I  + DLI+++  +M+++ N 
Sbjct: 235 NVVELIVEKDDQGKEKILEMTIEELDLSVRSFNCLKRAGINTVNDLIEKSAEEMMKVRNL 294

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPD 323
           G+KS  E++  L ++G  L     +
Sbjct: 295 GKKSFDEVREKLHSLGYELNSEEDN 319


>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 =  336 bits (863), Expect = 2e-90,   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|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 =  336 bits (863), Expect = 2e-90,   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|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 =  336 bits (863), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 130/311 (41%), Positives = 202/311 (64%), Gaps = 3/311 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  I+ +       N    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDG
Sbjct: 3   EMEKPR-IDCVE-KNSSSNYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDG 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 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI-GLITIDALYSPIKKVSYT 186
           LNPD  + +LD D  V +E+TV +G GYV +     +ND I 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|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 =  336 bits (863), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 136/311 (43%), Positives = 199/311 (63%), 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  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKRGPGVVTAGDIQTVNDIE 126
           VLHE S+I GV ED+  IILNIK I LK   +   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|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 =  336 bits (863), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 135/315 (42%), Positives = 206/315 (65%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAAI++V+IDG
Sbjct: 3   DFNKPN-IEITEI-SEDKKYGKFVVEPLERGYGITLGNSLRRIMLSSLPGAAISSVKIDG 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 VEIKGVLGTMGLFLG 318
            E+   L  + L L 
Sbjct: 301 EEVLAKLKELNLELN 315


>gi|190341367|gb|ACE74760.1| RpoA [Enterobacter radicincitans]
          Length = 308

 Score =  336 bits (863), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 137/314 (43%), Positives = 207/314 (65%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 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|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 =  336 bits (863), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 131/313 (41%), Positives = 196/313 (62%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +      E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPNITKI----DENKDYGKFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 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|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 =  336 bits (863), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 137/314 (43%), Positives = 207/314 (65%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 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|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 (863), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 133/315 (42%), Positives = 202/315 (64%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 3   DFEKPN-IEIAEI-SEDKRYGKFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDI 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 VEIKGVLGTMGLFLG 318
            E+   L  +GL L 
Sbjct: 301 EEVLAKLKELGLQLN 315


>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 =  336 bits (863), Expect = 2e-90,   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|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 =  336 bits (863), Expect = 2e-90,   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|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 =  336 bits (862), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 133/315 (42%), Positives = 202/315 (64%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 3   DFEKPN-IEIAEI-SEDKRYGKFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDI 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 VEIKGVLGTMGLFLG 318
            E+   L  +GL L 
Sbjct: 301 EEVLAKLKELGLQLN 315


>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 =  336 bits (862), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 134/314 (42%), 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   FLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 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 YNVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKE 237

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 238 EKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>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 =  336 bits (862), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 121/314 (38%), Positives = 193/314 (61%), Gaps = 7/314 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E I+P+    + + +   N   + AEPL RG+  TLGN+LRRVL+SSL G+A+ A+QID
Sbjct: 2   SEFIRPS----VSVEEIGANAARVSAEPLERGYGDTLGNSLRRVLLSSLEGSAVEAIQID 57

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDI 125
           GV HE +++ GV+ED+TDI+LN+K +  +   D  +   +I   GP VVT  DI      
Sbjct: 58  GVQHEFTTVDGVYEDVTDIVLNVKCLVFRSLEDIDEAEASITVDGPKVVTGADIDVPTGF 117

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++NP+  IC L   A + M L + KG GYV  + +  ++DPIG I++D+++SP+++ + 
Sbjct: 118 ELVNPEQHICTLSDGAHLAMRLRIGKGRGYVSGEDNERDDDPIGFISVDSIFSPVRRCAK 177

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE  R G+  DYD+L + ++T+G+I+  ++V  A+ I+   +G F+   E  + ++E  
Sbjct: 178 AVEPCRVGRHTDYDRLVLEVETNGAISPREAVVEAANIINQHMGAFMGLSEVDESLEETS 237

Query: 246 --NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               + +  +  L K+VE+L+LSVRS NCL+   I  +  L+  +E D+L + NFG KS+
Sbjct: 238 IFASEDVQDDSELDKQVEDLDLSVRSYNCLKRAGIHSVRQLVDFSENDLLNIRNFGVKSI 297

Query: 304 VEIKGVLGTMGLFL 317
            E+K  L  MGL L
Sbjct: 298 EEVKEKLEAMGLSL 311


>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 =  336 bits (862), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 134/315 (42%), Positives = 209/315 (66%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP  IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 3   DFEKP-KIEIAEI-SEDKTYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 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 VEIKGVLGTMGLFLG 318
            E+   L  +GL L 
Sbjct: 301 EEVLAKLKELGLELN 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 =  336 bits (862), Expect = 3e-90,   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|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 =  336 bits (862), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 136/314 (43%), Positives = 204/314 (64%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVDIEQVNS---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 +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 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKE 237

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 238 EKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>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 =  336 bits (862), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 137/314 (43%), Positives = 205/314 (65%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVD---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 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKE 237

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 238 EKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>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 (862), Expect = 3e-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|190341399|gb|ACE74776.1| RpoA [Cronobacter genomosp. 1]
          Length = 308

 Score =  336 bits (862), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 137/314 (43%), Positives = 207/314 (65%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 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 =  336 bits (862), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 137/314 (43%), Positives = 207/314 (65%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 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|190341387|gb|ACE74770.1| RpoA [Pantoea sp. E147]
          Length = 308

 Score =  336 bits (862), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 137/314 (43%), Positives = 206/314 (65%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 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|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 =  336 bits (861), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 140/330 (42%), Positives = 220/330 (66%), 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH--HRTENDPIGLITIDALYSP 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 PVAQEP---REEVDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 KKSLTEIKDVLASKGLQLGMRLENWPPASL 324


>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 =  336 bits (861), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 159/345 (46%), Positives = 232/345 (67%), Gaps = 12/345 (3%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           N   L KPN I+   +  +   ++ ++ EPL  GFA TLG+ALRRV++SSLRG+A+  ++
Sbjct: 12  NLDRLTKPNAIKV--ISGDSSKKSDIVLEPLESGFALTLGHALRRVMLSSLRGSAVYGIK 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 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--------ENDPIGLITIDAL 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|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 =  336 bits (861), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 124/329 (37%), Positives = 189/329 (57%), Gaps = 7/329 (2%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E        + R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLSE----ESLSDTRSRFSIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIKIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE ++I G  ED+ +++LN+K + +    D    + + K+GPG VTAGDIQ  + + V N
Sbjct: 61  HEFTTIPGAKEDVVELVLNVKQLCVSSELDEPVTMYLRKQGPGDVTAGDIQPPSGVTVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  +  L+    + MEL V +G GYV A  ++     IG I +D++YSP+ KVSY VE+
Sbjct: 121 PELKLATLNGKGRLDMELIVERGRGYVSAAQNKQAGAGIGRIPVDSIYSPVVKVSYRVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  S     ++A A   L +  G++   +   + +    +   
Sbjct: 181 TRVEQRTDFDKLIIDVETKPSTGPRTALASAGSTLVELFGLYRELDSAAEGIDVGPSPAD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +EELEL+VRS NCL+ E +  +G+LI RTEAD+L + NFG+KS+ E+K  
Sbjct: 241 AQLAADLALPIEELELTVRSYNCLKREGVDQVGELINRTEADLLDIRNFGQKSIDEVKMK 300

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYED 338
           L  +GL L  +   + P    E A  Y+D
Sbjct: 301 LAGLGLALKDSPGTFDPA---EAAAAYDD 326


>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 =  336 bits (861), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 131/313 (41%), Positives = 196/313 (62%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +      E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPNITKI----DENKDYGKFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 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|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 =  336 bits (861), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 129/313 (41%), Positives = 197/313 (62%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +      E ++  + + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPNITKI----DENKDYGVFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 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|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 =  336 bits (861), Expect = 4e-90,   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|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 =  336 bits (861), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 137/314 (43%), Positives = 205/314 (65%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVD---IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 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 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKE 237

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 238 EKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 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 =  336 bits (861), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 137/314 (43%), Positives = 207/314 (65%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 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|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 =  336 bits (861), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 140/330 (42%), Positives = 220/330 (66%), 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH--HRTENDPIGLITIDALYSP 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 PVAQEP---REEVDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 KKSLTEIKDVLASKGLQLGMRLENWPPASL 324


>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 =  336 bits (861), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 132/315 (41%), Positives = 202/315 (64%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP  IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 3   DFEKP-KIEIAEI-SEDKRYGKFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDI 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 VEIKGVLGTMGLFLG 318
            E+   L  +GL L 
Sbjct: 301 EEVLAKLKELGLQLN 315


>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 =  336 bits (861), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 137/314 (43%), Positives = 207/314 (65%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 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|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 =  336 bits (861), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 137/314 (43%), Positives = 207/314 (65%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 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|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 =  336 bits (861), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 135/315 (42%), Positives = 206/315 (65%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP  IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 3   DFQKP-KIEIAEI-SEDKKYGKFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 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 VEIKGVLGTMGLFLG 318
            E+   L  +GL L 
Sbjct: 301 EEVLAKLKELGLQLN 315


>gi|90194062|gb|ABD92592.1| RpoA [Pasteurella multocida subsp. septica]
          Length = 304

 Score =  335 bits (860), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 138/306 (45%), Positives = 204/306 (66%), Gaps = 7/306 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 2   LVDIEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 61

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI    D+E++NP+HVIC+
Sbjct: 62  GVQEDILEVLLNLKGLAVKVQNKDDVFLTLNKSGIGPVVAADITHDGDVEIVNPEHVICH 121

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D  A + M + V +G GYVPA    H + E  PIG + +DA YSP+ +++Y VE+AR 
Sbjct: 122 LTDESASINMRIRVQRGRGYVPASARVHAQDEERPIGRLLVDACYSPVDRIAYNVEAARV 181

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 182 EQRTDLDKLVIELETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEF 238

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 239 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 298

Query: 313 MGLFLG 318
            GL LG
Sbjct: 299 RGLSLG 304


>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 =  335 bits (860), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 144/329 (43%), Positives = 211/329 (64%), Gaps = 7/329 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q+  ++L+ P  ++   +       + +  EPL RGF HTLGNALRR+L+SS+ GAAI 
Sbjct: 1   MQEMLEQLLTPRLVDIKTV---NGFNSRVTLEPLERGFGHTLGNALRRILLSSMPGAAIV 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI-GLITIDALYSPI 180
            +D E++NPD VI +L   A + M+L V KG GY  A           G++ +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 VQEEEEN---EFDPIFLQPVDDLELTVRSANCLKAEQIYYIGDLVQRAESSLLKTPNLGK 294

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           KSL EIK VL   GL LG  L +WPP S+
Sbjct: 295 KSLQEIKDVLAQRGLGLGTKLENWPPSSL 323


>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 (860), Expect = 4e-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|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 =  335 bits (860), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 139/334 (41%), Positives = 213/334 (63%), Gaps = 12/334 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E + P  +    +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQSSVTEFLIPRLVNIEQI---SMTHVKITLEPLERGFGHTLGNALRRILLSSMPGFAVT 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-VDAVVRMELTVSKGHGYVPAKHH-----RTENDPIGLITIDA 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 DIRE---PEIKEEKPEFDPILLRPVDDLELTVRSANCLKAEMIHYIGDLVQKTEVELLRT 294

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
            N G+KSL EIK VL    L LGMNL +WPP++I
Sbjct: 295 PNLGKKSLTEIKDVLAAKNLSLGMNLENWPPDNI 328


>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 =  335 bits (860), Expect = 5e-90,   Method: Composition-based stats.
 Identities = 129/313 (41%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP   +      E ++    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++IDG
Sbjct: 3   EFEKPTITKI----DENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKIDG 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|190341305|gb|ACE74729.1| RpoA [Citrobacter koseri]
          Length = 308

 Score =  335 bits (860), Expect = 5e-90,   Method: Composition-based stats.
 Identities = 136/314 (43%), Positives = 205/314 (65%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 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 YNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKE 237

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 238 EKPEFAP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|58415734|emb|CAH57281.1| RNA polymerase alpha-subunit [Salinivibrio costicola subsp.
           costicola]
          Length = 308

 Score =  335 bits (860), Expect = 5e-90,   Method: Composition-based stats.
 Identities = 134/314 (42%), 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   FLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 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-DAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVS 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 YNVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKE 237

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 238 EKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GLFLG
Sbjct: 295 EIKDVLASRGLFLG 308


>gi|262370553|ref|ZP_06063878.1| RNA polymerase [Acinetobacter johnsonii SH046]
 gi|262314353|gb|EEY95395.1| RNA polymerase [Acinetobacter johnsonii SH046]
          Length = 335

 Score =  335 bits (860), Expect = 5e-90,   Method: Composition-based stats.
 Identities = 141/330 (42%), Positives = 221/330 (66%), 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH--HRTENDPIGLITIDALYSP 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 PVAQEP---REEVDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 KKSLTEIKDVLASKGLQLGMRLENWPPASL 324


>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 =  335 bits (860), Expect = 5e-90,   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|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 =  335 bits (860), Expect = 5e-90,   Method: Composition-based stats.
 Identities = 129/319 (40%), Positives = 203/319 (63%), Gaps = 5/319 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           ++I+P  IE + L   + +    +AEPL RGF  TLGN+LRRVL+SSL G A+ +V+IDG
Sbjct: 3   KIIEP-KIETVELKS-DGSYGKFVAEPLDRGFGTTLGNSLRRVLLSSLPGVAVISVKIDG 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 EIKGVLGTMGLFLGMNLPD 323
           E+   L ++G  L  +  +
Sbjct: 301 EVIWKLQSLGFDLSKDDDN 319


>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 =  335 bits (859), Expect = 5e-90,   Method: Composition-based stats.
 Identities = 132/313 (42%), Positives = 201/313 (64%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +      E +N  + + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPNITKI----DENKNYGIFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 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|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 =  335 bits (859), Expect = 6e-90,   Method: Composition-based stats.
 Identities = 121/307 (39%), Positives = 183/307 (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    G I +D +YSP+ KVSY VE+ R  Q  D+DKL +
Sbjct: 135 DIELVVERGRGYVPAATSTDEI---GRIPVDQIYSPVLKVSYKVEATRVEQRTDFDKLIL 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|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 =  335 bits (859), Expect = 6e-90,   Method: Composition-based stats.
 Identities = 134/315 (42%), Positives = 200/315 (63%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP  I+   +  +++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 3   DFNKP-KIQITEM-SDDKRYGKFVVEPLERGYGITLGNSLRRIMLSSLPGAAVSQVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE SSI GV ED+T+II+N+K + +K   D    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 VEIKGVLGTMGLFLG 318
            E+   L  +GL L 
Sbjct: 301 EEVLAKLKELGLQLN 315


>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 =  335 bits (859), Expect = 6e-90,   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|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 =  335 bits (859), Expect = 6e-90,   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|332077536|gb|EGI87997.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
           pneumoniae GA41301]
          Length = 311

 Score =  335 bits (859), Expect = 6e-90,   Method: Composition-based stats.
 Identities = 131/313 (41%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +      E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPNITKI----DENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIDG 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|329314907|gb|AEB89320.1| DNA-directed RNA polymerase subunit alpha [Staphylococcus aureus
           subsp. aureus T0131]
          Length = 314

 Score =  335 bits (859), Expect = 6e-90,   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|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 =  335 bits (859), Expect = 6e-90,   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|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 =  335 bits (859), Expect = 6e-90,   Method: Composition-based stats.
 Identities = 127/314 (40%), Positives = 194/314 (61%), Gaps = 7/314 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E I+P     + + +  EN   + AEPL RG+  TLGN+LRRVL+SSL GAA+ A+QID
Sbjct: 2   SEFIRPQ----VSVEEISENLARVSAEPLERGYGDTLGNSLRRVLLSSLEGAAVEAIQID 57

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDI 125
           GV HE ++++GV+ED+TDI+LN+KG+  +  G   +   +I   GP  VT GD +   + 
Sbjct: 58  GVQHEFTTVEGVYEDVTDIVLNVKGLVFRSMGTGDEATASISIDGPCTVTGGDFKVPAEF 117

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++N D VIC L   A + M++ +  G GYV    +  + DPIG+I +D+LYSP+++ + 
Sbjct: 118 ELVNEDQVICTLGEGAHLSMQMRIGTGRGYVAGDDNERDGDPIGIIHVDSLYSPVRRCAK 177

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE  R GQ  +YD+L + ++TDGSIT  D+V  A+ I+   +  F+   + ++ V++  
Sbjct: 178 AVEPCRVGQHTNYDRLVLEVETDGSITPRDAVVDAANIVNQHMSAFMALADEEEPVEDAS 237

Query: 246 --NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                    N  L K++E+L+LSVRS NCL+   I  +  L++ +E D+L + NFG KS+
Sbjct: 238 IFATGVEEDNTELDKQIEDLDLSVRSYNCLKRAGIHSVRQLVEFSENDLLNIRNFGVKSI 297

Query: 304 VEIKGVLGTMGLFL 317
            E+K  L TMGL L
Sbjct: 298 EEVKDKLETMGLGL 311


>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 =  335 bits (859), Expect = 6e-90,   Method: Composition-based stats.
 Identities = 140/330 (42%), Positives = 221/330 (66%), 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH--HRTENDPIGLITIDALYSP 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 PVAQEP---REEVDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 KKSLTEIKDVLASKGLQLGMRLENWPPASL 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 =  335 bits (859), Expect = 6e-90,   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|190341453|gb|ACE74803.1| RpoA [Cronobacter sakazakii]
          Length = 308

 Score =  335 bits (859), Expect = 7e-90,   Method: Composition-based stats.
 Identities = 138/314 (43%), Positives = 207/314 (65%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 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|179184384|gb|ACB78145.1| RNA polymerase alpha subunit [Aliivibrio finisterrensis]
 gi|179184823|gb|ACB78161.1| RNA polymerase alpha subunit [Aliivibrio finisterrensis]
          Length = 313

 Score =  335 bits (859), Expect = 7e-90,   Method: Composition-based stats.
 Identities = 140/319 (43%), Positives = 208/319 (65%), 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
              +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 VPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 294

Query: 299 GRKSLVEIKGVLGTMGLFL 317
           G+KSL EIK VL + GL L
Sbjct: 295 GKKSLTEIKDVLASRGLSL 313


>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 =  335 bits (859), Expect = 7e-90,   Method: Composition-based stats.
 Identities = 132/313 (42%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +      E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPNITKI----DENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIDG 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|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 =  335 bits (859), Expect = 7e-90,   Method: Composition-based stats.
 Identities = 137/315 (43%), Positives = 208/315 (66%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 3   DFEKPN-IEIAEI-SEDKKYGKFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVNDI 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 VEIKGVLGTMGLFLG 318
            E+   L  +GL L 
Sbjct: 301 EEVLAKLKELGLQLN 315


>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 =  335 bits (858), Expect = 8e-90,   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|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 =  335 bits (858), Expect = 8e-90,   Method: Composition-based stats.
 Identities = 136/310 (43%), Positives = 200/310 (64%), Gaps = 4/310 (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 GVLGTMGLFL 317
             L  +GL  
Sbjct: 299 NKLTELGLSF 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 =  335 bits (858), Expect = 8e-90,   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|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 =  335 bits (858), Expect = 8e-90,   Method: Composition-based stats.
 Identities = 119/314 (37%), Positives = 188/314 (59%), Gaps = 7/314 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E I+P     + + +  +    +  EPL RG+  TLGN+LRRVL+SSL GAA+ A+QID
Sbjct: 2   SEFIRPQ----VHVEEISDTAARVSVEPLERGYGDTLGNSLRRVLLSSLEGAAVEAIQID 57

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDI 125
           G  HE ++I  + ED+TDI+LN+KG+  +  G + +   TI   GP  VT  D    ++ 
Sbjct: 58  GAQHEFTTIPNMVEDVTDIVLNVKGLVFRTLGTTDEGTATISVDGPCEVTGADFFIPSEF 117

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++NPD  I  L     + M + +  G GYV  + ++ +NDPIG+I +D+L+SP+K+ + 
Sbjct: 118 ELVNPDQHIATLTEGGHLTMSMRIGYGRGYVSYEQNKRDNDPIGIIHVDSLFSPVKRCAK 177

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R GQ  DYD+L + I+T+G+I+  D+V  A+ I+   +  F+   +  +  +E  
Sbjct: 178 LVEACRVGQHTDYDRLVLEIETNGAISPRDAVVSAANIINQHMAAFMTLADEPEAEEEVS 237

Query: 246 --NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +    N  L K++E+L+LSVRS NCL+   I  +  L++ +E D+L + NFG KS+
Sbjct: 238 IFAPEVTSDNAELDKQIEDLDLSVRSYNCLKRAGIHSVRQLVEFSENDLLNIRNFGVKSI 297

Query: 304 VEIKGVLGTMGLFL 317
            E+K  L +MGL L
Sbjct: 298 EEVKDKLESMGLSL 311


>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 =  335 bits (858), Expect = 9e-90,   Method: Composition-based stats.
 Identities = 129/310 (41%), Positives = 194/310 (62%), Gaps = 4/310 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +      E +N    + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPNITKI----DENKNYGKFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 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|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 =  335 bits (858), Expect = 9e-90,   Method: Composition-based stats.
 Identities = 120/314 (38%), Positives = 190/314 (60%), Gaps = 7/314 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E I+PN    + + +   N   +  EPL RG+  TLGN+LRRVL+SSL GAA+ A+QID
Sbjct: 2   SEFIRPN----VSVDEIGANVARVSVEPLERGYGDTLGNSLRRVLLSSLEGAAVEAIQID 57

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDI 125
           GV HE ++++GV+ED+TDI+LN+KG+  + + +S +   +I   GP  VT  D+      
Sbjct: 58  GVQHEFTTVEGVYEDVTDIVLNVKGLVFRNTNNSDEAEASISVDGPCTVTGADLDVPMGY 117

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++NP   IC L   A + M L +  G GYV  + +  ENDPIG I +D+++SP+++ + 
Sbjct: 118 ELVNPAQHICALAEGAHLSMRLRIGNGRGYVSGEDNERENDPIGFIHVDSIFSPVRRCAK 177

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE  R G+  DYD+L + ++T+G+I+  ++V  A+ I+   +  F+   +  +  +E  
Sbjct: 178 AVEPCRVGRHTDYDRLVLEVETNGAISPREAVVEAANIINQHMSAFMGLTDFDETQEEAS 237

Query: 246 --NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                 +  +  L K+VE+L+LSVRS NCL+   I  +  L+  +E D+L + NFG KS+
Sbjct: 238 IFAKADVEDDSELEKQVEDLDLSVRSYNCLKRAGIHSVRQLVDFSENDLLNIRNFGVKSI 297

Query: 304 VEIKGVLGTMGLFL 317
            E+K  L +MGL L
Sbjct: 298 EEVKEKLESMGLSL 311


>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 =  335 bits (858), Expect = 9e-90,   Method: Composition-based stats.
 Identities = 132/313 (42%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +      E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPNITKI----DENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIDG 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|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 =  335 bits (858), Expect = 9e-90,   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 EVKEDINVKSLPFNPALL-KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 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|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 =  335 bits (858), Expect = 9e-90,   Method: Composition-based stats.
 Identities = 139/330 (42%), Positives = 221/330 (66%), 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH--HRTENDPIGLITIDALYSP 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 PVAQEP---REEVDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 KKSLTEIKDVLASKGLQLGMRLENWPPASL 324


>gi|251772518|gb|EES53084.1| DNA-directed RNA polymerase, alpha subunit [Leptospirillum
           ferrodiazotrophum]
          Length = 322

 Score =  335 bits (858), Expect = 9e-90,   Method: Composition-based stats.
 Identities = 132/316 (41%), Positives = 193/316 (61%), Gaps = 5/316 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
             P  +    +       + ++ EP  RGF  T+GNALRRVL+SS+ G AITA++   V 
Sbjct: 8   QMPKGL---AVSHSSARSSRVVVEPFERGFGITVGNALRRVLLSSIPGVAITAIRAKNVF 64

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I GV ED+TDIILN+K + +K        + +  +GP +V A DI TV  +E+++
Sbjct: 65  HEFSNIPGVVEDVTDIILNLKSLRMKPLLQGEHWLHLKVKGPRIVKASDIDTVGAVEMMD 124

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PDHVI  LD    + M+L    G GYVPA H R+    +G+I IDA+++PI KV+Y VES
Sbjct: 125 PDHVIATLDEGGHLDMDLKTEFGRGYVPADHSRSTETEVGIIPIDAIFTPINKVNYFVES 184

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP--KKEVKEDINV 247
            R G++ DYD+L   I+TDGSIT  ++++ A++IL+  L +F++ +           +  
Sbjct: 185 TRVGRITDYDRLIFEIETDGSITPGEALSEAAKILRTHLDLFVSSDLHLANDSSPLSLES 244

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            S      + K V ELELSVR+ NCL+  +I  +G+L+ RTE ++L+  NFG+KSL EIK
Sbjct: 245 NSSKEETIMDKSVNELELSVRAANCLKSSDIKKIGELVIRTEDELLQTKNFGKKSLDEIK 304

Query: 308 GVLGTMGLFLGMNLPD 323
             L  +GL LGM+L  
Sbjct: 305 EALENIGLSLGMDLSK 320


>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 =  334 bits (857), Expect = 9e-90,   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|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 (857), Expect = 9e-90,   Method: Composition-based stats.
 Identities = 136/310 (43%), Positives = 200/310 (64%), Gaps = 4/310 (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 GVLGTMGLFL 317
             L  +GL  
Sbjct: 299 NKLTELGLSF 308


>gi|90194008|gb|ABD92565.1| RpoA [Bibersteinia trehalosi]
          Length = 302

 Score =  334 bits (857), Expect = 9e-90,   Method: Composition-based stats.
 Identities = 136/305 (44%), Positives = 205/305 (67%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVNIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+       +T+ K G G VTA DI    D+E++NPDHVIC+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVQNKDDIILTLTKSGIGPVTAADITADADVEIVNPDHVICH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D +A + M + V +G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR 
Sbjct: 121 LTDKNASISMRIRVQRGRGYVPASARVHSQHEDRPIGRLLVDARFSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLAAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>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 =  334 bits (857), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 134/313 (42%), Positives = 197/313 (62%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +      E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPNITKI----DENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSIDIDG 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|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 =  334 bits (857), Expect = 1e-89,   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|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 = 134/315 (42%), Positives = 202/315 (64%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 13  DFEKPN-IEIAEI-SEDKRYGKFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 70

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDI 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 VEIKGVLGTMGLFLG 318
            E+   L  +GL L 
Sbjct: 311 EEVLAKLKELGLQLN 325


>gi|90194052|gb|ABD92587.1| RpoA [Mannheimia glucosida]
          Length = 304

 Score =  334 bits (857), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 135/305 (44%), Positives = 205/305 (67%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVNIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+       +T+ K G G VTA DI    D+E++NPDHVIC+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVQNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPDHVICH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D +A + M + V +G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+AR 
Sbjct: 121 LTDKNASINMRIRVQRGRGYVPASARLHTQNDDRPIGRLLVDARFSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLAAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>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 =  334 bits (857), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 120/318 (37%), Positives = 186/318 (58%), Gaps = 3/318 (0%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           + +R+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+V+IDGVLHE ++I GV ED++
Sbjct: 15  DNSRSRFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSVKIDGVLHEFTTITGVKEDVS 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           DI+LNIKG+ +    D    + +   G G VTAG I+    +E+ NPD  I  L+    +
Sbjct: 75  DILLNIKGLAISSDSDEPVVMYLRAEGAGEVTAGTIEPPAGVEIHNPDLHIATLNDQGRL 134

Query: 144 RMELTVSKGHGYVP---AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
            +E+ V +G GYVP   +    +    IG I +D +YSP+ KVSY VE+ R  Q  D+DK
Sbjct: 135 EIEMVVERGRGYVPVSSSTTTNSGTTEIGRIQVDQIYSPVLKVSYNVEATRVEQRTDFDK 194

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L++ ++T  SI+  ++ A A + L +  G+        + ++   + +      A    +
Sbjct: 195 LTIDVETKNSISPRNAFASAGKTLVELFGLARELNVSAEGIEVGPSPQETEHIAAYGMPI 254

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           EEL  SVRS NCL+ + I  +G+L + TE+D+L + NFG+KS+ E+K  L  +GL L   
Sbjct: 255 EELRFSVRSYNCLKRQEIHTVGELAECTESDLLDIRNFGQKSINEVKIKLAGLGLTLKDA 314

Query: 321 LPDWPPESIEELAKKYED 338
             D+ P  +E    +  D
Sbjct: 315 PEDFDPTQLEGYDAETGD 332


>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 =  334 bits (857), Expect = 1e-89,   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|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 =  334 bits (857), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 131/313 (41%), Positives = 198/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +      E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPNITKI----DENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIDG 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|295093661|emb|CBK82752.1| DNA-directed RNA polymerase subunit alpha [Coprococcus sp. ART55/1]
          Length = 318

 Score =  334 bits (857), Expect = 1e-89,   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|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 =  334 bits (856), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 134/313 (42%), Positives = 197/313 (62%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +      E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPNITKI----DENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSIDIDG 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|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 =  334 bits (856), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 139/330 (42%), Positives = 220/330 (66%), Gaps = 8/330 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +   E + P   + I +         +I EPL RGF HTLGNALRR+L+SSL GAA+ 
Sbjct: 1   MTRTANEFLTP---QAIKVEAASGTSAKVILEPLERGFGHTLGNALRRILLSSLPGAAVV 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH--HRTENDPIGLITIDALYSP 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 PVAQEP---REEVDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 KKSLTEIKDVLASKGLQLGMRLENWPPASL 324


>gi|90194004|gb|ABD92563.1| RpoA [Lonepinella koalarum]
          Length = 302

 Score =  334 bits (856), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 138/305 (45%), Positives = 204/305 (66%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE SS +
Sbjct: 1   LVDIEQISPTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI    D+E++NPDHVIC+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVQNKDDVFLTLNKSGIGPVVAADITHDGDVEIVNPDHVICH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D +A V M + V +G GYVPA    H + E  PIG + +DA YSP+ +++Y VE+AR 
Sbjct: 121 LTDENASVNMRIRVQRGRGYVPASARVHTQDEERPIGRLLVDACYSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLVIELETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>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 =  334 bits (856), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 128/313 (40%), Positives = 198/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP   +      E ++    + EPL RG+  TLGN+LRRVL+SSL GAA+T+++ DG
Sbjct: 3   EFEKPTITKI----DENKDYGRFVIEPLERGYGTTLGNSLRRVLLSSLPGAAVTSIKFDG 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|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 =  334 bits (856), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 131/313 (41%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +      E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPNITKI----DENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIDG 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|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 =  334 bits (856), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 124/310 (40%), Positives = 200/310 (64%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  ++ + L  E+      + EPL RGF  T+GNALRR+L+SSL G A+ AV+IDG
Sbjct: 3   EIEKP-KVDIVEL-SEDYRYGKFVVEPLERGFGITIGNALRRILLSSLPGVAVYAVRIDG 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 GVLGTMGLFL 317
             L  + L L
Sbjct: 301 QKLNELDLKL 310


>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 =  334 bits (856), Expect = 2e-89,   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+I+GV
Sbjct: 1   FLKPRLVD---IEQVSQTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 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 NPDHVICNLDV-DAVVRMELTVSKGHGYVPAK---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 YSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKE 237

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 238 EKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|90194046|gb|ABD92584.1| RpoA [Actinobacillus indolicus]
          Length = 303

 Score =  333 bits (855), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 136/305 (44%), Positives = 205/305 (67%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+       +T+ K G G VTA DI    D+E++NPDHVICN
Sbjct: 61  GVQEDILEVLLNLKGLAVKVQNKDDIILTLTKSGIGPVTAADITHDGDVEIVNPDHVICN 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D +A + M + V +G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+AR 
Sbjct: 121 LTDKNASINMRIRVQRGRGYVPASARVHTQDDDRPIGRLLVDARFSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLAAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>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 =  333 bits (855), Expect = 2e-89,   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|90194006|gb|ABD92564.1| RpoA [Mannheimia haemolytica]
          Length = 302

 Score =  333 bits (855), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 135/305 (44%), Positives = 205/305 (67%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVNIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+       +T+ K G G VTA DI    D+E++NPDHVIC+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVQNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPDHVICH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D +A + M + V +G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+AR 
Sbjct: 121 LTDKNASINMRIRVQRGRGYVPASARLHTQNDDRPIGRLLVDARFSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLAAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>gi|190341335|gb|ACE74744.1| RpoA [Enterobacter helveticus]
          Length = 307

 Score =  333 bits (855), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 137/313 (43%), Positives = 207/313 (66%), Gaps = 10/313 (3%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVL
Sbjct: 1   LKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVL 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|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 =  333 bits (855), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 139/330 (42%), Positives = 221/330 (66%), 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH--HRTENDPIGLITIDALYSP 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 PVAQEP---REEVDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 KKSLTEIKDVLASKGLQLGMRLENWPPASL 324


>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 =  333 bits (855), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 133/314 (42%), Positives = 204/314 (64%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL G+AI+ V+IDG
Sbjct: 6   DFNKPN-IEITEI-SEDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGSAISQVKIDG 63

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDI 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 VEIKGVLGTMGLFL 317
            E+   L  +GL L
Sbjct: 304 EEVLAKLDELGLCL 317


>gi|190341379|gb|ACE74766.1| RpoA [Escherichia vulneris]
          Length = 308

 Score =  333 bits (855), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 136/313 (43%), Positives = 206/313 (65%), Gaps = 10/313 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 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|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 =  333 bits (855), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 139/314 (44%), Positives = 207/314 (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---IEQVSQTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 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 YSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKE 237

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 238 EKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>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 =  333 bits (855), Expect = 2e-89,   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|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 =  333 bits (855), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 133/316 (42%), Positives = 203/316 (64%), Gaps = 7/316 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL G+AI++V+IDG
Sbjct: 3   DFNKPN-IEITDV-SEDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGSAISSVKIDG 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 LVEIKGVLGTMGLFLG 318
           L E+   L  + L L 
Sbjct: 301 LEEVLAKLKELNLELN 316


>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 =  333 bits (855), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 139/314 (44%), Positives = 206/314 (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---IEQVSQTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 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 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKE 237

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 238 EKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 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 =  333 bits (855), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 139/314 (44%), Positives = 206/314 (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---IEQVSQTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 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 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKE 237

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 238 EKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>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 =  333 bits (855), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 120/320 (37%), Positives = 186/320 (58%), Gaps = 4/320 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E     +  E R+    EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVL
Sbjct: 5   QRPTLSE----EKVSEARSRFTIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+T++ILNIK +      D      + K+G G +T  DI     +EV N
Sbjct: 61  HEFSTVPGVKEDVTELILNIKSLVFSSEHDEPVVAYLRKQGSGEMTGADISCPAGVEVHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  +  L+ +  + +ELT+ +G GYV A+ ++     IG I +D++YSP+  V+Y VE+
Sbjct: 121 PDLYLGALNDEGAIDLELTIERGRGYVSAQQNKGGEQEIGRIPVDSIYSPVLSVTYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+DKL + ++T  S++  D++A A + L +  G+  +     + ++       
Sbjct: 181 TRVEQRTDFDKLIVDVETKNSMSPADAMASAGKTLVELFGLARDLNVEAEGIEMGTVQTD 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   VEEL LSVRS NCL+ E I  +G+L+ R++AD+L + NFG KS+ E++  
Sbjct: 241 ASLAADLALPVEELNLSVRSYNCLKREGIHTVGELVARSQADLLDIRNFGNKSIDEVQVE 300

Query: 310 LGTMGLFLGMNLPDWPPESI 329
           L  +GL L     D+ P +I
Sbjct: 301 LHKLGLALKDTPADFDPSTI 320


>gi|90194032|gb|ABD92577.1| RpoA [Actinobacillus lignieresii]
          Length = 302

 Score =  333 bits (855), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 139/305 (45%), Positives = 206/305 (67%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVNIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+SG     +T+ K G G VTA DI    D+E++NP HVIC+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVSGKDDIILTLNKSGIGPVTAADITHDGDVEIVNPHHVICH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D DA + M + V +G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR 
Sbjct: 121 LTDKDASISMRIRVQRGRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>gi|179184358|gb|ACB78144.1| RNA polymerase alpha subunit [Vibrio gallaecicus]
          Length = 315

 Score =  333 bits (855), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 138/321 (42%), Positives = 207/321 (64%), Gaps = 11/321 (3%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T 
Sbjct: 1   QGSVTEFLKPRLVDIEQINT---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 SPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLG 318
            G+KSL EIK VL + GL LG
Sbjct: 295 LGKKSLTEIKDVLASRGLSLG 315


>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 =  333 bits (855), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 130/313 (41%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +      E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPNITKI----DENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 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|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 =  333 bits (855), Expect = 2e-89,   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-IEVEEYI-KDEFYGKFVIEPLKRGYGTTLGNSLRRVLLSSLPGAAVTSISIEG 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|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 =  333 bits (854), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 139/314 (44%), Positives = 207/314 (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---IEQVSQTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 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 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKE 237

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 238 EKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>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 =  333 bits (854), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 131/313 (41%), Positives = 201/313 (64%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +      E ++  + + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPNITKI----DENKDYGIFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 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|90193996|gb|ABD92559.1| RpoA [Volucribacter psittacicida]
          Length = 302

 Score =  333 bits (854), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 139/305 (45%), Positives = 206/305 (67%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVDIEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+       +T+ K G G V AGDI    D+E++NP+HVIC+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVQNKDDVLLTLSKSGIGPVVAGDIIHDGDVEIVNPEHVICH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D +A ++M + V +G GYVPA    H + E  PIG + +DA YSP+ +++Y VE+AR 
Sbjct: 121 LTDENASIQMRIRVQRGRGYVPASARVHAQDEERPIGRLLVDACYSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G+I  ED++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLVIELETNGTIDPEDAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>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 =  333 bits (854), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 140/330 (42%), Positives = 221/330 (66%), 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH--HRTENDPIGLITIDALYSP 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 PVAQEP---REEVDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 KKSLTEIKDVLASKGLQLGMRLENWPPASL 324


>gi|90194054|gb|ABD92588.1| RpoA [Mannheimia varigena]
          Length = 302

 Score =  333 bits (854), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 136/305 (44%), Positives = 206/305 (67%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTDVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+       +T+ K G G VTA DI    D+E++NPDHVICN
Sbjct: 61  GVQEDILEVLLNLKGLAVKVQNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPDHVICN 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D +A + M + V +G GYVPA    H ++++ PIG + +DA +SP+ +++Y VE+AR 
Sbjct: 121 LTDKNASINMRIRVQRGRGYVPASARLHTQSDDRPIGRLLVDARFSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLAAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>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 = 129/315 (40%), Positives = 199/315 (63%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP  IE   +  E+      + EPL RG+  TLGN+LRR+++SSL GAA++ V+I+G
Sbjct: 59  DFNKPR-IEIAEI-SEDRKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIEG 116

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDI 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 VEIKGVLGTMGLFLG 318
            E+   L  +GL L 
Sbjct: 357 EEVLAKLKELGLQLN 371


>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 =  333 bits (854), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 134/314 (42%), Positives = 205/314 (65%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL G+AI+ V+IDG
Sbjct: 6   DFNKPN-IEITEI-SEDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGSAISQVKIDG 63

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDI 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 VEIKGVLGTMGLFL 317
            E+   L  +GL L
Sbjct: 304 EEVLAKLDELGLSL 317


>gi|323126337|gb|ADX23634.1| DNA-directed RNA polymerase subunit alpha [Streptococcus
           dysgalactiae subsp. equisimilis ATCC 12394]
          Length = 312

 Score =  333 bits (854), Expect = 3e-89,   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|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 =  333 bits (854), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 140/330 (42%), Positives = 221/330 (66%), 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH--HRTENDPIGLITIDALYSP 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 PVAQEP---REEVDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 KKSLTEIKDVLASKGLQLGMRLENWPPASL 324


>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 =  333 bits (854), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 130/313 (41%), Positives = 199/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +      E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPNITKI----DENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 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|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 =  333 bits (854), Expect = 3e-89,   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  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQTVN 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|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 =  333 bits (854), Expect = 3e-89,   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|90194018|gb|ABD92570.1| RpoA [Actinobacillus ureae ATCC 25976]
          Length = 302

 Score =  333 bits (853), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 137/305 (44%), Positives = 206/305 (67%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVKIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           G+ ED+ +++LN+KG+ +K+S      +T+ K G G VTA DI    D+E++NPDHVIC+
Sbjct: 61  GIQEDILEVLLNLKGLAVKVSNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPDHVICH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D +A + M + V +G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR 
Sbjct: 121 LTDKNASINMCIRVQRGRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>gi|190341313|gb|ACE74733.1| RpoA [Enterobacter amnigenus]
          Length = 308

 Score =  333 bits (853), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 136/314 (43%), Positives = 206/314 (65%), Gaps = 10/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            + P  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGV
Sbjct: 1   FLNPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGV 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|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 =  333 bits (853), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 129/317 (40%), Positives = 204/317 (64%), Gaps = 6/317 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP  IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA++ V+IDG
Sbjct: 3   DFEKP-KIEIADI-SEDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSQVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDI 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|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 =  333 bits (853), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 130/313 (41%), Positives = 187/313 (59%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  I    L    +     I EPL  G+  T+GN+LRRVL+SSL GAA++ + I G
Sbjct: 3   EIEKP-KITIDKLDDSGK-YGKFIVEPLESGYGITIGNSLRRVLLSSLPGAAVSFINIRG 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 GVLGTMGLFLGMN 320
             L  M L L   
Sbjct: 301 SKLQEMNLSLKTE 313


>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 =  333 bits (853), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 133/320 (41%), Positives = 195/320 (60%), Gaps = 7/320 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             EL+ P  ++   +G    N + +  EPL RGF +TLG ALRRVL+SS+ GAA+T  +I
Sbjct: 3   LSELLTPRIVKIQEMG---LNTSRVTLEPLERGFGYTLGTALRRVLLSSIEGAAVTECEI 59

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           DGVLHE S I+GV ED+ D++LN+KG+ L +       + +     G V A D    +++
Sbjct: 60  DGVLHEYSGIEGVSEDVIDVLLNLKGLALILHEGERAEMRLSVNKAGEVKASDFSAPSNV 119

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSPIKKVS 184
           E+ NPDHVI +L  D    M + V KG GY  A            ++ +DA +SPIK+++
Sbjct: 120 EICNPDHVIAHLTQDVSFSMTVVVEKGRGYRVATQEIDTATHAPNVLRVDASFSPIKRIA 179

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE+AR  Q  D DKL + I+++G+I  E ++  A+ IL  Q+ +F+N E       E 
Sbjct: 180 YRVEAARVEQHTDLDKLVIDIESNGTIDPEQAIREAATILHKQIAVFVNLE---STEVEA 236

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              + +  +P LL+ V++LEL+VRS NCL+ ENI  +GDL++RTE ++L+  N G+KSL 
Sbjct: 237 EYEEEVQVDPVLLRPVDDLELTVRSANCLKAENINNIGDLVRRTEVELLKTPNLGKKSLN 296

Query: 305 EIKGVLGTMGLFLGMNLPDW 324
           EIK VL   GL LGM+L +W
Sbjct: 297 EIKEVLAAHGLELGMDLENW 316


>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 =  333 bits (853), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 138/330 (41%), Positives = 221/330 (66%), 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH--HRTENDPIGLITIDALYSP 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 PVAQEP---REEVDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 KKSLTEIKDVLASKGLQLGMRLENWPPASL 324


>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 =  333 bits (853), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 138/314 (43%), 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---IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 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 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKE 237

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 238 EKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>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 =  333 bits (853), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 133/329 (40%), Positives = 190/329 (57%), Gaps = 1/329 (0%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
              P N+  +      E     IAEP  +GF HTLGN LRRVL+ SL G A+T ++IDGV
Sbjct: 8   FAMPQNM-VLDEATATEKYGKFIAEPFEKGFGHTLGNGLRRVLLHSLEGVAVTWIKIDGV 66

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE +    V ED+T+I+LN K +     GD  +++ +     G VTA DI T    +V+
Sbjct: 67  LHEYAQAADVVEDVTEIVLNFKNVRFTAEGDLPRKLELRANTKGPVTAADIVTDGVTQVV 126

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  IC LD D  +R+E  V+ G G+  A  ++    PIGLI +D+L+SPI++VSY V 
Sbjct: 127 NPEQYICTLDKDTPLRIEFEVASGRGWKSADDNKPSEAPIGLIPVDSLFSPIERVSYDVS 186

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
             R GQ+ DYDKL + I TDG I+ ED++  ++ IL+D L +F +              +
Sbjct: 187 DTRVGQMTDYDKLELEIWTDGRISPEDALRKSAIILRDHLCVFTDDNPEDSTASLIQTPE 246

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  +L  V  +ELSVR+ NCLR   I Y+G+LIQ++E++ML+  NFG+KSL EIK 
Sbjct: 247 DEAILSKMLIPVTSVELSVRAQNCLRNAEIKYLGELIQKSESEMLKYRNFGKKSLDEIKD 306

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYE 337
            +  MG+ L M L D    +  +  +K E
Sbjct: 307 KMLEMGITLNMKLKDEVRVAFNKKLEKEE 335


>gi|90193990|gb|ABD92556.1| RpoA [Pasteurella multocida]
 gi|90194060|gb|ABD92591.1| RpoA [Pasteurella multocida subsp. gallicida]
          Length = 302

 Score =  333 bits (853), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 137/305 (44%), Positives = 203/305 (66%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVDIEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI    D+E++NP+HVIC+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVQNKDDVFLTLNKSGIGPVVAADITHDGDVEIVNPEHVICH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D  A + M + V +G GYVPA    H + E  PIG + +DA YSP+ +++Y VE+AR 
Sbjct: 121 LTDESASINMRIRVQRGRGYVPASARVHAQDEERPIGRLLVDACYSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLVIELETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>gi|90193998|gb|ABD92560.1| RpoA [Avibacterium gallinarum]
          Length = 302

 Score =  332 bits (852), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 136/305 (44%), Positives = 205/305 (67%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVDIEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+    +  +T+ K G G V A DI    D+E++NP+HVIC+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVQNKDNVFLTLSKSGIGPVVAADITYDGDVEIVNPEHVICH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D +A + M + V +G GYVPA    H + E  PIG + +DA YSP+++++Y VE+ R 
Sbjct: 121 LTDENASINMCIRVQRGRGYVPASARVHSQDEERPIGRLLVDACYSPVQRIAYNVEATRV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLVIELETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>gi|197288305|gb|ACH57435.1| RpoA [Aliivibrio finisterrensis]
          Length = 313

 Score =  332 bits (852), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 140/319 (43%), Positives = 207/319 (64%), Gaps = 10/319 (3%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E +K   +  + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I
Sbjct: 1   VTEFLK---LRLVDIEQVSMTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEI 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
           +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+K
Sbjct: 238 EKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKK 294

Query: 302 SLVEIKGVLGTMGLFLGMN 320
           SL EIK VL + GL LGM 
Sbjct: 295 SLTEIKDVLASRGLSLGMR 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 =  332 bits (852), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 129/313 (41%), Positives = 198/313 (63%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +      E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPNITKI----DENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 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|90194048|gb|ABD92585.1| RpoA [Actinobacillus porcinus]
          Length = 303

 Score =  332 bits (852), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 136/305 (44%), Positives = 204/305 (66%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE SS +
Sbjct: 1   LVNIEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI    D+E++NPDHV+C+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVQNKDDVFLTLNKSGIGPVVAADITHDGDVEIVNPDHVLCH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D +A + M + V +G GYVPA    H + E  PIG + +DA YSP+ +++Y VE+AR 
Sbjct: 121 LTDENASINMRIRVQRGRGYVPASARAHTQDEERPIGRLLVDACYSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLVIELETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>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 =  332 bits (852), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 138/314 (43%), 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---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 YAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKE 237

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 238 EKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|90194024|gb|ABD92573.1| RpoA [Actinobacillus genomosp. 1]
          Length = 303

 Score =  332 bits (852), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 139/305 (45%), Positives = 206/305 (67%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+SG     +T+ K G G VTA DI    D+E++NP HVIC+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVSGKDDIILTLNKSGIGPVTAADITHDGDVEIVNPHHVICH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D DA + M + V +G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR 
Sbjct: 121 LTDKDAAISMRIRVQRGRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>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 =  332 bits (852), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 144/339 (42%), Positives = 211/339 (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-AVVRMELTVSKGHGYVPAKHHRTEND-------PIGLIT 172
            +  ++++NP HVIC +  D A++ M + V +G GYVPA               PIG + 
Sbjct: 118 DSSIVKIVNPAHVICVITDDHAILSMRIKVQRGRGYVPAFSKFNSILDEQQTAIPIGRLV 177

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 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|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 =  332 bits (852), Expect = 4e-89,   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|90194016|gb|ABD92569.1| RpoA [Actinobacillus hominis]
          Length = 302

 Score =  332 bits (852), Expect = 4e-89,   Method: Composition-based stats.
 Identities = 137/305 (44%), Positives = 206/305 (67%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+S      +T+ K G G VTA DI    D+E++NP+HVIC+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVSNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPNHVICH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D +A + M + V +G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR 
Sbjct: 121 LTDKNASINMRIRVQRGRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>gi|90194064|gb|ABD92593.1| RpoA [Pasteurella canis]
          Length = 302

 Score =  332 bits (851), Expect = 5e-89,   Method: Composition-based stats.
 Identities = 136/305 (44%), Positives = 203/305 (66%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVDIEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI    D+E++NP+H+IC+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVQNKDDVFLTLNKSGIGPVVAADITHDGDVEIVNPEHIICH 120

Query: 137 LDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L  D A + M + V +G GYVPA    H + E  PIG + +DA YSP+ +++Y VE+AR 
Sbjct: 121 LTDDNASINMRIRVQRGRGYVPASARVHAQDEERPIGRLLVDACYSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLVIELETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>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 =  332 bits (851), Expect = 5e-89,   Method: Composition-based stats.
 Identities = 129/313 (41%), Positives = 195/313 (62%), Gaps = 4/313 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +      E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ I+G
Sbjct: 3   EFEKPNITKI----DENKDYGKFVVEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIEG 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|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 =  332 bits (851), Expect = 5e-89,   Method: Composition-based stats.
 Identities = 133/329 (40%), Positives = 206/329 (62%), Gaps = 10/329 (3%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQ    ++  P  +E              IA+PL RG+  T+GNA+RRVL+SSL G AI
Sbjct: 1   MIQ----QMQMPEKLEVDEA-SYSNYYGKFIAQPLERGYGVTIGNAIRRVLLSSLPGTAI 55

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           T ++I+GVLHE S+I GV ED+ DI+LN+K I  +     +  VT+  RGP    AGDI 
Sbjct: 56  TGIKIEGVLHEFSTIDGVKEDVPDIVLNLKQIRFRSISKRNAVVTLVLRGPKDFVAGDIV 115

Query: 121 TV-NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
           +   D EVLNP+H I  L+ DA ++++++V +G GY+PA+ ++ E  PIG I++D++++P
Sbjct: 116 SPEGDFEVLNPEHHIATLNEDATLKIDVSVGRGRGYMPAEDNKPETMPIGYISVDSIFTP 175

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           I+ V Y+VE+ R GQ  DY+KLS+ ++TDGSI  +++V++A +I+ D + +F  F   ++
Sbjct: 176 IRNVKYSVENTRVGQRTDYEKLSLEVETDGSIAPDEAVSMAGKIINDHVRLFSLFSPTQE 235

Query: 240 EVKEDINVKSLPFNPALLK----KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           E  E+   +       + K    ++E+LELSVRS NCLR   I  +G L+ + E ++L  
Sbjct: 236 EEVEEEVQQEDEEFENMRKLLMTRIEDLELSVRSHNCLRSAEIDTLGQLVSKREDELLGY 295

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDW 324
            NFG+KSL E+K +L +  L  GM +  +
Sbjct: 296 KNFGKKSLAELKELLESKNLSFGMEVTKY 324


>gi|90194030|gb|ABD92576.1| RpoA [Actinobacillus equuli subsp. haemolyticus]
          Length = 303

 Score =  332 bits (851), Expect = 5e-89,   Method: Composition-based stats.
 Identities = 137/305 (44%), Positives = 206/305 (67%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+S      +T+ K G G VTA DI    D+E++NP+HVIC+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVSNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPNHVICH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D +A + M + V +G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR 
Sbjct: 121 LTDKNASINMRIRVQRGRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>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 =  332 bits (851), Expect = 5e-89,   Method: Composition-based stats.
 Identities = 121/312 (38%), Positives = 180/312 (57%), Gaps = 4/312 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E     +  +NR+  I EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGV 
Sbjct: 15  QRPTLTE----EKVSDNRSRFILEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVQ 70

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+ +IILNIK I L    D    + + K G GVVTAGDI     +E+ N
Sbjct: 71  HEFSTVPGVKEDVAEIILNIKNIVLSSENDEPVVMYLRKTGAGVVTAGDITPPAGVEIHN 130

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  +  L     V +ELTV +G GYV A  ++  N  I  I ID++YSP+ KV+Y VE+
Sbjct: 131 PELELATLSEKGKVEIELTVERGRGYVSAMQNKDPNAEISRIPIDSIYSPVLKVTYKVEA 190

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R  Q  D+D+L + ++T  +IT  D++A A + L +  G+        + ++   +   
Sbjct: 191 TRVEQRTDFDRLIVDVETKPAITPRDALASAGKTLVELFGLARELNVEAEGIEIGPSATD 250

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L   +E L L  RS N LR   I+ +G+L+  +EAD+L + NFG KS+ EIK  
Sbjct: 251 ETLAADLALPIENLGLQSRSYNALRRRGILSVGELVAHSEADLLDIRNFGLKSIEEIKEK 310

Query: 310 LGTMGLFLGMNL 321
           L  +G+ L  ++
Sbjct: 311 LAGLGMTLKDSV 322


>gi|90193994|gb|ABD92558.1| RpoA [Gallibacterium anatis]
          Length = 300

 Score =  332 bits (851), Expect = 6e-89,   Method: Composition-based stats.
 Identities = 134/303 (44%), Positives = 201/303 (66%), Gaps = 5/303 (1%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVDIEQISPTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI    D+E++NPDH+IC+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVQNKDDVFLTLTKSGIGPVVAADITHDGDVEIVNPDHIICH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPA-KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
           L D +A + M + V +G GYVPA      E  PIG + +DA YSP+ +++Y VE+AR  Q
Sbjct: 121 LTDENASINMRIRVQRGRGYVPASSRTHDEERPIGRLLVDACYSPVDRIAYNVEAARVEQ 180

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
             D DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++    ++  +   F+P
Sbjct: 181 RTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEFDP 237

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
            LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + G
Sbjct: 238 ILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRG 297

Query: 315 LFL 317
           L L
Sbjct: 298 LSL 300


>gi|58416068|emb|CAH57448.1| RNA polymerase alpha-subunit [Vibrio sp. R-23695]
          Length = 308

 Score =  332 bits (851), Expect = 6e-89,   Method: Composition-based stats.
 Identities = 139/314 (44%), Positives = 206/314 (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 YSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKE 237

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 238 EKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLG 318
           EIK VL + GL LG
Sbjct: 295 EIKDVLASRGLSLG 308


>gi|302023188|ref|ZP_07248399.1| DNA-directed RNA polymerase subunit alpha [Streptococcus suis
           05HAS68]
          Length = 300

 Score =  331 bits (850), Expect = 6e-89,   Method: Composition-based stats.
 Identities = 129/302 (42%), Positives = 197/302 (65%), Gaps = 4/302 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP   +      E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T+++IDG
Sbjct: 3   EFEKPTITKI----DENKDYGRFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSIKIDG 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|90194022|gb|ABD92572.1| RpoA [Actinobacillus suis ATCC 33415]
          Length = 302

 Score =  331 bits (850), Expect = 6e-89,   Method: Composition-based stats.
 Identities = 138/305 (45%), Positives = 206/305 (67%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + L Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVNLEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+S      +T+ K G G VTA DI    D+E++NP+HVIC+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVSNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPNHVICH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D +A + M + V +G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR 
Sbjct: 121 LTDKNASINMRIRVQRGRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>gi|294842678|ref|ZP_06787361.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter sp.
           6014059]
          Length = 335

 Score =  331 bits (850), Expect = 7e-89,   Method: Composition-based stats.
 Identities = 140/330 (42%), Positives = 221/330 (66%), 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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH--HRTENDPIGLITIDALYSP 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 PVAQEP---REEVDPILLRPVDDLELTVRSANCLKAENIYYIGDLVQRTEVELLKTPNLG 294

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           +KSL EIK VL + GL LGM L +WPP S+
Sbjct: 295 KKSLTEIKDVLASKGLQLGMRLENWPPASL 324


>gi|179184592|gb|ACB78153.1| RNA polymerase alpha subunit [Vibrio breoganii]
          Length = 314

 Score =  331 bits (850), Expect = 7e-89,   Method: Composition-based stats.
 Identities = 139/319 (43%), Positives = 207/319 (64%), Gaps = 11/319 (3%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+
Sbjct: 2   SVTEFLKPRLVDIEQINT---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVE 58

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           I+GVLHE S+ +GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    
Sbjct: 59  IEGVLHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDG 118

Query: 124 DIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSP 179
           D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP
Sbjct: 119 DVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSP 178

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           + K++Y+VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + + 
Sbjct: 179 VDKIAYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRV 238

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
             KE+   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G
Sbjct: 239 PEKEEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLG 295

Query: 300 RKSLVEIKGVLGTMGLFLG 318
           +KSL EIK VL + GL LG
Sbjct: 296 KKSLTEIKDVLASRGLSLG 314


>gi|90194014|gb|ABD92568.1| RpoA [Actinobacillus genomosp. 2]
          Length = 303

 Score =  331 bits (850), Expect = 7e-89,   Method: Composition-based stats.
 Identities = 139/305 (45%), Positives = 206/305 (67%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+SG     +T+ K G G VTA DI    D+E++NP HVIC+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVSGKDDIILTLNKSGIGPVTAADITHDGDVEIVNPHHVICH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D DA + M + + +G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR 
Sbjct: 121 LTDKDASISMRIRIQRGRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    +I  +   F
Sbjct: 181 EQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EIKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>gi|91200694|emb|CAJ73745.1| strongly similar to DNA-directed RNA polymerase, alpha chain
           [Candidatus Kuenenia stuttgartiensis]
          Length = 338

 Score =  331 bits (850), Expect = 8e-89,   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|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 =  331 bits (850), Expect = 8e-89,   Method: Composition-based stats.
 Identities = 133/332 (40%), Positives = 191/332 (57%), Gaps = 26/332 (7%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +   P     I     EENR     EPL RGF +T GN+LRRVL+SSL GAA+T+V+I+G
Sbjct: 3   DFQVPR----ITTETVEENRGSFTIEPLDRGFGYTFGNSLRRVLLSSLAGAAVTSVRIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR-VTIFKRGPGVVTAGDIQTVNDIE 126
           V HE S+I GV ED+TDI+LN+KGI  +M  D+ +    +   GPG +TA DI   + +E
Sbjct: 59  VAHEFSTIPGVKEDVTDIVLNLKGIVCRMHSDATEIEAPLVVTGPGDITAKDIDLPSGVE 118

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +LNPD  I  L+    + + LT+ +G GY PA+ +++ + PIG+I ID+++SP+++V+Y 
Sbjct: 119 ILNPDAHIATLEKKTKLEVYLTIGRGRGYRPAEENKSPDQPIGVIPIDSIFSPVRRVAYA 178

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK------- 239
           VE AR GQ  DYDKL++ I+TDGSI    ++  A+ IL  QL +F + +   +       
Sbjct: 179 VEQARVGQKTDYDKLTLDIETDGSIDPHAALREAAEILISQLAIFTDADRVIELRDTGGL 238

Query: 240 --------------EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLI 285
                                    P N      +EELEL VRS NCL+   I  +GDLI
Sbjct: 239 GALEPGLAGGGVGGVGGHGAGPGGRPANAMDDILIEELELGVRSYNCLKRAGIQTVGDLI 298

Query: 286 QRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            +TE ++  + NFG+KS+ E+   L   GL L
Sbjct: 299 SKTENELNAIPNFGKKSIDEVIETLEGRGLHL 330


>gi|164608448|gb|ABY62527.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 309

 Score =  331 bits (850), Expect = 8e-89,   Method: Composition-based stats.
 Identities = 134/315 (42%), Positives = 207/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQIST---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 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 AYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDVFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>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 =  331 bits (849), Expect = 8e-89,   Method: Composition-based stats.
 Identities = 138/304 (45%), Positives = 205/304 (67%), Gaps = 7/304 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVNIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+SG     +T+ K G G VTA DI    D+E++NP HVIC+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVSGKDDIILTLNKSGIGPVTAADITHDGDVEIVNPHHVICH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D DA + M + V +G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR 
Sbjct: 121 LTDKDASISMRIRVQRGRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLF 316
            GL 
Sbjct: 298 RGLS 301


>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 =  331 bits (849), Expect = 9e-89,   Method: Composition-based stats.
 Identities = 131/314 (41%), Positives = 203/314 (64%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL G+AI+ V+IDG
Sbjct: 3   DFNKPN-IEITEI-SEDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGSAISYVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDI 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 VEIKGVLGTMGLFL 317
            E+   L  +GL L
Sbjct: 301 EEVLAKLKELGLEL 314


>gi|90194026|gb|ABD92574.1| RpoA [Actinobacillus capsulatus]
          Length = 303

 Score =  331 bits (849), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 136/305 (44%), Positives = 204/305 (66%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+S      +T+ K G G VTA DI    D+E++NP+HVIC+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVSNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPNHVICH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D  A + M + V +G GYV A    H + E+ PIG + +DA +SP+ +++Y VE+AR 
Sbjct: 121 LTDKSASINMRIRVQRGRGYVSASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>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 =  331 bits (849), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 134/315 (42%), Positives = 206/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQIST---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 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 AYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>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 =  331 bits (849), Expect = 1e-88,   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|179184569|gb|ACB78152.1| RNA polymerase alpha subunit [Vibrio crassostreae]
          Length = 315

 Score =  331 bits (849), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 137/321 (42%), Positives = 206/321 (64%), 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
           +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLG 318
            G+KSL EIK VL + GL LG
Sbjct: 295 LGKKSLTEIKDVLASRGLSLG 315


>gi|58415862|emb|CAH57345.1| RNA polymerase alpha-subunit [Vibrio gazogenes]
          Length = 309

 Score =  331 bits (849), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 139/315 (44%), Positives = 208/315 (66%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQIST---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 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 AYTVEAARVEQRTDLDKLVIDMETNGTIEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>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 =  331 bits (848), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 131/325 (40%), Positives = 190/325 (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 KEDINVKSLPFNPAL---LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + +    S   N         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|90194056|gb|ABD92589.1| RpoA [Mannheimia ruminalis]
          Length = 302

 Score =  331 bits (848), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 136/305 (44%), Positives = 206/305 (67%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q    R  +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVNIEQVSSTRAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+       +T+ K G G VTA DI    D+E++NPDH+IC+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVQNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPDHIICH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D +A + M + V +G GYVPA    H + ++ PIG + +DA YSP+ +++Y VE+AR 
Sbjct: 121 LTDKNASISMRIRVQRGRGYVPASARLHTQNDDRPIGRLLVDARYSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLAAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>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 =  331 bits (848), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 141/327 (43%), Positives = 220/327 (67%), Gaps = 9/327 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E IKP   +   +    + +  +  EPL RGF HT+GNALRR+L+SS+ G A+T V+IDG
Sbjct: 22  EFIKPKLADIQKI---SKTQARITLEPLERGFGHTIGNALRRILLSSMPGFAVTEVEIDG 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 + E K++
Sbjct: 199 YKVEATRVEQRTDLDKLIIEIETNGTIDPKEAIHKSATILANQLESFV---ELQNEDKKE 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|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 =  330 bits (847), Expect = 1e-88,   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|268609564|ref|ZP_06143291.1| DNA-directed RNA polymerase, alpha subunit [Ruminococcus
           flavefaciens FD-1]
          Length = 321

 Score =  330 bits (847), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 124/315 (39%), Positives = 199/315 (63%), Gaps = 6/315 (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 LVEIKGVLGTMGLFL 317
             E+K  L ++G  L
Sbjct: 302 FDEVKEKLQSLGFDL 316


>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 =  330 bits (847), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 112/311 (36%), Positives = 180/311 (57%), Gaps = 8/311 (2%)

Query: 15  IEYIVLGQEEEN--RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           IE +    E +N      + EPL RG   TLGNALRRVL+S+L G A+TAV+I GV HE 
Sbjct: 6   IECVETRTEADNGQYGKFVLEPLERGQGTTLGNALRRVLLSNLEGTAVTAVRITGVNHEF 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           +++KG+ ED+ DI+LN+K + L+      +   +  +GP  VTA D++   +++V++P H
Sbjct: 66  ATMKGIREDVLDILLNMKELVLRSYTSDIQIGRLAVQGPKRVTAADLELPTEVQVVHPRH 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  L  D  + ME  + +G GY   +    +   I  ++IDA++ P++KV++TVES R 
Sbjct: 126 YIATLAEDGQLEMEFQIERGKGYRAIERGSEDGAAIDYLSIDAIFMPVRKVNWTVESERS 185

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
              ++ D+L++ I T GS++ +++++ A++IL DQL         +   +     +    
Sbjct: 186 AANVEQDRLTLEIWTSGSLSPQEALSQAAKILVDQLRPL-----QEITFEPPAEPQRSAP 240

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG- 311
           N      +EEL+LSVR+ NCL+   I  + DL++ TE D+L + NFG+KS  E+   L  
Sbjct: 241 NTVGQVPIEELQLSVRAYNCLKRAQINTVADLLEYTEEDLLEIKNFGQKSAEEVIEALQD 300

Query: 312 TMGLFLGMNLP 322
            MGL L  + P
Sbjct: 301 KMGLSLPKDKP 311


>gi|179184612|gb|ACB78154.1| RNA polymerase alpha subunit [Vibrio breoganii]
          Length = 314

 Score =  330 bits (847), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 139/320 (43%), Positives = 207/320 (64%), Gaps = 11/320 (3%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T 
Sbjct: 1   QGSVTEFLKPRLVDIEQINT---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 SPVDKIAYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +   KE+   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPEKEEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFL 317
            G+KSL EIK VL + GL L
Sbjct: 295 LGKKSLTEIKDVLASRGLSL 314


>gi|179184539|gb|ACB78151.1| RNA polymerase alpha subunit [Vibrio gigantis]
          Length = 314

 Score =  330 bits (847), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 137/320 (42%), Positives = 206/320 (64%), Gaps = 11/320 (3%)

Query: 3   QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T 
Sbjct: 1   QGSVTEFLKPRLVDIEQINT---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 SPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFL 317
            G+KSL EIK VL + GL L
Sbjct: 295 LGKKSLTEIKDVLASRGLSL 314


>gi|90194000|gb|ABD92561.1| RpoA [Nicoletella semolina]
          Length = 302

 Score =  330 bits (847), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 134/305 (43%), Positives = 203/305 (66%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVSIEQVSLTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI    D+E++NP+HVIC+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVQNKDDVILTLTKSGIGPVIAADIVHDGDVEIVNPNHVICH 120

Query: 137 LDV-DAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L   +A + M + V +G GYVPA    H + +N PIG + +DA +SP+ ++SY VE+AR 
Sbjct: 121 LTDNNASINMRIRVRRGRGYVPASALVHTQDDNRPIGRLLVDARFSPVDRISYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLAAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>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 =  330 bits (847), Expect = 2e-88,   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|197288307|gb|ACH57436.1| RpoA [Vibrio gallaecicus]
          Length = 311

 Score =  330 bits (847), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 138/317 (43%), Positives = 206/317 (64%), Gaps = 11/317 (3%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVL
Sbjct: 1   LKPRLVDIEQINT---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVL 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 YAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKE 237

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL 
Sbjct: 238 EKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLT 294

Query: 305 EIKGVLGTMGLFLGMNL 321
           EIK VL + GL LGM L
Sbjct: 295 EIKDVLASRGLSLGMRL 311


>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 =  330 bits (847), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 134/315 (42%), Positives = 206/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQIST---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 +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 AYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|90194020|gb|ABD92571.1| RpoA [Actinobacillus arthritidis]
          Length = 303

 Score =  330 bits (846), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 138/305 (45%), Positives = 206/305 (67%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVNIEQISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+SG     +T+ K G G VTA DI    D+E++NP H+IC+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVSGKDDIILTLNKSGIGPVTAADITHDGDVEIVNPHHIICH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D DA + M + + +G GYVPA    H + E+ PIG + +DA +SP+ +++Y VE+AR 
Sbjct: 121 LTDKDASISMRIRIQRGRGYVPASARVHSQDEDRPIGRLLVDARFSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    +I  +   F
Sbjct: 181 EQRTDLDKLIIEMETNGTIDPEEAIRRAATILAEQLDAFVDLRDVRQP---EIKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>gi|58415962|emb|CAH57395.1| RNA polymerase alpha-subunit [Vibrio nereis]
          Length = 309

 Score =  330 bits (846), Expect = 2e-88,   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---IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 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 AYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|58415844|emb|CAH57336.1| RNA polymerase alpha-subunit [Vibrio fluvialis]
          Length = 309

 Score =  330 bits (846), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 134/315 (42%), Positives = 206/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQIST---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 +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 AYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFGP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>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 =  330 bits (846), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 134/315 (42%), 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---IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 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 AYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>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 =  330 bits (846), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 120/310 (38%), Positives = 196/310 (63%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  ++ + L  E+      + EPL RGF  T+GNALRR+L+SSL G A+ A++IDG
Sbjct: 3   EIEKP-KVDIVEL-SEDYRFGKFVVEPLERGFGITVGNALRRILLSSLPGVAVYAIRIDG 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 GVLGTMGLFL 317
             L  + L L
Sbjct: 301 HKLEELELRL 310


>gi|90193992|gb|ABD92557.1| RpoA [Histophilus somni]
          Length = 302

 Score =  330 bits (846), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 137/305 (44%), Positives = 204/305 (66%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +I EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVDIEQISSTHAKVILEPLERGFGHTLGNALRRILLSSMPGYAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+    +  +T+ K G G V A DI    D+E++NPDHVIC+
Sbjct: 61  GVQEDIIEVLLNLKGLAVKVQNKDNVFLTLSKSGIGPVVAADITHDGDVEIVNPDHVICH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D +A + M + V +G GYVPA    H   E  PIG + +DA YSP+ +++Y V++AR 
Sbjct: 121 LTDENASINMRIRVQRGRGYVPASSRVHSLDEERPIGRLLVDACYSPVDRIAYNVQAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLVIELETNGTIEPEEAIRRAATILAEQLDAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLVS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 302


>gi|58415948|emb|CAH57388.1| RNA polymerase alpha-subunit [Vibrio navarrensis]
          Length = 309

 Score =  330 bits (845), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 135/315 (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   FLKPRLVDIEQISS---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 +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 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|90194002|gb|ABD92562.1| RpoA [Phocoenobacter uteri]
          Length = 302

 Score =  330 bits (845), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 134/305 (43%), Positives = 205/305 (67%), Gaps = 7/305 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVNIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+       +T+ K G G V A DI    D+E++NP+HVIC+
Sbjct: 61  GVQEDILEVLLNLKGLAVKVQNKDDIVLTLNKSGIGPVIAADITHDGDVEIVNPEHVICH 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D DA + M + V +G GYVPA    H ++++ PIG + +DA +SP+ +++Y VE+AR 
Sbjct: 121 LTDKDASINMRIRVQRGRGYVPASARVHSQSDDRPIGRLLVDARFSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLIIEMETNGTLDPEEAIRRAATILAEQLAAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 297

Query: 313 MGLFL 317
            GL L
Sbjct: 298 RGLSL 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 =  330 bits (845), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 137/315 (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---IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 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 AYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|179184326|gb|ACB78143.1| RNA polymerase alpha subunit [Vibrio breoganii]
          Length = 311

 Score =  330 bits (845), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 139/317 (43%), Positives = 206/317 (64%), Gaps = 11/317 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+
Sbjct: 1   TEFLKPRLVDIEQINT---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 KIAYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPE 237

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           KE+   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+K
Sbjct: 238 KEEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKK 294

Query: 302 SLVEIKGVLGTMGLFLG 318
           SL EIK VL + GL LG
Sbjct: 295 SLTEIKDVLASRGLSLG 311


>gi|90194028|gb|ABD92575.1| RpoA [Actinobacillus equuli subsp. equuli]
          Length = 300

 Score =  330 bits (845), Expect = 3e-88,   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|45644721|gb|AAS73109.1| predicted DNA-directed RNA polymerase alpha subunit [uncultured
           marine gamma proteobacterium EBAC20E09]
          Length = 321

 Score =  330 bits (845), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 133/325 (40%), Positives = 204/325 (62%), Gaps = 6/325 (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 SLVEIKGVLGTMGLFLGMNLPDWPP 326
           SL EIK VL +  L LGMN+ +WPP
Sbjct: 295 SLNEIKDVLASKNLSLGMNVENWPP 319


>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 =  329 bits (844), Expect = 3e-88,   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---IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 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 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 AYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 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 =  329 bits (844), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 132/315 (41%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQIST---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 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 AYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>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 =  329 bits (844), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 128/316 (40%), Positives = 196/316 (62%), Gaps = 8/316 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP  IE   L Q+ +     + EPL RG+  TLGN+LRR+L SSL G+AI++V++DG
Sbjct: 3   EFEKP-QIEIKELSQDGK-YGCFVVEPLERGYGITLGNSLRRILSSSLPGSAISSVKVDG 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 SLVEIKGVLGTMGLFL 317
           SL E+   L  +G  L
Sbjct: 301 SLEEVFQKLNELGFQL 316


>gi|58416062|emb|CAH57445.1| RNA polymerase alpha-subunit [Vibrio sp. R-23692]
          Length = 309

 Score =  329 bits (844), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 135/315 (42%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQISS---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 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHNEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   ++
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>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 =  329 bits (844), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 118/314 (37%), Positives = 188/314 (59%), Gaps = 7/314 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E I+P     + + +  +    +  EPL RG+  TLGN+LRRVL+SSL GAA+ A+QID
Sbjct: 2   SEFIRPQ----VHVEEISDTAARVSVEPLERGYGDTLGNSLRRVLLSSLEGAAVEAIQID 57

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDI 125
           G  HE ++I  + ED+TDI+LN+KG+  +  G + +   TI   GP  VT  D    ++ 
Sbjct: 58  GAQHEFTTIPNMVEDVTDIVLNVKGLVFRTLGTTDEGTATISVDGPCEVTGADFFIPSEF 117

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++NP+  I  L     + M + +  G GYV  + ++ +NDPIG+I +D+L+SP+K+ + 
Sbjct: 118 ELVNPEQHIATLTEGGHLTMSMRIGYGRGYVSYEQNKRDNDPIGIIHVDSLFSPVKRCAK 177

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R GQ  DYD+L + I+T+G+I   D+V  A+ I+   +  F+   +  +  +E  
Sbjct: 178 LVEACRVGQHTDYDRLVLEIETNGAINPRDAVVSAANIINQHMAAFMTLADEPEAEEEIS 237

Query: 246 --NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +    N  L K++E+L+LSVRS NCL+  +I  +  L++ +E D+L + NFG KS+
Sbjct: 238 IFAPEVTSDNAELDKQIEDLDLSVRSYNCLKRASIHSVRQLVEFSENDLLNIRNFGVKSI 297

Query: 304 VEIKGVLGTMGLFL 317
            E+K  L +MGL L
Sbjct: 298 EEVKDKLESMGLSL 311


>gi|58416028|emb|CAH57428.1| RNA polymerase alpha-subunit [Vibrio sp. R-21415]
          Length = 309

 Score =  329 bits (844), Expect = 4e-88,   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---IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 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 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>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 =  329 bits (844), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 129/313 (41%), Positives = 201/313 (64%), Gaps = 5/313 (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 KGVLGTMGLFLGM 319
           K  L  + L L  
Sbjct: 299 KDKLDELELELKD 311


>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 =  329 bits (843), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 130/309 (42%), Positives = 190/309 (61%), Gaps = 2/309 (0%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           + KP  I+ I     ++     + EPL RG+  TLGN+LRR+L+SSL GAA  ++ I+GV
Sbjct: 4   IEKP-KIQIIE-ESSDKRFGRFVVEPLERGYGTTLGNSLRRMLISSLPGAAARSIDIEGV 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 VLGTMGLFL 317
            L  + L  
Sbjct: 302 KLQELELGF 310


>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 =  329 bits (843), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 140/334 (41%), Positives = 211/334 (63%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q   ++ +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGFVEDFLKPRLVDIQQI---SATHAKITLEPLERGFGHTLGNALRRILLSSISGCAVT 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-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALY 177
            N  E++N  H+ICNL   DA + + + V++G GY+ AK  +   D   +I    +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
           ++   ++   +  P    LL+ V++LEL+VRS NCL+ E+I Y+GDL+Q+TE ++L+  N
Sbjct: 238 REPEIKEEKPEFEP---VLLRPVDDLELTVRSANCLKAESIHYIGDLVQKTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP+S+ E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMKLDNWPPKSLLE 328


>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 =  329 bits (843), Expect = 4e-88,   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   FLKPRLVDIEQISS---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 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|32423696|gb|AAP81239.1| RNA polymerase alpha subunit [Candidatus Portiera aleyrodidarum]
          Length = 329

 Score =  329 bits (843), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 143/326 (43%), Positives = 208/326 (63%), Gaps = 7/326 (2%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           +  E ++P+ I    +     N  ++  EPL RGF HTLGNALRR+L+S + G A+   +
Sbjct: 3   SVNEFVRPSKINVEAISN---NHAIISLEPLERGFGHTLGNALRRILLSYMPGCAVVEAE 59

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           I GV HE S I G+ ED+ +IILNIK I +K+ G     + + K G GVV AGDI+   D
Sbjct: 60  IKGVQHEYSVIDGIKEDVIEIILNIKEIAIKLYGIDEIELELKKIGSGVVKAGDIKARQD 119

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           +EV+NPDHVI +L+    + M+L   +G GY PA      +   G I IDA +SP+K+V+
Sbjct: 120 VEVINPDHVIAHLNDHGELNMKLRFVRGRGYEPAYLRNKSDKNYGRIQIDAKFSPVKRVA 179

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN-FEEPKKEVKE 243
           Y VESAR  Q  D+DKL + ++T+G++  E+++  +++IL++QL  F++   E KK V+ 
Sbjct: 180 YFVESARVEQKTDFDKLIIELETNGTLDPEEAIRTSAKILRNQLDFFVDLSCENKKHVEN 239

Query: 244 DIN---VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           ++          + ALL  VE+LEL+VRS NCL+ ENI Y+GDL++RTE ++L+  N G+
Sbjct: 240 EVEHDRRTDTKIDKALLLPVEDLELTVRSANCLKAENIFYIGDLVKRTEGELLKTPNLGK 299

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPP 326
           KSL EIK VL   GL LGM++  WPP
Sbjct: 300 KSLNEIKKVLKVRGLALGMHIDLWPP 325


>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 =  329 bits (843), Expect = 4e-88,   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   FLKPRLVDIEQINT---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  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDDVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H   +  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 EEK---PEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|190341461|gb|ACE74807.1| RpoA [Cronobacter sakazakii]
          Length = 301

 Score =  329 bits (843), Expect = 4e-88,   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|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 =  329 bits (843), Expect = 4e-88,   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   FLKPRLVDIEQIST---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 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 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 =  329 bits (843), Expect = 4e-88,   Method: Composition-based stats.
 Identities = 136/315 (43%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQISS---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 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHNEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   ++
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>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 =  329 bits (843), Expect = 5e-88,   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   FLKPRLVDIEQINT---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 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 EEK---PEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 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 =  328 bits (842), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 126/325 (38%), Positives = 190/325 (58%), Gaps = 8/325 (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 VDIVSLDQPIATLDSEDATLSMQLTVQKGRGYVPAESQ--DFFEIGRIPVDAIYSPVTKV 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 VEIKGVLGTMGLFLGMNLPDWPPES 328
            E++  L   G +L  +LP+   E+
Sbjct: 315 HELEAKLKEFG-YLPSDLPEGAIEN 338


>gi|58415822|emb|CAH57325.1| RNA polymerase alpha-subunit [Vibrio diazotrophicus]
          Length = 309

 Score =  328 bits (842), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 133/315 (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   FLKPRLVDIEQIST---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 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 AYSVDPARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>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 =  328 bits (842), Expect = 6e-88,   Method: Composition-based stats.
 Identities = 130/309 (42%), Positives = 190/309 (61%), Gaps = 2/309 (0%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           + KP  I+ I     ++     + EPL RG+  TLGN+LRR+L+SSL GAA  ++ I+GV
Sbjct: 4   IEKP-KIQIIE-ESSDKRFGRFVVEPLERGYGTTLGNSLRRMLISSLPGAAARSIDIEGV 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 VLGTMGLFL 317
            L  + L  
Sbjct: 302 KLQELELGF 310


>gi|58415758|emb|CAH57293.1| RNA polymerase alpha-subunit [Vibrio campbellii]
          Length = 309

 Score =  328 bits (842), Expect = 6e-88,   Method: Composition-based stats.
 Identities = 136/315 (43%), Positives = 206/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQISS---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  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 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 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 (842), Expect = 6e-88,   Method: Composition-based stats.
 Identities = 122/314 (38%), Positives = 187/314 (59%), Gaps = 7/314 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E I+P     + + +  E    +  EPL RG+  TLGN+LRRVL+SSL GAA+ A+QID
Sbjct: 2   SEFIRPQ----VQVEEINETSARVSVEPLERGYGDTLGNSLRRVLLSSLEGAAVEAIQID 57

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDI 125
           G  HE  +I  + ED+TDI+LN+KG+  +  G + +   TI   GP  VT  D    ++ 
Sbjct: 58  GAQHEFMTIPNMVEDVTDIVLNVKGLVFRALGTTDEATATISVDGPCEVTGADFFIPSEF 117

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++NP+  I  L     + M + +  G GYV  + ++ +NDPIG+I +D+LYSP+ + + 
Sbjct: 118 ELVNPEQHIATLTEGGHLTMSMRIGYGRGYVSGEANKRDNDPIGVIHVDSLYSPVSRCAK 177

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R GQ  DYD+L + I+T+GSI   D+V  A+ I+   +  F+N  E  +  +E  
Sbjct: 178 LVEACRVGQHTDYDRLVLEIETNGSIAPRDAVVQAANIINQHMAAFMNLAETPEVEEEAS 237

Query: 246 --NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +    N  L K++E+L+LSVRS NCL+  +I  +  L++ +E D+L + NFG KS+
Sbjct: 238 IFAPEVTNDNAELDKQIEDLDLSVRSYNCLKRASIHSVRQLVEFSENDLLNIRNFGVKSI 297

Query: 304 VEIKGVLGTMGLFL 317
            E+K  L +MGL L
Sbjct: 298 EEVKDKLESMGLSL 311


>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 =  328 bits (842), Expect = 7e-88,   Method: Composition-based stats.
 Identities = 135/315 (42%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQIST---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 TNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   ++
Sbjct: 178 AYSVDAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|300244653|gb|ADJ93835.1| RNA polymerase alpha subunit [Vibrio sp. G21]
          Length = 309

 Score =  328 bits (842), Expect = 7e-88,   Method: Composition-based stats.
 Identities = 135/315 (42%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQIST---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  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 AYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATVLAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>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 =  328 bits (841), Expect = 7e-88,   Method: Composition-based stats.
 Identities = 136/315 (43%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQIST---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 AYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|40063201|gb|AAR38038.1| DNA-directed RNA polymerase, alpha subunit [uncultured marine
           bacterium 562]
          Length = 321

 Score =  328 bits (841), Expect = 7e-88,   Method: Composition-based stats.
 Identities = 133/325 (40%), Positives = 204/325 (62%), Gaps = 6/325 (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 SLVEIKGVLGTMGLFLGMNLPDWPP 326
           SL EIK VL +  L LGMN+ +WPP
Sbjct: 295 SLNEIKDVLASKELSLGMNVDNWPP 319


>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 =  328 bits (841), Expect = 7e-88,   Method: Composition-based stats.
 Identities = 133/315 (42%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQIST---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 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 AYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 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 =  328 bits (840), Expect = 9e-88,   Method: Composition-based stats.
 Identities = 135/315 (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   FLKPRLVDIEQISS---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 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 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|58415744|emb|CAH57286.1| RNA polymerase alpha-subunit [Vibrio alginolyticus]
          Length = 309

 Score =  328 bits (840), Expect = 9e-88,   Method: Composition-based stats.
 Identities = 135/315 (42%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQISS---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 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHNEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   ++
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASCGLSLG 309


>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 =  328 bits (840), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 138/315 (43%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQINT---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++  + +   KE
Sbjct: 178 AYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEKE 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 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 =  328 bits (840), Expect = 1e-87,   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   FLKPRLVDIEQINT---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 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>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 =  328 bits (840), Expect = 1e-87,   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---IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 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 AYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>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 =  327 bits (839), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 136/310 (43%), Positives = 197/310 (63%), Gaps = 2/310 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP+ IE + L +        + EPL  G+  T+GN+LRRVL+SSL GAAI+ + I G
Sbjct: 3   EIEKPS-IEKLELDE-SGVYGKFVVEPLESGYGITIGNSLRRVLLSSLPGAAISFINIRG 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|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 =  327 bits (839), Expect = 1e-87,   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---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-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H   +  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 AYAVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRSATILAEQLDAFVDLRDIRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>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 =  327 bits (839), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 112/311 (36%), Positives = 173/311 (55%), Gaps = 10/311 (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              ++     ++  
Sbjct: 185 VGGSLEKDRLILDIWTNGSLTPQEALSQAATILVDLFVPL-----KDITLESIKTDQTDD 239

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL+LSVR+ NCL+   I  + DL   T+ D+L + NFG+KS  E+   L 
Sbjct: 240 VDPTSQIPIEELQLSVRAYNCLKRAQINSVADLRDYTQEDLLEIKNFGQKSAEEVIEAL- 298

Query: 312 TMGLFLGMNLP 322
                LG+ LP
Sbjct: 299 --QKRLGITLP 307


>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 =  327 bits (839), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 127/301 (42%), Positives = 187/301 (62%), Gaps = 5/301 (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 L 317
            
Sbjct: 315 F 315


>gi|58415738|emb|CAH57283.1| RNA polymerase alpha-subunit [Vibrio aestuarianus]
          Length = 309

 Score =  327 bits (839), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 135/315 (42%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQIST---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 TNPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y+V++AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   ++
Sbjct: 178 AYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>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 =  327 bits (839), Expect = 1e-87,   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   MADHWNKLTRPSSIKV--VGGKEPCVMELVIEPLESGFALTLGNALRRVMMSSLRGFAVY 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|58384667|gb|AAW72682.1| DNA-directed RNA polymerase alpha chain [Buchnera aphidicola
           (Cinara cedri)]
          Length = 329

 Score =  327 bits (839), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 140/334 (41%), Positives = 211/334 (63%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q   ++ +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGFVEDFLKPGLVDIQQI---SATHAKITLEPLERGFGHTLGNALRRILLSSISGCAVT 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-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALY 177
            N  E++N  H+ICNL   DA + + + V++G GY+ AK  +   D   +I    +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
           ++   ++   +  P    LL+ V++LEL+VRS NCL+ E+I Y+GDL+Q+TE ++L+  N
Sbjct: 238 REPEIKEEKPEFEP---VLLRPVDDLELTVRSANCLKAESIHYIGDLVQKTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP+S+ E
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMKLDNWPPKSLLE 328


>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 =  327 bits (838), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 130/314 (41%), Positives = 203/314 (64%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KP  IE   +  E++     + EPL RG+  TLGN+LRR+++SSL G+A++ V+I+G
Sbjct: 3   DFNKP-KIEITEI-SEDKKFGRFVVEPLERGYGTTLGNSLRRIMLSSLPGSAVSQVKIEG 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 VEIKGVLGTMGLFL 317
            E+   L  +GL L
Sbjct: 301 EEVLAKLNELGLSL 314


>gi|58415894|emb|CAH57361.1| RNA polymerase alpha-subunit [Vibrio hispanicus]
          Length = 309

 Score =  327 bits (838), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 132/315 (41%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQIST---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 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 AYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>gi|58415996|emb|CAH57412.1| RNA polymerase alpha-subunit [Vibrio penaeicida]
          Length = 309

 Score =  327 bits (838), Expect = 2e-87,   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---IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 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-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H   +  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 AYTVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRSATILAEQLDAFVDLRDIRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>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 =  327 bits (838), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 129/309 (41%), Positives = 188/309 (60%), Gaps = 2/309 (0%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           + KP  I+ I     ++     + EPL RG+  TLGN+LRR+L+SSL GAA  ++ I GV
Sbjct: 4   IEKP-KIQIIE-ESSDKRFGRFVVEPLERGYGTTLGNSLRRMLISSLPGAAARSIDIQGV 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|58415964|emb|CAH57396.1| RNA polymerase alpha-subunit [Vibrio nigripulchritudo]
          Length = 309

 Score =  327 bits (838), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 137/315 (43%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQIST---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-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H   +  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 AYTVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRSATILAEQLDAFVDLRDIRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>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 =  326 bits (837), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 112/296 (37%), Positives = 183/296 (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 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           EL+LSVRS NCL+   I  + DL  ++E DM+++ N G+KSL E+K  L  +GL  
Sbjct: 255 ELDLSVRSYNCLKRAGIQTVQDLAAKSEDDMIKVRNLGKKSLKEVKEKLVELGLGF 310


>gi|326407604|gb|ADZ64675.1| DNA-directed RNA polymerase subunit alpha [Lactococcus lactis
           subsp. lactis CV56]
          Length = 312

 Score =  326 bits (837), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 127/310 (40%), Positives = 199/310 (64%), Gaps = 4/310 (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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 VKLTELGLSL 308


>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 =  326 bits (837), Expect = 2e-87,   Method: Composition-based stats.
 Identities = 136/306 (44%), Positives = 201/306 (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++  + +   +++   +  P    
Sbjct: 183 TDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---I 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|146742342|gb|ABQ42692.1| RNA polymerase alpha subunit [Vibrio porteresiae]
 gi|156106873|gb|ABU49636.1| RNA polymerase alpha subunit [Vibrio porteresiae]
          Length = 307

 Score =  326 bits (836), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 133/313 (42%), Positives = 203/313 (64%), Gaps = 11/313 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T  +I+GVLHE
Sbjct: 1   PRLVDIEQI---SATHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEAEIEGVLHE 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 VAAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEK 237

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EI
Sbjct: 238 PEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEI 294

Query: 307 KGVLGTMGLFLGM 319
           K VL + GL LGM
Sbjct: 295 KDVLASRGLSLGM 307


>gi|179184854|gb|ACB78162.1| RNA polymerase alpha subunit [Aliivibrio finisterrensis]
          Length = 306

 Score =  326 bits (836), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 139/312 (44%), Positives = 205/312 (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 EAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKP 237

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK
Sbjct: 238 EFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIK 294

Query: 308 GVLGTMGLFLGM 319
            VL + GL LGM
Sbjct: 295 DVLASRGLSLGM 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 =  326 bits (836), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 135/315 (42%), Positives = 205/315 (65%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQIST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 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 AYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>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 =  326 bits (836), Expect = 3e-87,   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|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 =  326 bits (836), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 123/311 (39%), Positives = 190/311 (61%), Gaps = 5/311 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I   +  +        PL RG+  TLGN+LRR+++SSL G A T+V+I+G
Sbjct: 3   EFEKP----AIERIESTDTYGKFAITPLERGYGITLGNSLRRIMLSSLPGTAPTSVKIEG 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 KGVLGTMGLFL 317
           K  L  + L L
Sbjct: 299 KDKLDELDLSL 309


>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 =  326 bits (836), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 102/311 (32%), Positives = 167/311 (53%), Gaps = 12/311 (3%)

Query: 16  EYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           +   +    +         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 VGGSTEKDRLIMEIWTNGSLTPQEALSQAASILVDLFSPL-----KDITLESLRSDVGSD 246

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL+LSVR+ NCL+   I  + DL+  T+ D+L + NFG+KS  E+   L 
Sbjct: 247 ADPTSQIPIEELQLSVRAYNCLKRAQINSVADLLDYTQEDLLEIKNFGQKSAEEVIEAL- 305

Query: 312 TMGLFLGMNLP 322
                LG+ LP
Sbjct: 306 --QKRLGITLP 314


>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 =  326 bits (836), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 127/318 (39%), Positives = 192/318 (60%), Gaps = 6/318 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           +  P  IE       ++     IA+PL RG+  TLGN +RRVL++SL G AIT +++DGV
Sbjct: 5   MQMPAKIEVDEATHTDQ-YGRFIAQPLERGYGVTLGNMMRRVLLASLPGTAITGIKVDGV 63

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEV 127
            HE SSI+GV ED+ +I+LN+K +  K +     + T+   GP   TAGDI     + EV
Sbjct: 64  FHEFSSIEGVREDVPEIVLNLKKVRFKSTCKRSCKTTLSIVGPKDFTAGDIVAQEGEFEV 123

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D  I  ++  + + +++ + +G GY PA+  R ++ PIG I IDA+Y+PI+ V + V
Sbjct: 124 LNKDLYIATVNEGSTLNIDVYIGRGRGYTPAEESRPDSMPIGYIAIDAIYTPIRNVKFAV 183

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK----E 243
           E+ R GQ  DY+K+ + ++TDGSIT +DS++LA RI+ + +  F NF   ++E      +
Sbjct: 184 ENTRVGQRTDYEKMVLDVETDGSITPDDSISLAGRIINEHVTFFANFSPTEEEFTEEEYK 243

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             + +       L  K+E+L+LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL
Sbjct: 244 QQDDEFETMRRLLNTKIEDLDLSVRSHNCLRLAEIDTIGDLVSRKEDELLNYKNFGKKSL 303

Query: 304 VEIKGVLGTMGLFLGMNL 321
            E+K  L    L  GM++
Sbjct: 304 TELKEQLEKFELKFGMDI 321


>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 =  326 bits (835), Expect = 3e-87,   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-IEIAEI-SEDKKFGRFICEPLERGYGTTLGNSLRRIMLSSLPGSAVSQVKIDG 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|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 =  326 bits (835), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 126/309 (40%), Positives = 194/309 (62%), Gaps = 2/309 (0%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           + KP     ++   E+ +    + EPL RG+  TLGN+LRRVL+S+L GAA+T+++IDG+
Sbjct: 4   IEKPTI--KMLHDNEKASEGRFVIEPLERGYGITLGNSLRRVLLSTLPGAAVTSIRIDGI 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE S+I GV ED+T+IILNIK + ++   +     TI   GP  +TA DI   +++++ 
Sbjct: 62  LHEFSTIPGVTEDVTEIILNIKRLAIRAWSEEPIVATIKASGPCEITAADIDCGSEVKIF 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           N DH I  LD DA + MEL + +G GY  A+ ++ ++DPI  I ID+++SP++K ++ V 
Sbjct: 122 NEDHHIATLDKDAELDMELVIDRGRGYSSAEQNKGKDDPISTIAIDSIFSPVEKANFIVS 181

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
             R GQV D+DKL + + TDGSI+  D+VA+A+RI+Q+ L +F+   E   E    +  +
Sbjct: 182 DTRVGQVTDFDKLELEVRTDGSISANDAVAVAARIMQEHLALFVELSEEATEYSIMLEHE 241

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
            +     L K +E+LEL+VRS N L    I  + DL+  TE ++  + N G+KSL EIK 
Sbjct: 242 DIEQTRVLEKNIEDLELTVRSLNALTQAGIDTVSDLVSMTEGELNSVKNLGKKSLSEIKD 301

Query: 309 VLGTMGLFL 317
            +  +GL L
Sbjct: 302 KIRELGLSL 310


>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 =  326 bits (835), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 104/311 (33%), Positives = 172/311 (55%), Gaps = 9/311 (2%)

Query: 14  NIEYIVLG--QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
            IE + L   + +      I EPL RG   T+GNALRRVL+S+L GAA+TA++I GV HE
Sbjct: 5   QIECVELKAHKNQGQYGKFILEPLDRGQGTTVGNALRRVLLSNLEGAAVTALRIAGVNHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            ++I GV ED+ ++ILN+K I LK      +   +   GP  VTAG     +++E+++P 
Sbjct: 65  FATISGVREDVMELILNMKEITLKSYTSQPQIGRLVATGPATVTAGQFDLPSEVEIVDPS 124

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  L   + + ME  + KG GY   +  + ++  +  + ID+++ P+ KV+Y+VE  R
Sbjct: 125 QYVATLAEGSKLEMEFRIEKGKGYRAIERGKDDSTSLDFLQIDSVFMPVTKVNYSVEDVR 184

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  D+L++ I T+GS+  +++++ A+ I+ D      +  E    ++   +     
Sbjct: 185 VDGTSSKDRLTIEIWTNGSVNPKEALSEAAAIIVDLFSPLRDLNE----LEATQSDYPDE 240

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            NP     +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L 
Sbjct: 241 VNPESQIPIEELQLSVRAYNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEEVIEAL- 299

Query: 312 TMGLFLGMNLP 322
                LG+ LP
Sbjct: 300 --QKRLGITLP 308


>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 =  326 bits (835), Expect = 3e-87,   Method: Composition-based stats.
 Identities = 133/310 (42%), Positives = 208/310 (67%), Gaps = 2/310 (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 GVLGTMGLFL 317
             L  + L L
Sbjct: 301 QKLANLELSL 310


>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 =  326 bits (835), Expect = 4e-87,   Method: Composition-based stats.
 Identities = 125/312 (40%), Positives = 187/312 (59%), Gaps = 2/312 (0%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           + KP  I+ I     ++     + EPL RG+  TLGN+LRR+L+SSL GAA  ++ I+GV
Sbjct: 4   IEKP-KIQIIE-ESSDKRFGRFVVEPLERGYGTTLGNSLRRMLISSLPGAAARSIDIEGV 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|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 =  326 bits (835), Expect = 4e-87,   Method: Composition-based stats.
 Identities = 121/314 (38%), Positives = 189/314 (60%), Gaps = 7/314 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E I+P     + + + +E    +  EPL RG+  TLGN+LRRVL+SSL GAA+ A+QID
Sbjct: 2   SEFIRPQ----VQVEEIDEVSARVSVEPLERGYGDTLGNSLRRVLLSSLEGAAVEAIQID 57

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDI 125
           G  HE  +I  + ED+TDI+LN+KG+  +  G + +   TI   GPG VT  D    +D 
Sbjct: 58  GAQHEFMTIPNMVEDVTDIVLNVKGLVFRSLGTTDEATATISVDGPGEVTGADFFVPSDF 117

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++NPD  I  L     + M + +  G GY+  + ++ +NDPIG+I +D+LYSP+++ + 
Sbjct: 118 ELVNPDQHIATLTEGGHLTMSMRIGYGRGYISYEANKHDNDPIGIIHVDSLYSPVRRCAK 177

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN--FEEPKKEVKE 243
            VE+ R GQ  DYD+L + I+T+G+++  D+V  A+ I+   +  F+N       +E   
Sbjct: 178 LVEATRVGQHTDYDRLVLEIETNGALSPRDAVVSAANIINQHMASFMNLAEVPEVEEEVS 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
               +    N  L K++E+L+LSVRS NCL+  +I  +  L++ +E D+L + NFG KS+
Sbjct: 238 IFAPEVTSDNAELDKQIEDLDLSVRSYNCLKRASIHSVRQLVEFSENDLLNIRNFGVKSI 297

Query: 304 VEIKGVLGTMGLFL 317
            E+K  L +MGL L
Sbjct: 298 EEVKDKLESMGLGL 311


>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 =  326 bits (835), Expect = 4e-87,   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|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 =  326 bits (835), Expect = 4e-87,   Method: Composition-based stats.
 Identities = 131/321 (40%), Positives = 196/321 (61%), Gaps = 6/321 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           +  P  IE        ++    IA+PL RG+  TLGN +RRVL++SL G AIT ++IDGV
Sbjct: 5   MQMPAKIEVDEA-NHTDSFGRFIAQPLERGYGVTLGNVMRRVLLASLPGTAITGLKIDGV 63

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEV 127
            HE +++ GV ED+ +I+LN+K +  K +   + + T+   GP   TAGDI     + EV
Sbjct: 64  FHEFAAVDGVREDVPEIVLNLKRVRFKSTCKRNCKTTLAIVGPKEFTAGDIIAQEGEFEV 123

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D  I  ++  A ++++L V +G GYVPA+ +R E  PIG I IDA+Y+PI+ V +TV
Sbjct: 124 LNKDMHIATVNAGATLKIDLYVGRGRGYVPAEENRPEGMPIGYIAIDAIYTPIRNVRFTV 183

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE----EPKKEVKE 243
           E+ R GQ  DY+K+ + ++TDGS+T +DS++LA +I+ D +  F NF     E  +E  +
Sbjct: 184 ENTRVGQRTDYEKMILDVETDGSVTPDDSISLAGKIITDHVTFFANFSPTEEEFTEEEFK 243

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             + +       L  K+E+L+LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL
Sbjct: 244 QQDDEFETMRRLLHTKIEDLDLSVRSHNCLRLAEIDTIGDLVSRKEDELLNYKNFGKKSL 303

Query: 304 VEIKGVLGTMGLFLGMNLPDW 324
            E+K  L    L  GM++  +
Sbjct: 304 TELKEQLEKFDLKFGMDITKY 324


>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 =  326 bits (835), Expect = 4e-87,   Method: Composition-based stats.
 Identities = 120/309 (38%), Positives = 174/309 (56%), Gaps = 4/309 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           + +P       LG E +NR      PL  GF H++GNALRRVL+SS+ GAAIT V+ D  
Sbjct: 4   MQRPT---VESLGDEVDNRQRFAIGPLEPGFGHSIGNALRRVLISSVPGAAITQVRFDDA 60

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           LHE ++I GV ED+ DIILN+K I  +   +    V +  RGP  VTAGD    +D+EV+
Sbjct: 61  LHEFTTIPGVKEDVIDIILNLKDIVWRSWSEEPVTVRLDVRGPKEVTAGDFMLPSDVEVI 120

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           N D  I ++     + ++  V +G GYV A         IG+I IDA++SP++ V+Y VE
Sbjct: 121 NRDLHIASVSEHGRLGLDAVVEQGRGYVSA-EGNKRTTTIGIIAIDAIFSPVRHVNYRVE 179

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
             R GQ  D+D++ + ++TDGS+T  ++VA A+R L    G+          ++      
Sbjct: 180 PVRVGQSTDFDQVVLEVETDGSVTPREAVASAARTLTSLFGLVAELATDVNALEVAATAD 239

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                      +EELEL+ R  NCL+  +I  +GDL++RT  D+L + NFG+KSL E+  
Sbjct: 240 DSVRPAEYDLPIEELELTERPRNCLKRASINTIGDLVERTPEDLLSITNFGQKSLDEVVE 299

Query: 309 VLGTMGLFL 317
            L   GL L
Sbjct: 300 RLTQRGLEL 308


>gi|58415864|emb|CAH57346.1| RNA polymerase alpha-subunit [Vibrio halioticoli]
          Length = 309

 Score =  325 bits (834), Expect = 4e-87,   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   FLKPRLVDIEQINT---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  LHEYSTKEGVQEDILEILLNLKGLAVRVAEGKDDVFITLNKSGSGPVVAGDITHDGDVEI 117

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKV 183
            NP+HVIC+L  D A + M + V +G GYVPA    H   +  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 EEK---PEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPSLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>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 =  325 bits (834), Expect = 4e-87,   Method: Composition-based stats.
 Identities = 119/296 (40%), Positives = 179/296 (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 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           EL+LSVRS NCL+   I  + +L  +TE DM+++ N G+KSL E+K  L  +GL  
Sbjct: 255 ELDLSVRSYNCLKRAGIQTVQELASKTEDDMIKVRNLGKKSLKEVKEKLNELGLGF 310


>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 =  325 bits (834), Expect = 5e-87,   Method: Composition-based stats.
 Identities = 127/310 (40%), Positives = 199/310 (64%), Gaps = 4/310 (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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 VKLTELGLSL 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 =  325 bits (834), Expect = 5e-87,   Method: Composition-based stats.
 Identities = 129/321 (40%), Positives = 200/321 (62%), Gaps = 6/321 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           +  P  I+       ++N  + IA+PL RG+  TLGNA+RRVL++SL G AIT ++IDGV
Sbjct: 5   MQMPEKIDVDEGTHNDKN-GIFIAQPLERGYGVTLGNAMRRVLLASLPGTAITGIKIDGV 63

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEV 127
            HE S+I GV ED+ DIILN+K +  + S     + T+   GP  VTAGDI     + EV
Sbjct: 64  FHEFSAIDGVREDVPDIILNLKKVRFRSSTKRSCKTTVTVDGPADVTAGDIVAQEGEFEV 123

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D  I  ++  + + M++ + +G GYVPA+ +R +  P+G I ID++++PIK V ++V
Sbjct: 124 LNTDLHIATVNEGSRLSMDVYIGRGRGYVPAEDNRGDGMPLGFIAIDSIFTPIKNVKFSV 183

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI-- 245
           E+ R GQ  DY+K+ + ++TDGS++ +DS++LA +I+ + + +F NF    +E  E+   
Sbjct: 184 ENTRVGQRTDYEKMILDVETDGSVSPDDSISLAGKIINEHVSLFANFSPTDEEFTEEEYK 243

Query: 246 --NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             + +       LL ++E+L+LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL
Sbjct: 244 QQDDEFENMRKMLLTRIEDLDLSVRSHNCLRLAEIDTLGDLVSRKEDELLTYKNFGKKSL 303

Query: 304 VEIKGVLGTMGLFLGMNLPDW 324
            E+K  L    L  GM++  +
Sbjct: 304 TELKEQLEKFELKFGMDITKY 324


>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 =  325 bits (834), Expect = 6e-87,   Method: Composition-based stats.
 Identities = 127/310 (40%), Positives = 199/310 (64%), Gaps = 4/310 (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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 VKLTELGLSL 308


>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 =  325 bits (833), Expect = 6e-87,   Method: Composition-based stats.
 Identities = 101/311 (32%), Positives = 170/311 (54%), Gaps = 11/311 (3%)

Query: 14  NIEYIV--LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
            IE +     +   + +  + 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              ++       +P
Sbjct: 185 -GDGSLKDRLLLEVWTNGSISPQEALSSAAGILVDLFNPL-----KDISLEPTDTGSDIP 238

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL+LSVR+ NCL+   +  + DL+  T+ D+L + NFG+KS  E+   L 
Sbjct: 239 DDPTAQIPIEELQLSVRAYNCLKRAQVNSVADLLDYTQEDLLEIKNFGQKSAEEVVEALQ 298

Query: 312 TMGLFLGMNLP 322
                LG+ LP
Sbjct: 299 RR---LGITLP 306


>gi|179184433|gb|ACB78147.1| RNA polymerase alpha subunit [Vibrio sp. CECT 7223]
          Length = 308

 Score =  325 bits (833), Expect = 7e-87,   Method: Composition-based stats.
 Identities = 135/314 (42%), Positives = 203/314 (64%), Gaps = 11/314 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQINT---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 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFL 317
            EIK VL + GL L
Sbjct: 295 TEIKDVLASRGLSL 308


>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 =  325 bits (832), Expect = 7e-87,   Method: Composition-based stats.
 Identities = 115/315 (36%), Positives = 182/315 (57%), Gaps = 4/315 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            +P   E     +  + R+     PL  GF +TLGN+LRR L+SS+ GAA+T++ IDGVL
Sbjct: 5   QRPTLTE----EKISDTRSRFTLNPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIHIDGVL 60

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I+GV ED+  IILN+K + +    D   ++ + K GPG VTA DI     +E+ N
Sbjct: 61  HEFSTIEGVKEDVAQIILNLKDLVVTSENDEPVQMYLRKAGPGQVTAEDITPPAGVEIHN 120

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+ +I  L+    + ++LTV +G GYV A+ + + +  IG I +D++YSP+ KVSY VE+
Sbjct: 121 PELLIATLNEKGKLEIDLTVERGRGYVSAQQNNSPDYEIGRIPVDSIYSPVVKVSYKVEA 180

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R GQ  D+DKL + ++T  S+   D+ A A + L +  G+     +  + ++       
Sbjct: 181 TRVGQRTDFDKLIVDVETKPSMAPRDAFASAGKTLVELFGLTTELNQEVEGLELKEAPVV 240

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              +  L + +  L L  RS NCL+ E I  +G+L+ R+EAD+L + NFG KS+ ++K  
Sbjct: 241 EQQSSDLQRPITILNLPARSQNCLQREGIHTIGELVLRSEADLLDIRNFGAKSIEDVKDE 300

Query: 310 LGTMGLFLGMNLPDW 324
           L  + L L  +   +
Sbjct: 301 LAKLDLRLKDSPAGF 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 =  325 bits (832), Expect = 8e-87,   Method: Composition-based stats.
 Identities = 137/339 (40%), Positives = 207/339 (61%), Gaps = 12/339 (3%)

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 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN---DPIGLITIDALYS 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+   E K
Sbjct: 178 PILRATYSVENARVEQRTDLDKLVIDLETNGTIDPEEAIRRAATIIQEQLRTFV---ELK 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 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337
           G+ SL EIK  L   GL LGM +   P + +  L K  E
Sbjct: 295 GKVSLWEIKTALQKRGLSLGMEV---PIQQLASLKKSLE 330


>gi|58415728|emb|CAH57278.1| RNA polymerase alpha-subunit [Photobacterium leiognathi subsp.
           leiognathi]
          Length = 292

 Score =  325 bits (832), Expect = 8e-87,   Method: Composition-based stats.
 Identities = 134/295 (45%), Positives = 198/295 (67%), 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++  + +   +++   +  P    LL+ V++L
Sbjct: 181 DMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDL 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|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 =  325 bits (832), Expect = 9e-87,   Method: Composition-based stats.
 Identities = 116/296 (39%), Positives = 182/296 (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 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           EL+LSVRS NCL+   I  + DL  ++E DM+++ N G+KSL E+K  L  +GL  
Sbjct: 255 ELDLSVRSYNCLKRAGIQTVQDLAAKSEDDMIKVRNLGKKSLKEVKEKLVELGLGF 310


>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 =  325 bits (832), Expect = 9e-87,   Method: Composition-based stats.
 Identities = 115/302 (38%), Positives = 177/302 (58%), Gaps = 3/302 (0%)

Query: 15  IEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS 74
           +  I   + + N      EPL  G+  TLGNALRRVL+SSL GAA+T+++I+GV HE   
Sbjct: 6   LPRIKNTKTQGNYASYDIEPLEAGYGQTLGNALRRVLLSSLPGAAVTSIRIEGVQHEFQD 65

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           + GV ED+TDI+LNIK + L+   +    + +   G   VTA DI   + +E++NP+  I
Sbjct: 66  VPGVLEDVTDIVLNIKKLRLRSFSEHPVTMRLEVNGEREVTAADIVAPSTVEIVNPELHI 125

Query: 135 CNLD-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            +LD  +A + MEL V  G  YVPA     E+ PIG+I +DA+Y+P++KV+YTVE  R G
Sbjct: 126 ASLDNDNAHLDMELVVETGRSYVPA--DSKEDQPIGVIPVDAIYTPVQKVNYTVEHTRVG 183

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q+ +YDK+ + + TDG+IT ++++  ++ +L     +  N+     E ++          
Sbjct: 184 QMTNYDKIVLEVTTDGTITPDEALRQSADVLVRHFTLLANYRASLPEPEKAPLSSLPIPQ 243

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                 +EEL+LSVR+ NCL+  NI  +G ++   E D+L + NFG KSL E++  L   
Sbjct: 244 KIYDTPIEELDLSVRAYNCLKRSNITKVGQVLSMNEEDLLGVRNFGEKSLQELRERLLAR 303

Query: 314 GL 315
             
Sbjct: 304 NF 305


>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 =  325 bits (832), Expect = 9e-87,   Method: Composition-based stats.
 Identities = 135/315 (42%), Positives = 202/315 (64%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQIST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 57

Query: 69  LHEISSIKGVHEDLTDIILNIKGINL-KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 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 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>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 =  325 bits (832), Expect = 9e-87,   Method: Composition-based stats.
 Identities = 111/317 (35%), Positives = 178/317 (56%), Gaps = 7/317 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           +E + P+ + +    +  +     + EPL RGF  TLGN+LRR L+SS++G AITAV+I 
Sbjct: 3   REFLFPSKVYW---EERGKTYGRFVVEPLERGFGITLGNSLRRTLLSSIQGTAITAVKIY 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           G+ HE S I+GV ED+ ++I N+K I   +     + + + K+G G VTA DI    +++
Sbjct: 60  GIYHEFSPIEGVQEDVLEVIANLKKIRFNLKSSDVETLYLKKKGEGTVTAKDITCPPNVD 119

Query: 127 VLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           ++NPD  I  +   +  + ME+ + +G GY+  +        +G I +DA +SP+++VS+
Sbjct: 120 IINPDQKIATITDPNKELNMEIRIERGFGYMTTEEMEV-IGEVGWILVDADFSPVRQVSF 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE  R  +  DYD+L M I T+G+ T E+ V  A  IL        +       V+E +
Sbjct: 179 RVEKTRVEKRSDYDRLIMEIYTNGTKTPEEVVKEAISILVKYFSSLEHISYELPVVEEPV 238

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                 F   L   VEEL++S R+ N ++   I  +GDL++ +E D+    N GRK++ E
Sbjct: 239 --IVDEFAEKLSLPVEELDVSQRALNSIKRMGINTIGDLVRLSEEDLKGTKNVGRKAINE 296

Query: 306 IKGVLGTMGLFLGMNLP 322
           IK  L  MGL+LGM++ 
Sbjct: 297 IKEALKQMGLYLGMDIE 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 =  324 bits (831), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 126/301 (41%), Positives = 191/301 (63%), Gaps = 5/301 (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 L 317
            
Sbjct: 315 F 315


>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 =  324 bits (831), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 128/318 (40%), Positives = 191/318 (60%), Gaps = 9/318 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           +E+ KP+ +  I     +      + EPL RG+  TLGN+LRRVL+SSL G A+T ++ID
Sbjct: 2   KEIEKPSLV--IDEISPDGRYGKFVWEPLERGYGITLGNSLRRVLLSSLSGMAVTGIKID 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS-----HKRVTIFKRGPGVVTAGDIQT 121
           GVLHE S+I+GV ED+ DI+LNIK +  K++ D       K   I K G G VT  DI T
Sbjct: 60  GVLHEFSTIEGVREDVADIVLNIKALCFKVNLDDQGTYEPKTFYIKKSGEGEVTGADIIT 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
             D EVLNP+  I  LD +A + ME+ V  G GYV A  +++++ PIG I +D++YSPI 
Sbjct: 120 DQDTEVLNPELHIATLDKNANLNMEIYVDIGRGYVSADKNKSKDQPIGFIPVDSIYSPIT 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +V + V   R G V +YD+L++ + TDGS+  +++V  A+ IL + L +F     PK + 
Sbjct: 180 RVKFGVTDTRVGNVTNYDRLTLEVWTDGSLGPDEAVTSAAEILINYLALFKTTNVPKIQG 239

Query: 242 KEDINVKSLP--FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            E+          +  L   +++L+L+VRS NCLR   I  + D+I +TE +++ + N G
Sbjct: 240 SEESGKPDEEGTKSSVLQMSIDDLDLTVRSNNCLRRAGINTVEDIINKTEDELICVRNLG 299

Query: 300 RKSLVEIKGVLGTMGLFL 317
            KSL E+K  +  +GL L
Sbjct: 300 SKSLEEVKNKIEELGLHL 317


>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 =  324 bits (830), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 127/310 (40%), Positives = 199/310 (64%), Gaps = 4/310 (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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 VKLTELGLSL 308


>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 =  324 bits (830), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 124/315 (39%), Positives = 197/315 (62%), Gaps = 6/315 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +   PN IE   +  E++     + EPL RG+  TLGN+LRR+++SSL GAA+T V+I+G
Sbjct: 3   DFKIPN-IEIAEI-SEDKKYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVTTVKIEG 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 EVLNPDHVICNLDVDAV--VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 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 VEIKGVLGTMGLFLG 318
            EIK  +  +GL L 
Sbjct: 301 EEIKAKIKALGLSLN 315


>gi|291334082|gb|ADD93755.1| DNA directed RNA polymerase alpha subunit [uncultured marine
           bacterium MedDCM-OCT-S05-C114]
          Length = 332

 Score =  324 bits (830), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 126/324 (38%), Positives = 185/324 (57%), Gaps = 4/324 (1%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +     +   PN +         ++    IA+P   G+ HT+GNA RRVL+SS+ GAAI+
Sbjct: 1   MATRLGKFELPNRL-VKEEDTSTDSYAKFIADPFESGYGHTIGNAFRRVLLSSIEGAAIS 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           ++++DGV HE  SI GV ED+TDI+LN+K + +         +TI     G VTAGDI  
Sbjct: 60  SLKLDGVQHEFQSIDGVVEDVTDIVLNLKKVLVISHKADPVTLTIDVEKDGEVTAGDISP 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
              IE++NP+ +I   D    V  E+ V+ G G+   +  +++  PIG+I +DALYSP+K
Sbjct: 120 AEGIEIINPEQIILTTDRKLQVTGEMIVTVGRGFCLGEDSKSDEQPIGMINVDALYSPVK 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
            V Y V++ R GQ+ DYDKL + + TDG IT +D++  ++ IL+  L +F    E + E 
Sbjct: 180 LVKYEVQNTRVGQMTDYDKLLLEVTTDGRITPDDALKQSAAILRHHLDVFDQISEEQIEF 239

Query: 242 KEDINVKSLPFNPALL---KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +      S   N         V E+ELSVR+ NCL   NI  +G+L  ++E +ML+  NF
Sbjct: 240 ESHTKEVSEEQNRLRNLLSMSVNEIELSVRAANCLNNANITTVGELATKSEPEMLKYRNF 299

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLP 322
           G+KSL EIK  L  +GL LGM   
Sbjct: 300 GKKSLNEIKAKLEQLGLSLGMKFE 323


>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 =  324 bits (830), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 126/310 (40%), Positives = 198/310 (63%), Gaps = 4/310 (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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 299 VKLTELGLSL 308


>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 =  324 bits (830), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 107/311 (34%), Positives = 170/311 (54%), Gaps = 9/311 (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 TMGLFLGMNLP 322
                LG+ LP
Sbjct: 300 --QKRLGITLP 308


>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 =  323 bits (829), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 124/310 (40%), Positives = 184/310 (59%), Gaps = 8/310 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           ++  P     I +    EN      EPL  G+ HTLGNALRRVL+SS+ GAAIT ++I+G
Sbjct: 3   DIAMPK----IEVVTAAENYGRFKIEPLDPGYGHTLGNALRRVLLSSIPGAAITKIKIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE S+I GV ED+T+I+LNIKGI L+   +   ++++ KRG GVV A DI   +++E+
Sbjct: 59  VFHEFSTIPGVKEDVTEIVLNIKGIRLRSYAERPVKISLSKRGAGVVRAADIDAPSNVEI 118

Query: 128 LNPDHVICNLD-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +NP+H IC +D  DA + ME+TV +G GY+PA     +  PIG I IDA+++P+ KV+Y 
Sbjct: 119 VNPNHYICTIDRDDAAIDMEMTVERGRGYLPADQR--DALPIGEIPIDAIFTPVPKVNYV 176

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE  R GQ  D D L + I TDG+I   D+++ A+++L        +F     E +    
Sbjct: 177 VEHIRVGQATDIDSLLIEIWTDGTIKPGDALSHAAQVLVQYSQTIADFNRLSTEAEPTTA 236

Query: 247 VKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
              L          +EEL+LS R+ NCL+  +I  +G +++  E  +L + N G+KS+ E
Sbjct: 237 PNGLAIPADIYDTPIEELDLSTRTYNCLKRADITKVGQVLEMDEKALLSVRNLGQKSMEE 296

Query: 306 IKGVLGTMGL 315
           I+  L   G 
Sbjct: 297 IRDKLIERGY 306


>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 =  323 bits (829), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 124/310 (40%), Positives = 191/310 (61%), Gaps = 2/310 (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 GVLGTMGLFL 317
             L  +GL L
Sbjct: 301 EKLDELGLSL 310


>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 =  323 bits (829), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 116/319 (36%), Positives = 191/319 (59%), 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 +   +    E     
Sbjct: 171 KKVSYTVEKTRVGRRTDLDRLILEIWTNGSISPEEAFREASRILMEYFRLLNEKEFQLPY 230

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +       L      L  +E+L LS R+ N LR   I  + DL+ +T  +++++ NFG+
Sbjct: 231 EEVKPENTYLEEEKKGLT-LEDLGLSTRAYNSLRHAGIHTIEDLLSKTREELMKIKNFGQ 289

Query: 301 KSLVEIKGVLGTMGLFLGM 319
           KSL E++  L   GL L  
Sbjct: 290 KSLQELEEKLREKGLSLKD 308


>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 =  323 bits (829), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 125/344 (36%), Positives = 192/344 (55%), 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   MARKNLLKGFVLPTSITVEHLD-TNAHYGKFAAYPFERGYGVTIGNTLRRILLSSIQGYA 59

Query: 60  ITAVQI-----DGVLH----EISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKR 109
           I+AV+I      G  H    E   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|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 =  323 bits (829), Expect = 2e-86,   Method: Composition-based stats.
 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|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 =  323 bits (829), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 99/311 (31%), Positives = 167/311 (53%), Gaps = 11/311 (3%)

Query: 14  NIEYIV--LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
            IE +     +   +    + 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 -GDGSLKDRLLLEVWTNGSISPQEALSSSAAILVELFNPL-----KDISLEPTDMGLDMP 238

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL+LSVR+ NCL+   +  + DL+  T+ D+L + NFG+KS  E+   L 
Sbjct: 239 DDPTAQIPIEELQLSVRAYNCLKRAQVNSVADLLDYTQEDLLEIKNFGQKSAEEVVEALQ 298

Query: 312 TMGLFLGMNLP 322
                LG+ LP
Sbjct: 299 RR---LGITLP 306


>gi|58415826|emb|CAH57327.1| RNA polymerase alpha-subunit [Vibrio diazotrophicus]
          Length = 309

 Score =  323 bits (829), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 132/315 (41%), Positives = 204/315 (64%), Gaps = 11/315 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNAL R+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQIST---THAKVTLEPLERGFGHTLGNALHRILLSSMPGCAVTEVEIEGV 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 AYSVDAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLGTMGLFLG 318
            EIK VL + GL LG
Sbjct: 295 TEIKDVLASRGLSLG 309


>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 =  323 bits (829), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 120/317 (37%), Positives = 191/317 (60%), Gaps = 10/317 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E ++P     I   +  +     + +PL RG+ +TLGN +RRVL++SL GAA TA+QID
Sbjct: 2   TEFMRPT----ITTEEVSDTVARFVVDPLERGYGYTLGNTMRRVLLNSLDGAAATAIQID 57

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQTVND 124
           GV HE ++ +GV ED+TDI+LN+KG+   +  +        +   GP  VT  D+Q   +
Sbjct: 58  GVQHEFATAEGVIEDITDIVLNVKGLVFSVFAEDAIEATAHVSAEGPCTVTGADLQVPTE 117

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
             ++NPDHVI  +     + M + +  G GYV A+ ++   DPIG+I +D+L+SP+++ +
Sbjct: 118 FTLVNPDHVIATVADGGQLDMTIRIGVGRGYVVAERNKRNEDPIGIIHVDSLFSPVRRCA 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
            +V   R GQ  DYDKL + ++TDGS+T  D+V  A+ I+   +G F++  E ++E + +
Sbjct: 178 LSVTDTRVGQSTDYDKLILEVETDGSLTPTDAVCQAANIVTQYMGAFLSLNESEEEEEGE 237

Query: 245 INVKSLPF----NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           +     P     N  L K++E+L+LSVRS NCL+   I  +  L++ +E D+L + NFG 
Sbjct: 238 VPSIFAPEGEETNAELDKQIEDLDLSVRSYNCLKRAGIHSVRQLVEYSENDLLNIRNFGA 297

Query: 301 KSLVEIKGVLGTMGLFL 317
           KS+ E+K  L +MGL L
Sbjct: 298 KSIEEVKDKLISMGLNL 314


>gi|125743179|gb|ABN54790.1| RpoA [Vibrio sp. RLUH-CZ]
          Length = 307

 Score =  323 bits (829), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 136/313 (43%), Positives = 204/313 (65%), Gaps = 11/313 (3%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T  +I+GVLH
Sbjct: 1   KPRLVD---IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEXEIEGVLH 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 SVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEE 237

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 238 KPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 294

Query: 306 IKGVLGTMGLFLG 318
           IK VL + GL LG
Sbjct: 295 IKDVLASRGLSLG 307


>gi|90194050|gb|ABD92586.1| RpoA [Haemophilus parasuis]
          Length = 302

 Score =  323 bits (828), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 132/296 (44%), Positives = 199/296 (67%), Gaps = 7/296 (2%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +GV 
Sbjct: 3   ILTISSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKEGVQ 62

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL-D 138
           ED+ +++LN+KG+ +K+       +T+ K G G VTA DI    D+E++NPDHVICNL D
Sbjct: 63  EDILEVLLNLKGLAVKVQNKDDIILTLTKSGIGPVTAADITHDGDVEIVNPDHVICNLTD 122

Query: 139 VDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
            +A + M + V +G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+AR  Q 
Sbjct: 123 KNASISMRIRVQRGRGYVPASARVHTQDDDRPIGRLLVDARFSPVDRIAYNVEAARVEQR 182

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
            D DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++    ++  +   F+P 
Sbjct: 183 TDLDKLVIEMETNGTLDPEEAIRRAATILAEQLAAFVDLRDVRQP---EVKEEKPEFDPI 239

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
           LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL 
Sbjct: 240 LLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLA 295


>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 =  323 bits (828), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 115/296 (38%), Positives = 178/296 (60%)

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 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           EL+LSVRS NCL+   I  + +L  ++E DM+++ N G+KSL E+K  L  +GL  
Sbjct: 255 ELDLSVRSYNCLKRAGIQTVQELAAKSEDDMIKVRNLGKKSLKEVKEKLVELGLGF 310


>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 =  323 bits (828), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 125/323 (38%), Positives = 206/323 (63%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            IKP+ +   +L   +E +      PL  GF  T+GNALRRVL+SSL G AI++++I+GV
Sbjct: 6   FIKPDKV---ILLNSDEFKGQFEFRPLEPGFGLTIGNALRRVLLSSLEGYAISSIKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE S+I GV ED+T+IILN+K + LK    G ++++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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++ ++ + GL  G ++  +
Sbjct: 303 SLTELEELVHSKGLNFGFDVAKY 325


>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 =  323 bits (828), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 114/312 (36%), Positives = 174/312 (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+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 DGGSLEKDRLTLEIWTSGSLTPQEAISQAAAILVDLFGAL-----KDINLESITSDQRDD 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 NR---LGITLPK 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 =  323 bits (828), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 123/317 (38%), Positives = 188/317 (59%), Gaps = 11/317 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E ++P     +   +  +     I EPL RGF +TLGN +RRVL+SSL GA  TA+QI+G
Sbjct: 3   EFMRPT----VTTEEVNDTIARFIVEPLERGFGYTLGNCMRRVLLSSLDGARATAIQIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQTVNDI 125
           V HE ++ +GV ED+TDI LN+KG+  +   +       T+   GP  VT  DIQ   + 
Sbjct: 59  VQHEFTTAEGVIEDVTDIALNVKGLVFQALSEDYTEATATVSVEGPCTVTGADIQVPTEF 118

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
            ++NP+HVIC +     + M + +  G GYVPA+ ++   DPIG+I +D+L+SP+++ + 
Sbjct: 119 TLVNPEHVICTVADGGTLNMTIRIGVGRGYVPAERNKRSEDPIGIIHVDSLFSPVQRCTA 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI-----NFEEPKKE 240
            V S R GQ  D+DKL + + TDGSIT +++V  A+ I+   +G F+       E+   E
Sbjct: 179 DVSSTRVGQRTDFDKLVLEVATDGSITPDEAVCRAANIINQYMGSFMALADIAGEDEDGE 238

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           +      +    N  L K++E+L+LSVRS NCL+   I  +  L++ +E D+L + NFG 
Sbjct: 239 IPSIFAPEGQESNAELDKQIEDLDLSVRSYNCLKRAGIHSVRQLVEFSENDLLNIRNFGA 298

Query: 301 KSLVEIKGVLGTMGLFL 317
           KS+ E+K  L +MGL L
Sbjct: 299 KSIEEVKDKLISMGLNL 315


>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 =  323 bits (827), Expect = 3e-86,   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-IEIAEI-SEDKKFGRFICEPLERGYGTTLGNSLRRIMLSSLPGSAVSQVKIDG 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|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 (827), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 123/315 (39%), Positives = 190/315 (60%), Gaps = 8/315 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E I+P     +V+    EN   +  EPL RG+  TLGN++RRVL+SSL GAA+ A+ ID
Sbjct: 2   SEFIRPQ----VVVEDISENLARVNVEPLERGYGDTLGNSMRRVLLSSLEGAAVEAISID 57

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDI 125
           GV HE S+I GV+ED+TDI+LN+KG+  + +G   +   +I   GP  V AGD     + 
Sbjct: 58  GVQHEFSTIPGVYEDVTDIVLNVKGLVFRSNGTGSEAEASISVDGPCTVVAGDFLIPAEF 117

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +++N DH IC L   A + M + +  G  YV    +  E+DPIG+I +D+L+SP+ + + 
Sbjct: 118 DLINKDHHICTLCEGAHLSMRMRIGMGRSYVSGDDNEREDDPIGVIHVDSLFSPVTRCAK 177

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE  R GQ  +YD+L + ++T+GSI+  D+V  A+ I+   +  F++  E ++E  ED 
Sbjct: 178 VVEPCRVGQHTNYDRLILEVETNGSISPRDAVIQAADIINQHMCAFMDLAEDEQEPLEDA 237

Query: 246 NVK---SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           ++        N  L K++E+L+LSVRS NCL+   I  +  L++ +E D+L + NFG KS
Sbjct: 238 SIFSTVEEEDNTELDKQIEDLDLSVRSYNCLKRAGIHNVRQLVEFSENDLLNIRNFGVKS 297

Query: 303 LVEIKGVLGTMGLFL 317
           + E++  L   GL L
Sbjct: 298 IEEVREKLEAAGLGL 312


>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 =  323 bits (827), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 99/311 (31%), Positives = 167/311 (53%), Gaps = 11/311 (3%)

Query: 14  NIEYIV--LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
            IE +     +   +    + 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 -GDGSLKDRLLLEVWTNGSISPQEALSSSAAILVELFNPL-----KDISLEPTDMGLDMP 238

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +P     +EEL+LSVR+ NCL+   +  + DL+  T+ D+L + NFG+KS  E+   L 
Sbjct: 239 DDPTAQIPIEELQLSVRAYNCLKRAQVNSVADLLDYTQEDLLEIKNFGQKSAEEVVEALQ 298

Query: 312 TMGLFLGMNLP 322
                LG+ LP
Sbjct: 299 RR---LGITLP 306


>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 =  323 bits (827), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 126/318 (39%), Positives = 190/318 (59%), Gaps = 9/318 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           +E+ KP+ +  +     +      + EPL RG+  TLGN+LRRVL+SSL G A+T ++ID
Sbjct: 2   KEIEKPSLV--VDEISPDGRYGKFVWEPLERGYGITLGNSLRRVLLSSLSGMAVTGIKID 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS-----HKRVTIFKRGPGVVTAGDIQT 121
           GVLHE S+I+GV ED+ DI+LNIK +  K+  D       K   I K G G VT  D+ T
Sbjct: 60  GVLHEFSTIEGVREDVADIVLNIKALCFKVGLDDQASFEPKTFYIKKAGEGEVTGADVIT 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
             D EVLNP+  I  LD +  + ME+ V  G GYV A+ +++++ PIG I +D++YSPI 
Sbjct: 120 DQDTEVLNPELHIATLDKNGALNMEIYVDVGRGYVQAEKNKSKDQPIGFIPVDSIYSPIT 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +V + V   R G V +YD+L++ + TDGS+  +++V  A+ IL   L +F     P+ + 
Sbjct: 180 RVKFGVTDTRVGNVTNYDRLTLEVWTDGSLGPDEAVTSAAEILIKYLALFKTTNVPRIQG 239

Query: 242 KEDINVKSLP--FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            ED    S     +  L   +++L+L+VRS NCLR   I  + D+I +TE +++ + N G
Sbjct: 240 DEDGTKTSDEGSKSSVLQMSIDDLDLTVRSNNCLRRAGINTVEDIINKTEDELICVRNLG 299

Query: 300 RKSLVEIKGVLGTMGLFL 317
            KSL E+K  +  +GL L
Sbjct: 300 SKSLEEVKNKIEELGLHL 317


>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 =  323 bits (827), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 99/311 (31%), Positives = 168/311 (54%), Gaps = 10/311 (3%)

Query: 14  NIEYIV--LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
            IE +     +   + +  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              ++       +P
Sbjct: 185 ADGSIPKDRLLLEVWTNGSISPQEALSSAAGILVDLFNPL-----KDISLEPTDTNSDIP 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 RR---LGITLP 307


>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 =  323 bits (827), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 129/306 (42%), Positives = 189/306 (61%), Gaps = 3/306 (0%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNI 89
             AEP   G+ HT+GN+LRR+L+SS+ GAAI++V+I+GV HE  S+ G+ ED+TDI+LN+
Sbjct: 2   FHAEPFEAGYGHTIGNSLRRILLSSIEGAAISSVKIEGVSHEFQSVDGIVEDITDIVLNL 61

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTV 149
           K + L        ++ I     G +TA DIQ  +++EV+NPD +IC LD +     EL +
Sbjct: 62  KKVLLVCHKREGVKLMINTNRSGAITAADIQPDSNVEVINPDQIICTLDREMPFTAELEI 121

Query: 150 SKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
             G GY P   ++ E DPIG+I ID+L+SP+  V Y VE+   GQ+ DYDKL + + TDG
Sbjct: 122 KVGRGYCPGDDNKDEEDPIGVIAIDSLFSPVSLVKYAVEATLVGQITDYDKLLLEVWTDG 181

Query: 210 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL---LKKVEELELS 266
            IT +D++  A+ IL+  L +F N  +   E +++    S   N         V E+ELS
Sbjct: 182 RITPDDALKQAAAILKHHLDVFDNVSDENYEFEDEGGEVSEEQNKLRKLLNMSVNEIELS 241

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           VR+ NCL   NI  +G+L  ++E +ML+  NFG+KSL EIK  L ++GL LGM   +   
Sbjct: 242 VRAANCLNNANITTVGELAMKSEQEMLKYRNFGKKSLNEIKDKLESLGLSLGMKFDERLL 301

Query: 327 ESIEEL 332
           +S +EL
Sbjct: 302 DSKKEL 307


>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 =  322 bits (826), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 98/311 (31%), Positives = 170/311 (54%), Gaps = 10/311 (3%)

Query: 14  NIEYIV--LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
            IE +     +   + +  + 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              ++       +P
Sbjct: 185 GEGLIPKDRLLLEVWTNGSISPQEALSSAAGILVDLFNPL-----KDISLEPTDTGSDIP 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 RR---LGITLP 307


>gi|90194058|gb|ABD92590.1| RpoA [Mannheimia granulomatis]
          Length = 303

 Score =  322 bits (826), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 132/297 (44%), Positives = 200/297 (67%), Gaps = 7/297 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+IDGVLHE SS +
Sbjct: 1   LVNIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSSKE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ +++LN+KG+ +K+       +T+ K G G VTA DI    D+E++NPDHVICN
Sbjct: 61  GVQEDILEVLLNLKGLAVKVQNKDDIILTLNKSGIGPVTAADITHDGDVEIVNPDHVICN 120

Query: 137 L-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           L D +A + M + V +G GYVPA    H + ++ PIG + +DA +SP+ +++Y VE+AR 
Sbjct: 121 LTDKNASINMRIRVQRGRGYVPASARLHTQNDDRPIGRLLVDARFSPVDRIAYNVEAARV 180

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + ++    ++  +   F
Sbjct: 181 EQRTDLDKLVIEMETNGTLDPEEAIRRAATILAEQLAAFVDLRDVRQP---EVKEEKPEF 237

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK V
Sbjct: 238 DPILLRPVDDLELTVRSANCLKAETIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDV 294


>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 =  322 bits (826), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 99/311 (31%), Positives = 168/311 (54%), Gaps = 10/311 (3%)

Query: 14  NIEYIV--LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
            IE +     +   + +  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              ++       +P
Sbjct: 185 ADGSIPKDRLLLEVWTNGSISPQEALSSAAGILVDLFNPL-----KDISLEPTDTNSDIP 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 RR---LGITLP 307


>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 =  322 bits (826), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 103/308 (33%), Positives = 168/308 (54%), Gaps = 9/308 (2%)

Query: 15  IEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS 74
           +E   L  + +  +  + EPL RG   T+GNALRRVL+S+L G AITAV+I GV HE ++
Sbjct: 9   VESKTLKNQSQ-YSKFVLEPLDRGQGTTVGNALRRVLLSNLEGTAITAVRIAGVNHEFAT 67

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           I G+ ED+ +I+LN+K + LK          +   GP  V +      +D+E ++P   I
Sbjct: 68  IAGIREDVLEILLNMKEVVLKSYTPGPHIGRVMITGPSTVRSAQFDLPSDVEFVDPGQYI 127

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
             L   A + ME  + +G GY   +  R E   +  + +DA++ P+ KV+Y+VE  R   
Sbjct: 128 ATLADGAKLEMEFRIERGKGYRSVERGRDETSSVDFLQLDAVFMPVTKVNYSVEDTRVDG 187

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
            L+ D+L + + T+GS++ +++++ A+ IL D      + E   + V    +      +P
Sbjct: 188 SLEKDRLILDVWTNGSVSPQEALSQAANILVDLFNPLKDIELKPEPVGRPEDE-----DP 242

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L    
Sbjct: 243 TSQIPIEELQLSVRAYNCLKRAQINSVADLLDYSQEDLLEIKNFGQKSAEEVIDAL---Q 299

Query: 315 LFLGMNLP 322
             LG+ LP
Sbjct: 300 KRLGITLP 307


>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 =  322 bits (826), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 125/321 (38%), Positives = 192/321 (59%), Gaps = 6/321 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           +  P  IE        +     +A+PL RG+  TLGN +RRVL++SL G AIT +++DGV
Sbjct: 5   MQMPAKIEVDET-THTDYFGRFVAQPLERGYGVTLGNMMRRVLLASLPGTAITGIKVDGV 63

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEV 127
            HE S+I+GV ED+ +I+LN+K +  + +     + T+   GP   TAGDI     + +V
Sbjct: 64  FHEFSAIEGVREDVPEIVLNLKKVRFRSTCKRSCKTTLTITGPKDFTAGDIVAMEGEFDV 123

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D  I  ++  + + +++ V +G GY PA+ +R E+ PIG I IDA+Y+PI+ V   V
Sbjct: 124 LNKDLHIATVNEGSTLNIDVFVGRGRGYTPAEDNRPESMPIGYIAIDAIYTPIRNVKVAV 183

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE----EPKKEVKE 243
           E+ R GQ  DY+K+ + ++TDGSIT +DS++LA RI+ + +  F +F     E  +E  +
Sbjct: 184 ENTRVGQRTDYEKMVLDVETDGSITPDDSISLAGRIINEHVAFFADFSPTEEEFTEEEFK 243

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             + +       L  K+E+L+LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL
Sbjct: 244 QQDDEFEAMRKLLNTKIEDLDLSVRSHNCLRLAEIDSIGDLVSRKEDELLNYKNFGKKSL 303

Query: 304 VEIKGVLGTMGLFLGMNLPDW 324
            E+K  L    L  GM++  +
Sbjct: 304 TELKEQLEKFELKFGMDITKY 324


>gi|189308771|gb|ACD87087.1| RpoA [Vibrio sp. PP-200]
          Length = 302

 Score =  322 bits (826), Expect = 5e-86,   Method: Composition-based stats.
 Identities = 134/304 (44%), Positives = 201/304 (66%), 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 V-DAVVRMELTVSKGHGYVPAK---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++  + +   +++   +  P   
Sbjct: 182 RTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP--- 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|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 =  322 bits (826), Expect = 5e-86,   Method: Composition-based stats.
 Identities = 124/323 (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  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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++ ++   GL  G ++  +
Sbjct: 303 SLTELEELVHAKGLNFGFDVAKY 325


>gi|309389906|gb|ADO77786.1| DNA-directed RNA polymerase subunit alpha [Halanaerobium praevalens
           DSM 2228]
          Length = 315

 Score =  322 bits (825), Expect = 5e-86,   Method: Composition-based stats.
 Identities = 127/312 (40%), Positives = 201/312 (64%), Gaps = 6/312 (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 IKGVLGTMGLFL 317
           I+  L  + L L
Sbjct: 299 IEKKLDELELDL 310


>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 =  322 bits (825), Expect = 5e-86,   Method: Composition-based stats.
 Identities = 121/321 (37%), Positives = 192/321 (59%), Gaps = 6/321 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           +  P  IE        +     +A+PL RG+  TLGN +RR L++SL G AIT ++IDGV
Sbjct: 5   MQMPAKIEVDEA-THTDRFGRFVAQPLERGYGVTLGNVMRRALLASLPGTAITGLKIDGV 63

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEV 127
            HE S+I GV ED+ +I+LN+K +  + +   + + ++   G    TAGDI     + EV
Sbjct: 64  FHEFSTINGVREDVPEIVLNLKKVRFRSNCKRNCKTSLVLNGQKEFTAGDIIAQEGEFEV 123

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D  I  ++  A +++++ V +G GY+P++ +R +  PIG I IDA+++PI+ V +TV
Sbjct: 124 LNKDLHIATVNEGATLKIDIFVGRGRGYLPSEENRPDGMPIGFIAIDAIFTPIRNVKFTV 183

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE----EPKKEVKE 243
           E+ R GQ  DY+K+ + ++TDGSIT +DS++LA +I+ + +  F +F     E  +E  +
Sbjct: 184 ENTRVGQRTDYEKMILDVETDGSITPDDSISLAGKIINEHVTFFADFSPTEEEFTEEEFK 243

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             + +          K+E+L+LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL
Sbjct: 244 QQDDEFENMRKLFNTKIEDLDLSVRSHNCLRLAEIDTIGDLVSRKEDELLNYKNFGKKSL 303

Query: 304 VEIKGVLGTMGLFLGMNLPDW 324
            E+K  L    L  GM++  +
Sbjct: 304 TELKEQLEKFDLKFGMDITKY 324


>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 =  322 bits (825), Expect = 5e-86,   Method: Composition-based stats.
 Identities = 131/316 (41%), Positives = 204/316 (64%), Gaps = 8/316 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP     I    E++     + EPL RG+  TLGN+LRR+++SSL G+A++ V+IDG
Sbjct: 3   EFEKPTI--RIEEISEDKRYGRFVVEPLERGYGTTLGNSLRRIMLSSLPGSAVSQVKIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRG---PGVVTAGDIQTVND 124
           VLHE S I GV ED++DII+NIK + +K S DS++    +       GVVTAGDI T +D
Sbjct: 61  VLHEFSPIPGVKEDVSDIIMNIKNLAIKNSSDSNEPKIAYIECDGREGVVTAGDIHTDSD 120

Query: 125 IEVLNPDHVICNLDV--DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           IE++NPD  I  L+   D  + MELT++ G GYV A+ ++ E+ PIG+++ID++Y+P+++
Sbjct: 121 IEIMNPDLPIATLNGGNDCKLFMELTITNGRGYVSAEKNKHEDTPIGVLSIDSIYTPVER 180

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE-V 241
           V+ TV++ R GQV D+DKL++ + T+G++  +D+V+LA+++L + L +F++  +  K+ V
Sbjct: 181 VNMTVQNTRVGQVTDFDKLTLEVYTNGTLAPDDAVSLAAKVLCEHLNLFVDLSDNTKDVV 240

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
              I              ++ELELSVRS NCL+   I  + +L  +T  DM+++ N GRK
Sbjct: 241 GTFIEKPEDEKVKTGAINIDELELSVRSYNCLKRAGINTVEELCSKTAEDMMKVRNLGRK 300

Query: 302 SLVEIKGVLGTMGLFL 317
           SL E+   L  +GL L
Sbjct: 301 SLEEVLAKLKELGLEL 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 =  321 bits (824), Expect = 7e-86,   Method: Composition-based stats.
 Identities = 123/313 (39%), Positives = 198/313 (63%), Gaps = 2/313 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP+ IE   L ++ +   + + EPL  G+  T+GN+LRRVL+SSL GA+++ V I G
Sbjct: 3   EIEKPS-IEIQELSEDGKK-GIFVVEPLESGYGITIGNSLRRVLLSSLPGASVSFVNIRG 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|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 =  321 bits (824), Expect = 7e-86,   Method: Composition-based stats.
 Identities = 99/306 (32%), Positives = 161/306 (52%), Gaps = 10/306 (3%)

Query: 16  EYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           +   +    E           EPL RG   T+GNALRRVL+S+L G A+TAV+I GV HE
Sbjct: 4   QVECVESRTEADQGQYGRFSIEPLARGQGTTVGNALRRVLLSNLEGTAVTAVRIGGVNHE 63

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            ++I GV ED+ DI+LN++ + +       +   +   GP  VTA D+    ++EV+NP+
Sbjct: 64  FATIPGVREDVLDILLNVRELVVHAHSPQPQIGRLRVVGPATVTAADVDFGPEVEVINPN 123

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
           H I +L   A + MEL V  G GY        E   +  + +DA++ P+++V+Y+VE AR
Sbjct: 124 HYIASLSEGATLEMELKVEWGTGYRAIDRSHDETTALDFLQLDAVFMPVRRVNYSVEDAR 183

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
            G+    D+L + + T+GS++ +++++ A+  L        N         +        
Sbjct: 184 VGESTAIDRLVLEVWTNGSLSPQEALSQAASCLVALFEPLKNVSVGSTHTADPEPTPESQ 243

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +E+L+LSVR+ NCL+   +  + DL+  T  D+L + NFG+KS  E+   L 
Sbjct: 244 ------TPIEDLQLSVRAYNCLKRAQVNSVADLLSYTYEDLLEIKNFGQKSAEEVVEALE 297

Query: 312 TMGLFL 317
            +G+ L
Sbjct: 298 RIGIKL 303


>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 =  321 bits (823), Expect = 8e-86,   Method: Composition-based stats.
 Identities = 130/301 (43%), Positives = 187/301 (62%), Gaps = 5/301 (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 L 317
            
Sbjct: 315 F 315


>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 =  321 bits (823), Expect = 9e-86,   Method: Composition-based stats.
 Identities = 123/300 (41%), Positives = 180/300 (60%), Gaps = 5/300 (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 VRMELTVSKGHGYVPAK----HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 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


>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 =  321 bits (823), Expect = 9e-86,   Method: Composition-based stats.
 Identities = 123/323 (38%), Positives = 193/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++    +        PL  G+  T+GNALRRVL+SSL G AIT+V+I+GV
Sbjct: 6   FQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSSLEGFAITSVRIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQ-TVNDI 125
            HE S++ GV ED+T+IILN+K +  K   +   ++ VTI   G   +TAGD Q  ++  
Sbjct: 63  DHEFSTLAGVVEDVTEIILNLKQVRFKRQIEEIDNETVTISLSGVDQLTAGDFQKFISGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNPD VI N+D    + ME+T+ KG GYVPA+ ++  N P+G I  D++Y+PI+ V Y
Sbjct: 123 QVLNPDMVIANMDKKVNLNMEITIEKGRGYVPAEENKKSNAPLGTIFTDSIYTPIRNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL   I TDGSI  ++++  A++ L     +F    I  E  +   
Sbjct: 183 SIENYRVEQKTDYEKLVFEIITDGSIHPKEALTEAAKTLIHHFMLFSDERITLEADEIAQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+K
Sbjct: 243 TETYDEESLHMRQLLKTKLIDMDLSVRALNCLKAAEVETLGDLVSYNKNDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++ ++   GL  GM+L  +
Sbjct: 303 SLTELEELVNVKGLSFGMDLAKY 325


>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 =  321 bits (823), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 109/311 (35%), Positives = 171/311 (54%), Gaps = 11/311 (3%)

Query: 16  EYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           +   +  + +      +  + EPL RG   T+GNALRRVL+++L G A+TA++I GV HE
Sbjct: 5   QIECIESKTQKNQSQYSKFVLEPLERGQGTTVGNALRRVLLANLEGTAVTAIRIGGVNHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            ++I GV ED+ +I+LN+K I LK   D  +   +   G   VTAG     +++EV+NP 
Sbjct: 65  FATIPGVREDVLEIMLNMKEIVLKSYTDQPQIGRLVATGAAHVTAGQFDLPSEVEVINPT 124

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             I  L   A + ME  + KG GYVP +    E   +  + IDA++ P+ KV+Y+VES R
Sbjct: 125 QPIATLTEGAKLEMEFRIEKGVGYVPVERSSDEPTALDFLQIDAVFMPVTKVNYSVESIR 184

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
             +    D+L + I T+GS   +++++ A+ IL D      +  + +  V E  +     
Sbjct: 185 GEEGEAKDRLMLEIWTNGSFNPKEALSRAADILVDLFNPLKDLNQLETAVPEYPD----E 240

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            NP     +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L 
Sbjct: 241 ENPQSQIPIEELQLSVRAYNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEEVIEAL- 299

Query: 312 TMGLFLGMNLP 322
                LG+ LP
Sbjct: 300 --QKRLGITLP 308


>gi|179184786|gb|ACB78160.1| RNA polymerase alpha subunit [Vibrio gallaecicus]
          Length = 306

 Score =  321 bits (822), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 136/304 (44%), Positives = 200/304 (65%), Gaps = 8/304 (2%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           L Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +GV 
Sbjct: 6   LEQINTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKEGVQ 65

Query: 80  EDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
           ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+ NP+HVIC+L 
Sbjct: 66  EDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVICHLT 125

Query: 139 VD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
            D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR  Q
Sbjct: 126 DDNAEIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAARVEQ 185

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
             D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   +++   +  P   
Sbjct: 186 RTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP--- 242

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
            LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + G
Sbjct: 243 ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRG 302

Query: 315 LFLG 318
           L LG
Sbjct: 303 LSLG 306


>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 =  321 bits (822), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 128/301 (42%), Positives = 187/301 (62%), Gaps = 5/301 (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 L 317
            
Sbjct: 315 F 315


>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 =  321 bits (822), Expect = 1e-85,   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-IEINEI-SEDNRFGRFVVEPLERGYGTTLGNSLRRIMLSSLPGAAVSSVKIKG 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|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 =  321 bits (822), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 125/323 (38%), Positives = 194/323 (60%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++    +        PL  G+  T+GNALRRVL+SSL G AIT+V+I+GV
Sbjct: 6   FQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSSLEGFAITSVRIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQ-TVNDI 125
            HE S+I GV ED+T+IILN+K +  K   D   ++ VTI   G   +TAG  Q  ++  
Sbjct: 63  DHEFSTIAGVVEDVTEIILNLKQVRFKRQIDEIDNESVTISVSGEEQLTAGHFQKFISGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNPD VIC++D    + ME+T+ KG GYVPA+ ++  N P+G I +D++Y+PIK V Y
Sbjct: 123 QVLNPDQVICHMDKKVSLNMEITIEKGRGYVPAEENKKANAPLGTIFVDSIYTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL   I +DGSI  +D++  A++ L     +F    I  E  +   
Sbjct: 183 SIENFRVEQKTDYEKLVFEIISDGSIHPKDALTEAAKTLIHHFMLFSDERITLEADEIAQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+K
Sbjct: 243 TETYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSYNKNDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++ ++   GL  GM+L  +
Sbjct: 303 SLTELEELVSNKGLNFGMDLSKY 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 =  321 bits (822), Expect = 1e-85,   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|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 =  321 bits (822), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 127/318 (39%), Positives = 191/318 (60%), Gaps = 6/318 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           +  P  IE        E     IA+PL RG+  T+GN +RRVL++SL G AIT V+I+GV
Sbjct: 5   MQMPAKIEVDEA-THTEMFGRFIAQPLERGYGVTIGNVMRRVLLASLPGTAITGVKIEGV 63

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEV 127
            HE S+I+GV ED+ +I+LN+K +  K +     + ++   G    TAGDI     + EV
Sbjct: 64  YHEFSAIEGVREDVPEIVLNLKRVRFKSNCKRSCKTSLSIAGTKDFTAGDIIAKEGEFEV 123

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D  I  ++  +V+ +E+ + +G GY+PA+ +  E  PIG I IDA+++PI+ V +TV
Sbjct: 124 LNKDLHIATVNDGSVLNIEIYIGRGRGYLPAEENHPEGMPIGFIAIDAIFTPIRNVKFTV 183

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE----EPKKEVKE 243
           E+ R GQ  DY+K+ + ++TDGSI  +DS++LA +I+ D +  F NF     E  +E  +
Sbjct: 184 ENTRVGQRTDYEKMILDVETDGSIAPDDSISLAGKIINDHIMYFANFSPTEEEFTEEEFK 243

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             + +       L  K+E+L+LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL
Sbjct: 244 QQDDEFESMRKLLHTKIEDLDLSVRSHNCLRLAEIDTIGDLVSRKEDELLNYKNFGKKSL 303

Query: 304 VEIKGVLGTMGLFLGMNL 321
            E+K  L    L  GM++
Sbjct: 304 TELKEQLEKFDLKFGMDI 321


>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 =  320 bits (821), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 124/310 (40%), Positives = 191/310 (61%), Gaps = 8/310 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           ++  P     I + Q  EN      EPL  G+ HTLGNALRRVL+SS+ G+AIT ++IDG
Sbjct: 3   DIAMPK----IEVVQAAENYGRFKIEPLDPGYGHTLGNALRRVLVSSIPGSAITKIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE S+I+GV ED+T+I+LNIKG+ L+   +   +V + KRGPG+VTA DI   ++IE+
Sbjct: 59  VFHEFSTIEGVKEDVTEIVLNIKGVRLRSYAERPVKVLLTKRGPGIVTAKDIDVPSNIEL 118

Query: 128 LNPDHVICNLDVD-AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +NP+H IC LD + A + +E+TV +G GYV A     +  PIG I +DA+++P+ +V+Y 
Sbjct: 119 VNPNHYICTLDSEVARLEIEMTVERGRGYVSADQR--DILPIGEIPVDAIFTPVPRVNYV 176

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+ R GQ  D+D+L + I TDG++   D+++ A+++L        +F     E +E   
Sbjct: 177 VENTRIGQATDFDRLLLEIWTDGTVKPGDALSHAAQVLVQYSQTIADFNRLAVEEEESPT 236

Query: 247 VKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
              L   +      +E+L+LS R+ NCL+  +I  +G ++Q  E  +L + N G+KS+ E
Sbjct: 237 PSGLTIPSDIYDTPIEDLDLSTRTYNCLKRADITKVGQVLQMDEKALLSVRNLGQKSMEE 296

Query: 306 IKGVLGTMGL 315
           I+  L   G 
Sbjct: 297 IRDRLVERGY 306


>gi|179184639|gb|ACB78155.1| RNA polymerase alpha subunit [Vibrio comitans]
          Length = 304

 Score =  320 bits (821), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 137/307 (44%), Positives = 201/307 (65%), Gaps = 9/307 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +
Sbjct: 2   LVDIEQINTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKE 61

Query: 77  GVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
           GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E+ NP+HVIC
Sbjct: 62  GVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVIC 121

Query: 136 NLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
           +L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K++Y+VE+AR
Sbjct: 122 HLTDDNADIAMRIKVERGRGYVPASARIHTEEDERPIGRLLVDATYSPVDKIAYSVEAAR 181

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
             Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   KE        
Sbjct: 182 VEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEKEREPR---- 237

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
           F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL 
Sbjct: 238 FDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLA 297

Query: 312 TMGLFLG 318
           + G  LG
Sbjct: 298 SRGWSLG 304


>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 =  320 bits (821), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 113/317 (35%), Positives = 191/317 (60%), Gaps = 11/317 (3%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M+++N +          +++ +  +     + EPL RG+  T+GN+LRR+L+SS+ GAA+
Sbjct: 1   MLEENVR----------VIIEKRSDEYGRFVIEPLERGYGWTIGNSLRRILLSSIEGAAV 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 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSYTVE  R G+  D D+L + I T+ S+T E++   ASRIL +   +    E     
Sbjct: 171 KKVSYTVEKTRVGRRTDLDRLIIEIWTNKSVTPEEAFREASRILMEYFKLLSEREFQLPH 230

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            +    + SL      L  +E+L LS R+ N LR   I  + DL+ ++  D++++ NFG+
Sbjct: 231 EEVGQEITSLEEEKKGLT-LEDLGLSTRAYNSLRHAGIHTIEDLLSKSREDLMKIKNFGQ 289

Query: 301 KSLVEIKGVLGTMGLFL 317
           KSL E++  L   GL L
Sbjct: 290 KSLQELEEKLREKGLSL 306


>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 =  320 bits (821), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 132/311 (42%), Positives = 199/311 (63%), Gaps = 1/311 (0%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             I+ + L ++  N    +  PL RG+  TLGN+LRRVL+SSL GAAI+ + I GV HE+
Sbjct: 7   TKIKIVELDEQN-NYGKFVIMPLERGYGTTLGNSLRRVLLSSLPGAAISKINIQGVAHEM 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           S+IKGV ED+ +IILN+KGI +K   +    + +  +GP V+TA DI    D+EV NPDH
Sbjct: 66  STIKGVKEDVPEIILNLKGIAVKKYNEEPISLNVDIKGPCVLTAKDILVDTDLEVKNPDH 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  L+ DA + M++TV  G GY  ++ ++TE D IG I ID+L+SP+KKV++TV++AR 
Sbjct: 126 YIATLNEDASLEMQITVINGKGYKISEFNKTEEDIIGDIAIDSLFSPVKKVNFTVDNARV 185

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           GQV+DYDKL++ + T+G+I  +D+++  S IL + L +F      +     D        
Sbjct: 186 GQVIDYDKLTIEVWTNGTIRPQDALSEGSNILINCLELFSELPNYECNTNSDDEDNQKDK 245

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
              ++  +EEL+ S+RS NCL+  NI  +GD++  T+ADM+++ NFG+KSL E++  L  
Sbjct: 246 ETQMVINIEELDFSLRSFNCLKRANINTVGDIVSHTKADMMKIKNFGKKSLDEVEEKLQE 305

Query: 313 MGLFLGMNLPD 323
           MGL     + D
Sbjct: 306 MGLAFKQEIKD 316


>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 =  320 bits (821), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 131/311 (42%), Positives = 199/311 (63%), Gaps = 1/311 (0%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             I+ + L ++  N    +  PL RG+  TLGN+LRRVL+SSL GAAI+ + I GV HE+
Sbjct: 7   TKIKIVELDEQN-NYGKFVIMPLERGYGTTLGNSLRRVLLSSLPGAAISKINIQGVAHEM 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           S+IKGV ED+ +IILN+KGI +K   +    + +  +GP V+TA DI    D+EV NPDH
Sbjct: 66  STIKGVKEDVPEIILNLKGIAVKKYNEEPISLNVDIKGPCVLTAKDILVDTDLEVKNPDH 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  L+ DA + M++TV  G GY  ++ ++T+ D IG I ID+L+SP+KKV++TV++AR 
Sbjct: 126 YIATLNEDASLEMQITVINGKGYKISEFNKTDEDIIGDIAIDSLFSPVKKVNFTVDNARV 185

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           GQV+DYDKL++ + T+G+I  +D+++  S IL + L +F      +     D        
Sbjct: 186 GQVIDYDKLTIEVWTNGTIRPQDALSEGSNILINCLELFSELPNYECNTNSDDEDNQKDK 245

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
              ++  +EEL+ S+RS NCL+  NI  +GD++  T+ADM+++ NFG+KSL E++  L  
Sbjct: 246 ETQMVINIEELDFSLRSFNCLKRANINTVGDIVSHTKADMMKIKNFGKKSLDEVEEKLQE 305

Query: 313 MGLFLGMNLPD 323
           MGL     + D
Sbjct: 306 MGLAFKQEIKD 316


>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 =  320 bits (820), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 125/323 (38%), Positives = 193/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++    +        PL  G+  T+GNALRRVL+SSL G AIT+V+I+GV
Sbjct: 6   FQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSSLEGFAITSVRIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQ-TVNDI 125
            HE S+I GV ED+T+IILN+K +  K   D   ++ VTI   G   +TAG  Q  ++  
Sbjct: 63  DHEFSTIPGVVEDVTEIILNLKQVRFKRQIDEIDNEAVTISVSGEEELTAGHFQKFISGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNP+ VIC+LD    + ME+T+ KG GYVPA+ ++  N P+G I  D++Y+PIK V Y
Sbjct: 123 QVLNPELVICHLDSKVNINMEITIEKGRGYVPAEENKKANAPLGTIFTDSIYTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL   I +DGSI  +D++  A++ L     +F    I  E  +   
Sbjct: 183 SIENYRVEQKTDYEKLVFEIISDGSIHPKDALTEAAKTLIHHFMLFSDERITLEADEIAQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+K
Sbjct: 243 TETYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSYNKNDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++ ++   GL  GM+L  +
Sbjct: 303 SLTELEELVSNKGLNFGMDLSKY 325


>gi|179184509|gb|ACB78150.1| RNA polymerase alpha subunit [Vibrio sp. RD 9.17]
          Length = 303

 Score =  320 bits (820), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 135/304 (44%), Positives = 200/304 (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++  + +   +++   +  P   
Sbjct: 183 RTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP--- 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|291166852|gb|EFE28898.1| DNA-directed RNA polymerase, alpha subunit [Filifactor alocis ATCC
           35896]
          Length = 315

 Score =  320 bits (820), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 127/312 (40%), Positives = 202/312 (64%), Gaps = 6/312 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KPN    + + +   +      EPL RGF  T+GN+LRRVL+SSL G A+ +++I+G
Sbjct: 3   EIEKPN----VTVLEYRNDYGKFALEPLERGFGITVGNSLRRVLLSSLPGVAVNSIKIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR--VTIFKRGPGVVTAGDIQTVNDI 125
           VLHE S+I GV ED+T+I+L +K + + M+ +  ++  + I + G 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 IKGVLGTMGLFL 317
           + G L  +G  L
Sbjct: 299 VVGKLHDLGFTL 310


>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 =  320 bits (820), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 108/311 (34%), Positives = 171/311 (54%), Gaps = 11/311 (3%)

Query: 16  EYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           +   +  + +      +  + EPL RG   T+GNALRRVL+++L G A+TA++I GV HE
Sbjct: 5   QIECIESKTQKNQSQYSKFVLEPLERGQGTTVGNALRRVLLANLEGTAVTAIRIGGVNHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            ++I GV ED+ +I+LN+K I LK   +  +   +   G   VTAG     +++EV+NP 
Sbjct: 65  FATIPGVREDVLEIMLNMKEIVLKSYTEQPQIGRLVATGAAHVTAGQFDLPSEVEVINPT 124

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             I  L   A + ME  + KG GYVP +    E   +  + IDA++ P+ KV+Y+VES R
Sbjct: 125 QPIATLTEGAKLEMEFRIEKGVGYVPVERSSDEPTALDFLQIDAVFMPVTKVNYSVESIR 184

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
             +    D+L + I T+GS   +++++ A+ IL D      +  + +  V E  +     
Sbjct: 185 GEEGEAKDRLMLEIWTNGSFNPKEALSRAADILVDLFNPLKDLNQLETAVPEYPD----E 240

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            NP     +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L 
Sbjct: 241 ENPQSQIPIEELQLSVRAYNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEEVIEAL- 299

Query: 312 TMGLFLGMNLP 322
                LG+ LP
Sbjct: 300 --QKRLGITLP 308


>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 =  320 bits (820), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 124/315 (39%), Positives = 191/315 (60%), Gaps = 8/315 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E I+P     + +    EN   +  EPL RG+  TLGN++RRVL+SSL GAA+ A+ ID
Sbjct: 2   SEFIRPQ----VSVVDISENLARVNVEPLERGYGDTLGNSMRRVLLSSLEGAAVEAISID 57

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKRGPGVVTAGDIQTVNDI 125
           GV HE S++ GV+ED+TDI+LN+KG+    +G       +I   GP  VT GD +   + 
Sbjct: 58  GVQHEFSTVDGVYEDVTDIVLNVKGLVFHANGSGETAEASISIDGPCTVTGGDFKIPAEF 117

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++N DHVIC L     + M + +  G GYV    +  + DPIG+I +D+LYSP+++ + 
Sbjct: 118 ELINKDHVICTLGEGGHLAMRMRIGVGRGYVSGDDNERDEDPIGVIHVDSLYSPVRRCAK 177

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           TVE  R GQ  +YD+L + I+T+GSI+  D+V  A+ I+   +  F++  E ++E +ED+
Sbjct: 178 TVEPCRVGQHTNYDRLILEIETNGSISPRDAVIEAADIINQHMAAFMDLAEDEEEPQEDV 237

Query: 246 NVKSLPFNPAL---LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           ++ S           K++E+L+LSVRS NCL+   I  +  L++ +E D+L + NFG KS
Sbjct: 238 SIFSNEEEEENTELDKQIEDLDLSVRSYNCLKRAGIHNVRQLVEFSENDLLNIRNFGVKS 297

Query: 303 LVEIKGVLGTMGLFL 317
           + E++  L   GL L
Sbjct: 298 IEEVRDKLEDAGLGL 312


>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 =  320 bits (820), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 108/314 (34%), Positives = 174/314 (55%), Gaps = 11/314 (3%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
              +   +  + +      +  + EPL RG   T+GN+LRRVL+++L GAA+TA++I GV
Sbjct: 2   TQFQIECIESKTQKNQSQYSKFVLEPLERGQGTTVGNSLRRVLLANLEGAAVTAIRIGGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE ++I GV ED+ +I+LN+K I LK   +  +   +   G   VTAG  +  +++EV+
Sbjct: 62  NHEFATIPGVREDVLEIMLNMKEIVLKSYTEQPQIGRLVATGAAHVTAGQFELPSEVEVV 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP   I  L   A + ME  + KG GYVP +    E   +  + IDA++ P+ KV+Y+VE
Sbjct: 122 NPTQPIATLTEGAKLEMEFRIEKGVGYVPVERSSEEPAALDFLQIDAVFMPVTKVNYSVE 181

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S R  +    D+L + I T+GS   +++++ A+ IL D      +  + +  V+E  +  
Sbjct: 182 SIRGEEGEAKDRLMLEIWTNGSFNPKEALSKAADILVDLFNPLKDLNQLETAVQEYPD-- 239

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
               NP     +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+  
Sbjct: 240 --EENPQSQIPIEELQLSVRAYNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEEVIE 297

Query: 309 VLGTMGLFLGMNLP 322
            L      LG+ LP
Sbjct: 298 AL---QKRLGITLP 308


>gi|168334324|ref|ZP_02692511.1| DNA-directed RNA polymerase, alpha subunit [Epulopiscium sp. 'N.t.
           morphotype B']
          Length = 319

 Score =  320 bits (819), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 122/314 (38%), Positives = 190/314 (60%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KP+ IE   L ++ +     + EPL RG+  TLGN LRR+L+S+L G+A++ V+ +G
Sbjct: 3   EFEKPS-IEIKALSEDGK-YGCFVIEPLERGYGMTLGNGLRRILLSTLPGSAVSNVKFEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           VLHE S+I GV ED+ +IILN+KG+ ++ S      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|58415736|emb|CAH57282.1| RNA polymerase alpha-subunit [Vibrio aerogenes]
          Length = 293

 Score =  320 bits (819), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 134/296 (45%), Positives = 199/296 (67%), 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++  + +   +++   +  P    LL+ V++
Sbjct: 181 IDMETNGTIEPEEAIRRAATVLAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDD 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|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 =  320 bits (819), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 127/303 (41%), Positives = 198/303 (65%), Gaps = 10/303 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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 FGR 300
            G+
Sbjct: 295 LGK 297


>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 =  320 bits (819), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 127/312 (40%), Positives = 203/312 (65%), Gaps = 5/312 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
              P  IE      E+      + EPL RG+  TLGN+LRR+++SSL G A+++++I+GV
Sbjct: 8   FKMP-KIEMTE-KSEDGKYGKFVVEPLERGYGLTLGNSLRRIMLSSLVGTAVSSIKIEGV 65

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           LHE SSI GV ED+T+I++NIK +++K +G+    K   I   G GVV A DIQ   DIE
Sbjct: 66  LHEFSSIPGVKEDVTEIVMNIKQLSIKNNGNSVEPKEAHIDFVGEGVVRASDIQVDPDIE 125

Query: 127 VLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           ++NPD VI +L+  D+ + MELT++ G GYV ++ ++ ++ P G+I ID++Y+P+++V+ 
Sbjct: 126 IINPDLVIAHLNGADSKLTMELTITNGRGYVSSEKNKRDDQPAGVIAIDSIYTPVERVNM 185

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            V++ R GQ  D+DKL++ I T+G+I  +++++LA+++L + L  FIN  E  ++V+  +
Sbjct: 186 AVQNTRVGQDTDFDKLTLDIFTNGTIEPDEALSLAAKVLSEHLKGFINLSENAQKVEIMV 245

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +       L   +E+LELSVRS+NCLR   I  + +L  +T  DM+++ N G+KSL E
Sbjct: 246 EQEEDETTKVLSMSIEDLELSVRSSNCLRRAGINTVEELCNKTSDDMMKVRNLGKKSLDE 305

Query: 306 IKGVLGTMGLFL 317
           +   L  MGL L
Sbjct: 306 VLLKLKEMGLHL 317


>gi|58415896|emb|CAH57362.1| RNA polymerase alpha-subunit [Vibrio ichthyoenteri ATCC 700023]
          Length = 297

 Score =  320 bits (819), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 133/300 (44%), Positives = 199/300 (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++  + +   +++   +  P    LL+
Sbjct: 181 DKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLR 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|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 =  320 bits (819), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 112/312 (35%), Positives = 172/312 (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 DGGSLEKDRLTLEIWTSGSLTPQEAISQAAAILVDLFGAL-----KDINLESITSDQRDD 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 NR---LGITLPK 308


>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 =  319 bits (818), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 132/330 (40%), Positives = 196/330 (59%), Gaps = 12/330 (3%)

Query: 1   MIQKNW-QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           M +KN  +   KP  I +    + + N    +A P  RGF  T+GN LRRVL+SS++G A
Sbjct: 1   MARKNLLKGFKKPRGITFEH-SELQSNYGKFVAYPFERGFGTTVGNTLRRVLLSSIQGYA 59

Query: 60  ITAVQI-----DGVLH----EISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKR 109
           ++AV+I     +G  H    E   +  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 ADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
            ++ +  NFG+KSL EIK  L    L LGM
Sbjct: 300 EEIAKTRNFGKKSLQEIKEKLKEWNLSLGM 329


>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 =  319 bits (818), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 122/342 (35%), Positives = 186/342 (54%), Gaps = 20/342 (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--------------------EEP 237
           YD+L + + T+G +T +++VA AS IL+       N                     E  
Sbjct: 199 YDRLVLEVWTNGVVTPKEAVAKASAILEGYFRSLTNVLSSRPSQGGALPEDAISSEGEGV 258

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
             E            N  L + V +LELSVRS NCL    +  +GDL+ R   D+L++ N
Sbjct: 259 PAEGDPAEEPVRFFENALLARPVRDLELSVRSENCLLRGGVHVIGDLVGRAREDLLKIRN 318

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            G+ SL EI+  L   GL LG        E+ ++L +  E++
Sbjct: 319 LGKISLKEIEEKLEKFGLSLGGEPLSDLGETEDDLPETKEEE 360


>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 =  319 bits (818), Expect = 4e-85,   Method: Composition-based stats.
 Identities = 123/333 (36%), Positives = 188/333 (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 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLG-MFINFEEPKKEVK------------ 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|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 =  319 bits (817), Expect = 4e-85,   Method: Composition-based stats.
 Identities = 122/310 (39%), Positives = 186/310 (60%), Gaps = 8/310 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           ++  P     I +    EN      EPL  G+ HTLGNALRRVL+SS+ GAAIT ++IDG
Sbjct: 3   DIAMPK----IEVVTAAENYGRFKIEPLDPGYGHTLGNALRRVLLSSIPGAAITKIKIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V HE S+I G+ ED+T+I+LNIKG+ L+   +   ++++ KRG G+V A DI   +++E+
Sbjct: 59  VFHEFSTISGIKEDVTEIVLNIKGVRLRSYAERPVKISLSKRGSGIVRAADIDAPSNVEI 118

Query: 128 LNPDHVICNLD-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +NP H IC +D  DA++ ME+TV +G GY+PA     +  PIG I IDA+++P+ KV+Y 
Sbjct: 119 VNPFHYICTIDRDDAMLEMEMTVERGRGYLPADQR--DALPIGEIPIDAIFTPVPKVNYV 176

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+ R GQ  D+D L + I TDG+I   D+++ A+++L        +F     E +    
Sbjct: 177 VENIRVGQATDFDSLLIEIWTDGTIKPGDALSHAAQVLVQYSQTIADFNRLSTETESTAA 236

Query: 247 VKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
              L          +EEL+LS R+ NCL+  +I  +G +++  E  +L + N G+KS+ E
Sbjct: 237 PNGLAIPADIYDTPIEELDLSTRTYNCLKRADITKVGQVLEMDEKALLSVRNLGQKSMEE 296

Query: 306 IKGVLGTMGL 315
           I+  L   G 
Sbjct: 297 IRDKLIERGY 306


>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 =  319 bits (817), Expect = 5e-85,   Method: Composition-based stats.
 Identities = 126/323 (39%), Positives = 193/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++    E        PL  G+  T+GNALRRVL+SSL G AIT+V+ID V
Sbjct: 6   FQKPDKV---IMIDSSEFDGKFEFRPLEPGYGLTIGNALRRVLLSSLEGFAITSVRIDKV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQ-TVNDI 125
            HE S+I GV ED+T+IILN+K +  K   D   ++ V+I   G   +TAGD Q  ++  
Sbjct: 63  DHEFSTISGVVEDVTEIILNLKQVRFKRQIDDIDNESVSISVSGKEQLTAGDFQKFISGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNPD VICN+D    + ME+T+ KG GYVPA+ ++  N P+G I  D++Y+P+K V Y
Sbjct: 123 QVLNPDLVICNMDASVNINMEITIEKGRGYVPAEENKKSNAPLGTIFTDSIYTPVKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL   I TDGSI  ++++  A++ L     +F    I  E  +   
Sbjct: 183 SIENYRVEQKTDYEKLVFEIITDGSIHPKEALTEAAKTLIHHFMLFSDERITLEADEIAQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+K
Sbjct: 243 TETYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSYNKNDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++ ++   GL  GM+L  +
Sbjct: 303 SLTELEELVNVKGLSFGMDLSKY 325


>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 =  318 bits (816), Expect = 5e-85,   Method: Composition-based stats.
 Identities = 114/300 (38%), Positives = 178/300 (59%), Gaps = 5/300 (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 VRMELTVSKGHGYVPAKHHRTENDPIGL----ITIDALYSPIKKVSYTVESAREGQVLDY 198
           + MEL    G GY+ A  ++  N         +  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


>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 =  318 bits (816), Expect = 5e-85,   Method: Composition-based stats.
 Identities = 131/311 (42%), Positives = 198/311 (63%), Gaps = 1/311 (0%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             I+ + L ++  N    +  PL RG+  TLGN+LRRVL+SSL GAAI+ + I GV HE+
Sbjct: 7   TKIKIVELDEQN-NYGKFVIMPLERGYGTTLGNSLRRVLLSSLPGAAISKINIQGVAHEM 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           S+IKGV ED+ +IILN+KGI +K   +    + +  +GP V+TA DI    D+EV NPDH
Sbjct: 66  STIKGVKEDVPEIILNLKGIAVKKYNEEPISLNVDIKGPCVLTAKDILVDTDLEVKNPDH 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  L+ DA + M++TV  G GY  ++ ++T+ D IG I ID+L+SP+KKV++TV++AR 
Sbjct: 126 YIATLNEDASLEMQITVINGKGYKISEFNKTDEDIIGDIAIDSLFSPVKKVNFTVDNARV 185

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           GQV+DYDKL++ + T+G+I  +D+++  S IL + L +F      +     D        
Sbjct: 186 GQVIDYDKLTIEVWTNGTIRPQDALSEGSNILINCLELFSELPNYECNTNSDDEDNQKDK 245

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
              +   +EEL+ S+RS NCL+  NI  +GD++  T+ADM+++ NFG+KSL E++  L  
Sbjct: 246 ETQMGINIEELDFSLRSFNCLKRANINTVGDIVSHTKADMMKIKNFGKKSLDEVEEKLQE 305

Query: 313 MGLFLGMNLPD 323
           MGL     + D
Sbjct: 306 MGLAFKEEIKD 316


>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 =  318 bits (816), Expect = 5e-85,   Method: Composition-based stats.
 Identities = 124/324 (38%), Positives = 193/324 (59%), Gaps = 6/324 (1%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
             L+     E +V+ +  +   +   +PL  GF  T+GNA+RRVL+SSL G AIT ++I 
Sbjct: 1   MSLLTFQIPEKVVMDKTTDFHGMFEFKPLEPGFGVTVGNAIRRVLLSSLEGYAITCIRIP 60

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS-HKRVTIFKRGPGVVTAGDI-QTVND 124
           GV HE SSIKGV +D+ +IILN+K +  K   ++   ++ +       +TAGDI +  + 
Sbjct: 61  GVQHEFSSIKGVMQDVAEIILNLKKVRFKKISENVDSKIVVEVSNQETLTAGDIGKFTSS 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            E+LNPD VICNLD    + +EL + KG GYV ++  +  +  IG I ID++++PIK V 
Sbjct: 121 FEILNPDLVICNLDESVDLEVELYIEKGRGYVSSEDQKLPDAAIGHIPIDSIFTPIKNVR 180

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF----EEPKKE 240
           Y VE+ R  Q  DY+KL + I TDGSI  E+++  A+ IL     +F +     E  KKE
Sbjct: 181 YAVENTRVEQRTDYEKLLLDIQTDGSIHPEEALKGAANILIQHFMLFSDQNIILETAKKE 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
             ++++   L     L   + +L+LSVR+ NCL+  +I  +GDL++   ADM++  NFG+
Sbjct: 241 EVQEVDEHFLHMRKLLKTPISDLDLSVRAYNCLKSADIRTLGDLVKLDIADMMKFRNFGK 300

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDW 324
           KSL E++ ++   GL  GM++  +
Sbjct: 301 KSLTELEQLVAEKGLSFGMDVSKY 324


>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 =  318 bits (816), Expect = 6e-85,   Method: Composition-based stats.
 Identities = 107/311 (34%), Positives = 170/311 (54%), Gaps = 11/311 (3%)

Query: 16  EYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           +   +           +    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|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 =  318 bits (816), Expect = 6e-85,   Method: Composition-based stats.
 Identities = 98/311 (31%), Positives = 167/311 (53%), Gaps = 11/311 (3%)

Query: 16  EYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           +   +  + +      +  + EPL RG   T+GNALRRVL+++L+GAA+TA++I GV HE
Sbjct: 7   QIECIESKTQKNQSQYSKFVLEPLARGQGTTVGNALRRVLLANLQGAAVTAIRIAGVNHE 66

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            ++I GV ED+ +I+LN+K I LK   D  +   +     G VTA + +  +++EV++P 
Sbjct: 67  FATIPGVREDVLEIMLNMKEIVLKSYSDQAQIGRLVATSAGTVTAANFELPSEVEVVDPT 126

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             +  L   + + ME  +  G GY   +  + +   +  + IDA++ P+ KV+Y VE  R
Sbjct: 127 QYVATLTEGSKLEMEFRIETGTGYKGVERGKDDGTSLDFLEIDAVFMPVTKVNYIVEDIR 186

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  D+L + I T+GS   +++++ A+ I+ D      +      +++         
Sbjct: 187 GEHGEAQDRLILEIWTNGSFNPKEALSEAAEIVVDLFSPLKDLN----QLETTTPDYQDD 242

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            NP     +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L 
Sbjct: 243 ENPQSQIPIEELQLSVRAYNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEEVIEAL- 301

Query: 312 TMGLFLGMNLP 322
                LG+ LP
Sbjct: 302 --QKRLGITLP 310


>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 =  318 bits (815), Expect = 7e-85,   Method: Composition-based stats.
 Identities = 116/316 (36%), Positives = 184/316 (58%), Gaps = 10/316 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E ++P     +   +  +     + EPL RGF +TLGN +RRVL+SSL GA  TA+QI+G
Sbjct: 3   EFMRPT----VTTEEVSDTDARFVVEPLERGFGYTLGNCMRRVLLSSLDGARATAIQIEG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKM--SGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           V HE ++ +GV ED+TDI+LN+KG+         +    TI   GP  VT  DIQ   + 
Sbjct: 59  VQHEFTTAEGVIEDVTDIVLNVKGLVFAALTEDYTEATATISVEGPCTVTGADIQVPTEF 118

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
            ++NP+HVI  +     + M + +  G GYV A+ ++   DPIG+I +D+L+SP+++ + 
Sbjct: 119 TLINPEHVIATVADGGTLNMSIRIGVGRGYVSAERNKRTEDPIGIIPVDSLFSPVRRCTL 178

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEV 241
            V   R GQ  D+D+L + ++TDGSI   ++V  A+ I+   +G F+      +E + ++
Sbjct: 179 AVNDTRVGQRTDFDQLLLEVETDGSIAPNEAVCRAANIINQYMGAFLTLADITDEDEGDI 238

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
                 +    N  L K++E+L+LSVRS NCL+   I  +  L++ +E D+L + NFG K
Sbjct: 239 PSIFATEGQESNAELDKQIEDLDLSVRSYNCLKRAGIHSVRQLVEFSENDLLNIRNFGAK 298

Query: 302 SLVEIKGVLGTMGLFL 317
           S+ E+K  L +M L L
Sbjct: 299 SIEEVKDKLISMDLNL 314


>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 =  318 bits (815), Expect = 8e-85,   Method: Composition-based stats.
 Identities = 98/311 (31%), Positives = 168/311 (54%), Gaps = 10/311 (3%)

Query: 14  NIEYIV--LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
            IE +     +   + +  + 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 TMGLFLGMNLP 322
                LG+ LP
Sbjct: 300 RR---LGITLP 307


>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 =  318 bits (815), Expect = 8e-85,   Method: Composition-based stats.
 Identities = 121/301 (40%), Positives = 182/301 (60%), Gaps = 5/301 (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 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL-PFNPAL 256
           YD+L M + T+GSI  + +++L S+IL D L   +  ++   E +  I        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 L 317
            
Sbjct: 315 F 315


>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 =  318 bits (815), Expect = 8e-85,   Method: Composition-based stats.
 Identities = 130/323 (40%), Positives = 195/323 (60%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++    +        PL  G+  T+GNALRRVL+SSL G AIT+V+I+GV
Sbjct: 6   FQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSSLEGFAITSVRIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQ-TVNDI 125
            HE S+I GV ED+T++ILN+K +N K   D   ++ VTI   G   +TAGD Q  ++  
Sbjct: 63  DHEFSTISGVVEDVTEMILNLKQVNFKRQIDEVDNETVTISISGQEQITAGDFQKFISGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLN D VICNLD    + MELT+ KG GYVPA+ ++  + PIG I  D++Y+PIK V Y
Sbjct: 123 QVLNTDLVICNLDPKVNINMELTIEKGRGYVPAEENKKASAPIGTIFTDSIYTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL   I TDGSI  +D++  A++IL     +F    I  E  +   
Sbjct: 183 SIENFRVEQKTDYEKLVFEIQTDGSINPKDALTEAAKILIHHFMLFSDERITLEADEIAQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+K
Sbjct: 243 TETYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++ ++   GL  GM+L  +
Sbjct: 303 SLTELEELVNVKGLNFGMDLSKY 325


>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 =  318 bits (815), Expect = 8e-85,   Method: Composition-based stats.
 Identities = 126/321 (39%), Positives = 196/321 (61%), Gaps = 6/321 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           +  P  IE        E+    +A+PL RG+  TLGNA+RRVL++SL G AIT ++IDGV
Sbjct: 5   MQMPERIEVDEA-THSESIGQFVAQPLERGYGVTLGNAMRRVLLASLPGTAITGIKIDGV 63

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEV 127
            HE S+I GV ED+ +I+LN+K +  K +     + ++   GP    AGDI     + EV
Sbjct: 64  FHEFSTIDGVREDVPEIVLNLKKVRFKSTTKRSCKTSLSIEGPADFKAGDIVAQEGEFEV 123

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D  I  L+ DA + +++ + +G GYVPA+ +R E  PIG I ID++++PIK V ++V
Sbjct: 124 LNKDMHIATLNGDAKLNIDIYIGRGRGYVPAEENRGEGMPIGFIAIDSIFTPIKNVKFSV 183

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK----E 243
           E+ R GQ  DY+K+ + ++TDGSI+ +DS++LA +++ + + +F NF   ++E      +
Sbjct: 184 ENTRVGQRTDYEKMILDVETDGSISPDDSISLAGKVINEHVSLFANFSPTEEEFAEEEYK 243

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             + +       L  ++E+L+LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL
Sbjct: 244 QQDDEFENMRKLLQTRIEDLDLSVRSHNCLRLAEIDTLGDLVSRKEDELLTYKNFGKKSL 303

Query: 304 VEIKGVLGTMGLFLGMNLPDW 324
            E+K  L    L  GM++  +
Sbjct: 304 TELKEQLDKCELKFGMDITKY 324


>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 =  318 bits (815), Expect = 9e-85,   Method: Composition-based stats.
 Identities = 110/310 (35%), Positives = 193/310 (62%), Gaps = 4/310 (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 GVLGTMGLFL 317
             L  +G  L
Sbjct: 299 HKLHELGFTL 308


>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 =  318 bits (814), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 103/315 (32%), Positives = 166/315 (52%), Gaps = 12/315 (3%)

Query: 13  NNIEYIVLGQEE----ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
              +   +  +        +  + EPL RG   TLGN+LRR+L+S+L G A+TA++I GV
Sbjct: 2   TQFQIECVESKTHKNQSQYSKFVFEPLERGQGTTLGNSLRRILLSNLEGTAVTALRIGGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE ++I GV ED  +IILN+K I LK      +   +   GPG VTA      +++EV+
Sbjct: 62  NHEFATIPGVREDALEIILNMKEIILKSYTHQPQIGRLTATGPGQVTAAQFDLPSEVEVV 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +P   I  L   A + ME  + KG  Y   + +R E   +  + IDA++ P+ KV+Y+V+
Sbjct: 122 DPTQYIATLADGAKLEMEFRIEKGKSYRAVQRNRDEATALDFLQIDAVFMPVTKVNYSVD 181

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S         D+L++ I T+GSI  E++++ A+ I  +              ++   +  
Sbjct: 182 SIHSEGDAVRDRLTLEIWTNGSIKPEEALSQAAAIAVELFNPL-----KDLTLEAIQDEL 236

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
               +P     +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+  
Sbjct: 237 QEDEDPTSQIPIEELQLSVRAYNCLKRAQINSVADLLDYSQEDLLEIKNFGQKSAEEVID 296

Query: 309 VLGTMGLFLGMNLPD 323
            L T    LG+ LP+
Sbjct: 297 ALKTR---LGITLPE 308


>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 =  318 bits (814), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 124/321 (38%), Positives = 193/321 (60%), Gaps = 6/321 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           +  P  IE        +     IA+PL RG+  TLGN +RRVL++SL G AIT ++IDGV
Sbjct: 5   MQMPAKIEVDE-SSHTDCFGRFIAQPLERGYGVTLGNVMRRVLLASLPGTAITGIKIDGV 63

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEV 127
            HE ++I GV ED+ +I+LN+K +  K +   + + ++   GP   TAGDI     + EV
Sbjct: 64  FHEFAAIDGVREDVPEIVLNLKKVRFKSTCKRNCKTSLTLVGPMDFTAGDIIAQEGEFEV 123

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D  +  ++  A V+++L + +G GY+PA+ +R E  PIG I +DA+Y+PI+ V +TV
Sbjct: 124 LNKDMHVATINAGATVKIDLYIGRGRGYMPAEENRPEGMPIGYIAVDAIYTPIRNVKFTV 183

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE----EPKKEVKE 243
           E+ R GQ  DY+K+ + ++TDGS++ +DS++LA +I+ D +  F NF     E  +E  +
Sbjct: 184 ENTRVGQRTDYEKMILDVETDGSVSPDDSISLAGKIITDHVTFFANFSPTEEEFTEEEFK 243

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             + +          K+E+L+LSVRS NCLR   I  +G+L+   E ++L   NFG+KSL
Sbjct: 244 QQDDEFETMRRLFHTKIEDLDLSVRSHNCLRLAEIDTIGELVSHKEDELLNYKNFGKKSL 303

Query: 304 VEIKGVLGTMGLFLGMNLPDW 324
            E+K  L    L  GM++  +
Sbjct: 304 TELKEQLEKFDLKFGMDITKY 324


>gi|315186306|gb|EFU20067.1| DNA-directed RNA polymerase subunit alpha [Spirochaeta thermophila
           DSM 6578]
          Length = 363

 Score =  317 bits (813), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 124/344 (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   MARKNLLKGFVLPTSITVEHLDTNT-HYGKFAAYPFERGYGVTIGNTLRRILLSSIQGYA 59

Query: 60  ITAVQI-----DGVLH----EISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKR 109
           I+AV+I      G  H    E   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|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 =  317 bits (813), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 127/315 (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  KGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDI-QTVNDIEVLNPDHV 133
           +G+ ED+T+IILN+K +  K   D  + 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 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKS 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|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 =  317 bits (813), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 123/323 (38%), Positives = 195/323 (60%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +  +               PL  G+  T+GNALRR+L+SSL G AIT+++IDGV
Sbjct: 6   FQKPDKVLMLEADN---FFGKFEFRPLEPGYGITIGNALRRILLSSLEGFAITSIKIDGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE  +I GV ED+T+IILN+K +  K   D   +++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 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL + I TDGSI  ++++  A++IL     +F    I  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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  GM++  +
Sbjct: 303 SLTELDELLESLNLSFGMDITKY 325


>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 =  317 bits (813), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 127/323 (39%), Positives = 192/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++    +        PL  G+  T+GNALRRVL+SSL G AIT+V+I+GV
Sbjct: 6   FQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSSLEGYAITSVRIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQ-TVNDI 125
            HE S+I GV ED+T+IILN+K +  K   +   ++ V+I   G   +TAGD Q  ++  
Sbjct: 63  EHEFSTISGVVEDVTEIILNLKQVRFKRQIEDIDNESVSISLSGKDKITAGDFQKFISGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNPD VICNLD    + MEL++ KG GYVPA+ ++  N PIG I  D++Y+P+K V Y
Sbjct: 123 QVLNPDLVICNLDSKTTLNMELSIEKGRGYVPAEENKKSNAPIGTIYTDSIYTPVKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           T+E+ R  Q  DY+KL   I TDGSI  +D++  A++ L     +F    I  E  +   
Sbjct: 183 TIENFRVEQKTDYEKLVFEIITDGSIHPKDALTEAAKTLIHHFMLFSDERITLEADEIAQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+K
Sbjct: 243 TESYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  ++    L  GM+L  +
Sbjct: 303 SLTELDELVANKNLTFGMDLAKY 325


>gi|126643071|ref|YP_001086055.1| DNA-directed RNA polymerase subunit alpha [Acinetobacter baumannii
           ATCC 17978]
          Length = 310

 Score =  317 bits (813), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 137/301 (45%), Positives = 212/301 (70%), 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 KGHGYVPAKH--HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 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 GTVDPEEAIRKAATILQQQIAIFVDLQKDQTPVAQEP---REEVDPILLRPVDDLELTVR 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|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 =  317 bits (812), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 124/322 (38%), Positives = 195/322 (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  LHEISSIKGVHEDLTDIILNIKGINLKMSGDS-HKRVTIFKRGPGVVTAGDI-QTVNDIE 126
           LHE SSI+GV ED+T+IILN+K +  K   D    ++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 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEVK 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|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 =  317 bits (812), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 139/324 (42%), Positives = 206/324 (63%), Gaps = 5/324 (1%)

Query: 1   MIQKNW-QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           M  KN  +   +P  IE+        N    +AEP  RG   T+GN+LRR LMSS+ GAA
Sbjct: 1   MSPKNLLKGFKRPKKIEF-TTDVNTPNYGKFVAEPFERGIGTTIGNSLRRTLMSSIEGAA 59

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS---HKRVTIFKRGPGVVTA 116
           I+A++I+GV HE S I+GV ED+T IILN+K + +K   +     K + +  +G G   A
Sbjct: 60  ISAIRIEGVSHEFSYIEGVAEDVTRIILNLKQVRIKYEPEDKEASKVIHLELKGAGYFRA 119

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
            D+   + IE++NPD  I  L+ DA + M+L + +G GYVPA+  + + + +G I ID++
Sbjct: 120 ADLAVDSSIEIMNPDLHIATLNEDANLIMDLEIQRGRGYVPAEDKKKDIEVLGTIPIDSI 179

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           +SPI+KV + V   R  Q  DY+KL+M + TDGS++ ED+VA A++IL+D L +FINFEE
Sbjct: 180 FSPIQKVLFEVSETRVAQRSDYEKLTMEVWTDGSVSPEDAVAQAAKILKDHLTVFINFEE 239

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
             +E +E+++        AL K VEELELSVRSTN LR   I ++G+L++R+E +M +  
Sbjct: 240 EIEEEEEELDEADEKLKAALSKHVEELELSVRSTNVLRSLEIDFIGELVKRSEDEMTKSK 299

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMN 320
           +F  +SL+E+K  L +MGL  GM 
Sbjct: 300 HFSEQSLLELKAKLSSMGLSFGMR 323


>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 =  317 bits (812), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 124/323 (38%), Positives = 195/323 (60%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +  +               PL  G+  T+GNALRR+L+SSL G AIT+++IDGV
Sbjct: 6   FQKPDKVLMLEADN---FFGKFEFRPLEPGYGITIGNALRRILLSSLEGFAITSIKIDGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE  +I GV ED+T+IILN+K +  K   D   +++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 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL + I TDGSI  ++++  A++IL     +F    I  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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  GM++  +
Sbjct: 303 SLTELDELLESLNLSFGMDITKY 325


>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 =  317 bits (812), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 125/323 (38%), Positives = 203/323 (62%), 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  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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|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 =  317 bits (812), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 132/318 (41%), Positives = 203/318 (63%), Gaps = 4/318 (1%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
            +   +P  IE+        N    +AEP  RGFA T+GN+LRR LMSS+ GAAI+A++I
Sbjct: 7   LKGFKRPKKIEFNT-EASTPNYGKFVAEPFERGFATTIGNSLRRTLMSSIEGAAISAIRI 65

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSG---DSHKRVTIFKRGPGVVTAGDIQTV 122
           +GV HE S I+GV ED+T IILN+K + +K      D  K + +  +G G   AGD+   
Sbjct: 66  EGVNHEFSFIEGVAEDVTRIILNLKQVRIKYEPEEKDQSKIIHLELKGAGYFRAGDLAVD 125

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IE++NPD  I  L+ DA + M+L + +G GYVPA+  + + + +G I +D+++SP++K
Sbjct: 126 SSIEIMNPDLHIATLNEDANLVMDLEIQRGRGYVPAEEKKKDIEVLGTIPVDSIFSPVQK 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V + V   R  Q  DY+KL++ + TDGS++ +D+VA A++IL++ L +FINFEE  +E  
Sbjct: 186 VVFEVSETRVAQRSDYEKLTLEVWTDGSVSPDDAVAQAAKILKEHLTVFINFEEELEEED 245

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           ++++        +L K VEELELSVRS N LR   I ++GDL++R+E +M +  ++  + 
Sbjct: 246 DELDEADEKLKASLSKHVEELELSVRSLNVLRSLEIDFIGDLVKRSEEEMSKSKHYSDQC 305

Query: 303 LVEIKGVLGTMGLFLGMN 320
           L E+KG L T+GL  GM 
Sbjct: 306 LQELKGKLSTLGLSFGMR 323


>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 =  317 bits (812), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 107/304 (35%), Positives = 169/304 (55%), Gaps = 8/304 (2%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +    +  + EPL RG   T+GNALRRVL+S+L+G A+TAV+I GV HE ++I GV
Sbjct: 11  RVEADYSQYSQFVLEPLERGQGTTVGNALRRVLLSNLKGTAVTAVRIAGVNHEFATIPGV 70

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED  DI+L +K + L+      +   +F +GP  VTA + +   D+EV+N DH I  L 
Sbjct: 71  REDALDILLRMKELVLRSYSPDPQIGRLFIQGPATVTAINFEVSPDVEVINLDHYIATLS 130

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            DA + ME  + +G GY   +  + E+  +  + IDA++ P++KV+YTVE AR G +++ 
Sbjct: 131 ADATLEMEFKIEQGKGYRAIERGKDESASLDFLQIDAIFMPVRKVNYTVEDARSGGLVEK 190

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           D+L + I T+GS+T ++++   + IL D               +      S   +     
Sbjct: 191 DRLVLEIWTNGSLTPQEALNQGASILVDLFNPL-----KDVPFRSSEPSHSTEEDETNQI 245

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +E L LSVR+ NCL+   I  + DL++ ++ D+L + NFG KS  E+   L      LG
Sbjct: 246 PIESLNLSVRAYNCLKRAQINTVADLLEYSQEDLLEIKNFGAKSAEEVIEALH---KNLG 302

Query: 319 MNLP 322
           + LP
Sbjct: 303 ITLP 306


>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 =  316 bits (811), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 129/315 (40%), Positives = 184/315 (58%), Gaps = 6/315 (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  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKRGPGVVTAGDIQTVNDIE 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 IVNPDVHIATVDKEIELRMELKIEKGRGYVMVEEMEPP-TEIGWIPIDTAFSPIKKCTFY 182

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE  R G+  +YDKL + + TDGSIT E+++  A+ IL +   + +N    K EV +   
Sbjct: 183 VEPTRVGEKTNYDKLILEVTTDGSITPEEALTKATNILIEHFQLLLNPTVRKVEVIKKAE 242

Query: 247 VKSLPFNPALLK---KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +S+       K    +EELE+S R+TN L+   I  +GDL++ TE D+    + GRK+L
Sbjct: 243 PESIAEKIEADKLSLAIEELEISSRATNTLKKLGIQTIGDLVKMTEEDLKEAKSIGRKAL 302

Query: 304 VEIKGVLGTMGLFLG 318
            EIK  L  +GL L 
Sbjct: 303 KEIKEALAELGLELA 317


>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 =  316 bits (811), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 116/293 (39%), Positives = 182/293 (62%), Gaps = 4/293 (1%)

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 DMELTVERHRGYLPAENRDP--VPIGEIPVDAIFTPVHKVNYVVEHTRIGGMTDFDRLLL 193

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL-PFNPALLKKVEE 262
            I TDG++   D+++ A+++L     +  +F     E ++  +   L   +      +E+
Sbjct: 194 EIWTDGTVKPGDALSYAAQVLVQYSSIIADFNRFDDEQEQVGDANGLVIPSEIYDMPIED 253

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           L+LS R+ NCL+  +I  +G +++  E  +L + N G+KS+ EI+  L    L
Sbjct: 254 LDLSTRTYNCLKRADITKVGQVLEMDEKQLLAVRNLGQKSMDEIREKLIERNL 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 =  316 bits (810), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 134/308 (43%), Positives = 200/308 (64%), Gaps = 11/308 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQINT---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++  + +   KE
Sbjct: 178 AYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEKE 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLG 311
            EIK VL 
Sbjct: 295 TEIKDVLA 302


>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 =  316 bits (810), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 128/318 (40%), Positives = 184/318 (57%), Gaps = 7/318 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E + PN I +    Q+E+N+ + + EPL RGF  TLGNALRRVL+SS+ G A+TAV+I
Sbjct: 2   LNEFVFPNKIYW---EQKEDNKGVFVVEPLERGFGTTLGNALRRVLLSSISGTAVTAVKI 58

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
            GV HE SS++GV ED+ +II NIKG+   +     + + + K+G G V AGDI    ++
Sbjct: 59  YGVYHEFSSLEGVAEDVVEIIANIKGVRFTLKDSDVEVLYLKKKGEGEVKAGDISLPPNV 118

Query: 126 EVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           EV NPD VI  +         E+ + +G GYV A+   T     G I +DA +SP+K VS
Sbjct: 119 EVANPDKVIATITDPEVEFNAEIRIERGKGYVLAEEMET-IGETGWILLDADFSPVKLVS 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y +E  R G+  DY+KL++ + TDG+ + E  V  A  ILQ  L +  +       ++E 
Sbjct: 178 YRIEQTRVGEKTDYEKLTVEVLTDGTKSPEAVVKEAVDILQRHLSLLEHISYEVPTLEEP 237

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           I       +  L   +EEL++S R+ N L+   I  +GDL+Q TE ++    N GRK+L 
Sbjct: 238 I--PVDELSEKLTLSIEELDISQRALNSLKRMGITTIGDLVQMTEEELKSTKNIGRKALA 295

Query: 305 EIKGVLGTMGLFLGMNLP 322
           EIK  L  MGL LG+N+ 
Sbjct: 296 EIKEALKQMGLQLGINIE 313


>gi|295111400|emb|CBL28150.1| DNA-directed RNA polymerase, alpha subunit, bacterial and
           chloroplast-type [Synergistetes bacterium SGP1]
          Length = 333

 Score =  316 bits (809), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 117/332 (35%), Positives = 189/332 (56%), Gaps = 15/332 (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 NFGRKSLVEIKGVLGTMGLFLGMNLPDWPPES 328
           N G+ SL EI+  L + GL L         E 
Sbjct: 302 NLGKISLTEIEEKLESAGLKLREKKEKAGKED 333


>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 =  316 bits (809), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 105/304 (34%), Positives = 171/304 (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 DRLILDIWTNGNLTPQESLSQAATILVDLFNPL-----KDATFNVVEDIELEEEDETNQI 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|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 =  316 bits (809), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 131/318 (41%), Positives = 202/318 (63%), Gaps = 4/318 (1%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
            +   +P  IE+        N    +AEP  RGFA T+GN+LRR LMSS+ GAAI+A++I
Sbjct: 7   LKGFKRPKKIEFNT-EANTPNYGKFVAEPFERGFATTIGNSLRRTLMSSIEGAAISAIRI 65

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSG---DSHKRVTIFKRGPGVVTAGDIQTV 122
           +GV HE S I+GV ED+T IILN+K + +K      D  K + +  +G G   AGD+   
Sbjct: 66  EGVNHEFSFIEGVAEDVTRIILNLKQVRIKYEPEEKDQSKIIHLELKGAGYFRAGDLAVD 125

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IE++NPD  I  L+ DA + M+L + +G GYVPA+  + + + +G I +D+++SP++K
Sbjct: 126 SSIEIMNPDLHIATLNEDANLVMDLEIQRGRGYVPAEEKKKDIEVLGTIPVDSIFSPVQK 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V + V   R  Q  DY+KL++ + TDGS++ +D+VA A++IL++ L +FINFEE  +E  
Sbjct: 186 VVFEVSETRVAQRSDYEKLTLEVWTDGSVSPDDAVAQAAKILKEHLTVFINFEEELEEED 245

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           ++++        +L K VEELELSVRS N LR   I ++GDL++R+E +M +  ++  + 
Sbjct: 246 DELDEADEKLKASLSKHVEELELSVRSLNVLRSLEIDFIGDLVKRSEEEMSKSKHYSDQC 305

Query: 303 LVEIKGVLGTMGLFLGMN 320
           L E+K  L T+GL  GM 
Sbjct: 306 LQELKVKLSTLGLSFGMR 323


>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 =  316 bits (809), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 121/324 (37%), Positives = 201/324 (62%), Gaps = 10/324 (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  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDI-QTVND 124
           V HE +++KGV ED+T+I+LN+K +  K   +    + 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 KSLVEIKGVLGTMGLFLGMNLPDW 324
           KSL E++ ++ + GL  GMN+  +
Sbjct: 302 KSLTELEDLVDSKGLNFGMNVAKY 325


>gi|5163231|gb|AAD40610.1|AF115283_29 RNA polymerase alpha-subunit [Leptospira interrogans]
          Length = 325

 Score =  316 bits (809), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 130/318 (40%), Positives = 201/318 (63%), Gaps = 4/318 (1%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
            +   +P  IE+        N    +AEP  RGFA T+GN+LRR LMSS+ GAAI+A++I
Sbjct: 7   LKGFKRPKKIEFNT-EANTPNYGKFVAEPFERGFATTIGNSLRRTLMSSIEGAAISAIRI 65

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSG---DSHKRVTIFKRGPGVVTAGDIQTV 122
           +GV HE S I+GV ED+T IILN+K + +K      D  K + +  +G G   AGD+   
Sbjct: 66  EGVNHEFSFIEGVAEDVTRIILNLKQVRIKYEPEEKDQSKIIHLELKGAGYFRAGDLAVD 125

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IE++NPD  I  L+ DA + M+L + +G GYVPA+  + + + +G I +D+++SP++K
Sbjct: 126 SSIEIMNPDLHIATLNEDANLVMDLEIQRGRGYVPAEEKKKDIEVLGTIPVDSIFSPVQK 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V + V   R  Q  DY+KL++ + TDGS++ +D+VA A++IL++ L +FINFEE  +E  
Sbjct: 186 VVFEVSETRVAQRSDYEKLTLEVWTDGSVSPDDAVAQAAKILKEHLTVFINFEEELEEED 245

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           ++++        +L K VEELELS RS N LR   I ++GDL++R+E +M +  ++  + 
Sbjct: 246 DELDEADEKLKASLSKHVEELELSARSLNVLRSLEIDFIGDLVKRSEEEMSKSKHYSDQC 305

Query: 303 LVEIKGVLGTMGLFLGMN 320
           L E+K  L T+GL  GM 
Sbjct: 306 LQELKVKLSTLGLSFGMR 323


>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 =  316 bits (809), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 118/317 (37%), Positives = 183/317 (57%), Gaps = 10/317 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E ++P     +   +  +     I EPL RG+ +TLGN +RRVL+SSL GA  TA+QI+
Sbjct: 2   TEFMRPT----VTTEEVNDTVARFIVEPLERGYGYTLGNCMRRVLLSSLDGAKATAIQIE 57

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT--IFKRGPGVVTAGDIQTVND 124
           GV HE ++ +GV ED+TDI+LN+KG+      D  +  T  +   GP  VT  D+    +
Sbjct: 58  GVQHEFTTAEGVIEDITDIVLNVKGLVFSALNDDIEEATAHVSAEGPCTVTGADLDIPTE 117

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
             ++NP+HVI  +     + M + +  G GYV A+ ++   DPIG+I +D+L+SP+++ +
Sbjct: 118 FTLVNPEHVIATVADGGQLDMTVRIGVGRGYVSAERNKRTEDPIGVIHVDSLFSPVRRCT 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ----LGMFINFEEPKKE 240
             V   R GQ  DYDKL + ++TDGSIT  ++V  AS I+       L +    +E + E
Sbjct: 178 LNVTDTRVGQRTDYDKLVLEVETDGSITPTEAVCRASNIINQYMGAFLSLSDVVDEEEGE 237

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           +      +    N  L K++E+L+LSVRS NCL+   I  +  L++ +E D+L + NFG 
Sbjct: 238 IPSIFAPEGQESNAELDKQIEDLDLSVRSYNCLKRAGIHSVRQLVEFSENDLLNIRNFGA 297

Query: 301 KSLVEIKGVLGTMGLFL 317
           KS+ E+K  L +M L L
Sbjct: 298 KSIEEVKDKLISMDLNL 314


>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 =  316 bits (809), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 121/323 (37%), Positives = 191/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++    +        PL  G+  T+GNALRRVL+S+L G AIT+++I+GV
Sbjct: 6   FQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSALEGYAITSIRIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQT-VNDI 125
            HE S+I GV ED+T+IIL++K +  K   +   ++ VTI   G   +TAGD Q  ++  
Sbjct: 63  DHEFSTIPGVVEDVTEIILSLKQVRFKRQIEDIDNESVTIAISGKNQITAGDFQKYISGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNP+ VICNLD      ME+T+ KG GYVPA+ ++ +N  IG I  D++++P+K V Y
Sbjct: 123 QVLNPELVICNLDSKVNFNMEMTIEKGRGYVPAEENKKQNAAIGTIFTDSIFTPVKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            +E+ R  Q  DY+KL   I TDGSI  +D++  A+++L     +F    I  E  +   
Sbjct: 183 AIENFRVEQKTDYEKLVFEIKTDGSINPKDALTEAAKVLIHHFMLFSDERITLEADEIAQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+K
Sbjct: 243 TESYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  ++    L  GM+L  +
Sbjct: 303 SLTELDELVAIKNLTFGMDLAKY 325


>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 =  315 bits (808), Expect = 5e-84,   Method: Composition-based stats.
 Identities = 123/323 (38%), Positives = 191/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++    +        PL  G+  T+GNALRRVL+S+L G AIT+V+I+GV
Sbjct: 6   FQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSALEGYAITSVRIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQ-TVNDI 125
            HE S+I GV ED+T+IILN+K +  K   +   ++ VTI   G   +TAGD Q  ++  
Sbjct: 63  DHEFSTISGVVEDVTEIILNLKQVRFKRQIEDIDNESVTISVSGKDQLTAGDFQKFISGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNPD VICNLD    +  +LT+ KG GYVPA+ ++ +N  IG I  D++++P+K V Y
Sbjct: 123 QVLNPDLVICNLDSKIKLNFDLTIEKGRGYVPAEENKKQNAAIGTIFTDSIFTPVKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            +E+ R  Q  DY+KL   I TDGSI  +D++  A+++L     +F    I  E  +   
Sbjct: 183 AIENFRVEQKTDYEKLVFEIKTDGSINPKDALTEAAKVLIHHFMLFSDERITLEADEIAQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+K
Sbjct: 243 TESYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  ++    L  GM+L  +
Sbjct: 303 SLTELDELVAVKNLTFGMDLAKY 325


>gi|179184696|gb|ACB78157.1| RNA polymerase alpha subunit [Vibrio inusitatus]
          Length = 294

 Score =  315 bits (808), Expect = 6e-84,   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-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV-DAVV 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 LVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVQEPIEEK---PEFDPILLRPV 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|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 =  315 bits (807), Expect = 6e-84,   Method: Composition-based stats.
 Identities = 106/304 (34%), Positives = 164/304 (53%), Gaps = 9/304 (2%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
              ++       I EPL RG   T+GNALRRVL+S+L G AIT+V+I GV HE ++IKGV
Sbjct: 19  KTDKDRSQYGKFIIEPLARGQGTTVGNALRRVLLSNLEGTAITSVRIAGVNHEFATIKGV 78

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+ +I+LN+K + LK   +  +   +   GP  VTA      +++EV++    I  L 
Sbjct: 79  REDVLEILLNMKEVVLKSYSEQPQIGRLRVEGPATVTADRFDVPSEVEVIDRSQYIATLS 138

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
             +++ ME  + KG GY      R +   +  + IDA++ P++KV+YT+E A  G  L+ 
Sbjct: 139 PGSILEMEFRIEKGTGYKAVDRTRDDVATLDFLQIDAIFMPVRKVNYTIEDAHIGSSLEQ 198

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           D+L M I T+GS T +D+++ A+ IL        +                   +P    
Sbjct: 199 DRLIMDIWTNGSYTPQDALSNAAGILMSLFEPLKDITNMADIPS------GETTDPTSQI 252

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L      LG
Sbjct: 253 PIEELQLSVRAYNCLKRAQINSVADLLDYSQEDLLEIKNFGQKSAEEVIEAL---QKRLG 309

Query: 319 MNLP 322
           + LP
Sbjct: 310 ITLP 313


>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 =  315 bits (807), Expect = 6e-84,   Method: Composition-based stats.
 Identities = 124/323 (38%), Positives = 196/323 (60%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            IKP+ +  I++  + +        PL  G+  T+GNALRRVL+SSL G AIT+++I+GV
Sbjct: 6   FIKPDKV--ILIESDTQF-GQFEFRPLEPGYGITVGNALRRVLLSSLEGYAITSIKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE S+I GV ED+T+IILN+K +  K   D    + VT    G   +TAGD+ + ++  
Sbjct: 63  EHEFSTIPGVVEDVTEIILNLKKVRFKKQIDESDAENVTATISGQDQLTAGDLGKFISGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNP+ VI NLD    + +  T+ KG GYVPA+ ++  + PIG I ID++Y+PIK V Y
Sbjct: 123 QVLNPELVIANLDSKVNLTISFTIEKGRGYVPAEENKKASAPIGTIAIDSIYTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            +E+ R  Q  DY+KL   I TDGSI+ +D++  A++IL     +F    I  E  +   
Sbjct: 183 AIENYRVEQKTDYEKLVFEITTDGSISPQDALTEAAKILIHHFMLFSDERITLEAEEVAS 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E  + ++L     L  K+ +L+LSVR+ NCL+   +  +G+L+   ++D+++  NFG+K
Sbjct: 243 GEAYDEEALHMRQLLKTKLVDLDLSVRALNCLKAAEVETLGELVSFAKSDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++ ++ + GL  GM+   +
Sbjct: 303 SLSELEELVDSKGLSFGMDTSKY 325


>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 =  315 bits (807), Expect = 7e-84,   Method: Composition-based stats.
 Identities = 123/323 (38%), Positives = 190/323 (58%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++    +        PL  G+  T+GNALRRVL+SSL G AIT+++I+GV
Sbjct: 6   FQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSSLEGFAITSIRIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQT-VNDI 125
            HE S+I+GV ED+T+IILN K I  +   D    + V +   G    TAGD+Q  ++  
Sbjct: 63  DHEFSTIEGVVEDVTEIILNFKQIRFRRQIDEVDSEVVNVSFSGKDTFTAGDMQKYISGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNP+ VICN +    + +ELT+ KG GYVPA+ ++  N  IG I ID++++PIK V Y
Sbjct: 123 QVLNPEMVICNTESSVSLNLELTIEKGRGYVPAEENKNPNAAIGTIAIDSIFTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL   I TDGSI  + ++  A++ L     +F    I  E  +   
Sbjct: 183 SIENYRVEQKTDYEKLVFEISTDGSIHPKQALTEAAKTLIHHFMLFSDERITLEADEIAQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E  + +SL     L  K+ ++ELSVR+ NCL+   +  +GDL+   + D+++  NFG+K
Sbjct: 243 TETYDEESLHMRQLLKTKLVDMELSVRALNCLKAAEVETLGDLVSYNKNDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++ ++   GL  GM+L  +
Sbjct: 303 SLTELEELVNVKGLNFGMDLSKY 325


>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 =  315 bits (807), Expect = 8e-84,   Method: Composition-based stats.
 Identities = 106/304 (34%), Positives = 164/304 (53%), Gaps = 9/304 (2%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
              ++       I EPL RG   T+GNALRRVL+S+L G AIT+V+I GV HE ++IKGV
Sbjct: 12  KTDKDRSQYGKFIIEPLARGQGTTVGNALRRVLLSNLEGTAITSVRIAGVNHEFATIKGV 71

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+ +I+LN+K + LK   +  +   +   GP  VTA      +++EV++    I  L 
Sbjct: 72  REDVLEILLNMKEVVLKSYSEQPQIGRLRVEGPATVTADRFDVPSEVEVIDRSQYIATLS 131

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
             +++ ME  + KG GY      R +   +  + IDA++ P++KV+YT+E A  G  L+ 
Sbjct: 132 PGSILEMEFRIEKGTGYKAVDRTRDDVATLDFLQIDAIFMPVRKVNYTIEDAHIGSSLEQ 191

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           D+L M I T+GS T +D+++ A+ IL        +                   +P    
Sbjct: 192 DRLIMDIWTNGSYTPQDALSNAAGILMSLFEPLKDITNMADIPS------GETTDPTSQI 245

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L      LG
Sbjct: 246 PIEELQLSVRAYNCLKRAQINSVADLLDYSQEDLLEIKNFGQKSAEEVIEAL---QKRLG 302

Query: 319 MNLP 322
           + LP
Sbjct: 303 ITLP 306


>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 =  314 bits (806), Expect = 9e-84,   Method: Composition-based stats.
 Identities = 122/323 (37%), Positives = 190/323 (58%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++    +        PL  G+  T+GNALRRVL+SSL G AIT+V+ID V
Sbjct: 6   FQKPDKV---IMIDSSDFEGKFEFRPLEPGYGLTVGNALRRVLLSSLEGHAITSVRIDKV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQ-TVNDI 125
            HE S I GV ED+T+IILN+K +  K   +    + V+I   G   +TAGD Q  ++  
Sbjct: 63  EHEFSVIPGVVEDVTEIILNLKQVRFKKQIEDSEAEVVSISVSGKDQLTAGDFQKFISGY 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNPD VICN+D    + ME+ + KG GYVPA+ ++  N  +G I +D++++PIK V Y
Sbjct: 123 QVLNPDLVICNMDSKVSINMEIVIDKGRGYVPAEENKKSNAALGTIAVDSIFTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL   I TDGSI  +D++   +++L     +F    I  E  +   
Sbjct: 183 SIENFRVEQKTDYEKLVFEIVTDGSIHPKDALTEGAKVLIHHFMLFSDERITLEADEIAQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+K
Sbjct: 243 TETYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++ ++   GL  GM+L  +
Sbjct: 303 SLTELEELVINKGLSFGMDLSKY 325


>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 =  314 bits (805), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 123/323 (38%), Positives = 193/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++    +        PL  G+  T+GNALRRVL+SSL G AIT+++++GV
Sbjct: 6   FQKPDKV---IMINSTDFEGKFEFRPLEPGYGLTIGNALRRVLLSSLEGFAITSLRVEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQ-TVNDI 125
            HE S+I GV ED+T+IILN+K +  K   D   ++ VTI   G   V AGD Q  ++  
Sbjct: 63  DHEFSTIAGVVEDVTEIILNLKQLRFKRQIDEIDNETVTISVSGNDKVVAGDFQKFISGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNPD +ICN+D    + ME+T+ KG GYVPA+ ++  N P+G I  D++++PIK V Y
Sbjct: 123 QVLNPDLIICNMDSKVNLNMEITIEKGRGYVPAEENKKANAPLGTIFTDSIFTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL   I +DGSI  +D++  A++ L     +F    I  E  +   
Sbjct: 183 SIENFRVEQKTDYEKLVFEITSDGSIHPKDALTEAAKTLIHHFMLFSDERITLEADEIAQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+K
Sbjct: 243 TETYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++ ++   GL  GM+L  +
Sbjct: 303 SLTELEELVLVKGLNFGMDLAKY 325


>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 =  314 bits (805), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 122/329 (37%), Positives = 193/329 (58%), Gaps = 7/329 (2%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M   +   L++P  +E         N      +PL RGF HTLGNA+RR+L+SSLRG+A+
Sbjct: 1   MATIDLSGLVRPQLVEATKRED-SPNLAEFRLQPLERGFGHTLGNAMRRLLLSSLRGSAV 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV-TIFKRGPGVVTAGDI 119
            A +IDGV+HE  +I GV ED+  II N+K + L +  +  + V  I K GPG VTA DI
Sbjct: 60  WAFRIDGVVHEHQTIGGVVEDVHQIIGNLKTLTLALPDEVEQTVLRISKSGPGTVTAADI 119

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR-TENDPIGLITIDALYS 178
                + +++P H I  +  +    +EL V+KG GY+ +  H   +N  + ++ IDA+YS
Sbjct: 120 IATGGVRIIDPSHHIFTITGERDFNIELYVNKGRGYIESDQHPADKNLSVDVVRIDAIYS 179

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF---- 234
           P+++V++TV   R GQ  DYD+L++T++T+G+++ E++V+ A+ + Q     F+ F    
Sbjct: 180 PVRRVNFTVAETRVGQRTDYDRLTLTVETNGTMSPEEAVSYAAALAQTHFQYFVGFGSSA 239

Query: 235 EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
                   +  N  ++         +++LELSVRS N L+  NI  +GDL+++TEA +L+
Sbjct: 240 SAQPGTAGDGANSDAIRLAELFRTPIDDLELSVRSVNSLKNSNIRSLGDLVRQTEAQILQ 299

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           + NFG+KSL EI  +L   GL  GM   +
Sbjct: 300 VKNFGKKSLQEIAALLEKEGLNFGMRYEE 328


>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 =  314 bits (805), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 123/322 (38%), Positives = 192/322 (59%), Gaps = 9/322 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
              P+ +   V+ + ++       +PL RG+  T+GNALRR+L+SSL G AIT+V+  GV
Sbjct: 6   FQMPDKV---VMEKADDFHGFFEFKPLERGYGVTIGNALRRILLSSLEGYAITSVRFPGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDS-HKRVTIFKRGPGVVTAGDI-QTVNDIE 126
           LHE S+I+GV +D+T+I+LN+K +  K   D    ++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 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEVK 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 LVEIKGVLGTMGLFLGMNLPDW 324
           L E++ ++    L  GM++  +
Sbjct: 303 LTELEQLIADKQLHFGMDVSKY 324


>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 =  314 bits (805), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 101/312 (32%), Positives = 168/312 (53%), Gaps = 16/312 (5%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            + +++         PL  G   T+GNALRRVL+S+L G+A+TAV+I GV HE S+I GV
Sbjct: 11  RVEEDQGQYGQFALHPLAPGQGITVGNALRRVLLSNLPGSAVTAVRIAGVNHEFSTIPGV 70

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG----VVTAGDIQTVNDIEVLNPDHVI 134
            ED+ DI+L +K + ++      +   +F + P      VTAG +Q  +++EV+NP+H I
Sbjct: 71  REDVMDILLQMKQLVIRSHTSEPQMGRLFAQAPENEPLTVTAGMVQLGSEVEVVNPNHYI 130

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR--- 191
             L   A + ME  + K  GY   +  R +   +  + +DA++ P+++V+YTV+S R   
Sbjct: 131 ATLMPGATLEMEFKIEKDRGYRSVERVRDDRLALDYLQLDAVFMPVRRVNYTVDSVRSAG 190

Query: 192 -EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
            EG     D L + I T+GS+T +D++  A+ IL D           +  +       + 
Sbjct: 191 AEGDRQLQDYLKLEIWTNGSLTPQDALNQAATILVDLFSPL-----KEVPLHTSEATATD 245

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
             +      +E+L LSVR+ NCL+   +  + DL++ ++ ++L + NFG+KS  E+   L
Sbjct: 246 DHDETGQIPIEQLNLSVRAYNCLKRAQVNTVADLLEYSQEELLEIKNFGQKSAEEVIEAL 305

Query: 311 GTMGLFLGMNLP 322
                 LG+ LP
Sbjct: 306 ---QKHLGITLP 314


>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 =  314 bits (805), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 125/323 (38%), Positives = 196/323 (60%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ +  +        PL  GF  T+GNALRRVL+SSL G AIT++++DGV
Sbjct: 6   FQKPDKV---IMIESTDFSGRFEFRPLEPGFGLTVGNALRRVLLSSLEGFAITSLRLDGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQ-TVNDI 125
            HE S++ GV ED+T+IILN+K +  K   +    + V+I   G    TAGD+Q  ++  
Sbjct: 63  EHEFSTVSGVVEDVTEIILNLKQVRFKKQIEETDRETVSISVSGQEQFTAGDLQKFISGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNPD VICN+D    +  E+T+ KG G+VPA+ ++  + PIG I  D++Y+PIK V Y
Sbjct: 123 QVLNPDLVICNMDKSVKLNAEITIEKGRGFVPAEENKKASAPIGTIFTDSIYTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE+ R  Q  DY+KL   IDTDGSI+ +D++  A++IL     +F    I  E  +   
Sbjct: 183 AVENFRVEQKTDYEKLVFDIDTDGSISPKDALTEAAKILIHHFMLFSDERITLEADEIAQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E  + +SL     L  ++ +++LSVR+ NCL+   +  +GDL+   ++D+++  NFG+K
Sbjct: 243 TETYDEESLHMRQLLKTRLIDMDLSVRALNCLKAAEVDTLGDLVSFNKSDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++ ++   GL  GM+L  +
Sbjct: 303 SLTELEELVIVKGLSFGMDLSKY 325


>gi|332042695|gb|EGI78895.1| DNA-directed RNA polymerase, alpha subunit [Lacinutrix algicola
           5H-3-7-4]
          Length = 330

 Score =  314 bits (804), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 123/323 (38%), Positives = 194/323 (60%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++    +        PL  G+  T+GNALRRVL+SSL G AIT+++I+GV
Sbjct: 6   FQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSSLEGFAITSIRIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQ-TVNDI 125
            HE S++ GV ED+T+IILN+K +  K   +   ++ V+I   G   +TAGD Q  ++  
Sbjct: 63  DHEFSTVAGVVEDVTEIILNLKQMRFKRQIEDVDNESVSISISGQDKITAGDFQKFISGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLN D VICNLD    + ME+T+ KG GYVPA+ ++  + PIG I  D++Y+PIK V Y
Sbjct: 123 QVLNSDLVICNLDPKVSITMEITIEKGRGYVPAEENKKASAPIGTIFTDSIYTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL   I +DGSI+ +D++  A++ L     +F    I  E  +   
Sbjct: 183 SIENYRVEQKTDYEKLVFEIQSDGSISPQDALTEAAKTLIHHFMLFSDERITLEADEIAQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+K
Sbjct: 243 TETYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++ ++   GL  GM+L  +
Sbjct: 303 SLTELEELVNVKGLNFGMDLSKY 325


>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 =  314 bits (804), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 122/318 (38%), Positives = 191/318 (60%), Gaps = 6/318 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           +  P  IE        ++    IA+PL RG+  TLGN +RRVL++SL G AIT ++I+ V
Sbjct: 5   MQMPAKIELDE-SSHSDSFGKFIAQPLERGYGVTLGNLMRRVLLASLPGTAITGIKIENV 63

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEV 127
            HE S+I+GV ED+ +I+LN+K +  +       + T+   GP   TAG IQ    + EV
Sbjct: 64  YHEFSTIQGVREDVPEIVLNLKKVRFRSQCKRSCKTTVTLVGPMEFTAGVIQPQEGEFEV 123

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D  I  ++    V +++ + +G GYVPA+ +R E  P+G I ID++++PI+ V +TV
Sbjct: 124 LNKDLHIATINAGTTVTLDIFIGRGRGYVPAEENRAEGMPLGFIPIDSIFTPIRNVKFTV 183

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK----E 243
           E+ R GQ  DY+K+ + ++TDGSIT +DS++LA R++ D + +F +F   ++E      +
Sbjct: 184 ENTRVGQRTDYEKMILEVETDGSITPDDSISLAGRVISDHVLLFADFSPAEEEYTEEEFK 243

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             + +       L  K+E+L+LSVRS NCLR   I  +G+L+   E ++L   NFG+KSL
Sbjct: 244 QQDDEFETMRRLLATKIEDLDLSVRSHNCLRLAEIDTLGELVSHKEDELLNYKNFGKKSL 303

Query: 304 VEIKGVLGTMGLFLGMNL 321
            E+K  L    L  GM++
Sbjct: 304 TELKEQLDKFDLKFGMDI 321


>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 =  314 bits (804), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 145/329 (44%), Positives = 210/329 (63%), 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
                +    P    LL  V+ELEL+VRS NCL+ E I Y+GDLIQ++E D+LR  N GR
Sbjct: 238 EALPTSEDFDPQ---LLAAVDELELTVRSANCLKAEQIYYIGDLIQKSEQDLLRTPNLGR 294

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           KSL EIK VL   GL L  ++ +WPP  +
Sbjct: 295 KSLNEIKEVLTEKGLNLATSIENWPPVDL 323


>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 =  314 bits (804), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 122/323 (37%), Positives = 196/323 (60%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +  +               PL  G+  T+GNALRR+L+SSL G AIT+++I+GV
Sbjct: 6   FQKPDKVLMLEADN---FFGKFEFRPLEPGYGITIGNALRRILLSSLEGFAITSIKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE  +I GV ED+T+IILN+K +  K   D   +++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 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL + I TDGSI  ++++  A++IL     +F    I  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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  GM++  +
Sbjct: 303 SLTELDELLESLNLSFGMDITKY 325


>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 =  313 bits (803), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 146/329 (44%), Positives = 209/329 (63%), 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    +    P    LL  V+ELEL+VRS NCL+ E I Y+GDLIQ++E D+LR  N GR
Sbjct: 238 VSLPTSEDFDPQ---LLAAVDELELTVRSANCLKAEQIYYIGDLIQKSEQDLLRTPNLGR 294

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESI 329
           KSL EIK VL   GL LG N+ +WPP  +
Sbjct: 295 KSLNEIKEVLTEKGLSLGTNIENWPPVDL 323


>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 =  313 bits (803), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 123/299 (41%), Positives = 183/299 (61%), Gaps = 1/299 (0%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            + +E+E   + +AEPLPRG  HTLGNALRRV++S L GAA+T ++I+GV HE S+I+GV
Sbjct: 11  RVEEEDERHGIFVAEPLPRGLGHTLGNALRRVMLSGLPGAAVTKLRIEGVQHEFSTIEGV 70

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+ DIILN+K +  ++  D    + I K GPG V   DI+   D+EV+NPD  I +L 
Sbjct: 71  REDVVDIILNVKQLKFRLERDEPIELQISKDGPGEVRGSDIELKADVEVVNPDAYIASLS 130

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + M LTV +G GYVPA+ ++++ DPIG+I +D+L+SP++KV Y V   R G  +D 
Sbjct: 131 EGGHLDMTLTVERGQGYVPAEQNKSDADPIGVIAVDSLFSPVEKVQYRVSETRAGARVDL 190

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           D L++ + TDG +   +++  ASR L D  G+F    +     +E       P      +
Sbjct: 191 DALTLEVFTDGRLGPREALREASRKLIDFFGLFAEGYQGAGAAEEPGRSGGRPV-ITDER 249

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            +E+LEL+VRS NCL+ E +  +G L   TE +++ + N G KS+ EI+  L   G  L
Sbjct: 250 PIEDLELTVRSYNCLKREGVDTIGQLATMTEEELMNIRNLGMKSVDEIRSKLEEYGYTL 308


>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 =  313 bits (803), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 130/318 (40%), Positives = 193/318 (60%), Gaps = 6/318 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           +  P  I+              IA+PL RG+  TLGNA+RRVL++SL G AIT ++IDGV
Sbjct: 5   MQMPTKIDVDEATHTGSF-GRFIAQPLERGYGVTLGNAMRRVLLASLPGTAITGIKIDGV 63

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEV 127
            HE S+I GV ED+ +I+LN+K +  K +     + T+   GP    AGDI     + EV
Sbjct: 64  FHEFSTIDGVREDVPEIVLNLKKVRFKSNCKRSCKTTLTLAGPKDFLAGDIVAQEGEFEV 123

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D  I  ++ +A V +++ + +G GYVPA+ +R++  PIG I ID++Y+PIK V  TV
Sbjct: 124 LNKDLHIATINSEATVTIDIYIGRGRGYVPAEENRSDGMPIGFIAIDSIYTPIKNVKLTV 183

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI-- 245
           E+ R GQ  DY+K+ + ++TDGSIT +D+++LA +I+ D +  F NF   ++E  E+   
Sbjct: 184 ENTRVGQKTDYEKMILDVETDGSITPDDAISLAGKIINDHITFFANFSPTEEEFSEEEYK 243

Query: 246 --NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             + +       L  K+E+L+LSVRS NCLR   I  +GDL+ R E ++L   NFG+KSL
Sbjct: 244 QLDDEFESMRKLLQTKIEDLDLSVRSHNCLRLAEIDSLGDLVSRREEELLNYKNFGKKSL 303

Query: 304 VEIKGVLGTMGLFLGMNL 321
            E+K  L    L  GM++
Sbjct: 304 TELKEQLEKFNLKFGMDI 321


>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 =  313 bits (802), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 120/323 (37%), Positives = 190/323 (58%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++    +        PL  G+  T+GNALRRVL+S+L G AIT+V++D V
Sbjct: 6   FQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSALEGFAITSVRMDKV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQ-TVNDI 125
            HE S I GV ED+T++ILN+K +  K   +    + V+I   G   +TAGD Q  ++  
Sbjct: 63  EHEFSVIPGVVEDVTEMILNLKQVRFKRQIEDVEAETVSISVSGKNQLTAGDFQKFISGY 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNPD VICN+D    + ME+ + KG GYVPA+ ++     IG I ID++++PIK V Y
Sbjct: 123 QVLNPDLVICNMDAKVSINMEIVIEKGRGYVPAEENKKPGAAIGTIPIDSIFTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL   I +DGSI  +D++  A+++L     +F    I  E  +   
Sbjct: 183 SIENYRVEQKTDYEKLVFEISSDGSINPKDALTEAAKVLIHHFMLFSDERITLEADEIAQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+K
Sbjct: 243 TETYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++ ++   GL  GM+L  +
Sbjct: 303 SLTELEELVINKGLSFGMDLSKY 325


>gi|58415796|emb|CAH57312.1| RNA polymerase alpha-subunit [Vibrio coralliilyticus]
          Length = 287

 Score =  313 bits (802), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 133/290 (45%), Positives = 197/290 (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++  + +   +++   +  P    LL+ V++LEL+VR
Sbjct: 181 GTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVR 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|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 =  313 bits (801), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 129/323 (39%), Positives = 197/323 (60%), Gaps = 10/323 (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  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLSELDDLLESLNLSFGTDISKY 325


>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 =  313 bits (801), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 121/300 (40%), Positives = 179/300 (59%), Gaps = 5/300 (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 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFI-NFEEPKKEVKEDINVKSLPFNPALL 257
           D+L+M + TDGSI  + +++LA++IL D L +     +E            +   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


>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 =  313 bits (801), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 124/323 (38%), Positives = 193/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++    +        PL  G+  T+GNALRRVL+SSL G AIT+V+I+GV
Sbjct: 6   FQKPDKV---IMIDSTDFEGTFEFRPLEPGYGLTVGNALRRVLLSSLEGFAITSVRIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQT-VNDI 125
            HE S+I+GV ED+T++ILN+K I  K   +   ++ V+I   G   +TAGD Q  +   
Sbjct: 63  DHEFSTIEGVVEDVTEMILNLKQIRFKKRAEDVDNETVSISFSGNDKMTAGDFQKYLTGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           ++LNPD  IC +D    + +ELTV KG GYVPA+ ++T   PIG I  D++++PIK V Y
Sbjct: 123 DILNPDLEICTMDKKVSLNLELTVQKGRGYVPAEENKTSKAPIGTIFTDSVFTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL   I +DGSI  +D++  A++ L     +F    I  E  +   
Sbjct: 183 SIENFRVEQKTDYEKLIFEIISDGSIHPKDALTEAAKTLIHHFMLFSDERITLETEEMSQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E  + +SL     L  K+ +L+LSVR+ NCL+   +  +GDL+   ++D+++  NFG+K
Sbjct: 243 AETYDEESLHMRQLLKTKLVDLDLSVRALNCLKAAEVETLGDLVSHNKSDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++ ++   GL  GM+L  +
Sbjct: 303 SLTELEELVENKGLDFGMDLSKY 325


>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 =  312 bits (800), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 115/318 (36%), Positives = 177/318 (55%), Gaps = 6/318 (1%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
            +E + P+ + +    ++ +     + EPL RGF  T+GNALRR L+SS+ G AIT V++
Sbjct: 2   LREFVYPSKVYW---EEKTKTYGRFVVEPLERGFGITVGNALRRTLLSSIEGTAITGVKV 58

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
            G  HE S+++GV ED+ +II N+K +  ++     + + + KRG G V A DI     +
Sbjct: 59  YGAYHEFSTVEGVLEDVLEIIANLKRVRFRLRESHVEILYLKKRGEGEVYARDIILPPSV 118

Query: 126 EVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           +++ PD  I  +   D  + +E+ V +G GYVP +   +    +G I +DA +SP++ VS
Sbjct: 119 DLITPDVKIATITSPDTELHIEIRVERGFGYVPTEEMESFG-EVGWILVDADFSPVRHVS 177

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           Y VE  R  +  DYD+L M I TDGS T E+ V  A +IL        N  +    V E+
Sbjct: 178 YRVEKTRVERRSDYDRLIMEIRTDGSKTPEEVVKEAVQILLRNFSSLENIAQEIPFVAEE 237

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
             V         L  +EEL++S RS N L+   I  +G+L++ TE D+    N GRK++ 
Sbjct: 238 PVVVDELMEKLSL-PIEELDISQRSLNSLKRIGINTLGELVRLTEEDLKSTKNVGRKAIN 296

Query: 305 EIKGVLGTMGLFLGMNLP 322
           EIK  L  MGL+LGM++ 
Sbjct: 297 EIKEALKQMGLYLGMDIE 314


>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 =  312 bits (799), Expect = 6e-83,   Method: Composition-based stats.
 Identities = 120/316 (37%), 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  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIE 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   +    + + IG I ID  +SPIK+ ++ 
Sbjct: 125 IVNPDEYICTLSENVKLQMEFRIERGRGYKTVEELE-DINEIGWILIDTSFSPIKRCTFF 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|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 =  311 bits (798), Expect = 7e-83,   Method: Composition-based stats.
 Identities = 121/310 (39%), Positives = 188/310 (60%), Gaps = 7/310 (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  LTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPDHVICNLD 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 LFLGMNLPDW 324
           L  GM+L  +
Sbjct: 303 LNFGMDLSKY 312


>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 =  311 bits (798), Expect = 7e-83,   Method: Composition-based stats.
 Identities = 121/323 (37%), Positives = 187/323 (57%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ +  +        PL  G+  T+GNALRRV++SSL G AIT+V+ D V
Sbjct: 6   FQKPDKV---IMIESSDFEGRFEFRPLEPGYGLTIGNALRRVMLSSLEGFAITSVKFDKV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQTV-NDI 125
            HE S+I GV ED+T+IILN+K +  K   +    +  TI   G   +TAGD Q   +  
Sbjct: 63  DHEFSTIPGVREDVTEIILNLKQVRFKRQVEDVEDETATITVSGKKQLTAGDFQKTLSGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNPD VICN++  A   ME+T+ KG GYV A+ +   N  IG+I  D++++PIK V Y
Sbjct: 123 QVLNPDLVICNMETSASFTMEITIEKGRGYVSAEENAKPNAAIGVIATDSIFTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           T+E+ R  Q  DY+KL   I TDGSI  + ++  A++ L     +F    I  E  +   
Sbjct: 183 TIENYRVEQKTDYEKLVFEIKTDGSIHPKQALTEAAKTLIHHFMLFSDERITLEADEVAQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            +  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   +AD+++  NFG+K
Sbjct: 243 TDAYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVETLGDLVSFNKADLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL+E+  ++   GL  GM+   +
Sbjct: 303 SLIELDELVANKGLVFGMDTSKY 325


>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 =  311 bits (798), Expect = 7e-83,   Method: Composition-based stats.
 Identities = 124/323 (38%), Positives = 194/323 (60%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ +  E        PL  G+  T+GNALRRV++SSL G AIT+V+ID V
Sbjct: 6   FQKPDKV---IMIESSEFEGKFEFRPLEPGYGLTIGNALRRVMLSSLEGYAITSVKIDSV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQ-TVNDI 125
            HE S+I GV ED+T+IILN+K +  K+  +    ++ +I   G   +TAGD Q  +   
Sbjct: 63  EHEFSTITGVVEDVTEIILNLKQVRFKLQTEGTDHEKASISVTGKKQLTAGDFQKFITGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNPD VICN++ D  ++M++T+ KG GYV A+ +   N P+G I  DA+++PIK V Y
Sbjct: 123 QVLNPDLVICNMEPDVAIKMDITIDKGMGYVFAEENTKPNMPMGTIPTDAIFTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL   I TDGSI  +D++  A++ L     +F    I  E  +   
Sbjct: 183 SIENYRVEQKTDYEKLIFEIKTDGSIHPKDALMEAAKTLIHHFMLFSDERITIEPEEVVQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+  T+ D+++  NFG+K
Sbjct: 243 PESYDEESLHMRQLLKTKLIDMDLSVRALNCLKAAEVDTLGDLVSFTKTDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  ++ + GL  GM+L  +
Sbjct: 303 SLTELDELVESKGLTFGMDLSRY 325


>gi|328814015|gb|AEB52123.1| DNA-directed RNA polymerase alpha chain [Lactobacillus rhamnosus]
          Length = 273

 Score =  311 bits (798), Expect = 7e-83,   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|208659518|gb|ACI31189.1| RpoA [Vibrio breoganii]
          Length = 302

 Score =  311 bits (798), Expect = 7e-83,   Method: Composition-based stats.
 Identities = 132/308 (42%), Positives = 199/308 (64%), Gaps = 11/308 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQINT---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++  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++  + +   KE
Sbjct: 178 AYSVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEKE 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GD +QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDXVQRTEVELLKTPNLGKKSL 294

Query: 304 VEIKGVLG 311
            EIK VL 
Sbjct: 295 TEIKDVLA 302


>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 =  311 bits (798), Expect = 7e-83,   Method: Composition-based stats.
 Identities = 122/310 (39%), Positives = 188/310 (60%), Gaps = 7/310 (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  LTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPDHVICNLD 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 LFLGMNLPDW 324
           L  GM+L  +
Sbjct: 303 LNFGMDLSKY 312


>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 =  311 bits (798), Expect = 7e-83,   Method: Composition-based stats.
 Identities = 121/323 (37%), Positives = 197/323 (60%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  +        PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---VMLEANDKFGKFEFRPLEPGFGVTIGNALRRILLSSLEGFAINTIKIGGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-QTVNDI 125
            HE SS+ GV ED+T+IILN+K +  K   D   +++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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLSELDDLLESLNLSFGTDISKY 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 =  311 bits (798), Expect = 8e-83,   Method: Composition-based stats.
 Identities = 120/322 (37%), Positives = 194/322 (60%), Gaps = 9/322 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
              P  +   V+ + ++   L   +PL +G+  T+GNALRR+L+SSL G AIT+++I GV
Sbjct: 6   FQMPEKV---VMEKADDFHGLFTFKPLEKGYGVTIGNALRRILLSSLEGYAITSIKIPGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINL-KMSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIE 126
           LHE S+I+GV ED+TDIILN+K +   K+      ++T+  +   V TAGDI +  +  E
Sbjct: 63  LHEFSTIEGVVEDVTDIILNLKQVRFKKVHEAFDGKITVEIKNQSVFTAGDIAKFTSSFE 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +LNPD VIC++D      +E+TV KG GY+PA+  + +    G I IDA+++PIK V Y+
Sbjct: 123 ILNPDLVICHIDESKNFEIEITVEKGRGYLPAEESKPKEQVFGQIAIDAIFTPIKNVKYS 182

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF----EEPKKEVK 242
           VE+ R  Q  D++KL + + TDGSI  E ++  +++IL     +F +     +       
Sbjct: 183 VENTRVEQKTDFEKLILEVSTDGSIHPEKALQESAKILIQHFMLFSDQTMVLDSTGIAEP 242

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           E I+ + L     L   + +L+LSVR+ NCL+  ++  +GDL +   +DM++  NFG+KS
Sbjct: 243 EPIDEEFLHMRKLLKTSLSDLDLSVRAFNCLKAADVKTLGDLAKLEISDMMKFRNFGKKS 302

Query: 303 LVEIKGVLGTMGLFLGMNLPDW 324
           L E++ ++   GL  GM++  +
Sbjct: 303 LAELEQLIQEKGLTFGMDISKY 324


>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 =  311 bits (798), Expect = 8e-83,   Method: Composition-based stats.
 Identities = 121/323 (37%), Positives = 191/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++    +        PL  G+  T+GNALRRVL+SSL G AIT++++D V
Sbjct: 6   FQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVLLSSLEGFAITSIRVDKV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQ-TVNDI 125
            HE S I G+ ED+T+IILN+K +  K   +    + V++   G   +TAGD Q  ++  
Sbjct: 63  EHEFSVISGIVEDVTEIILNLKQVRFKRQIEDVDSETVSVSVSGKNQLTAGDFQKFISGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNPD VICN+D      MEL + KG GYVPA+ ++    PIG I ID++++PIK V Y
Sbjct: 123 QVLNPDLVICNMDAKVNFNMELVIEKGRGYVPAEENKKSGAPIGTIAIDSIFTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL   I++DGSIT +D++   +++L     +F    I  E  +   
Sbjct: 183 SIENFRVEQKTDYEKLVFEIESDGSITPKDALTEGAKVLIHHFMLFSDERITLEADEIAQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+K
Sbjct: 243 TETYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++ ++   GL  GM+L  +
Sbjct: 303 SLTELEELVINKGLSFGMDLSKY 325


>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 =  311 bits (798), Expect = 8e-83,   Method: Composition-based stats.
 Identities = 124/323 (38%), Positives = 194/323 (60%), Gaps = 10/323 (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  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLSELDDLLESLNLSFGTDISKY 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 =  311 bits (797), Expect = 9e-83,   Method: Composition-based stats.
 Identities = 123/323 (38%), Positives = 194/323 (60%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ +  E        PL  G+  T+GNALRRV++SSL G AIT+V+ID V
Sbjct: 6   FQKPDKV---IMIESSEFEGKFEFRPLEPGYGLTIGNALRRVMLSSLEGYAITSVKIDTV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQ-TVNDI 125
            HE S+I GV ED+T+IILN+K +  K+  +    ++ +I   G   +TAGD Q  +   
Sbjct: 63  EHEFSTIAGVVEDVTEIILNLKQVRFKLQTEGTDHEKASISVTGKKQLTAGDFQKFITGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNPD VICN++ +  ++M++T+ KG GYV A+ +   N P+G I  DA+++PIK V Y
Sbjct: 123 QVLNPDLVICNMEPEVEIKMDITIDKGMGYVSAEENAKPNMPVGTIPTDAIFTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL   I TDGSI  +D++  A++ L     +F    I  E  +   
Sbjct: 183 SIENYRVEQKTDYEKLIFEIKTDGSIHPKDALMEAAKTLIHHFMLFSDERITIEPEEVVQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+  T+ D+++  NFG+K
Sbjct: 243 PESYDEESLHMRQLLKTKLIDMDLSVRALNCLKAAEVDTLGDLVSFTKTDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  ++ + GL  GM+L  +
Sbjct: 303 SLTELDELVESKGLTFGMDLSKY 325


>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 =  311 bits (797), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 124/323 (38%), Positives = 195/323 (60%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ +  +        PL  GF  T+GNALRRVL+SSL G AIT+++IDGV
Sbjct: 6   FQKPDKV---IMIESTDFSGRFEFRPLEPGFGLTVGNALRRVLLSSLEGFAITSLRIDGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQ-TVNDI 125
            HE S++ G+ ED+T+IILN+K +  K   D    + V++   G    TAGD+Q  ++  
Sbjct: 63  EHEFSTVSGIVEDVTEIILNLKQVRFKKQIDETDRETVSVSISGQEQFTAGDLQKFISGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNPD VICN+D    +  E+T+ KG G+VPA+ ++  + PIG I  D++Y+PIK V Y
Sbjct: 123 QVLNPDLVICNMDKSVKLNAEITIEKGRGFVPAEENKKASAPIGTIFTDSIYTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            +E+ R  Q  DY+KL   IDTDGSI  +D++  A++IL     +F    I  E  +   
Sbjct: 183 AIENFRVEQKTDYEKLVFDIDTDGSINPKDALTEAAKILIHHFMLFSDERITLEADEIAQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E  + +SL     L  ++ +++LSVR+ NCL+   +  +GDL+   ++D+++  NFG+K
Sbjct: 243 TETYDEESLHMRQLLKTRLIDMDLSVRALNCLKAAEVDTLGDLVSFNKSDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++ ++   GL  GM+L  +
Sbjct: 303 SLTELEELVIVKGLSFGMDLTKY 325


>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 =  311 bits (797), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 120/323 (37%), Positives = 192/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++    E        PL  G+  T+GNALRRVL+SSL G AIT+V+++ V
Sbjct: 6   FQKPDKV---IMIDSSEFEGKFEFRPLEPGYGLTVGNALRRVLLSSLEGFAITSVKLENV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQ-TVNDI 125
            HE S+I GV ED+T+IILN+K +  K   +    ++VT+   G   + A D+Q  ++  
Sbjct: 63  EHEFSTIPGVVEDVTEIILNLKQVRFKRQIEDTEEEKVTVIIGGQEQLKAADLQKFISGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNPD VIC+L+    + ME+ + KG GYVPA+ ++  N  +G+I ID++++PIK V Y
Sbjct: 123 QVLNPDLVICHLEKSVQLNMEIAIEKGRGYVPAEENKKANAELGVIAIDSIFTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL   I TDGSI  +D++  A++ L     +F    I  E  +   
Sbjct: 183 SIENFRVEQKTDYEKLVFEIITDGSIHPKDALTEAAKTLIHHFLLFSDERITLEADEIAQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+K
Sbjct: 243 TETYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSYNKNDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++ ++   GL  GM+L  +
Sbjct: 303 SLTELEELVVLKGLSFGMDLAKY 325


>gi|332176606|gb|AEE12296.1| DNA-directed RNA polymerase subunit alpha [Porphyromonas
           asaccharolytica DSM 20707]
          Length = 330

 Score =  311 bits (796), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 116/323 (35%), Positives = 190/323 (58%), Gaps = 7/323 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
              + +++    ++      +PL  G+A T+GNALRR+L+SSL G AI +++I+GV HE 
Sbjct: 7   QQPDSVLMLDASDHYAKFEFKPLEPGYAMTIGNALRRILLSSLEGYAIASIRIEGVEHEF 66

Query: 73  SSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLN 129
           ++I GV ED+T IILN+K I  K  +     + +T+   G     AGD+ Q +   +V N
Sbjct: 67  ATIPGVLEDVTHIILNLKQIRFKAAVEDPQEETITLHVTGRNTFQAGDLNQVLTSYKVQN 126

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD VICNL  DA   +EL ++KG GYV ++ +R E+DP+  + ID +Y+PI+KV+ T E+
Sbjct: 127 PDLVICNLAEDADFTIELRINKGRGYVVSEENRREDDPVNTLPIDGIYTPIRKVNQTTEA 186

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV-- 247
            R  Q  DY+KL + I+TDG+I   +++  A+ IL     +F + E   +  +E+ +   
Sbjct: 187 YRVDQRTDYEKLVLEIETDGTIHPREALRQAATILISHFALFTDKEFEVELPEEEPDQLL 246

Query: 248 --KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +++     L+  +   +LSVR+ NCL+   I  + DL+ R   ++L++ NFG+KSLVE
Sbjct: 247 DNQTMKVRTQLMTDLATTDLSVRALNCLKAAGISTIADLLSRDRDELLKIKNFGKKSLVE 306

Query: 306 IKGVLGTMGLFLGMNLPDWPPES 328
           I+  L    L   M+L  +  ++
Sbjct: 307 IEQFLADQDLDFDMDLTPYRLDN 329


>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 =  311 bits (796), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 122/323 (37%), Positives = 193/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++    +        PL  G+  T+GNALRRV++S+L G AIT+V++D V
Sbjct: 6   FQKPDKV---IMIDSTDFEGKFEFRPLEPGYGLTVGNALRRVMLSALEGFAITSVRMDKV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQ-TVNDI 125
            HE S I GV ED+T+IILN+K +  K   +   ++ ++I   G   +TAGD Q  ++  
Sbjct: 63  AHEFSVIPGVVEDVTEIILNLKQVRFKRQIEDVDNETISIALSGKQQLTAGDFQKFISGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLNPD VICN+D    + MELT+ KG GYVPA+ ++    PIG I ID++++PIK V Y
Sbjct: 123 QVLNPDLVICNMDAKVNINMELTIEKGRGYVPAEENKKSGAPIGTIAIDSIFTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL   I +DGSI  +D++  A+++L     +F    I  E  +   
Sbjct: 183 SIENFRVEQKTDYEKLVFEIVSDGSIHPKDALTEAAKVLIHHFMLFSDERITLEADEIAQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   + D+++  NFG+K
Sbjct: 243 TETYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVDTLGDLVSFNKNDLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++ ++   GL  GM+L  +
Sbjct: 303 SLTELEELVINKGLSFGMDLSKY 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 =  311 bits (796), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 129/318 (40%), Positives = 193/318 (60%), Gaps = 6/318 (1%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           +  P  I+              IA+PL RG+  TLGNA+RRVL++SL G AIT ++IDGV
Sbjct: 5   MQMPAKIDVDEATHTGSF-GRFIAQPLERGYGVTLGNAMRRVLLASLPGTAITGIKIDGV 63

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEV 127
            HE S+I GV ED+ +I+LN+K +  K +     + T+   GP    AGDI     + EV
Sbjct: 64  FHEFSTIDGVREDVPEIVLNLKKVRFKSNCKRSCKTTLTLAGPKDFLAGDIVAQEGEFEV 123

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LN D  I  ++ +A V +++ + +G GYVPA+ +R++  PIG I ID++Y+PIK V  TV
Sbjct: 124 LNKDLHIATINSEAAVTIDIYIGRGRGYVPAEENRSDGMPIGFIAIDSIYTPIKNVKLTV 183

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE----EPKKEVKE 243
           E+ R GQ  DY+K+ + ++TDGSI+ +D+++LA RI+ D +  F NF     E  +E  +
Sbjct: 184 ENTRVGQKTDYEKMILDVETDGSISPDDAISLAGRIINDHVTFFANFSPTEEEYAEEEYK 243

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            ++ +       L  K+E+L+LSVRS NCLR   I  + DL+ R E ++L   NFG+KSL
Sbjct: 244 QLDEEFENMRKKLQTKIEDLDLSVRSHNCLRLAEIDTLADLVSRREDELLNYKNFGKKSL 303

Query: 304 VEIKGVLGTMGLFLGMNL 321
            E++  L   GL  GM++
Sbjct: 304 TELREALEKEGLKFGMDI 321


>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 =  310 bits (795), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 115/323 (35%), Positives = 190/323 (58%), Gaps = 7/323 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
              + +++    ++      +PL  G+A T+GNALRR+L+SSL G AI +++I+GV HE 
Sbjct: 7   QQPDSVLMLDASDHYAKFEFKPLEPGYAMTIGNALRRILLSSLEGYAIASIRIEGVEHEF 66

Query: 73  SSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDI-QTVNDIEVLN 129
           ++I GV ED+T IILN+K I  K  +     + +T+   G     AGD+ Q +   +V N
Sbjct: 67  ATIPGVLEDVTHIILNLKQIRFKAAVEDPQEETITLHVTGRNTFQAGDLNQVLTSYKVQN 126

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD VICNL  DA   +E+ ++KG GYV ++ +R E+DP+  + ID +Y+PI+KV+ T E+
Sbjct: 127 PDLVICNLAEDADFTIEIRINKGRGYVVSEENRREDDPVNTLPIDGIYTPIRKVNQTTEA 186

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV-- 247
            R  Q  DY+KL + I+TDG+I   +++  A+ IL     +F + E   +  +E+ +   
Sbjct: 187 YRVDQRTDYEKLVLEIETDGTIHPREALRQAATILISHFALFTDKEFEVELPEEEPDQLL 246

Query: 248 --KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +++     L+  +   +LSVR+ NCL+   I  + DL+ R   ++L++ NFG+KSLVE
Sbjct: 247 DNQTMKVRTQLMTDLATTDLSVRALNCLKAAGISTIADLLSRDRDELLKIKNFGKKSLVE 306

Query: 306 IKGVLGTMGLFLGMNLPDWPPES 328
           I+  L    L   M+L  +  ++
Sbjct: 307 IEQFLADQDLDFDMDLTPYRLDN 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 =  310 bits (795), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 130/314 (41%), Positives = 201/314 (64%), Gaps = 11/314 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQISS---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 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 VRV---PEEKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 294

Query: 297 NFGRKSLVEIKGVL 310
           N G+  L+ +K  L
Sbjct: 295 NLGKNLLLRLKTYL 308


>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 =  310 bits (795), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 121/323 (37%), Positives = 195/323 (60%), Gaps = 10/323 (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  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLSELDDLLESLNLSFGTDISKY 325


>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 =  310 bits (795), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 121/323 (37%), Positives = 197/323 (60%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP  +   ++ + +  +      PL  G+  T+GNALRR+L+SSL G AIT+++I+G+
Sbjct: 6   FQKPEKV---IMLEADAFQGKFEFRPLEPGYGITIGNALRRILLSSLEGFAITSIKIEGI 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++  L ++ L  GM++  +
Sbjct: 303 SLTELEEKLESLNLSFGMDIAKY 325


>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 =  310 bits (794), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 130/323 (40%), Positives = 201/323 (62%), Gaps = 10/323 (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 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL EI+ ++ +  L  GMNL  +
Sbjct: 303 SLTEIQELVKSKSLSFGMNLSKF 325


>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 =  310 bits (794), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 133/300 (44%), Positives = 198/300 (66%), Gaps = 8/300 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +
Sbjct: 1   LVDIEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKE 60

Query: 77  GVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
           GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E++NP+HVIC
Sbjct: 61  GVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVIC 120

Query: 136 NLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
           +L  D A V M + V +G GYVPA    H   ++ PIG + +DA YSP+ K++YTVE+AR
Sbjct: 121 HLTDDNAEVAMRIKVQRGRGYVPASARIHTDEDDRPIGRLLVDATYSPVDKIAYTVEAAR 180

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
             Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + +   +++   +  P
Sbjct: 181 VEQRTDLDKLVIDMETNGTIEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP 240

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK  L 
Sbjct: 241 ---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDGLH 297


>gi|189308769|gb|ACD87086.1| RpoA [Vibrio sp. PP-203]
          Length = 295

 Score =  310 bits (794), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 130/298 (43%), Positives = 197/298 (66%), 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 LDV-DAVVRMELTVSKGHGYVPAK---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++  + +   +++   +  P 
Sbjct: 181 EQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP- 239

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
              LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL
Sbjct: 240 --ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVL 295


>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 =  309 bits (793), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 120/323 (37%), Positives = 195/323 (60%), Gaps = 11/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ I   VL +  +        PL  G+  T+GNALRRVL+SSL G AI  ++I+G 
Sbjct: 6   FQKPDKI---VLQKSTDFEAQFEFRPLEPGYGVTVGNALRRVLLSSLEGYAIVGIKIEGA 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSH---KRVTIFKRGPGVVTAGDIQ-TVND 124
            HE +++KG+ ED+T+IILN+K +  K   ++    +++ I  +G     A  I+   + 
Sbjct: 63  DHEFATLKGITEDVTEIILNLKQVRFKRIVENEVNNEKIQISIKGKTEFRADMIEKATSA 122

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
            +++NP+ +IC LD  A + +ELT+ KG GYVPA+ ++ ++   G I ID++++PIK V 
Sbjct: 123 FQIMNPELLICTLDPSAKLDIELTIGKGRGYVPAEENKPKDAVFGYIAIDSIFTPIKNVK 182

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKE 240
           Y++E+ R  Q  DY+KL M + TDG+I  E++V  ASRIL   L +     I+F+    E
Sbjct: 183 YSIENTRVEQKTDYEKLIMEVITDGTIHPEEAVKQASRILIQHLMIITDENISFDTKDTE 242

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            ++ ++ ++L     L   +E+L+LSVR+ NCL+   I  + +L+Q  + ++++  NFG+
Sbjct: 243 KEDVVDEQTLQLRKILKTPLEDLDLSVRAFNCLKAAKINSLSELVQYEQEELMKFRNFGQ 302

Query: 301 KSLVEIKGVLGTMGLFLGMNLPD 323
           KSL EI+ VL   GL  GM+L  
Sbjct: 303 KSLSEIEQVLNERGLHFGMDLSK 325


>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 =  309 bits (793), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 110/316 (34%), Positives = 179/316 (56%), Gaps = 7/316 (2%)

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 VLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           ++N D  I  ++  +  ++ME+ + +G GYV +          G + +DA +SPIK  ++
Sbjct: 119 IINKDAYIATINSANTTLKMEIRIERGKGYVMSDEMEQ-IGEAGWVVLDADFSPIKVAAF 177

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+ R G   DYDKL+  + T+G ++ + ++  A  ++   + M  N       + E +
Sbjct: 178 RVEATRVGDRTDYDKLTFELTTNGVVSPDTAIQQAVELIVKHMNMLTNISYEVPTLPEPM 237

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
               L         +EEL++S R+ N L+   +  +G+L+Q TE ++    N GRK+L E
Sbjct: 238 PPDELMEKLTF--SIEELDISQRALNSLKRIGVTTIGELVQLTEDELKSSKNIGRKALTE 295

Query: 306 IKGVLGTMGLFLGMNL 321
           IK  L  MG  LGMN+
Sbjct: 296 IKEALKNMGFSLGMNI 311


>gi|332181991|gb|AEE17679.1| DNA-directed RNA polymerase subunit alpha [Treponema brennaborense
           DSM 12168]
          Length = 350

 Score =  309 bits (793), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 128/349 (36%), Positives = 199/349 (57%), Gaps = 14/349 (4%)

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-----DGVLH----EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF-KR 109
           IT+V+I     D V H    E  +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 GPGTITSNDFSR-EGLEILSKDMLVFTMMENAHLEFEVQVDLGRGYTPAEVNEHYIEIVG 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       +++  L+KK E+
Sbjct: 299 DDIAKTRNFGKKSLTEIKEKLLEWNLNLGMTDYSHLKDAV-NLSKKKEE 346


>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 =  309 bits (793), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 121/323 (37%), Positives = 194/323 (60%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  +        PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---VMLEANDKFGKFEFRPLEPGFGVTIGNALRRILLSSLEGYAINTIRIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLSELDDLLESLNLSFGTDISKY 325


>gi|189308773|gb|ACD87088.1| RpoA [Vibrio sp. PP-204]
          Length = 295

 Score =  309 bits (793), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 130/297 (43%), Positives = 196/297 (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 V-DAVVRMELTVSKGHGYVPAK---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++  + +   +++   +  P   
Sbjct: 182 RTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP--- 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|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 =  309 bits (793), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 131/323 (40%), Positives = 200/323 (61%), Gaps = 10/323 (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 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL EI+ ++ +  L  GMNL  +
Sbjct: 303 SLTEIQELVKSKSLSFGMNLSKF 325


>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 =  309 bits (793), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 102/310 (32%), Positives = 169/310 (54%), Gaps = 11/310 (3%)

Query: 16  EYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           +   +  + +      +  + EPL RG   T+GNALRRVL+++L G A+TA++I GV HE
Sbjct: 5   QIECVESKTQKNQSQYSKFVLEPLERGQGITVGNALRRVLLANLEGTAVTAIRIGGVNHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            ++I GV ED+ +IILN+K I LK   D  +   +   G   VTA      +++E++NP 
Sbjct: 65  FATIPGVREDVLEIILNMKEIVLKSHTDQIQIGRLVAVGAAHVTAAQFDLPSEVEIINPT 124

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             I  L   A + ME  + KG GYVP +  + +   +  + IDA++ P+ KV+Y+VE+ R
Sbjct: 125 QPIATLTDGAKLEMEFRIEKGMGYVPVERGKEKQGALDFLQIDAVFMPVTKVNYSVENIR 184

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
             +    D L + I T+GS+  +++++ A+ +L +      N      +++  +      
Sbjct: 185 GERNEVKDSLMLEIWTNGSVNPKEALSQATEVLVNLFSPLKNIN----QIETVVPEYPDE 240

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            NP     +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L 
Sbjct: 241 ENPQSQIPIEELQLSVRAYNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEEVIEAL- 299

Query: 312 TMGLFLGMNL 321
                LG+ L
Sbjct: 300 --QKRLGITL 307


>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 =  309 bits (793), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 125/330 (37%), Positives = 189/330 (57%), Gaps = 12/330 (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-----DGVLH----EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF-KR 109
           I++V+I     DGV H    E  +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 ADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
            D+ +  NFG+KSL EIK  L   GL LGM
Sbjct: 300 DDITKTRNFGKKSLEEIKAKLEEHGLTLGM 329


>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 =  309 bits (792), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 119/319 (37%), Positives = 182/319 (57%), Gaps = 8/319 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E I P+ I +    ++ +    ++ EPL RGF  T+GN+LRRVL+SS+ G AITAV+I
Sbjct: 2   LNEFIYPDKIFW---EEKTDTYGRLVVEPLERGFGTTVGNSLRRVLLSSISGTAITAVKI 58

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKRGPGVVTAGDIQTVND 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 IEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           +E+LNPD  I  +   +  + +E+ V +G GYVP +        +G I +DA +SP+KKV
Sbjct: 119 VEILNPDQYIATITDPNKELNIEIRVERGRGYVPVEEMEA-IGEVGWILVDADFSPVKKV 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
            + V++ R G+   Y++L++ I T+G  T +  +  A  IL+    +  N    K  V  
Sbjct: 178 GFRVDNVRVGKKSTYERLTLEIFTNGIKTPDQCMQEAIEILKKHYELLENIFTEKPTV-- 235

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
              V        L   +EEL++S R+ N L+   I  +GDL++ TE ++    N GRK+L
Sbjct: 236 PQKVAVDELAEKLSLSIEELDISQRALNSLKRIGITTIGDLVRMTEDELKSTKNIGRKAL 295

Query: 304 VEIKGVLGTMGLFLGMNLP 322
            EIK  L  +GL LGMN+ 
Sbjct: 296 AEIKEALHKLGLELGMNIE 314


>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 =  309 bits (792), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 120/322 (37%), Positives = 193/322 (59%), Gaps = 9/322 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
              P  +   V+ + ++   L   +PL +G+  T+GNALRR+L+SSL G AIT +++ GV
Sbjct: 6   FQMPEKV---VMEKADDFHGLFEFKPLEKGYGVTIGNALRRILLSSLEGYAITGIKVPGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR-VTIFKRGPGVVTAGDI-QTVNDIE 126
           LHE S+I GV ED+T+IILN+K +  K   D ++  + +  +      AGDI +  +  +
Sbjct: 63  LHEFSTIPGVREDVTEIILNLKQVRFKKISDVNENKIVVSIKKQASFKAGDIAKFTSAYQ 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +LNP+ +ICN+D ++   +ELT+ KG GY+PA+ ++      G I IDA+++PIK V Y+
Sbjct: 123 ILNPELLICNVDSNSNFDIELTLEKGRGYLPAEENKPAEQIFGYIPIDAIFTPIKNVKYS 182

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEVK 242
           VE+ R  Q  DY+KL + I TDGSI  ED++  A+ IL     +F    + FE  K E +
Sbjct: 183 VENTRVEQRTDYEKLILEILTDGSIHPEDALKGAANILIKHFMLFSDQTMTFEAVKAEEE 242

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           E ++ + L     L   + +L+LSVR+ NCL+  +I  +G+L     +DM++  NFG+KS
Sbjct: 243 ETVDEEFLHMRKLLKTSLADLDLSVRAYNCLKAADIKTLGELATLDISDMMKFRNFGKKS 302

Query: 303 LVEIKGVLGTMGLFLGMNLPDW 324
           L E++ ++    L  GM+   +
Sbjct: 303 LNELEQLIIDKNLSFGMDTAKY 324


>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 =  309 bits (792), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 121/323 (37%), Positives = 194/323 (60%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  +        PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---VMLEANDKFGKFEFRPLEPGFGVTIGNALRRILLSSLEGYAINTIRIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLTELDDLLESLNLSFGTDISKY 325


>gi|179184670|gb|ACB78156.1| RNA polymerase alpha subunit [Vibrio rarus]
          Length = 301

 Score =  309 bits (792), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 131/303 (43%), 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-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
            D A + M + V +G GYVPA    H   +  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 RTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVQEPIEEK---PEFDP 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|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 =  309 bits (791), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 125/323 (38%), Positives = 195/323 (60%), Gaps = 10/323 (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  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLSELDDLLESLNLSFGTDISKY 325


>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 =  309 bits (791), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 121/323 (37%), Positives = 193/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ + +         PL  GF  T+GNALRR+L+SSL G A+  ++I GV
Sbjct: 6   FQKPDKV---VMLEADNKFGKFEFRPLEPGFGVTIGNALRRILLSSLEGYAVNTIRIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLSELDDLLESLNLSFGTDISKY 325


>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 =  308 bits (790), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 122/310 (39%), Positives = 186/310 (60%), Gaps = 7/310 (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  LTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPDHVICNLD 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 LFLGMNLPDW 324
           L  GM+L  +
Sbjct: 303 LNFGMDLSKY 312


>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 =  308 bits (790), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 134/331 (40%), Positives = 191/331 (57%), Gaps = 4/331 (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+  +  +K+V       
Sbjct: 185 AARVGEETEMDSLELEIWTDGRISPQNALEEAARILRDHLQPFMGNQVVEKDVVLTEEE- 243

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L   VE L+LSVR+ NCL   NI  +G+L  +TE+ ML+  NFG+KSL EIK 
Sbjct: 244 -TKMFKLLSHDVEILDLSVRAMNCLNSANIKLIGELCTKTESRMLKYRNFGKKSLDEIKE 302

Query: 309 VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +  +GL LGM+  D    ++E  + +   +
Sbjct: 303 KIEKLGLELGMSFSDRLMAALEAESVRVRSE 333


>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 =  308 bits (790), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 121/323 (37%), Positives = 195/323 (60%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AIT ++IDGV
Sbjct: 6   FQKPDKV---LMLEADSRFGKFEFRPLEPGFGITVGNALRRILLSSLEGFAITTIRIDGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLTELDDLLESLNLSFGTDISKY 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 =  308 bits (790), Expect = 7e-82,   Method: Composition-based stats.
 Identities = 122/323 (37%), Positives = 193/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP N+   ++ +  ++      +PL  G+  T+GNALRR+L+SSL G AITA++I+GV
Sbjct: 6   FQKPENV---LMMETSDSIAKFEFKPLEPGYGITIGNALRRILLSSLEGFAITAIKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMS--GDSHKRVTIFKRGPGVVTAGDIQT-VNDI 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 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE+ R  Q  DY+KL M + TDGSI   D++  A++IL     +F    I  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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L T+ L  GM++  +
Sbjct: 303 SLTELDELLATLNLSFGMDISKY 325


>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 =  308 bits (790), Expect = 7e-82,   Method: Composition-based stats.
 Identities = 121/323 (37%), Positives = 193/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AIT ++IDGV
Sbjct: 6   FQKPDKV---LMLEADSRFGKFEFRPLEPGFGITVGNALRRILLSSLEGFAITTIKIDGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLTELDDLLESLNLSFGTDISKY 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 =  308 bits (790), Expect = 7e-82,   Method: Composition-based stats.
 Identities = 121/323 (37%), Positives = 194/323 (60%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AIT ++IDGV
Sbjct: 6   FQKPDKV---LMLEADSRFGKFEFRPLEPGFGITVGNALRRILLSSLEGFAITTIRIDGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLTELDDLLESLNLSFGTDISKY 325


>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 =  308 bits (789), Expect = 7e-82,   Method: Composition-based stats.
 Identities = 131/301 (43%), Positives = 196/301 (65%), Gaps = 8/301 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +
Sbjct: 2   LVDIEQVSATHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKE 61

Query: 77  GVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
           GV ED+ +I+LN+KG+ +K+  G     +T+ K G G V AGDI    D+E+ NP+HVIC
Sbjct: 62  GVQEDILEILLNLKGLAVKVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVIC 121

Query: 136 NLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
           +L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR
Sbjct: 122 HLTDDNAEIAMRIKVERGRGYVPASSRIHTEEDERPIGRLLVDATYSPVDKIAYAVEAAR 181

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
             Q  D DKL + ++T+G++  E+++  ++ IL +QL  F++  + +   +++   +  P
Sbjct: 182 VEQRTDLDKLVIDMETNGTLDPEEAIRRSATILAEQLDAFVDLRDIRVPEEKEEKPEFDP 241

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
               LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G KSL EIK VL 
Sbjct: 242 ---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGNKSLTEIKDVLA 298

Query: 312 T 312
           +
Sbjct: 299 S 299


>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 =  308 bits (789), Expect = 8e-82,   Method: Composition-based stats.
 Identities = 112/306 (36%), Positives = 173/306 (56%), Gaps = 6/306 (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 YDKLSMTIDTDGSITGEDSVALASRILQDQLG------MFINFEEPKKEVKEDINVKSLP 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 TMGLFL 317
             GL L
Sbjct: 304 IFGLSL 309


>gi|159027085|emb|CAO89270.1| rpoA [Microcystis aeruginosa PCC 7806]
          Length = 313

 Score =  308 bits (789), Expect = 8e-82,   Method: Composition-based stats.
 Identities = 97/308 (31%), Positives = 166/308 (53%), Gaps = 8/308 (2%)

Query: 15  IEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS 74
           +E      + +  +  + EPL RG   T+GNALRR+L+S+L GAA+TA++I GV HE ++
Sbjct: 9   VEAKTYKNQSQ-YSKFVLEPLERGQGTTVGNALRRILISNLEGAAVTALRIAGVNHEFAT 67

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           ++GV ED+ +++LN+K I LK   +  +   +   GP  V A      +++E+++ +  +
Sbjct: 68  VEGVREDVMELMLNMKEITLKSYTNQTQIGRLVATGPATVVAAQFDLPSEVEIVDRNQYV 127

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
             L   A + ME  V KG GY      + E   +  + ID+++ P+ KV+Y+VE  R   
Sbjct: 128 ATLAEGAKLEMEFRVEKGKGYRAIDRSKEEATSLDFLQIDSIFMPVTKVNYSVEDIRSES 187

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
               D+L + I T+GSI  +++++ A+ +L +      +       ++   N      N 
Sbjct: 188 GQARDRLLLEIWTNGSINPKEALSQAADMLVNLFNPLKDLN----ALESSGNFDDQEINQ 243

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L    
Sbjct: 244 ENQIPIEELQLSVRAYNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEEVIEAL---Q 300

Query: 315 LFLGMNLP 322
             LG+ LP
Sbjct: 301 KRLGITLP 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 =  308 bits (789), Expect = 9e-82,   Method: Composition-based stats.
 Identities = 119/323 (36%), Positives = 191/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  +        PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---VMLEANDKFGKFEFRPLEPGFGVTIGNALRRILLSSLEGYAINTIKIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L  + L  G ++  +
Sbjct: 303 SLSELDDLLEGLNLSFGTDISKY 325


>gi|161511875|emb|CAP16948.1| DNA-directed RNA polymerase subunit alpha [Pediococcus siamensis]
          Length = 275

 Score =  308 bits (789), Expect = 9e-82,   Method: Composition-based stats.
 Identities = 121/269 (44%), Positives = 175/269 (65%), Gaps = 2/269 (0%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I    E EN    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+G
Sbjct: 3   IHKIDENENYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEG 62

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+T IILNIK ++LK+  D  K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +
Sbjct: 63  VVEDVTQIILNIKKVSLKIESDDEKSLEINVKGPATVTAGDIQGDSDVEILNPDQYICTV 122

Query: 138 DVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
                    LT   G GYV A     R ++ PIG++ ID++Y+PI++V+Y VE+ R GQ 
Sbjct: 123 ADGVTFHAVLTADTGRGYVSADENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQR 182

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
            DYDKL++ + TDGSI+  ++ +L+++IL + L +F+N  +  +E +  +  +       
Sbjct: 183 NDYDKLTLDVWTDGSISPSEATSLSAKILTEHLALFVNLTDEAQEAEIMVEKEETHKEKM 242

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDL 284
           L   +EEL+LSVRS NCL+   I  + +L
Sbjct: 243 LEMSIEELDLSVRSYNCLKRAGINTVQEL 271


>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 =  308 bits (788), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 121/323 (37%), Positives = 193/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + ++        PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---IMLENDDKFGKFEFRPLESGFGVTIGNALRRILLSSLEGFAINTIKIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L  + L  G ++  +
Sbjct: 303 SLTELDDLLAGLNLQFGTDISKY 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 =  308 bits (788), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 97/308 (31%), Positives = 166/308 (53%), Gaps = 8/308 (2%)

Query: 15  IEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS 74
           +E      + +  +  + EPL RG   T+GNALRR+L+S+L GAA+TA++I GV HE ++
Sbjct: 9   VEAKTYKNQSQ-YSKFVLEPLERGQGTTVGNALRRILISNLEGAAVTALRIAGVNHEFAT 67

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           ++GV ED+ +++LN+K I LK   +  +   +   GP  V A      +++E+++ +  +
Sbjct: 68  VQGVREDVMELMLNMKEIILKSYTNQTQIGRLVATGPATVVAAQFDLPSEVEIVDRNQYV 127

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
             L   A + ME  V KG GY      + E   +  + ID+++ P+ KV+Y+VE  R   
Sbjct: 128 ATLAEGAKLEMEFRVEKGKGYRAIDRSKDEATSLDFLQIDSIFMPVTKVNYSVEDIRSES 187

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
               D+L + I T+GSI  +++++ A+ +L +      +       ++   N      N 
Sbjct: 188 GQARDRLLLEIWTNGSINPKEALSQAADMLVNLFNPLKDLN----ALESSSNFDDQEINQ 243

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L    
Sbjct: 244 ENQIPIEELQLSVRAYNCLKRAQINTVADLLDYSQEDLLEIKNFGQKSAEEVIEAL---Q 300

Query: 315 LFLGMNLP 322
             LG+ LP
Sbjct: 301 KRLGITLP 308


>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 =  308 bits (788), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 122/323 (37%), Positives = 195/323 (60%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ + ++        PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---VMVEADDKFGKFEFRPLEPGFGVTIGNALRRILLSSLEGYAINTIRIGGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLSELDDLLESLNLSFGTDISKY 325


>gi|145577845|gb|ABP87373.1| RpoA [Vibrio ruber]
          Length = 294

 Score =  308 bits (788), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 131/296 (44%), Positives = 197/296 (66%), Gaps = 8/296 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +
Sbjct: 2   LVDIEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKE 61

Query: 77  GVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
           GV ED+ +I+LN+KG+ +++  G     +T+ K G G V AGDI    D+E++NP+HVIC
Sbjct: 62  GVQEDILEILLNLKGLAVRVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIVNPEHVIC 121

Query: 136 NLDV-DAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
           +L   +A V M + V +G GYVPA    H   ++ PIG + +DA YSP+ K++YTVE+AR
Sbjct: 122 HLTDGNAEVAMRIKVQRGRGYVPASARIHTDEDDRPIGRLLVDATYSPVDKIAYTVEAAR 181

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
             Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + +   +++   +  P
Sbjct: 182 VEQRTDLDKLVIDMETNGTIEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP 241

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
               LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK
Sbjct: 242 ---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIK 294


>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 =  307 bits (787), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 115/309 (37%), Positives = 193/309 (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 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI----NFEEPKKEVKEDINVK 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|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 =  307 bits (787), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 130/323 (40%), Positives = 201/323 (62%), Gaps = 10/323 (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 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL EI+ ++ + GL  GMNL  +
Sbjct: 303 SLTEIQDLVKSKGLSFGMNLSKF 325


>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 =  307 bits (787), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 120/323 (37%), Positives = 194/323 (60%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AIT ++IDGV
Sbjct: 6   FQKPDKV---LMLEADSRFGKFEFRPLEPGFGITVGNALRRILLSSLEGFAITTIRIDGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLTELDDLLESLNLSFGTDISKY 325


>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 =  307 bits (787), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 98/304 (32%), Positives = 168/304 (55%), Gaps = 8/304 (2%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
           ++  ++   +  + EPL R    T+GNALRRVL+S+L G A+T+V+I G  HE S+I GV
Sbjct: 12  IIEDDQSQFSRFVIEPLGRSQGTTVGNALRRVLLSNLEGTAVTSVRIAGASHEFSTIPGV 71

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+ DI+LN+K   LK      +   +  +GP  VTA +    +++E+++ D  I ++ 
Sbjct: 72  REDVLDILLNMKETVLKSYSAQPQIGRLVVQGPAKVTAANFDLPSEVELISTDRYIASVA 131

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + ME  + +G GY      R E   +  + IDA++ P++KV+Y+VE+  + +    
Sbjct: 132 AGHKLEMEFRIERGKGYKAIDRSREETGGVEFMQIDAVFMPVRKVNYSVENFIDPEGFPK 191

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           D+L M I T+GS+T + +++ A+ +L D              ++   +  +   +P    
Sbjct: 192 DRLVMEIWTNGSLTAQQAMSEAAALLVDMFNPL-----KDVTLEPKRDEDTKEEDPTYQI 246

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +EEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFG+KS  E+   L    + LG
Sbjct: 247 PIEELQLSVRAYNCLKRAQINAVSDLLDYSQEDLLEIKNFGQKSAEEVVEAL---QIHLG 303

Query: 319 MNLP 322
           + LP
Sbjct: 304 IMLP 307


>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 =  307 bits (787), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 129/330 (39%), Positives = 193/330 (58%), Gaps = 13/330 (3%)

Query: 1   MIQKNW-QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           M +KN  +   KP  I +      E N    IA P  RGF  T+GN LRRVL+SS++G A
Sbjct: 1   MARKNLLKGFKKPKGITFEH-SAVEPNYGKFIAYPFERGFGTTIGNTLRRVLLSSIQGYA 59

Query: 60  ITAVQI-----DGVLH----EISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKR 109
           +TAV+      DGV H    E   + 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 ADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
            ++ +  NFG+KSL EIK  L    L LGM
Sbjct: 299 EEIAKTRNFGKKSLQEIKEKLKEWNLSLGM 328


>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 =  307 bits (786), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 120/323 (37%), Positives = 194/323 (60%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AIT ++I+GV
Sbjct: 6   FQKPDKV---LMLEADAKFGKFEFRPLEPGFGITVGNALRRILLSSLEGFAITTIRIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLTELDDLLESLNLSFGTDISKY 325


>gi|254701949|ref|ZP_05163777.1| DNA-directed RNA polymerase subunit alpha [Brucella suis bv. 5 str.
           513]
          Length = 267

 Score =  307 bits (786), Expect = 2e-81,   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|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 =  307 bits (786), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 111/322 (34%), Positives = 187/322 (58%), Gaps = 9/322 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
              P  +    + + ++   L   +PL +G+  T+GNALRR+L+SSL G AIT ++I GV
Sbjct: 6   FQMPEKV---AMEKADDFHGLFTFKPLEKGYGVTVGNALRRILLSSLEGYAITGIKIPGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDS-HKRVTIFKRGPGVVTAGDI-QTVNDIE 126
           LHE S+++GV ED++++ILN+K +  K   ++   ++ I  +      AGDI +     E
Sbjct: 63  LHEFSAVEGVVEDVSELILNLKMVRFKKIAETADNKINISLKNTKEFKAGDINKFTTAFE 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +LNPD +IC++D      +ELT+ KG GYV ++ +   +     I ID++++PIK V Y+
Sbjct: 123 ILNPDLLICHMDESINFEIELTIEKGRGYVSSEENTLVDQVADYIAIDSIFTPIKNVKYS 182

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP----KKEVK 242
           VE+ R  Q  DY++L + I+TDGSI  E ++  A+ IL     +F +          +  
Sbjct: 183 VENTRVEQKTDYEQLVLDIETDGSIHPEVALKGAANILIKHFMLFSDQNMVLDAGGSDEP 242

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           E ++ + L     L   + +L+LSVR+ NCL+  ++  +GDL+    +DM++  NFG+KS
Sbjct: 243 EAVDEEMLHMRKLLKTALNDLDLSVRAYNCLKAADVKTLGDLVALEISDMMKFRNFGKKS 302

Query: 303 LVEIKGVLGTMGLFLGMNLPDW 324
           L E++ ++   GL  GM+L  +
Sbjct: 303 LAELEQLVADKGLTFGMDLSKY 324


>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 =  307 bits (786), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 108/327 (33%), Positives = 181/327 (55%), 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 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           ++ R GQ  DY+++ M +DT+G +  + +VA A+R+L+    + +   +     +     
Sbjct: 192 QAERVGQRTDYERIVMDVDTNGVVKPDLAVAEAARLLRKYFTIVVEEIQKLHPSEHTDPE 251

Query: 248 KSLPFNPAL-----------------LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
                  ++                  + 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|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 =  306 bits (785), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 119/323 (36%), Positives = 190/323 (58%), Gaps = 9/323 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
              P  I    + Q +E   +   +PL RG+  T+GNALRRV++SSL G AIT+++I G+
Sbjct: 6   FQIPGKI---SVKQADEFHGIFTFKPLERGYGVTIGNALRRVILSSLEGYAITSIRIPGI 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR-VTIFKRGPGVVTAGDI-QTVNDIE 126
            HE S+I+GV EDL +IILN+K I  K  GD+ +  + I      ++TAGD  Q     E
Sbjct: 63  YHEFSTIEGVTEDLVEIILNLKQIRFKKIGDTTENKIFISINNKKILTAGDFAQATAAFE 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           + NP+ VIC++D  A   +E+TV KG GYVPA+ ++ +    G+I ID++++P+K V Y 
Sbjct: 123 ITNPELVICHIDESARFEIEVTVEKGRGYVPAEENKIDAQVKGVIPIDSIFTPVKNVKYH 182

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI----NFEEPKKEVK 242
           VE+ R GQ  DY+ L  +++TDG+I  + ++  A+ I+     + I      E    +  
Sbjct: 183 VENTRVGQKTDYESLVFSVETDGTIHPQTAIERAADIMIKHFALLIDRNKMVETKDADEI 242

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           + ++  +L     L   + E+ LSVR+ NCL+  +I  +GDL+Q   +DM +  NFG+KS
Sbjct: 243 DVLDESTLQMRKLLKTPLSEMGLSVRAFNCLKAADIKTLGDLVQLKVSDMAQFRNFGKKS 302

Query: 303 LVEIKGVLGTMGLFLGMNLPDWP 325
           L E++ ++ +  L  GM+L  + 
Sbjct: 303 LKELQDLVASKDLTFGMDLSAYN 325


>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 =  306 bits (785), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 120/323 (37%), Positives = 192/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +  +    +          PL  GF  T+GNALRR+L+SSL G AIT ++IDGV
Sbjct: 6   FQKPDKVLMLEADSK---FGKFEFRPLEPGFGITVGNALRRILLSSLEGFAITTIKIDGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLTELDDLLESLNLSFGTDISKY 325


>gi|328813991|gb|AEB52111.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 269

 Score =  306 bits (785), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 124/269 (46%), Positives = 177/269 (65%), 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 VRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 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|328813951|gb|AEB52091.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 260

 Score =  306 bits (785), Expect = 3e-81,   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|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 =  306 bits (784), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 119/323 (36%), Positives = 192/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +  +    +          PL  GF  T+GNALRR+L+SSL G AIT ++I+GV
Sbjct: 6   FQKPDKVLMLEADSK---FGKFEFRPLEPGFGITVGNALRRILLSSLEGFAITTIKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLTELDDLLESLNLSFGTDISKY 325


>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 =  306 bits (784), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 124/325 (38%), Positives = 195/325 (60%), Gaps = 12/325 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  ++       PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---VMLEANDHFGKFEFRPLEPGFGVTIGNALRRILLSSLEGFAINTIRIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 RKSLVEIKGVLGTMGLFLGMNLPDW 324
           +KSL E+  +L ++ L  G ++  +
Sbjct: 303 KKSLSELDDLLESLNLSFGTDITKY 327


>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 =  306 bits (784), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 118/323 (36%), Positives = 193/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AIT ++I+GV
Sbjct: 6   FQKPDKV---LMLEADSRFGKFEFRPLEPGFGITVGNALRRILLSSLEGFAITTIKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLTELDDLLESLNLSFGTDISKY 325


>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 =  306 bits (784), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 119/323 (36%), Positives = 193/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AIT ++IDGV
Sbjct: 6   FQKPDKV---LMLEADSRFGKFEFRPLEPGFGITVGNALRRILLSSLEGFAITTIKIDGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLTELDDLLESLNLSFGTDISKY 325


>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 =  306 bits (784), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 120/323 (37%), Positives = 194/323 (60%), Gaps = 10/323 (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  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G +   +
Sbjct: 303 SLSELDDLLESLNLSFGTDTSKY 325


>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 =  306 bits (784), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 119/323 (36%), Positives = 192/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +  +    +          PL  GF  T+GNALRR+L+SSL G AIT ++I+GV
Sbjct: 6   FQKPDKVLMLEADSK---FGKFEFRPLEPGFGITVGNALRRILLSSLEGFAITTIKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLTELDDLLESLNLSFGTDISKY 325


>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 =  306 bits (784), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 127/330 (38%), Positives = 191/330 (57%), Gaps = 13/330 (3%)

Query: 1   MIQKNW-QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           M +KN  +   +P  I        + +     A P  RGF  T+GN LRR+L+SS++G A
Sbjct: 1   MARKNLMKGFKRPKGI-IFEHSDVKPDYGKFTAYPFERGFGTTIGNTLRRILLSSIQGYA 59

Query: 60  ITAVQI-----DGVLH----EISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKR 109
           ITAV+      DGV H    E  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 ADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
            ++ +  NFG+KSL EIK  L    L LGM
Sbjct: 299 EEIAKTRNFGKKSLSEIKAKLAEWNLSLGM 328


>gi|313158337|gb|EFR57739.1| DNA-directed RNA polymerase, alpha subunit [Alistipes sp. HGB5]
          Length = 330

 Score =  306 bits (784), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 116/321 (36%), Positives = 185/321 (57%), Gaps = 10/321 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP  +   ++ +   +       PL  GF  T+GNALRR+L+SSL G AIT V++ GV
Sbjct: 6   FQKPEKV---IMLESTSSFGKFEFRPLEPGFGMTVGNALRRILLSSLEGYAITTVKVAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQT-VNDI 125
            HE ++I GV ED+  IILN+K +    + D+   ++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 SLVEIKGVLGTMGLFLGMNLP 322
           SL E+  +L ++ L  GM++ 
Sbjct: 303 SLTELDELLTSLNLKFGMDVS 323


>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 =  306 bits (784), Expect = 4e-81,   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   TDLLRPNIKEVVTL---SRNVSRVILEPFEQHYAQVLGTALRRIMLSSIPGYAITEVEID 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+       +GQ    ++L + I+T+G+I   D+V  A+ I  DQL  F++      
Sbjct: 182 VLNVAVHTAPLNDGQ----EQLILDIETNGTIDPSDAVCSAATIFADQLNSFVDIRNSVA 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
              +         +P LL  VE+LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G
Sbjct: 238 PADD--ASFKPLIDPKLLCPVEDLELTVRSANCLKAEGIKYIGDLVQRTEVELLKTPNLG 295

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIE 330
           +KSL EIK VL   GL LGM L +WPP  +E
Sbjct: 296 KKSLTEIKDVLAERGLSLGMRLENWPPADLE 326


>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 =  306 bits (783), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 124/325 (38%), Positives = 195/325 (60%), Gaps = 12/325 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  ++       PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---VMLETNDHFGKFEFRPLEPGFGVTIGNALRRILLSSLEGFAINTIRIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 RKSLVEIKGVLGTMGLFLGMNLPDW 324
           +KSL E+  +L ++ L  G ++  +
Sbjct: 303 KKSLSELDDLLESLNLSFGTDITKY 327


>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 =  306 bits (783), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 119/323 (36%), Positives = 192/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +  +    +          PL  GF  T+GNALRR+L+SSL G AI  ++I+GV
Sbjct: 6   FQKPDKVLMLEADSK---FGKFEFRPLEPGFGITVGNALRRILLSSLEGYAINTIRIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLTELDDLLESLNLSFGTDISKY 325


>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 =  306 bits (783), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 114/315 (36%), Positives = 176/315 (55%), 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-VDAVVRMELTVSKGHGYVPAK--HHRTENDPIGLITIDALYSPIKKVS 184
           L PD  I  LD  ++ + + L + KG G+V ++      +   IG I +DA +SPIKKV+
Sbjct: 120 LTPDQEIATLDNENSEIEIYLRIDKGKGFVLSEDIQEIFDISTIGWIPLDADFSPIKKVA 179

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK-EVKE 243
           + VE  R G+  DY++L+M I TDGSIT +D+V  A+ IL +   M  +          +
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|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 =  306 bits (783), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 120/321 (37%), Positives = 181/321 (56%), 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  VLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDI 125
           V HE S+I+GV ED+T+I+LN+K + LK   +     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 EVVNPEHVIATLDNDDARLEMDLVIARGRGYQPA--ETQEIYTIGEIPVDAIFTPIEKVN 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|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 =  305 bits (782), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 110/301 (36%), Positives = 170/301 (56%), Gaps = 4/301 (1%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            I + +  E+      EPL  G+ HTLGNALRRVL++++ G+AIT V++ GV  E   I 
Sbjct: 8   KIEVVEATESFGRFKIEPLDPGYGHTLGNALRRVLLTAIPGSAITHVRVTGVYQETDRIP 67

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+ ++ILN+KGI+L+   +     TI K+GPGVVTA D+     + V++PDH IC 
Sbjct: 68  GVTEDMVELILNLKGIHLRGHHEGTVTATIRKQGPGVVTAADLVLPEGLAVVDPDHYICT 127

Query: 137 LD-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
           L+   A + +  T+ +G GY+ A        P+G I IDA+++P+ +V+Y VE+ R GQ 
Sbjct: 128 LEHEQAQIELTATIERGRGYLSADQRG--ILPLGEIPIDAIFTPVPRVNYIVENTRIGQA 185

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP-FNP 254
            D+D+L + + T+G++   D++  A+R+L        NF     E +       L     
Sbjct: 186 TDFDRLILEVWTNGTVRPVDALDYAARVLVHYNTTIANFNRMAVEPEAQPETTGLEIPPS 245

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +E LELS R+ NCL+   I  +G ++Q  E  +L + N G+KS+ EI+  L   G
Sbjct: 246 VYDTSIETLELSTRTYNCLKRAEITKIGQVLQMDEKALLSVRNLGQKSMEEIRDKLIERG 305

Query: 315 L 315
            
Sbjct: 306 Y 306


>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 =  305 bits (782), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 124/325 (38%), Positives = 195/325 (60%), Gaps = 12/325 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  ++       PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---VMLEANDHFGKFEFRPLEPGFGVTIGNALRRILLSSLEGFAINTIRIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 RKSLVEIKGVLGTMGLFLGMNLPDW 324
           +KSL E+  +L ++ L  G ++  +
Sbjct: 303 KKSLSELDDLLESLNLSFGTDITKY 327


>gi|328813947|gb|AEB52089.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 267

 Score =  305 bits (782), Expect = 5e-81,   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|328813955|gb|AEB52093.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 261

 Score =  305 bits (782), Expect = 5e-81,   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|58416044|emb|CAH57436.1| RNA polymerase alpha-subunit [Vibrio sp. R-21433]
          Length = 294

 Score =  305 bits (782), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 127/300 (42%), Positives = 194/300 (64%), Gaps = 11/300 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQISS---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 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294


>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 =  305 bits (782), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 126/289 (43%), Positives = 193/289 (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++  + +   +++   +  P    LL+
Sbjct: 182 DKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLR 238

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK
Sbjct: 239 PVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIK 287


>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 =  305 bits (782), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 98/305 (32%), Positives = 164/305 (53%), Gaps = 9/305 (2%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +          I EPL  G   T+GN+LRRVL+S + G+AITAV+I GV HE  SI GV
Sbjct: 12  KVESSCNQYGRFIVEPLEPGQGITIGNSLRRVLLSDIEGSAITAVRIAGVNHEFCSIPGV 71

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+ +++LN+K I LK   +  +   +  +G   VT  + +  +++E+++    +  + 
Sbjct: 72  KEDVLELLLNLKNIVLKSYTNEPQIGRLKIQGACKVTTANFELPSEVEIIHGTQYVATVA 131

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            +A++ ME  + KG GY      +TEN  I  + IDA++ P++KV+Y VE          
Sbjct: 132 ENAILEMEFKIEKGRGYKIIDKKQTENS-IDFLPIDAIFMPVRKVNYMVEEIFLRNSEIK 190

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           ++L + I  +GS+T +DS++ A+ +L +    F      K   +   +      +     
Sbjct: 191 ERLILEIWRNGSVTPQDSISQAAEVLLNLFNPF-----KKINFENTDDSTEQTEDKISQI 245

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +EEL+LSVR+ NCL+   I  +GDL+  ++ ++L + NFG+KS  E+   L      LG
Sbjct: 246 PIEELQLSVRAYNCLKRAQIHSIGDLLNVSQEELLEIRNFGQKSAKEVIDAL---QKRLG 302

Query: 319 MNLPD 323
           ++LP 
Sbjct: 303 ISLPK 307


>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 =  305 bits (781), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 127/300 (42%), Positives = 195/300 (65%), Gaps = 11/300 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQISS---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 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHNEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   ++
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294


>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 =  305 bits (781), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 129/323 (39%), Positives = 199/323 (61%), Gaps = 10/323 (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 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL EI+ ++ + GL  GMNL  +
Sbjct: 303 SLTEIQELVKSKGLSFGMNLSKY 325


>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 =  305 bits (781), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 127/323 (39%), Positives = 199/323 (61%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +P+ +   ++ +  +        PL  GF  T+GNALRR+L+SSL G AIT+++  GV
Sbjct: 6   FQRPDKV---IMQKSTDFDGTFEFRPLEPGFGVTIGNALRRILLSSLEGYAITSIRFSGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDI-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 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL EI+ ++ + GL  GMNL  +
Sbjct: 303 SLSEIQELVKSKGLSFGMNLSKF 325


>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 =  305 bits (781), Expect = 7e-81,   Method: Composition-based stats.
 Identities = 122/323 (37%), Positives = 190/323 (58%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ +  +        PL  G+  T+GNALRRV++SSL G AIT+V+ D V
Sbjct: 6   FQKPDKV---IMIESSDFEGRFEFRPLEPGYGLTIGNALRRVMLSSLEGFAITSVKFDKV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQ-TVNDI 125
            HE S+I GV ED+T+IILN+K I  K   +   ++  TI   G   +TAGD Q  ++  
Sbjct: 63  GHEFSTISGVREDVTEIILNLKQIRFKRQIEDIENETATITVSGKRQLTAGDFQKALSGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLN D VICN+D  A   +E+T+ KG GYV A+ +   N PIG+I  DA+++PIK V Y
Sbjct: 123 QVLNTDLVICNMDSSASFTIEITIEKGRGYVSAEENAKPNAPIGVIATDAIFTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL   I TDGSI  + ++  A++ L     +F    I  E  +   
Sbjct: 183 SIENYRVEQKTDYEKLVFEIKTDGSIHPKQALTEAAKTLIHHFMLFSDERITLEADEIAQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            +  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   +AD+++  NFG+K
Sbjct: 243 TDTYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVETLGDLVSFNKADLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL+E++ ++   GL  GM+   +
Sbjct: 303 SLIELEELVVNKGLVFGMDTSKY 325


>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 =  305 bits (781), Expect = 7e-81,   Method: Composition-based stats.
 Identities = 112/313 (35%), Positives = 188/313 (60%), Gaps = 6/313 (1%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
            NI+ + + +E EN       PL RG+  T+GN++RRVL+SSL G++++ + I+GVLHE 
Sbjct: 7   TNIQILDIDEE-ENYGKFALYPLERGYGTTIGNSMRRVLLSSLPGSSVSKILIEGVLHEF 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           S+I GV ED+ +I+LNIKG+++    D    + +   GP +VTA DI+  + +++ NPDH
Sbjct: 66  STIDGVVEDVPEIVLNIKGLDVTKHVDEDVTLFLDIEGPKIVTAKDIKADSSVDIANPDH 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  ++  + + + + V+ G GY  +  ++ E+DPIG I ID+ ++P++KV++TVE+ R 
Sbjct: 126 YIATVNEKSRLFIAMDVTDGKGYRVSDDNKKESDPIGAIAIDSSFTPVEKVNFTVENTRV 185

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           G+  DYDKL M + T+G+IT ++++A  S IL +    F      +   + +        
Sbjct: 186 GESTDYDKLVMEVWTNGTITPQEALAEGSSILIENFSFFNELPNQQFPPEVEEEEIEEVE 245

Query: 253 NPALL-----KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
               L       +EEL+LS+RS NCL+      +GD+I+ +E+++  + NFG+KSL E+ 
Sbjct: 246 EEDSLSEDLAMTIEELDLSLRSFNCLKRAGFDRVGDIIKVSESELKTIKNFGKKSLTEVI 305

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L   
Sbjct: 306 EKLDELGLSLKDE 318


>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 =  305 bits (781), Expect = 7e-81,   Method: Composition-based stats.
 Identities = 122/323 (37%), Positives = 194/323 (60%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + ++        PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---LMLEADDKYGKFEFRPLEPGFGITVGNALRRILLSSLEGYAINTMRIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLTELDDLLESLNLSFGTDISKY 325


>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 =  304 bits (780), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 128/323 (39%), Positives = 199/323 (61%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +P+ +   ++ +  +        PL  GF  T+GNALRR+L+SSL G AIT+++  GV
Sbjct: 6   FQRPDKV---IMQKSTDFDGTFEFRPLEPGFGVTIGNALRRILLSSLEGYAITSIRFSGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDI-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 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL EI+ ++ + GL  GMNL  +
Sbjct: 303 SLSEIQELVKSKGLSFGMNLSKF 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 =  304 bits (780), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 122/323 (37%), Positives = 189/323 (58%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ +  +        PL  G+  T+GNALRRV++SSL G AIT+V+ D V
Sbjct: 6   FQKPDKV---IMIESSDFEGRFEFRPLEPGYGLTIGNALRRVMLSSLEGFAITSVKFDKV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQ-TVNDI 125
            HE S+I GV ED+T+IILN+K I  K   +   ++  TI   G   +TAGD Q  ++  
Sbjct: 63  GHEFSTISGVREDVTEIILNLKQIRFKRQIEDIENETATITVSGKRQLTAGDFQKALSGF 122

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +VLN D VICN+D  A   +E+T+ KG GYV A+ +   N PIG+I  DA+++PIK V Y
Sbjct: 123 QVLNTDLVICNMDSSASFTIEVTIEKGRGYVSAEENAKPNAPIGVIATDAIFTPIKNVKY 182

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           ++E+ R  Q  DY+KL   I TDGSI  + ++  A++ L     +F    I  E  +   
Sbjct: 183 SIENYRVEQKTDYEKLVFEIKTDGSIHPKQALTEAAKTLIHHFMLFSDERITLEADEIAQ 242

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            +  + +SL     L  K+ +++LSVR+ NCL+   +  +GDL+   +AD+++  NFG+K
Sbjct: 243 TDTYDEESLHMRQLLKTKLVDMDLSVRALNCLKAAEVETLGDLVSFNKADLMKFRNFGKK 302

Query: 302 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL+E+  ++   GL  GM+   +
Sbjct: 303 SLIELDELVVNKGLVFGMDTSKY 325


>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 =  304 bits (779), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 119/323 (36%), Positives = 193/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AI  ++I+GV
Sbjct: 6   FQKPDKV---LMLEADSRFGKFEFRPLEPGFGITVGNALRRILLSSLEGFAINTIKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L  + L  G ++  +
Sbjct: 303 SLTELDDLLEGLNLSFGTDISKY 325


>gi|58415944|emb|CAH57386.1| RNA polymerase alpha-subunit [Vibrio mytili]
          Length = 294

 Score =  304 bits (779), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 126/300 (42%), Positives = 194/300 (64%), Gaps = 11/300 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQISS---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 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 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 294


>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 =  304 bits (779), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 128/323 (39%), Positives = 198/323 (61%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ +  +        PL  GF  T+GNALRR+L+SSL G AIT+V+  GV
Sbjct: 6   FQKPDKV---IMQKSTDFDGTFEFRPLEPGFGVTIGNALRRILLSSLEGYAITSVRFSGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVN-DI 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 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           T+E+ R  Q  DY+KL + I TDGSI  ED++  A++IL     +F    I  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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL EI+ ++ + GL  GMNL  +
Sbjct: 303 SLTEIQELVKSKGLSFGMNLSKY 325


>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 =  304 bits (779), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 112/304 (36%), Positives = 174/304 (57%), Gaps = 6/304 (1%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            +    E  N    I  PL  G+  TLGNALRRVL+SSL GAA+T+++I  VLHE S I 
Sbjct: 11  KVEREAEARNYGKFIIGPLEGGYGVTLGNALRRVLLSSLEGAAVTSIRISDVLHEFSDIP 70

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+  ++LNIK + L +       + +  RG G VTA DIQ   ++E++NP+  +  
Sbjct: 71  GVREDVIQVMLNIKQLRLILHDVETTHMHLEVRGEGTVTAADIQAPAEVEIVNPELELFT 130

Query: 137 LDV-DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
           +D  +  + ++ TVS+G GY PA        PIG + +DA++SP+K+V+++V +AR GQ 
Sbjct: 131 VDDPNTRLEIDFTVSRGRGYSPASERSGR-LPIGELPVDAIFSPVKRVNWSVTAARVGQS 189

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP-FNP 254
            +YD+L + I TDG+IT E++++ +++IL D L            V  +  V      + 
Sbjct: 190 TNYDRLILEIWTDGTITPENALSTSAKILIDHLRYITGVSAESLAVTVEKEVAGGRLTSE 249

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGD---LIQRTEADMLRMANFGRKSLVEIKGVLG 311
           A    +E L+LSVR  N L+   I  +GD   L+++ E  ++ + NFG KSL E++  + 
Sbjct: 250 AAETPIENLDLSVRVFNSLKRTGITTVGDVLELLEKGEDAVMSIRNFGEKSLDELRQKMR 309

Query: 312 TMGL 315
             G 
Sbjct: 310 EKGF 313


>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 =  304 bits (779), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 120/348 (34%), Positives = 190/348 (54%), Gaps = 12/348 (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-----DGVLH----EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIF-KR 109
           I+AV+I     D V H    E  +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 337
            ++ +  N G+KSL EI+  L    L LGM        SI+   +K E
Sbjct: 300 DEISKTRNVGKKSLQEIQEKLAERNLSLGMTDYSHLKNSIKLSRQKEE 347


>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 =  304 bits (778), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 124/323 (38%), Positives = 192/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  +        PL  GF  T+GNALRR+L+SSL G AI  ++I  V
Sbjct: 6   FQKPDKV---VMLEANDKFGKFEFRPLEPGFGVTIGNALRRILLSSLEGYAINTMRIGSV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           TVE  R  Q  DYDKL + +DTDGSI  +D++  A++IL     +F    I  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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLSELDDLLESLNLTFGTDISKY 325


>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 =  304 bits (778), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 122/325 (37%), Positives = 192/325 (59%), Gaps = 12/325 (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  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
            VE  R  Q  DYDKL + + TDGSI  +D++  A++IL     +F    I  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 RKSLVEIKGVLGTMGLFLGMNLPDW 324
           +KSL E+  +L ++ L  G ++  +
Sbjct: 303 KKSLSELDDLLESLNLTFGTDITKY 327


>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 =  304 bits (778), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 107/301 (35%), Positives = 167/301 (55%), Gaps = 4/301 (1%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            I + +  E       EPL  G+ HTLGNALRRVL++++ G+AIT V+I GV  E   I 
Sbjct: 8   KIEVVEATETFGRFKIEPLDPGYGHTLGNALRRVLLTAIPGSAITHVRIAGVYQETDVIP 67

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           G+ ED+ ++ILN+KGI+L+   +   + TI K+GP +VTA D+     + V++P H IC 
Sbjct: 68  GMTEDVVELILNLKGIHLRGRHEGTVQATIQKQGPAIVTAADLMLPEGLSVVDPTHYICT 127

Query: 137 LDVD-AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
           L+ D A + +  T+  G GY+ A        P+G   IDA+++P+ +V+Y VE+ R GQ 
Sbjct: 128 LEHDQARIEITATIEHGRGYLSADQRG--ILPLGEFPIDAIFTPVPRVNYVVENTRIGQA 185

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP-FNP 254
            DYD+L + + T+G+I  ++++  A+R+L        NF     E         L     
Sbjct: 186 TDYDRLILEVWTNGTIRAQEALDYAARVLVHYYTTIANFNRLMVEPAAQPETNGLEIPAH 245

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
                +E L+LS R+ NCL+   I  +G ++Q  E  +L + N G+KS+ EI+  L   G
Sbjct: 246 VYDTSIETLDLSTRTYNCLKRAEITKIGQVLQMDEKALLSVRNLGQKSMEEIRDKLIERG 305

Query: 315 L 315
            
Sbjct: 306 Y 306


>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 =  303 bits (777), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 118/323 (36%), Positives = 191/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +  +    +          PL  GF  T+GNALRR+L+SSL G AI  + I+GV
Sbjct: 6   FQKPDKVLMLEADSK---FGKFEFRPLEPGFGITVGNALRRILLSSLEGYAINTIHIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLTELDDLLESLNLSFGTDISKY 325


>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 =  303 bits (777), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 119/323 (36%), Positives = 190/323 (58%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +  +    +          PL  GF  T+GNALRR+L+SSL G AI  + IDGV
Sbjct: 6   FQKPDKVLMLEADSK---FGKFEFRPLEPGFGITVGNALRRILLSSLEGYAINTIHIDGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLTELDDLLESLNLSFGTDISKY 325


>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 (777), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 117/310 (37%), Positives = 193/310 (62%), 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 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF-----INFEEPKKEVKEDINV 247
           G+  DYDKL + + TDG+IT +++++  + IL + +  F       F    +E + +   
Sbjct: 186 GESTDYDKLILEVWTDGTITPQEALSEGASILMEDIRFFKDLPGQQFPPEVEEEEVEEIE 245

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           +       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|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 =  303 bits (777), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 126/299 (42%), Positives = 194/299 (64%), Gaps = 11/299 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVDIEQISS---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 ANPEHVICHLTDDNAEIAMRIKVERGRGYVPASARIHNEEDERPIGRLLVDATYSPVDKI 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           +Y VE+AR  Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   ++
Sbjct: 178 AYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KS
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKS 293


>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 =  303 bits (776), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 120/320 (37%), Positives = 173/320 (54%), Gaps = 7/320 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            +  + + P  I +     + +    +  EPL RGF  T+GNALRRVL+SSL G AITAV
Sbjct: 1   MSLLDFVMPTKIYWDEA-TKTDTYGKLYVEPLERGFGITIGNALRRVLLSSLPGGAITAV 59

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTV 122
           +I GV HE ++IKGV ED+ +I+LN+K I LK+  +  +    +     G V A DI+  
Sbjct: 60  KIMGVPHEFTTIKGVIEDVAEIVLNLKQIRLKIDENIERDFAILEAENVGKVYAKDIKFP 119

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
             IE++ PD  IC +     ++ME  V +G GY   +        IG I ID  +SPIK+
Sbjct: 120 AGIELVTPDVHICTISEPTKLQMEFRVERGIGYKTVEELEP-ISEIGWIIIDTAFSPIKR 178

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V++ VE  R G   DYDKL + I+TDG+IT ++++  AS IL D   +       K +V 
Sbjct: 179 VAFNVEPTRVGDKTDYDKLILEIETDGTITPDEALTKASNILIDHFNILQKPTVKKVQVI 238

Query: 243 EDINVKSLPFNPALLKK----VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +               K    ++ELE+S R+ N LR   I  +GDL++ +E D+    + 
Sbjct: 239 KKTVAPKPEEIKIEEDKLSLSIDELEISSRAINNLRKLGINTIGDLVRLSEEDLKEAKSI 298

Query: 299 GRKSLVEIKGVLGTMGLFLG 318
           GRKS+ EIK  L  MGL L 
Sbjct: 299 GRKSIKEIKDALAEMGLELA 318


>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 =  303 bits (776), Expect = 3e-80,   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  LTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDI-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|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 =  303 bits (776), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 118/323 (36%), Positives = 191/323 (59%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +  +    +          PL  GF  T+GNALRR+L+SSL G AI  + I+GV
Sbjct: 6   FQKPDKVLMLEADSK---FGKFEFRPLEPGFGITVGNALRRILLSSLEGYAINTIHIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLTELDDLLESLNLSFGTDISKY 325


>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 =  303 bits (776), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 121/320 (37%), Positives = 173/320 (54%), Gaps = 7/320 (2%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            +  + + P  I +     + +    +  EPL RGF  T+GNALRRVL+SSL G AITAV
Sbjct: 1   MSLLDFVMPTKIYWDEA-TKTDTYGKLYVEPLERGFGITIGNALRRVLLSSLPGGAITAV 59

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTV 122
           +I GV HE ++IKGV ED+ +I+LN+K I LK+  +  +    +     G V A DI+  
Sbjct: 60  KIMGVPHEFTTIKGVLEDVVEIVLNLKQIRLKIDENIERDFAILEAENVGKVYAKDIKFP 119

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
             IE++ PD  IC +     ++ME  V +G GY   +        IG I ID  +SPI+K
Sbjct: 120 AGIELVTPDVHICTISEPTKLQMEFRVERGIGYKTVEELEP-ISEIGWIIIDTAFSPIRK 178

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V++ VE  R G   DYDKL + I+TDG+IT ++++  AS IL D   +       K +V 
Sbjct: 179 VAFNVEPTRVGDKTDYDKLILEIETDGTITPDEALTKASNILIDHFNILQKPTVKKVQVI 238

Query: 243 EDINVKSLPFNPALLKK----VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           +               K    ++ELE+S R+ N LR   I  +GDL++ +E D+    + 
Sbjct: 239 KKTVAPKSEEIKIEEDKLSLSIDELEISSRAINTLRKLGINTIGDLVRLSEEDLREAKSI 298

Query: 299 GRKSLVEIKGVLGTMGLFLG 318
           GRKSL EIK  L  MGL L 
Sbjct: 299 GRKSLKEIKDALAEMGLELA 318


>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 =  303 bits (776), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 118/314 (37%), Positives = 189/314 (60%), Gaps = 11/314 (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  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR---VTIFKRGPGVVTAGDIQTVND 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 IYSVEKTRG----DLDELTIEIETNGAILAKEALALASKMLVDHFQVLVDISEKASEFDF 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             +++  P +     K+E+L+LSVR  N L+   I  +G+L++ +E +++R+ + GRKS 
Sbjct: 238 IRDIEEEPASKKSDTKIEQLDLSVRLFNSLKRSGITTVGELLKLSEEEVMRLRSLGRKSF 297

Query: 304 VEIKGVLGTMGLFL 317
            E+K  L   GL  
Sbjct: 298 KELKEKLAEHGLEF 311


>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 =  303 bits (776), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 112/346 (32%), Positives = 188/346 (54%), Gaps = 26/346 (7%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            E+++P     I + +       ++  PL RG+  T+GNALRRVL+SS++GAAI+AV+++
Sbjct: 1   MEIMRPE----IQVEECSSTAARLVIGPLERGYGQTIGNALRRVLLSSIKGAAISAVRVE 56

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
           G  HE ++I G+ ED+ +++LN+K + ++     ++ + +   G   VTA D Q  +DIE
Sbjct: 57  GAQHEFTTIPGMKEDVIELLLNLKHVPVRSHSAEYRTLKLDVEGGKKVTAADFQEDSDIE 116

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
            ++PD  IC L     + +E+ + +G GY      R    P+  + IDA+YSPI +V Y 
Sbjct: 117 FIDPDAYICTLAEGHSLSLEVYIEQGVGYATVDRPRPSYLPVDALMIDAIYSPILRVKYE 176

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF------------ 234
           V++ R GQ  DY+K+ M + T+G +  + +VA A+++L++   + I              
Sbjct: 177 VQNERVGQKTDYEKIVMNVTTNGVVAPDIAVAEAAKLLREYFDIVIQELRKLHPAEPGLF 236

Query: 235 -----EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
                 +P    +      + P N  L K V ELELS+RS NCL    I  +GDL+ R++
Sbjct: 237 DDESASQPSGNGQAGDGADNPPENALLNKPVRELELSIRSENCLLRGGIHTIGDLVSRSK 296

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
            D+L++ N G+ SL EI+  +   G+ L  +       S E  +K+
Sbjct: 297 DDLLKIRNLGKISLREIEEKMTKYGIVLSDD-----KASAENSSKE 337


>gi|157493247|gb|ABV57989.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 286

 Score =  303 bits (775), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 125/288 (43%), Positives = 192/288 (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++  + +   +++   +  P    LL+
Sbjct: 182 DKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLR 238

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EI
Sbjct: 239 PVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEI 286


>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 = 119/313 (38%), Positives = 196/313 (62%), Gaps = 6/313 (1%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
            NI+ + +  EEE+       PL RG+  T+GN++RRVL+SSL G++++ + I+GVLHE 
Sbjct: 7   TNIQILDI-NEEEHYGKFALYPLERGYGTTIGNSMRRVLLSSLPGSSVSKILIEGVLHEF 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|260656836|gb|ACX47808.1| RNA polymerase alpha-subunit [Vibrio casei]
          Length = 295

 Score =  303 bits (775), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 129/298 (43%), Positives = 193/298 (64%), Gaps = 8/298 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +
Sbjct: 1   LVDIEQISTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKE 60

Query: 77  GVHEDLTDIILNIKGINL-KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
           GV ED+ +I+LN+KG+ +    G     +T+ K G G V AGDI    D+E+ NP+HVIC
Sbjct: 61  GVQEDILEILLNLKGLAVSVAEGKDEVFITLKKSGSGPVVAGDIIHDGDVEIANPEHVIC 120

Query: 136 NLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
           +L  D A + M + V +G GYVP+    H   +  PIG + +DA YSP+ K++Y VE+AR
Sbjct: 121 HLTDDKAEIAMRIKVQRGRGYVPSSARIHTEEDERPIGRLLVDATYSPVDKIAYAVEAAR 180

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
             Q  D DKL + ++T+G++  E+++  A+ IL +QL  F++  + +   +++   +  P
Sbjct: 181 VEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP 240

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
               LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK V
Sbjct: 241 ---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDV 295


>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 =  303 bits (775), Expect = 4e-80,   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|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 =  302 bits (774), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 114/321 (35%), Positives = 185/321 (57%), Gaps = 10/321 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP  +   ++ +   +       PL  GF  T+GNALRR+L+SSL G AIT V++ GV
Sbjct: 6   FQKPEKV---IMLESTSSFGKFEFRPLEPGFGMTVGNALRRILLSSLEGYAITTVKVAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQT-VNDI 125
            HE ++I GV E + DIILN+K +    + D+   ++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 SLVEIKGVLGTMGLFLGMNLP 322
           SL E+  +L ++ L  GM++ 
Sbjct: 303 SLTELDELLASLNLKFGMDVS 323


>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 =  302 bits (773), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 114/316 (36%), 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 +     +EV  D   
Sbjct: 184 ENTRVEQTLNYDKLIIEIWTDGSVSPKDALMRSAEILRKILVIFTDNAFKTEEVSADKE- 242

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                +  L K V  +++SV++   L+   I  + DL++  E D+L   N  ++S  EIK
Sbjct: 243 ---EQDGILGKPVSIMDISVKTLKSLKSAGIETVEDLVKIKEEDLLNFNNLSKRSCEEIK 299

Query: 308 GVLGTMGLFLGMNLPD 323
             +  +GL LGM + D
Sbjct: 300 NRVKELGLSLGMKIED 315


>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 =  302 bits (773), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 120/327 (36%), Positives = 182/327 (55%), Gaps = 13/327 (3%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           + +L+ P  I+             +IAEP   G+ HT+GN+LRR+L+S L G+A+TAV++
Sbjct: 3   FNQLVLPTKIQLDE-KTVTPFYGRIIAEPYESGYGHTVGNSLRRILLSGLDGSAVTAVRV 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 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE AR GQ  DYD+L + I TDG++    ++  A+ +L   L +F    E       + 
Sbjct: 182 DVEPARVGQKTDYDRLVIQITTDGTLEPAKALHKAAVLLSQSLHIFTIEGEEVNAAAPET 241

Query: 246 NV------------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                          +      L + VE +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|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 =  302 bits (773), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 122/325 (37%), Positives = 190/325 (58%), Gaps = 12/325 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   V+ +  +        PL  GF  T+GNALRR+L+SSL G AI  ++I GV
Sbjct: 6   FQKPDKV---VMLEANDTFGKFEFRPLEPGFGVTIGNALRRILLSSLEGFAINTIRIAGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQT-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 RKSLVEIKGVLGTMGLFLGMNLPDW 324
           +KSL E+  +L  + L  G ++  +
Sbjct: 303 KKSLSELDDLLEGLNLSFGTDITKY 327


>gi|291514968|emb|CBK64178.1| DNA-directed RNA polymerase subunit alpha [Alistipes shahii WAL
           8301]
          Length = 317

 Score =  301 bits (772), Expect = 8e-80,   Method: Composition-based stats.
 Identities = 114/308 (37%), Positives = 181/308 (58%), Gaps = 7/308 (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  LTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLD 138
           + +IILN+K +    + D+   ++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 LFLGMNLP 322
           L  GM++ 
Sbjct: 303 LKFGMDVS 310


>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 =  301 bits (771), Expect = 9e-80,   Method: Composition-based stats.
 Identities = 122/325 (37%), Positives = 191/325 (58%), Gaps = 12/325 (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  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQT-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 RKSLVEIKGVLGTMGLFLGMNLPDW 324
           +KSL E+  +L  + L  G ++  +
Sbjct: 303 KKSLSELDDLLEGLNLSFGTDITKY 327


>gi|157493243|gb|ABV57987.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 286

 Score =  301 bits (771), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 125/289 (43%), Positives = 192/289 (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++  + +   +++   +  P    L
Sbjct: 181 DLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---IL 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|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 =  301 bits (771), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 124/312 (39%), Positives = 177/312 (56%), 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  LTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 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 KLSMTIDTDGSITGEDSVALASRILQDQLGMFIN---------FEEPKKEVKEDINVKSL 250
           KL++ ++TDGSI   D+VA A+ IL +   +F            +      +        
Sbjct: 195 KLTLELETDGSIKASDAVATAATILMNCFELFRPLATGPILEARDGSDMARQSSDQQAEE 254

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 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|145577855|gb|ABP87378.1| RpoA [Vibrio sp. MSSRF10]
          Length = 286

 Score =  301 bits (771), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 128/287 (44%), Positives = 192/287 (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-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV-DA 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++  + +   +++   +  P    LL+
Sbjct: 183 DKLVIDMETNGTIEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLR 239

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 240 PVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 286


>gi|145577841|gb|ABP87371.1| RpoA [Vibrio rhizosphaerae]
 gi|162955840|gb|ABY25295.1| RNA polymerase alpha subunit [Vibrio sp. MSSRF6]
          Length = 286

 Score =  301 bits (771), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 130/289 (44%), Positives = 194/289 (67%), 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++  + +   +++   +  P    L
Sbjct: 181 DLDKLVIDMETNGTIEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---IL 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|328814021|gb|AEB52126.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
          Length = 262

 Score =  301 bits (770), Expect = 1e-79,   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|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 =  301 bits (770), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 124/287 (43%), Positives = 191/287 (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++  + +   +++   +  P    LL+
Sbjct: 182 DKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLR 238

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 239 PVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 285


>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 =  301 bits (770), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 124/285 (43%), Positives = 191/285 (67%), 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++  + +   +++   +  P    LL+ V
Sbjct: 182 LVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPV 238

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           ++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 239 DDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 283


>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 =  301 bits (770), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 118/320 (36%), Positives = 174/320 (54%), Gaps = 10/320 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            I P     I L    EN       PL RG   +LGNALRRVL+SS+ GAA+T +++ GV
Sbjct: 8   FITPR----ITLVAAAENYGRFAIAPLQRGHGSSLGNALRRVLLSSIPGAAVTRIKVSGV 63

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE SSI GV ED T ++LNIKGI L+   D    + + K+GPG V A DI   + +E++
Sbjct: 64  IHEFSSIPGVVEDGTQLVLNIKGIRLRSYSDRAVALQLIKQGPGPVFARDIDAPSTVEIV 123

Query: 129 NPDHVICNLDVD-AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           NP H IC +D +     M+LTV +G G   A        PIG I +DAL+SPI +V++ V
Sbjct: 124 NPQHYICTIDDEHTTFEMQLTVERGRGVQLADTVS--GMPIGEIAVDALFSPIPRVNFLV 181

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E   +  +  YD+L + I TDG+I   D+++ A++IL    G  +N  +P+ E +   ++
Sbjct: 182 EEMGDDPLTGYDRLILEIWTDGTIKPGDALSHAAQILAQYFGRIVNLNQPE-EPEPSAHL 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                     + ++EL LS R+ N LR   I  +G L++  +  ++ + N G K + EI 
Sbjct: 241 PPPIPEEIASRTIDELGLSTRTYNSLRRAEIHTIGQLLRLDDRGLMSIRNLGAKGIEEIH 300

Query: 308 GVLGTMGLFLG--MNLPDWP 325
             L  +G   G    LP  P
Sbjct: 301 QRLEALGYRSGSSSRLPAAP 320


>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 =  300 bits (769), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 99/305 (32%), Positives = 156/305 (51%), Gaps = 9/305 (2%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +     +    +  PL  G   T+GN  RRVL+  L GA IT+VQI GV HE S+I GV
Sbjct: 17  RIESRRNHYGRFVIAPLEIGQGITVGNVFRRVLLGDLEGACITSVQIPGVNHEFSTIHGV 76

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + DI+LN+K I LK      +R  +  +GP  V A D+Q  + IE+++PD  I  + 
Sbjct: 77  REAVLDILLNLKEIVLKTQSQETQRGHLSVQGPSTVLARDLQLPSSIELVDPDQYIATIS 136

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + ME TV  G GY    + + +   + ++ IDA++ P+ KV+YTVE    G     
Sbjct: 137 GRVSLNMEFTVEVGKGYQLPDYEKKKTFQVDVLPIDAVFMPVTKVNYTVEENYGGDRS-Q 195

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           +++ + + T+GSI    ++ L+   + +      N    + E      +     +     
Sbjct: 196 ERVIIEVWTNGSINSRQAIDLSVNKIINLFSPLQNVRSIEHEP-----LVKEKDSKMTEV 250

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            VEEL+LSVR+ NCL+   I  + DL+  ++ D+L + NFGR+S  E+   L      LG
Sbjct: 251 LVEELDLSVRAYNCLKRAQIHTVSDLLSYSQEDLLEIKNFGRRSAEEVIEGL---QKRLG 307

Query: 319 MNLPD 323
           ++LP 
Sbjct: 308 IHLPK 312


>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 =  300 bits (769), Expect = 2e-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|325479152|gb|EGC82249.1| DNA-directed RNA polymerase, alpha subunit [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 318

 Score =  300 bits (769), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 113/313 (36%), Positives = 197/313 (62%), Gaps = 6/313 (1%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
            NI+ + + +E EN       PL RG+  T+GN++RRVL+SSL G++++ + I+GVLHE 
Sbjct: 7   TNIQILDIVEE-ENYGKFALYPLERGYGTTIGNSMRRVLLSSLPGSSVSKILIEGVLHEF 65

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           S+I GV ED+ +I+LNIKG+++    D    + +   GP +VTA DI+  + +++ NPDH
Sbjct: 66  STIDGVVEDVPEIVLNIKGLDVTKHTDEDVTLFLDVEGPKIVTAKDIKADSLVDIANPDH 125

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  ++  + + + + V+ G GY  +++++ E+DPIG I ID+ ++P++KV+YTVE+ R 
Sbjct: 126 YIATVNEKSRLFIAMDVTDGKGYRISENNKDESDPIGTIAIDSSFTPVEKVNYTVENTRV 185

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           G+  DYDKL + + T+G+I+ +++++L S IL + + +F N  + K   +E+I  +    
Sbjct: 186 GESTDYDKLILEVWTNGTISPQEALSLGSNILIEDVSLFNNLPDMKFPPEEEIIEEEENN 245

Query: 253 NPALL-----KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
               L       +EEL+LS+RS NCL+      + D+++ +E+++  + NFG+KSL E+ 
Sbjct: 246 EEEALSEDLSMTIEELDLSLRSFNCLKRAGFDKVADIVEVSESELKSIKNFGKKSLTEVM 305

Query: 308 GVLGTMGLFLGMN 320
             L  +GL L   
Sbjct: 306 DKLDELGLSLKDE 318


>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 =  300 bits (768), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 110/324 (33%), Positives = 178/324 (54%), Gaps = 4/324 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M+    + L  PN ++Y                PL  G+  T+GN LRR+L+SS++GAA+
Sbjct: 1   MMY--LEPLQMPNEVDYDKA-SYSRTYGKFEIGPLEPGYGTTIGNTLRRILLSSIQGAAV 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
             V+I+G+ HE   I G + D  D+IL +K + +  S      + +  +G GV+TA  IQ
Sbjct: 58  RFVRIEGLHHEFCPIPGTNSDYIDLILRLKQLVISSSSVEEVPLVLEHKGKGVITASMIQ 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               ++++N D  +  +  D   R+E+ V  G GYV A     E   +G I +D++YSP+
Sbjct: 118 ETAYVKIINKDLYLLEVVDDIDFRLEMIVGIGRGYVSADRQNPEGKAVGFIPVDSIYSPV 177

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE-EPKK 239
            KV+++V   R  + +++D+L M I T+G++    ++ LA++IL+D       FE EP+ 
Sbjct: 178 LKVNFSVSHQRVKERMNFDRLIMEIYTNGAVEPSIALFLAAKILKDMAAKISLFEIEPQY 237

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
               +++ +       L   V+E+ELSVR+ NCL    I  +GDL+ +TEA+ML+  NFG
Sbjct: 238 IRDIELDPELEEKERILKTSVKEIELSVRAANCLAQAKIETIGDLVSKTEAEMLKFRNFG 297

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPD 323
           +KSL EI   L    L LGM++  
Sbjct: 298 KKSLEEIVQKLKKYDLHLGMDVEG 321


>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 =  300 bits (768), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 115/310 (37%), Positives = 181/310 (58%), Gaps = 4/310 (1%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +   +E+        EPL RG+ +T+GNALRR+L+SS+ G AI  ++I+GVL+E S+I+G
Sbjct: 13  LTEEKEDNYTAKYTLEPLYRGYGNTIGNALRRILLSSIPGTAIKGIKIEGVLNEFSTIEG 72

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V E +TDIILN+K I ++      K++T+  +GP V+TA DI     + ++NP+ VI  +
Sbjct: 73  VKEAVTDIILNVKEIVVEADEPGEKKMTLSVKGPAVITAADIHVEPGLRIINPEQVIMTV 132

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D  + +E  V  G G+V +    T+  PIG + +DA+Y+PIK+V+Y+VE    G+V +
Sbjct: 133 TTDRQIDIEFLVDSGEGFVVSDEINTDGWPIGYLAVDAIYTPIKRVNYSVEDTMVGRVTN 192

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKSLPFN 253
           YDKL + I TDGSI  +D+++ A  +L   L  F N      + +    E     +   N
Sbjct: 193 YDKLILEIATDGSIEIKDALSYAVELLTWHLEPFTNIGNSMSKYRDSEDELAEADAENEN 252

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                K+EEL+ +VRS NCL+   +  + DL   T  ++L++ N G+KSL EI   +  +
Sbjct: 253 NIEDMKIEELDFTVRSYNCLKKAGVNTISDLTSMTYNELLKIKNLGKKSLNEIIDKMKEL 312

Query: 314 GLFLGMNLPD 323
           G  LG N  +
Sbjct: 313 GYDLGDNQSN 322


>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 =  300 bits (768), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 112/320 (35%), Positives = 176/320 (55%), Gaps = 8/320 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           LI P     + L    EN       PL RG   +LGNALRRVL+SS+ GAA+T ++I GV
Sbjct: 8   LITPR----VTLLAAAENYGRFAIAPLQRGHGTSLGNALRRVLLSSIPGAAVTRIKITGV 63

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
           +HE ++I GV ED T ++LN+KGI L+   D    + + K+GPG V AGDI   + +E++
Sbjct: 64  IHEFTAIPGVVEDGTQLVLNVKGIRLRSYSDRAVALQLVKQGPGPVFAGDIDAPSTVEIV 123

Query: 129 NPDHVICNLDVD-AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           NP H +C +D +   + M+LTV +G G   A        PIG I +DAL+SPI +V++ V
Sbjct: 124 NPQHYLCTIDDEHTTLEMQLTVERGRGVQLADTVS--GMPIGEIAVDALFSPIPRVNFLV 181

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E      +  YD+L + I TDG+I   D+++ A++IL       ++  +P+ E ++   +
Sbjct: 182 EEIGGDPLTGYDRLIIEIWTDGTIKPGDALSHAAQILTQYFSRIVSLNQPE-ESEQQPTL 240

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                +    + ++EL LS R+ N LR  +I  +G L++  +  ++ + N G K + EI 
Sbjct: 241 PPPIPDEIANRTIDELGLSTRTYNSLRRADIQTIGQLLRLDDRGLMSIRNLGAKGIEEIH 300

Query: 308 GVLGTMGLFLGMNLPDWPPE 327
             L  +G   G       P+
Sbjct: 301 QRLAALGYRSGETTSGHLPD 320


>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 =  299 bits (767), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 123/308 (39%), Positives = 189/308 (61%), Gaps = 4/308 (1%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            +   + ++   +   EPL RG+  T+GNALRRVL+SS+ G+AI  V+IDGVL+E S+I+
Sbjct: 12  KLKEDKTDDFHAIYTLEPLYRGYGATIGNALRRVLLSSIPGSAIKGVKIDGVLNEFSTIE 71

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV E +TDIILNIK I ++      K++++  +GP  +TA DI     ++++NPD VI  
Sbjct: 72  GVKEAVTDIILNIKEIVVESDEPGEKKMSLSVKGPREITARDIILEPGLKIINPDQVIAT 131

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +     + ME  V  G G+V ++   TEN PIG I +DA+Y+PIKK+SY+VE    G+  
Sbjct: 132 ITTKREINMEFLVDSGEGFVVSEEIETENWPIGYIAVDAIYTPIKKISYSVEDTMVGRAT 191

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKSLPF 252
           DYDKL++ I TDGSI   D+++ A  ++   L  F N     E+ + E + + +++ +  
Sbjct: 192 DYDKLTLDITTDGSIEIRDALSYAVELISFHLNPFTNIGNSMEKFRSEDEVESSIEVISE 251

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           N     K+EEL+ +VRS NCL+   +  +GDL + T A++L++ N GRKSL EI   +  
Sbjct: 252 NNMDDMKIEELDFTVRSYNCLKKAGVNTIGDLGKMTYAELLKIKNLGRKSLNEIIDKMKE 311

Query: 313 MGLFLGMN 320
           +G  L  N
Sbjct: 312 LGFDLNDN 319


>gi|328814007|gb|AEB52119.1| DNA-directed RNA polymerase alpha chain [Lactobacillus rhamnosus]
          Length = 258

 Score =  299 bits (766), Expect = 3e-79,   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|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 =  299 bits (766), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 117/313 (37%), Positives = 173/313 (55%), 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  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIE 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 VVNPDHVIATLDNDQARLEMDLWIGRGRGYLPA--EAQEIRSIGEIPIDAIFTPTLKVNY 176

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE  R G   DYD+L + I TDG++    ++  A+RIL         FE    E   + 
Sbjct: 177 VVEHTRVGGATDYDRLILEIVTDGTVEPAKALVEAARILVQHARWIAEFESEGAEEPVEE 236

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
              +   +    + + E+ LS R  N LR   I  +G ++      +L + NFG ++L E
Sbjct: 237 WSVA---HVDDTRLLSEIGLSQRVLNALRARGIERVGQVLAMRPDQLLGIRNFGPRALQE 293

Query: 306 IKGVLGTMGLFLG 318
           ++  L   G   G
Sbjct: 294 LRERLQENGYTEG 306


>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 =  299 bits (766), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 120/326 (36%), Positives = 183/326 (56%), Gaps = 18/326 (5%)

Query: 13  NNIEYIVLG-QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
             ++   +   E       + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDGVLHE
Sbjct: 5   KKLKIEKVDIAEGGRYGKFVCEPLDRGYGITLGNSLRRILLSSLDGAAITSIKIDGVLHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKR--VTIFKRGPGVVTAGDI--QTVNDIEV 127
            S+I G+ ED+TDIILN+K + +K+  D+     V    +  GV+TA D+  Q   ++EV
Sbjct: 65  FSTIPGIREDVTDIILNLKQLCIKLEEDAEWPLEVHFDFQKDGVLTAADLAEQFPPEVEV 124

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+ VI  +D  A + M++ + +G GYVP+  ++ + D IG I ID+++SPI +  Y V
Sbjct: 125 LNPELVIATMDETAHLVMDVVIERGKGYVPSTKNKKDTDVIGCIPIDSIFSPILRAKYEV 184

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK----- 242
              R G  +D+DKL++ + TDGSIT  D+VA ++ I+   LG F         V+     
Sbjct: 185 SDVRVGNEMDFDKLTLEVWTDGSITAADAVAKSAAIMIGYLGNFTKLAHSTSVVELDDQN 244

Query: 243 ------EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
                 +         +      ++ELELSVR+ NCL+   I  + DL+ +T  D+ ++ 
Sbjct: 245 LEGDVVDPTPQDVQEDDGPAKISIDELELSVRAYNCLKRAGINTIADLLDKTIDDLGKVR 304

Query: 297 NFGRKSLVEIKGVLGTM--GLFLGMN 320
           N G+KS+ EI   L     G  L   
Sbjct: 305 NLGKKSIDEIAEKLSNHPGGFSLKQK 330


>gi|328813969|gb|AEB52100.1| DNA-directed RNA polymerase alpha chain [Lactobacillus fermentum]
          Length = 275

 Score =  299 bits (765), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 119/270 (44%), Positives = 178/270 (65%), 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 VVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
            + +++T  KG GY  A     R 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|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 =  299 bits (765), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 127/289 (43%), Positives = 190/289 (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++  + +   +++   +  P    L
Sbjct: 181 DLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---IL 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|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 =  299 bits (765), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 111/314 (35%), Positives = 170/314 (54%), Gaps = 6/314 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E I P    +    +        + EPL +G+  T+GNALRRVL+SS+ GAA TAV+ +G
Sbjct: 3   EFITPERFTW---EEHTNTYGRFVVEPLEKGYGVTIGNALRRVLLSSIEGAAPTAVKFEG 59

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
             HE +++ GV EDLT+I+LNIK +   + G+    + + K+GPG V A D +  + +E+
Sbjct: 60  AYHEFTTLPGVVEDLTEIVLNIKKLRFVLHGEGPVFIELKKKGPGKVYAKDFELPSQLEL 119

Query: 128 LNPDHVICNLD-VDAVVRMELTVSKGHGYVPAK--HHRTENDPIGLITIDALYSPIKKVS 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|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 =  299 bits (765), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 121/309 (39%), 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 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP------KKEVKEDINVKSLP 251
           +DKL++ I+TDGSI   D+++ A  +L+     F+           + E +E+ +     
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|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 =  298 bits (764), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 113/323 (34%), Positives = 188/323 (58%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +PN +  +   +  E +      PL  G+  T+GNALRRVL+SSL G AIT+++I  V
Sbjct: 6   FQRPNQVYMV---EATEFKGRFEFAPLEPGYGITIGNALRRVLLSSLEGYAITSLKISEV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMS--GDSHKRVTIFKRGPGVVTAGDIQTV-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 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF----EEPKKEV 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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++  L ++ L  G+++  +
Sbjct: 303 SLTELEQKLESLNLHFGIDIAKY 325


>gi|328813997|gb|AEB52114.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 270

 Score =  298 bits (764), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 125/274 (45%), Positives = 176/274 (64%), Gaps = 6/274 (2%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            KPN    I    E +N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVL
Sbjct: 1   EKPN----IHKIDENDNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVL 56

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I+GV ED+T IILN+K I LK+  D  K + I  +GP  VTAGDI    D+EVLN
Sbjct: 57  HEFSTIEGVTEDVTAIILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEVLN 116

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTV 187
           PD  IC +   A   M +T + G GYV A    HR ++ PIG++ +D+LYSPI++V+Y V
Sbjct: 117 PDLPICTVADGAHFHMRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNYQV 176

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  D+DKL++ + T+GSIT  ++++L+++IL D L +F+N  +  K     +  
Sbjct: 177 ENTRVGQRDDFDKLTLDVWTNGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMVEK 236

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
           +       L   +EEL+LSVRS NCL+   I  +
Sbjct: 237 EETHKEKMLEMTIEELDLSVRSYNCLKRAGINTV 270


>gi|328814017|gb|AEB52124.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 263

 Score =  298 bits (764), Expect = 6e-79,   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|157493267|gb|ABV57999.1| RNA polymerase alpha subunit [Vibrio mimicus]
          Length = 283

 Score =  298 bits (764), Expect = 7e-79,   Method: Composition-based stats.
 Identities = 123/285 (43%), Positives = 190/285 (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++  + +   +++   +  P    LL+
Sbjct: 182 DKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLR 238

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 239 PVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 283


>gi|300089409|gb|ADJ67856.1| RNA polymerase alpha-subunit [Photobacterium jeanii]
          Length = 274

 Score =  298 bits (763), Expect = 7e-79,   Method: Composition-based stats.
 Identities = 124/277 (44%), Positives = 186/277 (67%), 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++  + +   +++   +  P    LL+ V++LEL
Sbjct: 181 QTNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLEL 237

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           +VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KS
Sbjct: 238 TVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKS 274


>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 =  298 bits (763), Expect = 8e-79,   Method: Composition-based stats.
 Identities = 119/322 (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 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 LTLDSDDAVLNVELEVELGRGYRP--PESTENTPIGTIPVDAIFTPIRKVNFTTEPMHVG 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|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 =  298 bits (763), Expect = 9e-79,   Method: Composition-based stats.
 Identities = 120/326 (36%), Positives = 183/326 (56%), Gaps = 18/326 (5%)

Query: 13  NNIEYIVLG-QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
             ++   +   E       + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDGVLHE
Sbjct: 5   KKLKIEKVDIAEGGRYGKFVCEPLDRGYGITLGNSLRRILLSSLDGAAITSIKIDGVLHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKR--VTIFKRGPGVVTAGDI--QTVNDIEV 127
            S+I G+ ED+TDIILN+K + +K+  D+     V    +  GV+TA D+  Q   ++EV
Sbjct: 65  FSTIPGIREDVTDIILNLKQLCIKLEEDAEWPLEVHFDFQKDGVLTAADLAEQFPPEVEV 124

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+ VI  +D  A + M++ + +G GYVP+  ++ + D IG I ID+++SPI +  Y V
Sbjct: 125 LNPELVIATMDETAHLVMDVVIERGKGYVPSTKNKKDTDVIGCIPIDSIFSPILRAKYEV 184

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK----- 242
              R G  +D+DKL++ + TDGSIT  D+VA ++ I+   LG F         V+     
Sbjct: 185 SDVRVGNEMDFDKLTLEVWTDGSITAADAVAKSAAIMIGYLGNFTKLAHSTSVVELDDQN 244

Query: 243 ------EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
                 +         +      ++ELELSVR+ NCL+   I  + DL+ +T  D+ ++ 
Sbjct: 245 LEGDVVDPTPQDVQEDDGPAKISIDELELSVRAYNCLKRAGINTIADLLDKTIDDLGKVR 304

Query: 297 NFGRKSLVEIKGVLGTM--GLFLGMN 320
           N G+KS+ EI   L     G  L   
Sbjct: 305 NLGKKSIDEIAEKLSNHPGGFNLKQK 330


>gi|328814009|gb|AEB52120.1| DNA-directed RNA polymerase alpha chain [Lactobacillus rhamnosus]
          Length = 257

 Score =  298 bits (762), Expect = 1e-78,   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|58415828|emb|CAH57328.1| RNA polymerase alpha-subunit [Vibrio diazotrophicus]
          Length = 285

 Score =  298 bits (762), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 123/285 (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: 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++  + +   +++   +  P    LL+ V
Sbjct: 184 LVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPV 240

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           ++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 241 DDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 285


>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 =  298 bits (762), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 118/319 (36%), Positives = 186/319 (58%), Gaps = 11/319 (3%)

Query: 13  NNIEYIVLG-QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           N  +   +   ++      + EPL RG+  TLGN+LRRVL+SSL G AIT+++IDGVLHE
Sbjct: 5   NKFKVKTVERSDDGTYGKFVCEPLDRGYGITLGNSLRRVLLSSLDGVAITSIKIDGVLHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
            S+I+GV ED+++IILN+K + L+ + D  +   +++   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|157493255|gb|ABV57993.1| RNA polymerase alpha subunit [Vibrio mimicus]
          Length = 285

 Score =  297 bits (761), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 123/287 (42%), Positives = 190/287 (66%), 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++  + +   +++   +  P    LL+
Sbjct: 182 DKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLR 238

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 239 PVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 285


>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 =  297 bits (761), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 115/323 (35%), Positives = 184/323 (56%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ +  +        PL  G+  T+GN LRR+L+SSL G AIT ++I GV
Sbjct: 6   FQKPDKV---IMLESTDKFGKFEFRPLEPGYGITIGNPLRRILLSSLEGFAITGIKIHGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E++ +L    L  GM++  +
Sbjct: 303 SLTELEALLENNNLEFGMDVTKY 325


>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 =  297 bits (761), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 119/322 (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 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 LTLDSDDAVLNVELEVELGRGYRA--PESTENTPIGTIPVDAIFTPIRKVNFTTEPMHVG 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|297180261|gb|ADI16480.1| DNA-directed RNA polymerase, alpha subunit/40 kd subunit
           [uncultured bacterium HF4000_05M23]
          Length = 362

 Score =  297 bits (760), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 113/320 (35%), Positives = 182/320 (56%), Gaps = 11/320 (3%)

Query: 11  KPNNIEY-IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            P   +  I + + EE     +AEPL RG+  TLGN +RR L+++L G AIT V+IDG+ 
Sbjct: 18  TPEVPDLSITIQENEETYGRFVAEPLERGWGVTLGNPIRRSLLNALSGTAITWVRIDGIH 77

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++K + E++ + +LN+KGI L+   D   R+ +   G G V AGDI    D E++N
Sbjct: 78  HEYSTVKHMREEVVEFLLNVKGIRLRSLADRPGRLRLEVDGEGEVRAGDIMATADFEIVN 137

Query: 130 PDHVICNLDVDA-VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           P+H +  LD     + +E  V +G GY PA H   E  PIG++ +DA+++P++K ++ VE
Sbjct: 138 PEHHLATLDNGGARLSVEFNVEQGVGYEPANH--EEGLPIGVLPVDAIFTPVRKANFAVE 195

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           + R GQ  D ++L + + TD +IT  D+V  A  +L ++  +F   ++P+ + +      
Sbjct: 196 ATRVGQRSDLERLVVEVWTDRTITPLDAVRAAGNLLMERFFLFKRLDKPQDDEEVLGVPG 255

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
            LP     L  VE L LS R+ NCL+   I  +G+++   + ++L++ NFG+KSL E+  
Sbjct: 256 VLPEVFNTL--VETLSLSARTLNCLKRAGINRVGEVLMMPKGELLKIRNFGQKSLDELYD 313

Query: 309 VLGTMGLFLGMNLPDWPPES 328
            L          LP+  PE 
Sbjct: 314 KLAEKNY-----LPEENPEG 328


>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 =  297 bits (760), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 114/310 (36%), Positives = 180/310 (58%), Gaps = 4/310 (1%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           +   +E+        EPL RG+ +T+GNALRR+L+SS+ G AI  ++I+GVL+E S+I+G
Sbjct: 13  LTEEKEDNYTAKYTLEPLYRGYGNTIGNALRRILLSSIPGTAIKGIKIEGVLNEFSTIEG 72

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V E +TDIILN+K I ++      K++T+  +GP V+TA DI     ++++NP+ VI  +
Sbjct: 73  VKEAVTDIILNVKEIVVESDEPGEKKMTLSVKGPAVITAADIHVEPGLKIINPEQVIMTV 132

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             D  + +E  V  G G+V +    T+  PIG + +DA+Y+PIK+V+Y+VE    G+V +
Sbjct: 133 TTDKQIDIEFLVDSGEGFVVSDEINTDGWPIGYLAVDAIYTPIKRVNYSVEDTMVGRVTN 192

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKSLPFN 253
           YDKL + I TDGSI  +D+++ A  +L   L  F N      + +    E         N
Sbjct: 193 YDKLILEIATDGSIEIKDALSYAVELLTWHLEPFTNIGNSMSKYRDSEDELTVTAEENEN 252

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                K+EEL+ +VRS NCL+   +  + DL   T  ++L++ N G+KSL EI   +  +
Sbjct: 253 NIEDMKIEELDFTVRSYNCLKKAGVNTISDLTSMTYNELLKIKNLGKKSLNEIIDKMKEL 312

Query: 314 GLFLGMNLPD 323
           G  LG    +
Sbjct: 313 GYDLGDTSSN 322


>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 =  296 bits (759), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 100/312 (32%), Positives = 163/312 (52%), Gaps = 13/312 (4%)

Query: 16  EYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           +   +    +         + EPL +G   TLGNALRR ++S L G AI AV+I GV HE
Sbjct: 5   QIECIESRTDGARGQYGSFVIEPLNQGQGITLGNALRRSILSDLEGTAIVAVRIAGVNHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            S+I GV ED+ +I+LN+K +  K      +   I  +GP +VTAG  +  +DIEV++P 
Sbjct: 65  FSTIPGVREDVLEILLNLKEVVFKSYNKESQIGRIRVQGPAIVTAGLFELSSDIEVVDPR 124

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             I  +  + +  ME  + K  GY  A+    E   +  + +D+++ P+ KV+Y VE  R
Sbjct: 125 QYIATICNNTIFEMEFKIEKNCGYRLAEKAVDE-LSVDFLQVDSVFMPVNKVNYKVEEVR 183

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
            G     D+L + I T+GSI+ +++++  + +L +             + K   N +S  
Sbjct: 184 IGSNSIKDRLIIQIWTNGSISPQEAISQGATVLTNLF-----CSLRNLDFKSADNYRSKE 238

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL+LSVR+ NCL+   I  + DL+  ++ ++L + NFG+KS  E+   L 
Sbjct: 239 DKKISQVLIEELQLSVRAYNCLKRAQIHSIADLLDYSQEELLEIKNFGQKSAEEVIYAL- 297

Query: 312 TMGLFLGMNLPD 323
                LG++LP 
Sbjct: 298 --QKKLGISLPK 307


>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 =  296 bits (759), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 125/285 (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: 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++  + +   +++   +  P    LL+
Sbjct: 181 DKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLR 237

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 PVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 282


>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 =  296 bits (759), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 118/310 (38%), Positives = 173/310 (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 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK----- 258
            I TDGS   + ++ +A   L+D+L +F N E  + E         LP   AL       
Sbjct: 192 RIWTDGSADPQSALDMAVDTLRDELSVFGNVETIQAETVVTPAAYDLPQPSALSINPQPY 251

Query: 259 ---------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 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|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 =  296 bits (759), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 118/319 (36%), Positives = 183/319 (57%), Gaps = 18/319 (5%)

Query: 13  NNIEYIVLG-QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
             ++   +   +       + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDGVLHE
Sbjct: 5   KKLKIEKVDIADGGRYGKFVCEPLDRGYGITLGNSLRRILLSSLDGAAITSIKIDGVLHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDI--QTVNDIEV 127
            S+I G+ ED+TDIILN+K + +K+  D+     V    +  GV+TA D+  Q   ++EV
Sbjct: 65  FSTIPGIREDVTDIILNLKQLCIKVEEDAQLPLEVHFDFQKDGVLTAADLAEQFPPEVEV 124

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+ VI  +D  A + M++ + +G GYVP+  ++ + D IG I ID+++SPI +  Y V
Sbjct: 125 LNPELVIATMDETAHLVMDVVIERGKGYVPSTKNKKDTDVIGCIPIDSIFSPILRAKYEV 184

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED--- 244
              R G  +D+DKL++ + TDGSIT  D+VA ++ I+   LG F         V  +   
Sbjct: 185 SDVRVGNEMDFDKLTLEVWTDGSITAADAVAKSAAIMIGYLGNFTKLAHSADVVDVNTGE 244

Query: 245 ----------INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
                      N +    +      ++ELELSVR+ NCL+   I  + DL+ +T  D+ +
Sbjct: 245 GGIVVDPVGSDNEEPAVDDGPAKISIDELELSVRAYNCLKRAGINTIADLLDKTIDDLGK 304

Query: 295 MANFGRKSLVEIKGVLGTM 313
           + N G+KS+ EI+  L   
Sbjct: 305 VRNLGKKSIDEIEEKLNNH 323


>gi|328813987|gb|AEB52109.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 262

 Score =  296 bits (758), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 120/259 (46%), Positives = 170/259 (65%), Gaps = 2/259 (0%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
            +N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+GV ED+T
Sbjct: 4   NDNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEGVTEDVT 63

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
            IILN+K I LK+  D  K + I  +GP  VTAGDI    D+EVLNPD  IC +   A  
Sbjct: 64  AIILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVADGAHF 123

Query: 144 RMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            M +T + G GYV A    HR ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL
Sbjct: 124 HMRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKL 183

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           ++ + T+GSIT  ++++L+++IL D L +F+N  +  K     +  +       L   +E
Sbjct: 184 TLDVWTNGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKEKMLEMTIE 243

Query: 262 ELELSVRSTNCLRGENIVY 280
           EL+LSVRS NCL+   I  
Sbjct: 244 ELDLSVRSYNCLKRAGINT 262


>gi|328813967|gb|AEB52099.1| DNA-directed RNA polymerase alpha chain [Lactobacillus fermentum]
          Length = 271

 Score =  296 bits (758), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 117/268 (43%), Positives = 176/268 (65%), 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 VVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
            + +++T  KG GY  A     R 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|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 =  296 bits (757), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 131/314 (41%), Positives = 186/314 (59%), Gaps = 11/314 (3%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            IV   +++       EPL RGF  TLGN+LRRVL+SSL G AIT+++IDGVLHE ++I+
Sbjct: 10  KIVELSDDKRYGKFECEPLERGFGITLGNSLRRVLLSSLDGVAITSIKIDGVLHEFTTIE 69

Query: 77  GVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           GV ED+TD+ILN+K I      +     +V I     G+  AGD+Q  ++I+VLN D  I
Sbjct: 70  GVREDVTDMILNLKKIRFIAHDEAVFPIQVRIDIDKEGIFHAGDMQLPSEIDVLNTDLEI 129

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
           C LD DA + MELT+ +GHGYVP   ++ +ND IG+I ID++++P+ K +Y V   R G 
Sbjct: 130 CTLDADAHLGMELTIDRGHGYVPFNKNK-KNDEIGIIPIDSIFTPVVKCNYKVSDTRVGN 188

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI-----NFEEPKKEVKEDINVKS 249
            +DYDKL++ ++TDGS+  ED+VA A+ IL      F         E   +  E    + 
Sbjct: 189 EMDYDKLTLELETDGSVKVEDAVAQAATILIKYFENFRRLATKQIPEIDVDEIEPEIEEK 248

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                  +  +EELELSVR+ NCL+   I  +  L  +TE ++ R+ N G+KS+ EIK  
Sbjct: 249 DDSPDLSVIPIEELELSVRAFNCLKRAEINMLDQLTDKTEDELTRVRNLGKKSVDEIKEK 308

Query: 310 LGTM---GLFLGMN 320
           L      GL L  N
Sbjct: 309 LAAYKGWGLHLKDN 322


>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 =  296 bits (757), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 118/309 (38%), 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 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI------NVKSLP 251
           +DKL++ I+TDGSI   D+++ A  +L+     F+      + ++ +        V    
Sbjct: 193 FDKLTLDIETDGSIEIRDALSYAVELLKLHFDPFLELGNKMENLRVEAEEEEENPVSHAK 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 ELGYDLSQN 321


>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 =  296 bits (757), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 119/309 (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 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI------NVKSLP 251
           +DKL++ I+TDGSI   D+++ A  +L+     F+      + ++ +        V    
Sbjct: 193 FDKLTLDIETDGSIEIRDALSYAVELLKLHFDPFLELGNKMENLRVEAEEEEENPVSHAK 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 ELGYDLSQN 321


>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 =  296 bits (757), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 116/305 (38%), Positives = 181/305 (59%), Gaps = 4/305 (1%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            +   +E         EPL RG+ +T+GNALRR+L+SS+ G+AI  ++IDGVL+E S+I 
Sbjct: 12  KLTEEKESRYTAKYTLEPLYRGYGNTIGNALRRILLSSIPGSAIKGLRIDGVLNEFSTIP 71

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV E +TDIILN+K I +++     K++ +  +GP V+TA DI+    I+++NP+ VI  
Sbjct: 72  GVKEAVTDIILNVKEIVVELDEPGEKKMVLSVKGPKVITAADIKPDPGIKIINPEQVIAT 131

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +  D  + ME  V  G G+V +    TE  PIG + +DA+Y+PIK+V+Y+VE    G+V 
Sbjct: 132 VTTDKEINMEFLVDSGEGFVVSDEIDTEGWPIGYLAVDAIYTPIKRVTYSVEDTMVGRVT 191

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN----FEEPKKEVKEDINVKSLPF 252
           +YDKL + I TDGSI   D+++ A  +L   +  F N      + +    E+ ++ S   
Sbjct: 192 NYDKLILEISTDGSIEIHDALSYAVELLILHVKPFTNIGNSMSKFRGNEDENSSLNSETE 251

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +     K+EEL+ +VRS NCL+   +  + DL   T  ++L++ N GRKSL EI   +  
Sbjct: 252 SNIEDMKIEELDFTVRSYNCLKKAGVNTISDLTSMTYVELLKIKNLGRKSLNEIIDKMKE 311

Query: 313 MGLFL 317
           +G  L
Sbjct: 312 LGYDL 316


>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 =  295 bits (756), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 117/331 (35%), Positives = 179/331 (54%), Gaps = 22/331 (6%)

Query: 8   ELIKPNNIEYIVLGQEEENR-TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI- 65
           E + P  ++     +E +   +     PL RG+A T+GNALRRVL+SS+   AI  V+  
Sbjct: 3   EFVIPKKLKVEEEREERDYYYSRFSLSPLERGYAITIGNALRRVLLSSIPSLAIVGVRFI 62

Query: 66  -DGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--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|300089407|gb|ADJ67855.1| RNA polymerase alpha-subunit [Photobacterium jeanii]
          Length = 270

 Score =  295 bits (756), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 123/273 (45%), Positives = 184/273 (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++  + +   +++   +  P    LL+ V++LEL+VRS
Sbjct: 181 TLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRS 237

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
            NCL+ E I Y+GDL+QRTE ++L+  N G+KS
Sbjct: 238 ANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKS 270


>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 =  295 bits (756), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 119/319 (37%), Positives = 181/319 (56%), Gaps = 18/319 (5%)

Query: 13  NNIEYIVLG-QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
             ++   +   E       + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDGVLHE
Sbjct: 8   KKLKIEKVDIAEGGRYGKFVCEPLDRGYGITLGNSLRRILLSSLDGAAITSIKIDGVLHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDI--QTVNDIEV 127
            S+I G+ ED+TDIILN+K + +K+  D      V    +  GV+TA D+  Q   ++EV
Sbjct: 68  FSTIPGIREDVTDIILNLKQLCIKVEEDVQLPLEVHFDFQKDGVLTAADLAEQFPPEVEV 127

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+ VI  +D  A + M++ + +G GYVP+  ++ + D IG I ID+++SPI +  Y V
Sbjct: 128 LNPELVIATMDETAHLVMDVVIERGKGYVPSTKNKKDTDVIGCIPIDSIFSPILRAKYEV 187

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED--- 244
              R G  +D+DKL++ + TDGSIT  D+VA ++ I+   LG F         V  +   
Sbjct: 188 SDVRVGNEMDFDKLTLEVWTDGSITAADAVAKSAAIMIGYLGNFTKLAHSADVVDVNTGE 247

Query: 245 ----------INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
                      N +           ++ELELSVR+ NCL+   I  + DL+ +T  D+ +
Sbjct: 248 GGIVVDPVGSDNEEPAVDEGPAKISIDELELSVRAYNCLKRAGINTIADLLDKTIDDLGK 307

Query: 295 MANFGRKSLVEIKGVLGTM 313
           + N G+KS+ EI+  L   
Sbjct: 308 VRNLGKKSIDEIEEKLNNH 326


>gi|311990454|gb|ADQ26357.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 260

 Score =  295 bits (755), Expect = 6e-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|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 =  294 bits (754), Expect = 9e-78,   Method: Composition-based stats.
 Identities = 111/298 (37%), Positives = 170/298 (57%), Gaps = 5/298 (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 TIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEVKEDINVKSLPFNPALLKK 259
            + TDGS++  +++  A  IL++QL +F    I+   P   +      + L         
Sbjct: 191 RVWTDGSVSPREALDSAVEILRNQLSVFSGGVIDEPLPVMAIPPRSADEPLSRAEPARIS 250

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +E LELS R  + L+ E I  +  L+  +E D+ ++   G KSL EIK  L   GL+L
Sbjct: 251 LESLELSSRVLHSLQEEGIDSVDALLALSERDLKKVGGVGDKSLEEIKERLQAQGLYL 308


>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 =  294 bits (754), Expect = 1e-77,   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 LTLDSDDAVLNVELEVELGRGYRPPESA--ENTPIGTIPVDAIFTPIRKVNFTTEPMHVG 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|46143635|ref|ZP_00134832.2| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Actinobacillus pleuropneumoniae serovar 1 str. 4074]
          Length = 279

 Score =  294 bits (754), Expect = 1e-77,   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|328814013|gb|AEB52122.1| DNA-directed RNA polymerase alpha chain [Lactobacillus rhamnosus]
          Length = 260

 Score =  294 bits (753), Expect = 1e-77,   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|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 =  294 bits (753), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 117/331 (35%), Positives = 177/331 (53%), Gaps = 22/331 (6%)

Query: 8   ELIKPNNIEYIVL-GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI- 65
           E + P  ++      +++         PL RG+A T+GNALRRVL+SS+   AI  V+  
Sbjct: 3   EFVIPKKLKVEEEREEKDYYYARFSLSPLERGYAITIGNALRRVLLSSIPSLAIVGVRFI 62

Query: 66  -DGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--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|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 =  294 bits (753), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 124/332 (37%), Positives = 183/332 (55%), 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 VNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPAKHH-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
                            L  V++LEL+VRS NCL+ E+I+Y+GDL+QRTE ++L+  N G
Sbjct: 238 RSMAPAAPPMPDPVLMQL--VDDLELTVRSANCLKAESIIYIGDLVQRTEVELLKTPNLG 295

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +KSL EIK VL   GL LGM L +WPP ++  
Sbjct: 296 KKSLTEIKDVLAQRGLSLGMRLTNWPPPNLRS 327


>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 =  294 bits (753), Expect = 1e-77,   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  ITAVQI--DGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--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|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 =  294 bits (752), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 111/301 (36%), Positives = 166/301 (55%), Gaps = 8/301 (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 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK----- 258
            I TDGS++  D++  A  IL++ LG F       +   E +            +     
Sbjct: 195 RIWTDGSVSPLDALQSAVGILREHLGFFDQAAVVAEAEAEPVEAAPEVEAVGAEEAAERP 254

Query: 259 --KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
              +++L LS R  + L+ E I  + +L+  TE ++ ++   G +S+ EIK  L   GL 
Sbjct: 255 ALTLDDLGLSTRVLHNLKEEGIDSIENLLALTERELKKVPGIGERSVEEIKERLAEHGLS 314

Query: 317 L 317
           L
Sbjct: 315 L 315


>gi|328813939|gb|AEB52085.1| DNA-directed RNA polymerase alpha chain [Lactobacillus brevis]
          Length = 265

 Score =  294 bits (752), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 117/265 (44%), Positives = 173/265 (65%), 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 ELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            +T  KG GYV A     R  + 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|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 =  294 bits (752), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 116/319 (36%), Positives = 183/319 (57%), Gaps = 18/319 (5%)

Query: 13  NNIEYIVLG-QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
             ++   +   +       + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDGVLHE
Sbjct: 5   KKLKIEKVDIADGGRYGKFVCEPLDRGYGITLGNSLRRILLSSLDGAAITSIKIDGVLHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDI--QTVNDIEV 127
            S+I G+ ED+TDIILN+K + +K+  ++     V    +  G++TA D+  Q   ++EV
Sbjct: 65  FSTIPGIREDVTDIILNLKQLCIKVEEEAQLPLEVHFDFQKDGILTAADLAEQFPPEVEV 124

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+ VI  +D  A + M++ + +G GYVP+  ++ + D IG I ID+++SPI +  Y V
Sbjct: 125 LNPELVIATMDETAHLVMDVVIERGKGYVPSTKNKKDTDVIGCIPIDSIFSPILRAKYEV 184

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED--- 244
              R G  +D+DKL++ + TDGSIT  D+VA ++ I+   LG F         V  +   
Sbjct: 185 SDVRVGNEMDFDKLTLEVWTDGSITAADAVAKSAAIMIGYLGNFTKLAHSADVVDVNTGE 244

Query: 245 ----------INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
                      N +    +      ++ELELSVR+ NCL+   I  + DL+ +T  D+ +
Sbjct: 245 GGIVIDPVGSDNEEPAVDDGPAKISIDELELSVRAYNCLKRAGINTIADLLDKTIDDLGK 304

Query: 295 MANFGRKSLVEIKGVLGTM 313
           + N G+KS+ EI+  L   
Sbjct: 305 VRNLGKKSIDEIEEKLNNH 323


>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 =  293 bits (751), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 116/319 (36%), Positives = 182/319 (57%), Gaps = 18/319 (5%)

Query: 13  NNIEYIVLG-QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
             ++   +   +       + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDGVLHE
Sbjct: 5   KKLKIEKVDIADGGRYGKFVCEPLDRGYGITLGNSLRRILLSSLDGAAITSIKIDGVLHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDI--QTVNDIEV 127
            S+I G+ ED+TDIILN+K + +K+  ++     V    +  G++TA D+  Q   ++EV
Sbjct: 65  FSTIPGIREDVTDIILNLKQLCIKVEEEAQLPLEVHFDFQKDGILTAADLAEQFPPEVEV 124

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+ VI  +D  A   M++ + +G GYVP+  ++ + D IG I ID+++SPI +  Y V
Sbjct: 125 LNPELVIATMDETAHFVMDVVIERGKGYVPSTKNKKDTDVIGCIPIDSIFSPILRAKYEV 184

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED--- 244
              R G  +D+DKL++ + TDGSIT  D+VA ++ I+   LG F         V  +   
Sbjct: 185 SDVRVGNEMDFDKLTLEVWTDGSITAADAVAKSAAIMIGYLGNFTKLAHSADVVDVNTGE 244

Query: 245 ----------INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
                      N +    +      ++ELELSVR+ NCL+   I  + DL+ +T  D+ +
Sbjct: 245 GGIVIDPVGSDNEEPAVDDGPAKISIDELELSVRAYNCLKRAGINTIADLLDKTIDDLGK 304

Query: 295 MANFGRKSLVEIKGVLGTM 313
           + N G+KS+ EI+  L   
Sbjct: 305 VRNLGKKSIDEIEEKLNNH 323


>gi|218674111|ref|ZP_03523780.1| DNA-directed RNA polymerase subunit alpha [Rhizobium etli GR56]
          Length = 237

 Score =  293 bits (751), Expect = 2e-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|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 =  293 bits (751), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 112/303 (36%), Positives = 165/303 (54%), Gaps = 3/303 (0%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
              +  +       + EPL RGF  TLGN LRR+L+SS+ G A+T+V I+ VLHE S+I 
Sbjct: 10  VFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIP 69

Query: 77  GVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           GV ED+ +IILN+K + ++          + +   GP VV AGD     D E+LNPD  I
Sbjct: 70  GVKEDVVEIILNLKELVVRFLDPKMQTTTLVLKAEGPKVVRAGDFVVPPDAEILNPDLTI 129

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
             LD    + ME+ V +G GYVPA+ H  ++  I  I +DA++SP+++V++ VE  R GQ
Sbjct: 130 ATLDKGGKLYMEVRVDRGVGYVPAERHGIKDR-INSIPVDAIFSPVRRVAFQVEDTRLGQ 188

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
             D DKL++ I TDGS+T  +++  A  IL++ L  F N +       E  +V+      
Sbjct: 189 RTDLDKLTLRIWTDGSVTPLEALNQAVEILKEHLSYFANPQATALPAPEPASVERAEGEE 248

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
            L   +EEL LS R  + L+ E I  +  L+     D+  +   G +SL EI+  L   G
Sbjct: 249 DLDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIREALAKKG 308

Query: 315 LFL 317
             L
Sbjct: 309 FAL 311


>gi|328813953|gb|AEB52092.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 250

 Score =  293 bits (751), Expect = 2e-77,   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|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 =  293 bits (750), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 115/304 (37%), Positives = 184/304 (60%), Gaps = 6/304 (1%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E E +   + EPL RG+ HTLGNALRRVL+SS+ GAAI  ++I+GVL E S + GV E +
Sbjct: 18  ESEFKGQFVVEPLYRGYGHTLGNALRRVLLSSIPGAAIKGIRIEGVLSEFSVMDGVKEAV 77

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T+IILN+K I +K      +++T+  +GP VVTA DI     +E++NPD  IC +  D  
Sbjct: 78  TEIILNVKEIVVKSETAGERKMTLSVKGPKVVTAADIIPDIGLEIINPDQEICTITTDRE 137

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +E  V  G G+V ++    +   +  I +DA+Y+PI+KVSY ++    G++ D+DKL+
Sbjct: 138 LDIEFLVDTGEGFVVSEEIERDGWAVDYIAVDAIYTPIRKVSYDIQDTMVGRMTDFDKLT 197

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI------NVKSLPFNPAL 256
           ++++TDGSI   D+++ A  +L+  L  F+      + ++ ++         S+  +  L
Sbjct: 198 LSVETDGSIEIRDALSYAVELLKLHLDPFLEIGNKMENLRVEVEEEVENQSSSIKDDINL 257

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
             K+EEL+L+VRS NCL+   I  +G L + +  ++L++ N GRKSL EI   +  +G  
Sbjct: 258 NIKIEELDLTVRSFNCLKKAGIEEVGQLSKLSMNELLKIKNLGRKSLDEILEKMKELGYD 317

Query: 317 LGMN 320
           L  N
Sbjct: 318 LAQN 321


>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 =  293 bits (750), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 117/331 (35%), Positives = 178/331 (53%), Gaps = 22/331 (6%)

Query: 8   ELIKPNNIEYIVL-GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI- 65
           E + P  ++      +++ +       PL RG+A T+GNALRRVL+SS+   AI  V+  
Sbjct: 3   EFVIPKKLKVEEEREEKDYHYARFSLSPLERGYAITIGNALRRVLLSSIPSLAIIGVRFI 62

Query: 66  -DGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--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|161511763|emb|CAP16892.1| DNA-directed RNA polymerase subunit alpha [Pediococcus parvulus]
          Length = 264

 Score =  293 bits (750), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 120/268 (44%), Positives = 173/268 (64%), Gaps = 6/268 (2%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            KPN    I    E  N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVL
Sbjct: 1   EKPN----IHKIDENANYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVL 56

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I+GV ED+T IILNIK ++LK+  D  K + I  +GP  VTAGDIQ  +D+E+LN
Sbjct: 57  HEFSTIEGVVEDVTQIILNIKKVSLKIESDDEKSLEINVKGPATVTAGDIQGDSDVEILN 116

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTV 187
           PD  IC +         LT   G GYV A     R ++ PIG++ ID++Y+PI++V+Y V
Sbjct: 117 PDQYICTVADGVTFHAVLTADTGRGYVSADENKARKDDMPIGVLPIDSIYTPIERVNYQV 176

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  DYDKL++ + TDGSI+  ++ +L+++IL + L +F+N  +  ++ +  +  
Sbjct: 177 ENTRVGQRDDYDKLTLDVWTDGSISPSEATSLSAKILTEHLALFVNLTDEAQDAEIMVEK 236

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRG 275
           +       L   +EEL+LSVRS NCL+ 
Sbjct: 237 EETHKEKMLEMSIEELDLSVRSYNCLKR 264


>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 =  293 bits (750), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 102/322 (31%), Positives = 174/322 (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 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF---------EEPKKEVKEDINVK 248
           Y+K+ M I ++G I  + +VA A+++L++   + +           E     V+ +    
Sbjct: 185 YEKVVMDIYSNGVIAPDMAVAEAAKLLREYFSIVVKEILKRYPASAEMAASPVEMEQEQP 244

Query: 249 SLPFNPALL----------KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           SL                   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|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 =  293 bits (750), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 116/319 (36%), Positives = 183/319 (57%), Gaps = 18/319 (5%)

Query: 13  NNIEYIVLG-QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
             ++   +   +       + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDGVLHE
Sbjct: 5   KKLKIEKVDIADGGRYGKFVCEPLDRGYGITLGNSLRRILLSSLDGAAITSIKIDGVLHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDI--QTVNDIEV 127
            S+I G+ ED+TDIILN+K + +K+  ++     V    +  G++TA D+  Q   ++EV
Sbjct: 65  FSTIPGIREDVTDIILNLKQLCIKVEEEAQLPLEVHFDFQKDGILTATDLAEQFPPEVEV 124

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           LNP+ VI  +D  A + M++ + +G GYVP+  ++ + D IG I ID+++SPI +  Y V
Sbjct: 125 LNPELVIATMDETAHLVMDVVIERGKGYVPSTKNKKDTDVIGCIPIDSIFSPILRAKYEV 184

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED--- 244
              R G  +D+DKL++ + TDGSIT  D+VA ++ I+   LG F         V  +   
Sbjct: 185 SDVRVGNEMDFDKLTLEVWTDGSITAADAVAKSAAIMIGYLGNFTKLAHSADVVDVNTGE 244

Query: 245 ----------INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
                      N +    +      ++ELELSVR+ NCL+   I  + DL+ +T  D+ +
Sbjct: 245 GGIVIDPVGSDNEEPAVDDGPAKISIDELELSVRAYNCLKRAGINTIADLLDKTIDDLGK 304

Query: 295 MANFGRKSLVEIKGVLGTM 313
           + N G+KS+ EI+  L   
Sbjct: 305 VRNLGKKSIDEIEEKLNNH 323


>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 =  293 bits (749), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 127/324 (39%), Positives = 194/324 (59%), Gaps = 6/324 (1%)

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 ELMDGAKLDAKIYLQRGIGYKQANYDAV-NREIGFIPVDALFSPIVRVAYHTKKSTMKDY 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 +E + +  E+K
Sbjct: 313 ELGM---KFSQEQLERIQQLIEEK 333


>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 =  292 bits (748), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 116/305 (38%), Positives = 181/305 (59%), Gaps = 2/305 (0%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
            NIE + +  E +N       PL RG+  TLGN++RRVL+ SL G+AI  V+IDGV HE 
Sbjct: 7   TNIEVLDIDLE-KNYGKFAIMPLDRGYGTTLGNSMRRVLLGSLPGSAIATVKIDGVGHEF 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  +     E   I  I +D+ +SP+KKV++ V + R 
Sbjct: 126 YITTLNEEGEIRMDLLVLNGKGYRVSD-LNKEYCDINSIAVDSSFSPVKKVNFIVGNTRV 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|328813965|gb|AEB52098.1| DNA-directed RNA polymerase alpha chain [Lactobacillus farraginis]
          Length = 270

 Score =  292 bits (748), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 123/270 (45%), Positives = 177/270 (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 VRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             M LT ++G GYV A     R    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|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 =  292 bits (748), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 97/312 (31%), Positives = 162/312 (51%), Gaps = 13/312 (4%)

Query: 16  EYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           +   +    +         + E L +G   TLGNALRR ++S L G AI AV+I GV HE
Sbjct: 5   QIECVESRTDGARGQYGSFVIEALNQGQGITLGNALRRSILSDLEGTAIVAVRIAGVNHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            S+I GV ED+ +I+LN+K +  K +    +   I  +GP +VTAG  +  +DIEV++P 
Sbjct: 65  FSTIPGVREDVLEILLNLKEVVFKSNNQESQIGRIKVQGPAIVTAGLFELSSDIEVVDPR 124

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             I  +  + +  ME  + K  GY  A+    E   +  + +D+++ P+ KV+Y VE  R
Sbjct: 125 QYIATICNNTIFEMEFKIEKSCGYRLAEKAVDE-LSLDFLQVDSVFMPVNKVNYKVEEVR 183

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
            G     D+L + I T+GSI+ +++++  + +L +             + K     ++  
Sbjct: 184 VGTNSIKDRLILQIWTNGSISPQEAISQGATVLTNLFCSLR-----NLDFKSVDTYRNKE 238

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL+LSVR+ NCL+   I  + DL+  ++ ++L + NFG+KS  E+   L 
Sbjct: 239 DKKISQVLIEELQLSVRAYNCLKRAQIHSIADLLDYSQEELLEIKNFGQKSAEEVIYAL- 297

Query: 312 TMGLFLGMNLPD 323
                LG++LP 
Sbjct: 298 --QKTLGISLPK 307


>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 =  292 bits (748), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 122/323 (37%), Positives = 192/323 (59%), Gaps = 10/323 (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  LHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDI-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 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           +VE  R  Q  DYDKL + + TDGSI+ +D++  A++IL     +F    I  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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L  + L  G ++  +
Sbjct: 303 SLTELDDLLLGLNLSFGTDISKY 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 =  292 bits (748), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 113/304 (37%), Positives = 183/304 (60%), Gaps = 6/304 (1%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E E +   + EPL RG+ HTLGNALRRVL+SS+ GAAI  ++I+GVL E S + GV E +
Sbjct: 18  ESEFKGQFVVEPLYRGYGHTLGNALRRVLLSSIPGAAIKGIRIEGVLSEFSVMDGVKEAV 77

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T+IILN+K I +K      +++T+  +GP VVTA DI     +E++NP+  IC +  D  
Sbjct: 78  TEIILNVKEIVVKSETAGERKMTLSVKGPKVVTAADIIPDIGLEIINPEQEICTITTDRE 137

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +E  V  G G+V ++    +   +  I +DA+Y+PI+KVSY ++    G++ D+DKL+
Sbjct: 138 LDIEFLVDTGEGFVVSEEIERDGWAVDYIAVDAIYTPIRKVSYDIQDTMVGRMTDFDKLT 197

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF------NPAL 256
           ++++TDGSI   D+++ A  +L+  L  F+      + ++ ++  +          +  L
Sbjct: 198 LSVETDGSIEIRDALSYAVELLKLHLDPFLEIGNKMENLRVEVEEEVENQSSSIRDDINL 257

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
             K+EEL+L+VRS NCL+   I  +G L + +  ++L++ N GRKSL EI   +  +G  
Sbjct: 258 NIKIEELDLTVRSFNCLKKAGIEEVGQLSKLSMNELLKIKNLGRKSLDEILEKMKELGYD 317

Query: 317 LGMN 320
           L  N
Sbjct: 318 LAQN 321


>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 =  292 bits (747), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 97/314 (30%), Positives = 158/314 (50%), Gaps = 10/314 (3%)

Query: 12  PNNIEYIV--LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           P+ I  I   +          + EPL  G   T+GN LRR+L+  + GAAIT+V+I G  
Sbjct: 8   PSTIYCIESKIESPRNLYGRFLIEPLAIGQGITVGNTLRRILLGDIEGAAITSVKIPGAN 67

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           +E S + G+ E + +I+LN+K I  +      ++  +  +GP VV A ++Q    IEV++
Sbjct: 68  NEFSILPGIRESVLEILLNLKEIVFRTKSLDVQKGYLSIQGPCVVKAANLQLPTSIEVVD 127

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
               I  L  +A + ME  ++ G GY  A +   +N  I  + +DA++ PI KV+Y VE 
Sbjct: 128 GGQYIATLSGNANLDMEFVINTGKGYQMADYAIKKNSYISSLPVDAIFMPIHKVNYMVEQ 187

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
               + L  +++ + I T+GSI+  D++ +  + + D      +        K D     
Sbjct: 188 DHTSKFLT-ERVILEIWTNGSISPRDALDIGIKKVIDLFNPLHHCSSEYSTNKND----F 242

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              +      VEELELSVR+ NCL+   I  + DL+  ++ D+L + NFGR+S  E+   
Sbjct: 243 STESKINDILVEELELSVRAYNCLKRAQIHTISDLLAYSQEDLLEIKNFGRRSAEEVIEA 302

Query: 310 LGTMGLFLGMNLPD 323
           L      L + LP 
Sbjct: 303 LE---KKLNIYLPK 313


>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 =  292 bits (747), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 112/314 (35%), Positives = 177/314 (56%), Gaps = 20/314 (6%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
           +      + +PL RG+  TLGN+LRR+L+SSL G AIT+++IDG+LHE ++I GV ED++
Sbjct: 17  DGTFGKFVCKPLDRGYGITLGNSLRRILLSSLEGVAITSIKIDGILHEFTTIPGVREDVS 76

Query: 84  DIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           +IILN+K + +K   +      + +   G    TA D+   +DIE+LNP   I  LD DA
Sbjct: 77  EIILNLKQVRMKFHKEDQMEADIIVDISGECDFTAADLNVNSDIEILNPTLHIATLDEDA 136

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            +RM+  + +G GYVP+  ++ + D IG+I ID+++SPI +  Y V + R G  +DYD L
Sbjct: 137 HIRMQCHIERGKGYVPSTKNKKDTDVIGVIPIDSIFSPILRAKYEVGNVRVGNEMDYDSL 196

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK------------------E 243
           +M + TDGS+T ED++A ++ IL   L        P + ++                  E
Sbjct: 197 TMEVLTDGSLTAEDAMAESASILSSYLEKIKQLAAPGRNLQQGKFTEDELGAGANGANAE 256

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                         + ++ L+LSVR++NCL+  NI  + +LI  T++D+ ++ N G KS+
Sbjct: 257 GAGADGTDMGEGGDESIDTLQLSVRASNCLKRANIYTIKELISHTKSDLGKIRNLGSKSV 316

Query: 304 VEIKGVLGTMGLFL 317
            EI   L   G  L
Sbjct: 317 EEIIEKLSQFGYKL 330


>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 =  292 bits (747), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 122/323 (37%), Positives = 192/323 (59%), Gaps = 10/323 (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  LHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDI-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 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF----INFEEPKKEV 241
           +VE  R  Q  DYDKL + + TDGSI+ +D++  A++IL     +F    I  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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L  + L  G ++  +
Sbjct: 303 SLTELDDLLLGLNLSFGTDISKY 325


>gi|312271196|gb|ADQ57295.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 253

 Score =  292 bits (747), Expect = 7e-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|297180267|gb|ADI16486.1| DNA-directed RNA polymerase, alpha subunit/40 kd subunit
           [uncultured bacterium HF4000_05M23]
          Length = 328

 Score =  292 bits (747), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 112/317 (35%), Positives = 174/317 (54%), 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 DIMATADFEIVNPEHHLATLDSAMARLSVEFNVEQGVGYQPAIQ--EEGLPIGVLLVDAI 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    ++D               VE L LS R+ NCL+      +G+++   +++++++ 
Sbjct: 239 PVGG-EDDKPGIDGVTPEVFNTLVETLALSARTHNCLKRAGFNRVGEILLLPKSELMKIR 297

Query: 297 NFGRKSLVEIKGVLGTM 313
            FG+KSL E+   L   
Sbjct: 298 GFGQKSLDELYVKLAEK 314


>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 =  292 bits (747), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 100/312 (32%), Positives = 168/312 (53%), Gaps = 13/312 (4%)

Query: 16  EYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           E   +    E    + +    EPL +G   TLGNALRR L++ L G AI AV+I GV HE
Sbjct: 5   EIECIESTREGLRDHYSKFCLEPLNQGQGTTLGNALRRTLLADLEGTAIVAVRIAGVSHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            S+I G+ ED+ +I+LN+K + LK    +     +  +GP +VT   ++  ++IE+++P+
Sbjct: 65  FSTIPGIREDVLEILLNLKEVVLKSQIGTSGVGRLRVQGPAIVTTNHLELPSEIELIDPN 124

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             I  +  + ++ ME  +  G GY   +    E   I  + +DA++ P+KKV+Y  +  R
Sbjct: 125 QYIATICGNNILEMEFRIETGKGYNLVERDSDE-SSIDFLQVDAIFMPVKKVNYLSKDIR 183

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
               L  ++L++ + T+GSI  +D+V+ A +IL + L         +   K D +   + 
Sbjct: 184 SENNLIQEQLTLEVWTNGSIDPQDAVSQAGKILTELLFPL-----KEINFKPDDSESIIE 238

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
            +      +EEL+LSVR+ NCL+   I  + DL+  ++ D++ + NFG+KS  E+   L 
Sbjct: 239 DSKINQILIEELQLSVRAYNCLKRAQIHSVADLLDYSQEDLIEIKNFGQKSAEEVIDAL- 297

Query: 312 TMGLFLGMNLPD 323
                LG+NLP 
Sbjct: 298 --QKRLGINLPK 307


>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 (745), Expect = 9e-77,   Method: Composition-based stats.
 Identities = 112/311 (36%), Positives = 188/311 (60%), Gaps = 4/311 (1%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
            NIE + + +E+ +       PL RG+  T+GN++RRVL+SSL G++++ + IDGVLHE 
Sbjct: 7   TNIEILDINEED-HYGKFALYPLERGYGTTIGNSMRRVLLSSLPGSSVSKILIDGVLHEF 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 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           G+  D+DKL + + T+G++T ++++A    IL ++   F    + K   +E    + L  
Sbjct: 186 GESTDFDKLIIEVWTNGTVTPQEALAEGLSILMNKFAFFKELPDKKFPPEEIETTEELAA 245

Query: 253 NPAL---LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           +       + +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|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 =  291 bits (745), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 94/305 (30%), Positives = 160/305 (52%), Gaps = 9/305 (2%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                 +     I EPL +G   TLGN+LRR ++S L+GAAI AV+I G+ HE S+I GV
Sbjct: 12  KTESNRQQYGRFILEPLNKGQGITLGNSLRRTILSDLQGAAIVAVRIAGINHEFSTITGV 71

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+ +I+LN+K + LK   D+ +   I  +GP ++T G  +   +I +++P   I  + 
Sbjct: 72  REDVLEILLNLKKVVLKSHSDTPQIGRIRLQGPAIITTGLFEVPPEILIIDPQQYIATIC 131

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            + +  ME  + KG GY        +   I  + IDA++ P+ K +YTVE  +   +L  
Sbjct: 132 NNTIFEMEFRIEKGSGYKLVNKG-FDKKSIDFLQIDAVFMPVTKFNYTVEEKKISPILIQ 190

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           +KL + + T+GS++ +++++  +++L                 +   N  +         
Sbjct: 191 EKLFLEVWTNGSLSPQEAISEGAQVLHSLFYPLT-----NLNFQNANNTDNEYEEEINQV 245

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +EEL+LSVR+ NCL+   I  + DL+  ++ ++L + NFG+KS  E+   L      LG
Sbjct: 246 LIEELQLSVRAYNCLKRAQINSISDLLDYSQDELLEIKNFGQKSAEEVIEALQNK---LG 302

Query: 319 MNLPD 323
           + LP 
Sbjct: 303 IRLPK 307


>gi|157493285|gb|ABV58008.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 272

 Score =  291 bits (745), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 122/275 (44%), Positives = 188/275 (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++  + +   +++   +  P    LL+ V++LEL+VR
Sbjct: 181 GTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVR 237

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL
Sbjct: 238 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL 272


>gi|318042541|ref|ZP_07974497.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp.
           CB0101]
          Length = 312

 Score =  291 bits (745), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 101/309 (32%), Positives = 165/309 (53%), Gaps = 14/309 (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 GQ-VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM---FINFEEPKKEVKEDINVK 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 I---------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIE 296

Query: 309 VLGTMGLFL 317
            L  +G+ L
Sbjct: 297 ALERIGISL 305


>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 =  291 bits (744), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 115/323 (35%), Positives = 188/323 (58%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +  +   +  +        PL  G+  T+GN+LRRVL+SSL G AIT+++I+GV
Sbjct: 6   FQKPDRVIEV---ESGDKYGKFEFHPLESGYGITIGNSLRRVLLSSLEGYAITSIKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR--VTIFKRGPGVVTAGDI-QTVNDI 125
            +E + + GV ED+T+IIL +K +  K      +   V +         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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SLVE+  +L  + L  GM++  +
Sbjct: 303 SLVELDELLAKLNLTFGMDIEKY 325


>gi|58416042|emb|CAH57435.1| RNA polymerase alpha-subunit [Vibrio sp. R-21432]
          Length = 287

 Score =  291 bits (744), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 123/293 (41%), Positives = 190/293 (64%), Gaps = 11/293 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +KP  ++   + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GV
Sbjct: 1   FLKPRLVD---IEQVSTTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGV 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 AYSVEAARVEQRTDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEK 237

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           +   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 238 EEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTP 287


>gi|308522652|dbj|BAJ22937.1| RNA polymerase alpha subunit [Aliivibrio sp. LC2-088]
          Length = 271

 Score =  291 bits (744), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 125/274 (45%), Positives = 187/274 (68%), 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++  + +   +++   +  P    LL+ V++LEL+V
Sbjct: 181 NGTLDPEEAIRRAATILAEQLDVFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTV 237

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+K
Sbjct: 238 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKK 271


>gi|328813979|gb|AEB52105.1| DNA-directed RNA polymerase alpha chain [Lactobacillus helveticus]
          Length = 263

 Score =  291 bits (744), Expect = 1e-76,   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|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 =  291 bits (744), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 115/355 (32%), Positives = 191/355 (53%), Gaps = 21/355 (5%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +   + +   P+ I        E N    +AEP  RGF HT+GNALRR+++SSL   AI 
Sbjct: 1   MSVKYGKFEMPHKITVDQ-ESPESNFARYVAEPFERGFGHTIGNALRRMMLSSLEAPAII 59

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM--SGDSHKRVTI------------- 106
           +V+++G+ HE  +I+G+ ED+T+IILN KG  L+   + ++ +   I             
Sbjct: 60  SVRVEGIPHEYMAIEGISEDMTNIILNFKGALLRKLPTEETPRDTRILTKVVEVTQDDLD 119

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
             +G   VT  D+    + E++NP+  +  +      +++L ++ G GYVP++ H   + 
Sbjct: 120 RNQGQYCVTLQDVVQEGNFEIVNPELHLFTVTKPMRRQVDLRIAFGRGYVPSERHVVRDK 179

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
               I +DA +SP++ ++Y +E+ R GQ  D+D+L M + TDG IT  ++++ A +I   
Sbjct: 180 TSDEILVDAAFSPVRLINYFIENTRVGQDTDFDRLIMEVTTDGRITPAEALSFAVQIGLK 239

Query: 227 QLGMFINFEEPKKEVKEDINVKSLPFNPALLKK---VEELELSVRSTNCLRGENIVYMGD 283
              +F  F        E    ++   +  + K    ++E+ELSVRS NCL G NI  + +
Sbjct: 240 HFEVFNQFNNYALSFDEKDGDRNGDQDELMDKLSLGIDEIELSVRSANCLTGANIETLAE 299

Query: 284 LIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP--PESIEELAKKY 336
           L+   E  ML   NFG+KSL EIK  L  M L LGM+L  +   P+++++  K+Y
Sbjct: 300 LVCIPERRMLEFRNFGKKSLNEIKAKLHEMSLHLGMDLSRFGVSPDNVKDKIKQY 354


>gi|328813937|gb|AEB52084.1| DNA-directed RNA polymerase alpha chain [Lactobacillus brevis]
          Length = 263

 Score =  291 bits (744), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 117/263 (44%), Positives = 173/263 (65%), 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 TVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           T  KG GYV A     R  + 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|260656834|gb|ACX47807.1| RNA polymerase alpha-subunit [Vibrio litoralis]
          Length = 276

 Score =  290 bits (743), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 126/279 (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  L-KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-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++  + +   +++   +  P    LL+ V++LEL+VR
Sbjct: 181 GTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVR 237

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
           S NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK
Sbjct: 238 SANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIK 276


>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 =  290 bits (743), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 125/274 (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  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++  + +   +++   +  P    LL+ V++LEL+V
Sbjct: 181 NGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTV 237

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           RS NCL+ E I Y+GDL+QRTE ++L+  N G+K
Sbjct: 238 RSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKK 271


>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 =  290 bits (742), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 121/358 (33%), Positives = 184/358 (51%), Gaps = 27/358 (7%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +   P  I         +     IAEP  +GF HT+GN+LRR+++SSL   AI +V+I+G
Sbjct: 7   KFEIPQQISVDE-ETLSQTFGRFIAEPFEKGFGHTVGNSLRRMMLSSLEAPAIVSVRIEG 65

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK---------MSGDSHKRVTIFKR--------G 110
           + HE  +I+G+ ED+T+IILN+KG  ++            D      +           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------PESIEELAKKYEDK 339
            E  ML   NFG+KSL EIK  L  MGL LGM+L  +        E I +  K+ +DK
Sbjct: 306 PERRMLEFRNFGKKSLNEIKAKLTEMGLHLGMDLSKYGITADNVKEKIAQYHKEAKDK 363


>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 =  289 bits (741), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 105/306 (34%), Positives = 166/306 (54%), Gaps = 8/306 (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 GQ-VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           G+     ++L + I+T+GSIT +D++A A+  L             ++  +E        
Sbjct: 186 GEGGSARERLRLEIETNGSITPDDAMAQAANQLIALFQPLATLSVVEEPGQEPEPSAEAQ 245

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 246 I------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLFL 317
            +G+ L
Sbjct: 300 RIGITL 305


>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 =  289 bits (741), Expect = 3e-76,   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 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV------KEDINVKSLP 251
           +DKL++ ++TDGSI   D+++ A  +L+     F++     + +      +E   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|270265495|emb|CBI68384.1| RNA polymerase alpha-subunit [Vibrio tapetis]
          Length = 286

 Score =  289 bits (741), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 123/288 (42%), Positives = 187/288 (64%), Gaps = 8/288 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            + + Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T V+I+GVLHE S+ +
Sbjct: 2   LVDIEQVSATHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIEGVLHEYSTKE 61

Query: 77  GVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
           GV ED+ +I+LN+KG+ +K+  G     +T+ K G G V AGDI    D+E+ NP+HVIC
Sbjct: 62  GVQEDILEILLNLKGLAVKVAEGKDEVFITLNKSGSGPVVAGDITHDGDVEIANPEHVIC 121

Query: 136 NLDVD-AVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
           +L  D A + M + V +G GYVPA    H   +  PIG + +DA YSP+ K++Y VE+AR
Sbjct: 122 HLTDDNAEIAMRIKVERGRGYVPASSRIHTEEDERPIGRLLVDATYSPVDKIAYAVEAAR 181

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
             Q  D DKL + ++T+G++  E+++  ++ IL +QL  F++  + +   +++   +  P
Sbjct: 182 VEQRTDLDKLVIDMETNGTLDPEEAIRRSATILAEQLDAFVDLRDIRVPEEKEEKPEFDP 241

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
               LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G
Sbjct: 242 ---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLG 286


>gi|328813995|gb|AEB52113.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 254

 Score =  289 bits (741), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 119/254 (46%), Positives = 169/254 (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 SKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 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 RSTNCLRGENIVYM 281
           RS NCL+   I  +
Sbjct: 241 RSYNCLKRAGINTV 254


>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 =  289 bits (740), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 108/297 (36%), Positives = 164/297 (55%), Gaps = 3/297 (1%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           + ++    + EPL RGF  TLGN LRR+L+SS+ G A+T+V I+ VLHE S+I GV ED+
Sbjct: 16  QGDHYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDV 75

Query: 83  TDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
            +IILN+K + ++      +  + +   GP  V A D     D+E++NPD  I  L+   
Sbjct: 76  VEIILNLKELVVRFLDPRWRTTLILRAEGPKEVRAVDFTPSADVEIMNPDLHIATLEEGG 135

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + ME+ V +G GYVPA+ H  ++  I  I +DA++SP+++V++ VE  R GQ  D DKL
Sbjct: 136 KLYMEVRVDRGVGYVPAERHGIKDR-INAIPVDAIFSPVRRVAFQVEDTRLGQRTDLDKL 194

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP-KKEVKEDINVKSLPFNPALLKKV 260
           ++ I TDGS+T  +++  A  IL++ L  F N E       +     K       L   +
Sbjct: 195 TLRIWTDGSVTPLEALNQAVAILKEHLNYFANPEASLLPTPEVSKGEKRESAEEDLDLPL 254

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           EEL LS R  + L+ E I  +  L+     D+  +   G +SL EI+  L   G  L
Sbjct: 255 EELGLSTRVLHSLKEEGIESVRALLALNLKDLRNIPGIGERSLEEIRQALAKKGFTL 311


>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 =  289 bits (740), Expect = 4e-76,   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|311990466|gb|ADQ26363.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 257

 Score =  289 bits (740), Expect = 4e-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|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 =  289 bits (739), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 109/298 (36%), Positives = 164/298 (55%), Gaps = 4/298 (1%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           + ++    + EPL RGF  TLGN LRR+L+SS+ G A+T+V I+ VLHE S+I GV ED+
Sbjct: 16  QGDHYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDV 75

Query: 83  TDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
            +IILN+K + ++          + +   GP  V AGD     D+E++NPD  I  L+  
Sbjct: 76  VEIILNLKELVVRFLDPKMASTTLILRAEGPKEVRAGDFTPSADVEIMNPDLHIATLEEG 135

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             + ME+ V +G GYVPA+ H  ++  I  I +DA++SP+++V++ VE  R GQ  D DK
Sbjct: 136 GKLYMEVRVDRGVGYVPAERHGIKDR-INAIPVDAIFSPVRRVAFQVEDTRLGQRTDLDK 194

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP-KKEVKEDINVKSLPFNPALLKK 259
           L++ I TDGS+T  +++  A  IL++ L  F N E       +     K       L   
Sbjct: 195 LTLRIWTDGSVTPLEALNQAVAILKEHLNYFANPEASLLPTPEVSKGEKRESAEEDLDLP 254

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +EEL LS R  + L+ E I  +  L+     D+  +   G +SL EI+  L   G  L
Sbjct: 255 LEELGLSTRVLHSLKEEGIESVRALLALNLKDLRNIPGIGERSLEEIRQALAKKGFTL 312


>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 =  289 bits (739), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 98/315 (31%), Positives = 165/315 (52%), Gaps = 13/315 (4%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
              E   +    +    + +    EPL +G   TLGNALRR L+S L G AI AV+I GV
Sbjct: 2   TKFEIECVESTTDGARDHYSKFCLEPLEQGQGVTLGNALRRTLLSDLEGTAIVAVRIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ ED+ +I+LN+K + LK    +     +  +GP +VT  +++  +++E++
Sbjct: 62  SHEFSTIPGIREDVLEILLNLKEVVLKSQTKNPSVGRLRVQGPAIVTTSNLELPSEVELI 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +P+  I  +  + ++ ME  +  G GY   +    E   I  + +DA++ P+KKV+Y  +
Sbjct: 122 DPNQYIATICGNNILEMEFRIETGKGYHLIERSIDE-TSIDFLQVDAIFMPVKKVNYLTK 180

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
             R    L  ++L + + T+GSI  +D+V+   +IL + L         +   K D    
Sbjct: 181 DIRSNDNLLQEQLLLEVWTNGSIDPQDAVSQGGKILTELLHPL-----KEINFKSDEEDT 235

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
               +      +EEL+LSVR+ NCL+   I  + DL+  ++ D++ + NFG+KS  E+  
Sbjct: 236 VAEDSKINQILIEELQLSVRAYNCLKRAQIHSVADLLDYSQEDLIEIKNFGQKSAEEVID 295

Query: 309 VLGTMGLFLGMNLPD 323
            L      LG+NLP 
Sbjct: 296 AL---QKRLGINLPK 307


>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 =  289 bits (739), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 120/323 (37%), Positives = 194/323 (60%), Gaps = 10/323 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             KP+ +   ++ + +         PL  GF  T+GNALRR+L+SSL G AIT ++IDGV
Sbjct: 6   FQKPDKV---LMLEADSRFGKFEFRPLEPGFGITVGNALRRILLSSLEGFAITTIKIDGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-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 SLVEIKGVLGTMGLFLGMNLPDW 324
           SL E+  +L ++ L  G ++  +
Sbjct: 303 SLTELDDLLESLSLSFGTDISKY 325


>gi|328814003|gb|AEB52117.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 261

 Score =  289 bits (739), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 121/261 (46%), Positives = 171/261 (65%), Gaps = 2/261 (0%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I    E +N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+G
Sbjct: 1   IHKIDENDNYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEG 60

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+T IILN+K I LK+  D  K + I  +GP  VTAGDI    D+EVLNPD  IC +
Sbjct: 61  VTEDVTAIILNVKKIALKLESDETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTV 120

Query: 138 DVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
              A   M +T + G GYV A    HR ++ PIG++ +D+LYSPI++V+Y VE+ R GQ 
Sbjct: 121 ADGAHFHMRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQR 180

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
            D+DKL++ + T+GSIT  ++++L+++IL D L +F+N  +  K     +  +       
Sbjct: 181 DDFDKLTLDVWTNGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKEKM 240

Query: 256 LLKKVEELELSVRSTNCLRGE 276
           L   +EEL+LSVRS NCL+  
Sbjct: 241 LEMTIEELDLSVRSYNCLKRA 261


>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 =  289 bits (739), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 109/298 (36%), Positives = 163/298 (54%), Gaps = 4/298 (1%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           +  +    + EPL RGF  TLGN LRR+L+SS+ G A+T+V I+ VLHE S+I GV ED+
Sbjct: 16  QGRHYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDV 75

Query: 83  TDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
            +IILN+K + ++          + +   GP  V AGD     D+E++NPD  I  L+  
Sbjct: 76  VEIILNLKELVVRFLDPKMASTTLILRAEGPKEVRAGDFTPSADVEIMNPDLHIATLEEG 135

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             + ME+ V +G GYVPA+ H  ++  I  I +DA++SP+++V++ VE  R GQ  D DK
Sbjct: 136 GKLYMEVRVDRGVGYVPAERHGIKDR-INAIPVDAIFSPVRRVAFQVEDTRLGQRTDLDK 194

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP-KKEVKEDINVKSLPFNPALLKK 259
           L++ I TDGS+T  +++  A  IL++ L  F N E       +     K       L   
Sbjct: 195 LTLRIWTDGSVTPLEALNQAVAILKEHLNYFANPEASLLPTPEVSKGEKRESAEEDLDLP 254

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +EEL LS R  + L+ E I  +  L+     D+  +   G +SL EI+  L   G  L
Sbjct: 255 LEELGLSTRVLHSLKEEGIESVRALLALNLKDLRNIPGIGERSLEEIRQALAKKGFTL 312


>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 =  288 bits (738), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 136/280 (48%), Positives = 188/280 (67%), 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 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLI 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 A---DLQGTPVEEVEEKAPPIDPVLLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETE 237

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +L+  N GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 238 LLKTPNLGRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 277


>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 =  288 bits (737), Expect = 9e-76,   Method: Composition-based stats.
 Identities = 90/347 (25%), Positives = 165/347 (47%), Gaps = 26/347 (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 DNTQHIASLTEPIELCIGLQIERNRGY--LIKTPNNNSKDGSYPIDAVFMPVRNANHSIH 188

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    +  + ++ 
Sbjct: 189 SYGNGND-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHTEEENLHLANNQHMV 247

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            LP      K                 +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 248 PLPPFTFHDKLDKLRKNKKKRALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQEDL 307

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           +++ +F  K   ++K +LG +     +NL   P    E LA+  + K
Sbjct: 308 MKIEHFRIK---DVKQILGILEKNFSINLGKKPKMGFESLAQLIDSK 351


>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 =  288 bits (737), Expect = 9e-76,   Method: Composition-based stats.
 Identities = 122/281 (43%), Positives = 185/281 (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++  + +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE 
Sbjct: 181 FVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEV 237

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           ++L+  N G+KSL EIK VL + GL LGM L +WPP SI E
Sbjct: 238 ELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAE 278


>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 =  288 bits (737), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 134/280 (47%), Positives = 186/280 (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 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLI 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 A---DLQGTPVEEVEEKAPPIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETE 237

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +L+  N GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 238 LLKTPNLGRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 277


>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 =  288 bits (736), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 111/315 (35%), Positives = 168/315 (53%), Gaps = 25/315 (7%)

Query: 27  RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDII 86
               + EPL RG+  T+GN +RR+LMSS+ G A+T+V I+ VLHE S+I GV ED+  II
Sbjct: 16  YGEFVLEPLTRGYGVTIGNPIRRILMSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVIRII 75

Query: 87  LNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           LN+K + +K      K +T+  +G GVV A   +  +D E++NPD  I  L  D  + ME
Sbjct: 76  LNLKELVVKFHAPGPKTLTLRAQGEGVVKASAFEVPSDAEIVNPDLTIATLAEDGKLVME 135

Query: 147 LTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
           + V +G GYVPA  H T++  I  I +DA++SP+++V+Y VE+ R GQ  D D+L + I 
Sbjct: 136 VRVEEGEGYVPADKHATKDR-INSIPVDAVFSPVRRVAYHVENTRVGQQTDLDRLILRIW 194

Query: 207 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL---------- 256
           TDGS+  ++++  A  IL+D+L +F N E       E  +V +                 
Sbjct: 195 TDGSVGPQEALDRAVEILRDELTVFGNVETVSAAAPELPSVYTPAAPIVSGYDLPRQPEL 254

Query: 257 --------------LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +E L L+ R  + L+ E I  +  L   ++ D+ ++   G +S
Sbjct: 255 SINPQPYPADLDTPRVTLEGLGLTTRVLHSLKEEGIDSVDALCALSDRDLKKVPGIGERS 314

Query: 303 LVEIKGVLGTMGLFL 317
           L EIK  L   GL L
Sbjct: 315 LDEIKQQLAQFGLAL 329


>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 =  288 bits (736), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 108/298 (36%), Positives = 163/298 (54%), Gaps = 4/298 (1%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           + ++    + EPL RGF  TLGN LRR+L+SS+ G A+T+V I+ VLHE S+I GV ED+
Sbjct: 16  QGDHYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDV 75

Query: 83  TDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
            +IILN+K + ++          + +   GP  V A D     D+E++NPD  I  L+  
Sbjct: 76  VEIILNLKELVVRFLDPKMASTTLILRAEGPKEVRAVDFTPSADVEIMNPDLHIATLEEG 135

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
             + ME+ V +G GYVPA+ H  ++  I  I +DA++SP+++V++ VE  R GQ  D DK
Sbjct: 136 GKLYMEVRVDRGVGYVPAERHGIKDR-INAIPVDAIFSPVRRVAFQVEDTRLGQRTDLDK 194

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK-KEVKEDINVKSLPFNPALLKK 259
           L++ I TDGS+T  +++  A  IL++ L  F N E       +     K       L   
Sbjct: 195 LTLRIWTDGSVTPLEALNQAVAILKEHLNYFANPEASSLPTPEVSKGEKRESAEEDLDLP 254

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +EEL LS R  + L+ E I  +  L+     D+  +   G +SL EI+  L   G  L
Sbjct: 255 LEELGLSTRVLHSLKEEGIESVRALLALNLKDLRNIPGIGERSLEEIRQALAKKGFTL 312


>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 =  287 bits (735), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 110/307 (35%), Positives = 181/307 (58%), Gaps = 7/307 (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 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV-------KEDINVKSL 250
           +DKL++ ++TDGSI   D+++ A  +L+  L  F+      + +        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 GTMGLFL 317
             +G  L
Sbjct: 329 KDLGYDL 335


>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 =  287 bits (735), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 113/308 (36%), Positives = 182/308 (59%), Gaps = 7/308 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            I   +E   +   I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + 
Sbjct: 18  KITEVKESNYKGQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMD 77

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV E +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ VIC 
Sbjct: 78  GVKEAVTEIILNVKEIVVKAESSGERRMTLSIKGPKVVKAADIVADIGLEIVNPEQVICT 137

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +  D  + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ 
Sbjct: 138 VTTDRTLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMT 197

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF---- 252
           D+DKL++ ++TDGSI   D+++ A  +L+  L  F+      + +++DI           
Sbjct: 198 DFDKLTLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEIIEEPMDIQ 257

Query: 253 ---NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   
Sbjct: 258 VVDDKSHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEK 317

Query: 310 LGTMGLFL 317
           +  +G  L
Sbjct: 318 MKDLGYDL 325


>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 =  287 bits (735), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 110/312 (35%), Positives = 182/312 (58%), Gaps = 8/312 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             I    + +E   +   + EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GV+ E 
Sbjct: 25  KQINITEV-KESNYKGQFVVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVMSEF 83

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           + + GV E +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ 
Sbjct: 84  TVMDGVKEAVTEIILNVKEIVVKAESSGERRMTLSVKGPKVVKAADIVADIGLEIVNPEQ 143

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           VIC +  D  + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    
Sbjct: 144 VICTVTTDRTLDMEFLVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMF 203

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV-------KEDI 245
           G++ D+DKL++ ++TDGSI   D+++ A  +L+  L  F+      + +        E+ 
Sbjct: 204 GRITDFDKLTLNVETDGSIEIRDALSYAVELLKLHLDPFLEIGNKMENLRDEIEEIIEEP 263

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
               +  + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL E
Sbjct: 264 IDIQVIDDKSHDMKIEELDLTVRSFNCLKKAGIEDVSQLASLSLNELLKIKNLGKKSLDE 323

Query: 306 IKGVLGTMGLFL 317
           I   +  +G  L
Sbjct: 324 ILEKMKDLGYDL 335


>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 =  287 bits (735), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 113/308 (36%), Positives = 182/308 (59%), Gaps = 7/308 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            I   +E   +   I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + 
Sbjct: 28  KITEVKESNYKGQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMD 87

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV E +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ VIC 
Sbjct: 88  GVKEAVTEIILNVKEIVVKAESSGERRMTLSIKGPKVVKAADIVADIGLEIVNPEQVICT 147

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +  D  + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ 
Sbjct: 148 VTTDRTLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMT 207

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF---- 252
           D+DKL++ ++TDGSI   D+++ A  +L+  L  F+      + +++DI           
Sbjct: 208 DFDKLTLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEIIEEPMDIQ 267

Query: 253 ---NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   
Sbjct: 268 VVDDKSHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEK 327

Query: 310 LGTMGLFL 317
           +  +G  L
Sbjct: 328 MKDLGYDL 335


>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 =  287 bits (735), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 137/280 (48%), Positives = 186/280 (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 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLI 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 ANLQGTPVE---EVEEKAPPIDPVLLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETE 237

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +L+  N GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 238 LLKTPNLGRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 277


>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 =  287 bits (735), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 112/303 (36%), Positives = 168/303 (55%), 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  DIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 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  I +DALYSP+++V+Y VE  R GQ  D DKL
Sbjct: 136 KLVMEIRVDEGVGYVPAEKHGIKDR-ISSIPVDALYSPVRRVAYQVEDTRLGQRTDLDKL 194

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK--- 258
           ++ I T+G+++  D++  A  IL++QLG F      + E K                   
Sbjct: 195 TLRIWTNGAVSPMDALQQAVAILREQLGYFDQSPVMRVEPKSTPAPAPAAPATTAPAAPA 254

Query: 259 ------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 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|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 =  287 bits (734), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 100/306 (32%), Positives = 165/306 (53%), Gaps = 8/306 (2%)

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 GQ-VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           G+     ++L + I+T+GSIT +D++A A+  L             ++  +E        
Sbjct: 186 GEGGSARERLRLEINTNGSITPDDALAYAANQLIALFQPLATVTLAEEPGQEPEPSAESQ 245

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 246 I------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGAKSADEVIEALE 299

Query: 312 TMGLFL 317
            +G+ L
Sbjct: 300 RIGISL 305


>gi|328813993|gb|AEB52112.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 253

 Score =  287 bits (734), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 119/253 (47%), Positives = 169/253 (66%), 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 MELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 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 LELSVRSTNCLRG 275
           L+LSVRS NCL+ 
Sbjct: 241 LDLSVRSYNCLKR 253


>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 =  287 bits (734), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 113/308 (36%), Positives = 182/308 (59%), Gaps = 7/308 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            I   +E   +   I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + 
Sbjct: 18  KITEVKESNYKGQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMD 77

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV E +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ VIC 
Sbjct: 78  GVKEAVTEIILNVKEIVVKAESSGERRMTLSIKGPKVVKAADIVADIGLEIVNPEQVICT 137

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +  D  + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ 
Sbjct: 138 VTTDRTLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMT 197

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF---- 252
           D+DKL++ ++TDGSI   D+++ A  +L+  L  F+      + +++DI           
Sbjct: 198 DFDKLTLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEIIEEPMDIQ 257

Query: 253 ---NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   
Sbjct: 258 VIDDKSHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEK 317

Query: 310 LGTMGLFL 317
           +  +G  L
Sbjct: 318 MKDLGYDL 325


>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 =  287 bits (734), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 110/312 (35%), Positives = 182/312 (58%), Gaps = 8/312 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             I    + +E   +   + EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GV+ E 
Sbjct: 25  KQINITEV-KESNYKGHFVVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVMSEF 83

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           + + GV E +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ 
Sbjct: 84  TVMDGVKEAVTEIILNVKEIVVKAESSGERRMTLSVKGPKVVKAADIVADIGLEIVNPEQ 143

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
           VIC +  D  + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    
Sbjct: 144 VICTVTTDRTLDMEFLVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMF 203

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV-------KEDI 245
           G++ D+DKL++ ++TDGSI   D+++ A  +L+  L  F+      + +        E+ 
Sbjct: 204 GRITDFDKLTLNVETDGSIEIRDAISYAVELLRLHLDPFLEIGNKMENLRDEIEEIIEEP 263

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
               +  + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL E
Sbjct: 264 IDIQVIDDKSHDMKIEELDLTVRSFNCLKKAGIEDVSQLASLSLNELLKIKNLGKKSLDE 323

Query: 306 IKGVLGTMGLFL 317
           I   +  +G  L
Sbjct: 324 ILEKMKDLGYDL 335


>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 =  286 bits (733), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 116/314 (36%), Positives = 184/314 (58%), Gaps = 9/314 (2%)

Query: 13  NNIEYIVLG-QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
              E  V+   E++        PL +G A  LGN+LRR+L+SS+ GAAI+ V+++ V HE
Sbjct: 5   RKPELEVIELSEDKRFGRFSCAPLVKGEATVLGNSLRRILLSSMPGAAISEVKVESVYHE 64

Query: 72  ISSIKGVHEDLTDIILNIKGINLK--MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
            SSI GV ED+++II+N+K + ++   S D      I   G GV+ A DI+  ++IE++N
Sbjct: 65  FSSIAGVKEDVSEIIMNLKKLAVRNTSSSDEAVMAYIDYAGEGVIRAADIRVSSEIEIVN 124

Query: 130 PDHVICNLD-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           P+ VI  L   DA + ME+ ++KG GY  A        PIG+I +DA+Y+P+ KV+ +V+
Sbjct: 125 PEQVIATLSGKDAKLYMEMKITKGRGYDGANTRDHSELPIGVIAVDAVYTPVTKVNVSVK 184

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
                     ++L + + T+G++  +D+V+LA++I+Q  L +FI+ +   KE     N  
Sbjct: 185 DLGRS-----ERLVLDVMTNGTLAPDDAVSLAAKIMQTHLQLFIDMDNTVKEPFLPGNTA 239

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  + K ++ELELSVRS NCL+   I  + DL ++T  D++++ N GRKSL EI  
Sbjct: 240 VEDVQDEMNKSIDELELSVRSYNCLKRAGINTVEDLCEKTMDDLMKVRNMGRKSLDEILN 299

Query: 309 VLGTMGLFLGMNLP 322
            L +MGL L   + 
Sbjct: 300 KLESMGLSLASKVE 313


>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 (733), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 133/280 (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 G V
Sbjct: 1   MNGFAPTEVAISGVLHEYSTVDGVQEDVVDILLNVKGIVFKLHGRGQVQLTLKKSGAGAV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLI 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 A---DLQGTPVEEVEEKAPPIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETE 237

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +L+  N GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 238 LLKTPNLGRKSLNEIKEVLASKGLTLGSKLEAWPPVGLEK 277


>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 =  286 bits (733), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 117/327 (35%), Positives = 173/327 (52%), Gaps = 18/327 (5%)

Query: 8   ELIKPNNIEYIVLGQEEENR-TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI- 65
           E + P  ++      E E      +  P+ +G+  T+GNALRRVL+SS+   AI  ++  
Sbjct: 3   EYVIPKKLKIEEERSETEYYYARYVLSPMEKGYGTTIGNALRRVLLSSIPSVAIVGIRFI 62

Query: 66  -DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV--TIFKRGPGVVTAGDIQTV 122
                HE  ++ GV ED+ +IILN+K I L+      +RV  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 AGFEIANPSLKIATLDEEADLFFELYAQAGKGFVPA-QEMDDHPEIGWIPIDGVFSPVMK 181

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG-----------MF 231
           V++ VESAR  +  DYDK+ + I T  +I   +++  A  IL + L              
Sbjct: 182 VNFRVESARVEKRTDYDKMILEIWTKKTIFPNEALKRAVDILMNHLQIITDSLPEGMPPL 241

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
                P  + +  +            KK++ELEL++RS NCLR + I  +GDL++RTE D
Sbjct: 242 TTEFVPISQEEVKVEQTVSEEEAVYSKKIDELELTIRSLNCLRRDKIETIGDLLKRTEED 301

Query: 292 MLRMANFGRKSLVEIKGV-LGTMGLFL 317
           +L++ NFG KSL E+K   L   GL L
Sbjct: 302 LLKIKNFGPKSLDEVKQKLLEKFGLSL 328


>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 =  286 bits (732), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 108/302 (35%), Positives = 171/302 (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  I +DAL+SP+++V++ VE  R GQ  D DKL++
Sbjct: 136 VMEVRVDEGVGYVPAEKHGIKDR-ISSIPVDALFSPVRRVAFQVEDTRLGQRTDLDKLTL 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|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 =  286 bits (732), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 89/307 (28%), Positives = 163/307 (53%), Gaps = 11/307 (3%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +    ++ +  + +PL  G   TLGNALRR L+S L G AITAV+I GV HE S+I G+
Sbjct: 12  KVYNARDHWSRFVIDPLKPGQGTTLGNALRRTLLSELEGLAITAVRIAGVSHEFSTINGI 71

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+ +I+LN+K I             +  +GP +VTA   +   +I++++P+  I  + 
Sbjct: 72  REDVLEILLNLKEIVFSGQLQESTIGRLTVQGPAIVTARSFELPPEIKLIDPEQYIATIC 131

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            +  + ME  +  G GY   +   +       + +D+++ P+KKV++ +E  R    +  
Sbjct: 132 GNNTLEMEFKIEVGSGYKIVEKDNSTE-HFEFLQVDSVFMPVKKVNFRIEETRGENNILN 190

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           ++L + I T+GSI+ +++++ A+  L +             + + + + ++   +     
Sbjct: 191 EQLILDIWTNGSISAKEAISNAADNLINLFSPL-----KTIDGESETDYETNETSHINQI 245

Query: 259 KVEELELSVRSTNCLRG--ENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
            +EEL+LSVR+ NCL+    +I  + DL+  ++ D++ + NFG+KS  E+   L      
Sbjct: 246 LIEELQLSVRAYNCLKRGCAHIHSVADLLDYSQEDLIEIKNFGQKSAEEVIDAL---QKR 302

Query: 317 LGMNLPD 323
           LG+NLP 
Sbjct: 303 LGINLPK 309


>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 =  286 bits (732), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 111/308 (36%), Positives = 182/308 (59%), Gaps = 7/308 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            I   +E   +   I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + 
Sbjct: 12  KITEVKESNYKGQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMD 71

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV E +T+IILN+K I +K      +R+++  +GP VV A DI     +E++NP+ VIC 
Sbjct: 72  GVKEAVTEIILNVKEIVVKAESSGERRMSLSIKGPKVVKAADIVADIGLEIVNPEQVICT 131

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +  D  + +E  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ 
Sbjct: 132 VTTDRTLDIEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMT 191

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF---- 252
           D+DKL++ ++TDGSI   D+++ A  +L+  L  F+      + +++DI           
Sbjct: 192 DFDKLTLNVETDGSIEIRDALSYAVELLKLHLDPFLEIGNKMENLRDDIEEMIEEPMDIQ 251

Query: 253 ---NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   
Sbjct: 252 VIDDKSHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEK 311

Query: 310 LGTMGLFL 317
           +  +G  L
Sbjct: 312 MKDLGYDL 319


>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 =  286 bits (732), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 111/308 (36%), Positives = 182/308 (59%), Gaps = 7/308 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            I   +E   +   I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + 
Sbjct: 28  KITEVKESNYKGQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMD 87

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV E +T+IILN+K I +K      +R+++  +GP VV A DI     +E++NP+ VIC 
Sbjct: 88  GVKEAVTEIILNVKEIVVKAESSGERRMSLSIKGPKVVKAADIVADIGLEIVNPEQVICT 147

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +  D  + +E  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ 
Sbjct: 148 VTTDRTLDIEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMT 207

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF---- 252
           D+DKL++ ++TDGSI   D+++ A  +L+  L  F+      + +++DI           
Sbjct: 208 DFDKLTLNVETDGSIEIRDALSYAVELLKLHLDPFLEIGNKMENLRDDIEEMIEEPMDIQ 267

Query: 253 ---NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   
Sbjct: 268 VIDDKSHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEK 327

Query: 310 LGTMGLFL 317
           +  +G  L
Sbjct: 328 MKDLGYDL 335


>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 =  286 bits (732), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 111/308 (36%), Positives = 182/308 (59%), Gaps = 7/308 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            I   +E   +   I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + 
Sbjct: 28  KITEVKESNYKGQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMD 87

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV E +T+IILN+K I +K      +R+++  +GP VV A DI     +E++NP+ VIC 
Sbjct: 88  GVKEAVTEIILNVKEIVVKAESSGERRMSLSIKGPKVVKAADIVADIGLEIVNPEQVICT 147

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +  D  + +E  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ 
Sbjct: 148 VTTDRALDIEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMT 207

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF---- 252
           D+DKL++ ++TDGSI   D+++ A  +L+  L  F+      + +++DI           
Sbjct: 208 DFDKLTLNVETDGSIEIRDALSYAVELLKLHLDPFLEIGNKMENLRDDIEEMIEEPMDIQ 267

Query: 253 ---NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   
Sbjct: 268 VIDDKSHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEK 327

Query: 310 LGTMGLFL 317
           +  +G  L
Sbjct: 328 MKDLGYDL 335


>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 =  286 bits (731), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 111/308 (36%), Positives = 182/308 (59%), Gaps = 7/308 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            I   +E   +   I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + 
Sbjct: 12  KITEVKESNYKGQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMD 71

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV E +T+IILN+K I +K      +R+++  +GP VV A DI     +E++NP+ +IC 
Sbjct: 72  GVKEAVTEIILNVKEIVVKAESSGERRMSLSIKGPKVVKAADIVADIGLEIVNPEQIICT 131

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +  D  + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ 
Sbjct: 132 VTTDRTLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMT 191

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF---- 252
           D+DKL++ ++TDGSI   D+++ A  +L+  L  F+      + +++DI           
Sbjct: 192 DFDKLTLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEMIEEPMDIQ 251

Query: 253 ---NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   
Sbjct: 252 VIDDKSHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEK 311

Query: 310 LGTMGLFL 317
           +  +G  L
Sbjct: 312 MKDLGYDL 319


>gi|34849417|gb|AAP58916.1| DNA-directed RNA polymerase alpha subunit [Spiroplasma kunkelii
           CR2-3x]
          Length = 317

 Score =  286 bits (731), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 106/316 (33%), Positives = 173/316 (54%), Gaps = 8/316 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           ++ I+P     +    +  N    + EPL RGF  TLGNA+RR L+S+  GAA+ AV+I 
Sbjct: 2   KQFIRPEF--KLQAEDKANNYGKFLVEPLERGFGVTLGNAIRRTLLSATPGAAVFAVRIK 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-----SHKRVTIFKRGPGVVTAGDIQT 121
           G  HE ++I GV E +T IILNIK + LK++ D         + +F    G + A D+  
Sbjct: 60  GSSHEFTAIPGVVEHVTKIILNIKNLVLKINQDIIPDGESVILKVFSSKEGEIYARDLVV 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
              +EV+N D ++  +     + +EL      GY     ++ E     LI ID+ Y PI+
Sbjct: 120 PTGVEVINGDLLLATIAKGGELDLELHARNSRGYKSFTDNKKEKKYADLIVIDSNYCPIQ 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +V+Y VE  + G+  D +KL + I TD SIT  ++VA+A++++ + L  F+N  E   + 
Sbjct: 180 RVAYNVEPTKVGKNADLEKLELEIQTDSSITPVNAVAMAAKVITEHLEFFVNLNE-AIKA 238

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            + I+ ++      L + ++ELE + RS NCL+   I  + DL+ ++E ++  + N G+K
Sbjct: 239 TQIISSEAEAEEDELDRSIDELEFTQRSQNCLKRAKIDTLRDLVSKSEDEIQEIRNLGKK 298

Query: 302 SLVEIKGVLGTMGLFL 317
           SL EIK  +  +GL  
Sbjct: 299 SLTEIKDKVAQLGLHF 314


>gi|324985144|gb|ADY69170.1| RNA polymerase subunit A [Photobacterium halotolerans]
          Length = 270

 Score =  286 bits (731), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 120/272 (44%), Positives = 182/272 (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++  + +   +++   +  P    LL+ V+
Sbjct: 182 VIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVD 238

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           +LEL+VRS NCL+ E I Y+GDL+QRTE ++L
Sbjct: 239 DLELTVRSANCLKAEAIHYIGDLVQRTEVELL 270


>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 =  286 bits (731), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 119/329 (36%), Positives = 183/329 (55%), Gaps = 18/329 (5%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQ   ++      +E   +  E+         PL +G+A T+GN LRRVL+SS+   AI
Sbjct: 1   MIQITGRKF----KLE-EQVEHEDHYYARYSLSPLEKGYAVTVGNTLRRVLLSSIPSFAI 55

Query: 61  TAVQI--DGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTA 116
           T V+       HE  +I+G  ED+ DI+LN+K + L++    +S  ++TI K+GPGV+TA
Sbjct: 56  TDVRFVKPEKYHEFDTIEGAKEDIMDILLNLKKVQLRVDTYVESPVKLTINKKGPGVLTA 115

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
           GDI+    + V+NP H +  L+ DA + +EL  + G G+VPA   R E   IG I +D +
Sbjct: 116 GDIECPAGVVVVNPGHYLATLNEDADLEIELYATFGKGFVPAA-DRNERPEIGWIVLDGV 174

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           YSP+ KV++ VE+ R  +  DY+KL + I T  SI   +++  + +I+ D          
Sbjct: 175 YSPVIKVNWLVENVRVDKRTDYEKLILEIWTKKSIKPSEALKHSLKIILDHFMFIEQSLS 234

Query: 237 PKKEVKED-------INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
             +E+          +  +       + KKVEELELS RS NCL+ + I  +GDL+ RTE
Sbjct: 235 DVEELPIPIIQETAVVTEEIGSPEDVMSKKVEELELSARSLNCLKRDKIETIGDLLSRTE 294

Query: 290 ADMLRMANFGRKSLVEIKGVL-GTMGLFL 317
            +++++ NFG KSL E++  L    GL L
Sbjct: 295 EELMKIKNFGLKSLEEVREKLRDKFGLSL 323


>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 =  286 bits (731), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 111/320 (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 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL------ 257
            + TDGS   +D++  +  IL+D+L +F N E     V +   V +    PA        
Sbjct: 192 RVWTDGSTGPQDALDKSVEILRDELTVFGNVEALPALVSDVAPVYTPTPVPAHNVYDLPP 251

Query: 258 --------------------KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
                                 +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 =  286 bits (731), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 112/308 (36%), Positives = 183/308 (59%), Gaps = 7/308 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            I   +E   ++  I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + 
Sbjct: 18  KITEVKESNYKSQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMD 77

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV E +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ +IC 
Sbjct: 78  GVKEAVTEIILNVKEIVVKAESSGERRMTLSIKGPKVVKAADIVADIGLEIVNPEQIICT 137

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +  D  + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ 
Sbjct: 138 VTTDRTLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMT 197

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF---- 252
           D+DKL++ ++TDGSI   D+++ A  +L+  L  F+      + +++DI           
Sbjct: 198 DFDKLTLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEMVDEPMDIQ 257

Query: 253 ---NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   
Sbjct: 258 VIDDKSHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEK 317

Query: 310 LGTMGLFL 317
           +  +G  L
Sbjct: 318 MKDLGYDL 325


>gi|328813971|gb|AEB52101.1| DNA-directed RNA polymerase alpha chain [Lactobacillus fermentum]
          Length = 257

 Score =  285 bits (730), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 114/257 (44%), Positives = 170/257 (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 SKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GY  A     R 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|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 =  285 bits (730), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 114/337 (33%), Positives = 186/337 (55%), Gaps = 12/337 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KN +  IKP  +E I    E         +PL RG+  T+GNALRRVL+SSL GAAI  V
Sbjct: 2   KNLK-FIKPFFVEEI---DENPISGKFTIKPLERGYGITVGNALRRVLLSSLPGAAIVNV 57

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG---DSHKRVTIFKRGPGVVTAGDIQ 120
           +I GV  E ++I GV+ED+  IILN+K I   +     D  +++ +  +GP  +TA   +
Sbjct: 58  KIQGVEQEFTTIPGVYEDVMTIILNLKKIVFAVDDESDDFEEKLELIAKGPQRLTAASFE 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSP 179
               ++++NPDH I  L  D    M +T+ KG GYV AK ++    + +G+I ID+L++P
Sbjct: 118 LPAGVKIINPDHYITTLSDDVCFHMTVTIKKGIGYVGAKENKVHIENQVGVIAIDSLFTP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +  VSY VE     ++ + D+L++ I T+G++  ++++A A+ IL D   + +   +   
Sbjct: 178 VVNVSYQVEK----KLGNKDELTIEITTNGALLAKEALATAASILVDHFNVLVELSQKPA 233

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            V+     K    N  L  ++E+L+LSVR  N L+   I  +  L++ +E +++++ + G
Sbjct: 234 HVEFVSESKKEAHNYVLDLEIEQLDLSVRLFNSLKRAGIDTVASLVKLSEKEVVKLKSLG 293

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKY 336
           RKS  E+K      GL     L +    S+EE   K+
Sbjct: 294 RKSFQELKDKFLEYGLEFNDYLKEALHHSVEEDKDKH 330


>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 =  285 bits (730), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 112/308 (36%), Positives = 183/308 (59%), Gaps = 7/308 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            I   +E   ++  I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + 
Sbjct: 28  KITEVKESNYKSQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMD 87

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV E +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ +IC 
Sbjct: 88  GVKEAVTEIILNVKEIVVKAESSGERRMTLSIKGPKVVKAADIVADIGLEIVNPEQIICT 147

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +  D  + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ 
Sbjct: 148 VTTDRTLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMT 207

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF---- 252
           D+DKL++ ++TDGSI   D+++ A  +L+  L  F+      + +++DI           
Sbjct: 208 DFDKLTLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEMVDEPMDIQ 267

Query: 253 ---NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   
Sbjct: 268 VIDDKSHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEK 327

Query: 310 LGTMGLFL 317
           +  +G  L
Sbjct: 328 MKDLGYDL 335


>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 =  285 bits (730), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 120/273 (43%), Positives = 185/273 (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++  + +   +++   +  P    LL+ V++LEL+
Sbjct: 181 TNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELT 237

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           VRS NCL+ E I Y+GDL+QRTE ++L+  N G
Sbjct: 238 VRSANCLKAEAIHYIGDLVQRTEVELLKTPNLG 270


>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 =  285 bits (730), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 108/315 (34%), Positives = 186/315 (59%), Gaps = 9/315 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  KPN I  + +  E+E     + EPL RG+  TLGN+L+R+++S+L G+A++A +I+G
Sbjct: 3   DFEKPN-IRVVEI-SEDERFGRFVCEPLERGYGTTLGNSLKRIMLSALPGSALSAAKIEG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQT---V 122
              +  S+ GV E L+++I+N+K + ++   DS   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 TEFVIANEEQSIATLTGEEALRIELLLSRGRGYVSAE--EQEELPEGMFALDSSYTPVER 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|328813981|gb|AEB52106.1| DNA-directed RNA polymerase alpha chain [Lactobacillus helveticus]
          Length = 249

 Score =  285 bits (730), Expect = 6e-75,   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|256027710|ref|ZP_05441544.1| DNA-directed RNA polymerase subunit alpha [Fusobacterium sp. D11]
          Length = 326

 Score =  285 bits (730), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 112/308 (36%), Positives = 183/308 (59%), Gaps = 7/308 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            I   +E   ++  I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + 
Sbjct: 12  KITEVKESNYKSQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMD 71

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV E +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ +IC 
Sbjct: 72  GVKEAVTEIILNVKEIVVKAESSGERRMTLSIKGPKVVKAADIVADIGLEIVNPEQIICT 131

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +  D  + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ 
Sbjct: 132 VTTDRTLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMT 191

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF---- 252
           D+DKL++ ++TDGSI   D+++ A  +L+  L  F+      + +++DI           
Sbjct: 192 DFDKLTLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEIVDEPMDIQ 251

Query: 253 ---NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   
Sbjct: 252 VIDDKSHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEK 311

Query: 310 LGTMGLFL 317
           +  +G  L
Sbjct: 312 MKDLGYDL 319


>gi|37912970|gb|AAR05302.1| DNA-directed RNA polymerase alpha subunit [uncultured marine gamma
           proteobacterium EB000-45B06]
          Length = 283

 Score =  285 bits (730), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 119/284 (41%), Positives = 183/284 (64%), Gaps = 3/284 (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 DLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
           DLI R+E D+L+  N G+KSL EIK VL +  L LGMN+ +WPP
Sbjct: 238 DLIHRSEFDLLKTPNLGKKSLNEIKDVLASKELSLGMNVDNWPP 281


>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 =  285 bits (729), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 118/334 (35%), Positives = 185/334 (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 DTNVLKASHFERD-GVEVFNKDLVIATLSHDVNLDFEFQINYGRGYVSSEQNSKYLEEVN 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 PLVDFED---SVSVSFDKSKSESSNLLDMSIEKLDLSVRSLNCLAKENVRTLGELISKNA 297

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            ++ +  NFG+KSL EI   LG+  LFLGM+  D
Sbjct: 298 EELSKARNFGKKSLEEIIEKLGSYQLFLGMSKED 331


>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 =  285 bits (729), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 116/330 (35%), Positives = 183/330 (55%), Gaps = 12/330 (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-----DGVLH----EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV-TIFKR 109
           IT+V+I     DGV H    E  SI  V ED  +I+ N+K I L +  +  +   T   +
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 ADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
             +    N G+KSL EI+G L    L LGM
Sbjct: 300 QTLASTRNVGKKSLSEIQGKLQEYNLRLGM 329


>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 =  285 bits (729), Expect = 7e-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|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 =  285 bits (729), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 111/297 (37%), Positives = 179/297 (60%), Gaps = 6/297 (2%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           E   +   + EPL RG+ HTLGNALRRVL+SS+ GAAI  ++I+GVL E S + GV E +
Sbjct: 18  ESAFKGQFVVEPLYRGYGHTLGNALRRVLLSSIPGAAIKGIRIEGVLSEFSVMDGVKEAV 77

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAV 142
           T+IILN+K I +K      +++T+  +GP VVTA DI     +E++NP+  IC +  D  
Sbjct: 78  TEIILNVKEIVVKSETAGERKMTLSVKGPKVVTAADIIPDIGLEIINPEQEICTITTDRS 137

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           + +E  V  G G+V ++    +   +  I +DA+Y+PI+KVSY ++    G++ D+DKL+
Sbjct: 138 LDIEFLVDTGEGFVVSEEIERDGWVVDYIAVDAIYTPIRKVSYEIQDTMVGRMTDFDKLT 197

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEP------KKEVKEDINVKSLPFNPAL 256
           ++++TDGSI   D+++ A  +L+  L  F+           + E + +    S+  +  L
Sbjct: 198 LSVETDGSIEIRDALSYAVELLKLHLDPFLEIGNKMENLRLEVEEEMENQSSSMKDDINL 257

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
             K+EEL+L+VRS NCL+   I  +G L + +  ++L++ N GRKSL EI   +  +
Sbjct: 258 NIKIEELDLTVRSFNCLKKAGIEEVGQLSKLSMNELLKIKNLGRKSLDEILEKMKEL 314


>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 =  285 bits (729), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 123/328 (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 VVNPSQYIATLNTDSVIYIELFAEIGRGFVPVSEMEIEHD-VEMIYIDGIFSPVLKVNFQ 192

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF--------------- 231
            E+ R G+  DYDKL + + T  SIT  D++  A+ IL     +F               
Sbjct: 193 TENVRVGKRTDYDKLILDVWTKKSITPSDALLRATDILIRHFEVFSNGLGKPGQGLTSSA 252

Query: 232 ------INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLI 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|317968839|ref|ZP_07970229.1| DNA-directed RNA polymerase subunit alpha [Synechococcus sp.
           CB0205]
          Length = 312

 Score =  285 bits (729), Expect = 8e-75,   Method: Composition-based stats.
 Identities = 96/306 (31%), Positives = 164/306 (53%), Gaps = 8/306 (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 GQ-VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           G+     ++L + I TDGS+T +D++A A+  L   +         +++ +E        
Sbjct: 186 GEGGSARERLRLEIQTDGSLTPDDAMAQAANQLITLIQPMATLTMEEEQGQEPEPSAEAQ 245

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 246 I------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLFL 317
            +G+ L
Sbjct: 300 RIGISL 305


>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 =  285 bits (729), Expect = 8e-75,   Method: Composition-based stats.
 Identities = 118/334 (35%), Positives = 185/334 (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 DTNVLKASHFERD-GVEVFNKDLVIATLSHDVNLDFEFQINYGRGYVSSEQNSKYLEEVN 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 PLVDFED---SVSVSFDKSKSESSNLLDMSIEKLDLSVRSLNCLAKENVRTLGELISKNA 295

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            ++ +  NFG+KSL EI   LG+  LFLGM+  D
Sbjct: 296 EELSKARNFGKKSLEEIIEKLGSYQLFLGMSKED 329


>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 =  285 bits (729), Expect = 8e-75,   Method: Composition-based stats.
 Identities = 126/351 (35%), Positives = 183/351 (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  LHEISSIKGVHEDLTDIILNIKGINLKMSG-----------------DSHKRVTIFKRGP 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 INFEEPKKEVKEDINVKSLPFNPALLK---KVEELELSVRSTNCLRGENIVYMGDLIQRT 288
              +       E         +  + K   +++E+ELSVRSTNCL G NI  + +L+   
Sbjct: 247 KKVQTQMVSFDEIKEDSDSDDDEIMDKLALRIDEIELSVRSTNCLSGANIETIAELVSIP 306

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYE 337
           E  ML   NFG+KSL EIK  L  MGL LGM+L  +    E++ E  K+Y+
Sbjct: 307 ERRMLEFRNFGKKSLTEIKAKLQEMGLGLGMDLSRYGITAENVREKIKEYQ 357


>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 =  285 bits (729), Expect = 8e-75,   Method: Composition-based stats.
 Identities = 112/308 (36%), Positives = 183/308 (59%), Gaps = 7/308 (2%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            I   +E   ++  I EPL RG+ +TLGNALRRVL+SS+ GAAI  ++I+GVL E + + 
Sbjct: 28  KITEVKESNYKSQFIVEPLYRGYGNTLGNALRRVLLSSIPGAAIKGMRIEGVLSEFTVMD 87

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV E +T+IILN+K I +K      +R+T+  +GP VV A DI     +E++NP+ +IC 
Sbjct: 88  GVKEAVTEIILNVKEIVVKAESSGERRMTLSIKGPKVVKAADIVADIGLEIVNPEQIICT 147

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +  D  + ME  V  G G+V ++    ++ P+  I +DA+Y+PI+KVSY ++    G++ 
Sbjct: 148 VTTDRTLDMEFIVDTGEGFVVSEEIDKKDWPVDYIAVDAIYTPIRKVSYEIQDTMFGRMT 207

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF---- 252
           D+DKL++ ++TDGSI   D+++ A  +L+  L  F+      + +++DI           
Sbjct: 208 DFDKLTLNVETDGSIEIRDAISYAVELLKLHLDPFLEIGNKMENLRDDIEEIVDEPMDIQ 267

Query: 253 ---NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              + +   K+EEL+L+VRS NCL+   I  +  L   +  ++L++ N G+KSL EI   
Sbjct: 268 VIDDKSHDMKIEELDLTVRSFNCLKKAGIEEVSQLASLSLNELLKIKNLGKKSLDEILEK 327

Query: 310 LGTMGLFL 317
           +  +G  L
Sbjct: 328 MKDLGYDL 335


>gi|110004254|emb|CAK98592.1| probable dna-directed rna polymerase alpha chain protein
           [Spiroplasma citri]
          Length = 317

 Score =  284 bits (728), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 105/316 (33%), Positives = 172/316 (54%), Gaps = 8/316 (2%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           ++ I+P     +    +  N    + EPL RGF  TLGNA+RR L+S+  GAA+ AV+I 
Sbjct: 2   KQFIRPEF--KLQAEDKANNYGKFLVEPLERGFGVTLGNAIRRTLLSATPGAAVFAVRIK 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-----SHKRVTIFKRGPGVVTAGDIQT 121
           G  HE ++I GV E +T IILNIK + LK++ D         + +     G + A D+  
Sbjct: 60  GASHEFTAIPGVVEHVTKIILNIKNLVLKINQDIIPDGESVILKVVSSKEGEIYARDLVV 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
              +EV+N D ++  +     + +EL      GY     ++ E     LI ID+ Y PI+
Sbjct: 120 PTGVEVINGDLLLATIAKGGELDLELYARNSRGYKSFTDNKKEKKYADLIVIDSNYCPIQ 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +V+Y VE  + G+  D +KL + I TD SIT  ++VA+A++++ + L  F+N  E   + 
Sbjct: 180 RVAYNVEPTKVGKNADLEKLELEIQTDSSITPVNAVAMAAKVITEHLEFFVNLNE-AIKA 238

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            + I+ ++      L + ++ELE + RS NCL+   I  + DL+ ++E ++  + N G+K
Sbjct: 239 TQIISSEAEAEEDELERSIDELEFTQRSQNCLKRAKIDTLRDLVSKSEDEIQEIRNLGKK 298

Query: 302 SLVEIKGVLGTMGLFL 317
           SL EIK  +  +GL  
Sbjct: 299 SLTEIKDKVAQLGLNF 314


>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 =  284 bits (728), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 111/327 (33%), Positives = 175/327 (53%), Gaps = 16/327 (4%)

Query: 7   QELIKPNNIEYIV-LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
            E + P  ++       E+      +  PL +G+A T+GN LRRVL+SS+   AIT V+ 
Sbjct: 1   MEFVMPKRLKMEEHKESEDYYYARYVLSPLEKGYATTIGNTLRRVLLSSIPSLAITDVKF 60

Query: 66  --DGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQT 121
                 HE  +I+GV ED+ +I+LN+K + L M    +    +TI  +G G + AGDI  
Sbjct: 61  VRPEKYHEFDTIEGVKEDILEILLNLKKVQLSMEDYVEDPVELTIQHKGAGEIKAGDIIV 120

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
              + V NP+  I  L+ DA + ++L  + G G+VPA   R E   IG I +D +Y+P+ 
Sbjct: 121 PAGVSVTNPNLHIATLNEDADLEIKLYATIGKGFVPAAE-RNEKPDIGWIVLDGVYNPVL 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KV++  E+ R G+  DYDKL + I T  +I   D++  A +I+ D   +         E 
Sbjct: 180 KVNWIAENVRVGKKTDYDKLVLEIWTKKNIKPSDALKKAVKIINDHFRIIEESFGEFDEE 239

Query: 242 KE---------DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            +             + +  N  L +K++EL+LS+R+ NCL+ + I  +GDL+ R E ++
Sbjct: 240 NDIAEVSEVSTVEEEEVVDENDILSRKIDELDLSMRALNCLKRDKIETIGDLLSRGEEEL 299

Query: 293 LRMANFGRKSLVEIKGVL-GTMGLFLG 318
           L++ NFG+KSL E+K  L    GL  G
Sbjct: 300 LKIKNFGQKSLDEVKEKLMEKFGLSFG 326


>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 =  284 bits (728), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 99/296 (33%), Positives = 166/296 (56%), Gaps = 2/296 (0%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
            EN      EPL +G   T+GNALRR L+S++ G AI   +I GV HE S I GV ED  
Sbjct: 15  TENVAKFCIEPLSKGQGITIGNALRRTLLSNIPGTAIVGTRISGVDHEFSVIPGVKEDAL 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV 143
           +I+LN+K +  K + +      +  +GP +VTAGDI    D+E+++P   I  +   + +
Sbjct: 75  EILLNLKQLVFKGNLNEPIITRLNIQGPCIVTAGDIDIPTDLELIDPQQYIATITDFSHL 134

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            ME  + +G  YV ++   + N+P G + +DA+++PIKKV++ VE++   + L+ ++L +
Sbjct: 135 EMEFILEQGESYVLSEKTAS-NNPRGFLAVDAVFTPIKKVNFFVETSSSKERLEKERLII 193

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            I+T+GSI   +++ LA+  L     +  + +   +   E  N+  +         +EEL
Sbjct: 194 EIETNGSILPLEALNLAAERLSSLFKLVNSADLTAEFPTEVENIVQVSQTDVTGVLIEEL 253

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT-MGLFLG 318
           ELSVR+ NCL+   I  +G+L++ ++ ++L   NFG+KS  E+   L     L L 
Sbjct: 254 ELSVRAYNCLKRAQIHTLGELLKYSKENLLEFKNFGQKSANEVCENLHERFNLTLN 309


>gi|218462761|ref|ZP_03502852.1| DNA-directed RNA polymerase subunit alpha [Rhizobium etli Kim 5]
          Length = 247

 Score =  284 bits (728), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 173/246 (70%), Positives = 209/246 (84%), 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 EDAVAFAARILQDQLGVFVNFDEPQKETEE-EAVTELAFNPALLKKVDELELSVRSANCL 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|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 =  284 bits (728), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 107/303 (35%), Positives = 169/303 (55%), Gaps = 3/303 (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 LDDAESHLYVEMEVEVGRGFVEATSA--DNVAIGTIPQDAIFNPVEKVNYEIEPVHMGQE 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 FLG 318
              
Sbjct: 306 SFN 308


>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 =  284 bits (727), Expect = 1e-74,   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   DRIEH-QISDDRAQTGVFLIGPLERGQATTLGNALRRVLMGGLEGSAVTAVRIAGVNHEY 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 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM---FINFEEPKKEVKEDINVK 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 I---------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIE 296

Query: 309 VLGTMGLF 316
            L  +G+ 
Sbjct: 297 ALERIGIS 304


>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 =  284 bits (727), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 114/337 (33%), Positives = 186/337 (55%), Gaps = 12/337 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KN +  IKP  +E I    E       I +PL RG+  T+GNALRRVL+SSL G AI  V
Sbjct: 2   KNIK-FIKPFFVEEI---DENPISGKFIIKPLERGYGITVGNALRRVLLSSLPGTAIVNV 57

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS---GDSHKRVTIFKRGPGVVTAGDIQ 120
           +I GV  E ++I GV+ED+  IILN+K I   +     D  +++ +  +GP  +TA   +
Sbjct: 58  KIQGVEQEFTTIPGVYEDVMTIILNLKKIVFAVDDESDDFEEKLELIAKGPQRLTASSFE 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSP 179
               ++++NPDH I  L  D    M +T+ KG GYV AK ++    + +G+I ID+L++P
Sbjct: 118 LPAGVKIINPDHYITTLSDDVCFHMTVTLKKGIGYVGAKDNKVHGENQVGVIAIDSLFTP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +  VSY VE     ++ + D+L++ I T+G++  ++++A A+ IL D   + +   +   
Sbjct: 178 VVNVSYQVEK----KLGNKDELTIEITTNGALLAKEALATAASILVDHFNVLVELSQKPA 233

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            V+     K    N  L  ++E+L+LSVR  N L+   I  +  L++ +E +++++ + G
Sbjct: 234 HVEFVSESKKEAHNSVLDLEIEQLDLSVRLFNSLKRAGIDTVAALVKLSEKEVVKLKSLG 293

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKY 336
           RKS  E+K      GL     L +    S+EE   K+
Sbjct: 294 RKSFQELKDKFLEYGLEFNDYLKEVLHHSVEEDKDKH 330


>gi|328813963|gb|AEB52097.1| DNA-directed RNA polymerase alpha chain [Lactobacillus farraginis]
          Length = 264

 Score =  284 bits (727), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 119/264 (45%), Positives = 172/264 (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 ELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            LT ++G GYV A     R    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|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 =  284 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 127/279 (45%), Positives = 180/279 (64%), Gaps = 5/279 (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 ---DLQGTPVEEVEEKTPPIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETEL 237

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           L+  N GRKSL EIK VL + GL LG  L  WPP  +E 
Sbjct: 238 LKTPNLGRKSLNEIKEVLASKGLTLGSKLEAWPPAGLER 276


>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 =  284 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 105/309 (33%), Positives = 164/309 (53%), Gaps = 14/309 (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 GQ-VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM---FINFEEPKKEVKEDINVK 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 I---------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIE 296

Query: 309 VLGTMGLFL 317
            L  +G+ L
Sbjct: 297 ALERIGISL 305


>gi|157493263|gb|ABV57997.1| RNA polymerase alpha subunit [Vibrio mimicus]
          Length = 270

 Score =  284 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 120/273 (43%), Positives = 186/273 (68%), 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++  + +   +++   +  P    LL+ V++LEL+VRS NC
Sbjct: 181 PEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANC 237

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
           L+ E I Y+GDL+QRTE ++L+  N G+KSL E
Sbjct: 238 LKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTE 270


>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 =  284 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 102/322 (31%), Positives = 170/322 (52%), Gaps = 10/322 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +   + + +K   +E   +          + + L  G   T+GN  RRVL+S L G AIT
Sbjct: 1   MNNFYIKCLKSKKVESGSI------YGQFVIKSLHPGQGITIGNLFRRVLLSDLGGTAIT 54

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+I GV  E S+I G+ ED+ +I+LN+KGI LK   +  K   +  +GP VVTA  IQ 
Sbjct: 55  GVRIAGVRDEFSTIPGIREDILEILLNLKGIVLKSKTNDLKFGRLKIKGPAVVTANCIQL 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
            +++E++NP+H I  +    V+ +E  +  G GY  A     +      + IDA++ P++
Sbjct: 115 PSEVEIVNPNHYIATITTSNVLEIEFKIESGTGYKLAGQTFCKKSQ-DYLQIDAIFMPVQ 173

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KV + +E+  +      ++L + I T+GS++ E++V+ ASR +       +  + P++  
Sbjct: 174 KVDFKIENIYDNSNDLTERLFLDIWTNGSMSPEEAVSSASRFIISFFSSLLENKLPQETK 233

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           + +    S P NP     +EEL LSVR+ NCL+   I  +GDL++ +   +  + NFGRK
Sbjct: 234 ESENKTLSAPKNPHTNIAIEELHLSVRAYNCLKRAQINTIGDLLKYSPEKLQELKNFGRK 293

Query: 302 SLVEIKGVLGTMGLFLGMNLPD 323
           S  E+   L      LG+ L +
Sbjct: 294 SADEVFTTLKNK---LGIVLSN 312


>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 (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 88/359 (24%), Positives = 168/359 (46%), Gaps = 28/359 (7%)

Query: 1   MIQKNWQELIKPNNIEYIVLG----QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLR 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 QDIISPPYVEIVDNTQHIASLAEPIDLCIGLQIERNRGY--LIKTPNNNFQDGSYPIDAV 176

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           + P++  ++++ S   G     + L + I T+GS+T ++++  ASR L D    F++ EE
Sbjct: 177 FMPVRNANHSIHSYGNGNE-KQEILFLEIWTNGSLTPKEALHQASRNLIDLFIPFLHTEE 235

Query: 237 PKKEVKEDINVKSLPFNPALLK----------------KVEELELSVRSTNCLRGENIVY 280
               + ++ +   LP      K                 +++ EL  R  NCL   NI  
Sbjct: 236 ENLHLADNQHTVPLPPFTFHEKLTKLRKNKKKIALKSIFIDQSELPPRIYNCLIRSNIYT 295

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           + DL+  ++ D++++ +F    + ++K +LG +     ++LP       E LA+    +
Sbjct: 296 LLDLLNNSQEDLMKIEHF---RIEDVKAILGILEKHFAIDLPKKLKIGFESLAQSIYSE 351


>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 =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 119/334 (35%), Positives = 183/334 (54%), Gaps = 17/334 (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---------VLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGP 111
           A++I           V  E   I GV ED  ++I NIK I+LK+  G+  K ++    G 
Sbjct: 62  AMRIQSNNKDSSSKVVSSEFDLIPGVSEDTLEVIANIKNIHLKLGEGEQRKTISFSVSGK 121

Query: 112 --GVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
              V+ A   +    +EV N D VI  L  D  + +E  ++ G GYV ++ +    + + 
Sbjct: 122 DTKVLKASHFERD-GVEVFNRDLVIATLSQDVNLDLEFQINYGRGYVSSEQNSKYLEEVN 180

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ L 
Sbjct: 181 VIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIIREFLY 240

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
             ++FE+    V           +  L   +E+L+LSVRS NCL  EN+  +G+LI +  
Sbjct: 241 PLVDFED---NVNTSFEKSKSESSNLLDMSIEKLDLSVRSLNCLAKENVRTLGELISKNA 297

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            ++ +  NFG+KSL EI   L +  LFLGM+  D
Sbjct: 298 EELSKARNFGKKSLEEIIEKLSSYQLFLGMSKED 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 =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 119/334 (35%), Positives = 183/334 (54%), Gaps = 17/334 (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---------VLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGP 111
           A++I           V  E   I GV ED  ++I NIK I+LK+  G+  K ++    G 
Sbjct: 62  AMRIQSNNKDSSSKVVSSEFDLIPGVSEDTLEVIANIKNIHLKLGEGEQRKTISFSVSGK 121

Query: 112 --GVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
              V+ A   +    +EV N D VI  L  D  + +E  ++ G GYV ++ +    + + 
Sbjct: 122 DTKVLKASHFERD-GVEVFNRDLVIATLSQDVNLDLEFQINYGRGYVSSEQNSKYLEEVN 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
             ++FE+    V           +  L   +E+L+LSVRS NCL  EN+  +G+LI +  
Sbjct: 241 PLVDFED---NVNTSFEKSKSESSNLLDMSIEKLDLSVRSLNCLAKENVRTLGELISKNA 297

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            ++ +  NFG+KSL EI   L +  LFLGM+  D
Sbjct: 298 EELSKARNFGKKSLEEIIEKLSSYQLFLGMSKED 331


>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 =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 83/331 (25%), Positives = 159/331 (48%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    +++  +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEEENLHLEDGEHTI 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            L       K                 +++LE   +  NCL+  NI  + DL+ +++ D+
Sbjct: 247 PLSPLSFHDKVAKLRKNKKKLALKSIFIDQLEFPPKIYNCLKKSNISTLLDLLNKSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F    + ++K +LG +     ++LP 
Sbjct: 307 MKIEHF---HIEDVKQILGILEKHFAIDLPK 334


>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 =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 114/330 (34%), Positives = 179/330 (54%), Gaps = 12/330 (3%)

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-----DGVLH----EISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKR 109
           +T V+I     DGV H    E   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 ADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
             +    N G+KSL EI+G L    L LGM
Sbjct: 300 QTLANTRNVGKKSLSEIQGKLQEYNLRLGM 329


>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 =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 105/306 (34%), Positives = 163/306 (53%), 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 GQ-VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           G+     ++L + I+T+GSIT ED++A A+  L        N    ++ + E        
Sbjct: 186 GEGGSARERLRLEIETNGSITPEDAMAEAANQLISMFQPLANLTMVEEPIPEPEPPTEAQ 245

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 246 I------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLFL 317
            +GL L
Sbjct: 300 RIGLSL 305


>gi|312148520|gb|ADQ31179.1| DNA-directed RNA polymerase, alpha subunit [Borrelia burgdorferi
           JD1]
          Length = 344

 Score =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 118/335 (35%), Positives = 184/335 (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---------VLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRG 110
           TA+++           V  E   I GV ED  ++I NIK I+LK+  G+  K ++    G
Sbjct: 61  TAMRVQSNNKDASLKVVSSEFDLIPGVSEDTLEVIANIKNIHLKLGEGEQKKTISFSVSG 120

Query: 111 P--GVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 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|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 =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 118/335 (35%), Positives = 184/335 (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---------VLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRG 110
           TA+++           V  E   I GV ED  ++I NIK I+LK+  G+  K ++    G
Sbjct: 61  TAMRVQSNNKDASSKVVSSEFDLIPGVSEDTLEVIANIKNIHLKLGEGEQKKTISFSVSG 120

Query: 111 P--GVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 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|312386519|gb|ADQ74778.1| RNA polymerase alpha subunit [Lactobacillus sp. MWBPC 1-3-1]
          Length = 248

 Score =  283 bits (723), Expect = 3e-74,   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|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 =  283 bits (723), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 121/334 (36%), 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---------VLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGP 111
           A+++           V  E   I GV ED  ++I NIK I+LK+  G+  K ++    G 
Sbjct: 62  AMRVQSNNKDSSSKIVSSEFDLIPGVSEDTLEVIANIKNIHLKLGEGEQRKTISFSISGK 121

Query: 112 G--VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
              V+ A   +    +EV N D VI NL  DA +  E  ++ G GYV ++ +    + + 
Sbjct: 122 DTSVLKASHFERD-GVEVFNKDLVIANLSHDANLDFEFQINYGRGYVSSEQNSKYLEEVN 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 PLVDFED---NVNISFEKSKSESYNLLDMSIEKLDLSVRSLNCLAKENVRTLGELISKNA 297

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            ++ +  NFG+KSL EI   LG+  LFLGM+  D
Sbjct: 298 EELSKARNFGKKSLEEIIEKLGSYRLFLGMSKED 331


>gi|328813957|gb|AEB52094.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 255

 Score =  283 bits (723), Expect = 4e-74,   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|328814005|gb|AEB52118.1| DNA-directed RNA polymerase alpha chain [Lactobacillus rhamnosus]
          Length = 250

 Score =  283 bits (723), Expect = 4e-74,   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|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 =  283 bits (723), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 115/328 (35%), Positives = 186/328 (56%), Gaps = 16/328 (4%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           K  ++   P+ IE++  G+++ +    +  P  +GF  T+GN LRRVL+SS+ G AI+A+
Sbjct: 5   KLLKDFTIPDRIEFVR-GEDDGSYGKFVIYPFEKGFGVTIGNTLRRVLLSSIEGYAISAM 63

Query: 64  QIDG--------VLHEISSIKGVHEDLTDIILNIKGINLKMSG---DSHKRVTIFKRGPG 112
           +I          V  E   I GV ED  ++I NIK ++LK+     ++   +++  +   
Sbjct: 64  RIQSNQEESLKIVSSEFDLIPGVMEDTLEVIANIKNVHLKLDEGVTNTTINLSVNGKDNN 123

Query: 113 VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT 172
           V+ AG ++    +EV N D VI  L  DA +  E  V+ G GYV ++ +    + +  I 
Sbjct: 124 VLKAGHLER-EGVEVFNKDLVIATLSSDANLDFEFQVNYGRGYVSSEQNAKYLEEVNTIA 182

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           +D+++SPI+KV+Y+VE  R GQ  DYDKL M I T G I+ +D++  A+ ++++ L   +
Sbjct: 183 LDSIFSPIEKVTYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASVVREFLLPLV 242

Query: 233 NFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           NFE+        ++      +  L   VE+L LSVRS NCL  EN+  +G+LI ++  ++
Sbjct: 243 NFEDKVIH---SVDYAEFRDSDILSMNVEKLNLSVRSLNCLIKENVKTLGELISKSPVEL 299

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMN 320
            +  NFG+KSL EI   L   GLFLGM+
Sbjct: 300 SKARNFGKKSLEEIVEKLNAYGLFLGMS 327


>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 =  282 bits (722), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 119/334 (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---------VLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGP 111
           A++I           V  E   I GV ED  ++I NIK I+LK+  G+  K ++    G 
Sbjct: 62  AMRIQSNNKDSSSKVVSSEFDLIPGVSEDTLEVIANIKNIHLKLGEGEQRKIISFSVSGK 121

Query: 112 --GVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
              V+ A   +    +EV N D VI  L  D  + +E  ++ G GYV ++ +    + + 
Sbjct: 122 DTKVLKASHFERD-GVEVFNRDLVIATLSQDVNLDLEFQINYGRGYVSSEQNSKYLEEVN 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|157493277|gb|ABV58004.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 269

 Score =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 119/272 (43%), Positives = 184/272 (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++  + +   +++   +  P    LL+ V++LEL+
Sbjct: 181 TNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELT 237

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           VRS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 VRSANCLKAEAIHYIGDLVQRTEVELLKTPNL 269


>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 =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 121/366 (33%), Positives = 194/366 (53%), Gaps = 28/366 (7%)

Query: 2   IQKNWQ-----ELIKPNNIEYIVLGQ-EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSL 55
           + +N Q     +   P +++ + +     +     +AEPL +G  HTLGNALRR L+  L
Sbjct: 1   MSENLQNLLYDKFELPESVKMLSMEGFSTDTHARFVAEPLEKGMGHTLGNALRRALLIGL 60

Query: 56  RGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-------GDSHKRVTIFK 108
              AI +  + GVLHE  +I+G+ ED+T+IILN+K   LK         G S + +    
Sbjct: 61  EAPAIISFSMTGVLHEYMAIEGIIEDVTNIILNLKSALLKKHPMQGSEEGRSTQLLKSSI 120

Query: 109 R----------GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 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 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK---VEELELSVRSTNCLRG 275
            +++IL     +F   +E +   +E ++++    +  L K    + E+ELSVRSTNCL  
Sbjct: 241 FSTQILTKHFSIFEKMDEKRIVFEEAVSIEKENKDDILHKLILGINEIELSVRSTNCLSN 300

Query: 276 ENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELA 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|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 =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 131/280 (46%), Positives = 183/280 (65%), 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 VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLI 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+      P +P LL+ V++LEL+VRS NCL+ E+I Y+GDLIQRTE +
Sbjct: 181 ADLEGTPIEVEEEKA---PPIDPVLLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETE 237

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +L+  N GRKSL EIK VL + GL LG  L  WPP  +E+
Sbjct: 238 LLKTPNLGRKSLNEIKEVLASKGLTLGSKLESWPPAGLEK 277


>gi|328814019|gb|AEB52125.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 263

 Score =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 121/267 (45%), Positives = 172/267 (64%), Gaps = 4/267 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            KP   +      EE++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVL
Sbjct: 1   EKPRIAKI----DEEKDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVL 56

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+IKGV ED+T IILNIKG+ LKM G   K + I   GP  VTAGDI   +D+E+LN
Sbjct: 57  HEFSTIKGVREDVTQIILNIKGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSDVEILN 116

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
            D  IC++   A     LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+
Sbjct: 117 KDMYICSVSEGATFHARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVEN 176

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R G   D+DKL+M I TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  + 
Sbjct: 177 TRVGHREDFDKLTMEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEE 236

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGE 276
                 L   +EEL+LSVRS NCL+  
Sbjct: 237 TQKEKMLEMTIEELDLSVRSYNCLKRA 263


>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 =  282 bits (722), Expect = 5e-74,   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|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 =  282 bits (721), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 116/328 (35%), Positives = 186/328 (56%), Gaps = 16/328 (4%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           K  ++   P+ IE++  G+++ +    I  P  +GF  T+GN LRRVL+SS+ G AI+A+
Sbjct: 5   KLLKDFTIPDRIEFVR-GEDDGSYGKFIIYPFEKGFGVTIGNTLRRVLLSSIEGYAISAM 63

Query: 64  QIDG--------VLHEISSIKGVHEDLTDIILNIKGINLKMSG---DSHKRVTIFKRGPG 112
           +I          V  E   I GV ED  ++I NIK ++LK+     ++   +++  +   
Sbjct: 64  RIQSNQEESLKIVSSEFDLIPGVMEDTLEVIANIKNVHLKLDEGVTNTTINLSVNGKDNN 123

Query: 113 VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT 172
           V+ AG ++    +EV N D VI  L  DA +  E  V+ G GYV ++ +    + +  I 
Sbjct: 124 VLKAGHLER-EGVEVFNKDLVIATLSSDANLDFEFQVNYGRGYVSSEQNAKYLEEVNTIA 182

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           +D+++SPI+KV+Y+VE  R GQ  DYDKL M I T G I+ +D++  A+ ++++ L   +
Sbjct: 183 LDSIFSPIEKVTYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASVVREFLLPLV 242

Query: 233 NFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           NFE+        ++      +  L   VE+L LSVRS NCL  EN+  +G+LI ++  ++
Sbjct: 243 NFEDKVIH---SVDYAEFRDSDILSMNVEKLNLSVRSLNCLIKENVKTLGELISKSPVEL 299

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMN 320
            +  NFG+KSL EI   L   GLFLGM+
Sbjct: 300 SKARNFGKKSLEEIVEKLNAYGLFLGMS 327


>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 =  282 bits (721), Expect = 6e-74,   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 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM---FINFEEPKKEVKEDINVK 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 I---------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIE 296

Query: 309 VLGTMGLF 316
            L  +G+ 
Sbjct: 297 ALERIGIS 304


>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 =  282 bits (721), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 117/336 (34%), Positives = 194/336 (57%), 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  VLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDI-QTVND 124
           V +E S+I+GV ED+T+I+LN K I LK        + 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 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN-----FEEPK 238
            YT+E+ R GQ  D++ LS+ I TDGSI  + ++  AS+IL     +F +      ++ +
Sbjct: 182 KYTIENCRVGQKTDFENLSLEIQTDGSICPKSALMEASKILIQYFSIFSHEKIGKKKQEE 241

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 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|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 = 6e-74,   Method: Composition-based stats.
 Identities = 89/334 (26%), Positives = 161/334 (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 DNTQHIASLTEPIELCIGLQIERNRGY--LIKTPNNNSQDGSYPIDAVFMPVRNANHSIH 188

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    + ++ ++ 
Sbjct: 189 SYGNGND-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFITFLHTEEENLHLADNQHMV 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|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 =  282 bits (721), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 125/355 (35%), Positives = 192/355 (54%), Gaps = 23/355 (6%)

Query: 8   ELIKPNNIEYIVLGQEE-ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           +   P  ++ + +     +     IAEPL RG  HTLGNALRR L+  L   AI +  + 
Sbjct: 12  KFELPEAVKMLPVEGLPIDKHARFIAEPLERGMGHTLGNALRRALLIGLEAPAIISFAMT 71

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMS-------GDSHKRVTIFKR---------- 109
           GVLHE  +I+GV ED+T+IILN+KG  LK         G + + +               
Sbjct: 72  GVLHEYMAIEGVIEDVTNIILNLKGALLKKYPMQDSSLGRTTQVLKASISIDASDLAAAN 131

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           G   VT  D+    D E +NPD VI  +     + + L ++ G GY P++    E+  + 
Sbjct: 132 GQKEVTLQDLLQEGDFEAVNPDQVIFTVTQPIQLEVVLRIAFGRGYTPSERIVLEDKGVY 191

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +T ++++A +++IL     
Sbjct: 192 EIVLDAAFSPVTLVNYFVEDTRVGQDTDFDRLVLIVETDGRVTPKEALAFSTQILTKHFS 251

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKK---VEELELSVRSTNCLRGENIVYMGDLIQ 286
           +F N +E K   +E I+++    +  L K    + E+ELSVRSTNCL   NI  +G+L+ 
Sbjct: 252 IFENMDEKKIVFEEAISIEKENKDDILHKLILGINEIELSVRSTNCLSNANIETIGELVI 311

Query: 287 RTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
             E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 312 MPEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLTQFGVGLDNVKEKMKWYAEK 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 =  282 bits (721), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 125/355 (35%), Positives = 192/355 (54%), Gaps = 23/355 (6%)

Query: 8   ELIKPNNIEYIVLGQEE-ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           +   P  ++ + +     +     IAEPL RG  HTLGNALRR L+  L   AI +  + 
Sbjct: 29  KFELPEAVKMLPVEGLPIDKHARFIAEPLERGMGHTLGNALRRALLIGLEAPAIISFAMT 88

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMS-------GDSHKRVTIFKR---------- 109
           GVLHE  +I+GV ED+T+IILN+KG  LK         G + + +               
Sbjct: 89  GVLHEYMAIEGVIEDVTNIILNLKGALLKKYPMQDSSLGRTTQVLKASISIDASDLAAAN 148

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           G   VT  D+    D E +NPD VI  +     + + L ++ G GY P++    E+  + 
Sbjct: 149 GQKEVTLQDLLQEGDFEAVNPDQVIFTVTQPIQLEVVLRIAFGRGYTPSERIVLEDKGVY 208

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +T ++++A +++IL     
Sbjct: 209 EIVLDAAFSPVTLVNYFVEDTRVGQDTDFDRLVLIVETDGRVTPKEALAFSTQILTKHFS 268

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKK---VEELELSVRSTNCLRGENIVYMGDLIQ 286
           +F N +E K   +E I+++    +  L K    + E+ELSVRSTNCL   NI  +G+L+ 
Sbjct: 269 IFENMDEKKIVFEEAISIEKENKDDILHKLILGINEIELSVRSTNCLSNANIETIGELVI 328

Query: 287 RTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
             E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 329 MPEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLTQFGVGLDNVKEKMKWYAEK 383


>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 =  281 bits (720), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 125/355 (35%), Positives = 192/355 (54%), Gaps = 23/355 (6%)

Query: 8   ELIKPNNIEYIVLGQEE-ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           +   P  ++ + +     +     IAEPL RG  HTLGNALRR L+  L   AI +  + 
Sbjct: 12  KFELPEAVKMLPVEGLPIDKHARFIAEPLERGMGHTLGNALRRALLIGLEAPAIISFAMT 71

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMS-------GDSHKRVTIFKR---------- 109
           GVLHE  +I+GV ED+T+IILN+KG  LK         G + + +               
Sbjct: 72  GVLHEYMAIEGVIEDVTNIILNLKGALLKKYPMQDSSLGRTTQVLKASISIDASDLAAAN 131

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           G   VT  D+    D E +NPD VI  +     + + L ++ G GY P++    E+  + 
Sbjct: 132 GQKEVTLQDLLQEGDFEAVNPDQVIFTVTQPIQLEVVLRIAFGRGYTPSERIVLEDKGVY 191

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +T ++++A +++IL     
Sbjct: 192 EIVLDAAFSPVTLVNYFVEDTRVGQDTDFDRLVLIVETDGRVTPKEALAFSTQILTKHFS 251

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKK---VEELELSVRSTNCLRGENIVYMGDLIQ 286
           +F N +E K   +E I+++    +  L K    + E+ELSVRSTNCL   NI  +G+L+ 
Sbjct: 252 IFENMDEKKIVFEEAISIEKENKDDILHKLILGINEIELSVRSTNCLSNANIETIGELVI 311

Query: 287 RTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
             E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 312 MPEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLTQFGVGLDNVKEKMKWYAEK 366


>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 =  281 bits (720), Expect = 8e-74,   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|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 =  281 bits (720), Expect = 8e-74,   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|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 =  281 bits (720), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 99/305 (32%), Positives = 160/305 (52%), 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        
Sbjct: 186 AEGGSARERLRMEIVTDGSITPDEALAQSANQLIELFQPLATVTLVEEVPAEPEPSAEAQ 245

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 246 I------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLF 316
            +G+ 
Sbjct: 300 RIGIS 304


>gi|269302410|gb|ACZ32510.1| DNA-directed RNA polymerase, alpha subunit [Chlamydophila
           pneumoniae LPCoLN]
          Length = 374

 Score =  281 bits (719), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 125/355 (35%), Positives = 192/355 (54%), Gaps = 23/355 (6%)

Query: 8   ELIKPNNIEYIVLGQEE-ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           +   P  ++ + +     +     IAEPL RG  HTLGNALRR L+  L   AI +  + 
Sbjct: 12  KFELPEAVKMLPVEGLPIDKHARFIAEPLERGMGHTLGNALRRALLIGLEAPAIISFAMT 71

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMS-------GDSHKRVTIFKR---------- 109
           GVLHE  +I+GV ED+T+IILN+KG  LK         G + + +               
Sbjct: 72  GVLHEYMAIEGVIEDVTNIILNLKGALLKKYPMQDSSLGRTTQVLKASISIDASDLAAAN 131

Query: 110 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           G   VT  D+    D E +NPD VI  +     + + L ++ G GY P++    E+  + 
Sbjct: 132 GQKEVTLQDLLQEGDFEAVNPDQVIFTVTQPIQLEVVLRIAFGRGYTPSERIVLEDKGVY 191

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +T ++++A +++IL     
Sbjct: 192 EIILDAAFSPVTLVNYFVEDTRVGQDTDFDRLVLIVETDGRVTPKEALAFSTQILTKHFS 251

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKK---VEELELSVRSTNCLRGENIVYMGDLIQ 286
           +F N +E K   +E I+++    +  L K    + E+ELSVRSTNCL   NI  +G+L+ 
Sbjct: 252 IFENMDEKKIVFEEAISIEKENKDDILHKLILGINEIELSVRSTNCLSNANIETIGELVI 311

Query: 287 RTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
             E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 312 MPEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLTQFGVGLDNVKEKMKWYAEK 366


>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 =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 119/271 (43%), Positives = 184/271 (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++  + +   +++   +  P    LL+ V++LEL+V
Sbjct: 181 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTV 237

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           RS NCL+ E I Y+GDL+QRTE ++L+  N 
Sbjct: 238 RSANCLKAEAIHYIGDLVQRTEVELLKTPNL 268


>gi|110589176|gb|ABG77097.1| DNA-directed RNA polymerase alpha subunit [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 303

 Score =  281 bits (719), Expect = 1e-73,   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 RRVAYSIESARVEQRTNMDRLVIELQTDGTIDPEEAIRRSAGILRDQLSVFVDL-EGGGA 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|328813989|gb|AEB52110.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 264

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 123/266 (46%), Positives = 172/266 (64%), 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 LNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSY 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|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 =  281 bits (718), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 85/331 (25%), Positives = 157/331 (47%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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   N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDLCIGLQIKRNRGYLIKMPH---NFQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  A R L D    F++ EE    ++++ +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEACRNLIDLFIPFLHKEEENLPLEDNQHTV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            L       K                 +++ E S R  NCL+  NI  + DL+  +  D+
Sbjct: 247 PLSPLTFHDKLDKLRKNKKKIALKSIFIDQSEFSPRVYNCLKRSNIYTLLDLLNNSPEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +     L +IK +L  +     ++LP 
Sbjct: 307 MKIEHL---RLEDIKQILVILEKHFAIDLPK 334


>gi|161511759|emb|CAP16890.1| DNA-directed RNA polymerase subunit alpha [Pediococcus damnosus]
          Length = 265

 Score =  281 bits (718), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 114/269 (42%), Positives = 170/269 (63%), Gaps = 6/269 (2%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            KP   +      E+ N    + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDGVL
Sbjct: 1   EKPKIHKV----DEKSNYGRFVVEPLERGYGTTLGNSLRRILLSSLPGAALTSVQIDGVL 56

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S+I+GV ED+T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LN
Sbjct: 57  HEFSTIEGVVEDVTQIILNLKKVSLKVESDEEKSLEINVMGPANVTAGDIVGDGDVTILN 116

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTV 187
           P+  IC +         LT  KG GY  A  ++    + PIG++ ID++Y+PI++V+Y V
Sbjct: 117 PELPICTVAEGTTFHAVLTAEKGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQV 176

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+ R GQ  DYDKL++ + TDGS+   ++++L+++IL + L +F+N ++  K+ +  +  
Sbjct: 177 ENTRVGQRDDYDKLTLDVWTDGSLAASEAISLSAKILTEHLTIFVNLDDQAKDTEIMVEK 236

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGE 276
           +       L   +EEL+LSVRS NCL+  
Sbjct: 237 EETHKEKMLEMTIEELDLSVRSYNCLKRA 265


>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 =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 119/335 (35%), Positives = 184/335 (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---------VLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRG 110
           TA+++           V  E   I GV ED  +II NIK I+LK+  G+  K ++    G
Sbjct: 61  TAMRVQSNNKDSSSKVVSSEFDLIPGVSEDTLEIIANIKNIHLKLGEGEQRKTISFSVSG 120

Query: 111 P--GVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 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|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 =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 112/315 (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-------------------PKKEVKED 244
            I TDGS + +D +  A  IL+++L +F + EE                   P+ EV  +
Sbjct: 192 RIWTDGSASPQDVLDQAIDILREELLVFGSVEELEDSESSALDYTISAETVQPEAEVAPE 251

Query: 245 INVKSLPFNPALLKKV--EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
               +     +    V  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|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 =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 111/305 (36%), Positives = 165/305 (54%), Gaps = 5/305 (1%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
              +  +       + EPL RGF  TLGN LRR+L+SS+ G A+T+V I+ VLHE S+I 
Sbjct: 10  VFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIP 69

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVT--IFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           GV ED+ +IILN+K + ++    S + VT  +   GP  V A D   V D+E++NPD  I
Sbjct: 70  GVKEDVVEIILNLKELVVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIMNPDLHI 129

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
             L+    + ME+ V +G GYVPA+ H  ++  I  I +DA++SP+++V++ VE  R GQ
Sbjct: 130 ATLEEGGRLNMEVRVDRGVGYVPAEKHGIKDR-INAIPVDAVFSPVRRVAFQVEDTRLGQ 188

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--EPKKEVKEDINVKSLPF 252
             D DKL++ I TDGS+T  +++  A  IL++ L  F N +        +          
Sbjct: 189 RTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQAAAVAAPEEAKEPEAPPEQ 248

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
              L   +EEL LS R  + L+ E I  +  L+     D+  +   G +SL EIK  L  
Sbjct: 249 EEELDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALEK 308

Query: 313 MGLFL 317
            G  L
Sbjct: 309 KGFTL 313


>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 =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 119/333 (35%), Positives = 186/333 (55%), Gaps = 18/333 (5%)

Query: 1   MIQ--KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGA 58
           M+   K  ++   P+ IE++  G+++ +    I  P  +GF  T+GN LRRVL+SS+ G 
Sbjct: 1   MMSLGKLLKDFTIPDRIEFLR-GEDDGSYGKFIIYPFEKGFGVTIGNTLRRVLLSSIEGY 59

Query: 59  AITAVQIDG--------VLHEISSIKGVHEDLTDIILNIKGINLKMSG---DSHKRVTIF 107
           AI+A++I          V  E   I GV ED  ++I NIK I+LK+      +   V++ 
Sbjct: 60  AISAMRIQSNQGGSLKIVSSEFDLIPGVVEDTLEVIANIKNIHLKLDEGVKSATISVSVN 119

Query: 108 KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
            +   V+ A  ++    +EV N D VI  L  +A +  E  V  G GYV ++H+    + 
Sbjct: 120 GKDTNVLKAVHLER-EGVEVCNKDLVIATLSSEANLDFEFQVDYGRGYVSSEHNAKYLEE 178

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           +  I +D+++SPI+KV+Y+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ 
Sbjct: 179 VNTIALDSIFSPIEKVTYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVREF 238

Query: 228 LGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
           L   +NFE+      +D   +       L   +E+L LSVRS NCL  EN+  +G+LI +
Sbjct: 239 LLPLVNFEDKVVHSVDDSEFRDS---DILNMNIEKLNLSVRSLNCLTKENVKTLGELISK 295

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           +  ++ +  NFG+KSL EI   L   GLFLGM+
Sbjct: 296 SAEELSKARNFGKKSLEEIVEKLSVYGLFLGMS 328


>gi|328813943|gb|AEB52087.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 250

 Score =  280 bits (717), Expect = 2e-73,   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|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 =  280 bits (717), Expect = 2e-73,   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|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 =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 112/312 (35%), Positives = 175/312 (56%), Gaps = 8/312 (2%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
              +   + +  +     + EPL   +   LGNALRRVL+SS+ G AI +++IDGV HE 
Sbjct: 3   TKYKISTIEETTK-EGKFLFEPLEYRYGTPLGNALRRVLLSSIPGGAIFSIRIDGVYHEF 61

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHK--RVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           + IKGV ED+  IILN+K + L +    ++   + I + GP  V AGDI+    + VLN 
Sbjct: 62  TGIKGVKEDVASIILNLKQLILDIDIHDNEVYTLRIDQEGPKTVVAGDIECPTGVTVLNK 121

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPA----KHHRTENDPIGLITIDALYSPIKKVSYT 186
           D  IC L     + MEL    G G+V +    + ++ E  P+G+I  D+LYSP+K VSY 
Sbjct: 122 DLPICTLSEGGSIHMELQARLGRGFVRSDVNKRMYQNEGQPLGIIYTDSLYSPVKNVSYV 181

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK-KEVKEDI 245
               +      YD L + I TD +I   +++A+A++IL+D L +  + +E   +  ++++
Sbjct: 182 ANPIKSEDGSMYDSLELEITTDETIKPSEALAVAAKILRDHLSILASVDEASLEVKEQEV 241

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            V   P      K +E+LELSVRS NCL+   I  + +L Q+TE +M+ + N G+KSL E
Sbjct: 242 EVSEEPVVHTTHKMIEDLELSVRSYNCLKRAGIATVDELTQKTEEEMIHVRNLGKKSLQE 301

Query: 306 IKGVLGTMGLFL 317
           +K  +  +GL  
Sbjct: 302 VKDKIKELGLSF 313


>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 =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 100/305 (32%), Positives = 161/305 (52%), 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        
Sbjct: 186 AEGGSARERLRMEIVTDGSITPDDALAQSANQLIELFQPLATVTLVEEVPAEPEPSAEAQ 245

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 246 I------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLF 316
            +G+ 
Sbjct: 300 RIGIS 304


>gi|290489678|gb|ADD31223.1| RNA polymerase alpha subunit protein [Berberidopsis corallina]
          Length = 337

 Score =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 82/331 (24%), Positives = 160/331 (48%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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         N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDLCIGLQIERNRGYRIKT---LNNFQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENLHLEDNQHKA 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 MKIEHF---RIEDVKQILGILEKHFTIDLPK 334


>gi|317016847|gb|ADU85964.1| DNA-directed RNA polymerase alpha chain [Lactobacillus sp. 3.1.1]
          Length = 249

 Score =  280 bits (716), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 118/249 (47%), Positives = 168/249 (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 SKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 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 RSTNCLRGE 276
           RS NCL+  
Sbjct: 241 RSYNCLKRA 249


>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 =  280 bits (716), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 119/335 (35%), Positives = 184/335 (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---------VLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRG 110
           TA+++           V  E   I GV ED  +II NIK I+LK+  G+  K ++    G
Sbjct: 61  TAMRVQSNNKDSSSKVVSSEFDLIPGVSEDTLEIIANIKNIHLKLGEGEQRKTISFSVSG 120

Query: 111 P--GVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
               V+ A   +    +EV N D VI  L  D  + +E  ++ G GYV ++ +    + +
Sbjct: 121 KDTNVLKASHFERD-GVEVFNKDLVIATLSHDVNLDLEFQINYGRGYVSSEQNSKYLEEV 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|225544155|ref|YP_002720144.1| rpoA [Jatropha curcas]
 gi|224979596|gb|ACN72723.1| rpoA [Jatropha curcas]
          Length = 339

 Score =  280 bits (716), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 85/334 (25%), 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       T N   G   IDA++ P++  ++
Sbjct: 128 EIIDNTQHIASLTESIDLCIGLQIERNRGYRIKP---TNNFQDGSYPIDAVFMPVRNANH 184

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           +V S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + 
Sbjct: 185 SVHSYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENLHLEINQ 243

Query: 246 NVKSLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTE 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|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 =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 119/335 (35%), Positives = 184/335 (54%), Gaps = 17/335 (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---------VLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRG 110
           TA+++           V  E   I GV ED  +II NIK I+LK+  G+  K ++    G
Sbjct: 62  TAMRVQSNNKDSSSKVVSSEFDLIPGVSEDTLEIIANIKNIHLKLGEGEQRKTISFSVSG 121

Query: 111 P--GVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
               V+ A   +    +EV N D VI  L  D  + +E  ++ G GYV ++ +    + +
Sbjct: 122 KDTNVLKASHFERD-GVEVFNKDLVIATLSHDVNLDLEFQINYGRGYVSSEQNSKYLEEV 180

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
            +I +D+++SPI+KVSY+VE  R GQ  DYDKL M I T G I+ +D++  A+ I+++ L
Sbjct: 181 NVIALDSIFSPIEKVSYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVREFL 240

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
              ++FE+    V           +  L   +E+L LSVRS NCL  EN+  +G+LI + 
Sbjct: 241 FPLVDFED---NVNTSFEKSKSESSNLLDMSIEKLNLSVRSLNCLAKENVRTLGELISKN 297

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
             ++ +  NFG+KSL EI   LG+  L+LGM+  D
Sbjct: 298 AEELSKARNFGKKSLEEIIEKLGSYRLYLGMSKED 332


>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 =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 120/333 (36%), Positives = 188/333 (56%), Gaps = 18/333 (5%)

Query: 1   MIQ--KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGA 58
           M+   K  ++   P+ IE++  G+++ +    I  P  +GF  T+GN LRRVL+SS+ G 
Sbjct: 1   MMSLGKLLKDFTIPDRIEFVR-GEDDSSYGKFIMYPFEKGFGVTIGNTLRRVLLSSIEGY 59

Query: 59  AITAVQIDG--------VLHEISSIKGVHEDLTDIILNIKGINLKMS---GDSHKRVTIF 107
           AI+A++I          V  E   I GV ED  ++I NIK I+LK+      +   +++ 
Sbjct: 60  AISAMRIQSNQGGSLKIVSSEFDLIPGVVEDTLEVIANIKNIHLKLDEGVNSTTISLSVN 119

Query: 108 KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
            +   V+ A  ++    +EV N D VI  L  +A +  E  ++ G GYV ++ +    + 
Sbjct: 120 GKDTNVLKAVHLER-EGVEVFNKDLVIATLSSEANLDFEFQINYGRGYVSSEQNAKYLEE 178

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           +  I +D+++SPI+KV+Y+VE  R GQ  DYDKL M I T G I+ +D++  A+ I++D 
Sbjct: 179 VNTIALDSIFSPIEKVTYSVEDTRVGQRSDYDKLVMEIWTTGVISAKDAIKKAASIVRDF 238

Query: 228 LGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
           L   +NFE+    V   +    L  +  L   +E+L LSVRS NCL  EN+  +G+LI +
Sbjct: 239 LLPLVNFEDK---VVHSVENSELRDSDILSINIEKLNLSVRSLNCLTKENVKTLGELISK 295

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           +  D+ +  NFG+KSL EI   L T GLFLGM+
Sbjct: 296 SAEDLSKARNFGKKSLEEIIEKLNTYGLFLGMS 328


>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 =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 120/334 (35%), Positives = 186/334 (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---------VLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGP 111
            +++           V  E   I GV ED  ++I NIK I+LK+  G+  K ++    G 
Sbjct: 62  TMRVQSNNKDSSSKVVSSEFDLIPGVSEDTLEVIANIKNIHLKLREGEQRKIISFSVSGK 121

Query: 112 --GVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 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|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 =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 119/335 (35%), Positives = 184/335 (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---------VLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRG 110
           TA+++           V  E   I GV ED  +II NIK I+LK+  G+  K ++    G
Sbjct: 61  TAMRVQSNNKDSSSKVVSSEFDLIPGVSEDTLEIIANIKNIHLKLGEGEQKKTISFSVSG 120

Query: 111 P--GVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 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|290489670|gb|ADD31219.1| RNA polymerase alpha subunit protein [Nerium oleander]
          Length = 337

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 88/331 (26%), Positives = 159/331 (48%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 DNTQHIASLMEPINLCIGLQIERNRGY---LIQTPQNFQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEEENSHLENNQHAV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            L       K                 +++LEL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 PLFPFIFHDKLTKLIKNKKEIALKSIFIDQLELPPRIYNCLKRSNIYTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F    + ++K +L  +   L + LP 
Sbjct: 307 MKIEHF---RIEDVKQILVILEKHLAIFLPK 334


>gi|165910447|gb|ABY73978.1| RNA polymerase alpha subunit [Cuscuta japonica]
          Length = 332

 Score =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 83/327 (25%), Positives = 157/327 (48%), Gaps = 26/327 (7%)

Query: 14  NIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 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 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
               +    + L + I T+GS+T ++++  ASR L D    F++ E+    +++  +   
Sbjct: 189 YGNEK---QEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEKENLPLEDADHTIP 245

Query: 250 LPFNPALLK-------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
           L       K              +++LE   +  NCL+  NI  + DL+  ++ D++++ 
Sbjct: 246 LSPFTVYYKVAKNKKKLSLESLFIDQLEFPPKIYNCLKKSNIFTLLDLLNNSQEDLIKIE 305

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +F    L ++K +L  +G    ++LP 
Sbjct: 306 HF---RLEDVKQILAILGKHFALDLPK 329


>gi|260656838|gb|ACX47809.1| RNA polymerase alpha-subunit [Vibrio casei]
          Length = 275

 Score =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 120/277 (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  ILNIKGINL-KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD-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++  + +   +++   +  P    LL+ V
Sbjct: 182 LVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPV 238

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 239 DDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 275


>gi|161511757|emb|CAP16889.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 263

 Score =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 111/264 (42%), Positives = 169/264 (64%), Gaps = 3/264 (1%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
             +   + ++  N    + EPL RG+  TLGN+LRR+L+SSL GAA+T+VQIDGVLHE S
Sbjct: 1   KPKIHKVDEKS-NYGRFVVEPLERGYGTTLGNSLRRILLSSLPGAALTSVQIDGVLHEFS 59

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           +I+GV ED+T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  
Sbjct: 60  TIEGVVEDVTQIILNLKKVSLKVESDEEKSLEINVMGPANVTAGDIVGDGDVTILNPELP 119

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAR 191
           IC +         LT  KG GY  A  ++    + PIG++ ID++Y+PI++V+Y VE+ R
Sbjct: 120 ICTVAEGTTFHAVLTAEKGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTR 179

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
            GQ  DYDKL++ + TDGS+   ++++L+++IL + L +F+N ++  K+ +  +  +   
Sbjct: 180 VGQRDDYDKLTLDVWTDGSLAASEAISLSAKILTEHLTIFVNLDDQAKDTEIMVEKEETH 239

Query: 252 FNPALLKKVEELELSVRSTNCLRG 275
               L   +EEL+LSVRS NCL+ 
Sbjct: 240 KEKMLEMTIEELDLSVRSYNCLKR 263


>gi|161511769|emb|CAP16895.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 262

 Score =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 116/261 (44%), Positives = 165/261 (63%), Gaps = 2/261 (0%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            I    E +N    + EPL RG+  TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+
Sbjct: 2   KIHKIDENDNYGRFVIEPLERGYGTTLGNSLRRILLSSLPGAAITSVQIDSVLHEFSTIE 61

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  IC 
Sbjct: 62  GVVEDVTQIILNLKKVSLKIESDEDKTLEINVAGPANVTAGDIMGDGDVVILNPELPICT 121

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQ 194
           +         LT   G GY  A  ++    + PIG++ ID++Y+PI++V+Y VE+ R GQ
Sbjct: 122 VAEGTTFHAVLTADTGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTRVGQ 181

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
             DYDKL++ I TDGSIT  ++ +L+++IL + L +F+N  +  KE +  +  +      
Sbjct: 182 RDDYDKLTLDIWTDGSITPSEATSLSAKILTEHLAIFVNLNDQAKETEIMVEKEETHKEK 241

Query: 255 ALLKKVEELELSVRSTNCLRG 275
            L   +EEL+LSVRS NCL+ 
Sbjct: 242 MLEMTIEELDLSVRSYNCLKR 262


>gi|156597913|gb|ABU85224.1| RNA polymerase alpha subunit [Anethum graveolens]
          Length = 338

 Score =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 86/332 (25%), Positives = 159/332 (47%), Gaps = 26/332 (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 DNTQHIASLTEPIELHIGLQIERSRGY--LIKTPNNNFQDGSYPIDAVFMPIRNANHSIH 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 KSLPFNPALL----------------KKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
             LP                        +++ EL  R  NCL+  NI  + DL+  ++ D
Sbjct: 249 VPLPPFTFHDNLDKLRKNKKKIALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQED 308

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++++ +F    + ++K +LG +     ++LP 
Sbjct: 309 LMKIEHF---RINDVKQILGILEKHFSIDLPK 337


>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 =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 97/311 (31%), Positives = 174/311 (55%), Gaps = 5/311 (1%)

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  LSG--DKVSGIQESFPELLTNLKSIAVILPEEVESLEVSVDLSGKSEILAEDFIGESELK 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 KGVLGTMGLFL 317
              L  + L L
Sbjct: 299 LAKLRDLNLGL 309


>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 =  279 bits (713), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 123/357 (34%), Positives = 192/357 (53%), Gaps = 25/357 (7%)

Query: 8   ELIKPNNIEYIVLGQEE---ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           +   P +++ + +       + +   IAEPL RG  HTLGNALRR L+  L   AI +  
Sbjct: 12  KFELPESVKMMAVEGSGGSVDKQASFIAEPLERGMGHTLGNALRRALLIGLEAPAIISFS 71

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMS----GDSHKRVTIFKR----------- 109
           + GVLHE  +I G+ ED+T+IILN+KG  LK       ++ +   + K            
Sbjct: 72  MTGVLHEYMAINGIIEDVTNIILNLKGALLKKYPFQDSENGRCTQLLKSKVSIDASDLAA 131

Query: 110 --GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
             G   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 LGMFINFEEPKKEVKEDINVKSLPFNPALLKK---VEELELSVRSTNCLRGENIVYMGDL 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|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 =  279 bits (713), Expect = 5e-73,   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 SEGGSTRERLRMEIVTDGSITPDDAVAEAANQLIELFQPLATVTMVEEVPQEPEPTAEAQ 245

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 246 I------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLF 316
            +G+ 
Sbjct: 300 RIGIS 304


>gi|315134694|dbj|BAJ41855.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus ozensis]
          Length = 264

 Score =  279 bits (713), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 120/262 (45%), Positives = 171/262 (65%), Gaps = 4/262 (1%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I    E +N   ++ EPL RG+  TLGN+LRR+L+SSL GAA+T++QID VLHE S++KG
Sbjct: 3   IHKIDETDNYGEVVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDDVLHEFSTVKG 62

Query: 78  VHEDLTDIILNIKGINLKMS--GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
           V ED+  IILN+K I+LK+    D  K + I   GP  VTAGDIQ   D+ VLNPD  IC
Sbjct: 63  VVEDVAQIILNVKKISLKLDIADDEEKSMEINVTGPAQVTAGDIQADGDVTVLNPDLKIC 122

Query: 136 NLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
            +   A   M +T +KG GYV A     R +  PIG++ +D++Y+PI++V+Y VE+AR G
Sbjct: 123 TVAEGATFHMRMTANKGRGYVSADENKARNDGMPIGVLPVDSIYTPIERVNYQVENARVG 182

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           Q  D+DKL++ + TDGSIT  ++V+LA++IL + L MF++  +  K  +  +  +     
Sbjct: 183 QRADFDKLTLDVWTDGSITPSEAVSLAAKILSEHLSMFVDLTDEAKNAEVMVEKEETHKE 242

Query: 254 PALLKKVEELELSVRSTNCLRG 275
             L   +EEL+LSVRS NCL+ 
Sbjct: 243 KMLEMTIEELDLSVRSYNCLKR 264


>gi|290489662|gb|ADD31215.1| RNA polymerase alpha subunit protein [Ilex cornuta]
          Length = 337

 Score =  279 bits (713), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 84/331 (25%), Positives = 159/331 (48%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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+        N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDLCIGLQIERNRGYLIKT---PNNFQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S R G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +  
Sbjct: 188 SYRNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEEENLHLEDNQHTI 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 MKIEHF---RIEDVKQILGVLEKHFAIDLPK 334


>gi|328813961|gb|AEB52096.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 248

 Score =  279 bits (713), Expect = 5e-73,   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|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 =  278 bits (712), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 117/334 (35%), Positives = 182/334 (54%), Gaps = 17/334 (5%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           ++   ++   P  IE++   Q + +       P  RGF  T+GN LRRVL+SS+ G AIT
Sbjct: 3   VENFLKDFTIPEKIEFLK-SQGDGSYGKFTIYPFERGFGITIGNTLRRVLLSSIEGYAIT 61

Query: 62  AVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGP 111
           A+++           V  E   I GV ED  ++I NIK I+LK+  G+  K ++    G 
Sbjct: 62  AMRVQSNNKDSSSKVVSSEFDLIPGVSEDTLEVIANIKNIHLKLGEGEQKKTISFSVSGK 121

Query: 112 --GVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
              V+ A   +    +EV N D VI  L  D  + +E  ++ G GYV ++ +    + + 
Sbjct: 122 DTNVLKASHFERD-GVEVFNKDLVIATLSRDVNLDLEFQINYGRGYVSSEQNSKYLEEVN 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 PLVDFED---NVNTSFEKSKSESSNLLDMSIEKLNLSVRSLNCLAKENVRTLGELISKNA 297

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            ++ +  NFG+KSL EI   LG+  L+LGM+  D
Sbjct: 298 EELSKARNFGKKSLEEIIEKLGSYRLYLGMSKED 331


>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 =  278 bits (712), Expect = 7e-73,   Method: Composition-based stats.
 Identities = 83/331 (25%), Positives = 162/331 (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 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++  E    +K++ N  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHANEENFILKDNQNKV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP      +                 +++ EL  R+ NCL+  NI  + DL+  ++ D+
Sbjct: 247 ALPLFTFHDRLAKQRKNKKEISFQCIFIDQSELPPRTYNCLKRSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F    + ++K +LG +     ++LP 
Sbjct: 307 MKIEHF---RIEDVKQILGILQKHFAIDLPK 334


>gi|290489702|gb|ADD31235.1| RNA polymerase alpha subunit protein [Trochodendron aralioides]
          Length = 337

 Score =  278 bits (712), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 86/329 (26%), Positives = 163/329 (49%), Gaps = 27/329 (8%)

Query: 15  IEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +++  +    +         I  PL +G A T+G A+RR L+  + G  IT  + + + H
Sbjct: 13  LQWKCVESRADSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPH 72

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S+I G+ E + +I+LN+K I L+ +       +I  RGPG VTA DI +   +E+++ 
Sbjct: 73  EYSTIVGIEESVQEILLNLKEIVLRSNLYGTLDASICVRGPGYVTAQDIISPPSVEIVDA 132

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
              I +L     + + L + +  GY   +     N   G   IDA++ P++  S+++ S 
Sbjct: 133 TQHIASLTEPIDLCIGLQIERNRGY---RMKTPNNSQDGSYPIDAVFMPVRNASHSIHSY 189

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
             G     + L + I T+GS+T ++++  ASR L D    F++ EE   +++++ N  SL
Sbjct: 190 GNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEESIKLEDNQNGISL 248

Query: 251 PFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           PF     +                 +++ EL  R+ NCL+  NI  + DL+  ++ D+++
Sbjct: 249 PFFAFHDRLANLKKKKKEIAFKCIFIDQSELPPRTYNCLKRSNIYTLLDLLNNSQEDLMK 308

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           + +F    + ++K +L  +     ++LP 
Sbjct: 309 IDHF---HIEDVKQILDILQKHFSIDLPK 334


>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 =  278 bits (711), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 99/299 (33%), Positives = 156/299 (52%), Gaps = 7/299 (2%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +     L +  PL RG A TLGN+LRRVLM  L G+A+TAV+I GV HE ++I GV
Sbjct: 12  QISDDRSQTGLFLIGPLERGQATTLGNSLRRVLMGGLEGSAVTAVRISGVNHEYATIPGV 71

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+ DI+LN K +++       +   +   GP  V A D+Q  + ++V++ D  I  + 
Sbjct: 72  REDVLDILLNCKQLSVNSRSPELEIGRLVVNGPAEVKARDVQFSSQVQVVDGDRPIATVH 131

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE-GQVLD 197
               + +EL V +G GY P   H  E   I L+ IDA++ PIKKV++ ++          
Sbjct: 132 SGHSLELELHVERGVGYRPVDRHNEETTSIDLLHIDAVFMPIKKVNFNIDETAVAEGGST 191

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
            ++L M I TDGS++ +D++A A+  L +           ++  +E              
Sbjct: 192 RERLKMEIVTDGSMSPDDALAEAANQLIELFQPLATVTMVEEIPQEPEPSAEAQI----- 246

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
             +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L  +G+ 
Sbjct: 247 -PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALERIGIS 304


>gi|332144664|dbj|BAK19492.1| RNA polymerase alpha subunit [Lactobacillus sp. YIT 12363]
          Length = 251

 Score =  278 bits (711), Expect = 8e-73,   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|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 =  278 bits (711), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 82/328 (25%), Positives = 157/328 (47%), Gaps = 26/328 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S    +    + L + I T+GS+T ++++  ASR L D    F++ E+    +++  +  
Sbjct: 188 SYGNEK---QEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEKENLPLEDADHTI 244

Query: 249 SLPFNPALLK-------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
            L       K              +++LE   +  NCL+  NI  + DL+  ++ D++++
Sbjct: 245 PLSPFTVYYKVAKNKKKLSLESLFIDQLEFPPKIYNCLKKSNIFTLLDLLNNSQEDLIKI 304

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            +F    L ++K +L  +G    ++LP 
Sbjct: 305 EHF---RLEDVKQILAILGKHFALDLPK 329


>gi|290489654|gb|ADD31211.1| RNA polymerase alpha subunit protein [Antirrhinum majus]
          Length = 336

 Score =  278 bits (711), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 87/330 (26%), Positives = 162/330 (49%), Gaps = 26/330 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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   N   G  +IDA++ P++ V++++ 
Sbjct: 131 DNTQHIASLTEPINFCIGLEIERNRGYLIKMPH---NFQDGSYSIDAVFMPVRNVNHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    + ++ +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHKEEENLPLDDNQHTI 246

Query: 249 SLPFNPALLK---------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            L       K                +++ ELS R+ NCL+  NI  + DL+  ++ D++
Sbjct: 247 PLSPFSFHDKLDKLRKNKKIALKSIFIDQSELSPRAYNCLKRSNIYTLFDLLNNSQEDLM 306

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++ +F    L ++K +LG +     ++LP 
Sbjct: 307 KIEHF---RLKDVKEILGILEKHFAIDLPK 333


>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 =  278 bits (711), Expect = 9e-73,   Method: Composition-based stats.
 Identities = 126/279 (45%), Positives = 182/279 (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 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL--IT 172
            A DI+  +D EV+NP+H+IC+L  +A + ME+ V KG GY      +   +   +  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 ---DLQGTPVEEVEEVAPPIDPILLRPVDDLELTVRSANCLKAEDIYYIGDLIQRTETEL 237

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           L+  N GRKSL EIK VL + GL LG  L  WPP ++E+
Sbjct: 238 LKTPNLGRKSLNEIKEVLASKGLTLGSKLEAWPPVNLEK 276


>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 =  278 bits (711), Expect = 1e-72,   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 TIDTDGSITGEDSVALASRILQDQLGMFINFE-EPKKEVKEDINVKSLPFNPALLK---- 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|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 =  278 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 114/317 (35%), Positives = 175/317 (55%), 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   + +I ID ++SP+ KV++
Sbjct: 132 EVVNPSQYIATLNEDAAVYMELFAEIGKGFVPVSEMELE-QDVEMIYIDGIFSPVLKVNF 190

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF-------------- 231
             E+ R G+  DYDKL + + T  SI   +++  A+ IL     +               
Sbjct: 191 ISENVRVGKKTDYDKLILEVWTKKSIKPTEALLKATDILIKHFEVTTSSLNQVLDNSGIL 250

Query: 232 -----INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQ 286
                I   E  +  +E +       +  L +++EELELSVRS NCL+ + I  +GDLI 
Sbjct: 251 VNSASIFEPEEPQPEEEPVEEPISEEDSVLSRRIEELELSVRSLNCLKRDKINTIGDLIS 310

Query: 287 RTEADMLRMANFGRKSL 303
           RTEAD+L++ NFG KS+
Sbjct: 311 RTEADLLKIRNFGDKSM 327


>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 =  278 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 93/300 (31%), Positives = 157/300 (52%), Gaps = 4/300 (1%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +        + + L  G   T+GN LRRVL++ L G AI+AV+I GV HE S+I GV ED
Sbjct: 15  ESGACHGQFLIQTLRPGQGITIGNQLRRVLLNDLGGVAISAVRIAGVSHEFSTIPGVRED 74

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + +I+LN+K I L+    + +   +  +GP VVTA  IQ  + +E++NP+  I  +    
Sbjct: 75  ILEILLNLKEIVLRSKTQTPQFGRLKIQGPAVVTADLIQLPSTVEIVNPNQYIMTISTSN 134

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
           ++ +E     G GY  A     E +    + +DA++ PI+KV + +E+  +      ++L
Sbjct: 135 ILEIEFKFDYGTGYRLASQTFLEENE-NYLQLDAIFMPIQKVDFKIENVYDKANNITERL 193

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + I T+GSI+  +++  A++I  D     +  ++     +      ++   P     +E
Sbjct: 194 FLDIWTNGSISPTEAMKSAAQITIDVFTSLLENKDTNSSNEVPSKTSAISLEPYTNIAIE 253

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           EL+LSVR+ NCL+   I  +GDL+  +   +  + NFGRKS  E+   L      LG+ L
Sbjct: 254 ELQLSVRAYNCLKKAQINTVGDLLHYSPEKLQELKNFGRKSADEVFSTLKNK---LGIIL 310


>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 =  278 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 97/305 (31%), Positives = 158/305 (51%), Gaps = 8/305 (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 AEGGSARERLRMEVVTDGSITPDDAIAQAANQLIELFQPLATVTMVEEVSAEPEPTAEAQ 245

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 246 I------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLF 316
            +G+ 
Sbjct: 300 RIGIQ 304


>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 =  278 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 96/308 (31%), Positives = 164/308 (53%), Gaps = 11/308 (3%)

Query: 15  IEYIVLGQEE----ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +E   +  E             +PL  G   T+GNALRRVL+S L G AIT+ ++ G +H
Sbjct: 4   LEIKYIESETYTNTSYYGRFTFQPLKLGQGLTIGNALRRVLLSDLEGIAITSARVSGSVH 63

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S I G  ED+ +I+LN+K I LK S        +  +GP +VTA D +  + ++ ++P
Sbjct: 64  EFSEIPGTREDVLEILLNLKKIVLKGSSKDAGIARLKVQGPCIVTASDFELPSFVKAVDP 123

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
              I  +    V+ +E+++S G GY      ++ +     + +DA++ P+ KV+YT+E  
Sbjct: 124 SQYIATICDSNVLEIEVSISAGRGYKLVNR-QSLDSGKDSLELDAVFMPVNKVNYTIEEI 182

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
                +  +KL++ I T+GS+T E+S+  A+ +L D L         +  + ++ +  + 
Sbjct: 183 NTDFPIAEEKLTLEIWTNGSLTPEESLMQAATVLTDILAPI-----QRIHLTDEEDFPAD 237

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                    +E+L+LSVR+ NCL+  NI Y  DL+ R++ ++L + NFG+K   E+   L
Sbjct: 238 KEPEVKNLPIEDLKLSVRAYNCLKQINIDYTEDLLTRSQEELLEIKNFGKKCCEEVTQAL 297

Query: 311 GTM-GLFL 317
             + GL L
Sbjct: 298 KNIVGLTL 305


>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 =  278 bits (710), Expect = 1e-72,   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|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 =  277 bits (709), Expect = 1e-72,   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 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM---FINFEEPKKEVKEDINVK 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 I---------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIE 296

Query: 309 VLGTMGLF 316
            L  +G+ 
Sbjct: 297 ALERIGIS 304


>gi|261876120|gb|ACY04590.1| DNA-directed RNA polymerase [Lactobacillus sp. DCY 50T]
          Length = 251

 Score =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 117/251 (46%), Positives = 167/251 (66%), 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 TVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           T  KG GYV A     R  + 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|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 =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 116/334 (34%), Positives = 186/334 (55%), Gaps = 17/334 (5%)

Query: 9   LIKPNNIEYIVLG-------QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 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-QTVNDIEVLNPDHVICNLDVDA--VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDA 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 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           +L+  NFG+K+  E++G L  +GL    +L  + 
Sbjct: 306 LLKFRNFGKKTFEELEGFLAEVGLEFATDLSKYN 339


>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 =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 122/357 (34%), Positives = 192/357 (53%), Gaps = 25/357 (7%)

Query: 8   ELIKPNNIEYIVLGQEE---ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           +   P +++ + +       + +   IAEPL RG  HTLGNALRR L+  L   AI +  
Sbjct: 12  KFELPESVKMMAVEGSGGSVDKQASFIAEPLERGMGHTLGNALRRALLIGLEAPAIISFS 71

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMS----GDSHKRVTIFKR----------- 109
           + GVLHE  +I G+ ED+T+IILN+KG  LK       ++ +   + K            
Sbjct: 72  MTGVLHEYMAINGIIEDVTNIILNLKGALLKKYPFQDSENGRCTQLLKSKVSIDASDLAA 131

Query: 110 --GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
             G   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 LGMFINFEEPKKEVKEDINVKSLPFNPALLKK---VEELELSVRSTNCLRGENIVYMGDL 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|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 =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 98/305 (32%), Positives = 159/305 (52%), Gaps = 8/305 (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 AEGGSARERLRMEVVTDGSITPDDAIAQAANQLIELFQPLATVTMVEEVSAEPEPTAEAQ 245

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 246 I------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLF 316
            +G+ 
Sbjct: 300 RIGIQ 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 =  277 bits (708), Expect = 2e-72,   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 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM---FINFEEPKKEVKEDINVK 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 I---------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIE 296

Query: 309 VLGTMGLF 316
            L  +G+ 
Sbjct: 297 ALERIGIS 304


>gi|167946610|ref|ZP_02533684.1| DNA-directed RNA polymerase subunit alpha [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 280

 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: 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 RRVAYSIESARVEQRTNMDRLVIELQTDGTIDPEEAIRRSAGILRDQLSVFVDL-EGGGA 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|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 =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 88/321 (27%), Positives = 159/321 (49%), Gaps = 19/321 (5%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  E  +       P   G A+T+G ++++ L+  + GAA++      V  E +++KGV
Sbjct: 133 QVEGERLHYGRFAVSPFRSGQANTVGVSMQKALLGEVEGAAVSCATFKNVKSEYAAMKGV 192

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E   DI++N+K + ++   D  ++  I   GPG VTAGDI     +EV +P   I  L 
Sbjct: 193 EETPMDILVNLKELVIRSDSDEPQKAIISAIGPGPVTAGDIVLPPSLEVTDPTQHIAYLT 252

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            +  + +EL V KG GY    H ++ +   G   ID+++ P++  +Y+V S      +  
Sbjct: 253 KEVSLDIELDVEKGCGYRMGDHTKSGD---GRFYIDSVFMPVRNANYSVHSYESEPDVTQ 309

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK---KEVKEDINVKSLPFNPA 255
           + L + I T+GSIT E+++  A+R L D    F++ ++ +      K   +     FN +
Sbjct: 310 EILFLEIWTNGSITPEEALHEAARCLIDLFLPFLHPKKKEVTNSATKMHKSFTMSQFNSS 369

Query: 256 LLKKVEELE----------LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                +E++          +  ++ N L+  NI  + DL+  T+ D+L + NFGRKS+ +
Sbjct: 370 AEMSAKEVDLRHVYVDQLRIPSKAYNSLKRANINTVSDLLDYTQDDLLSIPNFGRKSVDD 429

Query: 306 IKGVLGTMGLFLGMNLPDWPP 326
           I   L  +     ++LP+  P
Sbjct: 430 I---LEALQAQFSIDLPENNP 447


>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 =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 84/319 (26%), Positives = 150/319 (47%), Gaps = 23/319 (7%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
             +  +       PL +G A T+G A+RR L+  + G  IT  +++ V HE S+I G+ E
Sbjct: 23  DSKRLHYGRFALSPLRKGQASTIGIAMRRALLGEIEGTCITHAKLEKVTHEYSAIIGIEE 82

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
            + DI++N+K I L+      +  +I   GP  VTA DI     + +++    I +L   
Sbjct: 83  SVHDILINLKEIVLRSDPYGTREASICIVGPRNVTAQDIILPPSVRIIDATQHIASLTKS 142

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
               + L + K  GY        +N   G+  IDA++ P++  +Y++ S   G  +  + 
Sbjct: 143 ITFDIRLWIEKDRGYRI---QSPKNYQDGIFPIDAVFMPVRNANYSIHSYGNGNDI-QEI 198

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK- 259
           L + I T+GS+   +++  ASR L D    F+  EE   +  ++ N  ++P         
Sbjct: 199 LFLEIWTNGSLAPREALYRASRNLIDLFIPFLRAEEQNIDGMDNQNGSNMPSFSFSNISA 258

Query: 260 ---------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
                          +++ EL  R  NCL   NI  + DL+  ++ D++R+ +FG+KS+ 
Sbjct: 259 DMERMEEEVAFKHIFIDQSELPPRVYNCLGRVNIHTLSDLLNYSQEDLMRIGHFGKKSVE 318

Query: 305 EIKGVLGTMGLFLGMNLPD 323
           ++  VL        ++LP 
Sbjct: 319 QVSEVL---QKHFAVDLPK 334


>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 =  276 bits (707), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 100/308 (32%), Positives = 164/308 (53%), Gaps = 14/308 (4%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           + IE+  + ++     + +  PL RG A TLGNALRRVLM  L G+A+TA++I GV HE 
Sbjct: 7   DRIEH-QVEEDRSQSGVFLIGPLERGQATTLGNALRRVLMGGLEGSAVTAIRIAGVNHEY 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 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM---FINFEEPKKEVKEDINVK 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 I---------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIE 296

Query: 309 VLGTMGLF 316
            L  +G+ 
Sbjct: 297 ALERIGIS 304


>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 =  276 bits (707), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 121/357 (33%), Positives = 192/357 (53%), Gaps = 25/357 (7%)

Query: 8   ELIKPNNIEYIVLGQEE---ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           +   P +++ + +       +     +AEPL RG  HTLGNALRR L+  L   AI +  
Sbjct: 12  KFELPKSVKMMTVEGSGGSIDKHARFVAEPLERGMGHTLGNALRRALLIGLEAPAIISFS 71

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-------GDSHK----RVTIFKR---- 109
           + GVLHE  +I+G+ ED+T+I+LN+KG  LK         G   +     ++I       
Sbjct: 72  MTGVLHEYMAIEGIIEDVTNIVLNLKGALLKKYPFQDSEDGRRPQLLKSMISIDASDLAA 131

Query: 110 --GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
             G   VT  D+      E +NP+HVI  +     V + L V+ G GY  ++    E+  
Sbjct: 132 CGGQRAVTLADLLQEGGFEAVNPEHVIFTVTQPMQVEVALRVAFGRGYSTSERIILEDKG 191

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           +  I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG ++ ++++A +++IL   
Sbjct: 192 VNEIVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLILYVETDGRVSPKEALAFSTQILTKH 251

Query: 228 LGMFINFEEPKKEVKEDINVKSLPFNPALLKK---VEELELSVRSTNCLRGENIVYMGDL 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 +K
Sbjct: 312 VIMPEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYAEK 368


>gi|326200311|gb|ADZ52350.1| RNA polymerase alpha subunit [Asclepias syriaca]
          Length = 340

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 88/331 (26%), Positives = 157/331 (47%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 DNTQHIANLTEPINLCIVLKIERNRGY---LIQTPQNVPDGSYPIDAVFMPVRNANHSVH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEEENSHLENNQHRV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            L       K                 +++LEL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 PLFPFTFHDKLTKLIKNKKEIALKSIFIDQLELPPRIYNCLKRSNIYTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F    + ++K +L  +   L + LP 
Sbjct: 307 MKIEHF---RIEDVKQILVVLEKHLAIFLPK 334


>gi|290489690|gb|ADD31229.1| RNA polymerase alpha subunit protein [Heuchera sanguinea]
          Length = 337

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 81/331 (24%), Positives = 159/331 (48%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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         N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDLCIGLQIEKNRGYRIKT---PNNFQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENLHLEDNQHKV 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 MKIEHF---RIEDVKEILGFLEKHFEIDLPK 334


>gi|58758770|gb|AAW81775.1| RNA polymerase alpha subunit [Oedipodium griffithianum]
          Length = 340

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 86/321 (26%), Positives = 154/321 (47%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  E  + +     P   G A+T+G A+RR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  KVDSERLHYSRFAISPFRCGQANTVGIAMRRALLGEVEGTCITCAKFKKVTHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + DI++N+K I L+ +    ++  I   GP  VTA DI     +++++    I  L 
Sbjct: 81  QESVHDILINLKEIVLRSNSYETQKAFISILGPKKVTAQDIILPPSVKIIDTTQYIATLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + K  GY      ++ +   G   IDA++ PI+  +Y+V S         
Sbjct: 141 KTIHLDIELEIEKDCGYRIQDSIKSTD---GHFPIDAIFMPIRNANYSVHSFEHENKT-Q 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GSIT ++++  ASR L D    F++ E+ +     +   +S   +     
Sbjct: 197 EILFIEIWTNGSITPKEALYEASRSLIDLFIPFLHAEKKEIINGLENKYESNNMSYFSSF 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  N+  + DL+  ++ D++++ NFG+KS
Sbjct: 257 SPLADRITKEVTFKHIFIDQLELPARAYNCLKRVNVHTISDLLNYSQDDLMKIKNFGKKS 316

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
              ++ VL  +     +NLP 
Sbjct: 317 ---VEQVLEALQKQFSINLPK 334


>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 =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 115/271 (42%), Positives = 176/271 (64%), Gaps = 4/271 (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 RTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           RT  DM+++ N GRKSL E+   L  +GL L
Sbjct: 241 RTPEDMMKVRNLGRKSLEEVLAKLDELGLSL 271


>gi|319827245|gb|ADV74822.1| RNA polymerase subunit A [Vibrio coralliilyticus]
          Length = 276

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 119/277 (42%), Positives = 181/277 (65%), 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++  + +   +++   +  P    
Sbjct: 183 TDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---I 239

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++
Sbjct: 240 LLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVEL 276


>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 =  276 bits (706), Expect = 3e-72,   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 -GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM---FINFEEPKKEVKEDINVK 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 I---------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIE 296

Query: 309 VLGTMGLF 316
            L  +G+ 
Sbjct: 297 ALERIGIS 304


>gi|319827247|gb|ADV74823.1| RNA polymerase subunit A [Vibrio neptunius]
          Length = 275

 Score =  276 bits (706), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 119/277 (42%), Positives = 181/277 (65%), 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++  + +   +++   +  P    
Sbjct: 182 TDLDKLVIDMETNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---I 238

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++
Sbjct: 239 LLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVEL 275


>gi|325473246|gb|EGC76441.1| DNA-directed RNA polymerase subunit alpha [Treponema denticola
           F0402]
          Length = 351

 Score =  276 bits (706), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 117/348 (33%), Positives = 178/348 (51%), Gaps = 12/348 (3%)

Query: 1   MIQKNW-QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           M +KN  +   KP  +E+       E+     A P   GF  T+GN LRR+L+SS++G A
Sbjct: 1   MARKNLLKGFKKPKGLEFAQQES-TESYGKFTASPFETGFGTTIGNCLRRILLSSIQGYA 59

Query: 60  ITAVQI-----DGVLH----EISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKR 109
           I+AV I     DGV H    E  +I  V ED  +I+  +K I L++S +S +       +
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 337
            ++  M N GR +L EI   L    L LGM        +I+   +K E
Sbjct: 300 DEIESMRNVGRMTLNEIHAKLAEYNLRLGMTDYSHLKNTIKVSRQKEE 347


>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 =  276 bits (706), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 114/305 (37%), Positives = 167/305 (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  ++  I  I +DAL+SPIK+V++ VE  R GQ  D DKL +
Sbjct: 137 VMEVRVDEGVGYVAAEKHGIKDR-INSIPVDALFSPIKRVAFHVEDTRLGQRTDLDKLIL 195

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK---- 259
            I TDGS+T + ++A A  IL+ QLG F           E     +    PA  ++    
Sbjct: 196 RIWTDGSVTPDAALAQAVEILRGQLGYFDQLAPQAAPEPEAAEAPAPEAAPAEPEEAAAE 255

Query: 260 -------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 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|290489666|gb|ADD31217.1| RNA polymerase alpha subunit protein [Meliosma aff. cuneifolia
           Moore 333]
          Length = 337

 Score =  276 bits (706), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 86/331 (25%), Positives = 168/331 (50%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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   +    +N   G   IDA++ P++  ++++ 
Sbjct: 131 DTTQHIASLTEPINLCIGLQIERNHGY---RMKTPKNSQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ N  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHTEEEDIIIEDNQNRF 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           ++PF     +                 +++ EL  R+ NCL+  NI  + DL+ +++ D+
Sbjct: 247 TVPFFTFHDRLAKLRKNKKEIALKFIFIDQSELPPRTYNCLKRSNIHTLLDLLNKSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +R+ +F    + ++K +LG +     +NLP 
Sbjct: 307 MRIEHF---RIEDVKHILGILQKHFEINLPK 334


>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 =  276 bits (706), Expect = 3e-72,   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|290489692|gb|ADD31230.1| RNA polymerase alpha subunit protein [Liquidambar styraciflua]
          Length = 338

 Score =  276 bits (705), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 78/332 (23%), Positives = 156/332 (46%), Gaps = 28/332 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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         N       IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDLCIGLKMERNRGYRIKT---PNNFQDRSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S         + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +  
Sbjct: 188 SYGNENE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENLHLEDNQHKT 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 LMKIEHF---RIEDVKKILGILEKHFAIDLPK 335


>gi|153012268|gb|ABS50355.1| DNA-directed RNA polymerase alpha chain [Enterococcus thailandicus]
          Length = 250

 Score =  276 bits (705), Expect = 4e-72,   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|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 =  276 bits (705), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 119/359 (33%), Positives = 191/359 (53%), Gaps = 25/359 (6%)

Query: 6   WQELIKPNNIEYIVLGQEE---ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           + +   P +++   +       +     +A+PL +G  HTLG+ALRR L+  L   AI +
Sbjct: 10  YNKFELPESVKMSPVEGAVGGIDKVARFVADPLEKGMGHTLGSALRRALLIGLEAPAIVS 69

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-------GDSHKRVTIFKR------ 109
             + GVLHE  +++G+ ED+T+I+LN+KG  LK         G   +++           
Sbjct: 70  FSMTGVLHEYMAVEGIIEDVTNIVLNLKGSLLKKYPLQDCEGGRCSQKLRATISVDASDL 129

Query: 110 ----GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
               G   VT GD+      E +NP+HVI  +     + + L V+ G GY P++    E 
Sbjct: 130 AAAGGQKEVTLGDLLQEGTFEAVNPEHVIFTVTRPMQLEVMLRVAFGRGYSPSERIVLEE 189

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
             +  I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +  +++VA A++IL 
Sbjct: 190 RGMNEIVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLVLQVETDGRVAPKEAVAFATQILS 249

Query: 226 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK---VEELELSVRSTNCLRGENIVYMG 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|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 =  276 bits (705), Expect = 4e-72,   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|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 =  276 bits (705), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 119/359 (33%), Positives = 191/359 (53%), Gaps = 25/359 (6%)

Query: 6   WQELIKPNNIEYIVLGQEE---ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           + +   P +++   +       +     +A+PL +G  HTLG+ALRR L+  L   AI +
Sbjct: 10  YNKFELPESVKMSPVEGAVGGIDKVARFVADPLEKGMGHTLGSALRRALLIGLEAPAIVS 69

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-------GDSHKRVTIFKR------ 109
             + GVLHE  +++G+ ED+T+I+LN+KG  LK         G   +++           
Sbjct: 70  FSMTGVLHEYMAVEGIIEDVTNIVLNLKGSLLKKYPLQDCEGGRCSQKLRATISIDASDL 129

Query: 110 ----GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
               G   VT GD+      E +NP+HVI  +     + + L V+ G GY P++    E 
Sbjct: 130 AAAGGQKEVTLGDLLQEGTFEAVNPEHVIFTVTRPMQLEVMLRVAFGRGYSPSERIVLEE 189

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
             +  I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +  +++VA A++IL 
Sbjct: 190 RGMNEIVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLVLQVETDGRVAPKEAVAFATQILS 249

Query: 226 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK---VEELELSVRSTNCLRGENIVYMG 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|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 =  276 bits (705), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 117/348 (33%), Positives = 178/348 (51%), Gaps = 12/348 (3%)

Query: 1   MIQKNW-QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAA 59
           M +KN  +   KP  +E+       E+     A P   GF  T+GN LRR+L+SS++G A
Sbjct: 1   MARKNLLKGFKKPKGLEFAQQES-TESYGKFTASPFETGFGTTIGNCLRRILLSSIQGYA 59

Query: 60  ITAVQI-----DGVLH----EISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKR 109
           I+AV I     DGV H    E  +I  V ED  +I+  +K I L++S +S +       +
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 337
            ++  M N GR +L EI   L    L LGM        +I+   +K E
Sbjct: 300 DEIESMRNVGRMTLNEIHAKLAEYNLRLGMTDYSHLKNTIKVSRQKEE 347


>gi|165910449|gb|ABY73979.1| RNA polymerase alpha subunit [Cuscuta lupuliformis]
          Length = 335

 Score =  276 bits (705), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 84/331 (25%), Positives = 156/331 (47%), Gaps = 29/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S    +    + L + I T+GS+T ++++  ASR L D    F++ E+    +++     
Sbjct: 188 SYGNEK---QEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHIEKENLHLEDADRTI 244

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            L       K                 +++LE      NCL+  NI  + DL+  ++ D+
Sbjct: 245 PLSPFTVYDKVAKLRKNKKKLALESLFIDQLEFPPNIYNCLKKSNIFTLLDLLNNSQEDL 304

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F    L ++K +LG +G    ++LP 
Sbjct: 305 MKIEHF---RLEDVKQILGILGKHFALDLPK 332


>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 =  276 bits (705), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 119/357 (33%), Positives = 192/357 (53%), Gaps = 25/357 (7%)

Query: 8   ELIKPNNIEYIVLGQEE---ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           +   P +++ + +       + +   +AEPL RG  HTLGNALRR L+  L   AI +  
Sbjct: 12  KFELPESVKMMAVEGSGGSVDKQASFVAEPLERGMGHTLGNALRRALLIGLEAPAIISFS 71

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMS----GDSHKRVTIFKR----------- 109
           + GVLHE  +I+G+ ED+T+I+LN+KG  LK       +  +   + K            
Sbjct: 72  MTGVLHEYMAIEGIVEDVTNIVLNLKGALLKKYPFQDSEDGRCTQLLKSTISVDASDLAA 131

Query: 110 --GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
             G   +T  D+      E +NPDHVI  +     + + L V+ G GY  ++    E+  
Sbjct: 132 CGGQKSITLADLLQEGGFESVNPDHVIFTVTQPMQLEIALRVAFGRGYSTSERIVLEDKG 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 LGMFINFEEPKKEVKEDINVKSLPFNPALLKK---VEELELSVRSTNCLRGENIVYMGDL 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 +K
Sbjct: 312 VIMPEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKSYAEK 368


>gi|290489668|gb|ADD31218.1| RNA polymerase alpha subunit protein [Nelumbo nucifera]
          Length = 339

 Score =  276 bits (705), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 83/323 (25%), Positives = 160/323 (49%), Gaps = 25/323 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I L+ +    +   I  RGPG VTA DI +   +E+++    I +L 
Sbjct: 81  EESVHEILMNLKEIVLRSNLYGTRDAFICVRGPGYVTAQDIISPPSVEIVDTTQHIASLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + + L + +  GY   +     N   G   IDA++ P++  ++++ S   G     
Sbjct: 141 EPIDLCIGLQIERNRGY---RMKTPNNSQDGSYPIDAVFMPVRNANHSIHSYGNGNE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ +E   +++++ N  +LPF     +
Sbjct: 197 EILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLDAQEEDIQLEDNQNKVTLPFFTFHDR 256

Query: 259 ------------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                              +++ EL  R+ NCL+  NI  + DL+  ++ D+++M +F  
Sbjct: 257 LTKLRKNKKEKEIALKCIFIDQSELPPRTYNCLKRSNIHTLLDLLNNSQEDLMKMFHF-- 314

Query: 301 KSLVEIKGVLGTMGLFLGMNLPD 323
             + ++K +L  +     ++LP 
Sbjct: 315 -QIEDVKQILDILQKHFAIDLPK 336


>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 =  275 bits (704), Expect = 5e-72,   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|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 =  275 bits (704), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 87/331 (26%), Positives = 163/331 (49%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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         N   G   ID ++ P++ V++++ 
Sbjct: 131 DTTQHIANLTEPIDLRIELQLERNRGYRIKT---PNNFQDGSYPIDVVFMPVRNVNHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F+  E+    ++++ +  
Sbjct: 188 SYSNGNE-KQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLYAEKENFHLEDNQDRV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP      +                 +++LEL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPLFLFHDRLIELRKNKKKIALKSIFIDQLELPPRIYNCLKNSNIHTLLDLLTNSQDDI 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F   S+ ++K +L T+     +NLP 
Sbjct: 307 MKIEHF---SIEDVKQILDTLEKHFAINLPK 334


>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 =  275 bits (704), Expect = 5e-72,   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|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 =  275 bits (704), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 119/359 (33%), Positives = 191/359 (53%), Gaps = 25/359 (6%)

Query: 6   WQELIKPNNIEYIVLGQEE---ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           + +   P +++   +       +     +A+PL +G  HTLG+ALRR L+  L   AI +
Sbjct: 10  YNKFELPESVKMSPVEGAVGGIDKVARFVADPLEKGMGHTLGSALRRALLIGLEAPAIVS 69

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-------GDSHKRVTIFKR------ 109
             + GVLHE  +++G+ ED+T+I+LN+KG  LK         G   +++           
Sbjct: 70  FSMTGVLHEYMAVEGIIEDVTNIVLNLKGSLLKKYPLQDCEGGRCSQKLRATISIDASDL 129

Query: 110 ----GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
               G   VT GD+      E +NP+HVI  +     + + L V+ G GY P++    E 
Sbjct: 130 AAAGGQKEVTLGDLLQEGTFEAVNPEHVIFTVTRPMQLEVMLRVAFGRGYSPSERIVLEE 189

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
             +  I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +  +++VA A++IL 
Sbjct: 190 RGMNEIVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLVLQVETDGRVAPKEAVAFATQILS 249

Query: 226 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK---VEELELSVRSTNCLRGENIVYMG 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|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 =  275 bits (704), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 119/359 (33%), Positives = 191/359 (53%), Gaps = 25/359 (6%)

Query: 6   WQELIKPNNIEYIVLGQEE---ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           + +   P +++   +       +     +A+PL +G  HTLG+ALRR L+  L   AI +
Sbjct: 10  YNKFELPESVKMSPVEGAVGGIDKVARFVADPLEKGMGHTLGSALRRALLIGLEAPAIVS 69

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-------GDSHKRVTIFKR------ 109
             + GVLHE  +++G+ ED+T+I+LN+KG  LK         G   +++           
Sbjct: 70  FSMTGVLHEYMAVEGIIEDVTNIVLNLKGSLLKKYPLQDCEGGRCSQKLRATISIDASDL 129

Query: 110 ----GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
               G   VT GD+      E +NP+HVI  +     + + L V+ G GY P++    E 
Sbjct: 130 AAAGGQKEVTLGDLLQEGTFEAVNPEHVIFTVTRPMQLEVMLRVAFGRGYSPSERIVLEE 189

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
             +  I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +  +++VA A++IL 
Sbjct: 190 RGMNEIVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLVLQVETDGRVAPKEAVAFATQILS 249

Query: 226 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK---VEELELSVRSTNCLRGENIVYMG 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|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 =  275 bits (704), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 119/357 (33%), Positives = 192/357 (53%), Gaps = 25/357 (7%)

Query: 8   ELIKPNNIEYIVLGQEE---ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           +   P +++ + +       + +   +AEPL RG  HTLGNALRR L+  L   AI +  
Sbjct: 29  KFELPESVKMMAVEGSGGSVDKQASFVAEPLERGMGHTLGNALRRALLIGLEAPAIISFS 88

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMS----GDSHKRVTIFKR----------- 109
           + GVLHE  +I+G+ ED+T+I+LN+KG  LK       +  +   + K            
Sbjct: 89  MTGVLHEYMAIEGIVEDVTNIVLNLKGALLKKYPFQDSEDGRCTQLLKSTISVDASDLAA 148

Query: 110 --GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
             G   +T  D+      E +NPDHVI  +     + + L V+ G GY  ++    E+  
Sbjct: 149 CGGQKSITLADLLQEGGFESVNPDHVIFTVTQPMQLEIALRVAFGRGYSTSERIVLEDKG 208

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
           +  I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG ++ ++++A +++IL   
Sbjct: 209 VNEIVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLILHVETDGRVSPKEALAFSTQILTKH 268

Query: 228 LGMFINFEEPKKEVKEDINVKSLPFNPALLKK---VEELELSVRSTNCLRGENIVYMGDL 284
             +F   +E K   +E I+++    +  L K    + E+ELSVRSTNCL   NI  +G+L
Sbjct: 269 FSIFEKMDEKKIVFEEAISIEKENKDDILHKLVLGINEIELSVRSTNCLSNANIETIGEL 328

Query: 285 IQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
           +   E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  K Y +K
Sbjct: 329 VIMPEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKSYAEK 385


>gi|290489682|gb|ADD31225.1| RNA polymerase alpha subunit protein [Cornus florida]
          Length = 337

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 82/329 (24%), Positives = 158/329 (48%), Gaps = 27/329 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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         N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQYIASLTEPIDLCIGLQIERNRGYRIKP---PNNFQDGNYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHTEEENLHLEDNQHKV 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 MKMKDF---RIEDVKEILDILEKRFATDL 332


>gi|290489694|gb|ADD31231.1| RNA polymerase alpha subunit protein [Oxalis latifolia]
          Length = 339

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 81/331 (24%), Positives = 161/331 (48%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    +         I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 13  RTLQWKCVESRADGKRLYYGRFILSPLMKGQADTIGIAIRRALLGEIEGTCITRAKSEKI 72

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S++ G+ E + +I++N+K I L+ +       ++  +GPG VTA DI     +E++
Sbjct: 73  PHEYSTLAGIQESIHEILMNLKEIVLRSNLYGTHDASLCVKGPGYVTAQDIILPPSVEII 132

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY         N   G   IDA++ P++  ++++ 
Sbjct: 133 DNTQHIASLTEPIELCIGLQIERNRGY---HKKTPNNFQDGSYPIDAVFMPVRNANHSIH 189

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S R G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + +  
Sbjct: 190 SYRNGNE-KQEMLFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENSHLETNQHKV 248

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP      +                 +++LEL+ R  NCL+  NI  + DL+  ++ D+
Sbjct: 249 TLPLFTFHDRLAKLRKIKKKISLKYIFIDQLELTPRIYNCLKRSNIHTLLDLLNNSQEDL 308

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           + + +F    + ++K ++G +   L ++LP 
Sbjct: 309 MNIEHF---HIEDVKHIMGVLENNLAIDLPK 336


>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 =  275 bits (704), Expect = 6e-72,   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|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 =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 85/333 (25%), Positives = 159/333 (47%), Gaps = 29/333 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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   +     N   G   IDA+  P++  ++++ 
Sbjct: 131 DTTQHIASLTEPINLCIELQIERDRGY---RMKAPNNYQDGSYPIDAVSMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    +  + N  
Sbjct: 188 SYGSGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEQDIHLNLEDNQN 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 DLMRIEHF---RIEDIKQILDILQKHFGIDLPK 336


>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 =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 115/273 (42%), Positives = 177/273 (64%), Gaps = 5/273 (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 QRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            +T  DM+++ N GRKSL E+   L  + L L 
Sbjct: 241 NKTPEDMMKVRNLGRKSLEEVLAKLKELNLELN 273


>gi|161511761|emb|CAP16891.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           ethanolidurans]
          Length = 251

 Score =  275 bits (703), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 110/250 (44%), Positives = 162/250 (64%), Gaps = 2/250 (0%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I    E  N    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVLHE S+I+G
Sbjct: 2   IHKIDENANYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVLHEFSTIEG 61

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V ED+T IILNIK ++LK+  D  K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +
Sbjct: 62  VVEDVTQIILNIKKVSLKIESDDEKSLEINVKGPATVTAGDIQGDSDVEILNPDQYICTV 121

Query: 138 DVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
                    LT   G GYV A     R ++ PIG++ ID++Y+PI++V+Y VE+ R GQ 
Sbjct: 122 ADGVTFHAVLTADTGRGYVSADENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQR 181

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
            DYDKL++ + TDGSI+  ++ +L+++IL + L +F+N  +  ++ +  +  +       
Sbjct: 182 DDYDKLTLDVWTDGSISPSEATSLSAKILTEHLALFVNLTDEAQDAEIMVEKEETHKEKM 241

Query: 256 LLKKVEELEL 265
           L   +EEL+L
Sbjct: 242 LEMSIEELDL 251


>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 (703), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 122/337 (36%), Positives = 185/337 (54%), Gaps = 22/337 (6%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           + +   IAEPL RG  HTLGNALRR L+  L   AI +  + GVLHE  +I G+ ED+T+
Sbjct: 12  DKQASFIAEPLERGMGHTLGNALRRALLIGLEAPAIISFSMTGVLHEYMAINGIIEDVTN 71

Query: 85  IILNIKGINLKMS----GDSHKRVTIFKR-------------GPGVVTAGDIQTVNDIEV 127
           IILN+KG  LK       ++ +   + K              G   VT  D+      E 
Sbjct: 72  IILNLKGALLKKYPFQDSENGRCTQLLKSKVSIDASDLAACGGQKAVTLADLLQEGGFES 131

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NPDHVI  +     + + L V+ G GY  ++    E+  +  I +DA +SP+  V+Y V
Sbjct: 132 VNPDHVIFTVTQPMQLDITLRVAFGRGYTTSERIVLEDKGVNEIVLDAAFSPVVLVNYFV 191

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E  R GQ  D+D+L + ++TDG ++ ++++A +++IL     +F   +E K   +E I++
Sbjct: 192 EDTRVGQDTDFDRLILHVETDGRVSPKEALAFSTQILTKHFSIFEKMDEKKIVFEEAISI 251

Query: 248 KSLPFNPALLKK---VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +    +  L K    + E+ELSVRSTNCL   NI  +G+L+   E  +L+  NFG+KSL 
Sbjct: 252 EKENKDDILHKLVLGINEIELSVRSTNCLSNANIETIGELVIMPEPRLLQFRNFGKKSLC 311

Query: 305 EIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYEDK 339
           EIK  L  M L LGM+L  +    ++++E  K Y DK
Sbjct: 312 EIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYADK 348


>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 =  275 bits (703), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 85/331 (25%), Positives = 161/331 (48%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    +         I  PL +G A T+G A+RR L+  + G  IT  + + V
Sbjct: 11  RALQWKCVESRADSKRLYYGRFILSPLLKGQADTIGIAMRRALLGEIEGTCITRAKSEKV 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +    +  +I  RGP  VTA DI +   +EV+
Sbjct: 71  PHEYSTIAGIEESVHEILMNLKEIVLRSNLYGTRDASICVRGPRCVTAQDIISPPSVEVV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY   +   T+N   G   IDA+  P++  ++++ 
Sbjct: 131 DTTQHIASLTEPIDLCIGLQIQRDRGY---RMKTTKNSQDGSYPIDAVSMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  
Sbjct: 188 SYGNGNQ-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEEDINFEENQNRF 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           ++P      +                 +++ EL  R+ NCL+  NI  + DL+  ++ D+
Sbjct: 247 TVPPFTFPDRLANLKKNKKEIALKCIFIDQSELPPRTYNCLKRSNIHTLLDLLSNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++  F    + ++K +L T+     ++LP 
Sbjct: 307 MKIEYF---RIEDVKQILDTLQKHFAIDLPK 334


>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 =  275 bits (703), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 110/305 (36%), Positives = 173/305 (56%), Gaps = 5/305 (1%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            +   + ++       EPL RG+ +T+GNALRRVL+SS+ G+AI  V+IDGVL+E S I+
Sbjct: 12  KLTEEKIDQYSAKYTLEPLYRGYGNTIGNALRRVLLSSIPGSAIKGVRIDGVLNEFSMIE 71

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV E +TDI+LNIK I +++     KR+ +   GP V+TA DI     I ++NP+ VI  
Sbjct: 72  GVKEAVTDIVLNIKEIVVELDEPVEKRMKLSVVGPKVITAADIVPEAGITIVNPEQVIAT 131

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +     + ME  V  G G+V +    T       + +DA+Y+PI+KVSY VE    G+V 
Sbjct: 132 ITTKKAIDMEFIVDSGEGFVVSDEINTSGWEADFLAVDAIYTPIRKVSYQVEDTMVGRVT 191

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
           +YDKL++T+ TDGSI   D+++ A  ++      F N      + + +  ++    N + 
Sbjct: 192 NYDKLTLTVTTDGSIDIHDALSYAVELINIHTKPFANIGTAMAKFRSEEELELEVSNDSY 251

Query: 257 -----LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                  ++EEL L++RS NCL+  +I  +G+LI+ T+ D+ ++ N G KS  EI   + 
Sbjct: 252 PSLVEDTRIEELGLTIRSYNCLKKVDINTVGELIRLTKEDLKKIKNLGNKSAKEIIEKMK 311

Query: 312 TMGLF 316
             G  
Sbjct: 312 EYGYE 316


>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 =  274 bits (702), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 118/359 (32%), Positives = 192/359 (53%), Gaps = 25/359 (6%)

Query: 6   WQELIKPNNIEYIVLGQEE---ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           + +   P +++   +       +     +A+PL +G  HTLG+ALRR L+  L   AI +
Sbjct: 10  YNKFELPESVKMSPVEGAAGGIDKVARFVADPLEKGMGHTLGSALRRALLIGLEAPAIVS 69

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-------GDSHKRVTIFKR------ 109
             + GVLHE  +++G+ ED+T+I+LN+KG  LK         G + +++           
Sbjct: 70  FSMTGVLHEYMAVEGIIEDVTNIVLNLKGSLLKKYPLQDCEGGRASQKLRATISIDASDL 129

Query: 110 ----GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
               G   +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 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK---VEELELSVRSTNCLRGENIVYMG 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|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 =  274 bits (702), Expect = 9e-72,   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   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 +           ++  +E        
Sbjct: 186 AEGGTGRERLTMEVVTDGSTSPDDAIAEAANQLIELFQPLATVTMVEEIPEEPEPSPEAQ 245

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 246 I------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLF 316
            +G+ 
Sbjct: 300 RIGIS 304


>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 =  274 bits (702), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 84/331 (25%), Positives = 158/331 (47%), Gaps = 29/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S    +    + L + I T+GS+T ++++  ASR L D    F++ EE    +++  +  
Sbjct: 188 SYGNEK---QEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEEENLHLEDADHTI 244

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           SL       K                 +++LE   +  NCL+  NI  + DL+  ++ D+
Sbjct: 245 SLSPFTVYDKVAKLRKNKKKRSLESIFIDQLEFPPKIYNCLKKSNIFTLLDLLNNSQEDL 304

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F    L ++K +LG +G    ++LP 
Sbjct: 305 IKIEHF---RLEDVKQILGILGKHFALDLPK 332


>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 =  274 bits (702), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 119/359 (33%), Positives = 191/359 (53%), Gaps = 25/359 (6%)

Query: 6   WQELIKPNNIEYIVLGQEE---ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           + +   P +++   +       +     +A+PL +G  HTLG+ALRR L+  L   AI +
Sbjct: 27  YNKFELPESVKMSPVEGAVGGIDKVARFVADPLEKGMGHTLGSALRRALLIGLEAPAIVS 86

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-------GDSHKRVTIFKR------ 109
             + GVLHE  +++G+ ED+T+I+LN+KG  LK         G   +++           
Sbjct: 87  FSMTGVLHEYMAVEGIIEDVTNIVLNLKGSLLKKYPLQDCEGGRCSQKLRATISIDASDL 146

Query: 110 ----GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
               G   VT GD+      E +NP+HVI  +     + + L V+ G GY P++    E 
Sbjct: 147 AAAGGQKEVTLGDLLQEGTFEAVNPEHVIFTVTRPMQLEVMLRVAFGRGYSPSERIVLEE 206

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
             +  I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +  +++VA A++IL 
Sbjct: 207 RGMNEIVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLVLQVETDGRVAPKEAVAFATQILS 266

Query: 226 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK---VEELELSVRSTNCLRGENIVYMG 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|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 =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 109/244 (44%), Positives = 163/244 (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 MGDL 284
           + +L
Sbjct: 241 VQEL 244


>gi|329565863|gb|AEB92268.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
          Length = 250

 Score =  274 bits (701), Expect = 1e-71,   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|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 =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 94/299 (31%), Positives = 156/299 (52%), Gaps = 7/299 (2%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       +  PL RG A TLGN+LRRVLM  L G+A+TAV+I G+ HE ++I GV
Sbjct: 12  QISDDRSQTGTFLIGPLERGQATTLGNSLRRVLMGGLEGSAVTAVRISGINHEYATIPGV 71

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+ DI+LN K +++  S    +   +   GP  V A DIQ  + +E+++ +  I  + 
Sbjct: 72  REDVLDILLNCKQLSINSSNPETEIGRLVVNGPMEVKANDIQFSSQVEIVDGEKPIATIQ 131

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE-GQVLD 197
               + +E+ V +G GY P      E   I L+ IDA++ P+K+V++T++          
Sbjct: 132 EGHNLELEIHVERGVGYRPVDRRNQETTAIDLLQIDAVFMPVKRVNFTIDETAVAEGATG 191

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
            ++L+M + TDGS + +D++A A+  L +           ++  +E              
Sbjct: 192 RERLTMEVVTDGSTSPDDAIAEAANQLIELFQPLATVTMVEEIPEEPEPSPEAQI----- 246

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
             +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L  +G+ 
Sbjct: 247 -PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALERIGIS 304


>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 =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 116/320 (36%), Positives = 169/320 (52%), Gaps = 10/320 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           ++  KP     IV     +      A PL RGFA TLGNALRR L+SS  GA++ A++I 
Sbjct: 2   KQFNKPEF--GIVKESPNKFYGKFEAAPLERGFAVTLGNALRRTLLSSTPGASVFAIKIA 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSG-----DSHKRVTIFKRGPGVVTAGDIQT 121
           G  HE +SI G+ E++T I+LN+K + L++       D    + +     G VTAG +  
Sbjct: 60  GAQHEFTSISGIEENVTRIVLNVKKLILRIDSAIYNDDETVELKVGTSTIGPVTAGSLVL 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT-ENDPIGLITIDALYSPI 180
              +EVLN D VI N+     + + L      GY   K ++  ++   G+ITID+ YSPI
Sbjct: 120 PAGVEVLNKDLVIANVAEGGNLDLVLYAKNSRGYKTFKENKELKDVVPGMITIDSNYSPI 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KV+Y       G+  D++KL + ++TDGSI   D+V+LAS+IL     +F    E  +E
Sbjct: 180 IKVAYGSTPINLGKAQDFEKLILEVETDGSILASDAVSLASKILISHFDVFTTLAEEVEE 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           V              L K VEELE + RS NCL+   I  + +L+ +TE ++  + N GR
Sbjct: 240 VAIMGVETVEEKE--LDKPVEELEFTQRSLNCLKRAGISTLRELVSKTEDEIQDIRNLGR 297

Query: 301 KSLVEIKGVLGTMGLFLGMN 320
           KSL EIK  +  + L    N
Sbjct: 298 KSLKEIKDKVAALELTFKQN 317


>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 = 84/333 (25%), Positives = 160/333 (48%), Gaps = 29/333 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID-- 66
             +++  +    +         I  PL +G A T+G A+RR L+  + G +IT V+ +  
Sbjct: 11  RTLQWKCVESRTDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTSITRVKSESE 70

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
            V HE S+I G+ E + +I++N+K I L+ +       +I  RGPG VTA DI     +E
Sbjct: 71  KVPHEYSTISGIQESVHEILMNLKEIVLRSNLYGTCDASICVRGPGYVTAQDIILPPYVE 130

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           +++    I +L     + + L + +  GY+    H   N   G   IDA++ P++  +++
Sbjct: 131 IVDNTQHIASLTEPIDLCIGLQIERNRGYLIKTPH---NFQDGSYPIDAVFMPVRNANHS 187

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           + S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +
Sbjct: 188 IHSYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEEENVHLEDNQH 246

Query: 247 VKSLPFNPALLKK----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
              L       K                 +++ EL  R  NCL+  NI  + DL+  ++ 
Sbjct: 247 TVPLSPFIFHDKLAKLRKKKKKIALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQE 306

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           D++++ +F    + ++K +LG +     ++L  
Sbjct: 307 DLMKIEHF---RIEDVKQILGILEKHFAIDLSK 336


>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 =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 94/305 (30%), Positives = 158/305 (51%), 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        
Sbjct: 186 AEGGSARERLRIEICTDGSITPDDALAQTANQLLELFQPLATVTLVEEVGVEPEPSAEAQ 245

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 246 I------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLF 316
            +G+ 
Sbjct: 300 RIGIS 304


>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 =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 112/317 (35%), Positives = 180/317 (56%), Gaps = 10/317 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           ++ ++P  I       +++N       PL RGF  TLGNA+RR L+++  GA++ A++I 
Sbjct: 2   KQFVRPEFILLK--EGQDKNYGKFSVSPLERGFGITLGNAIRRTLLAATPGASVYAIKIA 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMS-----GDSHKRVTIFKRGPGVVTAGDIQT 121
           G  HE +SI G+ E++T IILNIK + LK+       D   ++ I     G V AGD+  
Sbjct: 60  GATHEFTSIPGIIENVTKIILNIKQLVLKIDTSIYSDDEVVQLRIRSDIQGPVYAGDLDI 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND-PIGLITIDALYSPI 180
              +E+LN D +I  +    V+ + L      GY   K ++ E +   G+ITID+ YSPI
Sbjct: 120 PAGVEILNKDLLIATISEGGVLDLVLYAKNSRGYKTFKDNKNEKNIEPGMITIDSNYSPI 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KV+Y+V+SA+ G+ +D +KL + + TDGSIT  D++++ASRIL   L  FI+       
Sbjct: 180 IKVAYSVDSAKIGRAIDLEKLELEVTTDGSITAIDAISIASRILVAHLEFFIDLNREISV 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           ++     ++   +  L + VEEL+ + RS NCL+   I  + +L+ + E ++  + N GR
Sbjct: 240 LEVIGTNQTD--DKELDRTVEELDFTQRSLNCLKRAGINTLRELVSKNEDEIGSIRNLGR 297

Query: 301 KSLVEIKGVLGTMGLFL 317
           KSL EIK  + ++GL  
Sbjct: 298 KSLKEIKDKVASLGLAF 314


>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 =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 118/359 (32%), Positives = 192/359 (53%), Gaps = 25/359 (6%)

Query: 6   WQELIKPNNIEYIVLGQEE---ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           + +   P +++   +       +     +A+PL +G  HTLG+ALRR L+  L   AI +
Sbjct: 27  YNKFELPESVKMSPVEGAAGGIDKVARFVADPLEKGMGHTLGSALRRALLIGLEAPAIVS 86

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-------GDSHKRVTIFKR------ 109
             + GVLHE  +++G+ ED+T+I+LN+KG  LK         G + +++           
Sbjct: 87  FSMTGVLHEYMAVEGIIEDVTNIVLNLKGSLLKKYPLQDCEGGRASQKLRATISIDASDL 146

Query: 110 ----GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
               G   +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 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK---VEELELSVRSTNCLRGENIVYMG 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|76665073|emb|CAJ17984.1| DNA-directed RNA polymerase alpha subunit [Candidatus Phytoplasma
           solani]
          Length = 318

 Score =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 102/321 (31%), Positives = 174/321 (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  GVHEDLTDIILNIKGINLKMS---GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
           GV+ED+  IILN+K I  K+     D  +++ 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 ITTISDNINFHMTVTIKKGIGYVGAKDNKIHSENQIGVIAIDSLFTPVLDVAYQVGK--- 178

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            ++ + D+L++ I T+G+   ++++  A++IL +   + +   +    ++     K    
Sbjct: 179 -KLGNKDELTIQITTNGAAVAKEALVTAAKILVEHFNVIVELSQKVANIEFIPETKEEAH 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|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 =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 97/300 (32%), Positives = 163/300 (54%), Gaps = 4/300 (1%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +    +   +   L  G   T+GN LRRVL+  L G AI+AV+I G+ HE S+I GV ED
Sbjct: 15  ESGACQGRFVINALRAGQGITIGNQLRRVLLGDLGGMAISAVRIAGITHEFSTIPGVRED 74

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + +I+LN+KGI LK   +  +   +  +GP VVTA  IQ  +++E++NP+H I  +    
Sbjct: 75  ILEILLNLKGIVLKSEINDIQFGRLKVQGPAVVTADLIQLPSNLEIINPNHYIATISTSN 134

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
           ++ +E     G GY  A    T++     + +D ++ PI+KV + +E+  +      ++L
Sbjct: 135 ILEIEFKFEYGTGYKLATQTFTDDSE-NYLQLDTVFMPIQKVDFKIENVYDSANNITERL 193

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + I T+GSI+  +++  A++++ D   + IN +      + +   +S    P     +E
Sbjct: 194 LLDIWTNGSISPNEALESAAQVIVDLFTLLINNKNMVNTNQLESKPESSSIEPYTNIAIE 253

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           EL+LSVR+ NCL+   I  +GDL+Q +   +  + NFGRKS  E+   L      LG+ L
Sbjct: 254 ELQLSVRAYNCLKKAQINTVGDLLQYSPEKLQELKNFGRKSADEVFSTLKNK---LGIIL 310


>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 =  274 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 117/271 (43%), Positives = 180/271 (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++  + +   +++   +  P    LL+
Sbjct: 182 DKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLR 238

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
            V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 239 PVDDLELTVRSANCLKAEAIHYIGDLVQRTE 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 =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 117/271 (43%), Positives = 180/271 (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++  + +   +++   +  P    LL+
Sbjct: 182 DKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLR 238

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
            V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 239 PVDDLELTVRSANCLKAEAIHYIGDLVQRTE 269


>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 =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 80/328 (24%), Positives = 154/328 (46%), Gaps = 27/328 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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         N   G   IDA+  P++  ++++ 
Sbjct: 131 DTTQYIASLTEPIDLCIELQIERDRGYRIKT---PNNYQDGSYPIDAVSMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS T ++++  ASR L D    F++ EE    V+++ N  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSFTPKEALYEASRNLIDLFLPFLHAEEQDINVEDNQNRA 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 MRIEHF---RIEDVKQILGILQKRFAID 331


>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 =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 116/326 (35%), Positives = 197/326 (60%), Gaps = 12/326 (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 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP-IGLITIDALYSPIKKV 183
            +VLN D VIC+ +    + M  T+ +G GYVPA+ ++  N+  IG I ID++Y+PIK V
Sbjct: 122 FQVLNTDVVICHKEKSIPLEMSFTIEEGRGYVPAEENKKNNNDLIGNIPIDSIYTPIKNV 181

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN-----FEEPK 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 GRKSLVEIKGVLGTMGLFLGMNLPDW 324
           GRKSL E++  +   GL+ GM++ ++
Sbjct: 302 GRKSLEELESQMKEKGLYFGMDISEY 327


>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 =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 94/305 (30%), Positives = 158/305 (51%), 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        
Sbjct: 186 AEGGSARERLRIEISTDGSITPDDALAQTANQLLELFQPLATVTLVEEVGVEPEPSAEAQ 245

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 246 I------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLF 316
            +G+ 
Sbjct: 300 RIGIS 304


>gi|254553679|gb|ACT67298.1| RNA polymerase alpha subunit [Joinvillea plicata]
          Length = 339

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 92/321 (28%), Positives = 160/321 (49%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLIKGQADTIGIAMRRALLGEIEGTCITRAKSGKVPHEYSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI +   +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIISPPSVEIVDTTQHIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + +  GY        +N   G   IDA+  P++ V+Y++ S        Y
Sbjct: 141 EPIDLCIELQIKRDRGYHTEPR---KNSQDGSYPIDAVSMPVRNVNYSIYSCGNENE-KY 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +LP      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEEDTNFEENKNRFTLPLLTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ ++E D++++ NF    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRSNIHTLLDLLSKSEEDLMKIENF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + + K +L T+   L M+LP 
Sbjct: 314 MEDGKQILDTLQKHLSMDLPK 334


>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 =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 81/335 (24%), Positives = 162/335 (48%), Gaps = 26/335 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    +         +  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWRCVESRTDSKRLYYGRFVLSPLMKGQADTIGIAMRRALLGEIEGTCITHAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +       +I  +GP  +TA DI +   +E++
Sbjct: 71  PHEYSTIVGIEESVHEILMNLKEIVLRSNLYGTCDASICVKGPINITAKDIISPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY   +         G   IDA++ P++  ++++ 
Sbjct: 131 DTTQHIASLTEPFDLCIGLQIERNRGY---RMKTPNKAQNGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ N  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEQDIILEDNQNRV 246

Query: 249 SLPFNPALL---------------KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           +LPF                      +++ EL  R+ NCL+  NI  + DL+ +++ D+L
Sbjct: 247 TLPFFTFHDGLAKLKKKNEIALKFIFIDQSELPSRTYNCLKKSNINTLLDLLNKSQEDLL 306

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPES 328
           ++ +F    + ++K VLG +     ++LP     +
Sbjct: 307 KIEHF---RIEDVKRVLGILQKRFVIDLPKNKFSN 338


>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 =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 85/331 (25%), Positives = 161/331 (48%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    +         I  PL +G A T+G A+RR L+  + G  IT  + + V
Sbjct: 11  RALQWKCVESRADSKRLYYGRFILSPLLKGQADTIGIAMRRALLGEIEGTCITRAKSEKV 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +    +  +I  RGP  VTA DI +   +EV+
Sbjct: 71  PHEYSTIAGIEESVHEILMNLKEIVLRSNLYGTRDASICVRGPRCVTAQDIISPPSVEVV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY   +   T+N   G   IDA+  P++  ++++ 
Sbjct: 131 DTTQHIASLTEPIDLCIGLQIQRDRGY---RMKTTKNSQDGSYPIDAVSMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  
Sbjct: 188 SYGNGNQ-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEEDINFEENQNRF 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           ++P      +                 +++ EL  R+ NCL+  NI  + DL+  ++ D+
Sbjct: 247 TVPPFTFPDRLANLKKNKKEIALKCIFIDQSELPPRTYNCLKRSNIHTLLDLLSNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++  F    + ++K +L T+     ++LP 
Sbjct: 307 MKIEYF---RIEDVKQILDTLRKHFAIDLPK 334


>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 =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 100/313 (31%), Positives = 163/313 (52%), Gaps = 8/313 (2%)

Query: 13  NNIEYIVLGQE----EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           NNI    L  E           +   L  G   T+GN LRRVL+  L G AI+AV+I G+
Sbjct: 2   NNISIKCLKSEKIQSGACHGQFLINSLNPGQGITIGNQLRRVLLGDLGGVAISAVRIAGI 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I GV ED+ +I+LN+KGI         +   +  +GP VVTA  IQ    +E++
Sbjct: 62  THEFSTIPGVREDILEILLNLKGIICTSQIQDTQFGHLKVQGPSVVTADLIQLPPGVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+H I  +    ++ +E     G GY  A  +  E D    + +D ++ P++KV + +E
Sbjct: 122 NPNHYIATISTSNILEIEFKFEYGSGYHLASQNFVEEDE-NYLQLDTIFMPVQKVDFKIE 180

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +  +      ++L + I T+GSI+  D++  A++++ D   + IN +      + ++  +
Sbjct: 181 NIYDATNNISERLFLDIWTNGSISPNDALESAAQVIIDLFTLLINNKNINNNNRLELKPE 240

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
           ++   P     +EEL+LSVR+ NCL+   I  +GDL+Q +   +  + NFGRKS  E+  
Sbjct: 241 TISIEPYTNIAIEELQLSVRAYNCLKKAQINTVGDLLQYSPEKLQELKNFGRKSADEVFS 300

Query: 309 VLGTMGLFLGMNL 321
            L      LG+ L
Sbjct: 301 TLKNK---LGIIL 310


>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 =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 111/317 (35%), Positives = 180/317 (56%), Gaps = 10/317 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           ++ ++P  I       +++N       PL RGF  TLGNA+RR L+++  GA++ A++I 
Sbjct: 2   KQFVRPEFILLK--EGQDKNYGKFSVSPLERGFGITLGNAIRRTLLAATPGASVYAIKIA 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMS-----GDSHKRVTIFKRGPGVVTAGDIQT 121
           G  HE +SI G+ E++T IILNIK + LK+       D   ++ I     G + AGD+  
Sbjct: 60  GATHEFTSIPGIIENVTKIILNIKQLVLKIDTSIYSDDEVVQLRIRSDIQGPIYAGDLDI 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND-PIGLITIDALYSPI 180
              +E+LN D +I  +    V+ + L      GY   K ++ E +   G+ITID+ YSPI
Sbjct: 120 PAGVEILNKDLLIATISEGGVLDLVLYAKNSRGYKTFKDNKNEKNIEPGMITIDSNYSPI 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KV+Y+V+SA+ G+ +D +KL + + TDGSIT  D++++ASRIL   L  FI+       
Sbjct: 180 IKVAYSVDSAKIGRAIDLEKLELEVTTDGSITAIDAISIASRILVAHLEFFIDLNREISV 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           ++     ++   +  L + VEEL+ + RS NCL+   I  + +L+ + E ++  + N GR
Sbjct: 240 LEVIGTNQTD--DKELDRTVEELDFTQRSLNCLKRAGINTLRELVSKNEDEIGSIRNLGR 297

Query: 301 KSLVEIKGVLGTMGLFL 317
           KSL EIK  + ++GL  
Sbjct: 298 KSLKEIKDKVASLGLAF 314


>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 =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 81/331 (24%), Positives = 159/331 (48%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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   +     N   G   IDA+  P++  ++++ 
Sbjct: 131 DTTQHIASLTEPIDLCIELQIERDRGY---RMKTPNNYQDGSYPIDAVSMPVRNANHSIH 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 MRIEHF---RIEDVKQILDILQKHFTIDLPK 334


>gi|332178481|gb|AEE14170.1| DNA-directed RNA polymerase subunit alpha [Thermodesulfobium
           narugense DSM 14796]
          Length = 341

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 101/324 (31%), Positives = 176/324 (54%), Gaps = 14/324 (4%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
            I+  +  +     +  + EPLP G+  T+GNALRRVL++S+ G+A+ AV++D   HE  
Sbjct: 11  EIKEQLEIENGGKYSKFVLEPLPPGYGATIGNALRRVLLTSIPGSAVIAVRVDDAPHEYM 70

Query: 74  SIKGVHEDLTDIILNIKGINLK----MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           ++ G+ ED+ +  LN+K + +     +S +  +++ +  +GP +V A DIQ   +++++N
Sbjct: 71  TLPGMVEDILEFHLNLKKLVVVVSPDISEEETRKLILDVKGPKIVKASDIQPNAEVQIIN 130

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND--PIGLITIDALYSPIKKVSYTV 187
            D  +  L+ +  +R E+TV KG GY+  +  +        G I +DA + PI +V+Y+V
Sbjct: 131 KDLYLATLEENGELRAEITVKKGKGYISIEKMKENTRWLSPGSIPLDANFLPITRVNYSV 190

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF------EEPKKEV 241
           ES R GQ  D+DKL   I T+G+I   +++ +A+  L     +F  +      E+P  + 
Sbjct: 191 ESTRVGQETDWDKLIFEIWTNGAIEPVNALRIAAEDLISHFRIFAEYGTFLDSEKPVSDY 250

Query: 242 KEDINVKS--LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           KE              L + +EE+ L  R  N L+   I  +GDLI +T  D+L + +FG
Sbjct: 251 KETKKDSYLRSQAKMDLEQSIEEIGLQTRIANVLKRSGISTLGDLISKTREDILNVPSFG 310

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPD 323
           +KSL E++ +L   G  L  +  +
Sbjct: 311 KKSLDELEEILHAKGYRLKSSDEN 334


>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 =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 86/331 (25%), Positives = 156/331 (47%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLG----QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 DNTQHIARLMEPINLCIRLEIERNRGYLIKTPQ---NFQDGSYPIDAVFMPIRNANYSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHQASRNLIDLFIPFLHMEEQNSHLENNQHTV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            L       K                 +++ EL  R  NCL+  NI  + DL+  ++ ++
Sbjct: 247 PLAPFFFHDKLDKLRKNKKEIALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQENL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F    + ++K +LG +   L + LP 
Sbjct: 307 MKIEHF---HIEDVKEILGILEKQLVIFLPK 334


>gi|47679557|gb|AAT36722.1| RNA polymerase alpha subunit [Navicula salinicola]
          Length = 298

 Score =  273 bits (697), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 97/298 (32%), Positives = 156/298 (52%), Gaps = 5/298 (1%)

Query: 13  NNIEYIVLGQE----EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           NNI    L  E           +   L  G   T+GN LRRVL+  L G AI+AV+I GV
Sbjct: 2   NNISIKCLKSEKIQSGTCHGQFLINSLRPGQGITIGNQLRRVLLGDLGGVAISAVRIAGV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I GV ED+ +I+LN+KGI L       +   +  +GP VVTA  IQ   ++E++
Sbjct: 62  SHEFSTIPGVREDILEILLNLKGIVLTSKTQETQFGRLKIQGPCVVTADLIQLPPNLEIV 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+  I  +    ++ +E     G GY  A    ++      + +D ++ P+ KV + +E
Sbjct: 122 NPNQYIATITTSNIIEIEFKFEYGIGYKFASQTFSDEAD-NFLQLDTVFMPVPKVDFKIE 180

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +  +      ++L + I T+GSI   D++  A++I+ D   + IN ++  +  +     +
Sbjct: 181 NVYDTANNITERLFIDIWTNGSIPPNDALESAAQIIIDLFTLLINNKDTNESSQLKTKAR 240

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           S+   P     +EEL+LSVR+ NCL+   I  +GDL+Q +   +  + NFGRKS  E+
Sbjct: 241 SISMEPYTNIAIEELQLSVRAYNCLKKAQINTVGDLLQYSPEKLQELKNFGRKSADEV 298


>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 =  273 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 95/305 (31%), 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   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 +           ++  +E        
Sbjct: 185 AEGGTGRERLKMEVVTDGSTSPDDAIAEAANQLIELFQPLATVTMVEEIPEEPEPSPEAQ 244

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 245 I------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIDALE 298

Query: 312 TMGLF 316
            +G+ 
Sbjct: 299 RIGIS 303


>gi|267798457|gb|ACY78909.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 269

 Score =  273 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 117/271 (43%), Positives = 180/271 (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++  + +   +++   +  P    LL+
Sbjct: 182 DKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLR 238

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
            V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 239 PVDDLELTVRSANCLKAEAIHYIGDLVQRTE 269


>gi|213420654|ref|ZP_03353720.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. E01-6750]
          Length = 271

 Score =  273 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 114/277 (41%), Positives = 179/277 (64%), Gaps = 10/277 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 120/312 (38%), Positives = 190/312 (60%), Gaps = 11/312 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           ++KP  +E     +E+      + + L +G A  LGN+LRR+L+SS+ G+A++ V++D V
Sbjct: 4   IMKP-VLEVKEFVEEQG-YARFVCDSLAKGEATVLGNSLRRILLSSMPGSAVSEVKLDSV 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMS--GDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
            HE SSI GV ED+++II+N+K + L+ +  G+      +   G GVV A DI+  +++E
Sbjct: 62  YHEFSSIPGVKEDVSEIIMNLKNLALRYTGSGEEPVMAYVDYMGEGVVKASDIKVSSEVE 121

Query: 127 VLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           ++NPD V+ +L   DA + ME+ VSKG GY  A      +  IG+I +DA+YSP+KKV+ 
Sbjct: 122 IMNPDLVLAHLSGKDAKIYMEMKVSKGKGYDGANTRDHSDLAIGVIAVDAIYSPVKKVNV 181

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE     +  + ++L + + TD ++  E++V+LA+RILQ  L +F++ +   KE    +
Sbjct: 182 FVE-----EQGNTERLILDVTTDRTMMPEEAVSLAARILQTHLQLFMHMDTSAKEQGAAV 236

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                     L K ++ELELSVRS NCL+   I  + DL  +T  D++++ N GRKSL E
Sbjct: 237 -ANQEAGRDELNKSIDELELSVRSYNCLKRAGINTVEDLCAKTMDDLMKVRNMGRKSLDE 295

Query: 306 IKGVLGTMGLFL 317
           I   L +MGLFL
Sbjct: 296 ILNKLESMGLFL 307


>gi|69215824|gb|AAZ03868.1| RNA polymerase alpha chain [Ranunculus macranthus]
          Length = 339

 Score =  272 bits (696), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 79/333 (23%), Positives = 158/333 (47%), Gaps = 29/333 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 DTTQHIASLTEPVDFCIGLQIESNRGY---RMKTPNNAQKGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G   + + L + I T+GS+T ++++  ASR L D    F++ EE  + +K++    
Sbjct: 188 SYGNGNE-NQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEQDQNLKDNQKNG 246

Query: 249 SLPFNPALL-----------------KKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
                                       +++ EL  R+ NCL+  NI  + DL+ +++ D
Sbjct: 247 VTLPFFTFHDGFDKLKKNKKEIELKCIFIDQSELPSRTYNCLKRANIHTLLDLLNKSQED 306

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFL-GMNLPD 323
           ++++ +F    + ++K +L  +      ++LP 
Sbjct: 307 LMKIEHF---RIEDVKQILDIIQKHFVVIDLPK 336


>gi|47679549|gb|AAT36718.1| RNA polymerase alpha subunit [Chaetoceros gracilis]
          Length = 300

 Score =  272 bits (696), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 92/285 (32%), Positives = 152/285 (53%), Gaps = 1/285 (0%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +        +   L  G   T+GN LRRVL+S L G  ITAV+I GV  E S I G+ ED
Sbjct: 17  ESGSMYGQFLINSLRPGQGITIGNLLRRVLLSDLEGTTITAVRIAGVQDEFSIIPGIRED 76

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + +I+LN+KG+ +K +        +  +GP VVTA  IQ   +IE++NP+H I  +    
Sbjct: 77  ILEILLNLKGVVVKSATPDISFGRLKIKGPAVVTADSIQLPPNIEIINPNHYIATISTSN 136

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
           V+ +E    +G GY  A     +      + IDA++ PI+KV + +E+  +      ++L
Sbjct: 137 VLEIEFKFERGTGYKLAGQTFCDKSE-DFLQIDAIFMPIQKVDFKIENVYDNSNSITERL 195

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + I T+GSI+ +D+++ AS+ + +     +  +  +     +        NP +   +E
Sbjct: 196 FLDIWTNGSISPDDAISYASKFIIEFFNSLLENKITQNLEIIEDTNSLTQLNPHINIAIE 255

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           EL+LSVR+ NCL+   I  +GDL++ +   +  + NFGRKS  E+
Sbjct: 256 ELQLSVRAYNCLKRAQINTIGDLLEYSPEKLQELKNFGRKSADEV 300


>gi|328813975|gb|AEB52103.1| DNA-directed RNA polymerase alpha chain [Lactobacillus fermentum]
          Length = 248

 Score =  272 bits (696), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 111/248 (44%), Positives = 165/248 (66%), 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 KGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           KG GY  A     R 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|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 =  272 bits (695), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 110/317 (34%), Positives = 180/317 (56%), Gaps = 10/317 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           ++ ++P  I       +++N       PL RGF  TLGNA+RR L+++  GA++ A++I 
Sbjct: 2   KQFVRPEFILLK--EGQDKNYGKFSVSPLERGFGITLGNAIRRTLLAATPGASVYAIKIA 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMS-----GDSHKRVTIFKRGPGVVTAGDIQT 121
           G  HE +SI G+ E++T IILNIK + L++       D   ++ I     G V AGD++ 
Sbjct: 60  GATHEFTSIPGIIENVTKIILNIKQLVLRIDTSIYGDDEVVQLKIRSDIQGPVYAGDLEL 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND-PIGLITIDALYSPI 180
              +EVLN D +I  +    ++ + L      GY   K ++ E +   G+ITID+ YSPI
Sbjct: 120 PAGVEVLNQDLLIATISEGGILDLVLYAKNSRGYKTFKDNKNEKNIEPGMITIDSNYSPI 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KV+Y+V+SA+ G+ +D +KL + + TDGSIT  D++++AS+IL   L  FI+       
Sbjct: 180 IKVAYSVDSAKIGRAIDLEKLELEVTTDGSITAIDAISIASKILVAHLEFFIDLNREISV 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           ++      +   +  L + VEEL+ + RS NCL+   I  + +L+ + E ++  + N GR
Sbjct: 240 LEVI--GVNQTDDKELDRTVEELDFTQRSLNCLKRAGINTLRELVTKNEDEIGSIRNLGR 297

Query: 301 KSLVEIKGVLGTMGLFL 317
           KSL EIK  + ++GL  
Sbjct: 298 KSLKEIKDKVASLGLAF 314


>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 =  272 bits (695), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 81/334 (24%), Positives = 161/334 (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     +  +        IDA++ P++  ++
Sbjct: 128 EIIDNTQHIASLTEAIDLCIGLQIERNRGYRINPTNNFQVQDGSYS-IDAVFMPVRNANH 186

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           +V S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ 
Sbjct: 187 SVHSYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDFFIPFLHAEEENLHLEKNQ 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|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 = 84/323 (26%), Positives = 158/323 (48%), Gaps = 25/323 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  E  + +  I  PL  G A+TLG A+RR  +  L G  IT+ + + ++HE S++ G+
Sbjct: 22  KIENERLHHSRFIISPLGIGQANTLGIAMRRASLGELEGTCITSAKFEKIIHEYSTVVGI 81

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + D ++N+K I L+ +    ++  I   GPG +TA DI     IE+++P   I  L 
Sbjct: 82  QESVHDTLINLKEIVLRSNSSEIQKAYISIIGPGEITAQDIILPPSIEIIDPAQHIATLT 141

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR-EGQVLD 197
               + +EL + +  GY      ++++   G   ++A++ PI+ V+Y++       + + 
Sbjct: 142 KKIHLNIELRIERDRGYRRQNIVKSQD---GNFPLNAVFMPIRNVNYSIHCFESHDKKIM 198

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK------------------ 239
            + L + I T+GSIT  +++  ASR L +    F++ E  +K                  
Sbjct: 199 KEMLLLEIWTNGSITPREAIYEASRSLINLFIPFLHAENGEKIYGMGNINESNALSCSVL 258

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
                   +           +++LEL  R+ NCL+  N+  + DL+  ++ D++++ NFG
Sbjct: 259 PPMSIQVDQMAKEVTFRHIFIDQLELPPRAYNCLKRINVHTISDLLDYSQDDLMKIKNFG 318

Query: 300 RKSLVEIKGVLGTMGLFLGMNLP 322
            KS   ++ VL  +    G++LP
Sbjct: 319 IKS---VEQVLEALWKRFGISLP 338


>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 =  272 bits (695), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 79/333 (23%), Positives = 158/333 (47%), Gaps = 29/333 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 DTTQHIASLTEPVDFCIGLQIESNRGY---RMKTPNNAQKGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G   + + L + I T+GS+T ++++  ASR L D    F++ EE  + +K++    
Sbjct: 188 SYGNGNE-NQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEQDQNLKDNQKNG 246

Query: 249 SLPFNPALL-----------------KKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
                                       +++ EL  R+ NCL+  NI  + DL+ +++ D
Sbjct: 247 VTLPFFTFHDGFDKLKKNKKEIELKCIFIDQSELPSRTYNCLKRANIHTLLDLLNKSQED 306

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFL-GMNLPD 323
           ++++ +F    + ++K +L  +      ++LP 
Sbjct: 307 LMKIEHF---RIEDVKQILDIIQKHFVVIDLPK 336


>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 =  272 bits (695), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 95/305 (31%), 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   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 +           ++  +E        
Sbjct: 186 AEGGTGRERLKMEVVTDGSTSPDDAIAEAANQLIELFQPLATVTMVEEIPEEPEPSPEAQ 245

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 246 I------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIDALE 299

Query: 312 TMGLF 316
            +G+ 
Sbjct: 300 RIGIS 304


>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 =  272 bits (695), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 110/317 (34%), Positives = 180/317 (56%), Gaps = 10/317 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           ++ ++P  I       +++N       PL RGF  TLGNA+RR L+++  GA++ A++I 
Sbjct: 2   KQFVRPEFILLK--EGQDKNYGKFSVSPLERGFGITLGNAIRRTLLAATPGASVYAIKIA 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMS-----GDSHKRVTIFKRGPGVVTAGDIQT 121
           G  HE +SI G+ E++T IILNIK + L++       D   ++ I     G V AGD++ 
Sbjct: 60  GATHEFTSIPGIIENVTKIILNIKQLVLRIDTSIYSDDEVVQLKIRSDIQGPVYAGDLEL 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND-PIGLITIDALYSPI 180
              +EVLN D +I  +    ++ + L      GY   K ++ E +   G+ITID+ YSPI
Sbjct: 120 PAGVEVLNQDLLIATISEGGILDLVLYAKNSRGYKTFKDNKNEKNIEPGMITIDSNYSPI 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KV+Y+V+SA+ G+ +D +KL + + TDGSIT  D++++AS+IL   L  FI+       
Sbjct: 180 IKVAYSVDSAKIGRAIDLEKLELEVTTDGSITAIDAISIASKILVAHLEFFIDLNREISV 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           ++      +   +  L + VEEL+ + RS NCL+   I  + +L+ + E ++  + N GR
Sbjct: 240 LEVI--GVNQTDDKELDRTVEELDFTQRSLNCLKRAGINTLRELVTKNEDEIGSIRNLGR 297

Query: 301 KSLVEIKGVLGTMGLFL 317
           KSL EIK  + ++GL  
Sbjct: 298 KSLKEIKDKVASLGLAF 314


>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 = 7e-71,   Method: Composition-based stats.
 Identities = 92/331 (27%), Positives = 160/331 (48%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    +         I  PL +G A T+G ALRR L+  + G  IT  + + V
Sbjct: 11  RRLQWKCVESRVDSKRLYYGRFILSPLIKGQADTVGIALRRALLGEIEGTCITRAKSENV 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI +   +E++
Sbjct: 71  PHEYSTIVGIEESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIISPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L       +EL + +  GY        +N       IDA+  P++ V+Y++ 
Sbjct: 131 DTAQHIATLTEPIDFCIELQIKRDRGYYTELR---KNSQDESYPIDAVSMPVQNVNYSIF 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  
Sbjct: 188 SCGNGNE-KQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEESTNFEENKNRF 246

Query: 249 SLPF----------------NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           + P                  P     +++L+L  R+ NCL+  NI  + DL+ +TE D+
Sbjct: 247 TQPPLTLQKKLTNLKKNKKGVPLNSIFIDQLKLPSRTYNCLKRANIHTLLDLLSKTEEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           LR+ NF    + + K +L T+   L ++LP 
Sbjct: 307 LRIDNF---RMEDGKQILDTLEKDLPIDLPK 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 =  272 bits (695), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 95/305 (31%), 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: 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 +           ++  +E        
Sbjct: 214 AEGATGRERLKMEVVTDGSTSPDDAIAEAANQLIELFQPLATVTMVEEIPEEPEPSPEAQ 273

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 274 I------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 327

Query: 312 TMGLF 316
            +G+ 
Sbjct: 328 RIGIS 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 =  271 bits (694), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 97/299 (32%), Positives = 154/299 (51%), Gaps = 7/299 (2%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +     + +  PL RG A TLGN+LRRVLM  L G+A+TAV+I GV HE ++I GV
Sbjct: 12  QVSNDRSQTGVFLIGPLERGQATTLGNSLRRVLMGGLEGSAVTAVRIAGVNHEYATIPGV 71

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            ED+ DI+LN K I++       +   +   GP  V A DIQ  + +EV++ D  I  + 
Sbjct: 72  REDVLDILLNCKQISVDSRSQELEIGRLVVTGPADVKAKDIQFSSQVEVVDGDRPIATVQ 131

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE-GQVLD 197
               + +E+ V +G GY P      E   I L+ IDA++ PI +V++T++          
Sbjct: 132 EGHNLELEIHVERGVGYRPVDRKNEETSAIDLLQIDAVFMPINRVNFTIDETAVAEGGST 191

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
            ++L M + TDGS + +D++A A+  L +           ++  +E              
Sbjct: 192 RERLKMELVTDGSTSPDDALAEAANQLIELFQPLATVSMVEEIPEEPEPAAEAQI----- 246

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
             +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L  +G+ 
Sbjct: 247 -PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALERIGIS 304


>gi|290489688|gb|ADD31228.1| RNA polymerase alpha subunit protein [Gunnera manicata]
          Length = 330

 Score =  271 bits (694), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 82/325 (25%), Positives = 159/325 (48%), Gaps = 27/325 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 DNTQHIASLTEPIDLCIQLQIEKNRGYRIKT---PNTYQDGSYPIDAVFMPVRNANHSIH 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|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 =  271 bits (694), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 95/305 (31%), 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   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 +           ++  +E        
Sbjct: 186 AEGATGRERLKMEVVTDGSTSPDDAIAEAANQLIELFQPLATVTMVEEIPEEPEPSPEAQ 245

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 246 I------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLF 316
            +G+ 
Sbjct: 300 RIGIS 304


>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 =  271 bits (694), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 83/331 (25%), Positives = 157/331 (47%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 DNTQHIASLTEPIDFCIGLQIERNRGYLIKTPQ---NFQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEEDNLYLQDNQHTV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            L       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|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 =  271 bits (694), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 90/321 (28%), Positives = 158/321 (49%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       +  PL +G A T+G A+RR L+  + G  IT    + VLHE S I G+
Sbjct: 21  RVDSKRLYYGRFVLSPLMKGQADTIGIAMRRALLGRIEGTCITRATSENVLHEYSMIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + DI++N+K I LK +    +  +I  RGP  +TA DI +   +++++    I NL 
Sbjct: 81  EESVHDILINLKEIVLKSNLYGVRDASICVRGPKYITAQDIISPPSVKIVDTTQHIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + +G GY       T     G   ID +  P++  ++++ S   G     
Sbjct: 141 EPIDLCIELQIKRGRGY---HMKSTNESHDGSYPIDIVSMPVRNANHSIHSYGNGNE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D L  F++ EE    ++E+    +LP      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLLIPFLHAEEEDMNLEENEKRWNLPLFSFQDR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++ ELS R+ NCL+  NI  + DL+  ++ D+++M  F    
Sbjct: 257 FTNLKKNKKGIPLTCIFIDQSELSSRTYNCLKRSNIHTLLDLLNHSQEDLMKMEYF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + ++K +LGT+     +NLP 
Sbjct: 314 IEDVKQILGTLQKHFAINLPK 334


>gi|290489696|gb|ADD31232.1| RNA polymerase alpha subunit protein [Plumbago auriculata]
          Length = 333

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 81/329 (24%), Positives = 158/329 (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         N   G   IDA++ P++ V++++ 
Sbjct: 131 DNTQHIATLTEPIDLCIGLQLERNRGYRIQTQ---NNFQDGSYPIDAVFMPVRNVNHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE     + + +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEENLHFEANQHKV 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 MQIEDF---RIEDLKQIWGTLEKNFSIDL 332


>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 =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 94/305 (30%), Positives = 158/305 (51%), 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 +           ++  +E        
Sbjct: 186 AEGGTGRERLKMEVVTDGSTSPDDAIAEAANQLIELFQPLATVTMVEEIPEEPEPSPEAQ 245

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 246 I------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 299

Query: 312 TMGLF 316
            +G+ 
Sbjct: 300 RIGIS 304


>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 =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 92/331 (27%), Positives = 161/331 (48%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             I++  +    +         I  PL +G A T+G A+RR L+  + G  IT  + + V
Sbjct: 11  RTIQWKCVESRVDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSERV 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I+LN+K I L+ +    +  +I  RGP  VTA DI     +E++
Sbjct: 71  PHEYSTIIGIEESVHEILLNLKEIVLRSNLYGVRDASICVRGPRYVTAQDIILPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +P   I NL     + +EL + +  GY   +   T N   G   IDA+  P++  ++++ 
Sbjct: 131 DPTQHIANLTEPIDLYIELQIKRDRGY---RMEPTNNSQDGSYPIDAVSMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEEDINFEENKNRF 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LPF     +                 +++LEL  R+ NCL+  NI  + DL+   + D+
Sbjct: 247 TLPFLTFQDRLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRSNIHTLLDLLSNGQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +R+       + ++K +L T+     ++LP 
Sbjct: 307 MRIEYL---RMEDVKQILDTLQKNFAIDLPK 334


>gi|303308472|gb|ADM14339.1| RNA polymerase alpha subunit [Punica granatum]
          Length = 337

 Score =  271 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 80/309 (25%), Positives = 150/309 (48%), Gaps = 20/309 (6%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFEKIPHEYSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I L+         +I  +GPG VTA DI     +E+++    I +L 
Sbjct: 81  QESVHEILMNLKEIVLRSYLYGTCNASICVKGPGCVTAQDIILPPSVEIIDNTQHIASLM 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + + L + +  GY         N   G   IDA++ P++  ++++ S   G     
Sbjct: 141 EPINLCIGLQIERNRGYHIKT---PNNFQDGSYPIDAVFMPVRNANHSIHSYGNGNE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D L  F++ EE    ++ +    +LP      +
Sbjct: 197 EILFLEIWTNGSLTPKEALHEASRNLIDLLIPFLHAEEENLHLENNQYKVTLPLFTFHDR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R  N L+  NI  + DL+ +++ D++++ +F R+ 
Sbjct: 257 LTKLRKTKKEIALKYIFIDQLELPPRIYNFLKKSNIHTLLDLLNKSQEDLMKIKHFRRED 316

Query: 303 LVEIKGVLG 311
           + +I  +L 
Sbjct: 317 VEQILDILE 325


>gi|329565843|gb|AEB92258.1| DNA-directed RNA polymerase alpha subunit [Thermoanaerobacter
           thermohydrosulfuricus]
          Length = 250

 Score =  271 bits (692), Expect = 1e-70,   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|620029|gb|AAA74989.1| RNA polymerase alpha-subunit [Chlamydia trachomatis]
          Length = 380

 Score =  271 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 118/362 (32%), Positives = 191/362 (52%), Gaps = 28/362 (7%)

Query: 6   WQELIKPNNIEYIVLGQ---EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
           + +   P +++   +       +     +A+PL +G  HTLG+ALRR L+  L   AI +
Sbjct: 10  YNKFELPESVKMSPVEGAVGSIDKVARFVADPLEKGMGHTLGSALRRALLIGLEAPAIVS 69

Query: 63  VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS-------GDSHKRVTIFKR------ 109
             + GVLHE  +++G+ ED+T+++LN+KG  LK         G   +++           
Sbjct: 70  FSMTGVLHEYMAVEGIIEDVTNMLLNLKGSLLKKYPLQDCEGGRCSQKLRATISVDASDL 129

Query: 110 ----GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
               G   VT GD+      E +NP+HVI  +     + + L V+ G GY P++    E 
Sbjct: 130 AAAGGQKEVTLGDLLQEGTFEAVNPEHVIFTVTRPMQLEVMLRVAFGRGYSPSERIVLEE 189

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
             +  I +DA +SP+  V+Y VE  R GQ  D+D+L + ++TDG +  +++VA A++IL 
Sbjct: 190 RGMNEIVLDAAFSPVVLVNYFVEDTRVGQDTDFDRLVLQVETDGRVAPKEAVAFATQILS 249

Query: 226 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK---VEELELSV---RSTNCLRGENIV 279
               +F   +E +   +E I+V+    +  L K    + E+ELSV   RSTNCL   NI 
Sbjct: 250 KHFSVFEKMDEKRIVFEEAISVEKENKDDILHKLVLGINEIELSVRLIRSTNCLSNANIE 309

Query: 280 YMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP--ESIEELAKKYE 337
            +G+L+   E  +L+  NFG+KSL EIK  L  M L LGM+L  +    ++++E  K Y 
Sbjct: 310 TIGELVIMPEPRLLQFRNFGKKSLCEIKNKLKEMKLELGMDLSQFGVGLDNVKEKMKWYA 369

Query: 338 DK 339
           +K
Sbjct: 370 EK 371


>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 = 80/309 (25%), Positives = 151/309 (48%), Gaps = 20/309 (6%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFEKIPHEYSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I L+ +       +I  +GPG VTA DI     +E+++    I +L 
Sbjct: 81  QESVHEILMNLKEIVLRSNLYGTCNASICVKGPGCVTAQDIILPPSVEIIDNTQHIASLM 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + + L + +  GY         N   G   IDA++ P++  ++++ S   G     
Sbjct: 141 EPINLCIGLQIERNRGYHIKT---PNNFQDGSYPIDAVFMPVRNANHSIHSYGNGNE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D L  F++ EE    ++ +    +LP      +
Sbjct: 197 EILFLEIWTNGSLTPKEALHEASRNLIDLLIPFLHAEEENLHLENNQYKVTLPLFTFHDR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R  N L+  NI  + DL+ +++ D++++ +F R+ 
Sbjct: 257 LTKLRKTKKGIALKYIFIDQLELPPRIYNFLKKSNIHTLLDLLNKSQEDLMKIKHFRRED 316

Query: 303 LVEIKGVLG 311
           + +I  +L 
Sbjct: 317 VKQILDILE 325


>gi|68124013|emb|CAJ01914.1| DNA-directed RNA polymerase alpha chain [Chrysanthemum x
           morifolium]
          Length = 335

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 83/331 (25%), Positives = 161/331 (48%), Gaps = 29/331 (8%)

Query: 13  NNIEYIVLGQ----EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +      +       I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESAADSKRPFYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +       +I  RGPG VTA DI     +E++
Sbjct: 71  SHEYSTIMGIQESVHEILMNLKEIVLRSNLYGTCEASICVRGPGYVTAQDIILPPYVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L     + + L + K  GY+    +  ++   G   ID ++ P++  ++++ 
Sbjct: 131 DNTQHIATLTEPIELVIGLQIEKNRGYLIKAPNTFQD---GSYPIDPVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D L  F++ +E    ++++ ++ 
Sbjct: 188 SYENGNK---EILFLEIWTNGSLTPKEALHEASRNLIDLLIPFLHTKEENLNLEDNQHMI 244

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            LP      K                 +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 245 PLPPFTFYDKLAKLTKNKKKMALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQDDL 304

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++M +F    + ++K +LG +     ++LP 
Sbjct: 305 MKMEHF---HIEDVKQILGILEKNFVIDLPK 332


>gi|47679553|gb|AAT36720.1| RNA polymerase alpha subunit [Thalassionema frauenfeldii]
          Length = 298

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 94/296 (31%), Positives = 159/296 (53%), Gaps = 4/296 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           KP   E +   Q        + + L  G   T+GN LRRVL+  + G AI+AV+I G+ H
Sbjct: 7   KPLKSEKL---QSGGYYGQFLIDKLKLGQGITIGNQLRRVLLGEIGGTAISAVRIVGIRH 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 NHYIATISTSINLELEFKIEHGIGYKLASQLFNDEN-KNFLQIDSIFMPVQKVNFKIENL 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|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 =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 85/331 (25%), Positives = 158/331 (47%), Gaps = 29/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S    +    + L + I T+GS+T ++++  ASR L D    F++ EE    +++  +  
Sbjct: 188 SYGNEK---QEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEEENLHLEDADHTI 244

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            L       K                 +++LE   +  NCL+  NI  + DL+  ++ D+
Sbjct: 245 PLSPFTVYDKVAKLRKNKKKLSLESIFIDQLEFPPKIYNCLKKSNIFTLLDLLNNSQEDL 304

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F    L ++K +LG +G    ++LP 
Sbjct: 305 IKIEHF---HLEDVKQILGILGKHFALDLPK 332


>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 =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 97/300 (32%), Positives = 156/300 (52%), Gaps = 4/300 (1%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +        +   L  G   T+GN LRRVL++ L G AI+AV+I G+ HE S+I GV ED
Sbjct: 15  ESGACHGQFLINSLRPGQGITIGNQLRRVLLNDLGGVAISAVRIAGISHEFSTIPGVRED 74

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + +I+LN+K I LK    + +   +  +GP VVTA  IQ  + IE++N    I  +    
Sbjct: 75  ILEILLNLKEIVLKSKTQTPQFGRLKIQGPAVVTADLIQLPSTIEIVNSHQYIMTISTSN 134

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
           +V +E     G GY  A     E +    + +DA++ PI+KV + +E+  + +    ++L
Sbjct: 135 IVEIEFKFEYGTGYKLASQSFLEENE-NYLQLDAIFMPIQKVDFKIENVYDNRNSLTERL 193

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + I T+GSI+  +++ +A+ I  D     +  +    + +      SL   P     +E
Sbjct: 194 LLDIWTNGSISPNEAIKMAAEITIDLFTALLENKATNSQEEVKSKTSSLSIEPYTNIAIE 253

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           EL+LSVR+ NCL+   I  +GDL+Q +   +  + NFGRKS  E+   L      LG+ L
Sbjct: 254 ELQLSVRAYNCLKKAQINTVGDLLQYSPEKLQELKNFGRKSADEVFFTLKNK---LGIIL 310


>gi|12661177|gb|AAK01152.2|AF311314_2 RPoA [Marsilea quadrifolia]
          Length = 347

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 159/327 (48%), Gaps = 21/327 (6%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +  +    +  P  +G A+T+G A+RR L+  + GA+IT+ + +GV HE S++ G+
Sbjct: 27  RIESKRLHYGRFVISPFKKGQANTVGIAMRRALLGEVGGASITSARFEGVAHEYSTVAGI 86

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + DI++N+K I L+   D +++  +   GP  VTAGDI     ++V++    I  + 
Sbjct: 87  QETIHDILVNLKEIVLRSDSDGNQKAILSVTGPKRVTAGDISLPPSVKVIDDSQYIVTIT 146

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               V +EL +    GY     +   +       +DA++ P++ V+Y+V     G+ +  
Sbjct: 147 QPISVNIELNIECDCGYRIESLNEYRDGE---FPVDAVFMPVRNVNYSVHPFGSGKEM-R 202

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED-------------- 244
           + L + + T+GS+T  ++++ AS+   D L  F++ +       E               
Sbjct: 203 EILFIEVWTNGSLTPTEAISKASKSSIDLLSPFLHTKHEDIPDFESNRDSSSLMKFSSRV 262

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
            +V     +      +++LEL  R+ NCL+   I  + DL+  +  D+L++ +FG+KS+ 
Sbjct: 263 DDVDKSEGDFFKNTFIDQLELPARAFNCLKRAEIHTISDLLSYSRDDLLKLKSFGKKSVD 322

Query: 305 EIKGVLGTMGLFLGMNLPDWPPESIEE 331
           ++   L          LP+  P  + +
Sbjct: 323 QVSRALWER---FATELPNEKPRVVGD 346


>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 =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 81/327 (24%), Positives = 159/327 (48%), Gaps = 21/327 (6%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +  +    +  P  +G A+T+G A+RR L+  + GA+IT+ + +GV HE S++ G+
Sbjct: 21  RIESKRLHYGRFVISPFKKGQANTVGIAMRRALLGEVGGASITSARFEGVAHEYSTVAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + DI++N+K I L+   D +++  +   GP  VTAGDI     ++V++    I  + 
Sbjct: 81  QETIHDILVNLKEIVLRSDSDGNQKAILSVTGPKRVTAGDISLPPSVKVIDDSQYIVTIT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               V +EL +    GY     +   +       +DA++ P++ V+Y+V     G+ +  
Sbjct: 141 QPISVNIELNIECDCGYRIESLNEYRDGE---FPVDAVFMPVRNVNYSVHPFGSGKEM-R 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED-------------- 244
           + L + + T+GS+T  ++++ AS+   D L  F++ +       E               
Sbjct: 197 EILFIEVWTNGSLTPTEAISKASKSSIDLLSPFLHTKHEDIPDFESNRDSSSLMKFSSRV 256

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
            +V     +      +++LEL  R+ NCL+   I  + DL+  +  D+L++ +FG+KS+ 
Sbjct: 257 DDVDKSEGDFFKNTFIDQLELPARAFNCLKRAEIHTISDLLSYSRDDLLKLKSFGKKSVD 316

Query: 305 EIKGVLGTMGLFLGMNLPDWPPESIEE 331
           ++   L          LP+  P  + +
Sbjct: 317 QVSRALWER---FATELPNEKPRVVGD 340


>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 =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 84/321 (26%), Positives = 157/321 (48%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ++RR L+  + G  IT  + D V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLMKGQADTIGISMRRALLGEIEGTCITRAKFDKVTHEYSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I L+ +       +I  RGP  VTA DI +   +E+++    I NL 
Sbjct: 81  EESVHEILMNLKEIVLRSNLYGTLDASICVRGPRSVTAQDIISPPSVEIVDTTQHIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + + L + +  GY         N   G   ID ++ P++  ++++ S   G     
Sbjct: 141 EPIDLCIGLQIERDRGYRLKT---PNNYQDGSYPIDTVFMPVRNANHSIHSYGNGTE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L +    F++ EE +  +++  N+ ++P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLINLFIPFLHAEEQEILLEDSENISTVPLFTFHNE 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+  ++ D++R+ +F    
Sbjct: 257 LANLKKNKKGIALKCIFIDQLELPSRTYNCLKRSNIHTLFDLLSNSKEDLMRIEHF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + ++K +L  +     MNLP 
Sbjct: 314 VEDVKQILDILQKNFAMNLPK 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 =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 94/305 (30%), Positives = 158/305 (51%), 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 +           ++  +E        
Sbjct: 185 AEGGTGRERLKMEVVTDGSTSPDDAIAEAANQLIELFQPLATVTMVEEIPEEPEPSPEAQ 244

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
                   +EEL LSVR+ NCL+   +  + DL+  +  D+L + NFG KS  E+   L 
Sbjct: 245 I------PLEELNLSVRAYNCLKRAQVNSVSDLMGFSYEDLLEIKNFGSKSADEVIEALE 298

Query: 312 TMGLF 316
            +G+ 
Sbjct: 299 RIGIS 303


>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 =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 85/331 (25%), Positives = 159/331 (48%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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   N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDFCIGLQIERNRGYLIKTPH---NFQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +  
Sbjct: 188 SYGNGNE-KQEILFIEIWTNGSLTPKEALHDASRNLIDLFIPFLHMEEDNLYLQDNQHTV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            L       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|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 =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 116/284 (40%), Positives = 178/284 (62%), Gaps = 11/284 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  +    +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVYIEQINT---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 YSPVDKIAYAVEAARVEQRTDLDKLVIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRD 237

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVY 280
            +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y
Sbjct: 238 VRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHY 278


>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 =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 85/331 (25%), Positives = 162/331 (48%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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   +     N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIANLTEPIDFCIELEIERNRGY---RMKTPNNSQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ +E    ++++ N  
Sbjct: 188 SYANGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAQEENILLEDNQNGV 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 MKIEDF---RIEDVKQILGILQKHFTVDLPK 334


>gi|306486177|gb|ADM92734.1| RNA polymerase alpha subunit protein [Davidia involucrata]
          Length = 328

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 79/325 (24%), Positives = 154/325 (47%), Gaps = 27/325 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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         N   G   IDA++ P++  ++++ 
Sbjct: 131 DSTQYIASLTEPIDLCIGLQIERNRGYRIKM---PNNFQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHTEEENLHLEDNQHKV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP      K                 +++ EL  R  NCL+  NI  + D +  ++ D+
Sbjct: 247 TLPLFTFHEKLAKLRKNKKKIALKYIFIDQSELPTRIYNCLKRSNIYTLLDFLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFL 317
           +++ +F    + ++K +LG +    
Sbjct: 307 MKIEHF---RIEDVKEILGILEKQF 328


>gi|290489700|gb|ADD31234.1| RNA polymerase alpha subunit protein [Staphylea colchica]
          Length = 342

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 81/334 (24%), Positives = 159/334 (47%), 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     +           IDA++ P++ V+Y++ 
Sbjct: 131 DNTQHIASLTEPMDLCIGLQIERNRGYSIKTPNNFHFQDGSY-PIDAVFMPVRNVNYSIH 189

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + +  
Sbjct: 190 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEDNGHLENNHHKL 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 EDLLKIEDL---RIEDVKQILDILEIENTIDLPK 339


>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 =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 84/331 (25%), Positives = 158/331 (47%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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   N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDFCIGLQIERNRGYLIKTPH---NFQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +  
Sbjct: 188 SYGNGNE-KQEILFIEIWTNGSLTPKEALHDASRNLIDLFIPFLHMEEDNLYLQDNQHTV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            L       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|290489656|gb|ADD31212.1| RNA polymerase alpha subunit protein [Aucuba japonica]
          Length = 349

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 80/328 (24%), Positives = 155/328 (47%), Gaps = 27/328 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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+        N   G   IDA++ P++ V+Y++ 
Sbjct: 131 DKTQHIASLTEPIDLCIGLQIERNRGYLIKT---PNNFQDGSYPIDAVFMPVRNVNYSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEEENLHLEDNQHTV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            L       K                 +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 PLSPFTFHDKLAKLRKNKNKIALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           +++  F    + ++K +LG +     ++
Sbjct: 307 MKIEQF---RIQDVKQILGILEKHFAID 331


>gi|311990462|gb|ADQ26361.1| RNA polymerase alpha subunit [Lactobacillus plantarum]
          Length = 252

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 114/253 (45%), Positives = 161/253 (63%), Gaps = 6/253 (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 LNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSY 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 NVKSLPFNPALLK 258
             +       L  
Sbjct: 239 EKEETHKEKMLEM 251


>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 =  269 bits (688), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 80/331 (24%), Positives = 159/331 (48%), 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 DTTQHIASLTEPIDLCIGLQIERDRGYRMKTPNNDQDGSYP-IPIEAVSMPVRNANHSIH 189

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  AS  L D    F++ EE    +++ +N  
Sbjct: 190 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASHNLIDLFIPFLHGEEEDINLEDSLNRG 248

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LPF     K                 +++ EL  R+ NCL+  NI  + DL+  ++ D+
Sbjct: 249 TLPFFTFQDKLANLRKNKKAIALECIFIDQSELPPRTYNCLKRSNIHTLLDLLSNSQEDL 308

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +R+ +     + ++K +L  +     ++LP 
Sbjct: 309 MRIEHL---RIEDVKRILDILQKHFTIDLPK 336


>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 =  269 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 119/265 (44%), 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  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++  + +   +++   +  P    LL+ V++LEL+VR
Sbjct: 181 GTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVR 237

Query: 269 STNCLRGENIVYMGDLIQRTEADML 293
           S NCL+ E I Y+GDL+QRTE ++L
Sbjct: 238 SANCLKAEAIHYIGDLVQRTEVELL 262


>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 (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 78/324 (24%), Positives = 154/324 (47%), Gaps = 27/324 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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         N   G   +DA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDLCIGLQIERNRGYRIKT---PNNFHDGSYPLDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
                     + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + +  
Sbjct: 188 CYGNDNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENLHLENNQHNV 246

Query: 249 SLPFNPALLKK----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LPF P   +                 +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPFFPFHDRLAKLRKKKKEIALKYIFIDQSELPPRIYNCLKKSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLF 316
           +++ +F    + ++K +LG +   
Sbjct: 307 MKIEHF---RIEDVKQILGILEKE 327


>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 =  269 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 83/331 (25%), Positives = 158/331 (47%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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   N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDFCIGLQIERNRGYLIKTPH---NFQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEEDNLYLQDNQHTV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            L       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|158148901|dbj|BAF81985.1| RNA polymerase alpha subunit [Lactobacillus parabrevis]
          Length = 246

 Score =  269 bits (687), Expect = 6e-70,   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|47679551|gb|AAT36719.1| RNA polymerase alpha subunit [Thalassiosira sp. Cleve BA153110]
          Length = 300

 Score =  269 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 96/299 (32%), Positives = 154/299 (51%), Gaps = 7/299 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E +K   IE              + + L  G   T+GN LRRVL+  L+G AIT V+I G
Sbjct: 9   ECLKSEKIE------SGSMYGQFLIDSLSSGQGITIGNLLRRVLLGDLKGTAITGVRIAG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           V  E S I GV ED+ +I+LN+KGI LK    + +   +   GP V+TA  IQ   D+E+
Sbjct: 63  VKDEFSLIPGVREDILEILLNLKGIVLKSKNSTRQFARLRLHGPAVITASSIQLPPDVEI 122

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NP+H I  L    ++ +E  +  GH Y  A    ++      I  DA++ P +K  + V
Sbjct: 123 INPNHYIATLSSSHILEIEFKIESGHDYRLANETFSDKLS-NFIETDAIFMPDQKDDFKV 181

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+  +      +++ + + T+GSI+ E ++  AS ++ D        +  +++       
Sbjct: 182 ENVYDNSNNVKERVFLDVWTNGSISPEQAIFSASNLIIDLFKSITEHKINQEKESIKEKT 241

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           ++ P +P     +EEL+LSVR  NCL+   I  +GDL+  +   +L + NFGRKS  E+
Sbjct: 242 QTKPVDPYTHIAIEELQLSVRPYNCLKRAQINTIGDLLDYSPEKLLELKNFGRKSADEV 300


>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 = 6e-70,   Method: Composition-based stats.
 Identities = 81/328 (24%), Positives = 152/328 (46%), Gaps = 26/328 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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         N   G   IDA+  P++  ++++ 
Sbjct: 131 DTTQHIAVLTEPVDLCIELKIERGRGYCTRTQ---NNYQDGSYPIDAVSMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE       + N+K
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEQDINRNMEDNLK 246

Query: 249 SLPFNPALL---------------KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                                     +++LEL  R+ NCL+  NI  + DL+ +++ D++
Sbjct: 247 RASVPFFAFDDGLDNIKREIILKRIFIDQLELPPRTYNCLKRSNIHTLLDLLSKSQEDLM 306

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           R+ +F    + ++K +   +     ++L
Sbjct: 307 RIEHF---RVEDVKQIFDILQKGFTIDL 331


>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 =  268 bits (686), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 80/319 (25%), Positives = 154/319 (48%), Gaps = 24/319 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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         N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIANLTEPINLCIELQIERNRGYRIKT---PNNFQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE   +++ + +  
Sbjct: 188 SYVNGNE-KQEILFLEIWTNGSLTPKEALHDASRNLIDLFIPFLHAEEENLQLENNQHKV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP      +                 +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPLFTFHGRLAKQRKNKKEIALQYIFIDQSELFPRVYNCLKRSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLG 311
           +++ +F  + +  I  +L 
Sbjct: 307 MKIKHFRIEDVKHILNILE 325


>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 =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 87/321 (27%), Positives = 154/321 (47%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RR L+  + G  IT  + + V HE  +I G+
Sbjct: 21  RIDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKVPHEYFTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I L+ +    +   I  RGP  VTA DI +   +E+++    I  L 
Sbjct: 81  KESVHEILINLKEIVLRSTLYGVRDAAICVRGPRYVTAQDIISPPSVEIVDTTQHIATLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + + L + +  GY   +   T N   G   IDA+  P++  ++++ S   G     
Sbjct: 141 EPIDLCIGLQIKRDRGY---RMKPTNNSKDGSYPIDAVSMPVRNANHSIHSYGNGNE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     KE+ N  +LP      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEEGINFKENENRFTLPPFTLQDR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+  ++ D++R+       
Sbjct: 257 LINLKKTKKCIPLKCIFIDQLELPPRTYNCLKRSNIHTLLDLLSNSQEDLMRIDYL---R 313

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + ++K +L T+   L  +LP 
Sbjct: 314 IEDVKQILDTLQKHLASDLPK 334


>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 =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 82/321 (25%), Positives = 157/321 (48%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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         N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDLRIGLQIERNRGYGIKT---PNNFQDGSYPIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE K  ++ + +  
Sbjct: 188 SYGTGNE-KQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHAEEEKFYLENNQHKV 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|32487326|emb|CAE05901.1| OSJNBa0061C08.8 [Oryza sativa Japonica Group]
 gi|57834095|emb|CAE04760.3| OSJNBa0079C19.1 [Oryza sativa Japonica Group]
          Length = 446

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 93/321 (28%), Positives = 157/321 (48%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+
Sbjct: 130 RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGI 189

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 190 EESVQEILLNLKEIVLRSNLYGVRTASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 249

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                R+EL + +  GY        +N   G   IDA+  P++ V+Y++ +   G    Y
Sbjct: 250 EPTDFRIELRIKRDRGYHTEVR---KNTQDGSYPIDAVSMPVRNVNYSIFACGNGNA-KY 305

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 306 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKR 365

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 366 LTNLKKNKKRIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 422

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + + K +  T+   L M+LP 
Sbjct: 423 MQDGKQIWDTLEKHLPMDLPK 443


>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 = 81/326 (24%), Positives = 156/326 (47%), Gaps = 24/326 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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         N   G   IDA+  P++  ++++ 
Sbjct: 131 DTTQHIAILTEPVDLCIELKIERGRGYC---MRTPNNYQDGSYPIDAVSMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    +++++   
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEQDINIEDNLKRA 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 EHF---RVEDVKQIFDILQKGFTIDL 329


>gi|58758781|gb|AAW81783.1| RNA polymerase alpha subunit [Polytrichastrum pallidisetum]
          Length = 338

 Score =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 85/319 (26%), Positives = 151/319 (47%), Gaps = 21/319 (6%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  E  + +     P   G A+T+G A+RR L+  + G  IT      V HE S+I G+
Sbjct: 21  KVDSERLHYSRFAISPFRCGQANTVGIAMRRALLGEIEGTCITCAIFKKVTHEYSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + DI++N+K I LK +    ++  I   GP  +TA DI     +++++    I  + 
Sbjct: 81  QESVHDILINLKEIVLKSNSSETQKAFISILGPKKITAQDIILPPSVKIIDTTQYIATIT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + K  GY      ++ +   G   IDA++ PI+  +Y+V S      +  
Sbjct: 141 KPIHLDIELEIEKDCGYRIQDSVKSID---GYFPIDAIFMPIRNANYSVHSFENNNKI-Q 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK--------------EVKED 244
           + L + I T+GSIT ++++  ASR L D    F++ E+ +                    
Sbjct: 197 EILFIEIWTNGSITPKEALYEASRSLIDLFIPFLHPEKKETIDRLKYTPNDISDFSSFSP 256

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           +  K           +++LEL  R+ NCL+  N   + DL+  ++ D++++ NFG+KS  
Sbjct: 257 VTGKLTKEITFKHIFIDQLELPARAYNCLKRVNGHTISDLLNYSQDDLMKIKNFGKKS-- 314

Query: 305 EIKGVLGTMGLFLGMNLPD 323
            ++ VL  +     +NLP 
Sbjct: 315 -VEQVLEALEKQFSINLPK 332


>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 =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 81/324 (25%), Positives = 158/324 (48%), Gaps = 27/324 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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        +N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQYIANLTEPINLCIGLQIERNRGYHIKT---PKNFQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++ +    
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENLHLENNQYKV 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 MKMEYF---RIEDVKQILDSLEIE 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 =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 80/321 (24%), Positives = 150/321 (46%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 DNTQHIANLTEPINLCIELQIERNRGYRIKT---PNNFQEGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE     + + +  
Sbjct: 188 SYVNGNE-KQEILFIEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENLHFENNQHKV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP      K                 +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPLFTFHGKLANPKKIKKENTLKYIFIDQSELPPRVYNCLKRSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTM 313
           +++ +   + +  I  +L   
Sbjct: 307 MKIKHLRIEDVKHILNILEIK 327


>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 =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 80/336 (23%), Positives = 157/336 (46%), 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     +  +        IDA++ P++  ++
Sbjct: 128 EIIDNTQHIASLTKAIDLCIGLQIERNRGYRIKPTNNFQVQDGSYS-IDAVFMPVRNANH 186

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           +V S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + 
Sbjct: 187 SVHSYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDFFIPFLHAEEENLHLEIEK 245

Query: 246 NVKSLPFNPA------------------LLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
           N   +                           +++ EL+ +  NCL+  NI  + DL+ +
Sbjct: 246 NQHKVTLPLFCFHDKLTKLRKNKKEIVLKYIFIDQSELTPKIYNCLKRSNIHTLSDLLNK 305

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++ D++++ +F    +  I G+L  +     ++LP 
Sbjct: 306 SQEDLMKIEHFRIDDVKHILGIL-EIEKHFTIDLPK 340


>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 =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 119/265 (44%), Positives = 180/265 (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++  + +   +++   +  P    LL+ V++LEL+VR
Sbjct: 181 GTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVR 237

Query: 269 STNCLRGENIVYMGDLIQRTEADML 293
           S NCL+ E I Y+GDL+QRTE ++L
Sbjct: 238 SANCLKAEAIHYIGDLVQRTEVELL 262


>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 =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 101/316 (31%), Positives = 158/316 (50%), Gaps = 10/316 (3%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
             E IK   IE              + + L  G   T+GN LRRVL+  L+G AIT V+I
Sbjct: 7   LMECIKSEKIE------SGPMYGQFLIDSLSSGQGITIGNLLRRVLLGDLQGTAITGVRI 60

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
            GV  E S I GV ED+ +I+LN+KGI LK    + +   +  +GP V+TA  IQ   +I
Sbjct: 61  AGVKDEFSLIPGVREDILEILLNLKGIVLKSKTPNRQFGRLRLQGPAVITASSIQLPPEI 120

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           E++NP+H I  +    ++ +E  +  G  Y  A    ++      I  DA++ P++KV +
Sbjct: 121 EIINPNHYIATISSSHILEIEFKIESGSKYRLANELFSDKFE-DFIETDAIFMPVQKVDF 179

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            VE+  +      ++L + I T+GSI+ E ++   S ++ +        +  K++     
Sbjct: 180 KVENVYDNSNNIKERLLIDIWTNGSISPEQAIFSGSNLIINLFKSIGEQKINKEKENIKE 239

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                P +P     +EEL+LSVR  NCL+   I  +GDL+  +   +L + NFGRKS  E
Sbjct: 240 KNHIKPIDPYTHIAIEELQLSVRPYNCLKRAQINTIGDLLDYSPEKLLELKNFGRKSADE 299

Query: 306 IKGVLGTMGLFLGMNL 321
           +   L      LG+ L
Sbjct: 300 VFATLKNK---LGIVL 312


>gi|156598421|gb|ABU85470.1| RNA polymerase alpha subunit [Musa acuminata]
          Length = 339

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 87/321 (27%), Positives = 155/321 (48%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       +  PL +G A T+G A+RR L+  + G  IT    + V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFVLSPLMKGQADTIGIAMRRALLGEIEGTCITRANSEKVPHEYSTIIGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  RGP  VTA DI +   +E+++    I NL 
Sbjct: 81  EESVHEILLNLKEIVLRSNIYGVRDASICARGPKYVTAQDIISPPSVEIVDTTQHIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + + L + +  GY       T N   G   IDA+  P++  ++++ S   G     
Sbjct: 141 EPIDLCIGLQIRRDRGYRTKP---TTNSQNGSYPIDAVSMPVRNANHSIHSYGNGNE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     KE+ N  +LP      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEEDINFKENKNRFTLPIFTFQDR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++ EL  R+ NCL+  NI  + DL+ +++ D++R+  F    
Sbjct: 257 LTNLKKNKKEIPLKCIFIDQSELPSRTYNCLKRSNIHTLLDLLNKSQEDLMRIEYF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + ++K +  T+     ++LP 
Sbjct: 314 IEDVKEISDTLQKHFAIDLPK 334


>gi|4379135|emb|CAA83722.1| DNA-directed RNA Polymerase (alpha) [Mycoplasma capricolum subsp.
           capricolum ATCC 27343]
          Length = 317

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 111/317 (35%), Positives = 180/317 (56%), Gaps = 10/317 (3%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           ++ ++P  I       +++N       PL RGF  TLGNA+RR L+++  GA++ A++I 
Sbjct: 2   KQFVRPEFILLK--EGQDKNYGKXXVSPLERGFGITLGNAIRRTLLAATPGASVYAIKIA 59

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMS-----GDSHKRVTIFKRGPGVVTAGDIQT 121
           G  HE +SI G+ E++T IILNIK + L++       D   ++ I     G V AGD++ 
Sbjct: 60  GATHEFTSIPGIIENVTKIILNIKQLVLRIDTSIYSDDEVVQLKIRSDIQGPVYAGDLEL 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSPI 180
              +EVLN D +I  +    ++ + L      GY   K ++ E N   G+ITID+ YSPI
Sbjct: 120 PAGVEVLNQDLLIATISEGGILDLVLYAKNSRGYKTFKDNKNEKNVEPGMITIDSNYSPI 179

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            KV+Y+V+SA+ G+ +D +KL + + TDGSIT  D++++AS+IL   L  FI+       
Sbjct: 180 IKVAYSVDSAKIGRAIDLEKLELEVTTDGSITAIDAISIASKILVAHLEFFIDLNREISV 239

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           ++      +   +  L + VEEL+ + RS NCL+   I  + +L+ + E ++  + N GR
Sbjct: 240 LEVI--GVNQTDDKELDRTVEELDFTQRSLNCLKRAGINTLRELVTKNEDEIGSIRNLGR 297

Query: 301 KSLVEIKGVLGTMGLFL 317
           KSL EIK  + ++GL  
Sbjct: 298 KSLKEIKDKVASLGLAF 314


>gi|47679555|gb|AAT36721.1| RNA polymerase alpha subunit [Cylindrotheca fusiformis]
          Length = 291

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 93/286 (32%), Positives = 158/286 (55%), Gaps = 2/286 (0%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
           +        +   L  G   T+GN LRRVL++ L G AI+A +I GV HE S+I GV ED
Sbjct: 7   ESGACHGQFLINSLKPGQGITIGNQLRRVLLNDLGGVAISAARIAGVSHEFSTIPGVRED 66

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + +I+LN+KGI LK    + +   +  +GP VVTA  IQ  +D+E++NP+H +  +    
Sbjct: 67  ILEILLNLKGIVLKSKTQTAQFGRLKIQGPTVVTADLIQLPSDLEIVNPNHYLMTISTSN 126

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
           V+ +E     G GY        +      + +D ++ P++KV++ +E+  +      +++
Sbjct: 127 VLEIEFKFEYGTGYKLTSQAFLDESD-NYLQLDTIFMPVQKVNFKIENVYDNNNNITEQV 185

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK-EDINVKSLPFNPALLKKV 260
            + I T+GSI+  +++  A++I  D   + +  +E K++ K E   V S+   P     +
Sbjct: 186 FLDIWTNGSISPNEALKSAAQITIDLFELLLKNKETKEKNKLEATKVPSISIEPYTNIAI 245

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           EEL+LSVR+ NCL+   I  +GDL++ +   +  + NFGRKS  E+
Sbjct: 246 EELQLSVRAYNCLKKAQINTVGDLLKYSPEKLQELKNFGRKSADEV 291


>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 =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 84/334 (25%), Positives = 163/334 (48%), Gaps = 25/334 (7%)

Query: 10  IKPNNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 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        +N   G  +IDA++ P++  ++
Sbjct: 128 EIIDNTQHIASLREPIDLHIGLEIERNRGYC---MKPPKNFQDGSYSIDAVFMPVRNANH 184

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           +V S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ 
Sbjct: 185 SVHSYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEESFHLEKNQ 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|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 =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 95/298 (31%), Positives = 163/298 (54%), Gaps = 2/298 (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 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +E+L+LSVRS NCL+   I  + +L Q+TE +M+ + N G+KSL E+K  +  +GLF 
Sbjct: 260 IEDLDLSVRSYNCLKRAGIQTVDELTQKTEDEMMHVKNLGKKSLKEVKDKMYQLGLFF 317


>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 =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 84/334 (25%), Positives = 163/334 (48%), Gaps = 25/334 (7%)

Query: 10  IKPNNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 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        +N   G  +IDA++ P++  ++
Sbjct: 128 EIIDNTQHIASLREPIDLHIGLEIERNRGYC---MKPPKNFQDGSYSIDAVFMPVRNANH 184

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           +V S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ 
Sbjct: 185 SVHSYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENFHLEKNQ 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|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 =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 93/321 (28%), Positives = 157/321 (48%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+
Sbjct: 130 RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGI 189

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 190 EESVQEILLNLKEIVLRSNLYGVRTASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 249

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                R+EL + +  GY        +N   G   IDA+  P++ V+Y++ +   G    Y
Sbjct: 250 EPTDFRIELRIKRDRGYHTEVR---KNTQDGSYPIDAVSMPVRNVNYSIFACGNGNAR-Y 305

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 306 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKR 365

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 366 LTNLKKNKKRIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 422

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + + K +  T+   L M+LP 
Sbjct: 423 MQDGKQIWDTLEKHLPMDLPK 443


>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 =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 83/328 (25%), Positives = 160/328 (48%), 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      R  N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIARLMEPIDLCIGLQIERNRGY---SIKRPNNFQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + +  
Sbjct: 188 SYGNGNER-QEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEETLHLEYNQHKS 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP      +                 +++LEL  R  NCL+  NI  + DL+ +++ D+
Sbjct: 247 TLPPLTFHDRLAKLRKNKKEIELKYIFIDQLELPPRIYNCLKRSNIHTLLDLLNKSQKDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           +++ +F    + ++K +LG +     ++
Sbjct: 307 MKIEDF---RIEDVKQLLGILEKHFTID 331


>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 =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 100/302 (33%), Positives = 166/302 (54%), Gaps = 10/302 (3%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +    E     + EPL  G A T+GNALRRVL+S + G  I +V+I G+ HE S++KGV 
Sbjct: 17  VINSREIYGKFMIEPLSYGQAITVGNALRRVLLSDVPGVTIVSVRIAGINHEFSTVKGVK 76

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           ED+ +I+LN+K I LK +   ++   +  +GP +VT+G I+   DI V++P   I  +  
Sbjct: 77  EDVLEILLNLKNIVLKGNVLKNQIGRLKVQGPAIVTSGQIEFPLDITVVDPCQYIATISG 136

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           +  + MEL V K  GY   +   ++  P+  + ID+++ P+KKV+Y VE   + +V  Y+
Sbjct: 137 NDYLEMELKVEKSSGYKLVETF-SKKSPLDFLPIDSIFMPVKKVNYYVEEILDSKVA-YE 194

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
           KL + + T+GS++ + S+  AS  L               +  ++ +      +    K 
Sbjct: 195 KLILELWTNGSLSPQQSINYASDNLVKLFNPLRV-----LDFSKESSSVYEQNSLIKQKL 249

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +EEL LSVR+ NCL+   +  +GDL++ +  D+L + NFG+KS+ E+   L       G+
Sbjct: 250 IEELCLSVRAYNCLKRVQVDSIGDLLEYSIGDLLEIKNFGQKSVEEVSKALY---KKFGV 306

Query: 320 NL 321
            L
Sbjct: 307 KL 308


>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 =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 81/322 (25%), Positives = 151/322 (46%), Gaps = 24/322 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +     + +     P   G A T+G A+RR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSARLHYSRFAISPFRSGQASTVGIAMRRALLGEVEGTCITCAEFKRVTHEYSTILGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + D+++N+  I L+      ++  I   GP  VTA DI     +++++    I  + 
Sbjct: 81  QESVHDVLINLGEIVLRSDSYETQKAFISILGPKKVTAQDIILPPSVKIIDTTQYIATVT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + K  GY      ++ +   G   +DA++ PI+ V+Y+V S   G     
Sbjct: 141 KAIHLDIELKIEKDFGYRIEDPIKSAD---GNFPVDAVFMPIRNVNYSVHSFENGNET-Q 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP----------KKEVKEDINVK 248
           + L + I T+GS+T ++++  ASR L +    F++ E+           +  +    +  
Sbjct: 197 EILFLEIWTNGSVTPKEALYEASRSLINLFIPFLHAEKKEFIYGLKNTYESNMSYFSSPS 256

Query: 249 SLPFNPALLK-------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
                  + K        +++LEL  R+ NCL+  N   + DL+  ++ D++++ NFG+K
Sbjct: 257 LSADIDEMTKGVTFKHIFIDQLELPARAYNCLKRVNAHTISDLLNYSQDDLMKIKNFGKK 316

Query: 302 SLVEIKGVLGTMGLFLGMNLPD 323
           S   ++ VL  +     +NLP 
Sbjct: 317 S---VEQVLEALQKRFSINLPK 335


>gi|58491826|gb|AAW78552.1| RNA polymerase alpha subunit [Sphagnum fimbriatum]
          Length = 338

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 84/318 (26%), Positives = 154/318 (48%), Gaps = 20/318 (6%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  E  +       P   G A+T+G A+RR L+  + G  IT  + + V HE S+I G+
Sbjct: 22  KVDSERLHYGRFAISPFRSGQANTVGIAVRRALLGGVEGTCITRAKSEKVTHEYSTILGI 81

Query: 79  HEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
            E + DI++N+K I LK   +    ++  +   GP  VTA DI     +EV++    I  
Sbjct: 82  QESVRDILINLKEIVLKSKSNSCETQKAFLSIFGPKEVTARDIIFPPSVEVIDTTQYIAT 141

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           L     + +EL + K  GY      ++ +   G  ++DA+++PI+  +Y+V S       
Sbjct: 142 LTKAIHLDIELKIEKDCGYRTQDSIKSAD---GYFSVDAVFTPIRNANYSVHSFENKNET 198

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI----------- 245
             + L + I T+GS+T ++++  ASR L D    F++ E+ +    ++            
Sbjct: 199 -QEILFIEIWTNGSVTPKEALYEASRSLIDLFIPFLHAEKEEVMHDKNESNTLHFSSSPS 257

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             K           +++LEL  R+ NCL+  ++  + DL+  ++ D++++ NFG+KS   
Sbjct: 258 ENKMEKEMTFKHIFIDQLELPARAYNCLKRVDVHTISDLLSYSQDDLMKIKNFGKKS--- 314

Query: 306 IKGVLGTMGLFLGMNLPD 323
           ++ VL  +     + LP 
Sbjct: 315 VEQVLEALQKRFSIKLPK 332


>gi|156598227|gb|ABU85377.1| RNA polymerase alpha subunit [Elaeis oleifera]
          Length = 339

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 88/321 (27%), Positives = 156/321 (48%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RR L+  + G  IT  + + V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKVAHEYSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +       +I  RGP  VTA DI +   +E+++    I NL 
Sbjct: 81  EESVHEILLNLKEIILRSNLYGVIDASICVRGPRYVTAQDIISPPYVEIVDTTQHIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + +  GY   +     N   G   IDA+  P++  ++++ S   G     
Sbjct: 141 EPIDLCIELQIKRDRGY---RMKSANNSQDGSYPIDAVSMPVRNANHSIHSYGNGNE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N   LP      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEEDINFEENKNRFPLPLFTFQNR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++ EL  R+ NCL+G NI  + DL+  ++ D++R+  F    
Sbjct: 257 LTNLKKNKKGIPLKCIFIDQSELPSRTYNCLKGSNIHTLSDLLSNSQEDLMRIKFF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + ++K +L T+  +  ++L  
Sbjct: 314 IEDVKQILDTLQKYFAIDLSK 334


>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 =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 102/243 (41%), Positives = 153/243 (62%), Gaps = 4/243 (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 SLP 251
           +  
Sbjct: 237 NDK 239


>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 =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 102/243 (41%), Positives = 152/243 (62%), Gaps = 4/243 (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 SLP 251
              
Sbjct: 237 DDK 239


>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 =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 85/326 (26%), Positives = 158/326 (48%), Gaps = 25/326 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +    +  I  PL +G A  +G A+RR L+  + G  IT V+ + V HE S+I G+
Sbjct: 21  RIDSKRLYYSRFILSPLMKGQADMIGIAMRRALLGEIEGTCITRVKSEKVPHEFSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I L+ +       +I  RGP  VTA DI     +E+++    I NL 
Sbjct: 81  EESVHEIVMNLKEIVLRSNLYGTLDASICIRGPRYVTAQDIILPPSVEIVDATQHIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + ++L + +  GY     H  E+   G   IDA++ P++  +++V S   G     
Sbjct: 141 ERVDLCIKLQIERDRGYSMKTPHNDED---GSYPIDAIFMPVRNANHSVHSYGNGNE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE +  ++++ N   L       +
Sbjct: 197 EILFIEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEREIHLEDNANGVPLALFTFHDE 256

Query: 259 ------------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                              +++ EL  ++ NCL+  NI  + DL+  ++ D+L++ +F  
Sbjct: 257 FAITNIRKNKKKMALKSIFIDQSELPSKTYNCLKKSNIHTLLDLLNNSQEDLLKIEHF-- 314

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPP 326
             + ++K +L  +    G +LP    
Sbjct: 315 -CMEDVKRILDILQKHFGFDLPKNGK 339


>gi|296936704|gb|ADH94376.1| RNA polymerase alpha subunit [Syzygium cumini]
          Length = 337

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 79/324 (24%), Positives = 157/324 (48%), Gaps = 27/324 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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        +N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQYIASLTEPINLCIGLQIERNRGYHIKT---PKNFQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++ +    
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENLHLENNQYKV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP      +                 +++ EL  R+ NCL+  NI  + DL+ +++ D+
Sbjct: 247 TLPLFTFHDRLVKLRKTKKEIALKSIFIDQFELPPRTYNCLKRYNIHTLFDLLNKSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLF 316
           ++M  F    + ++K +L ++ + 
Sbjct: 307 MKMEYF---RIEDVKQILNSLEIE 327


>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 =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 81/331 (24%), Positives = 157/331 (47%), Gaps = 31/331 (9%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +  + +         +  PL +G A T+G A+RR L+  + G  IT  + + V
Sbjct: 11  RTLQWKCVESKADSKRLYYGRFVLSPLMKGQADTIGTAMRRSLLGEIEGTCITCAKSERV 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I ++      +   I  RGP  VTA DI +   ++++
Sbjct: 71  PHEYSTIVGIEESVHEILMNLKEIIVRSDLYGTRDAFICVRGPKYVTAQDIISPPSVKIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I ++       + L + +  GY     ++          IDA+  P++  +Y+++
Sbjct: 131 DTTQHIASITEPINFCIGLEIERNRGYRTRTTNQD-----ASYPIDAVSMPVRNANYSIQ 185

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
                     + L + I T+GS+T ++++  ASR L D    F++ EE    + +D N+ 
Sbjct: 186 CYGNENE-KQEILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEERDLHLDDDQNIF 244

Query: 249 SLPFNPALL------------------KKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
           + PF P                       +++LELS R+ NCL+  NI  + DL+ +++ 
Sbjct: 245 TAPFFPFHEGLAYIGIGESKKRIALKRIFIDQLELSPRTYNCLKRSNIHTLLDLLSKSQE 304

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           D+ ++ +F    + ++K VL  +     MNL
Sbjct: 305 DLRKIQHF---RVEDVKRVLDILKKRFAMNL 332


>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 (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 79/328 (24%), Positives = 162/328 (49%), Gaps = 25/328 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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+       +N   G   IDA++ P++ V++++ 
Sbjct: 131 DNTQHIASLTEPIELCIGLQIERNRGYLIKT---AKNFQDGSYPIDAVFMPVRNVNHSIY 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G    ++ L + I T+GS+T ++++  A+R L D    F++ EE   +++++ ++ 
Sbjct: 188 SYGTGND-KHEILFLEIWTNGSLTPKEALHEAARNLIDLFIPFLHTEEENLDLEDNQHML 246

Query: 249 SLPFNPALLK--------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
               +    K               +++ EL  R  NCL+  NI  + DL+  ++ D+++
Sbjct: 247 PFRPSILPEKFVKIKNKKISLKSIFIDQSELPPRVYNCLKRSNIYTLLDLLNNSQEDLMK 306

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           + +F    + ++K +L  +    G++LP
Sbjct: 307 IEHF---RVEDLKRILDILEKNFGIDLP 331


>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 =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 108/335 (32%), Positives = 182/335 (54%), Gaps = 12/335 (3%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KN +  IKP  +E +    E+      I  PL +G A ++GN+LRR L+SSL G AI  V
Sbjct: 2   KNLK-FIKPFFVEEL---DEKLTSGKFIFYPLVKGHATSIGNSLRRTLLSSLPGTAIVNV 57

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG---DSHKRVTIFKRGPGVVTAGDIQ 120
            I+GV HE ++I GV+ED+  IILN+K I  K+     D  +++ I   GP  +TA    
Sbjct: 58  SIEGVEHEFTTISGVYEDVMTIILNLKKIIFKVDDESNDFEEKLKISLSGPQKITAASFG 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR-TENDPIGLITIDALYSP 179
               ++++NP+  I  +  D    M  T+ KG GYV AK ++    + +G+I ID+L++P
Sbjct: 118 LPEGVKIINPEAPIATISSDINFNMTATIKKGIGYVSAKDNKVHSENQLGVIPIDSLFTP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +  V+Y VE     ++ + ++L+M I T+G++  ++++A A++IL +   +     +   
Sbjct: 178 VVNVAYQVEK----KIGNKEELTMEITTNGALLAKEALATAAKILVEHFNVVSELSQQTP 233

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
            V+     K    N  L  ++E+L+LSVR  N L+   I  + DL++ +E +++++ + G
Sbjct: 234 NVEFVSERKPEAHNYFLDLEIEQLDLSVRLFNSLKRAGINTVADLVKLSEREVVKLKSLG 293

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334
           RKS  E+K      GL     L +    S EE  +
Sbjct: 294 RKSFQELKDKFVEYGLEFNDCLKEALHNSDEEEKE 328


>gi|161513438|emb|CAP16862.1| DNA-directed RNA polymerase subunit alpha [Pediococcus damnosus]
          Length = 234

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 103/234 (44%), Positives = 153/234 (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 TVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           T   G GYV A     R ++ 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|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 =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 88/321 (27%), Positives = 156/321 (48%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RR L+  + G  IT  + + V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKVAHEYSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +       +I  RGP  VTA DI +   +E+++    I NL 
Sbjct: 81  EESVHEILLNLKEIILRSNLYGVIDASICVRGPRYVTAKDIISPPYVEIVDTTQHIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + +  GY   +     N   G   IDA+  P++  ++++ S   G     
Sbjct: 141 EPIDLCIELQIKRDRGY---RMKSANNSQDGSYPIDAVSMPVRNANHSIHSYGNGNE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N   LP      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEEDINFEENKNRFPLPLFTFQDR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++ EL  R+ NCL+G NI  + DL+  ++ D++R+  F    
Sbjct: 257 LTNLKKNKKGIPLKCIFIDQSELPSRTYNCLKGSNIHTLSDLLNNSQEDLMRIEFF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + ++K +L T+  +  ++L  
Sbjct: 314 IEDVKQILDTLQKYFAIDLSK 334


>gi|290489676|gb|ADD31222.1| RNA polymerase alpha subunit protein [Ximenia americana]
          Length = 337

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 81/321 (25%), Positives = 152/321 (47%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RRVL+  + G  IT  + + V HE S+  G+
Sbjct: 21  RVDSKRLYYGRFILSPLMKGRADTIGIAMRRVLLGEIEGTCITRAKSEQVPHEYSTAIGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I L+ +       +I  RGP  +TA DI +   +E+++    I +L 
Sbjct: 81  QESIHEILMNLKEIVLRSNLYGTCNASICVRGPRYITAQDIISPPSVEIVDNTQYIASLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY         N   G   IDA++ P++  ++++ S   G     
Sbjct: 141 EPIDFCIELQIERNRGYHIKM---PNNFQDGSYPIDAVFMPVRNANHSIHSYGNGNE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T + ++  AS+ L D    F++ EE    ++++ +   LP      +
Sbjct: 197 EILFLEIWTNGSLTPKKALYEASQNLIDLFIPFLHAEEENLHLEDNQHKVILPLFTPHDR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++ EL  R  NCL+  NI  + DL   ++ D++++ +F    
Sbjct: 257 LAKLRKNKEKIALKSIFIDQSELPSRIYNCLKRSNIHTLLDLFNNSQKDLMKIEHF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + + K +LG +     ++LP 
Sbjct: 314 VEDGKQILGILEKHFAVDLPK 334


>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 =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 83/331 (25%), 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 SYENGNK---EILFLEIWTNGSLTPKEALHEASRNLIDLLIPFLHTKEENLNLEDNQHIV 244

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            LP      K                 +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 245 PLPPFTFYDKLAKLTKNKKKMALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQEDL 304

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F    + ++K +LG +     ++LP 
Sbjct: 305 MKIEHF---RIEDVKQILGILEKNFVIDLPK 332


>gi|150036782|emb|CAM98034.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. dextranicum]
          Length = 248

 Score =  266 bits (680), Expect = 4e-69,   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|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 =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 111/325 (34%), Positives = 181/325 (55%), Gaps = 14/325 (4%)

Query: 7   QELIKPNNIEYIVLGQEEENR-TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
            + I P N++     + +E+     +  PL +G+A T+GN LRRVL+SS+   AIT V+ 
Sbjct: 1   MDFIMPKNLKMEDHSETDEHYYARFVLSPLEKGYATTIGNTLRRVLLSSIPSLAITDVKF 60

Query: 66  --DGVLHEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQT 121
                 HE  +I+GV ED+ +I+LN+K + LKM    ++   +TI  +G G + AGDI  
Sbjct: 61  VRPEKYHEFDTIEGVKEDIIEILLNLKKVQLKMESYVNTPVELTIQHKGEGEIKAGDIVV 120

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
              + V NP+  I  L+ DA + +++  + G G+VPA   R E   IG I +D +Y+PI 
Sbjct: 121 PAGVTVTNPNLHIATLNEDADIEIKMYATVGKGFVPAAE-RNERPDIGWIVLDGVYNPIL 179

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KV++ +E+ R G+  DYDKL + + T  +I   +++  A +I+ D   +        ++ 
Sbjct: 180 KVNWKIENVRVGKKTDYDKLILEVWTKKNIKPVEALKQAVKIINDHFKLIEESFGDMEDA 239

Query: 242 KEDINVKSLP-------FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
              I              N  L KK++EL+LS+R+ NCL+ + I  +GDL++R E ++L+
Sbjct: 240 GIVIETTKAEIVEEKIDENEILNKKIDELDLSMRALNCLKRDKIETIGDLLERGEEELLK 299

Query: 295 MANFGRKSLVEIKGVL-GTMGLFLG 318
           + NFG+KSL E+K  L    G+  G
Sbjct: 300 IKNFGQKSLDEVKEKLMEKFGISFG 324


>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 =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 80/326 (24%), Positives = 152/326 (46%), Gaps = 25/326 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    +         I  PL +G A T+G A+R+ L+  + G  IT  + + +
Sbjct: 11  RTLKWKCVESRADSKRLYYGRFILSPLMKGQADTIGIAMRKALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I +N+K I L+ +    +  +I  +GPG VTA DI     +E++
Sbjct: 71  PHEYSTIVGIQESVHEIFMNLKEIVLRSNLYGTRDASICVKGPGYVTAQDIILPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I NL     + +EL + +  GY         N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIANLTEPINLCIELQIERNRGYRIKT---PNNFQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    +K + +  
Sbjct: 188 SYVNGNE-KQEILFLEIWTNGSLTPKEALYEASRNLIDFFIPFLHAEEENFHLKNNQHKV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP      +                 +++ EL  R  NCL+  NI  + DL+  +  D+
Sbjct: 247 TLPLFTFHDRLAKLRKNKKEIALKYIFIDQSELPPRIYNCLKRSNIHTLLDLLNNSPDDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLG 318
           +++ +F  + +  I  +L  +     
Sbjct: 307 MKIKHFRIEDVKHILDIL-EIEKHFA 331


>gi|269784296|emb|CBH50793.1| alpha subunit of RNA polymerase [Vibrio sp. Cmj 13.4]
          Length = 270

 Score =  266 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 118/273 (43%), Positives = 179/273 (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++  + +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE 
Sbjct: 181 FVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEV 237

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++L+  N G+KSL EIK VL + GL LGM L +
Sbjct: 238 ELLKTPNLGKKSLTEIKDVLASRGLSLGMRLEN 270


>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 =  266 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 121/306 (39%), Positives = 175/306 (57%), Gaps = 6/306 (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  TDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
            D+ LN+K + LK    +    + +   G G V +  I   +D EV+N D +ICN+    
Sbjct: 85  ADLALNLKKVVLKSVSGATCGNLHLSVTGGGAVFSNMISPSHDFEVVNADLLICNVAEGV 144

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDP-IGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
            + ME+ VS G GYV +   R +     G + IDA+Y+P++ V++TV+    G  + +DK
Sbjct: 145 SLEMEMKVSSGFGYVSSVSVRKDEYDLEGAVPIDAIYNPVRAVNFTVKPTSAGSFVGHDK 204

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK-- 258
           L + ++T+G++  + +V  AS+IL  Q   F+N  +P+  V       S           
Sbjct: 205 LILYVETNGAMDPKTAVLEASKILSTQARCFLNIADPEHRVHGVPYSVSTSDRNDTSDLL 264

Query: 259 --KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
             +++ L LS R+  CL GENIVY+ DL+ RTEAD+L+  NFGR+SL E+K  L + GL 
Sbjct: 265 SARIDRLYLSARARKCLNGENIVYIRDLVSRTEADLLKAPNFGRRSLEEVKKELFSKGLS 324

Query: 317 LGMNLP 322
           LGMNL 
Sbjct: 325 LGMNLD 330


>gi|187233921|gb|ACD01207.1| RNA polymerase alpha subunit [Phyllostachys propinqua]
          Length = 339

 Score =  266 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 91/321 (28%), Positives = 157/321 (48%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIELQIKRDRGYHTELR---KNSQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLLTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + + K +  T+   L ++LP 
Sbjct: 314 MEDGKQIWDTLEKHLPIDLPK 334


>gi|328813977|gb|AEB52104.1| DNA-directed RNA polymerase alpha chain [Lactobacillus helveticus]
          Length = 237

 Score =  266 bits (679), Expect = 4e-69,   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|165910441|gb|ABY73975.1| RNA polymerase alpha subunit [Cuscuta nitida]
          Length = 339

 Score =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 77/330 (23%), Positives = 154/330 (46%), Gaps = 28/330 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    ++        I  PL +G A T+  A+RR L+S + G  IT V     
Sbjct: 11  RTLKWKCVESRTDSKRLSYGRFILSPLMKGQADTIAIAMRRALLSEIEGTCITRVTFQNA 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S I G+ E + DI++N+K I LK +       +++ +GP  VTA DI     +E++
Sbjct: 71  SHEYSIIAGIQESVHDILMNLKEIVLKSNLYGTCDASLYIKGPRYVTAQDIILPPHVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L     + + L + +  GY+   H   +N      ++DA++ P+  V++++ 
Sbjct: 131 DSTQHIASLTEPINLCIGLKIERNRGYLIKAHPPFQN---ETYSLDAVFMPVLNVNHSIY 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S    +    + L + I T+GS+T ++++  A++ L D    F+  EE    +++  +  
Sbjct: 188 SYGNEKK---EILFLEIWTNGSLTPKEALHEAAQNLMDLFIPFLQMEEENLNLEDAEHQI 244

Query: 249 SLPFNPALLKK---------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                    K                +++L    +  NCL   NI  + DL+ +++ D+L
Sbjct: 245 PFSPFTFYDKVSKLIKKKKRSLKSIFIDQLAFPPKIYNCLTKSNIFTLLDLLNKSQEDLL 304

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++ +F    + ++K +LG +     ++LP 
Sbjct: 305 KIEHF---HIEDVKQILGILEKNFALDLPK 331


>gi|86438808|emb|CAJ43369.1| RNA polymerase alpha subunit [Lactobacillus casei]
          Length = 233

 Score =  266 bits (679), Expect = 5e-69,   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|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 =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 83/331 (25%), Positives = 158/331 (47%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    +         I  PL +G A T+G A+RR L+  + G  IT V+ + V
Sbjct: 11  RTLKWKCVESRTDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRVKSEKV 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +       +I  +GPG VTA DI     +E++
Sbjct: 71  PHEYSTIMGIQESVHEILMNLKEIVLRSNLYGTSDASICVKGPGYVTAQDIILPPYVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I +L       + L + +  GY+    H   N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTETIDFCIGLQIKRNRGYLIKTPH---NFQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHIEEDNLYLQDNQHTV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            L       K                 +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 PLSPFTFHDKLAKLIKNKKKIALKSIFIDQSELPSRIYNCLKMSNIYTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F      ++K +LG +  +  ++L  
Sbjct: 307 MKIEHFRS---EDVKQILGILEKYFVIDLAK 334


>gi|290489658|gb|ADD31213.1| RNA polymerase alpha subunit protein [Dillenia indica]
          Length = 353

 Score =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 79/311 (25%), Positives = 151/311 (48%), Gaps = 20/311 (6%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+++G+
Sbjct: 21  RIDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSTMRGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I L+ +    +  +I  RGPG VTA DI     +E+++    I +L 
Sbjct: 81  QESVHEILMNLKEIVLRSNLYGTRNASICARGPGYVTAQDIILPPSVEIIDNTQHIASLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + +  GY         N       IDA++ P++  ++++ S   G     
Sbjct: 141 EPINLYIELQIERNRGYHIKT---PNNFQDESYPIDAVFMPVRNANHSIHSYGNGNE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR   D    FI+ E+    + ++ +  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALHEASRNFIDLFIPFIHVEKENLYLGDNQDKDTFPLFTFHDE 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R  NCL+  NI  + DL+  ++ D++++  F R+ 
Sbjct: 257 LAKLRKNKKEIALKYLFIDQLELPPRIYNCLKRSNIHTLLDLLNNSQEDLMKIEYFRRED 316

Query: 303 LVEIKGVLGTM 313
           + +I G+L   
Sbjct: 317 VKQIFGILEKH 327


>gi|290489686|gb|ADD31227.1| RNA polymerase alpha subunit protein [Ficus sp. Moore 315]
          Length = 323

 Score =  266 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 85/328 (25%), Positives = 158/328 (48%), Gaps = 23/328 (7%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLR 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 QDIILPPSVEIVDNTQHIANLTEPITLCIELQIKRDRGYRIKT---PNNFQNGSYPIDAV 175

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           + P++  ++++ S   G   + + L + I T+GS+T ++++  ASR L D    F + EE
Sbjct: 176 FMPVRNANHSIHSYVNGNE-NQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFFHAEE 234

Query: 237 PKKEVKEDINVKSLPFNPALLKK-------------VEELELSVRSTNCLRGENIVYMGD 283
             +  +    +    F+  L K              +++ EL+ R  NCL+  NI    D
Sbjct: 235 HLENNQHKGTLPLFNFHGRLAKPRKTKKEKALKYIYIDQSELTPRVYNCLKRSNINTFLD 294

Query: 284 LIQRTEADMLRMANFGRKSLVEIKGVLG 311
           L+  ++ +++++ +F  + +  I  VL 
Sbjct: 295 LLNNSQEELMKIKDFTIEDVKHILDVLE 322


>gi|71056814|emb|CAH58962.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
          Length = 243

 Score =  266 bits (679), Expect = 5e-69,   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|194132131|gb|ACF33385.1| RNA polymerase alpha subunit [Gonystylus bancanus]
          Length = 329

 Score =  265 bits (678), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 82/311 (26%), Positives = 152/311 (48%), Gaps = 20/311 (6%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RR L+  + G  IT  + + + HE S I G+
Sbjct: 23  RIDSKHLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPHEYSIIAGI 82

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I L+ +    +   I  +GPG VTA DI     +E+++    I +L 
Sbjct: 83  QESVHEILMNLKEIVLRSNLYGTRNAFICAKGPGYVTAQDIILPPSVEIVDNTQHIASLT 142

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + + L + +  GY         N   G   ID ++ P++ V++++ S   G     
Sbjct: 143 EPIDLCIGLQIERNRGYGIKT---PNNFHDGSYPIDVVFMPVRNVNHSIHSYGNGNE-KQ 198

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE    ++   +  +LPF P   K
Sbjct: 199 EILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENSHLENSQHKVTLPFFPFHDK 258

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++ EL  R  NCL+  NI  + DL+ +++ D++++ +F R+ 
Sbjct: 259 LTKLRKKKKEIALKYFFIDQSELPPRIYNCLKTSNIHTLFDLLNKSQEDLMKIEHFHRED 318

Query: 303 LVEIKGVLGTM 313
           + +I G++   
Sbjct: 319 VKQILGIIENK 329


>gi|317016849|gb|ADU85965.1| DNA-directed RNA polymerase alpha chain [Lactobacillus
           fabifermentans]
          Length = 235

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 105/234 (44%), Positives = 153/234 (65%), Gaps = 2/234 (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 LTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
           +T + G GYV A    HR ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ 
Sbjct: 121 MTANTGRGYVSAEDNKHREDDMPIGVLPVDSLYSPIERVNYQVENTRVGQRDDFDKLTLD 180

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + T+GSIT  ++++L+++IL D L +F+N  +  K     +  +       L  
Sbjct: 181 VWTNGSITPSEAISLSAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKEKMLEM 234


>gi|300431307|gb|ADK12618.1| RNA polymerase alpha subunit [Achnatherum chingii]
          Length = 339

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 92/319 (28%), Positives = 154/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY         N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIELQIKRDRGYQTELR---NNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T GS+T ++++  ASR L D    F++ EE     +E+ N  + P      K
Sbjct: 197 EILFLEIWTTGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKK 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ NF    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDNF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDGKQIWDTLEKHLPIDL 332


>gi|84874038|gb|ABC68042.1| RNA polymerase subunit [Oryza rhizomatis]
          Length = 317

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 94/321 (29%), Positives = 157/321 (48%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+
Sbjct: 1   RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGI 60

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 61  EESVQEILLNLKEIVLRSNLYGVRNASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 120

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                R+EL + +  GY        +N   G   IDA+  P++ V+Y++ S   G    Y
Sbjct: 121 EPTDFRIELRIKRDRGYHTEVR---KNTQDGSYPIDAVSMPVRNVNYSIFSCGNGNA-KY 176

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 177 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENQNRFTSPLLSFQKR 236

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 237 LTNLKKNKKRIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 293

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + + K +  T+   L M+LP 
Sbjct: 294 MQDGKQIWDTLEKHLPMDLPK 314


>gi|47679559|gb|AAT36723.1| RNA polymerase alpha subunit [Phaeodactylum sp. Bohlin BA153065]
          Length = 298

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 95/298 (31%), Positives = 155/298 (52%), Gaps = 5/298 (1%)

Query: 13  NNIEYIVLGQE----EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           NNI    L  E           +   L  G   T+GN LRRVL+  L G AI+AV+I G+
Sbjct: 2   NNISIKCLKSEKIQSGACHGQFLINSLNPGQGITIGNQLRRVLLGDLGGVAISAVRIAGI 61

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I GV ED+ +I+LN+KGI         +   +  +GP VVTA  IQ   ++E++
Sbjct: 62  THEFSTIPGVREDILEILLNLKGIICTSQIQDTQFGHLKVQGPSVVTADLIQLPPEVEII 121

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+H I  +    ++ +E     G GY  A       D    + +D ++ P++KV + +E
Sbjct: 122 NPNHYIATITTSNILEIEFKFVYGGGYHLASQKFCREDE-NYLQLDTIFMPVQKVDFKIE 180

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +  +      ++L + I T+GSI+  D++  A++++ D   + IN        +    ++
Sbjct: 181 NIYDATNNISERLFLDIWTNGSISPNDALESAAQVIIDLFTLLINNTNINNNNRLVKAIR 240

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           ++   P     +EEL+LSVR+ NCL+   I  +GDL+Q +   +  + NFGRKS  E+
Sbjct: 241 AISIEPYTNIAIEELQLSVRAYNCLKKAQINTVGDLLQYSPEKLQELKNFGRKSADEV 298


>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 =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 91/321 (28%), Positives = 156/321 (48%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDMAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY        +N   G   IDA+  P++ V+Y++     G    +
Sbjct: 141 EPIDFCIELQIKRDRGYHTELR---KNSQDGSYPIDAVSMPVRNVNYSIFYCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      K
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLLTFQKK 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + + K +  T+   L ++LP 
Sbjct: 314 MEDGKQIWDTLEKHLPIDLPK 334


>gi|69215828|gb|AAZ03870.1| RNA polymerase alpha chain [Yucca schidigera]
          Length = 337

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 92/321 (28%), Positives = 158/321 (49%), Gaps = 25/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RR L+  + G  IT  + + V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKVPHEYSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I +N+K I L + G   +  +I  RGP  VTA DI +   +E+++    I NL 
Sbjct: 81  EESVHEIFINLKEIVLNLYG--VRDASICVRGPRYVTAQDIISPPSVEIVDTTQHIANLT 138

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               +R+EL + +  GY     + T N   G   IDA+  P++  ++++ S   G     
Sbjct: 139 EPIDLRIELQIKRDRGYRI---NPTNNSQDGSYPIDAVSMPVRNANHSIHSYGNGNE-KQ 194

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +LP      +
Sbjct: 195 EILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEGDIHFEENKNRFTLPLFTFQNR 254

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+  ++ D++R+  F    
Sbjct: 255 LTNLKKNKKGIPLKCIFIDQLELPPRTYNCLKRSNIHTLLDLLSNSQEDLMRIEYFRT-- 312

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
             ++K +L T+     +NLP 
Sbjct: 313 -EDVKQILDTLQKHFAINLPK 332


>gi|20160832|dbj|BAB89772.1| Chloroplast RNA polymerase alpha chain [Oryza sativa Japonica
           Group]
          Length = 337

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 93/321 (28%), Positives = 157/321 (48%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRTASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                R+EL + +  GY        +N   G   IDA+  P++ V+Y++ +   G    Y
Sbjct: 141 EPTDFRIELRIKRDRGYHTEVR---KNTQDGSYPIDAVSMPVRNVNYSIFACGNGNA-KY 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKRIPLSCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + + K +  T+   L M+LP 
Sbjct: 314 MQDGKQIWDTLEKHLPMDLPK 334


>gi|153799470|gb|ABS50510.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
          Length = 240

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 102/243 (41%), Positives = 154/243 (63%), Gaps = 4/243 (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 SLP 251
           +  
Sbjct: 237 NDK 239


>gi|300431329|gb|ADK12627.1| RNA polymerase alpha subunit [Achnatherum diegoense]
          Length = 339

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 91/319 (28%), Positives = 156/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I+ +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY         N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIELQIQRDRGYQTELR---NNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      K
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKK 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDGKQIWDTLEKHLPIDL 332


>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 =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 84/331 (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 SYENGNK---EILFLEIWTNGSLTPKEALYEASRNLIDLLIPFLHTKEENLNLEGNQHMV 244

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            LP      K                 +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 245 PLPPFTFYDKLAKLTKNKKKMALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQEDL 304

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++M +F    + ++K +LG +     ++LP 
Sbjct: 305 MKMEHF---RIEDVKQILGILEKNFVIDLPK 332


>gi|153799484|gb|ABS50517.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
          Length = 240

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 102/242 (42%), Positives = 152/242 (62%), Gaps = 4/242 (1%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            KPN    I + ++E++    + EPL RGF  TLGN+LRRVL++S+ G  +  VQIDGVL
Sbjct: 2   EKPN----ITVVEQEDSYGKFVVEPLERGFGTTLGNSLRRVLLTSIPGTGLVYVQIDGVL 57

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           HE S++ GV ED+T IILN+K + LK   D  K + +   GP  VTA D++   D++VLN
Sbjct: 58  HEFSTVPGVREDVTKIILNLKKLELKSLSDEQKVIELDVEGPATVTADDLKVDADVQVLN 117

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  IC +     + MEL V  G GYV A  +++++ PIG+I +D+L+SPIKKV+Y VES
Sbjct: 118 PDQYICTIAEGGHLHMELAVKNGRGYVTASDNKSDDMPIGVIPVDSLFSPIKKVNYQVES 177

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
            R G+  D+DKL+  I TDGSI   D+++ A++IL +   +F + +   +  +  +  + 
Sbjct: 178 TRVGKRDDFDKLTFEIWTDGSIKPNDALSFAAKILVEHFKVFESADANTQFSEVMVEKED 237

Query: 250 LP 251
             
Sbjct: 238 DK 239


>gi|300431291|gb|ADK12610.1| RNA polymerase alpha subunit [Jarava plumosula]
          Length = 339

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 155/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I+ +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY         N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIELQIKRDRGYQTELR---NNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  AS  L D    F++ EE     +E+ N  + P      K
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASHNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKK 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDGKQIWDTLEKHLPIDL 332


>gi|153799478|gb|ABS50514.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
          Length = 240

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 102/243 (41%), Positives = 153/243 (62%), Gaps = 4/243 (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 SLP 251
              
Sbjct: 237 DDK 239


>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 =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 93/321 (28%), Positives = 157/321 (48%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRTASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                R+EL + +  GY        +N   G   IDA+  P++ V+Y++ +   G    Y
Sbjct: 141 EPTDFRIELRIKRDRGYHTEVR---KNTQDGSYPIDAVSMPVRNVNYSIFACGNGNA-KY 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKRIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + + K +  T+   L M+LP 
Sbjct: 314 MQDGKQIWDTLEKHLPMDLPK 334


>gi|328813959|gb|AEB52095.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 231

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 101/230 (43%), Positives = 153/230 (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 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           GSI+  ++++LA++IL + L +F+N  +  K  +  +  +       L  
Sbjct: 181 GSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEM 230


>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 =  264 bits (676), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 97/327 (29%), Positives = 172/327 (52%), Gaps = 14/327 (4%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           ++ +K   ++   +  E++NRT++   PL  GF  TLGNALRR+ +SS+ GA++ AV+  
Sbjct: 2   RKFLK-YQLDVPSINSEDKNRTVVKIAPLEIGFGDTLGNALRRICLSSIPGASMFAVKFG 60

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSG-------------DSHKRVTIFKRGPGV 113
           G  HE    +GV ED+T IILN+K + +K+               D   ++ I  +GPGV
Sbjct: 61  GYSHEFQPYEGVKEDITHIILNLKNLAIKIDELIYSEDYFNNLLIDKWPKMKINFKGPGV 120

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITI 173
           +TA DI      E++N D  I  +     V +E+    G G V    ++     + +I  
Sbjct: 121 ITAKDIVCPVGFEIVNQDLYIAEVTKPIDVEIEIFAKTGRGRVDFNTNKDFVSTLHIIAT 180

Query: 174 DALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           D+ YSP+   +Y VE  ++ +    + L++ I T+G+I+G +++A+A++I+Q  L   +N
Sbjct: 181 DSNYSPVLHYAYNVEMIKDSKSSMSEILTIDIATNGTISGSEAIAIAAKIMQAHLEPIVN 240

Query: 234 FEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            ++   E+      +           +++L+L+VR+ N L+   I    +LI+ T++ + 
Sbjct: 241 IDKTINEMIIMREREEEEKRQNASISIDDLDLTVRAYNALKQSGINTTAELIELTKSQLE 300

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMN 320
           ++ N GRKS+ EI   L    L L  +
Sbjct: 301 KIKNLGRKSVTEIIQKLTERSLELKKD 327


>gi|300431299|gb|ADK12614.1| RNA polymerase alpha subunit [Hesperostipa comata]
          Length = 339

 Score =  264 bits (676), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 91/319 (28%), Positives = 155/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY         N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIELQIKRDRGYQTELR---NNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      K
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPRFTFQKK 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDGKQIWDTLEKHLPIDL 332


>gi|290790733|gb|ADD62991.1| RNA polymerase alpha subunit [Oryza australiensis]
          Length = 337

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 94/321 (29%), Positives = 157/321 (48%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRNASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                R+EL + +  GY        +N   G   IDA+  P++ V+Y++ S   G    Y
Sbjct: 141 EPTDFRIELRIKRDRGYHTEVR---KNTQDGSYPIDAVSMPVRNVNYSIFSCGNGNA-KY 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKRIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + + K +  T+   L M+LP 
Sbjct: 314 MQDGKQIWDTLEKHLPMDLPK 334


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 79/318 (24%), Positives = 152/318 (47%), Gaps = 24/318 (7%)

Query: 16  EYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           ++  +    +         I  PL +G A T+G A+RR L+  L G  IT  + + + HE
Sbjct: 16  QWKCVESRTDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGELEGTCITRAKSEKIPHE 75

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            S+I G+ E + +I++N+K I L+ +    +   I  +GPG VTA DI     +E+++  
Sbjct: 76  YSTIVGIQESVHEILMNLKEIVLRGNLYGTRNAFICAKGPGYVTAQDIILPPSVEIVDNT 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             + +L     + + L + +  GY        +N   G   IDA++ P++  ++++    
Sbjct: 136 QHVASLTEPIDLCIGLQIERNRGYGIKT---PKNFHDGSYPIDAVFMPVRNANHSIHCYG 192

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + +  +LP
Sbjct: 193 NDNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHTEEENLHLENNQHDVTLP 251

Query: 252 FNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
           F P   +                 +++ EL  R  NCL+  NI  + DL+  +  D++++
Sbjct: 252 FFPFHDRLVKLTKKKKEIALKYIFIDQSELPPRIYNCLKKSNIHTLLDLLNNSREDLMKI 311

Query: 296 ANFGRKSLVEIKGVLGTM 313
            +F  + + +I G+L   
Sbjct: 312 EHFRIEDVKQILGILEKK 329


>gi|300431293|gb|ADK12611.1| RNA polymerase alpha subunit [Piptatherum miliaceum]
          Length = 339

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 156/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S++ G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTLAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASISVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPVDFCIELQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      K
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKK 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDGKQIWDTLEKHLPIDL 332


>gi|307683477|dbj|BAJ19717.1| RNA polymerase alpha chain [Pseudotsuga sinensis var. wilsoniana]
          Length = 335

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 88/317 (27%), Positives = 151/317 (47%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RRVL+  + G  IT VQ D + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRVLLGEVEGTCITHVQFDNIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILVNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY     H   N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIRLRIEKNRGY---IMHSPNNYKDGIFPIDAVFMPVRDANYSIHSYGSGNEI-REVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP------- 254
            + I T+G +T  +++  ASR L D    F++ EE   +   +    ++P  P       
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNRKGSNMPPFPLSHVLTD 259

Query: 255 ---------ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                         +++LEL  R  NCLR  NI  + DL+  +  D++R+ N G++S+ +
Sbjct: 260 TRETIEKIAFQYIFIDQLELPPRIYNCLRRANIHTLLDLLNYSREDLMRIENLGKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL        ++ P
Sbjct: 320 VLEVLR---KRFAIDPP 333


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 120/301 (39%), Positives = 173/301 (57%), Gaps = 6/301 (1%)

Query: 28  TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIIL 87
              I EPL  GF  T+GNA+RRVL+SSL G AI+AV I G+ HE S I GV ED  D+ L
Sbjct: 30  AEFIVEPLRVGFGLTIGNAMRRVLLSSLSGFAISAVGIKGLTHEFSCIPGVREDFADLAL 89

Query: 88  NIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           N+K + LK    +    + +     G V +  I   +D EV+N D +ICN+     + ME
Sbjct: 90  NLKKVVLKSISGATCGNLHLSVTDGGAVFSNMISPSHDFEVVNGDLLICNVAEGVSLEME 149

Query: 147 LTVSKGHGYVPAKHHRTENDP-IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           + VS G GYV +   R +     G + IDA+Y+P++ V++TV+    G    +DKL + +
Sbjct: 150 MKVSSGFGYVSSVSVRKDEYDLEGAVPIDAIYNPVRAVNFTVKPTSAGSFAGHDKLILYV 209

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI----NVKSLPFNPALLKKVE 261
           +T+G++  + +V  AS+IL  Q   F+N  +P+  V               +  L  +++
Sbjct: 210 ETNGAMDPKTAVLEASKILSTQARCFLNIADPEHRVHGVPCGVSTSDRNDASDLLSARID 269

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
            L LS R+  CL GENIVY+ DL+ RTEAD+L+  NFGR+SL E+K  L + GL LGMNL
Sbjct: 270 RLYLSARARKCLNGENIVYIRDLVSRTEADLLKAPNFGRRSLEEVKKELFSKGLSLGMNL 329

Query: 322 P 322
            
Sbjct: 330 D 330


>gi|300431309|gb|ADK12619.1| RNA polymerase alpha subunit [Achnatherum psilantherum]
          Length = 339

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 91/319 (28%), Positives = 156/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I+ +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVDTGQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY         N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIELQIKRDRGYQTELR---NNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      K
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKK 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDGKQIWDTLEKHLPIDL 332


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 91/319 (28%), Positives = 156/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I+ +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY         N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIELQIKRDRGYQTELR---NNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      K
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKK 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDGKQIWDTLEKHLPIDL 332


>gi|88657014|gb|ABD47264.1| RNA polymerase alpha subunit [Lactuca sativa]
          Length = 337

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 84/331 (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 SYENGNK---EILFLEIWTNGSLTPKEALYEASRNLIDLLIPFLHTKEENLNLEGNQHMV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            LP      K                 +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 PLPPFTFYDKLAKLTKNKKKMALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++M +F    + ++K +LG +     ++LP 
Sbjct: 307 MKMEHF---RIEDVKQILGILEKNFVIDLPK 334


>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 =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 91/319 (28%), Positives = 155/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDITLPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY         N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIELQIKRDRGYQTELR---NNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      K
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKK 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDGKQIWDTLEKHLPIDL 332


>gi|300431303|gb|ADK12616.1| RNA polymerase alpha subunit [Aciachne flagellifera]
          Length = 339

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 91/319 (28%), Positives = 155/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY         N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIELQIKRDRGYQTELR---NNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      K
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKK 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDGKQIWDTLEKHLPIDL 332


>gi|84874028|gb|ABC68037.1| RNA polymerase subunit [Oryza sativa]
          Length = 317

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 92/321 (28%), Positives = 156/321 (48%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+
Sbjct: 1   RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGI 60

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 61  EESVQEILLNLKEIVLRSNLYGVRTASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 120

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY        +N   G   IDA+  P++ V+Y++ +   G    Y
Sbjct: 121 EPTDFHIELRIKRDRGYHTEVR---KNTQDGSYPIDAVSMPVRNVNYSIFACGNGNA-KY 176

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 177 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKR 236

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 237 LTNLKKNKKRIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 293

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + + K +  T+   L M+LP 
Sbjct: 294 MQDGKQIWDTLEKHLPMDLPK 314


>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 =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 97/327 (29%), Positives = 172/327 (52%), Gaps = 14/327 (4%)

Query: 7   QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           ++ +K   ++   +  E++NRT++   PL  GF  TLGNALRR+ +SS+ GA++ AV+  
Sbjct: 2   RKFLK-YQLDVPSINSEDKNRTVVKIAPLEIGFGDTLGNALRRICLSSIPGASMFAVKFG 60

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSG-------------DSHKRVTIFKRGPGV 113
           G  HE    +GV ED+T IILN+K + +K+               D   ++ I  +GPGV
Sbjct: 61  GYSHEFQPYEGVKEDITHIILNLKNLAIKIDELIYSEDYFNNLLIDKWPKMKINFKGPGV 120

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITI 173
           +TA DI      E++N D  I  +     V +E+    G G V    ++     + +I  
Sbjct: 121 ITAKDIVCPVGFEIVNQDLYIAEVTKPIDVEIEIFAKTGRGRVDFNTNKDFVSTLHIIAT 180

Query: 174 DALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           D+ YSP+   +Y VE  ++ +    + L++ I T+G+I+G +++A+A++I+Q  L   +N
Sbjct: 181 DSNYSPVLHYAYNVEMIKDSKSSMSEILTIDIATNGTISGSEAIAIAAKIMQAHLEPIMN 240

Query: 234 FEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            ++   E+      +           +++L+L+VR+ N L+   I    +LI+ T++ + 
Sbjct: 241 IDKTINEMIIMREREEEEKRQNASISIDDLDLTVRAYNALKQSGINTTAELIELTKSQLE 300

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMN 320
           ++ N GRKS+ EI   L    L L  +
Sbjct: 301 KIKNLGRKSVTEIIQKLTERSLELKKD 327


>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 =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 93/321 (28%), Positives = 157/321 (48%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+
Sbjct: 1   RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGI 60

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 61  EESVQEILLNLKEIVLRSNLYGVRTASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 120

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                R+EL + +  GY        +N   G   IDA+  P++ V+Y++ +   G    Y
Sbjct: 121 EPTDFRIELRIKRDRGYHTEVR---KNTQDGSYPIDAVSMPVRNVNYSIFACGNGNA-KY 176

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 177 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKR 236

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 237 LTNLKKNKKRIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 293

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + + K +  T+   L M+LP 
Sbjct: 294 MQDGKQIWDTLEKHLPMDLPK 314


>gi|71056830|emb|CAH58970.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
          Length = 243

 Score =  264 bits (675), Expect = 1e-68,   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|328813949|gb|AEB52090.1| DNA-directed RNA polymerase alpha chain [Lactobacillus casei]
          Length = 241

 Score =  264 bits (675), Expect = 1e-68,   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|84874036|gb|ABC68041.1| RNA polymerase subunit [Oryza officinalis]
 gi|84874042|gb|ABC68044.1| RNA polymerase subunit [Oryza australiensis]
          Length = 317

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 94/321 (29%), Positives = 157/321 (48%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+
Sbjct: 1   RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGI 60

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 61  EESVQEILLNLKEIVLRSNLYGVRNASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 120

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                R+EL + +  GY        +N   G   IDA+  P++ V+Y++ S   G    Y
Sbjct: 121 EPTDFRIELRIKRDRGYHTEVR---KNTQDGSYPIDAVSMPVRNVNYSIFSCGNGNA-KY 176

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 177 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKR 236

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 237 LTNLKKNKKRIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 293

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + + K +  T+   L M+LP 
Sbjct: 294 MQDGKQIWDTLEKHLPMDLPK 314


>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 =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 85/321 (26%), Positives = 158/321 (49%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ++RR L+  + G  IT  + + V HE S++ G+
Sbjct: 21  RVDSKRLYYGRFILSPLMKGQADTIGISMRRALLGEIEGTCITRAKSEKVPHEYSTVVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+ N+K I L+ +    +  +I  RGP  VTA DI +   +E+++    I NL 
Sbjct: 81  EESVHEILFNLKEIVLRSNLYEIRDASICVRGPRYVTAQDIISPPYVEIVDTTQYIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + +  GY   +     N   G   IDA++ P++  ++++ S   G     
Sbjct: 141 EPIDLCIELEIKRDRGY---RMKPITNSQDGSYPIDAVFMPVRNANHSIHSYGNGNE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  +LP      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFVPFLHAEEEDINFEENKNKFTLPPLTFQDR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ + + ++++M  F    
Sbjct: 257 LSNLKKNKKGIPLKYIFIDQLELPSRTYNCLKRSNIHTLLDLLSKGQENLIKMEYF---H 313

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + ++K +L T+     ++LP 
Sbjct: 314 IEDVKQILDTLQKHFAVDLPK 334


>gi|300431322|gb|ADK12624.1| RNA polymerase alpha subunit [Amelichloa brevipes]
          Length = 339

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 91/319 (28%), Positives = 155/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + +  GY         N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDLCIELQIKRDRGYQTELR---NNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      K
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKK 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +   +   L +NL
Sbjct: 314 MEDGKQIWDNLEKHLPINL 332


>gi|19702212|emb|CAD28795.1| RNA polymerase alpha subunit [Cuscuta reflexa]
          Length = 335

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 84/331 (25%), Positives = 156/331 (47%), Gaps = 29/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    +         I  PL +G A T+G A+RR L++ + G  IT V+    
Sbjct: 11  RTLQWKCVESRTDSKRPYYGRFILSPLTKGQADTIGIAMRRALLAEIEGTRITRVKFANT 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---GSYPIDALLMPVRNANHSIN 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S    +    + L + I T+GS+T ++++  ASR L D    F++ EE    +++  +  
Sbjct: 188 SYGNEK---QEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHMEEENLHLEDADHTI 244

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            L       K                 +++LE   +  NCL+  NI  + DL+  ++ D+
Sbjct: 245 PLSPFTVYDKVAKLRKNKKKLSLESIFIDQLEFPPKIYNCLKKSNIFTLLDLLNNSQEDL 304

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +++ +F    L ++K +LG +G    ++ P 
Sbjct: 305 IKIEHF---HLEDVKQILGILGKHFALDSPK 332


>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 =  264 bits (674), 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  + + +
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 SYENGNK---EILFLEIWTNGSLTPKEALHEASRNLIDLLIPFLHTKEENLSLEDNQHIV 244

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            LP      K                 +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 245 PLPPFTFYDKLAKLTKNKKKMALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQEDL 304

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++M +F    + ++K +LG +     ++LP 
Sbjct: 305 MKMEHF---RIEDVKQILGILEKNFVIDLPK 332


>gi|84874032|gb|ABC68039.1| RNA polymerase subunit [Oryza glumipatula]
          Length = 317

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 93/321 (28%), Positives = 156/321 (48%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+
Sbjct: 1   RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGI 60

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 61  EESVQEILLNLKEIVLRSNLYGVRTASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 120

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                R+EL + +  GY        +N   G   IDA+  P++ V+Y++ +   G    Y
Sbjct: 121 EPTDFRIELRIKRDRGYHTEVR---KNTQDGSYPIDAVSMPVRNVNYSIFACGNGNA-KY 176

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T  +++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 177 EILFLEIWTNGSLTPMEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKR 236

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 237 LTNLKKNKKRIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 293

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + + K +  T+   L M+LP 
Sbjct: 294 MQDGKQIWDTLEKHLPMDLPK 314


>gi|300431288|gb|ADK12609.1| RNA polymerase alpha subunit [Jarava leptostachya]
          Length = 339

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 156/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I+ +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY         N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIELQIKRDRGYQTELR---NNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +++ N  + P      K
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEKNKNRFTPPLFTFQKK 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDGKQIWDTLEKHLPIDL 332


>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 =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 85/318 (26%), Positives = 153/318 (48%), Gaps = 24/318 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E  +       PL +G A T+G A+RRVL+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SERLHYGRFALSPLRKGRADTIGIAMRRVLLGEVEGTCITHVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I   GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVLRSDSYGIRGASICIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-REVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP------- 254
            + I T+G +T  ++++ ASRIL +    F++ EE   +   +    ++P  P       
Sbjct: 200 FLEIWTNGGLTPREALSEASRILIELFIPFLHGEEQNIDGMNNRKGSNMPPFPLSHVLTD 259

Query: 255 ----------ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
                          +++LE   R  NCLR  NI  + DL+  +  D++R+  FG++S+ 
Sbjct: 260 TGETKEKKIAFQHIFIDQLEFPPRVYNCLRRANIHTLSDLLNYSREDLMRIERFGKESVE 319

Query: 305 EIKGVLGTMGLFLGMNLP 322
           ++  +L        ++ P
Sbjct: 320 QVFEILR---KRFAIDPP 334


>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 =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 91/319 (28%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIELQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIESF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+  +L M+L
Sbjct: 314 MEDRKQIWDTLEKYLPMDL 332


>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 = 83/321 (25%), Positives = 151/321 (47%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  E  +       P   G A+T+G A+RR L+  + G  IT  + + V HE S+I G+
Sbjct: 22  KVDSERLHYGRFAISPFRSGQANTVGIAVRRALLGGVEGTCITRAKSEKVTHEYSTILGI 81

Query: 79  HEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
            E + DI++N+K I LK   +    ++  +   GP  VTA DI     +EV++    I  
Sbjct: 82  QESVRDILINLKEIVLKSKSNSCETQKAFLSIFGPKEVTARDIVFPPSVEVIDTTQYIAT 141

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           L     + +EL + K  GY      ++ +   G  ++DA+++PI+  +Y+V S       
Sbjct: 142 LTKAIHLDIELKIEKDCGYRTQDSIKSAD---GYFSVDAVFTPIRNANYSVHSFENKNET 198

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE--------------VK 242
             + L + I T+GS+T ++++  ASR L D    F++ E+ +                  
Sbjct: 199 -QEILFIEIWTNGSVTPKEALYEASRSLIDLFIPFLHAEKEEVMHGLGNKNESNTLHFSS 257

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                K           +++LEL  R+ NC +  ++  + DL+  ++ D++++ NFG+KS
Sbjct: 258 SPSENKMEKEMTFKHIFIDQLELPARAYNCPKRVDVHTISDLLSYSQDDLMKIKNFGKKS 317

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
              ++ VL  +     + LP 
Sbjct: 318 ---VEQVLEALQKRFSIKLPK 335


>gi|228016583|gb|ACP51413.1| RNA polymerase alpha subunit [Abies firma]
          Length = 336

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 88/318 (27%), Positives = 153/318 (48%), Gaps = 24/318 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V++D + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLCKGRADTIGIAMRRALLGEVEGTCITHVKLDNIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TFDIRLRIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-REVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP------- 254
            + I T+G +T  +++  ASR L D L  F++ EE   +   +    S            
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLLIPFLHGEEQNIDGMNNRKGSSNMPPFPLSHVFT 259

Query: 255 ----------ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
                          +++LEL  R+ NCLR  NI  + DL+  +  D++R+ +FG++S+ 
Sbjct: 260 DTGETKEKIAFQHIFIDQLELPPRTYNCLRRANIHTLLDLLNYSREDLMRIEHFGKESIE 319

Query: 305 EIKGVLGTMGLFLGMNLP 322
           ++  VL        +NLP
Sbjct: 320 QVLEVLR---KRFAINLP 334


>gi|300431278|gb|ADK12604.1| RNA polymerase alpha subunit [Piptochaetium montevidense]
          Length = 339

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 155/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDRAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY         N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIELQIKRDRGYQTELR---NNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      K
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKK 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++++ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMKIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDGKQIWDTLEKHLPIDL 332


>gi|119662349|emb|CAJ33163.1| RNA polymerase alpha subunit [Lactobacillus rhamnosus]
          Length = 223

 Score =  264 bits (674), Expect = 2e-68,   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|58758766|gb|AAW81772.1| RNA polymerase alpha subunit [Buxbaumia aphylla]
          Length = 340

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 86/321 (26%), Positives = 155/321 (48%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  E  + +     P   G A+T+G A+RR L+  ++G +IT  + + V HE S+I G+
Sbjct: 21  KIDNERLHYSRFAISPFRCGQANTVGIAMRRALLGEVKGTSITCAKFEKVTHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + DI +N K I L+ +    ++  I   GP  +TA DI     +++++    I  L 
Sbjct: 81  QESVHDISINSKEIVLESNSSETQKAFISILGPKKITAQDIILPPSVKIIDGKQYIATLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + K +GY     +++ N       IDA++ PI+  +Y+V S         
Sbjct: 141 KAIQLDIELEIEKDYGYRIQNSNKSTNSH---FFIDAIFMPIRNANYSVHSFENENKT-Q 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GSIT +D++  ASR L D    F++ E  +   + +   K    +     
Sbjct: 197 EMLFIEIWTNGSITPKDALYEASRSLIDLFIPFLHAERREIINELENEYKLSNISYFSSF 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  N+  + DL+  ++ D++++ NFG+KS
Sbjct: 257 SPLADKITKEVSFKHIFIDQLELPARAYNCLKRVNVNTLADLLNYSQEDLMKIKNFGKKS 316

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
              ++ VL  +     +NLP 
Sbjct: 317 ---VEQVLEALQKQFSINLPK 334


>gi|119662337|emb|CAJ33157.1| RNA polymerase alpha subunit [Lactobacillus paracasei subsp.
           tolerans]
          Length = 230

 Score =  264 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 101/229 (44%), Positives = 152/229 (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 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           SI+  ++++LA++IL + L +F+N  +  K  +  +  +       L  
Sbjct: 181 SISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLEM 229


>gi|307683665|dbj|BAJ19811.1| RNA polymerase alpha chain [Picea morrisonicola]
          Length = 336

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 86/318 (27%), Positives = 154/318 (48%), Gaps = 24/318 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            E  +       PL +G A T+G A+RRVL+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SERLHYGRFALSPLRKGRADTIGIAMRRVLLGEVEGTCITHVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I   GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVLRSDSYGIRGASICIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGNGNEI-REVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP------- 254
            + I T+G +T  ++++ ASRIL +    F++ EE   +   +    ++P  P       
Sbjct: 200 FLEIWTNGGLTPREALSEASRILIELFIPFLHGEEQNIDGMNNRKGSNMPPFPLSHVLTD 259

Query: 255 ----------ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
                          +++LEL  R  NCLR  NI  + DL+  +  D++R+  FG++S+ 
Sbjct: 260 TGETKEKKIAFQHIFIDQLELPPRVYNCLRRANIHTLSDLLNYSREDLMRIERFGKESVE 319

Query: 305 EIKGVLGTMGLFLGMNLP 322
           ++  +L        ++ P
Sbjct: 320 QVFEILR---KRFAIDPP 334


>gi|300431284|gb|ADK12607.1| RNA polymerase alpha subunit [Nassella arcuata]
          Length = 339

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 91/319 (28%), Positives = 156/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I+ +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY         N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPMDFCIELQIKRDRGYQTELR---NNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      K
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKK 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDGKQIWDTLEKHLPIDL 332


>gi|290489680|gb|ADD31224.1| RNA polymerase alpha subunit protein [Bulnesia arborea]
          Length = 352

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 82/320 (25%), Positives = 156/320 (48%), Gaps = 24/320 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 DNTQHIANLTEPIDFCIRLQIERNRGYRIKTPNQF---QEGIYPIDAVFMPVRNANHSIH 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|88656926|gb|ABD47177.1| RNA polymerase alpha subunit [Helianthus annuus]
          Length = 337

 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  + + +
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 SYENGNK---EILFLEIWTNGSLTPKEALHEASRNLIDLLIPFLHTKEENLSLEDNQHIV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
            LP      K                 +++ EL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 PLPPFTFYDKLAKLTKNKKKMALKSIFIDQSELPPRIYNCLKRSNIYTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           ++M +F    + ++K +LG +     ++LP 
Sbjct: 307 MKMEHF---RIEDVKQILGILEKNFVIDLPK 334


>gi|300431280|gb|ADK12605.1| RNA polymerase alpha subunit [Piptochaetium napostaense]
          Length = 339

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 89/319 (27%), Positives = 155/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDRAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY         N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIELQIKRDRGYQTELR---NNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      K
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKK 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  ++ NCL+  NI  + DL+ +TE D++++ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSKTYNCLKRANIHTLLDLLSKTEEDLMKIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDGKQIWDTLEKHLPIDL 332


>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 =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 93/331 (28%), Positives = 160/331 (48%), Gaps = 27/331 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +E+  +    +         I  PL +G A T+G ALRR L+  + G  IT  +   V
Sbjct: 11  QKLEWKCVESRVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGNV 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E++
Sbjct: 71  PHEYSTIVGIEESIQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I NL       +EL + +  GY        +N   G   IDA++ P++ V+Y++ 
Sbjct: 131 DTAQPIANLREPIDFCIELQIKRDRGYHTELR---KNSQDGSYPIDAVFMPVRNVNYSIF 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G    ++ L + I T+GS+T ++++  ASR L D    FI+ EE     +E  N  
Sbjct: 188 SCGNGNE-KHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFIHTEEEGTSFEESKNRL 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           + P      +                 +++LEL  R+ NCL+  NI  + DL+ +TE D+
Sbjct: 247 TPPLLTFQKRFTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +R+ +F    + + K +  T+   L ++LP 
Sbjct: 307 MRINSF---RMEDGKLIWDTLEKHLPIDLPK 334


>gi|71056838|emb|CAH58974.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
          Length = 237

 Score =  263 bits (673), Expect = 3e-68,   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|283945407|dbj|BAI66457.1| RNA polymerase alpha-subunit [Vibrio tapetis]
          Length = 260

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 119/262 (45%), Positives = 177/262 (67%), 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 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++  + +   +++   +  P    LL+ V++LEL+V
Sbjct: 181 NGTLDPEEAIRRSATILAEQLDAFVDLRDIRVPEEKEEKPEFDP---ILLRPVDDLELTV 237

Query: 268 RSTNCLRGENIVYMGDLIQRTE 289
           RS NCL+ E I Y+GDL+QRTE
Sbjct: 238 RSANCLKAEAIHYIGDLVQRTE 259


>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 =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 77/321 (23%), Positives = 153/321 (47%), Gaps = 23/321 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRSLIDLFIPFLQAEDENLPLENNQYKV 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|119662385|emb|CAJ33181.1| RNA polymerase alpha subunit [Lactobacillus zeae]
          Length = 227

 Score =  263 bits (672), Expect = 3e-68,   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|290489684|gb|ADD31226.1| RNA polymerase alpha subunit protein [Euonymus americanus]
          Length = 338

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 82/331 (24%), Positives = 158/331 (47%), Gaps = 26/331 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 DNTQHIAILTEPIYFCIELQIERHRGYHIKT---PNNFQEGSFPIDAVFMPVRNTNYSIQ 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 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 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|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 = 80/316 (25%), Positives = 151/316 (47%), Gaps = 21/316 (6%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    +         +  PL RG A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RPLQWKCVESRADSKRLYYGRFLLAPLMRGQADTIGIAMRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +    +  +I  +GPG VTA DI     +E++
Sbjct: 71  PHEYSTIVGIQESVHEILMNLKEIVLRSNLYGTRDASICVKGPGYVTAQDIILPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I NL     + +EL + +  GY         N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIANLTEPITLCIELQIERNRGYRIKT---PNNFQNGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G   + + L + I T+GS+T ++++  ASR L D    F + EE  +  +    + 
Sbjct: 188 SYVNGNE-NQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFFHAEEHLENNQHKGTLP 246

Query: 249 SLPFNPALLKK-------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
              F+  L K              +++ EL  R  NCL+  NI    +L+  ++ +++++
Sbjct: 247 LFNFHGRLAKPRKTKKEIALKYIYIDQSELPPRVYNCLKRSNINTFLELLNNSQEELMKI 306

Query: 296 ANFGRKSLVEIKGVLG 311
            +F  + +  I  VL 
Sbjct: 307 QDFRIEDVKHILDVLE 322


>gi|228016968|gb|ACP51792.1| RNA polymerase alpha subunit [Pinus banksiana]
          Length = 335

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 83/317 (26%), Positives = 152/317 (47%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-REVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL----------- 250
            + I T+G +T  +++  ASR L D    F++ EE   +   +    ++           
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHLLTD 259

Query: 251 -----PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                      L  +++LEL  +  N LR  NI  + DL+  +  D++R+ NFG++S+ +
Sbjct: 260 TGETKEKIAFQLIFIDQLELPPKIYNSLRRANIHTLLDLLNYSREDLMRIKNFGKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL  +     ++ P
Sbjct: 320 VLEVLQKL---FAIDPP 333


>gi|167957552|ref|ZP_02544626.1| DNA-directed RNA polymerase subunit alpha [candidate division TM7
           single-cell isolate TM7c]
          Length = 294

 Score =  262 bits (671), Expect = 3e-68,   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 EKLIVVIDTDGSITPRDAFEEAAAILVNQYTALAGSTVVESAPALGQER--EEESNELNT 250

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            +E+L+L+ R+ N L   +I  + DL+  TE D+  +  FG K
Sbjct: 251 SIEDLDLTARTANALINNDIRTVQDLVTLTEQDLRELKGFGSK 293


>gi|71056822|emb|CAH58966.1| DNA-directed RNA polymerase alpha chain [Enterococcus avium]
          Length = 245

 Score =  262 bits (671), Expect = 4e-68,   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|228017404|gb|ACP52221.1| RNA polymerase alpha subunit [Larix occidentalis]
          Length = 335

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 86/317 (27%), Positives = 155/317 (48%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIRLRIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-REVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP------- 254
            + I T+G +T  +++  ASR L D L  F++ EE   +   +    ++P  P       
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLLIPFLHGEEQNIDGMNNRKGSNMPPFPLSHVLTD 259

Query: 255 ---------ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                         +++LEL  R+ NCLR  NI  + DL+  +  D++R+ +FG++S+ +
Sbjct: 260 TRETKEKIAFKHIFIDQLELPPRTYNCLRRANIHTLLDLLNYSREDLMRIEHFGKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL        ++ P
Sbjct: 320 VLEVL---QKRFAIDPP 333


>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 =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 81/321 (25%), Positives = 160/321 (49%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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   +     N       IDA++ P++  ++++ 
Sbjct: 131 DITQHIASLTEPIDLCIELQIERNRGY---RMKTPNNAQERSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I TDGS+T ++++  ASR L D    F++ EE   +++++ +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTDGSLTPKEALYEASRNLIDLFIPFLHAEEQDTKLEDNQSRV 246

Query: 249 SLPFNPALL----------------KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 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|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 =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 85/320 (26%), Positives = 155/320 (48%), Gaps = 23/320 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +  +    +  PL +G A T+G A+RR L+  ++G  IT V+++ + HE S+I G+
Sbjct: 21  RVYSKRFHYGRFVLSPLRKGRADTIGIAMRRALLGEVKGTCITHVKLENIKHEYSAIIGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + DI++N+K I L+      +  +I+  GP  VTA DI     +++++    I  L 
Sbjct: 81  EESVHDILMNLKEIVLRSDSYGIQEASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 + L + K  GY     H   N   G+  IDA++ P++  +Y++ S   G  +  
Sbjct: 141 KSITFDIRLRIEKNRGY---LIHSPTNYGDGIFPIDAVFMPVRDANYSIHSYGSGNEI-R 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP---- 254
           + L + I T+G +T  +++  ASR L +    F++ EE   +        ++P  P    
Sbjct: 197 EVLFLEIWTNGGLTPREALYEASRNLINFFIPFLHGEEQNIDGMNSRKGSNIPSFPLSHV 256

Query: 255 ------------ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R  NCLR  NI  + DL+  ++ D++R+  FG+KS
Sbjct: 257 LTNTGETKEIFEFQHIFIDQLELPSRIYNCLRRANIYTLLDLLNYSQEDLMRIEQFGKKS 316

Query: 303 LVEIKGVLGTMGLFLGMNLP 322
           + ++  +L        ++LP
Sbjct: 317 VEQVLEILR---KRFAIDLP 333


>gi|84874040|gb|ABC68043.1| RNA polymerase subunit [Oryza punctata]
          Length = 317

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 94/321 (29%), Positives = 157/321 (48%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+
Sbjct: 1   RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGI 60

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 61  EESVQEILLNLKEIVLRSNLYGVRNASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 120

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                R+EL + +  GY        +N   G   IDA+  P++ V+Y++ S   G    Y
Sbjct: 121 EPEDFRIELRIKRDRGYHTEVR---KNTQDGSYPIDAVSMPVRNVNYSIFSCGNGNA-KY 176

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 177 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKR 236

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 237 LTNLKKNKKRIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 293

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + + K +  T+   L M+LP 
Sbjct: 294 MQDGKQIWDTLEKHLPMDLPK 314


>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 =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 85/317 (26%), Positives = 155/317 (48%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVLRSDSYGVREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              ++L + K  GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIKLRIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-REVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP------- 254
            + I T+G +T  +++  ASR L D    F++ EE   +   +    ++P  P       
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNRKGSNMPPFPLSHVLTD 259

Query: 255 ---------ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                         +++LEL  R+ NCLR  NI  + DL+  +  D++R+ +FG++S+ +
Sbjct: 260 TGETKEKIAFQHIFIDQLELPPRTYNCLRRANIHTLLDLLNYSREDLMRIEHFGKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL        ++ P
Sbjct: 320 VLEVLR---KRFAIDPP 333


>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 (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 77/321 (23%), Positives = 155/321 (48%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 DNTQHIATLTEPIDLCIELKIERNRGYSLKMSNNFEDRSY---PIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQV 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|300431320|gb|ADK12623.1| RNA polymerase alpha subunit [Amelichloa caudata]
          Length = 339

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 91/319 (28%), Positives = 155/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I+ +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY         N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIELQIKRDRGYQTELR---NNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS T ++++  ASR L D    F++ EE     +E+ N  + P      K
Sbjct: 197 EILFLEIWTNGSSTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKK 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDGKQIWDTLEKHLPIDL 332


>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 =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 110/324 (33%), Positives = 179/324 (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   MALKEILESIKHPHRVTFEK-KDLTPTYGKFIAQPFERGYAVTVGNALRRVLLSSIPGYA 59

Query: 60  ITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKRGPGVVTAGD 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 KKEVKEDINVKSLPF-NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
             + ++          +    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|119668363|emb|CAK95475.1| RNA polymerase alpha subunit [Lactobacillus rhamnosus]
          Length = 228

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 100/228 (43%), Positives = 152/228 (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 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           SI+  ++++LA++IL + L +F+N  +  K  +  +  +       L 
Sbjct: 181 SISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETHKEKMLE 228


>gi|332144686|dbj|BAK19503.1| RNA polymerase alpha subunit [Lactobacillus camelliae]
          Length = 228

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 104/228 (45%), Positives = 150/228 (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 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           SI+  ++++LA++IL + L +F+N  +  K  +  +  +       L 
Sbjct: 181 SISPREAISLAAKILTEHLDIFVNLTDSAKNAEIMVEKEETHKEKMLE 228


>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 (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 77/321 (23%), Positives = 155/321 (48%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 DNTQHIATLTEPIDLCIELKIERNRGYSLKMSNNFEDRSY---PIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETVYLENNQHQV 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|289524818|emb|CBJ94465.1| alpha subunit of RNA polymerase [Vibrio sp. Rd 16.2]
          Length = 267

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 117/270 (43%), Positives = 178/270 (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++  + +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
            ++L+  N G+KSL EIK VL + GL LGM
Sbjct: 238 VELLKTPNLGKKSLTEIKDVLASRGLSLGM 267


>gi|300431270|gb|ADK12600.1| RNA polymerase alpha subunit [Piptochaetium medium]
          Length = 339

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 155/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDRAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY         N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIELQIKRDRGYQTELR---NNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      K
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTCFEENKNRFTPPLFTFQKK 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++++ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMKIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDGKQIWDTLEKHLPIDL 332


>gi|124020697|gb|ABM88794.1| DNA-directed RNA polymerase alpha chain [Enterococcus camelliae]
          Length = 223

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 104/221 (47%), Positives = 149/221 (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 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           TDGSI   D+++LA++I+ + L +F+N  +  K  +  +  
Sbjct: 182 TDGSIEPLDAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEK 222


>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 =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 86/329 (26%), Positives = 162/329 (49%), Gaps = 28/329 (8%)

Query: 15  IEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +++  +    +    +    I  PL +G A T+G A+RR L+  + G  IT  + + + H
Sbjct: 13  LQWKCVESRTDSKCLHYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPH 72

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S+I G+ E + +I++N+K I L+ +       +I  RGP  VTA DI     +E+++ 
Sbjct: 73  EYSTILGIQESVHEILMNLKEIVLRSNLYGTCEASICVRGPRGVTAQDIILPPYVEIVDN 132

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
              I +L     + + L + +  GY         N   G   IDAL+ P++ V++++ S 
Sbjct: 133 TQHIASLTEPIDLCIGLQLERNRGY---HIKAPNNFQDGSFPIDALFMPVRNVNHSIHSY 189

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
             G     + L + I T+GS+T ++++  ASR L D L  F++ EE    ++++ +  SL
Sbjct: 190 GNGNE-KQEILFLEIWTNGSLTPKEALYEASRNLIDLLIPFLHAEE-NVNLEDNQHKVSL 247

Query: 251 PFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           P      +                 +++LEL  R  NCL+  NI  + DL+  ++ D+++
Sbjct: 248 PLFTFHNRLAEIRKNKKKIALKFIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLIK 307

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           M +F    + ++K + GT+     ++L +
Sbjct: 308 MKHF---RIEDVKQIFGTLEKHFVIDLKN 333


>gi|300431335|gb|ADK12628.1| RNA polymerase alpha subunit [Achnatherum eminens]
          Length = 339

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 155/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I+ +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY         N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIELQIKRDRGYQTELR---NNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+G +T ++++  ASR L D    F++ EE     +E+ N  + P      K
Sbjct: 197 EILFLEIWTNGRLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKK 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDGKQIWDTLEKHLPIDL 332


>gi|190411117|gb|ACE78313.1| RpoA [Vibrio parahaemolyticus]
 gi|190411119|gb|ACE78314.1| RpoA [Vibrio parahaemolyticus]
          Length = 263

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 116/266 (43%), Positives = 179/266 (67%), 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++  + +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y
Sbjct: 181 ATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHY 237

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEI 306
           +GDL+QRTE ++L+  N G+KSL EI
Sbjct: 238 IGDLVQRTEVELLKTPNLGKKSLTEI 263


>gi|300431295|gb|ADK12612.1| RNA polymerase alpha subunit [Aciachne acicularis]
          Length = 339

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 91/319 (28%), Positives = 154/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDITLPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY         N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIELQIKRDRGYQTELR---NNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      K
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKK 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D+ R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLRRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDGKQIWDTLEKHLPIDL 332


>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 =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 77/321 (23%), Positives = 155/321 (48%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 DNTQHIATLTEPIDLCIGLKIERNRGYSLKISNNLEDRSY---PIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQV 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|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 =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 89/318 (27%), Positives = 159/318 (50%), Gaps = 21/318 (6%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  E    +  I  PL  G A+T+G  +RR L+  ++G  IT  + + + HE S++ G+
Sbjct: 24  KVESERLFYSRFILSPLKVGQANTIGLVMRRALLGEIKGTCITCAKFENITHEYSTMDGI 83

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + DI++N K I LK      ++  I   GP  VTA DI+    +EV++P   I  + 
Sbjct: 84  QESVHDILINSKEIVLKSKSSEAQKAFISIVGPRRVTAQDIELPTSVEVIDPMQHIATIT 143

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR-EGQVLD 197
               + +EL + K  GY        ++   G  T+DA+++PI+ V+Y++       + + 
Sbjct: 144 KKVKLNIELKIEKDSGYRRQNIVEYKD---GNFTVDAVFTPIRSVNYSIHCFESHDKSIM 200

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP--- 254
            + L   I ++GSIT E+++  ASR   +    F+  E+ K++ K +   +S   +P   
Sbjct: 201 KEMLLYEIWSNGSITPEEAIYEASRSSINLFLPFLQAEKEKEDFKGEDIHESNALHPSVS 260

Query: 255 -----------ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                           +E+LELS ++ N L+  N+  + DL+  ++ D+++M NFG+KS+
Sbjct: 261 IVVDQMAKKVTFQHIFIEQLELSPKAYNFLKKINVHTISDLLDYSQDDLMKMKNFGKKSV 320

Query: 304 VEIKGVLGTMGLFLGMNL 321
            +I   L  +    GM L
Sbjct: 321 EQI---LEALQKRFGMRL 335


>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 =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 83/318 (26%), Positives = 153/318 (48%), Gaps = 23/318 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RRVL+  + G  IT V+ + + HE S+I G+
Sbjct: 21  RIDSKRLYYGRFILSPLMKGQADTIGIAMRRVLLGEIEGTCITRVKSEKIPHEYSTIIGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I L+ +    +  +I  +GPG VTA DI     +E+++    I N+ 
Sbjct: 81  EESVHEILMNLKEIVLRSNLYGTRDASICFKGPGYVTAQDIILPPSVEIVDNTQHIANVT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + +  GY        +N   G   IDA + P++ V++++ S   G     
Sbjct: 141 EPVNLCIELKIERNRGYRIKT---LKNFQDGSYPIDATFMPVRNVNHSIHSYVNGNE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL- 257
           + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + +  +LP       
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEDNFNLENNQHKVTLPLFTFHDI 256

Query: 258 -----------------KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                              +++LEL  R  NCL+  NI  + +L+  ++ D+L++ +F  
Sbjct: 257 LAKEKLRKKKKEIALKSIFIDQLELPPRIYNCLKRSNIHTLLELLNNSQEDLLKIEHFRV 316

Query: 301 KSLVEIKGVLGTMGLFLG 318
           + +  I   L  +     
Sbjct: 317 EDVKYILDFL-EIEKHFA 333


>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 =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 113/331 (34%), Positives = 182/331 (54%), Gaps = 27/331 (8%)

Query: 9   LIKPNNIEYIVLGQEEE-NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           LIKP     +   +++E N +     PL +G+A TLGNALRRVL+SS+   AIT ++I G
Sbjct: 4   LIKPEKFRIVQKEEQDEYNYSKYELFPLEKGYAITLGNALRRVLLSSIPSLAITGLRIPG 63

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSG-------DSHKRVTIFKRGP--GVVTAGD 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 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|228017032|gb|ACP51855.1| RNA polymerase alpha subunit [Pinus canariensis]
          Length = 335

 Score =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 82/317 (25%), Positives = 153/317 (48%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I  +      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVFRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H   N   G+  IDA++ P++ V+Y++ S   G  +  + L
Sbjct: 144 TSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDVNYSIHSYGSGNEI-REVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL----------- 250
            + I T+G +T  +++  ASR L D    F++ EE   +   +    ++           
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTD 259

Query: 251 -----PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                      L  +++LEL  ++ N LR  NI  + DL+  +  D++R+ +FG++S+ +
Sbjct: 260 TGETKEKIAFQLIFIDQLELPPKTYNSLRRANIHTLSDLLNYSREDLMRIEHFGKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL  +     ++ P
Sbjct: 320 VLEVLQKL---FAIDPP 333


>gi|71056806|emb|CAH58958.1| DNA-directed RNA polymerase alpha chain [Enterococcus italicus DSM
           15952]
          Length = 234

 Score =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 105/232 (45%), Positives = 150/232 (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 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           TDGSI   D+++LA++I+ + L +F+N  +  K  +  +  +       L  
Sbjct: 182 TDGSIEPLDAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEM 233


>gi|12265|emb|CAA27214.1| unnamed protein product [Spinacia oleracea]
          Length = 335

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 86/329 (26%), Positives = 162/329 (49%), Gaps = 28/329 (8%)

Query: 15  IEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           +++  +    +    +    I  PL +G A T+G A+RR L+  + G  IT  + + + H
Sbjct: 13  LQWKCVESRTDSKCLHYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSEKIPH 72

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S+I G+ E + +I++N+K I L+ +       +I  RGP  VTA DI     +E+++ 
Sbjct: 73  EYSTILGIQESVHEILMNLKEIVLRSNLYGACEASICVRGPRGVTAQDIILPPYVEIVDN 132

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
              I +L     + + L + +  GY         N   G   IDAL+ P++ V++++ S 
Sbjct: 133 TQHIASLTEPIDLCIGLQLERNRGY---HIKAPNNFQDGSFPIDALFMPVRNVNHSIHSY 189

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
             G     + L + I T+GS+T ++++  ASR L D L  F++ EE    ++++ +  SL
Sbjct: 190 GNGNE-KQEILFLEIWTNGSLTPKEALYEASRNLIDLLIPFLHAEE-NVNLEDNQHKVSL 247

Query: 251 PFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           P      +                 +++LEL  R  NCL+  NI  + DL+  ++ D+++
Sbjct: 248 PLFTFHNRLAEIRKNKKKIALKFIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDLIK 307

Query: 295 MANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           M +F    + ++K + GT+     ++L +
Sbjct: 308 MKHF---RIEDVKQIFGTLEKHFVIDLKN 333


>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 =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 92/321 (28%), Positives = 158/321 (49%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFWNVPHEYSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESIQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTTQPIANLR 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY        +N   G   IDA++ P++ V+Y++ S   G    +
Sbjct: 141 EPVDFCIELQIKRDRGYHTELR---KNSQDGSYPIDAVFMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    FI+ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFIHTEEEGTSFEENKNRLTPPLLTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 FTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRINSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + + K +  T+   L ++LP 
Sbjct: 314 MEDGKLIWDTLEKHLPIDLPK 334


>gi|283945397|dbj|BAI66454.1| RNA polymerase alpha subunit [Lactobacillus similis]
          Length = 248

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 110/252 (43%), Positives = 162/252 (64%), Gaps = 7/252 (2%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
            KPN    I   +E ++    + EPL RG+  TLGN+LRR+L+SSL GAA+T++QIDGVL
Sbjct: 1   EKPN----IHKIEESDDYGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTSIQIDGVL 56

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           HE S+++GV ED+T IILN K I+LK+ G  D  + + I  +GP  VTAGDI   +D+ V
Sbjct: 57  HEFSTVEGVVEDVTQIILNTKKISLKLEGPDDEIESMEIDVKGPAQVTAGDITADSDVTV 116

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR-TENDPIGLITIDALYSPIKKVSYT 186
           LNPD  I  +   A   M +T +KG GYV A  ++  E+ PIG++ ID++Y+PI++V+Y 
Sbjct: 117 LNPDLYIATVAEGATFHMRMTANKGRGYVSADRNKAKEDMPIGVLPIDSIYTPIERVNYQ 176

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           VE+ R GQ  DYDKL++ + TD SIT  +S++LA++IL + L MF++  +  K  +  + 
Sbjct: 177 VENTRVGQRDDYDKLTLDVWTDSSITPSESISLAAKILTEHLAMFVDLTDEAKNAEIMVE 236

Query: 247 VKSLPFNPALLK 258
            +       L  
Sbjct: 237 KEETHKEKMLEM 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 =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 87/344 (25%), Positives = 156/344 (45%), Gaps = 30/344 (8%)

Query: 2   IQKNWQELIKPNNIEYI----VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRG 57
           ++KN     K   I++      +  +  +    +  P  RG A T+G A+RR L+  + G
Sbjct: 1   MRKNEMSTSK-QAIQWKCLESKIESKRLHYGRFLVSPFKRGQASTVGIAMRRALLQEIEG 59

Query: 58  AAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG-DSHKRVTIFKRGPGVVTA 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 GDLSLPPGVEAIDNSQYIATITQPISLTIELEIEKDCGYRIENLAK---SGKGQFPIDAV 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 YMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            + DL+  +  D+ ++ NFGRKS+ ++   L          LPD
Sbjct: 296 TIADLLNYSREDLSKLKNFGRKSVDQVSEALWDR---FAKELPD 336


>gi|307697293|gb|ADN86101.1| RNA polymerase alpha subunit [Chasmanthium latifolium]
          Length = 339

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 91/320 (28%), Positives = 157/320 (49%), Gaps = 23/320 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGNVPHEYSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESIQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLR 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIELQIKRDRGYHTELR---KNSQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGSSFEENKNRFTPPLLTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 FTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNLP 322
           + + K +  T+   L ++LP
Sbjct: 314 MEDGKLIWDTLEKHLPIDLP 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 =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 92/321 (28%), Positives = 158/321 (49%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGNVPHEYSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESIQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTTQPIANLR 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY        +N   G   IDA++ P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIELQIKRDRGYHTELR---KNSQDGSYPIDAVFMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    FI+ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFIHTEEEGTSFEENKNRLTPPLLTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 FTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRSNIHTLLDLLSKTEEDLMRINSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + + K +  T+   L ++LP 
Sbjct: 314 MEDGKLIWDTLEKHLPIDLPK 334


>gi|71056824|emb|CAH58967.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
          Length = 235

 Score =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 107/234 (45%), Positives = 154/234 (65%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S++KGV ED+  
Sbjct: 1   KDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTVKGVREDVAQ 60

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILNIKG+ LKM GD  K + I   GP  VTAGDI   +D+E+LN D  ICN+   A   
Sbjct: 61  IILNIKGLALKMYGDEEKTLEIDITGPATVTAGDIIVDSDVEILNKDMYICNVSEGASFH 120

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
             LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G+  D+DKL+M 
Sbjct: 121 ARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGRRDDFDKLTME 180

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           I TDGSI   ++++LA++I+ + L +F+N  +  K  +  +  +       L  
Sbjct: 181 IWTDGSIEPLEAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEM 234


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 82/317 (25%), Positives = 152/317 (47%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-REVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL----------- 250
            + I T+G +T  +++  ASR L D    F++ EE   +   +    ++           
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHLLTD 259

Query: 251 -----PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                      L  +++LEL  +  N LR  NI  + DL+  +  D++R+ +FG++S+ +
Sbjct: 260 TGETKEKIAFQLIFIDQLELPPKIYNSLRRANIHTLLDLLNYSREDLMRIKHFGKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL  +     ++ P
Sbjct: 320 VLEVLQKL---FAIDPP 333


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 74/321 (23%), Positives = 153/321 (47%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    +         I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWRCVESRRDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENI 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 + +  GY     +  E+       IDA++ P++  ++++ 
Sbjct: 131 DNTQHIATVTESIDLCIGLKIERNRGYSLKMSNNFEDRSY---PIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGNGNG-KQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETFHLENNQHQV 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|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 =  261 bits (667), Expect = 1e-67,   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  HEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQ--TVNDIEVLNPDHVIC 135
            ED+  I+LN+K I  +           +  +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 +  +  L     
Sbjct: 194 LVDKALHLEIWTNGSISPQEALHQAARILTHWFNPLQTLEWKTSHTKNEQTMAQL----- 248

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
               +EEL+LSVR+ NCL+   I  + DL+Q T+ ++L + NFG+KS+ E+   L   
Sbjct: 249 SNMLIEELDLSVRAYNCLKRAQIHSVADLMQYTQEELLALKNFGQKSVEEVNKALEQK 306


>gi|283945395|dbj|BAI66453.1| RNA polymerase alpha subunit [Lactobacillus odoratitofui]
          Length = 247

 Score =  261 bits (667), 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: 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|161513430|emb|CAP16858.1| DNA-directed RNA polymerase subunit alpha [Pediococcus parvulus]
          Length = 224

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 101/224 (45%), Positives = 152/224 (67%), 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 SKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
             G GYV A     R ++ 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|290489698|gb|ADD31233.1| RNA polymerase alpha subunit protein [Quercus nigra]
          Length = 331

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 83/319 (26%), Positives = 154/319 (48%), Gaps = 24/319 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    +         I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRGDSNSLYYGRFILSPLMKGQADTIGIAVRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +       +I  +GP  VTA DI     ++++
Sbjct: 71  PHEYSTIIGIQESVHEILMNLKEIVLRSNLYGISGASICVKGPRYVTAQDIILPPSVQIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I NL     + +EL + +  GY       T N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIANLTEPINLYIELQIERDRGYRIKT---TNNSQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE K  ++ +    
Sbjct: 188 SYVNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIELFIPFLHAEEEKLHLENNQQKV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LPF     +                 +++ EL  R  NCL+G NI  + DL+  ++ D 
Sbjct: 247 TLPFFTCHDRLAKLNKNSTEIALKSIFIDQSELPPRIYNCLKGSNIHTLLDLLNNSQTDF 306

Query: 293 LRMANFGRKSLVEIKGVLG 311
           ++M +F R+ +  I  +L 
Sbjct: 307 MKMKHFRREDIKHILDILE 325


>gi|157493287|gb|ABV58009.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 259

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 114/267 (42%), Positives = 178/267 (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++  + +   +++   +  P    LL+ V++LEL+VRS
Sbjct: 176 TLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRS 232

Query: 270 TNCLRGENIVYMGDLIQRTEADMLRMA 296
            NCL+ E I Y+GDL+QRTE ++L+  
Sbjct: 233 ANCLKAEAIHYIGDLVQRTEVELLKTP 259


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 91/319 (28%), Positives = 158/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + GA IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGACITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>gi|190411121|gb|ACE78315.1| RpoA [Vibrio parahaemolyticus]
          Length = 263

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 116/266 (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++  + +   +++   +  P    LL+ V +LEL+VRS NCL+ E I Y
Sbjct: 181 ATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVNDLELTVRSANCLKAEAIHY 237

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEI 306
           +GDL+QRTE ++L+  N G+KSL EI
Sbjct: 238 IGDLVQRTEVELLKTPNLGKKSLTEI 263


>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 (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 80/330 (24%), Positives = 156/330 (47%), Gaps = 29/330 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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   +         G   IDA+  P++  ++++ 
Sbjct: 131 DTTQHIASLTEPIDLCIELQIQRDRGY---RMKTPNKYQNGSYPIDAVSMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE    ++++ N  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEEGIRLEDNPNRF 246

Query: 249 SLPFNPALL------------------KKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
           ++PF                         +++ EL  R+ N L+  NI  + DL+  ++ 
Sbjct: 247 NIPFFTFHDGLANTNIRKKKKGIALKCIFIDQSELPPRTYNYLKRSNINTLLDLLSNSQE 306

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           D L++ +F    + ++K +L  +     ++
Sbjct: 307 DFLKIEHF---RIEDVKQILDILQKHFTID 333


>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 =  261 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPPFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>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 =  261 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 83/319 (26%), Positives = 154/319 (48%), Gaps = 24/319 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    +         I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESRGDSNSLYYGRFILSPLMKGQADTIGIAVRRALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +       +I  +GP  VTA DI     ++++
Sbjct: 71  PHEYSTIIGIQESVHEILMNLKEIVLRSNLYGISGASICVKGPRYVTAQDIILPPSVQIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I NL     + +EL + +  GY       T N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIANLTEPINLYIELQIERDRGYRIKT---TNNSQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE K  ++ +    
Sbjct: 188 SYVNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIELFIPFLHAEEEKLHLENNQQKV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LPF     +                 +++ EL  R  NCL+G NI  + DL+  ++ D 
Sbjct: 247 TLPFFTCHDRLAKLNKNSTEITLKSIFIDQSELPPRIYNCLKGSNIHTLLDLLNNSQTDF 306

Query: 293 LRMANFGRKSLVEIKGVLG 311
           ++M +F R+ +  I  +L 
Sbjct: 307 MKMKHFRREDIKHILDILE 325


>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 =  261 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 79/309 (25%), Positives = 147/309 (47%), Gaps = 20/309 (6%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFEKIPHEYSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I L+ +       +I  +GPG VTA DI     +E+++    I +L 
Sbjct: 81  QESVHEILMNLKEIVLRSNLYGTCNASICVKGPGCVTAQDILLPPSVEIIDNTQHIASLM 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + + L + +  GY         N   G   IDA++ P++  ++++ S    Q    
Sbjct: 141 EPIHLCIGLQIERNRGY---HIKSPNNFQDGSYPIDAVFMPVRNANHSIHSYGN-QNEKQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE    +  +    + P      K
Sbjct: 197 EILFLEIWTNGSLTPKEALHEASRNLIDLFLPFLHAEEENLHLGNNKYNVTFPLFTFHKK 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R  N L+G  I  + DL+ +++ D+++M +F  + 
Sbjct: 257 LAKLRKPKNEIALKSIFIDQLELPPRIYNSLKGSKIHTLSDLLNKSQEDLMKMKHFRIED 316

Query: 303 LVEIKGVLG 311
           + +I  +L 
Sbjct: 317 VKQILDILE 325


>gi|313292082|gb|ADR51230.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
          Length = 241

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 109/236 (46%), Positives = 156/236 (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 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +M I TDGSI   ++++LA++I+ + L +F+N  +  K  +  +  +       L 
Sbjct: 186 TMEIWTDGSIEPLEAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLE 241


>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 = 153/321 (47%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 DNTQHIATLTEPINLCIGLKIERNRGYSLKMSNNFEDRSY---PIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQV 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|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 =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       +  PL +G A T+G A+RR L+  + G  IT    + VLHE S+I G+
Sbjct: 21  RVDSKRLYYGRFVLSPLMKGQADTIGIAIRRALLGEIEGTCITRATSENVLHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  RGP  +TA DI +   +E+++    I NL 
Sbjct: 81  EESVHEILLNLKDIVLRSNLYGVRNASICVRGPKYITAQDIISPPSVEIVDTTQHIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + +  GY   +   T +   G   ID +  P++  ++++ S   G     
Sbjct: 141 EPINLCIELQIKRDRGY---RMKSTNDSHDGSYPIDIVSMPVRNANHSIHSYGNGNE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D L  F++ EE     KE+ N  +LP      K
Sbjct: 197 EILFIEIWTNGSLTPKEALYEASRNLIDLLIPFLHAEEEDMNFKENENRWNLPPFSFQDK 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++ ELS R+ NCL+  NI  + DL+  ++ D+++M  F    
Sbjct: 257 FTNFKKNKKGIPLTCIFIDQSELSSRTYNCLKRSNIHTLLDLLSHSQEDLMKMEYFRT-- 314

Query: 303 LVEIKGVLGTMGLFLGMNL 321
             ++K +L T+     +NL
Sbjct: 315 -EDVKQILSTVQKHFAINL 332


>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 =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 79/309 (25%), Positives = 148/309 (47%), Gaps = 20/309 (6%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RR L+  + G  IT  + + + HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKFEKIPHEYSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I L+ +       +I  +GPG VTA DI     +E+++    I +L 
Sbjct: 81  QESVHEILMNLKEIVLRSNLYGTCNASICVKGPGCVTAQDILLPPSVEIIDNTQHIASLM 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + + L + +  GY         N   G   IDA++ P++  ++++ S    Q    
Sbjct: 141 EPIHLCIGLQIERNRGY---HIKSPNNFQDGSYPIDAVFMPVRNANHSIHSYGN-QNEKQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE    + ++    + P      K
Sbjct: 197 EILFLEIWTNGSLTPKEALHEASRNLIDLFLPFLHAEEENLHLGKNKYNVTFPLFTFHKK 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R  N L+G  I  + DL+ +++ D+++M +F  + 
Sbjct: 257 LAKLRKPKNEIALKSIFIDQLELPPRIYNSLKGSKIHTLSDLLNKSQEDLMKMKHFRIED 316

Query: 303 LVEIKGVLG 311
           + +I  +L 
Sbjct: 317 VKQILDILE 325


>gi|84874044|gb|ABC68045.1| RNA polymerase subunit [Oryza granulata]
          Length = 317

 Score =  261 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 94/321 (29%), Positives = 158/321 (49%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+    G  IT  +   V HE S+I G+
Sbjct: 1   RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGETEGTCITHAKFGSVPHEYSTIAGI 60

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 61  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDMAQPIANLT 120

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                R+EL + +  GY        +N   G   IDA+  P++ V+Y++ S   G    Y
Sbjct: 121 EPMDFRIELRIKRDRGYHTEVR---KNAQDGSYPIDAVSMPVRNVNYSIFSCGNGNA-KY 176

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 177 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTRFQENKNRFTSPLLSFQKR 236

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 237 LTNLKKNKKRIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 293

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + + K +  T+  +L M+LP 
Sbjct: 294 MQDGKQIWDTLEKYLPMDLPK 314


>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 (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 75/321 (23%), Positives = 153/321 (47%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 DNTQHIATLTEPIDLCIGLKIERNRGYSLKMSNNFEDRSY---PIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQV 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|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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 79/316 (25%), Positives = 158/316 (50%), Gaps = 25/316 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RR+L+  + G  IT  + + + HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLMKGQADTIGIAMRRILLGEIEGTCITRAKSEKIPHEYSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I L+ +    +  +I  +GPG VTA DI     +E+++    I NL 
Sbjct: 81  QESIHEILMNLKEIVLRSNLYGTRDASICFKGPGSVTAQDIILPPSVEIVDNTQHIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + MEL + +  GY     +  +++      IDA++ P++  ++++ S   G     
Sbjct: 141 EPINLCMELKLERNRGYRIKTLNNIQDESYT---IDAVFMPVRNANHSIHSYGNGNE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE K  ++ +    +LP      +
Sbjct: 197 EILFLEIWTNGSLTPKEALFEASRNLIDLFIPFLHAEEDKLNLENNQQKVTLPLFTFHDR 256

Query: 259 ------------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                              +++LEL  R  NCL+  NI  + +L+ +++ +++++ +F  
Sbjct: 257 FVKDKLRKNKKEIALKSIFIDQLELPPRIYNCLKKSNIHTLLELLNKSQEELMKIEHF-- 314

Query: 301 KSLVEIKGVLGTMGLF 316
             + ++K +L  + + 
Sbjct: 315 -RVEDVKNILNLLQIE 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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 75/321 (23%), Positives = 153/321 (47%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 DNTQHIATLTEPIDLCIGLKIERNRGYSLKMSNNFEDRSY---PIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQV 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|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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F    
Sbjct: 257 LTNPKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 77/321 (23%), Positives = 156/321 (48%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +  + +         I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESKRDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENI 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 DNTQHIATLTETIDLCIELKIERNRGYSLKMSNNFEDRSY---PIDAVFMPVENANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQV 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|99024202|dbj|BAE94567.1| plastid DNA-dependent RNA polymerase subunit alpha [Takakia
           lepidozioides]
          Length = 341

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 79/322 (24%), Positives = 149/322 (46%), Gaps = 24/322 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +     + +     P   G A T+G A+RR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSARLHYSRFAISPFRSGQASTVGIAMRRALLGEVEGTCITCAEFKRVTHEYSTILGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + D+++N+  I L+      ++  I   GP  VTA DI     +++++    I  + 
Sbjct: 81  QESVHDVLINLGEIVLRSDSYETQKAFISILGPKKVTAQDIILPPSVKIIDTTQYIATVX 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + K  GY      ++ +   G   +DA++ PI+ V+Y+V S   G     
Sbjct: 141 KAIHLDIELKIEKDFGYRIEDPIKSAD---GNFPVDAVFMPIRNVNYSVHSFENGNET-Q 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP----------KKEVKEDINVK 248
           + L + I T+GS+T ++++  ASR L +    F++ E+           +  +    +  
Sbjct: 197 EILFLEIWTNGSVTPKEALYEASRSLINLFIPFLHAEKKEFIYGLKNTYESNMSYFSSPS 256

Query: 249 SLPFNPALLK-------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
                  + K        +++LEL  R+ NC +  N   + DL+  ++ D++++ NFG+K
Sbjct: 257 LSADIDEMTKGVTFKHIFIDQLELPARAYNCXKRVNXHTISDLLNYSQDDLMKIKNFGKK 316

Query: 302 SLVEIKGVLGTMGLFLGMNLPD 323
           S   ++ VL  +     +N P 
Sbjct: 317 S---VEQVLEALQKRFSINXPK 335


>gi|51859683|gb|AAU11121.1| RNA polymerase alpha subunit [Psathyrostachys fragilis subsp.
           secaliformis]
          Length = 339

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 89/319 (27%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIXIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPPFTFKKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 89/319 (27%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 89/319 (27%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---H 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>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 = 155/321 (48%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 DNTQHIATLTEPIDLCIELKIERNRGYSLKMSNNFEDRSY---PIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQV 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|228016017|gb|ACP50856.1| RNA polymerase alpha subunit [Pinus resinosa]
          Length = 335

 Score =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 81/317 (25%), Positives = 152/317 (47%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I  +      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVFRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-REVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL----------- 250
            + I T+G +T  +++  ASR L D    F++ EE   +   +    ++           
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTD 259

Query: 251 -----PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                      L  +++LEL  ++ N LR  NI  + DL+  +  D++R+ +FG++S+ +
Sbjct: 260 TGETKEKIAFQLIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMRIEHFGKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL  +     ++ P
Sbjct: 320 VLEVLQKL---FAIDPP 333


>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 =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 86/318 (27%), Positives = 151/318 (47%), Gaps = 24/318 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V ++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVTLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TFDIRLRIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-REVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP------- 254
            + I T+G +T  +++  ASR L D    F++ EE   +   +    S            
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDFFIPFLHGEEQNIDGINNRKGSSNMPPFPLLHVLT 259

Query: 255 ----------ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
                          +++LEL  R+ NCLR  NI  + DL+  +  D++RM +FG++S+ 
Sbjct: 260 DTGETKEKIAFQHIFIDQLELPPRTYNCLRRANIHTLLDLLNYSREDLMRMEHFGKESVE 319

Query: 305 EIKGVLGTMGLFLGMNLP 322
           ++  VL        ++LP
Sbjct: 320 QVLEVLR---KRFAIDLP 334


>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 =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 77/323 (23%), Positives = 156/323 (48%), Gaps = 26/323 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +  + +         I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWKCVESKRDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            H+ S+I G+ E + +I++N+  I L+ +    +   I  +GPG +TA DI     +E++
Sbjct: 71  PHDYSNIAGIQESVHEILMNLNEIVLRSNLYGTRNALICVQGPGYITARDIILPPAVEII 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L     + +EL + +  GY     +  E+       IDA++ P++  ++++ 
Sbjct: 131 DNTQHIATLTEPIDLCIELKIERNRGYSLKMSNNFEDRSY---PIDAVFMPVENANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHQASRNLINLFIPFLHVEEETFYLENNQHQV 246

Query: 249 SLPFNPALLK------------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
           +LPF P   +                   +++LEL  R  NCL+  NI  + DL+  ++ 
Sbjct: 247 TLPFFPFHNRLVNLRKKKKTKELAFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQE 306

Query: 291 DMLRMANFGRKSLVEIKGVLGTM 313
           D++++ +F  + + +I  +L   
Sbjct: 307 DLIKIEHFHVEDVKKILDILEKK 329


>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 =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 82/318 (25%), Positives = 153/318 (48%), Gaps = 23/318 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-REVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL----------- 250
            + I T+G +T  +++  ASR L D    F++ EE   +   +    ++           
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHLLTD 259

Query: 251 -----PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                      L  +++LEL  ++ N LR  NI  + DL+  +  D++R+ +FG++S+ +
Sbjct: 260 TGETKEKIAFQLIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMRIEHFGKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLPD 323
           +  VL  +     ++ P 
Sbjct: 320 VLEVLQKL---FAIDPPK 334


>gi|22657232|gb|AAM97419.1| RNA polymerase alpha subunit [Aegilops tauschii]
          Length = 339

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F    
Sbjct: 257 LTNLKKNKKGIPLNSIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 89/319 (27%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ ++Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNLNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 89/319 (27%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGXVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>gi|165910445|gb|ABY73977.1| RNA polymerase alpha subunit [Cuscuta europaea]
          Length = 329

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 80/316 (25%), Positives = 147/316 (46%), Gaps = 25/316 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RR L+  + G  IT V+ +   HE S+I G+
Sbjct: 21  RIDSKRLFYGRFILSPLIKGQADTIGIAMRRALLGEIEGTCITRVKSEKASHEYSTIGGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I L+ +       +I  +GP  VTA DI     +++++    I  L 
Sbjct: 81  QESVHEILMNLKEIVLRSNLYESCDASICIKGPRHVTAQDIILPPHVQIVDNTQHIAWLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 + L + +  GY        ++   G   IDAL+ P++  ++++ S    +    
Sbjct: 141 EPIDFFIGLKIERNRGYFNKVDLHFDD---GSYPIDALFMPVQNANHSIHSYGNEK---Q 194

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ++RIL D    F   EE    + +  +   LP      K
Sbjct: 195 EILFLEIWTNGSLTPKEALHESARILIDFFIPFFQMEEENLYLADAKHTIPLPPLIFYNK 254

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LE   +  NCL+  NI  + DL  + + D+L++ +F    
Sbjct: 255 VTTLIKKKKKLSLKLIFIDQLEFPPKIYNCLKKSNIFTLFDLFNQKQEDLLKIEHF---Q 311

Query: 303 LVEIKGVLGTMGLFLG 318
           L +IK +LG +G +  
Sbjct: 312 LEDIKHILGILGKYFA 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 =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F    
Sbjct: 257 LTNLKKNKKGIPLNSIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>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 =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 75/316 (23%), Positives = 152/316 (48%), Gaps = 23/316 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G  +RR+L+  + G  IT  + + + HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLMKGQADTIGITMRRILLGEIEGTCITRAKSEKIPHEYSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I L+ +    +  +I  +GPG VTA DI     +E+++    I NL 
Sbjct: 81  QESIHEILMNLKQIVLRSNLYGTRDASICFKGPGYVTARDIILPPSVEIVDNTQHIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + +  GY        ++     I +D ++ P+   +Y++ S         
Sbjct: 141 EPINLCIELQIERARGYRKKTIDNIQD-GSYTIDVDPVFMPVIHANYSIHSYLNANE-KQ 198

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  A+R L D    F++ EE     + + +  +LP      +
Sbjct: 199 EILFLEIWTNGSLTPKEALYEAARNLIDLFIPFLHAEEENFHFENNQHKVTLPLFAFHDR 258

Query: 259 ------------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                              +++LEL  R  NCL+  +I  +  L+ +++ D++++ +F  
Sbjct: 259 LVKDKLRKNKKQIELKSVFIDQLELPPRIYNCLKKSDIHTLYQLLNKSQEDLMKIEDF-- 316

Query: 301 KSLVEIKGVLGTMGLF 316
            S+ ++K +L  + + 
Sbjct: 317 -SVEDVKNILNILQID 331


>gi|161511773|emb|CAP16897.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 249

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 107/248 (43%), Positives = 154/248 (62%), Gaps = 2/248 (0%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            I    E +N    + EPL RG+  TLGN+LRR+L+SSL GAAIT+VQID VLHE S+I+
Sbjct: 2   KIHKIDENDNYGRFVIEPLERGYGTTLGNSLRRILLSSLPGAAITSVQIDSVLHEFSTIE 61

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  IC 
Sbjct: 62  GVVEDVTQIILNLKKVSLKIESDEDKTLEINVAGPANVTAGDIMGDGDVVILNPELPICT 121

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESAREGQ 194
           +         LT   G GY  A  ++    + PIG++ ID++Y+PI++V+Y VE+ R GQ
Sbjct: 122 VAEGTTFHAVLTADTGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTRVGQ 181

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
             DYDKL++ I TDGSIT  ++ +L+++IL + L +F+N  +  KE +  +  +      
Sbjct: 182 RDDYDKLTLDIWTDGSITPSEATSLSAKILTEHLAIFVNLNDQAKETEIMVEKEETHKEK 241

Query: 255 ALLKKVEE 262
            L   +EE
Sbjct: 242 MLEMTIEE 249


>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 =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 116/269 (43%), Positives = 177/269 (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++  + +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            ++L+  N G+KSL EIK VL + GL LG
Sbjct: 238 VELLKTPNLGKKSLTEIKDVLASRGLSLG 266


>gi|300431272|gb|ADK12601.1| RNA polymerase alpha subunit [Piptochaetium lasianthum]
          Length = 339

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 88/319 (27%), Positives = 152/319 (47%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDRAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY         N   G   IDA+  P++ V+Y       G    +
Sbjct: 141 EPIDFCIELQIKRDRGYQTELR---NNYQDGSYPIDAVSMPVRNVNYXXXXXGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + + T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      K
Sbjct: 197 EILFLELWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKK 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++++ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMKIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDGKQIWDTLEKHLPIDL 332


>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 =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFKKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>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 =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 82/317 (25%), Positives = 153/317 (48%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-REVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL----------- 250
            + I T+G +T  +++  ASR L D    F++ EE   +   +    ++           
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHLLTD 259

Query: 251 -----PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                      L  +++LEL  ++ N LR  NI  + DL+  +  D++R+ +FG++S+ +
Sbjct: 260 TGETKEKIAFQLIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMRIEHFGKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL  +     ++ P
Sbjct: 320 VLEVLQKL---FAIDPP 333


>gi|58758777|gb|AAW81780.1| RNA polymerase alpha subunit [Dendroligotrichum dendroides]
          Length = 340

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 85/321 (26%), Positives = 153/321 (47%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  E  + +     P   G A+T+G A+RR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  KVDSERLHYSRFAISPFRCGQANTVGIAMRRALLGEIEGTCITCARSKKVTHEYSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E   DI++N+K I LK +    ++  +   GP  +TA DI     +++++    I  + 
Sbjct: 81  QESAHDILINLKEIVLKSNSYETQKAFLSILGPKKITAQDIILPPSVKIIDTTQYIATIT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + K  GY      ++ +   G  +IDA++ PI+  +Y+V S      +  
Sbjct: 141 KPIHLDIELEIDKDCGYRIXDSVKSID---GYFSIDAIFMPIRNANYSVHSFENNNKI-Q 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GSIT ++++  ASR L D    F++ E+ +         KS   +     
Sbjct: 197 EILFIEIWTNGSITPKEALYEASRSLIDLFIPFLHTEKKETINGLKTEYKSNDMSDFSSF 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  N+  + DL+   + D +++ NFG+KS
Sbjct: 257 SPLADKLTKEIKFKHIFIDQLELPARAYNCLKRVNVHPISDLLNYXQDDFMKIKNFGKKS 316

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
              ++ VL  +     +NLP+
Sbjct: 317 ---VEQVLEALQKQFSINLPE 334


>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 =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 89/319 (27%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGXVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTXQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNYIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>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 =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVXMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>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 =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 81/317 (25%), Positives = 152/317 (47%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLHKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I  +      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVFRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-REVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL----------- 250
            + I T+G +T  +++  ASR L D    F++ EE   +   +    ++           
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTD 259

Query: 251 -----PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                      L  +++LEL  ++ N LR  NI  + DL+  +  D++R+ +FG++S+ +
Sbjct: 260 TGETKEKIAFQLIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMRIEHFGKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL  +     ++ P
Sbjct: 320 VLEVLQKL---FAIDPP 333


>gi|119662335|emb|CAJ33156.1| RNA polymerase alpha subunit [Lactobacillus paracasei subsp.
           paracasei]
          Length = 213

 Score =  259 bits (663), Expect = 4e-67,   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|73747868|gb|AAZ82835.1| RNA polymerase subunit a [Elymus dentatus]
          Length = 339

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICIKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>gi|313292084|gb|ADR51231.1| DNA-directed RNA polymerase alpha chain [Enterococcus malodoratus]
          Length = 241

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 107/240 (44%), Positives = 155/240 (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 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL+M I TDGSI  +++++LA++IL + L +F+N  +  K  +  +  +       L 
Sbjct: 182 FDKLTMEIWTDGSIIAQEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLE 241


>gi|313292086|gb|ADR51232.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
          Length = 241

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 107/240 (44%), Positives = 155/240 (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 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +DKL+M I TDGSI  +++++LA++IL + L +F+N  +  K  +  +  +       L 
Sbjct: 182 FDKLTMEIWTDGSIIAQEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLE 241


>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 =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 89/319 (27%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFWSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---H 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>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 =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 102/251 (40%), Positives = 161/251 (64%), Gaps = 2/251 (0%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  ++ + L  E+      + EPL RG+  T+GNALRR+L+SSL G A+ A++IDG
Sbjct: 3   EIEKP-KVDIVEL-SEDYRYGKFVIEPLERGYGITIGNALRRILLSSLPGVAVNAIKIDG 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 KSLPFNPALLK 258
           +       L  
Sbjct: 241 EEDQKEKVLEM 251


>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 =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFWSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>gi|66876504|gb|AAY58043.1| RpoA [Cuscuta europaea]
          Length = 329

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 80/316 (25%), Positives = 147/316 (46%), Gaps = 25/316 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RR L+  + G  IT V+ +   HE S+I G+
Sbjct: 21  RIDSKRLFYGRFILSPLIKGQADTIGIAMRRALLGEIEGTCITRVKSEKASHEYSTIGGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I L+ +       +I  +GP  VTA DI     +++++    I  L 
Sbjct: 81  QESVHEILMNLKEIVLRSNLYESCDASICIKGPRHVTAQDIILPPHVQIVDNTQHIAWLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 + L + +  GY        ++   G   IDAL+ P++  ++++ S    +    
Sbjct: 141 EPIDFFIGLKIERNRGYFNKVDLHFDD---GSYPIDALFMPVQNANHSIHSYGNEK---Q 194

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ++RIL D    F   EE    + +  +   LP      K
Sbjct: 195 EILFLEIWTNGSLTPKEALHESARILIDFFIPFFQMEEENLYLADAKHTIXLPPLIFYNK 254

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LE   +  NCL+  NI  + DL  + + D+L++ +F    
Sbjct: 255 VTTLIKKKKKLSLKLIFIDQLEFPPKIYNCLKKSNIFTLFDLFNQKQEDLLKIEHF---Q 311

Query: 303 LVEIKGVLGTMGLFLG 318
           L +IK +LG +G +  
Sbjct: 312 LEDIKHILGILGKYFA 327


>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 = 85/317 (26%), Positives = 153/317 (48%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H   N   G+  IDA++ P+   +Y++ S    +    + L
Sbjct: 144 TSDIRLRIEKNRGYII---HSPNNYQDGIFPIDAVFMPVPDANYSIHSYG-SRNEIREVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP------- 254
            + I T+G +T  +++  ASR L D L  F++ EE   +   +    ++P  P       
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLLIPFLHGEEQNIDGMNNRKGSNMPPFPLSHVLTD 259

Query: 255 ---------ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                         +++LEL  R+ NCLR  NI  + DL+  +  D++R+ +FG++S+ +
Sbjct: 260 TRETKEKIAFQHIFIDQLELPPRTYNCLRRANIHTLLDLLNYSREDLMRIEHFGKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL        ++ P
Sbjct: 320 VLEVL---QKRFAIDPP 333


>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 =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDRAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>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 =  259 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 75/321 (23%), Positives = 153/321 (47%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 DNTQHIATLMEPIDLCIGLKIERNRGYSLKMSNNFEDRSY---PIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQV 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|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 =  259 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 105/329 (31%), Positives = 170/329 (51%), Gaps = 11/329 (3%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
            P  I    +    EN   + A P   G+A TL + LRR+L SS  G A T V+I+GV H
Sbjct: 1   MPTEI---SVESISENVARITAYPFETGYAVTLAHPLRRLLYSSTVGFAATGVKIEGVSH 57

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           E  S++G+ ED+   I+N+K I  K+  +S  + V    +GP  + AGD+++   ++++N
Sbjct: 58  EFDSMRGMLEDVAQFIINLKNIRFKLKNESEREVVEYSFKGPKEIKAGDLKSDV-VDIVN 116

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  +  ++ DA ++  + + KG GYVP++  R  +   G I +DA ++P+KK  Y + +
Sbjct: 117 PDAYLATINEDAELKFSVIIQKGIGYVPSEEIRG-DTEEGYIALDAFFTPVKKAVYELVN 175

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                  DY+K+  T+ TDG +   ++   A   +  Q+ +F            +     
Sbjct: 176 VLVEDNPDYEKIIFTVTTDGQVGAIEAFKHAIEAMYQQMSVFKGVLNIDISAGLNAQTSG 235

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              +  LL+ VEEL LS RS NCL    I ++G+L    E ++  + N G+KSL EIK V
Sbjct: 236 SE-HAKLLQSVEELNLSARSFNCLDKAEIRFIGELALMDENELKELKNLGKKSLEEIKAV 294

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYED 338
           +  +G  +G +L        E+L KK  D
Sbjct: 295 MQEIGYPVGGDLGG----GKEQLKKKIAD 319


>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 =  259 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 89/321 (27%), Positives = 156/321 (48%), Gaps = 25/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  I   +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCIARAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTSQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIELQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ------------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                              +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F  
Sbjct: 257 LTNLNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF-- 314

Query: 301 KSLVEIKGVLGTMGLFLGMNL 321
             + + K +  T+  +L ++L
Sbjct: 315 -HMEDGKQIWDTLEKYLPIDL 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 =  259 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 89/319 (27%), Positives = 156/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E ++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVETVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>gi|228017468|gb|ACP52284.1| RNA polymerase alpha subunit [Pinus merkusii]
          Length = 335

 Score =  259 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 81/317 (25%), Positives = 151/317 (47%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I  +      +  +I+  GP  VTA DI     ++ ++    I  L    
Sbjct: 84  VHDILMNLKEIVFRSDSYGIREASIYIVGPRNVTAQDIILPPSVKTIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-REVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL----------- 250
            + I T+G +T  +++  ASR L D    F++ EE   +   +    ++           
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTD 259

Query: 251 -----PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                      L  +++LEL  ++ N LR  NI  + DL+  +  D++R+ +FG++S+ +
Sbjct: 260 TGETKEKIAFQLIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMRIEHFGKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL  +     ++ P
Sbjct: 320 VLEVLQKL---FAIDPP 333


>gi|22657314|gb|AAM97460.1| RNA polymerase alpha subunit [Heteranthelium piliferum]
          Length = 339

 Score =  259 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFWSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPKYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTEL---IKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>gi|51859695|gb|AAU11127.1| RNA polymerase alpha subunit [Psathyrostachys caduca]
          Length = 339

 Score =  259 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 89/319 (27%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKNLPIDL 332


>gi|119663518|emb|CAK22330.1| RNA polymerase alpha subunit [Lactobacillus algidus]
          Length = 230

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 102/229 (44%), Positives = 153/229 (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 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           SIT  ++++L+++IL + L +F++  +  K  +  +  +       L  
Sbjct: 181 SITPSEAISLSAKILTEHLTLFVDLTDEAKNAEIMVEKEETHKEKMLEM 229


>gi|71056828|emb|CAH58969.1| DNA-directed RNA polymerase alpha chain [Enterococcus sulfureus]
          Length = 234

 Score =  258 bits (660), Expect = 7e-67,   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|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 =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 104/313 (33%), Positives = 173/313 (55%), Gaps = 4/313 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
            P+ + +             IA+P  RG+A T+GNALRRVL+SS+ G AIT ++IDGV +
Sbjct: 12  HPHRVTFEK-KDLTPTYGKFIAQPFERGYAVTVGNALRRVLLSSIPGYAITTIKIDGVSN 70

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDS-HKRVTIFKRGPGVVTAGDIQTVN-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 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
             R GQ +DY KL++ I+T G+I  + +++ A++IL+D L  F++ EE   + ++     
Sbjct: 191 PIRVGQRIDYGKLTLEIETKGNIAPDKALSQAAKILRDNLKHFMDPEEANGDDEKIEETP 250

Query: 249 SLPF-NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                +    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|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 =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 78/328 (23%), Positives = 150/328 (45%), Gaps = 27/328 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    +         I  PL +G   T+G A+R+ L+  + G  IT  + + +
Sbjct: 11  RTLKWKCVESRADSKRLYYGRFILSPLMKGQGDTIGIAMRKALLGEIEGTCITRAKSEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I++N+K I L+ +    +  +I  +GPG VTA DI     +E++
Sbjct: 71  PHEYSTIVGIQESVHEILMNLKEIVLRSNLYGTRDASICVKGPGCVTAQDIILPPSVEIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I NL     + +EL + +  GY         N       +DA++ P++ V++++ 
Sbjct: 131 DNTQHIANLMEPINLCIELKIERNRGY---HIQTPNNFQDASYPMDAIFMPVRNVNHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L D    F++ EE K+      N K
Sbjct: 188 SYVNGNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEEKENFHLKNNKK 246

Query: 249 SLPFNPALLKK------------------VEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
            +        +                  +++ EL  R  NCL+  NI  + DL+  +  
Sbjct: 247 KVTLPLFTFHEKLAKLRKKKKEIALKYIFIDQSELPPRIYNCLKRCNIHTLFDLLNNSPD 306

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           +++++ +F  + +  I  +L  M     
Sbjct: 307 ELMKIKHFRIEDVKHILDIL-EMEKNFA 333


>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 =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 115/269 (42%), 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++  + +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            ++L+  N G+KSL EIK VL + GL L 
Sbjct: 238 VELLKTPNLGKKSLTEIKDVLASRGLSLA 266


>gi|169788447|emb|CAP58145.1| RNA polymerase [Lactobacillus rossiae]
          Length = 235

 Score =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 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 PA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A     R ++ 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|71056812|emb|CAH58961.1| DNA-directed RNA polymerase alpha chain [Enterococcus hirae]
          Length = 237

 Score =  258 bits (660), Expect = 8e-67,   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|311990458|gb|ADQ26359.1| RNA polymerase alpha subunit [Lactobacillus fermentum]
          Length = 242

 Score =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 108/242 (44%), Positives = 161/242 (66%), 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 KGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           KG GY  A     R 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|161513428|emb|CAP16857.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           argentinicus]
          Length = 225

 Score =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 103/225 (45%), Positives = 149/225 (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 VSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
             KG GY  A     R  + 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|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 =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 84/321 (26%), Positives = 153/321 (47%), Gaps = 25/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            + +   +    I  PL +G A+T+G ALRR L+S + G  IT+V+I   +HE SS+ GV
Sbjct: 21  KIEKSTLHYGRFIISPLWKGQANTIGLALRRTLLSEVEGTCITSVKIKNAIHEYSSLSGV 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + DI++N+K I L  S        +   GP  V A D+   + I+++NPD  I  ++
Sbjct: 81  QESVHDILINLKKIILSSSFSGIFEGFLSVVGPKTVLASDLNLPSFIKIVNPDQYIATVN 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +++ + KG GY        +    G   +D ++ PI+ V+Y++ S  + +    
Sbjct: 141 KPINFNLQIYIQKGKGYSLKNPISIK---QGFFLVDPVFIPIRSVNYSIHSFEDEKAT-K 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK------------------KE 240
           + L + + T+GSI  ++++  AS  L +     ++ E  +                  + 
Sbjct: 197 EFLIVEVWTNGSIEPKEAIKEASYNLVNLFTPLVSQEYQQLKNQLFKEDEKNKELNFIET 256

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
               I+     +N      +++LELS R+ N L+  NI  + DL++ +  D+L++ NFG+
Sbjct: 257 NSNAISDNENSYNLYNQIFLDQLELSSRAYNSLKKNNINTISDLLKYSYEDLLKIKNFGK 316

Query: 301 KSLVEIKGVLGTMGLFLGMNL 321
           KS  ++   L        + L
Sbjct: 317 KSADQVIEQLK---KRFKIQL 334


>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 =  258 bits (659), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 84/321 (26%), Positives = 152/321 (47%), Gaps = 24/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +  +       P  +G A+T+G A+RR L+  + G AIT  +   V+HE S+I G+
Sbjct: 21  KIESKRLHYGRFAISPFRKGQANTVGIAIRRSLLGEIEGTAITYAKSKNVIHEYSTIIGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + DI++N K I L+      ++  I   GP  +TA DI     ++ ++    I  + 
Sbjct: 81  EESINDILINFKEIVLRSDSYETQKAYISITGPKDITAEDILLPPSVQAIDDSQHIATIT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D  + +E+ + K  GY       ++    G   IDA++ PI+K +Y+V S    +    
Sbjct: 141 KDITLDIEIEIQKDRGYRI---QDSKESQAGEFFIDAVFMPIRKANYSVHSFGNNKKF-Q 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV----------- 247
           + L + I TDGS+T ++++  ASR L D    F++ EE +     D              
Sbjct: 197 EILFIEIWTDGSLTPKEALYEASRNLIDLFLPFLHTEEEEIISDRDEKSESNGNILLSNS 256

Query: 248 ------KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
                 +           +++LEL  R+ NCL+  ++  + DL++ ++ D+ ++ NFG+K
Sbjct: 257 ISTDIDRMAKEVAFKHIFIDQLELPARAYNCLKKVDVHTISDLLKYSQDDLRKIKNFGKK 316

Query: 302 SLVEIKGVLGTMGLFLGMNLP 322
           S+ ++   L        +NLP
Sbjct: 317 SVDQVLEALQER---FAINLP 334


>gi|71056884|emb|CAH58998.1| DNA-directed RNA polymerase alpha chain [Enterococcus pseudoavium]
          Length = 236

 Score =  258 bits (659), Expect = 9e-67,   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|71056888|emb|CAH59000.1| DNA-directed RNA polymerase alpha chain [Enterococcus mundtii]
          Length = 238

 Score =  258 bits (659), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 107/238 (44%), Positives = 156/238 (65%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T 
Sbjct: 1   KDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQ 60

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILNIKG+ LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A   
Sbjct: 61  IILNIKGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFH 120

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
             LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M 
Sbjct: 121 ARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTME 180

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
           I TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  +       L   +EE
Sbjct: 181 IWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEMTIEE 238


>gi|311990563|gb|ADQ26408.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           helveticus]
          Length = 243

 Score =  258 bits (659), Expect = 9e-67,   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|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 =  258 bits (659), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 89/321 (27%), Positives = 157/321 (48%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGNVPHEYSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESIQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTTQPIANLR 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +   Y        +N   G   IDA++ P++ V+Y++ S   G    +
Sbjct: 141 EPVDFCIELQIKRDRAYHTELR---KNSQDGSYPIDAVFMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHTEEEGTSFEENKNRLTPPLLTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++++ +F    
Sbjct: 257 FTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMQINSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + + K +  T+   L ++LP 
Sbjct: 314 MEDGKLIWDTLEKHLPIDLPK 334


>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 =  258 bits (659), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 156/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLX 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+  F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDXF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>gi|228016331|gb|ACP51165.1| RNA polymerase alpha subunit [Pinus taeda]
          Length = 335

 Score =  258 bits (659), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 82/317 (25%), Positives = 151/317 (47%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+         +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKXIVLRSDSYGIXEASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-REVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL----------- 250
            + I T+G +T  +++  ASR L D    F++ EE   +   +    ++           
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHLLTD 259

Query: 251 -----PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                      L  +++LEL  +  N LR  NI  + DL+  +  D++R+ +FG++S+ +
Sbjct: 260 TGETKEKIAFQLIFIDQLELPPKIYNSLRRANIHTLLDLLNYSREDLMRIEHFGKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL  +     ++ P
Sbjct: 320 VLEVLQKL---FAIDPP 333


>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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 95/344 (27%), Positives = 161/344 (46%), Gaps = 29/344 (8%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLR 56
           MIQ+   E+     + +  +    E+           P  +G A+T+G A+RR L++ + 
Sbjct: 1   MIQEEI-EISTRTLLRWRCIESRTESKRLLYGRFAISPFRKGQANTVGIAMRRALLNEIE 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 RDIQGSSLIHVIDNTQYVATITGKISLDIELDIEKDRGY---RMENSRKYREGFFPIDAV 176

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF-- 234
           + PI+  +Y+V S    +    + L + I T+GS+T E ++  ASR L D     +N   
Sbjct: 177 FMPIRNANYSVHSFGSREKT-KEILLLEIWTNGSLTPEKALYEASRNLIDLFIPSMNPGG 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|311990464|gb|ADQ26362.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 243

 Score =  258 bits (659), Expect = 1e-66,   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|73747870|gb|AAZ82836.1| RNA polymerase subunit a [Elymus mutabilis]
          Length = 339

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 158/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICIKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G +  +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNG-IEKH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>gi|1771084|emb|CAB01369.1| alpha subunit of RNA polymerase [Hordeum vulgare subsp. spontaneum]
          Length = 339

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 89/319 (27%), Positives = 155/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E ++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVETVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+  F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDXF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>gi|156598719|gb|ABU85614.1| RNA polymerase alpha subunit [Scaevola aemula]
          Length = 332

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 84/333 (25%), Positives = 161/333 (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 SIHSSGNGK---QEILFLEIWTNGSLTPKEALHEACRNLIDLFIPFLHKEEGNLENNQDR 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 MKKAHL---HIEDVKRILGLLEKNCVIDLPKNP 331


>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 =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 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 PA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A     R ++ 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|228017724|gb|ACP52536.1| RNA polymerase alpha subunit [Pinus pinaster]
          Length = 335

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 81/317 (25%), Positives = 151/317 (47%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I  +      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVFRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-REVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL----------- 250
            + I T+G +T  +++  ASR L D    F++ EE   +   +    ++           
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTD 259

Query: 251 -----PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                      L  +++LEL  ++ N LR  NI  + DL+  +  D++R+  FG++S+ +
Sbjct: 260 TGETKEKIAFQLIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMRIERFGKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL  +     ++ P
Sbjct: 320 VLEVLQKL---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 (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 77/319 (24%), Positives = 149/319 (46%), Gaps = 25/319 (7%)

Query: 16  EYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           ++  +    +         I  PL +G A T+G A+RR L+  L G  IT  + + + HE
Sbjct: 16  QWKCVESRTDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGELEGTCITRAKSEKIPHE 75

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            S+I G+ E + +I++N+K I L+ +    +   I  +GPG VTA DI     +E+++  
Sbjct: 76  YSTIVGIQESVHEILMNLKEIVLRGNLYGTRNAFICAKGPGYVTAQDIILPPSVEIVDNT 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             + +L     + + L + +  GY        +N   G   IDA++ P++  ++++    
Sbjct: 136 QHVASLTEPIDLCIGLQIERNRGYGIKT---PKNFHDGSYPIDAVFMPVRNANHSIHCYG 192

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  + L + I T+GS+T ++++  ASR L D    F++ +E    ++ + +  +L 
Sbjct: 193 NDNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIHFLHAKEENLHLENNQHDVTLH 251

Query: 252 FNPALL-----------------KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           F                        +++ EL  R  NCL+  NI  + DL+  +  D+++
Sbjct: 252 FFFPFHYRLVKLTKKKKEIALKYIFIDQSELPPRIYNCLKKSNIHTLLDLLNNSREDLMK 311

Query: 295 MANFGRKSLVEIKGVLGTM 313
           M +F  + + +I G+L   
Sbjct: 312 MEHFRIEDVKQILGILEKK 330


>gi|71056876|emb|CAH58993.1| DNA-directed RNA polymerase alpha chain [Enterococcus canis]
          Length = 235

 Score =  257 bits (657), Expect = 1e-66,   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|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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 80/317 (25%), Positives = 150/317 (47%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIKES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H + N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIRLQIEKNRGYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHSYGNGNEI-QEVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL----------- 250
            + I T+G +T  +++  ASR L D    F++ EE   +        ++           
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNKKKGSNMLPFPLSHVLTD 259

Query: 251 -----PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                         +++LEL  ++ N LR  NI  + DL+  +  D++R+ + G++S+ +
Sbjct: 260 TGETKEKIAFQHIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMRIEHLGKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL        ++ P
Sbjct: 320 VLEVLR---KRFAIDPP 333


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 156/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA   P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAESMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>gi|51859679|gb|AAU11119.1| RNA polymerase alpha subunit [Psathyrostachys lanuginosa]
          Length = 339

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 89/319 (27%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGXVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDMAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLRIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>gi|300431286|gb|ADK12608.1| RNA polymerase alpha subunit [Nassella novarae]
          Length = 339

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 155/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I+ +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY         N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIELQIKRDRGYQTELR---NNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      K
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGXXFEENKNRFTPPLFTFQKK 256

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++ + +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTILDLLSKTEEDLMXIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDGKQIWDTLEKHLPIDL 332


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 76/324 (23%), Positives = 155/324 (47%), Gaps = 27/324 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 SYGTGNE-KQEILFLEIWTNGNLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHKV 246

Query: 249 SLPFNPALLKK----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP  P   +                 +++LEL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPLFPFHNRLVKLRKKKKELVFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLF 316
           +++ +F    + ++K +L  +   
Sbjct: 307 IKIEHF---HIEDVKKILEILEKN 327


>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 =  257 bits (657), Expect = 2e-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|51859681|gb|AAU11120.1| RNA polymerase alpha subunit [Psathyrostachys lanuginosa]
          Length = 339

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 88/319 (27%), Positives = 154/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTXQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+   ++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMXVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLLTFQKR 256

Query: 259 KVE----------------ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                              +LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIXQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 110/329 (33%), Positives = 176/329 (53%), Gaps = 10/329 (3%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
            P  IE + +    EN   +IA P   G+A TL + LRR+L +S  G A TAV+IDGV H
Sbjct: 10  MPTEIEVVNV---SENVAKIIAYPFETGYAVTLAHPLRRLLYTSTVGFAPTAVKIDGVAH 66

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           E  S++G+ ED+T  I+N+K +  K+  D   + +    +GP  +T  D+     +E++N
Sbjct: 67  EFDSMRGMLEDVTLFIINLKNLRFKLKNDSKREVIEYSFKGPKEITGIDLNNDI-VEIVN 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 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                  DY+K+ +T+ TDG ++  ++   +   +  Q+ +F N       +    +  S
Sbjct: 185 VLVEDNPDYEKIVLTVTTDGQVSPIEAFKHSIEAMYKQMSIFNNVLNIDVNMALTSSQNS 244

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              +  LL+ VE L LS RS NCL   +I Y+G+L    E+++  + N G+KSL EIK V
Sbjct: 245 NEHSK-LLESVENLNLSARSFNCLDKADIRYIGELALMEESELKDLKNLGKKSLDEIKAV 303

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYED 338
           +  +G   G    +   +S E L KK  +
Sbjct: 304 MAEIGYPFG---ENTLGDSKEALRKKISE 329


>gi|71056800|emb|CAH58955.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
          Length = 233

 Score =  257 bits (657), Expect = 2e-66,   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|300431268|gb|ADK12599.1| RNA polymerase alpha subunit [Poa holciformis]
          Length = 341

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 91/321 (28%), Positives = 154/321 (47%), Gaps = 25/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIGGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     IE+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSIEIVDTSQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIELQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLLTFQKR 256

Query: 259 ------------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                              +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F  
Sbjct: 257 LTNLNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSFRM 316

Query: 301 KSLVEIKGVLGTMGLFLGMNL 321
           +   +I   L      L ++L
Sbjct: 317 EDRKQIWDTLENY---LPIDL 334


>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 =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 76/320 (23%), Positives = 155/320 (48%), Gaps = 24/320 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 SYGTGNE-NQEILFLEIWTNGNLTPKEALHEASRNLINLFIPFLHVEEETFYLENNEDKV 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|313292080|gb|ADR51229.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 241

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 108/236 (45%), Positives = 155/236 (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 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +M I TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  +       L 
Sbjct: 186 TMEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLE 241


>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 =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 78/320 (24%), Positives = 154/320 (48%), Gaps = 22/320 (6%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  E  +       PL  G A+T+G A+RR L+  + G  IT V+ + V HE S+I G+
Sbjct: 21  KIDSERLHYGRFAISPLRPGQANTVGIAIRRALLGEIEGTCITYVKFEKVTHEYSTIMGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + DI++N+K I LK +    +  +I   GP  VTA DI   + +EV++    I  + 
Sbjct: 81  QESVHDILINLKEIVLKSNSYKTQEASISILGPKRVTAEDIVLPSSVEVIDATQHIATIT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + K  GY      + E+   G   ++A ++PI+  +Y+V S    +    
Sbjct: 141 KAVYFNIKLGIRKDRGYRIENPVKYED---GNFAVNAAFTPIRNANYSVHSFENEKE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL- 257
           + L + + T+GS+T ++++  AS+ L +     ++ ++ ++  K +   +          
Sbjct: 197 EILFIEVWTNGSLTPKEALREASQSLINLFIPLLHEKKERENRKLENKDEYNVLRSCFSL 256

Query: 258 --------------KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                           +++LEL  R+ N L+  ++  + DL+  ++ D++++ NFG+KS+
Sbjct: 257 TNIGEVRKEISFKHIFIDQLELPARAYNGLKKVDVHTISDLLNYSQEDLMKIKNFGKKSI 316

Query: 304 VEIKGVLGTMGLFLGMNLPD 323
            ++   L        ++LP 
Sbjct: 317 QQVVEAL---QKHFAIHLPK 333


>gi|289524822|emb|CBJ94467.1| alpha subunit of RNA polymerase [Vibrio sp. Cmf 5.9]
          Length = 265

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 115/268 (42%), Positives = 176/268 (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++  + +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            ++L+  N G+KSL EIK VL + GL L
Sbjct: 238 VELLKTPNLGKKSLTEIKDVLASRGLSL 265


>gi|197131698|gb|ACH47367.1| RNA polymerase alpha subunit [Sarcocaulon vanderietiae]
          Length = 333

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 81/323 (25%), Positives = 156/323 (48%), Gaps = 14/323 (4%)

Query: 1   MIQKNWQ-ELIKPN-NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGA 58
           MI++  +     P           +       I  PL +G A  +G A+RR L+  + G 
Sbjct: 1   MIREKVRVSTQTPRWKCVESRADDKRLYYGRFILSPLKKGQADIIGIAMRRALLVEIEGT 60

Query: 59  AITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGD 118
            IT  +   + HE +++ G+ E + +I++N+K I L+ +    +  +I  RGP  VTA D
Sbjct: 61  CITHAKFAKIPHEYTTMAGIKESIYEILMNLKEIVLRSNLYGTRDASICVRGPRDVTAQD 120

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE---NDPIGLITIDA 175
           I       +++    I  L       +EL + +G GY       T    +D    I IDA
Sbjct: 121 IILPPSTAIVDNTQHIVTLTEPIDFCVELKIERGRGYSIKIPMPTNPFHHDSGYPIPIDA 180

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           ++ P++ V++++ S + G     + L + I T+GS+T ++++  ASR L +    F++ E
Sbjct: 181 VFMPVRNVNHSIYSYKRGSR---EILFLEIWTNGSLTPKEALREASRKLINLFIPFLHAE 237

Query: 236 EPK---KEVKEDINVKSLPFNPALLKKV---EELELSVRSTNCLRGENIVYMGDLIQRTE 289
           E      E  ++ + + LP +   LK++   + +EL  R  NCL+   I  + DL+ ++ 
Sbjct: 238 EENFYLLENNQNQHTEELPIDSCGLKEIYIDQLVELPPRFYNCLKRSGIHTVMDLLDKSR 297

Query: 290 ADMLRMANFGRKSLVEIKGVLGT 312
            D++++ +F ++ +  +  +L  
Sbjct: 298 DDLMKITHFRQEDVERVMNILNN 320


>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 =  257 bits (656), Expect = 2e-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|71056886|emb|CAH58999.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           saccharolyticus]
          Length = 231

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 105/230 (45%), Positives = 150/230 (65%)

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 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           GSI   D+++LA++I+ + L +F+N  +  K  +  +  +       L  
Sbjct: 181 GSIEPLDAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEM 230


>gi|71056912|emb|CAH59015.1| DNA-directed RNA polymerase alpha chain [Enterococcus raffinosus]
          Length = 235

 Score =  257 bits (656), Expect = 2e-66,   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|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 =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 114/259 (44%), Positives = 172/259 (66%), 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-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV-DAVVR 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++  + +   +++   +  P    LL+ V+
Sbjct: 181 VIDMETNGTIEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVD 237

Query: 262 ELELSVRSTNCLRGENIVY 280
           +LEL+VRS NCL+ E I Y
Sbjct: 238 DLELTVRSANCLKAEAIHY 256


>gi|71056880|emb|CAH58996.1| DNA-directed RNA polymerase alpha chain [Enterococcus avium]
          Length = 235

 Score =  257 bits (656), Expect = 2e-66,   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|165910443|gb|ABY73976.1| RNA polymerase alpha subunit [Cuscuta epilinum]
          Length = 330

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 81/319 (25%), Positives = 148/319 (46%), Gaps = 25/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +  +    I  PL +G A T+G A+RR L+  + G  IT V+ +   HE S+I G+
Sbjct: 21  RIDSKRLSYGRFILSPLIKGQADTIGIAMRRALLGEIEGTCITRVKSEKASHEYSTIGGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I L+ +       +I  +GP  VTA DI     +++++    I  L 
Sbjct: 81  QESVHEILMNLKEIVLRSNLYGTCDASICIKGPRHVTAQDIILPPHVQIVDNTQHIAWLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 + L + +  GY        ++   G+  IDAL+ P++  ++++ S    +    
Sbjct: 141 EPIDFFIGLKIERNRGYFNKVDLHFDD---GIYPIDALFMPVQNANHSIHSYGNEK---Q 194

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  A+RIL D    F + EE    + +  +   L       K
Sbjct: 195 EILFLEIWTNGSLTPKEALHEAARILIDFFIPFFHMEEENLYLADAEHTIPLSSLIFYNK 254

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LE   +  NCL   NI  + DL    E D+L++ +F    
Sbjct: 255 VTKLIKKKKKLSLKLIFIDQLEFPPKIYNCLTKSNIFTLFDLFNHKEEDLLKIEHF---Q 311

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           L +IK +LG +  +  + L
Sbjct: 312 LEDIKKILGILAKYFALYL 330


>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 (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 75/321 (23%), Positives = 153/321 (47%), Gaps = 24/321 (7%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    +         I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 11  RTLQWRCVESRRDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGEIEGTCITRAKSENI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            H+ S+I G+ E + +I++N+  I L+ +    +   I  +GPG +TA DI     +E++
Sbjct: 71  PHDYSNIVGIQESVHEILMNLNEIVLRSNLYGARNAIICVQGPGYITARDIILPPSVEII 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L     + + L + +  GY     +  E+       IDA++ P++  ++++ 
Sbjct: 131 DNTQHIATLTESIDLCIGLKIERNRGYSLKILNTFEDRSY---PIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGNGNG-KQEILFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHHV 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|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 =  256 bits (655), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 88/319 (27%), Positives = 156/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  I   +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCIARAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFKKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>gi|71056890|emb|CAH59001.1| DNA-directed RNA polymerase alpha chain [Enterococcus cecorum]
          Length = 235

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 105/232 (45%), Positives = 152/232 (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 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           TDGSI   D+++LA++IL + L +F+N  +  +  +  +  +       L  
Sbjct: 183 TDGSIEPLDAMSLAAKILTEHLDIFVNLTDEARHAEIMVEKEETQKEKMLEM 234


>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 =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 77/317 (24%), Positives = 153/317 (48%), Gaps = 23/317 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RR+L+  + G  IT  + + + HE S+I G+
Sbjct: 21  RIDSKRLYYGRFILSPLMKGQADTIGIAMRRILLGEMEGTCITRAKSEKISHEYSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I LK +    +  +I  +GPG VTA +I     + +++    I N+ 
Sbjct: 81  QEPVHEILMNLKEIVLKSNLYGIRDASICFKGPGYVTAQNIILPPSVVIVDNTQHIANVT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + + L + +  GY     +  +N   G   IDA++ P++  ++++ S   G     
Sbjct: 141 EPIQLCIGLQIERDRGYRI---NTLKNFQDGSYNIDAIFMPVRNANHSIHSYVNGNE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE K   + + +  +LP       
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEEKLNFENNEHKVTLPLFTCHDL 256

Query: 259 K------------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                              +++LEL  +  NCL+  NI  + +L+ +++ D++++ +F  
Sbjct: 257 LAKTKLKKKKKEIAFKSIFIDQLELPPKIYNCLKKSNIHTLLELLTKSKEDLMKIEHFRV 316

Query: 301 KSLVEIKGVLGTMGLFL 317
           + +  I  +L  +    
Sbjct: 317 EDVKHILDIL-EIEKHF 332


>gi|71833746|emb|CAH59013.1| DNA-directed RNA polymerase alpha chain [Enterococcus canintestini]
          Length = 233

 Score =  256 bits (655), Expect = 3e-66,   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|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 =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 97/302 (32%), Positives = 153/302 (50%), Gaps = 6/302 (1%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
                    + + L  G   T GN LRRVL+  L G AIT V+I GV  E S I GV ED
Sbjct: 34  DSGAMYGQFLIDSLNSGQGITNGNLLRRVLLGDLEGIAITGVRIAGVKDEFSLIPGVRED 93

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + +I+LN+KG+ LK +  + +   +  +GP V+TA  IQ   +IE +NP+H I  +    
Sbjct: 94  ILEILLNLKGVILKSNIVTRQFGRLRIQGPAVITASSIQLPPEIETINPNHYIATISTSD 153

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
           +V +E  +  G  Y  A    ++      I  DA++ P++KV + VE+  +      ++L
Sbjct: 154 IVEIEFKIESGRQYRLANELFSDKFE-DFIETDAIFMPVQKVDFKVENVYDNSNNIKERL 212

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED--INVKSLPFNPALLKK 259
            + + T+GSI  +D++  AS  +          +      KE+     +  P +P +   
Sbjct: 213 FLDVWTNGSIAPQDAIISASNSIIAFFQSISEQKVKNALEKENIIEKNQVKPIDPYIHIA 272

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +EEL+LSVR  NCL+   I  +GDL++ +   +L + NFGRKS  E+   L      LG+
Sbjct: 273 IEELQLSVRPYNCLKRARINTIGDLLEYSPEKLLELKNFGRKSADEVFATLKNK---LGI 329

Query: 320 NL 321
            L
Sbjct: 330 VL 331


>gi|228016715|gb|ACP51543.1| RNA polymerase alpha subunit [Pinus aristata]
          Length = 335

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 80/317 (25%), Positives = 151/317 (47%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H + N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIRLQIEKNRGYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-QEVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL----------- 250
            + I T+G +T  +++  ASR L D    F++ EE   +        ++           
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNKKKGSNMLPFPLSHVLTD 259

Query: 251 -----PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                         +++LEL  ++ N LR  NI  + DL+  +  D++R+ + G++S+ +
Sbjct: 260 TGETKEKIAFQHIFIDQLELPPQTYNSLRRANIHTLLDLLNYSREDLMRIEHLGKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL  +     ++ P
Sbjct: 320 VLEVLRKL---FAIDPP 333


>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 =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 157/319 (49%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFWSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPKYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTEL---IKNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTXNCLKRANIHTLLDLLSKTEEDLLRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>gi|76563869|gb|ABA46366.1| RNA polymerase alpha subunit [Photobacterium halotolerans]
          Length = 252

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 110/253 (43%), Positives = 168/253 (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++  + +   +++   +  P    LL+ V++LEL+
Sbjct: 183 TNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELT 239

Query: 267 VRSTNCLRGENIV 279
           VRS NCL+ E I 
Sbjct: 240 VRSANCLKAEAIH 252


>gi|119662309|emb|CAJ33142.1| RNA polymerase alpha subunit [Lactobacillus gasseri]
          Length = 232

 Score =  256 bits (654), 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|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 =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 80/317 (25%), Positives = 150/317 (47%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H + N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIRLQIEKNRGYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-QEVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL----------- 250
            + I T+G +T  +++  ASR L D    F++ EE   +        ++           
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNKKKGSNMLPFPLSHVLTD 259

Query: 251 -----PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                         +++LEL  ++ N LR  NI  + DL+  +  D++R+ + G++S+ +
Sbjct: 260 TGETKEKIAFQHIFIDQLELPPQTYNSLRRANIHTLLDLLNYSREDLMRIEHLGKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL        ++ P
Sbjct: 320 VLEVLR---KRFAIDPP 333


>gi|71056840|emb|CAH58975.1| DNA-directed RNA polymerase alpha chain [Enterococcus hirae]
          Length = 235

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 105/234 (44%), Positives = 153/234 (65%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
           ++    I EPL RG+  TLGN+LRR+L+SSL GAAIT +QIDGVLHE S+IKGV ED+T 
Sbjct: 1   KDYGKFIVEPLERGYGTTLGNSLRRILLSSLPGAAITNIQIDGVLHEFSTIKGVREDVTQ 60

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVR 144
           IILNIKG+ LKM G   K + I   GP  VTAGDI   +++E+LN D  IC++   A   
Sbjct: 61  IILNIKGLALKMYGQEEKTLEIDITGPATVTAGDIIVDSEVEILNKDMYICSVSEGATFH 120

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
             LTV  G GYV A  ++ E+ PIG++ +D++Y+P+++V+Y VE+ R G   D+DKL+M 
Sbjct: 121 ARLTVKPGRGYVQADENKKEDMPIGVLPVDSIYTPVRRVNYQVENTRVGHREDFDKLTME 180

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           I TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  +       L  
Sbjct: 181 IWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEM 234


>gi|328813941|gb|AEB52086.1| DNA-directed RNA polymerase alpha chain [Lactobacillus brevis]
          Length = 248

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 109/248 (43%), Positives = 163/248 (65%), 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 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHR 162
            I  +GP  +TAGDI    D+++LNPD  I  +   A   M +T  KG GYV A     R
Sbjct: 61  EINVKGPAQITAGDIVAGADVDILNPDLYIATVADGATFHMRMTADKGRGYVSADENKTR 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 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|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 =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 80/311 (25%), Positives = 151/311 (48%), Gaps = 22/311 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RR+L+  + G  IT V+ + + HE S+I G+
Sbjct: 21  RIESKRLYYGRFILSPLMKGQADTIGIAIRRILLGEIEGTCITRVKSEKIPHEYSTIIGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I +N+K I LK +    +  +I  +GPG +TA DI     +E+++    I N+ 
Sbjct: 81  EESVHEIFMNLKEIVLKSNMYGTQDASISFKGPGYITAQDIILPPSVEIVDNRQHIANVT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY        +++      IDA + P++ V+Y++ S   G     
Sbjct: 141 EPVNFCIELKIERNRGYRIKTLKNFQDESYD---IDARFMPVRNVNYSIHSYVNGNE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL- 257
           + L + I T+GS+T ++++  AS+ L D    F++ EE    ++++ +  +LP       
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASQNLIDLFIPFLHAEEENFNLEKNKDKVTLPLFTFHDI 256

Query: 258 -----------------KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                              +++LEL  R  NCL+  NI  + +L+  ++ D+L++ +F  
Sbjct: 257 LVKDKLRKNKKEIALKSIFIDQLELPPRIYNCLKRSNIHTLLELLNNSQEDLLKIEHFRV 316

Query: 301 KSLVEIKGVLG 311
           +    I  +L 
Sbjct: 317 EDGKSILDILK 327


>gi|153012181|ref|YP_001381697.1| RNA polymerase alpha subunit [Medicago truncatula]
          Length = 333

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 80/316 (25%), Positives = 157/316 (49%), Gaps = 25/316 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RR+L+  + G  IT  + + + HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTIGIAMRRILLGEIEGTCITRAKSEKIPHEYSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I LK +    +  +I  +GPG VTA DI     +E+++    I NL 
Sbjct: 81  QESIHEILMNLKEIVLKSNLYGTRDASICFKGPGYVTAQDIILPPSVEIVDNTQHIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + +  GY     +  ++       IDA++ P++  ++++ S   G     
Sbjct: 141 EPINLCIELQIERKRGYRIKTLNNIQDGSYT---IDAVFMPVRNANHSIHSYVNGNE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     + + +  +LP      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEENLNFENNQHKVTLPLFTFHDR 256

Query: 259 ------------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                              +++LELS R  NCL+  NI  + +L+ +++ D++++ +F  
Sbjct: 257 LLKDKLRKNKKEIALKSIFIDQLELSPRIYNCLKKSNIHTLLELLNKSQEDLMKIEHF-- 314

Query: 301 KSLVEIKGVLGTMGLF 316
             + ++K +L  + + 
Sbjct: 315 -RVEDVKNILNILQIE 329


>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 =  256 bits (653), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 80/335 (23%), Positives = 153/335 (45%), Gaps = 31/335 (9%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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         N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDLCIGLQIERNRGY---LMKMPHNSQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G    ++ L + I T+GS+T ++++  A R L D    F++ EE    ++++ +  
Sbjct: 188 SYGSGNE-KHEILFLEIWTNGSLTPKEALHEACRNLIDLFIPFLHKEEETSPLEDNHHTV 246

Query: 249 SLPFNPALLK--------------------KVEELELSVRSTNCLRGENIVYMGDLIQRT 288
            L       K                     +++ EL  +  NCL+G N+  + DL+ ++
Sbjct: 247 PLSPLTFHDKADKLRKRKKEIKKKIALKSIFIDQSEL-PKVYNCLKGSNLYTLLDLLNKS 305

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           + D+++M +   + +  I  +L        + LP+
Sbjct: 306 QEDLMKMEHLRLEDVNHILVILAR--KHFAIYLPN 338


>gi|71056826|emb|CAH58968.1| DNA-directed RNA polymerase alpha chain [Tetragenococcus
           solitarius]
          Length = 226

 Score =  256 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 100/225 (44%), Positives = 148/225 (65%)

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 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           TDGSI   D+++L+++IL + L +F+N  +  K  +  +  +   
Sbjct: 182 TDGSIEPLDALSLSAKILTEHLEIFVNMTDEAKNTEIMVEKEETK 226


>gi|72534399|emb|CAH59014.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
          Length = 227

 Score =  256 bits (653), Expect = 5e-66,   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|300431314|gb|ADK12620.1| RNA polymerase alpha subunit [Pappostipa vaginata]
          Length = 319

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 90/319 (28%), Positives = 152/319 (47%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A  +G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 1   RVDSKRLYYGRFILSPLRKGQADPVGIALRRALLXEIEGTCITRAKFGSVPHEYSTIAGI 60

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+ +    I NL 
Sbjct: 61  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIXDTAQPIANLT 120

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + +  GY         N   G   IDA+  P++ V+Y++ S   G     
Sbjct: 121 EPIDLCIELQIKRDRGYQTELR---NNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNEKP- 176

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      K
Sbjct: 177 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKK 236

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 237 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 293

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +   +   L +NL
Sbjct: 294 MEDGKQIWDNLEKHLPINL 312


>gi|71056810|emb|CAH58960.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
          Length = 230

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 107/229 (46%), Positives = 152/229 (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 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           SI   ++++LA++I+ + L +F+N  +  K  +  +  +       L  
Sbjct: 181 SIEPLEAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEM 229


>gi|313292078|gb|ADR51228.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
          Length = 241

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 107/236 (45%), Positives = 155/236 (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 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +M I TDGSI   ++++L+++I+ + L +F+N  +  K  +  +  +       L 
Sbjct: 186 TMEIWTDGSIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLE 241


>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 =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 107/329 (32%), Positives = 169/329 (51%), Gaps = 9/329 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
            P  I    +    EN   +IA P   G+A TL + LRR+L +S  G A TAV+I+GV H
Sbjct: 1   MPTEI---KVENVSENVAKIIAYPFETGYAVTLAHPLRRLLYTSTVGFAPTAVKIEGVSH 57

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDS-HKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           E  S++G+ ED+   I+N+KG+  K+ GDS  + V    +GP  +   D+     +E++N
Sbjct: 58  EFDSMRGMLEDMAAFIINLKGLRFKIKGDSLREVVEYSFKGPKEIYGSDLNNDA-VEIVN 116

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P   +  ++ DA ++  L + KG GYVP++  R EN     I +DA ++P+ K  Y +E+
Sbjct: 117 PSAYLATINEDADLKFTLIIEKGIGYVPSEEIR-ENLDADFIALDAFFTPVTKAVYDIEN 175

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                  DY+K+  TI TDG I+  D+   A   +  QL +F               + +
Sbjct: 176 VFVEDNPDYEKVVFTITTDGQISAIDAFKNALEAMYQQLAVFKGIVNISAADTFGRAIPA 235

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L + V  L LS RS NCL   +I ++G+L    E+++  + N G+KSL EIK V
Sbjct: 236 NSEFAKLFESVSNLSLSARSFNCLDRADIRFIGELAIMEESELKDLKNLGKKSLEEIKAV 295

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYED 338
           +  +G  +G        E  E+L +K ++
Sbjct: 296 MEEIGYPIGNQ---ELGEKKEQLKRKLDE 321


>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 =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 105/329 (31%), Positives = 170/329 (51%), Gaps = 11/329 (3%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
            P  I    +    EN   + A P   G+A TL + LRR+L SS  G A T V+I+GV H
Sbjct: 1   MPTEI---SVESISENVARITAYPFETGYAVTLAHPLRRLLYSSTVGFAATGVKIEGVSH 57

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           E  S++G+ ED+   I+N+K I  K+  +S  + V    +GP  + AGD+++   ++++N
Sbjct: 58  EFDSMRGMLEDVAQFIINLKNIRFKLKNESEREVVEYSFKGPKEIKAGDLKSDV-VDIVN 116

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
            D  +  ++ DA ++  + + KG GYVP++  R +N   G I +DA ++P+KK  Y + +
Sbjct: 117 LDAYLATINEDAELKFSVIIQKGIGYVPSEEIR-DNTEEGYIALDAFFTPVKKAVYELVN 175

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                  DY+K+  T+ TDG +   ++   A   +  Q+ +F            +     
Sbjct: 176 VLVEDNPDYEKIIFTVTTDGQVGAIEAFKHAIEAMYQQMSVFKGVLNIDVSAGLNAQTSG 235

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              +  LL+ VEEL LS RS NCL    I ++G+L    E ++  + N G+KSL EIK V
Sbjct: 236 SE-HAKLLQSVEELNLSARSFNCLDKAEIRFIGELALMDENELKELKNLGKKSLDEIKAV 294

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYED 338
           +  +G  +G +L        E+L KK  D
Sbjct: 295 MQEIGYPVGGDLGG----GKEQLKKKIAD 319


>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 =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 104/229 (45%), Positives = 153/229 (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 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           SI  +++++LA++I+ + L +F+N  +  K  +  +  +       L  
Sbjct: 181 SIIPQEALSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEM 229


>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 =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 88/319 (27%), Positives = 155/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLIKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I L+ +    +  +I  +GP  +TA DI     +EV++    I NL 
Sbjct: 81  EESVQEILVNLKEIVLRSNLYGVRDASICVKGPRCITAQDIILPPSVEVVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIQLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTGFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ N L+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNRKKNKKGIPLNFIFIDQLELPSRTYNYLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDGKQIWDTLEKHLPVDL 332


>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 =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 81/311 (26%), Positives = 151/311 (48%), Gaps = 22/311 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RR+L+  + G  IT V+ + + HE S+I G+
Sbjct: 21  RIDSKRLYYGRFILSPLMKGQADTIGIAIRRILLGEIEGTCITCVKSEKIPHEYSTIIGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I +N+K I LK +    +  +I  +GPG +TA DI     +E+++    I N+ 
Sbjct: 81  EESVHEIFMNLKEIVLKSNMYGIQDASISFKGPGYITAQDIILPPSVEIVDNRQHIANVT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + +  GY        +N   G   IDA + P++ V+Y++ S   G     
Sbjct: 141 EPVHLCIELKIERNRGYRIKT---LKNFQDGSYDIDARFMPVRNVNYSIHSYVNGNE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL- 257
           + L + I T+GS+T ++++  AS+ L +    F++ EE    ++++ +  +LP       
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASQNLIELFIPFLHAEEDNFHLEKNQHKVTLPLFTFHDI 256

Query: 258 -----------------KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                              +++LEL  R  NCL+  NI  + +L+  ++ D+L+  +F  
Sbjct: 257 LVKDKLRKNQKEIALKSIFIDQLELPPRIYNCLKRSNIHTLLELLSNSQEDLLKFEHFHV 316

Query: 301 KSLVEIKGVLG 311
           +    I  +L 
Sbjct: 317 EDGKSILDILK 327


>gi|57115498|gb|AAW33058.1| RNA polymerase alpha subunit [Plantago rugelii]
          Length = 308

 Score =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 82/311 (26%), Positives = 151/311 (48%), Gaps = 25/311 (8%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
               +  +    +  PL +G A T+G A+RR L+  ++G  IT V+ + V HE S+I G+
Sbjct: 6   RTDSKRLHYGRFVLSPLMKGQADTIGIAMRRALLGEIQGTCITRVKSENVPHEYSTIAGI 65

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I L+ +       +I  RGPG VTA DI     +E+ +    I  L 
Sbjct: 66  QESVPEILMNLKEIVLRSNLYGTCGASICARGPGYVTAQDIILPPCVEIGDNTQHIARLT 125

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 + L + +  GY+    H  ++       IDA++ P++ V++++ S    +    
Sbjct: 126 EPISFCIGLEIERSRGYLIKSPHIFQDRSY---PIDAVFMPVRNVNHSIHSYGNEK---Q 179

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + +  S        K
Sbjct: 180 EILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHKEEENLPLENNQDTVSFSPFSFHEK 239

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++ ELS R  NCL+  NI  + D + +++ D+++M +F    
Sbjct: 240 LDQFRKNKKKKALQSIFIDQFELSPRVYNCLKKSNIYTLFDFLTKSQEDLMKMEHF---R 296

Query: 303 LVEIKGVLGTM 313
           L ++K  LG +
Sbjct: 297 LEDLKQTLGIL 307


>gi|71056802|emb|CAH58956.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 234

 Score =  255 bits (651), Expect = 7e-66,   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|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 =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 103/326 (31%), Positives = 167/326 (51%), Gaps = 7/326 (2%)

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  ISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNP 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 ELKPF-LVPVDALGLGARSFNSLDRAGIKYLGELVLMSENELKEIKNLGKKSLDEIQEVL 304

Query: 311 GTMGLFLGMNLPDWPPESIEELAKKY 336
              G   G +      E+   L KK 
Sbjct: 305 AEHG--FGPDYE-MDEETRAALTKKI 327


>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 =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 77/324 (23%), Positives = 153/324 (47%), Gaps = 27/324 (8%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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 DNTQHIATLTEPINLCIGLKIERNRGYSLKMSNNFEDRSY---PIDAVFMPVQNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G     + L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  
Sbjct: 188 SYGNGNE-KQEILFIEIWTNGSLTPKEALYEASRNLINLFIPFLHVEEETFYLENNQHQV 246

Query: 249 SLPFNPALLK----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +LP  P   K                 +++LEL  R  NCL+  NI  + DL+  ++ D+
Sbjct: 247 TLPVFPFHNKLVNLRQKKKELAFQYIFIDQLELPPRIYNCLKKSNIHTLLDLLNNSQEDL 306

Query: 293 LRMANFGRKSLVEIKGVLGTMGLF 316
           ++M +F    + ++K +L  +   
Sbjct: 307 IKMEHF---HIEDVKKLLDILEKK 327


>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 =  254 bits (650), Expect = 1e-65,   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|71056878|emb|CAH58995.1| DNA-directed RNA polymerase alpha chain [Enterococcus avium]
          Length = 231

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 105/230 (45%), Positives = 151/230 (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 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           GSI  +++++LA++IL + L +F+N  +  K  +  +  +       L  
Sbjct: 181 GSIIAQEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEM 230


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 99/327 (30%), Positives = 172/327 (52%), Gaps = 4/327 (1%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + +  +N+  + A P   G+A TL + LRR+L+ S  G A TA++I+G  HE
Sbjct: 8   PYIPTDISIQEIGKNKIKISAYPFESGYAITLAHPLRRLLLGSSVGFAPTALKIEGAAHE 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 +            + +  
Sbjct: 186 LVEDNPTYEKIVLEIETDGLIEPIAAFKDALGVMQKQMSVFNSEWSVSSAESTSSDEEDP 245

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
              P LL+K+E L LS RS NCL    + ++G+L+   E ++  + N G+KS  EIK  L
Sbjct: 246 ELKP-LLQKIEALNLSARSFNCLDRAGMKFVGELVLLGENELKEVKNLGKKSFDEIKDKL 304

Query: 311 GTMGLFLGMNLPDWPPESIEELAKKYE 337
             +G  +G +L +    ++++   K +
Sbjct: 305 EEIGYPVGSDLAEEVSSALQKRLNKLK 331


>gi|71056917|emb|CAH59017.1| DNA-directed RNA polymerase alpha chain [Enterococcus columbae]
          Length = 234

 Score =  254 bits (650), Expect = 1e-65,   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|119662395|emb|CAJ33187.1| RNA polymerase alpha subunit [Lactobacillus aviarius subsp.
           aviarius]
          Length = 231

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 100/231 (43%), Positives = 149/231 (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 SKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 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|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 =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 106/229 (46%), Positives = 152/229 (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 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           SI   ++++LA++I+ + L +F+N  +  +  +  +  +       L  
Sbjct: 181 SIEPLEAMSLAAKIMTEHLDIFVNLTDEARNAEIMVEKEETQKEKMLEM 229


>gi|119662325|emb|CAJ33150.1| RNA polymerase alpha subunit [Lactobacillus intestinalis]
          Length = 211

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 96/206 (46%), Positives = 140/206 (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 SITGEDSVALASRILQDQLGMFINFE 235
           SI   D+++ A++IL +   +F + +
Sbjct: 181 SIKPNDALSFAAKILVEHFKVFESAD 206


>gi|197131686|gb|ACH47361.1| RNA polymerase alpha subunit [Erodium chrysanthum]
          Length = 329

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 77/297 (25%), Positives = 139/297 (46%), Gaps = 8/297 (2%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
             +       I  PL +G A  +G A+RR L+  + G  IT  Q + + HE ++  G+ E
Sbjct: 23  DGKRLYYGRFILSPLKKGQADIIGIAMRRALLGEIEGTCITHAQFEKIPHEYTTRVGIQE 82

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
            + +I++N+K I L+ S    +  +I  RGP  VTA DI     + +++    I  L   
Sbjct: 83  SVYEIVMNLKEIVLRSSLYGTRDASICVRGPRDVTAQDIILPPSVSIVDNTQHIVTLTEP 142

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
               + L + +  GY         +       IDA++ P+K V++++ S   G    ++ 
Sbjct: 143 IEFCVALQIERNRGYSLRIPTPNNSHDERGYPIDAVFMPVKNVNHSIHSYENGS---HEM 199

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L   I T+GS+T ++++  ASR L +    F++ EE K   + + N         L +  
Sbjct: 200 LFFEIWTNGSLTPKEALREASRKLINLFIPFLHAEEEKPHFENNQNEPRDELLVDLCELK 259

Query: 261 EE-----LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           E      +ELS R  N L+G  I  + DL+ +   D+L++ +F ++ +  +  +L  
Sbjct: 260 EIYIDQLVELSPRLYNILKGSGIHTVMDLLDKNPDDLLKLRHFRQEDVERVMNILNN 316


>gi|317016851|gb|ADU85966.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 238

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 93/228 (40%), Positives = 141/228 (61%), Gaps = 2/228 (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 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           +  I T+GSI   D+++L ++IL + L +F++      E    +  + 
Sbjct: 181 TFDIWTNGSIKPSDALSLGAKILAEHLNLFMDISPVAAEAXVMVEAEP 228


>gi|328813983|gb|AEB52107.1| DNA-directed RNA polymerase alpha chain [Lactobacillus
           parabuchneri]
          Length = 244

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 115/244 (47%), 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 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 VRST 270
           VRS 
Sbjct: 241 VRSY 244


>gi|301633194|gb|ADK86748.1| DNA-directed RNA polymerase, alpha subunit [Mycoplasma pneumoniae
           FH]
          Length = 327

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 90/307 (29%), Positives = 160/307 (52%), Gaps = 13/307 (4%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
             N  +    PL  GF  T+GNA+RRVL+S + GA++ A+ I G   E ++++G+ ED+T
Sbjct: 19  NPNYGIFEVGPLESGFGITIGNAMRRVLLSCIPGASVFALSISGAKQEFAAVEGMKEDVT 78

Query: 84  DIILNIKGINLKMSG-------------DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           +++LN K + +K+S              +    +T+     G V A D++     EV+N 
Sbjct: 79  EVVLNFKQLVVKISDLLFEDGEMVEPPLERWPLLTVTAEKAGPVYAKDLECPAGFEVVNK 138

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  + +L  D  V + + V +G G+V    +R   + +G+I  D+ +SP+    Y V+  
Sbjct: 139 DLYLFSLQTDKKVTVNVYVKQGRGFVTFLENREMINSLGIIATDSNFSPVLHCGYEVQEL 198

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           +  +    D L+  I T+G+I+  D+ A+A++IL + L   +N  E  K +         
Sbjct: 199 KTSKQKITDHLTFKIATNGAISAVDAFAMAAKILIEHLNPIVNVNESIKALNIIQEKAEE 258

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
               +  K++EEL+ +VR+ NCL+   I  + +L+ ++ AD+  + N G+KS  EI   +
Sbjct: 259 RRVRSFAKQIEELDFTVRTFNCLKRSGIHTLQELLSKSLADIREIRNLGKKSEREIIKKV 318

Query: 311 GTMGLFL 317
             +GL L
Sbjct: 319 HELGLKL 325


>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 =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 107/338 (31%), Positives = 170/338 (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   MRKITTSAYMPTEIEVQSI---SENVAKITAYPFETGYAVTLAHPLRRLLYTSTVGFAPI 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 NDV-VEIVNPDAYLATINEDAELNFSVIIQKGIGYVPSEEIREEIE-DDYIALDAFFTPV 175

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KK  Y +E+       DY+K+  TI TDG +   ++       +  Q+ +F    +    
Sbjct: 176 KKAVYELENVLVEDDPDYEKIVFTITTDGQVGPIEAFKHCLEAMYQQMSVFKGVLDIDVN 235

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                +      +  LL  VEEL LS RS NCL    I Y+G+L    E ++  + N G+
Sbjct: 236 APMMSSSVGGE-HAKLLSSVEELNLSARSFNCLDKAEIRYIGELALMDENELKDLKNLGK 294

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK V+  +G  +G ++     +S E+L KK  +
Sbjct: 295 KSLEEIKAVMEEIGYPVGSDV---LKDSKEQLRKKIAE 329


>gi|71056852|emb|CAH58981.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
          Length = 232

 Score =  254 bits (649), Expect = 1e-65,   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|300431305|gb|ADK12617.1| RNA polymerase alpha subunit [Achnatherum inebrians]
          Length = 330

 Score =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 88/319 (27%), Positives = 152/319 (47%), Gaps = 32/319 (10%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   + HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSLPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I+ +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASIWVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY         N   G   IDA+  P++ V+Y            +
Sbjct: 141 EPIDFCIELQIKRDRGYQTELR---NNYQDGSYPIDAVSMPVRNVNYR----------KH 187

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      K
Sbjct: 188 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKK 247

Query: 259 K----------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL  R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 248 LTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 304

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 305 MEDGKQIWDTLEKHLPIDL 323


>gi|72534397|emb|CAH59002.1| DNA-directed RNA polymerase alpha chain [Enterococcus cecorum]
          Length = 231

 Score =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 105/230 (45%), Positives = 151/230 (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 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           GSI   D+++LA++IL + L +F+N  +  +  +  +  +       L  
Sbjct: 181 GSIEPLDAMSLAAKILTEHLDIFVNLTDEARHAEIMVEKEETQKEKMLEM 230


>gi|71056882|emb|CAH58997.1| DNA-directed RNA polymerase alpha chain [Enterococcus malodoratus]
          Length = 227

 Score =  254 bits (648), Expect = 2e-65,   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|119663520|emb|CAK22331.1| RNA polymerase alpha subunit [Lactobacillus hammesii]
          Length = 227

 Score =  254 bits (648), Expect = 2e-65,   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|108792409|emb|CAJ33153.1| RNA polymerase alpha subunit [Lactobacillus murinus]
          Length = 222

 Score =  254 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 102/221 (46%), Positives = 150/221 (67%), 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 HGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 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|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 =  254 bits (648), Expect = 2e-65,   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|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|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 =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 115/270 (42%), Positives = 176/270 (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++  + +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
            ++L+  N G+KSL EIK V  + GL L M
Sbjct: 238 VELLKTPNLGKKSLTEIKDVHASRGLSLRM 267


>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 =  253 bits (647), Expect = 2e-65,   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|228017530|gb|ACP52345.1| RNA polymerase alpha subunit [Pinus monticola]
          Length = 335

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 78/317 (24%), Positives = 150/317 (47%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H + N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TFDIRLQIEKNRGYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-QEVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL----------- 250
            + I T+G +T  +++  ASR L D    F++ EE   +   +    ++           
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTD 259

Query: 251 -----PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                         +++LEL  ++ N LR  NI  + DL+  +  D++++ +  ++S+ +
Sbjct: 260 TGETKEKIAFKHIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMKIEHLEKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL        ++ P
Sbjct: 320 VLEVLR---KRFAIDPP 333


>gi|71056870|emb|CAH58990.1| DNA-directed RNA polymerase alpha chain [Enterococcus malodoratus]
          Length = 231

 Score =  253 bits (647), Expect = 2e-65,   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|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 =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 75/306 (24%), Positives = 145/306 (47%), Gaps = 12/306 (3%)

Query: 16  EYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           ++  +    +         I  PL +G A  +G A+RR L+  L G  IT  +   + HE
Sbjct: 14  QWKCVESRADGKRLYYGRFILSPLKKGQADIIGIAMRRALLGELEGTCITHAKFGKIPHE 73

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            ++I G+ E + +I++N+K I L+ +    +  +I  RGP  VTA DI     + +++  
Sbjct: 74  YTTIVGIQESVYEILMNLKEIVLRSNLYGTRGASICVRGPRDVTAQDIVLPPSVAIVDNT 133

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             I  L       + L + +  GY       T +   G   IDA++ P+K V++++ S  
Sbjct: 134 QHIVTLTEPIDFCVGLQIERNRGYSIKIPTATNSHNDGGYPIDAVFMPVKNVNHSIHSYE 193

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
            G    ++ L + I T+GS+T ++++  ASR L +    F+N EE    ++ + N  +  
Sbjct: 194 NGS---HEMLFLEIWTNGSLTPKEALREASRKLINLFIPFLNAEEENSHLENNQNEHTEE 250

Query: 252 FNPALLKKVEE-----LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       +      +EL  R  N L+G  I  + DL+ +   D++++ +F ++ + ++
Sbjct: 251 LSRDFCGLKDIYIDQLVELPPRLYNSLKGSGIHTVMDLLDKNPDDLMKITHFRQEDVEKV 310

Query: 307 KGVLGT 312
             +L  
Sbjct: 311 MNILNN 316


>gi|71056868|emb|CAH58989.1| DNA-directed RNA polymerase alpha chain [Enterococcus pseudoavium]
          Length = 229

 Score =  253 bits (647), Expect = 3e-65,   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|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 =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 78/299 (26%), Positives = 146/299 (48%), Gaps = 10/299 (3%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
             +       I  PL +G A  +G A+RR L+  + G  IT  +   + HE ++I G+ E
Sbjct: 23  DDKRLFYGRFILSPLKKGQADIIGIAMRRALLGEIEGTCITHAKFAKIPHEYTTIAGIKE 82

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
            + +I++N+K I L+ +    +  +I  RGP  VTA DI       +++    I  L   
Sbjct: 83  SIYEILMNLKEIVLRSNLYGTRDASICVRGPRDVTAQDIILPPSTAIVDNTQHIFTLTEP 142

Query: 141 AVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
               + L + +G GY       T+         IDA++ P++ V++++ S   G    ++
Sbjct: 143 IDFCVGLKIERGRGYSIKIPMPTDLFHHDSAYPIDAVFMPVRNVNHSIHSYERGS---HE 199

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK---KEVKEDINVKSLPFNPAL 256
            L + I T+GS+T ++++  ASR L + L  F++ EE      E  ++ + + LP +   
Sbjct: 200 MLFLEIWTNGSLTPKEALREASRKLINLLMPFLHAEEENFYLVENNQNQDTEELPIDLCG 259

Query: 257 LKKV---EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           LK +   + +EL  R  NCL+   I  + DL+ +   D+++M +F ++ +  +  +L  
Sbjct: 260 LKDIYIDQLVELPPRFYNCLKRSGIHTVMDLLDKNRDDLMKMTHFRQEDIEGVMNILNN 318


>gi|71056898|emb|CAH59006.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           hermanniensis]
          Length = 234

 Score =  253 bits (646), Expect = 3e-65,   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|71056914|emb|CAH59016.1| DNA-directed RNA polymerase alpha chain [Enterococcus cecorum]
          Length = 229

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 105/229 (45%), Positives = 151/229 (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 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           GSI   D+++LA++IL + L +F+N  +  +  +  +  +       L 
Sbjct: 181 GSIEPLDAMSLAAKILTEHLDIFVNLTDEARHAEIMVEKEETQKEKMLE 229


>gi|300089411|gb|ADJ67857.1| RNA polymerase alpha-subunit [Photobacterium jeanii]
          Length = 248

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 110/251 (43%), Positives = 166/251 (66%), 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++  + +   +++   +  P    LL+ V++LEL
Sbjct: 181 QTNGTLDPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLEL 237

Query: 266 SVRSTNCLRGE 276
           +VRS NCL+ E
Sbjct: 238 TVRSANCLKAE 248


>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 =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 81/311 (26%), Positives = 150/311 (48%), Gaps = 22/311 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RR+L+  + G  IT V+ + + HE S+I G+
Sbjct: 21  RIESKRLYYGRFILSPLMKGQADTIGIAIRRILLGEIEGTCITRVKSEKIPHEYSTIIGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I +N+K I LK +    +  +I  +GPG +TA DI     +E+++    I N+ 
Sbjct: 81  EESVHEIFMNLKEIVLKSNMYGTQDASISFKGPGYITAQDIILPPSVEIVDNRQHIANVT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + +  GY        +N   G   IDA + P++ V+Y++ S   G     
Sbjct: 141 EPVNLCIELKIERNRGYRIKT---LKNFQDGSYDIDARFMPVRNVNYSIHSYVNGNE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL- 257
           + L + I T+GS+T ++++  AS+ L D    F++ EE    +++  +  +LP       
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASQNLIDLFIPFLHAEEENFNLEKKKHKVTLPLFTFHDI 256

Query: 258 -----------------KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                              +++LEL  R  NCL+  NI  + +L+  ++  +L++ +F  
Sbjct: 257 LVKDKLRKNKKEIALKSIFIDQLELPPRIYNCLKRSNIHTLLELLNNSQEXLLKIEHFRV 316

Query: 301 KSLVEIKGVLG 311
           +    I  +L 
Sbjct: 317 EDGKSILDILK 327


>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 =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 108/329 (32%), Positives = 173/329 (52%), Gaps = 10/329 (3%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
            P  IE   +     N+  + A P   GFA TL + LRR+L+ S  G+A TAV+I+GV H
Sbjct: 10  MPTEIE---VENISANKVQISAYPFESGFAVTLAHPLRRLLLGSTIGSAPTAVKIEGVTH 66

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDS-HKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           E  S++G+ ED+   I+N+K I  K+ GD     V     GP  +   D+   + IE++ 
Sbjct: 67  EFDSMRGMLEDVALFIINLKNIRFKIKGDEKRVEVNYSFSGPKEIKGSDLA-NSHIEIVT 125

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           PD  +  ++ DA     L + KG GYVP+++ R +      I +DA ++P+K+  Y +E+
Sbjct: 126 PDTYLATINEDAEFNFSLIIEKGIGYVPSENIR-DLLTDDYIALDAFFTPVKRAVYDIEN 184

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                  +Y+K+  TI+TDG ++  ++   A   +  Q+ +F    +     K + +  +
Sbjct: 185 VLVEDNPNYEKIVFTIETDGLVSPIEAFKNALEAMYAQMSVFNGILDIAVAPKNETSHDN 244

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           +     LL+ VEEL LS RS NCL    + Y+G+L   +E ++  + N G+KSL EI+ V
Sbjct: 245 VEL-GKLLQSVEELNLSARSFNCLDRAEVKYIGELALMSETELKDLKNLGKKSLEEIRQV 303

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYED 338
           +   G  +G N  D   E+   L KK ED
Sbjct: 304 MEESGYPVGYNFSD---ETASLLKKKIED 329


>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 =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 97/319 (30%), Positives = 165/319 (51%), Gaps = 15/319 (4%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
           NI+      ++ +  + + +PL RGF HTLGN+LRRVL+S++ G ++ A++I  V HE  
Sbjct: 8   NIQIGKDQNKDADYGVFVFKPLERGFGHTLGNSLRRVLLSNIIGHSLFAIKIPNVSHEFQ 67

Query: 74  SIKGVHEDLTDIILNIKGINLKMSG-------------DSHKRVTIFKRGPGVVTAGDIQ 120
           SIKGV EDLT IILN+K + +K+               +    + I     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 GRKSLVEIKGVLGTMGLFL 317
           G+KS  EI   +    L L
Sbjct: 308 GKKSFKEIIKKIQDRNLKL 326


>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 =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 81/336 (24%), Positives = 152/336 (45%), Gaps = 28/336 (8%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
              E   +    EN     +     PL +G A+T+G+A+RRVL+  + G  IT  +   +
Sbjct: 11  KIPELKCVESRTENKRFHYSRFTLSPLRKGQANTIGSAIRRVLLGEVEGTCITRAKFHNI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            +E S I G+ E + +I++N+K I L+      +  +I   GP  VTA DI     + ++
Sbjct: 71  SNEYSVIIGIEESIHEILMNLKEIVLRSDAYGIREGSIHVVGPKKVTAQDIMLPPSVRII 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-------NDPIGLITIDALYSPIK 181
           +    I N++    + + L + KG GY+    +           D   +  IDA ++P++
Sbjct: 131 DTTQHIANINKSITLDISLQIEKGRGYIIQNPNNYNPKDEIFAIDAAFVFPIDAAFAPVQ 190

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
            V+Y++ S         + L + I T+G +  ++++  ASR L D    F+N +E   + 
Sbjct: 191 NVNYSIHSYWSENET-QEILFLEIWTNGGLAPKEALYEASRNLIDFFLPFLNAKEENSDG 249

Query: 242 KEDINVKSLPFNP------------ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
              ++    P  P                 +++L  S R  NCL+  NI  + DL+  + 
Sbjct: 250 TNSLSDDITPSLPILHISTDTKRIAFDQMYIDQLNFSTRVYNCLKKANINTVSDLLNYSR 309

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
            D++++ + G +S+ EI   +  +     ++ P  P
Sbjct: 310 EDLMKIKHLGEQSVKEILEFIRNIQ----IDSPGNP 341


>gi|71056818|emb|CAH58964.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 232

 Score =  252 bits (645), Expect = 4e-65,   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|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 =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 90/322 (27%), Positives = 158/322 (49%), Gaps = 24/322 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +    +     P  +G A+T+G A+RR L++ + GA+IT  +I  V HE S+I G+
Sbjct: 21  KIESKRLLYSRFAISPFRKGQANTVGIAMRRALLNEIEGASITYAKIKKVKHEYSTIIGL 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + DI++N+K I LK      ++  I   GP  +TA DI+  + I+++     I  L+
Sbjct: 81  QESIHDILINLKEIVLKSESFEPQKAYISVLGPKKITAQDIKGPSCIKIMIIAQYIATLN 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D ++ +EL + K  GY      +      GL  +DA++ PI+  +Y+V S    + +  
Sbjct: 141 KDILLEIELNIEKDRGYRIENLQK---YQEGLFPVDAVFMPIRNANYSVHSFESEKKI-K 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN------------ 246
           + L + I TDGS+T ++++  ASR L D     IN E+ +K    +              
Sbjct: 197 EILFLEIWTDGSLTPKEALYEASRNLIDLFIPLINSEKKEKNFGIEKTNESNMSYFPFQS 256

Query: 247 -----VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
                 K           +++LEL  R+ NCL+  N+  + DL+  +E D++++ NFG+K
Sbjct: 257 VSLDIEKMTKDVAFKHIFIDQLELPARAYNCLKKVNVHTIADLLHYSEDDLIKIKNFGKK 316

Query: 302 SLVEIKGVLGTMGLFLGMNLPD 323
           S+ ++   L        + LP 
Sbjct: 317 SVEQVLEALK---KRFSIQLPK 335


>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 =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 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|161513440|emb|CAP16863.1| DNA-directed RNA polymerase subunit alpha [Pediococcus inopinatus]
          Length = 229

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 103/229 (44%), Positives = 152/229 (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 YVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           YV A     R ++ 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|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 =  252 bits (644), Expect = 6e-65,   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|228017657|gb|ACP52470.1| RNA polymerase alpha subunit [Pinus peuce]
          Length = 335

 Score =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 78/317 (24%), Positives = 150/317 (47%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H + N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIRLQIEKNRGYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-QEVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL----------- 250
            + I T+G +T  +++  ASR L D    F++ EE   +   +    ++           
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTD 259

Query: 251 -----PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                         +++LEL  ++ N LR  NI  + DL+  +  D++++ +  ++S+ +
Sbjct: 260 TGETKEKIAFQHIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMKIEHLEKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL        ++ P
Sbjct: 320 VLEVLR---KRFAIDPP 333


>gi|119668315|emb|CAK95458.1| RNA polymerase alpha subunit [Lactobacillus gallinarum]
          Length = 214

 Score =  252 bits (644), Expect = 6e-65,   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|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 =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 103/314 (32%), Positives = 170/314 (54%), Gaps = 5/314 (1%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
            P+ + +        N    +A+P  RG+A T+GNALRRVL+SS+ G AITA++IDGV +
Sbjct: 12  HPHRVTF-EARDLTPNYGKFVAQPFERGYATTIGNALRRVLLSSIPGYAITAIKIDGVTN 70

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKRGPGVVT-AGDIQTVNDIEVL 128
           E  ++ G+ ED   +I+++K + + +  +   K + I K GP  VT A       D+ V 
Sbjct: 71  EFENVPGMKEDTIVMIMHLKNVVVALPENVDAKTIHIKKEGPCTVTAADFASADADVSVF 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           NP+H I  +       M++ +  G+ YVPA+ +    + +  I IDA+YSPI  V + V+
Sbjct: 131 NPEHHIATIAEGYTFEMDVQIESGYNYVPAEVNMELLEDVNAIAIDAIYSPIVSVKFAVD 190

Query: 189 SAREGQVLD-YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
             R GQ ++ Y KL++ I+T G+I  E +++ A+++L+D L  F+  EE   + ++    
Sbjct: 191 DVRVGQRINYYGKLTLEIETKGNIAPEKALSWAAKLLRDNLTPFMLPEEANGDDEKIEET 250

Query: 248 KSLPF-NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
                 +    K VEE+E SVR+ N L   ++  +  +  +T+AD+LR+       + EI
Sbjct: 251 PKDSVLDSLKDKHVEEVEFSVRTANFLISSDLKTLDKVALKTDADLLRLIGANEMIIEEI 310

Query: 307 KGVLGTMGLFLGMN 320
           K  L      LGM 
Sbjct: 311 KEKLAEYNAHLGMR 324


>gi|71056894|emb|CAH59004.1| DNA-directed RNA polymerase alpha chain [Enterococcus italicus]
          Length = 229

 Score =  252 bits (643), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 105/228 (46%), Positives = 151/228 (66%)

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 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           I   D+++LA++I+ + L +F+N  +  K  +  +  +       L  
Sbjct: 181 IEPLDAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEM 228


>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 =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 78/317 (24%), Positives = 150/317 (47%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H + N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIRLQIEKNRGYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-QEVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL----------- 250
            + I T+G +T  +++  ASR L D    F++ EE   +   +    ++           
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTD 259

Query: 251 -----PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                         +++LEL  ++ N LR  NI  + DL+  +  D++++ +  ++S+ +
Sbjct: 260 TGETKEKIAFQHIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMKIEHLEKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL        ++ P
Sbjct: 320 VLEVLR---KRFAIDPP 333


>gi|156752145|gb|ABU93823.1| RNA polymerase subunit A [Vibrio sp. 23023]
          Length = 256

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 112/259 (43%), Positives = 173/259 (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++  + +   +++   +  P    LL+ V++LEL+VRS NCL+ E I
Sbjct: 181 RAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAI 237

Query: 279 VYMGDLIQRTEADMLRMAN 297
            Y+GDL+QRTE ++L+  N
Sbjct: 238 HYIGDLVQRTEVELLKTPN 256


>gi|213584847|ref|ZP_03366673.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. E98-0664]
          Length = 253

 Score =  252 bits (643), Expect = 7e-65,   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|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 =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 80/317 (25%), Positives = 151/317 (47%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H + N   G+  IDA++ P++ V+Y++ S   G  +  + L
Sbjct: 144 TSDIRLQIEKNRGYII---HSSNNYQDGIFPIDAVFMPVRDVNYSIHSYGSGNEI-QEVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL----------- 250
            + I T+G +T  +++  ASR L D    F++ EE   +   +    ++           
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTD 259

Query: 251 -----PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                         +++LEL  ++ N LR  NI  + DL+  +  D++R+ +  ++S+ +
Sbjct: 260 TGETKEKIAFQHIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMRIEHLEKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL        ++ P
Sbjct: 320 VLEVLR---KRFAIDPP 333


>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 =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 99/236 (41%), Positives = 152/236 (64%), Gaps = 7/236 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALR +L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRAILLSSMPGCAVT 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 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVD 233


>gi|228016207|gb|ACP51043.1| RNA polymerase alpha subunit [Pinus squamata]
          Length = 335

 Score =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 79/317 (24%), Positives = 150/317 (47%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H + N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIRLQIEKNRGYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-QEVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN--------------- 246
            + I T+G +T  +++  ASR L D    F++ EE   +   +                 
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTD 259

Query: 247 -VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             ++          +++LEL  ++ N LR  NI  + DL+  +  D++R+ +  ++S+ +
Sbjct: 260 TRETKEKIAFQHIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMRIEHLEKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL        ++ P
Sbjct: 320 VLEVLR---KRFAIDPP 333


>gi|72534409|emb|CAH59041.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 229

 Score =  252 bits (643), Expect = 8e-65,   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|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 =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 94/316 (29%), Positives = 163/316 (51%), Gaps = 5/316 (1%)

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  HEISSIKGVHEDLTDIILNIKGINL--KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           HE  SI+G+ ED++  I N+K I    K +   + ++    +GP V++A ++     + +
Sbjct: 66  HEFDSIRGIVEDVSHFITNLKNIRFLIKDTESDNVQLHYEFKGPMVLSANELVNDM-VGI 124

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NP+  +  ++ +A +   L V KG GYVP++  R +      I +DA ++P+KK  Y +
Sbjct: 125 VNPEAYLATINENASLSFSLIVQKGIGYVPSESIRGKISE-DYIPLDAYFTPVKKAVYEI 183

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+       +Y+K+   I+TDG I    +   A  I+  Q+ +F            +I+ 
Sbjct: 184 ENVLVEDNPNYEKIVFDIETDGQIEPITAFKEAIAIMHKQMSIFGVDLSTASSGTRNISE 243

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            S      ++K ++ L LS R  NCL    + Y+G+L+  +E ++  + N G+KS  EI 
Sbjct: 244 DSGELKTLMIK-IDTLNLSARCFNCLDRSGLKYVGELVIMSENELKNIKNMGKKSYDEIA 302

Query: 308 GVLGTMGLFLGMNLPD 323
             L  +G  +G  + D
Sbjct: 303 DKLEELGYPVGGEIAD 318


>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 =  251 bits (642), Expect = 8e-65,   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|119672801|emb|CAK95516.1| RNA polymerase alpha subunit [Lactobacillus agilis]
          Length = 217

 Score =  251 bits (642), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 99/217 (45%), Positives = 145/217 (66%), 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 SKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GYV A     + +  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|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 (642), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 78/317 (24%), Positives = 150/317 (47%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H + N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIRLQIEKNRGYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-QEVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL----------- 250
            + I T+G +T  +++  ASR L D    F++ EE   +   +    ++           
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTD 259

Query: 251 -----PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                         +++LEL  ++ N LR  NI  + DL+  +  D++++ +  ++S+ +
Sbjct: 260 TGETKEKIAFKHIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMKIEHLEKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL        ++ P
Sbjct: 320 VLEVLR---KRFAIDPP 333


>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 =  251 bits (642), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 86/319 (26%), Positives = 154/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +     HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSXPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTXQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   I  +  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIXXVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D++R+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLMRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 71/309 (22%), Positives = 142/309 (45%), Gaps = 9/309 (2%)

Query: 10  IKPN-NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +P           +       I  PL +G A  +G A+RR L+  + G  IT  + + +
Sbjct: 11  QRPRWKCVEFRADGKRLYYGRFILSPLKKGQADIIGIAMRRALLGEIEGTCITYAKFEKI 70

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE +++ G+ E + +I++N+K I L+ +    +  +I  RGP  VTA DI     + ++
Sbjct: 71  PHEYTTLVGIQESVYEIVMNLKEIVLRSNLYGTRDASICVRGPRDVTAQDIILPPSVAIV 130

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I  L       + L + +  GY       T +       IDA++ P+K V++++ 
Sbjct: 131 DNTQHIVTLTEPIDFCVGLQIERNRGYSMKIPMPTNSHDDRGYPIDAVFMPVKNVNHSIH 190

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           +   G    ++ L   I T+GS+T ++++  ASR L +    F++ EE    ++ + N  
Sbjct: 191 AYENGS---HEMLFFEIWTNGSLTPKEALREASRKLINLFIPFLHAEEENSHLENNQNQH 247

Query: 249 SLPFNPALLKKVEE-----LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
           +   +  L    +      +EL  R  N L+G  I  + DL+ +    ++++ +F  + +
Sbjct: 248 TEELSIDLCGLKDIYIDQLVELPPRLYNSLKGSGIHTVMDLMDKNTDALMKIPHFRHEDV 307

Query: 304 VEIKGVLGT 312
            ++  +L  
Sbjct: 308 EKVMNILNK 316


>gi|229915452|gb|ACQ90797.1| alpha subunit of RNA polymerase [Oocystis solitaria]
          Length = 356

 Score =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 85/341 (24%), Positives = 161/341 (47%), Gaps = 36/341 (10%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            + + +      I  P   G   TL N+LRR L+S + G AI A++I+G LHE S++ GV
Sbjct: 18  RIEENKNFYGRFILGPFEVGQGLTLANSLRRTLLSEISGLAIVAMEIEGALHEYSNLPGV 77

Query: 79  HEDLTDIILNIKGINL--KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
            E + DI+LN+K I L  +   D      +  +GPG+VTA D++  + I+ ++P   I  
Sbjct: 78  QESILDILLNLKQIVLVSRFEMDQPVFGFLKVQGPGIVTASDLKLPSSIQCVDPHQYIAT 137

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTE--------------------------NDPIGL 170
           L  +  + ++  V +   Y+  K+   +                          N    +
Sbjct: 138 LSYNGFLSIKFFVCQKKNYIFLKNASLKKKKIYKLKKNKIQSPILEKKKSNFLINKTSNV 197

Query: 171 ITIDALYSPIKKVSYTVE-SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           ++ID  +  + KV+Y +E  +        +++ + I T+GS+    ++  A++ + +   
Sbjct: 198 VSIDPNFFSVNKVNYLIETCSLFLFEKPKEQIFLEIWTNGSLHPRQAINEAAKRIVNIFS 257

Query: 230 MF---INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQ 286
            F     ++  + +  +  ++K   F       +  L+LS+RS  CL+  NI  + +L+Q
Sbjct: 258 PFQETRFYKPGRLKSSKLFSLKRENFKKFTSLDIANLDLSLRSYTCLKRANIHTIDNLLQ 317

Query: 287 RTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
            +  ++L + NFG +SL E+  +L  +GL    NL D+  +
Sbjct: 318 YSSEELLLLKNFGTRSLEEVLNILQQIGL----NLRDFDKD 354


>gi|156788956|gb|ABU96049.1| RNA polymerase subunit A [Vibrio parahaemolyticus]
          Length = 258

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 111/260 (42%), Positives = 174/260 (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++  + +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y
Sbjct: 182 ATILTEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHY 238

Query: 281 MGDLIQRTEADMLRMANFGR 300
           +GDL+QRTE ++L+  N G+
Sbjct: 239 IGDLVQRTEVELLKTPNLGK 258


>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 =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 79/317 (24%), Positives = 150/317 (47%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVLRSDSYGIREASIYIVGPKNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H + N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIRLQIEKNRGYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-QEVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL----------- 250
            + I T+G +T  +++  ASR L D    F++ EE   +   +    ++           
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHVLTD 259

Query: 251 -----PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                         +++LEL  ++ N LR  NI  + DL+  +  D++R+ +  ++S+ +
Sbjct: 260 TGETKEKIAFQHIFIDQLELPSKTYNSLRRANIHTLLDLLNYSREDLMRIEHLEKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL        ++ P
Sbjct: 320 VLEVLR---KRFAIDPP 333


>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 =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 94/293 (32%), Positives = 148/293 (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 TKLKLELQIESGCGYRLVTDELHRDS-GTFLNIDAIFTPVKNVSYKVLDLYRFDEKLLED 192

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L + I TDGS+  +D++  A+ ILQ+  G     E    +    I+ + +         +
Sbjct: 193 LVLEITTDGSLNPKDALIQAANILQNMFGSLTVGEPKALKQTTTISSRQI--------LI 244

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           EEL+LSVR+ NCL+  NI  + DL Q +  ++  + NFG+KS  E+   L   
Sbjct: 245 EELQLSVRAYNCLKRANIRTIDDLTQYSIKELKELKNFGQKSANEVIQKLQDR 297


>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 =  251 bits (641), Expect = 1e-64,   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|12372|emb|CAA33618.1| unnamed protein product [Triticum aestivum]
          Length = 339

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 88/319 (27%), Positives = 155/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G     
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KL 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L +   ++GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEYGSNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D+LR+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEEDLLRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>gi|228016646|gb|ACP51475.1| RNA polymerase alpha subunit [Pinus albicaulis]
          Length = 335

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 78/317 (24%), Positives = 149/317 (47%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +       PL +G A T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFALSPLRKGRADTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H + N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIRLQIEKNRGYII---HSSNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-QEVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL----------- 250
            + I T+G +T  +++  ASR L D    F++ EE   +        ++           
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNKKKGSNMLPFPLSHVLTD 259

Query: 251 -----PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                         +++LEL  ++ N LR  NI  + DL+  +  D++++ +  ++S+ +
Sbjct: 260 TGETKEKIAFKHIFIDQLELPPKTYNSLRRANIHTLLDLLNYSREDLMKIEHLEKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL        ++ P
Sbjct: 320 VLEVLR---KRFAIDPP 333


>gi|71056906|emb|CAH59010.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
          Length = 228

 Score =  251 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 104/227 (45%), Positives = 152/227 (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 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
             +++++LA++I+ + L +F+N  +  K  +  +  +       L  
Sbjct: 181 IPQEALSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEM 227


>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 =  251 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 100/363 (27%), Positives = 171/363 (47%), Gaps = 42/363 (11%)

Query: 1   MIQKNWQELIKPNNIEYI----VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLR 56
           MIQ N  +    + I++      +  +  +       PL +G A+TLG  LRR L+S L 
Sbjct: 1   MIQ-NVTD----DKIQWKCLESKIESQRIHYGRFAIAPLKKGQANTLGITLRRTLLSDLD 55

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           G  IT+V+ID + HE  ++ GV E + DI+LN+K I  K   D  ++  IF +GP  +TA
Sbjct: 56  GICITSVKIDNIKHEYCTLTGVRESIQDILLNLKEIVFKGVCDKTQKGFIFVKGPKKITA 115

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
            DIQ    IE+L+ + +I +L      ++ELT+ K  G+      +   D      IDA+
Sbjct: 116 SDIQIEPCIEILDSNQIIAHLTEPIDFKVELTIEKSMGFRLQNATQISKDSFS---IDAI 172

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           + PI+ V+Y++    +      + L + I T+GSIT +++   AS  + +      N  +
Sbjct: 173 FMPIRNVNYSIHPVEKAGDWKSELLILEIWTNGSITPKEAFHQASEKIMNIFLSLSNSSD 232

Query: 237 PKKEV--------------------KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGE 276
            + +                     K+D   K           + +LELS R+ NCL+ E
Sbjct: 233 NQIQEKSTKNFEEKEEFIFQNIDGFKQDKETKVQESLGWKKISINQLELSARAYNCLKNE 292

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKY 336
            I  + DL+  ++ D+L++ NFG++S  ++   L        M L         + +KK+
Sbjct: 293 KISTLFDLLNYSQEDLLKIKNFGKRSFEQVVNALE---KHFDMKLSK-------DSSKKF 342

Query: 337 EDK 339
            ++
Sbjct: 343 YEQ 345


>gi|71056842|emb|CAH58976.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
          Length = 215

 Score =  251 bits (640), Expect = 2e-64,   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|47679547|gb|AAT36717.1| RNA polymerase alpha subunit [Corethron hystrix]
          Length = 301

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 87/287 (30%), Positives = 145/287 (50%), Gaps = 3/287 (1%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
              E         L  G   T+G  LRR L+S L   AIT V+I GV +E S I+GV ED
Sbjct: 16  DSGEIYGQFQINDLNPGQGITIGTVLRRFLLSELNATAITGVRIAGVNNEFSIIEGVRED 75

Query: 82  LTDIILNIKGINLKMSGDSHKR--VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           + +++LN++ I +K + D+ +     +  +GP V+TA  IQ   ++E+LNP+  I  +  
Sbjct: 76  VLELLLNLRPIVIKNNSDNSEMKFGRLKVQGPAVITANAIQLPTELEILNPNQYIATISR 135

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
             ++ ME     G GY      + E      + IDA++ P++KV + VE+  +      +
Sbjct: 136 SMILEMEFKFESGIGYRLVNQTKME-SSSDFLEIDAVFMPVQKVDFKVENIYDKNKHISE 194

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
            L + I T+GSI+ E ++  +S  + +     I  +  K+ ++       +         
Sbjct: 195 NLIIDIWTNGSISPETALYESSNNIIELFNSLIENKFKKEILEPLPENTRINSENHTNIS 254

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           +EEL+LSVRS NCL+   I  + DL++ +   +  + NFGRKS  E+
Sbjct: 255 IEELQLSVRSYNCLKRAQINSISDLLKYSPEKLQEIKNFGRKSADEV 301


>gi|197131690|gb|ACH47363.1| RNA polymerase alpha subunit [Geranium carolinianum]
          Length = 329

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 77/322 (23%), Positives = 149/322 (46%), Gaps = 16/322 (4%)

Query: 1   MIQKNWQ-ELIKPNNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSL 55
           MI++  +     P    +  +    +         I  PL +G A  +G A+RR L+  +
Sbjct: 1   MIREKVRVSTQTPR---WKCVESRADGKRLYYGRFILSPLKKGQADIIGIAMRRALLGEI 57

Query: 56  RGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVT 115
            G  IT  + + + HE ++I G+ E + +I++N+K I L+ + D  +  +I  RGP  VT
Sbjct: 58  EGTCITHAKFEKIPHEYTTIVGIQESIYEILMNLKEIVLRSNLDGTRDASICVRGPRDVT 117

Query: 116 AGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDA 175
           A DI   N   +++    I  L       + L + +  GY       T         IDA
Sbjct: 118 AQDIILPNSAAIVDNTQHIVTLTEPIDFCIGLQIDRNRGYSRKIPMPTNFHDDRGYPIDA 177

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           ++ P+K V++++ S   G    ++ L + I T+GS+T ++++  ASR L +    F++ E
Sbjct: 178 VFLPVKNVNHSIHSYENGS---HEMLFLEIWTNGSLTPKEALREASRKLINLFIPFLHAE 234

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEE-----LELSVRSTNCLRGENIVYMGDLIQRTEA 290
           E     + + N  +      L +  +      +EL  R  NCL+   I  + DL+ +   
Sbjct: 235 EENFHFENNQNEHTDELPIDLCELKDIYIDQLVELPARFYNCLKRSGIHTVMDLLNKNTD 294

Query: 291 DMLRMANFGRKSLVEIKGVLGT 312
            ++++ +F ++ + ++  +L  
Sbjct: 295 GLMKITHFRQEDVEKVMNILNN 316


>gi|119672799|emb|CAK95483.1| RNA polymerase alpha subunit [Lactobacillus agilis]
          Length = 214

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 98/214 (45%), Positives = 144/214 (67%), 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 SKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GYV A     + +  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|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 =  250 bits (639), Expect = 2e-64,   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|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 =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 90/307 (29%), Positives = 160/307 (52%), Gaps = 13/307 (4%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
             N  +    PL  GF  T+GNA+RRVL+S + GA++ A+ I G   E ++++G+ ED+T
Sbjct: 19  NPNYGIFEVGPLESGFVITIGNAMRRVLLSCIPGASVFALSISGAKQEFAAVEGMKEDVT 78

Query: 84  DIILNIKGINLKMSG-------------DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           +++LN K + +K+S              +    +T+     G V A D++     EV+N 
Sbjct: 79  EVVLNFKQLVVKISDLLFEDGEMVEPPLERWPLLTVTAEKAGPVYAKDLECPAGFEVVNK 138

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  + +L  D  V + + V +G G+V    +R   + +G+I  D+ +SP+    Y V+  
Sbjct: 139 DLYLFSLQTDKKVTVNVYVKQGRGFVTFLENREMINSLGIIATDSNFSPVLHCGYEVQEL 198

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           +  +    D L+  I T+G+I+  D+ A+A++IL + L   +N  E  K +         
Sbjct: 199 KTSKQKITDHLTFKIATNGAISAVDAFAMAAKILIEHLNPIVNVNESIKALNIIQEKAEE 258

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
               +  K++EEL+ +VR+ NCL+   I  + +L+ ++ AD+  + N G+KS  EI   +
Sbjct: 259 RRVRSFAKQIEELDFTVRTFNCLKRSGIHTLQELLSKSLADIREIRNLGKKSEREIIKKV 318

Query: 311 GTMGLFL 317
             +GL L
Sbjct: 319 HELGLKL 325


>gi|119662353|emb|CAJ33165.1| RNA polymerase alpha subunit [Lactobacillus saerimneri]
          Length = 213

 Score =  250 bits (639), Expect = 2e-64,   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|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 =  250 bits (638), Expect = 2e-64,   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|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 =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 105/229 (45%), 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   +++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 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           SI   ++++L+++I+ + L +F+N  +  K  +  +  +       L  
Sbjct: 181 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEM 229


>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 =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 102/332 (30%), Positives = 178/332 (53%), Gaps = 12/332 (3%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           I P+   ++ + + +EN   +   P   G+A ++ + LRR+L+SS  G A   ++I+GV 
Sbjct: 6   ITPSVPTHMEVEKIKENAIRLHVYPYESGYAISVAHPLRRLLLSSTAGYAPIGLKIEGVQ 65

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI--FKRGPGVVTAGDIQTVNDIEV 127
           HE  S++G+ ED+   I+N+K +  K+     + VT+     GP  +   D +    +EV
Sbjct: 66  HEFDSVRGMLEDVAAFIINLKNVRFKLRDSEQENVTLEYEFSGPKELFGKDFENDL-VEV 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 EKVLVEDNPNYEKIVFDIETDGQVDPVSALKMAMNVMQSQMEIFTNDIEVTETVGQNIE- 242

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                +    + ++ L+LS RS NCL    I Y+G+L+  +   +  + N G+KSL EI+
Sbjct: 243 ----NSEIFYQPLDILDLSARSYNCLDKAGIKYVGELLLMSNEALKSIKNLGKKSLDEIQ 298

Query: 308 GVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             L  + + LG  L D   E+I  L K  ++K
Sbjct: 299 EKLSELNIDLG-KLSDQEKETI--LKKIEQNK 327


>gi|71056896|emb|CAH59005.1| DNA-directed RNA polymerase alpha chain [Enterococcus italicus]
          Length = 223

 Score =  250 bits (638), Expect = 3e-64,   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|108792411|emb|CAJ33183.1| RNA polymerase alpha subunit [Lactobacillus agilis]
          Length = 227

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 99/227 (43%), Positives = 147/227 (64%), 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 SKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GYV A     + +  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|156752143|gb|ABU93822.1| RNA polymerase subunit A [Vibrio sp. 0908]
          Length = 257

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 108/258 (41%), Positives = 173/258 (67%), 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++  + +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y
Sbjct: 183 ATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHY 239

Query: 281 MGDLIQRTEADMLRMANF 298
           +GDL+QRTE ++L+  N 
Sbjct: 240 IGDLVQRTEVELLKTPNL 257


>gi|261886106|ref|ZP_06010145.1| DNA-directed RNA polymerase subunit alpha [Campylobacter fetus
           subsp. venerealis str. Azul-94]
          Length = 326

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 105/318 (33%), Positives = 170/318 (53%), Gaps = 7/318 (2%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
              EN   +IA P    +A TL + LRR+L +S  G A TAV+IDGV HE  S++G+ ED
Sbjct: 12  NVSENVAKIIAYPFETVYAVTLAHPLRRLLYTSTVGFAPTAVKIDGVAHEFDSMRGMLED 71

Query: 82  LTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           +T  I+N+K +  K+  D   + +    +GP  +T  D+     +E++NPD  +  ++ D
Sbjct: 72  VTLFIINLKNLRFKLKNDSKREVIEYSFKGPKEITGIDLNNDI-VEIVNPDSYLATINED 130

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
           A ++  L V KG GYVP++  R   D    I +DA ++P+KK  Y +E+       DY+K
Sbjct: 131 AELKFSLIVEKGIGYVPSEEIRDYIDS-EYIALDAFFTPVKKAVYEIENVLVEDNPDYEK 189

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           + +++ TDG ++  ++   +   +  Q+ +F N       +    +  S   +  LL+ V
Sbjct: 190 IVLSVSTDGQVSPIEAFKHSIEAMYKQMSIFNNVLNIDVNMALTSSQNSNEHSK-LLESV 248

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           E L LS RS NCL   +I Y+G+L    E+++  + N G+KSL EIK V+  +G   G  
Sbjct: 249 ENLNLSARSFNCLDKADIRYIGELALMEESELKDLKNLGKKSLDEIKAVMAEIGYPFG-- 306

Query: 321 LPDWPPESIEELAKKYED 338
             +   +S E L KK  +
Sbjct: 307 -ENTLGDSKEALRKKISE 323


>gi|119668369|emb|CAK95477.1| RNA polymerase alpha subunit [Lactobacillus ruminis]
          Length = 201

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 98/201 (48%), Positives = 143/201 (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 SKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 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|71056923|emb|CAH59020.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
          Length = 226

 Score =  249 bits (637), Expect = 4e-64,   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|119662297|emb|CAJ33135.1| RNA polymerase alpha subunit [Lactobacillus curvatus]
          Length = 223

 Score =  249 bits (637), Expect = 4e-64,   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|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 =  249 bits (637), Expect = 4e-64,   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|269784300|emb|CBH50795.1| alpha subunit of RNA polymerase [Vibrio sp. C 14.7]
          Length = 261

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 112/264 (42%), Positives = 173/264 (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++  + +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADMLRMANFGRKSLVEIKGVLGTM 313
            ++L+  N G+KSL EIK VL + 
Sbjct: 238 VELLKTPNLGKKSLTEIKDVLASR 261


>gi|161511719|emb|CAP16870.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           acidilactici]
          Length = 235

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 109/235 (46%), Positives = 150/235 (63%), 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 GYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 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|302584003|gb|ADL57236.1| RNA polymerase A [Paralactobacillus selangorensis]
          Length = 222

 Score =  249 bits (636), Expect = 4e-64,   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|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 =  249 bits (636), Expect = 5e-64,   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|157493283|gb|ABV58007.1| RNA polymerase alpha subunit [Vibrio cholerae]
          Length = 249

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 109/252 (43%), Positives = 169/252 (67%), 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++  + +   +++   +  P    LL+ V++LEL+V
Sbjct: 181 NGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTV 237

Query: 268 RSTNCLRGENIV 279
           RS NCL+ E I 
Sbjct: 238 RSANCLKAEAIH 249


>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 =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 82/334 (24%), Positives = 148/334 (44%), Gaps = 28/334 (8%)

Query: 10  IKPNNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
           I    I++  L  + E    +    +  P  RG A T+G A+RR L   + G +IT  + 
Sbjct: 8   ISTQRIQWKCLESKTESKRLHYGRFVVSPFKRGQASTVGIAMRRALSQEVGGTSITRAKF 67

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
            GV+HE S+I G+ E + D+++N+K I LK   +          GP  VTAGD      +
Sbjct: 68  HGVVHEYSTITGIQETIHDVLVNLKEIVLKSDSNDIWEAFPSVMGPKEVTAGDTSLPPRV 127

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           + ++    I  +       +EL + +  GY     +   +   G  +IDA++ P++ V+Y
Sbjct: 128 KAIDNSQYIATITQPISSNIELKIERDCGYRIENSNECRD---GQFSIDAVFMPVRNVNY 184

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF-------INFEEPK 238
           ++     G+    +   + I T+GS T  ++++ AS+ L D    F       ++F E  
Sbjct: 185 SIHLFGNGRAT-QEISFIEIWTNGSPTPHEALSEASKKLIDLSTPFSGVKCRDVSFLEDH 243

Query: 239 KEVKEDINVKSLPFNP----------ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
           ++  +      L                   +++LEL  R+ NCL+   I  + D +  +
Sbjct: 244 EDSSDSTRSPFLQLQFGNACKLEGKLFENMFIDQLELPARAFNCLKRAEIHTIADSLNYS 303

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
             D+ ++ NFG+KS+ ++   L          LP
Sbjct: 304 REDLSKIRNFGQKSVDQVSKALWER---FSKELP 334


>gi|119662319|emb|CAJ33147.1| RNA polymerase alpha subunit [Lactobacillus kalixensis]
          Length = 208

 Score =  249 bits (635), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 94/203 (46%), Positives = 139/203 (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 GEDSVALASRILQDQLGMFINFE 235
             D+++ A++IL +   +F + +
Sbjct: 181 PNDALSFAAKILVEHFKVFESAD 203


>gi|71056808|emb|CAH58959.1| DNA-directed RNA polymerase alpha chain [Enterococcus raffinosus]
          Length = 228

 Score =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 105/227 (46%), Positives = 150/227 (66%)

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 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
             +++++LA++IL + L +F+N  +  K  +  +  +       L  
Sbjct: 181 IAQEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEM 227


>gi|161511767|emb|CAP16894.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 219

 Score =  249 bits (635), Expect = 6e-64,   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|156752147|gb|ABU93824.1| RNA polymerase subunit A [Vibrio sp. 09022]
          Length = 256

 Score =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 110/259 (42%), Positives = 172/259 (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++  + +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+
Sbjct: 181 TILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYI 237

Query: 282 GDLIQRTEADMLRMANFGR 300
           GDL+QRTE ++L+  N G+
Sbjct: 238 GDLVQRTEVELLKTPNLGK 256


>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 =  249 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 105/229 (45%), 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   +++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 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           SI   ++++L+++I+ + L +F+N  +  K  +  +  +       L  
Sbjct: 181 SIEPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEM 229


>gi|328814001|gb|AEB52116.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 232

 Score =  249 bits (635), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 108/232 (46%), Positives = 155/232 (66%), 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 VPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           V A    HR ++ 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|71056832|emb|CAH58971.1| DNA-directed RNA polymerase alpha chain [Enterococcus dispar]
          Length = 226

 Score =  248 bits (634), Expect = 7e-64,   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|328813973|gb|AEB52102.1| DNA-directed RNA polymerase alpha chain [Lactobacillus fermentum]
          Length = 243

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 106/243 (43%), Positives = 160/243 (65%), 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 KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTEN 165
            +GP  VTA DIQ   D+ +LN D  I  +   A + +++T  KG GY  A     R 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|71056921|emb|CAH59019.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
          Length = 226

 Score =  248 bits (634), Expect = 8e-64,   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|71056804|emb|CAH58957.1| DNA-directed RNA polymerase alpha chain [Enterococcus italicus]
          Length = 224

 Score =  248 bits (634), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 103/224 (45%), Positives = 148/224 (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 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
            D+++LA++I+ + L +F+N  +  K  +  +  +       L 
Sbjct: 181 LDAMSLAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLE 224


>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 =  248 bits (633), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 79/313 (25%), Positives = 150/313 (47%), Gaps = 24/313 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RR+L+  + G  IT  + + + HE S++ G+
Sbjct: 21  RVDSKRLYYGRFILSPLLKGQADTIGIAMRRILLGEIDGTCITRAKSEKIPHEYSTVVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I L+ +    +  +I  +GPG VTA DI     +EV++    I NL 
Sbjct: 81  QESIHEILMNLKEIVLRSNLYGTREASISFKGPGYVTAQDIILPPSVEVIDKTQHIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + +  GY     +  ++       IDA++ P++  +Y++ S   G     
Sbjct: 141 EPINLCIELQIERKRGYRIKTLNNIQDGSYT---IDAVFMPVRNANYSIHSYVNGNE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           D L + I T+GS T ++++  ASR L D    F++ EE    ++ + +  + P       
Sbjct: 197 DILFLEIWTNGSFTPKEALYEASRNLIDLFIPFLHAEEENFNLENNQHKMTWPLFTFHDH 256

Query: 259 K--------------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                                +++LEL  R  NCL+  NI  + + + +++ D++++ +F
Sbjct: 257 DRFVKDKLTNTQKEITLKSIFIDQLELPPRIYNCLKKSNIHTVFEFLNKSQEDLMKIEHF 316

Query: 299 GRKSLVEIKGVLG 311
             + L  I  +L 
Sbjct: 317 RVEDLKNILNILK 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 =  248 bits (633), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 105/312 (33%), Positives = 161/312 (51%), Gaps = 13/312 (4%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            L +  +    ++  PL +GF  T+GNALRRVL+ S+ GAA+ A++IDGV HE  + +GV
Sbjct: 12  KLLESSQYMASVVISPLKQGFGTTIGNALRRVLLGSIPGAAVFAIKIDGVDHEFMAPEGV 71

Query: 79  HEDLTDIILNIKGINLKMSGD-------------SHKRVTIFKRGPGVVTAGDIQTVNDI 125
            ED+T+IILN+K + + +                    + I K   GVV A DI+    +
Sbjct: 72  LEDVTNIILNVKKLVISIDEKVVDVQSLEEKSISEWPTMKIKKNKAGVVYANDIECPPGM 131

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +V+N D  IC L  D    MEL  +   GY     +R   D + +I+ID+L+SPI KV +
Sbjct: 132 KVINKDLKICELSKDVEFGMELYATLDRGYRSFSENRERLDTLKIISIDSLFSPIVKVEW 191

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            V   +  +    DKL +T+ T+GS+   D+++LA+  L   L     F     + K   
Sbjct: 192 KVVEEKTTKQGTTDKLHLTLVTNGSVKAADALSLAAHTLISLLEPISAFNPETSKRKLIG 251

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
             +      A+   ++ELEL++RS NCL+   I  + +L + T A+   + N G+KSL E
Sbjct: 252 EAEVATKKVAMATPIDELELTMRSFNCLKQNGINTITELAEMTRAEAENIKNLGKKSLNE 311

Query: 306 IKGVLGTMGLFL 317
           I   L   GL  
Sbjct: 312 IIAKLAEKGLKF 323


>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 =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 70/305 (22%), Positives = 138/305 (45%), Gaps = 12/305 (3%)

Query: 17  YIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           +  +    +         I  PL +G A  +G A+RR L+  + G  IT  + D + HE 
Sbjct: 15  WKCVESRADGKRLYYGRFILSPLKKGQADIIGIAMRRALLGEIEGTCITHAKFDKIPHEY 74

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH 132
           +++ G+ E + +I++N+K I L+      +  +I  RGP  VTA DI       +++   
Sbjct: 75  TTLVGIQESIYEILMNLKEIVLRSHLYGTRDASICVRGPRDVTAQDIILPTSATIVDNTQ 134

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  +       + L + +  GY       T         ID+++ P+K V++++ S   
Sbjct: 135 HIVTITEPIDFCVGLQIERNRGYFIQIPMLTNLHDDRGYPIDSVFMPVKNVNHSIHSYEN 194

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           G    +  L + I T+GS+T ++++  ASR L +    F++ EE     + + N  +   
Sbjct: 195 G---IHAMLFLEIWTNGSLTPKEALREASRKLSNLFIPFLHAEEQNFHFENNQNEHTDEL 251

Query: 253 NPALLKKVEE-----LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
                   +      +EL  R  NCL+   I  + DL+ +   D++++ +F ++ + ++ 
Sbjct: 252 PIDFCALKDIYIDQLVELPARFYNCLKISGIHTVMDLLNKNTEDLMKITHFRQQDIEKVM 311

Query: 308 GVLGT 312
            +L  
Sbjct: 312 HILNN 316


>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 =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 104/337 (30%), Positives = 172/337 (51%), Gaps = 13/337 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+ + 
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSD 127

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IE++NP+  +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKK
Sbjct: 128 H-IEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKK 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             EI   L  +G  +G  L     ES+++  +K EDK
Sbjct: 304 YDEIAEKLNDLGYPVGTELSSEQRESLKKRLEKLEDK 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 =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 88/322 (27%), Positives = 154/322 (47%), Gaps = 24/322 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +          P  +G A+T+G A+RR L++ + GA+IT V+I  V HE S+I G+
Sbjct: 21  RMESKRLLYGRFAISPFRKGQANTIGIAMRRALLNEIEGASITYVEIKKVKHEYSTITGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + DI++N+K I  K      ++  I   GP  +TA DI+  + I +++    I  L 
Sbjct: 81  QESIHDILINLKEIVSKSDSYEPQKAYISIYGPKKITARDIKGTSSIRIIDNTQYIATLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + K HGY      +  +   G+ TIDA++ PI+ V+Y+V S   G+    
Sbjct: 141 EAISLDIELNIEKDHGYRIENLQKYRD---GIFTIDAVFMPIRNVNYSVHSFESGEKT-K 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN------------ 246
           + L + I TDGS+T ++++  ASR L D     +N E  +                    
Sbjct: 197 EILFLEIWTDGSLTPKEALYEASRSLIDLFIPLMNSERKEINSGMKKKNELDIPCFPFRF 256

Query: 247 -----VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
                 +           +++LEL  R+ NCL+  N+  + D +  +E D++++ NFG+K
Sbjct: 257 ISLDMEEMTKDIAFKHIFIDQLELPARAYNCLKRVNVHTIADSLNYSEDDLVKIKNFGKK 316

Query: 302 SLVEIKGVLGTMGLFLGMNLPD 323
           S+ ++   L        ++L  
Sbjct: 317 SIEQVLEALK---KRFSIDLQK 335


>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 =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 105/227 (46%), Positives = 150/227 (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 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
              ++++L+++I+ + L +F+N  +  K  +  +  +       L  
Sbjct: 181 EPLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEM 227


>gi|71056834|emb|CAH58972.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
          Length = 227

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 105/226 (46%), Positives = 150/226 (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 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
            +++++LA++IL + L +F+N  +  K  +  +  +       L  
Sbjct: 181 AQEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEM 226


>gi|71056798|emb|CAH58954.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
          Length = 224

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 103/224 (45%), Positives = 149/224 (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 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
            ++++L+++I+ + L +F+N  +  K  +  +  +       L 
Sbjct: 181 LEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLE 224


>gi|72534405|emb|CAH59039.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 221

 Score =  247 bits (632), Expect = 1e-63,   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|300431316|gb|ADK12621.1| RNA polymerase alpha subunit [Lorenzochloa erectifolia]
          Length = 339

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 85/319 (26%), Positives = 143/319 (44%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDITLPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +  GY         N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIELQIKRDRGYQTELR---NNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F+           + N  + P      K
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLXXXXXXXXXXXNKNRFTPPLFTFQKK 256

Query: 259 KVE----------------ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                              +LEL  R+ NCL+   I  + DL+ +TE  ++ + +F    
Sbjct: 257 LTNLXKNKKGIPXXCIFXXQLELPSRTYNCLKRAXIHTLLDLLSKTEEXLMXIDSFRX-- 314

Query: 303 LVEIKGVLGTMGLFLGMNL 321
               K +  T+   L ++L
Sbjct: 315 -EXGKQIWDTLEKHLPIDL 332


>gi|119668287|emb|CAK95499.1| RNA polymerase alpha subunit [Lactobacillus brevis]
          Length = 228

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 101/227 (44%), Positives = 151/227 (66%), 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 KGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           KG GYV A     R  + 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|161513432|emb|CAP16859.1| DNA-directed RNA polymerase subunit alpha [Pediococcus parvulus]
          Length = 224

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 100/224 (44%), Positives = 149/224 (66%), Gaps = 2/224 (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 VPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           V A     R ++ PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSI+ 
Sbjct: 121 VSADENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSISP 180

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
            ++ +L+++IL + L +F+N  +  ++ +  +  +       L 
Sbjct: 181 SEATSLSAKILTEHLALFVNLTDEAQDAEIMVEKEETNKEKMLE 224


>gi|332144698|dbj|BAK19509.1| RNA polymerase alpha subunit [Lactobacillus sunkii]
          Length = 235

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 109/235 (46%), 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 ELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
            LT +KG GYV A     R+   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|161513424|emb|CAP16855.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           dextrinicus]
          Length = 222

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 100/222 (45%), Positives = 151/222 (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 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
            ++++LA++IL D L +FI+  +  K  +  +  +       
Sbjct: 181 REAISLAAKILSDHLNIFIDLSDEAKNTEIMVEKEETQKRRN 222


>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 =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 107/342 (31%), Positives = 177/342 (51%), 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   MRKITTSAYMPTEIE---VENVSENVAKIIAYPFETGYAVTLAHPLRRLLYTSTVGYAPT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQ 120
           AV+IDGV HE  S++G+ ED+   I+N+KGI  K+ GD   + +     GP  +T  D+ 
Sbjct: 58  AVKIDGVSHEFDSMRGMLEDVAIFIINLKGIRFKIKGDSKREVIEYNFTGPKEITGKDLN 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               +E++NPD  +  ++ DA ++  + + KG GYVP++  R +      I +DA ++P+
Sbjct: 118 NDI-VEIVNPDAYLATINEDADLKFSVVIEKGIGYVPSESIR-DYVSSDYIALDAFFTPV 175

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
            +  Y +E+       DY+K+  TI TDG ++  D+   A   +  Q+ +F    +    
Sbjct: 176 IRAIYDIENVFVEDNPDYEKIIFTITTDGQVSAVDAFKNALEAMYQQMSVFKGIVDIDTG 235

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            K          +  L + +E L LS RS NCL   +I ++G+++   E+++  + N G+
Sbjct: 236 -KSFTKQIPSGEHSKLFESIENLNLSARSFNCLEKADIKFVGEIVIMDESELKGIKNLGK 294

Query: 301 KSLVEIKGVLGTMGLFLG----MNLPDWPPESIEELAKKYED 338
           KSL EIK V+  +G  +G     +  +   + I EL KK +D
Sbjct: 295 KSLEEIKSVMEEIGYPIGNEEIKDKKEVLSKKIAELKKKAKD 336


>gi|119662289|emb|CAJ33131.1| RNA polymerase alpha subunit [Lactobacillus casei]
          Length = 211

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 96/210 (45%), Positives = 146/210 (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 ALASRILQDQLGMFINFEEPKKEVKEDINV 247
           +LA++IL + L +F+N  +  K  +  +  
Sbjct: 181 SLAAKILTEHLDIFVNLTDEAKNAEIMVEK 210


>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 =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 87/319 (27%), Positives = 154/319 (48%), Gaps = 23/319 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDTAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGASFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            +++LEL+ R+ NC +      + DL+ +TE D+LR+ +F    
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCXKRXXXXTLLDLLSKTEEDLLRIDSF---R 313

Query: 303 LVEIKGVLGTMGLFLGMNL 321
           + + K +  T+   L ++L
Sbjct: 314 MEDRKHIWDTLEKHLPIDL 332


>gi|190411113|gb|ACE78311.1| RpoA [Vibrio campbellii]
          Length = 257

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 110/260 (42%), 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: 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++  + +   +++   +  P    LL+ V++LEL+VRS NC + E I Y
Sbjct: 181 ATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCRKAEAIHY 237

Query: 281 MGDLIQRTEADMLRMANFGR 300
           +GDL+QRTE ++L+  N G+
Sbjct: 238 IGDLVQRTEVELLKTPNLGK 257


>gi|150036758|emb|CAM98029.1| DNA-directed RNA polymerase alpha chain [Leuconostoc lactis KCTC
           3528]
          Length = 228

 Score =  247 bits (631), Expect = 2e-63,   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|108792407|emb|CAJ33136.1| RNA polymerase alpha subunit [Lactobacillus acidipiscis]
          Length = 224

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 102/224 (45%), Positives = 150/224 (66%), 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 GYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 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|72534411|emb|CAH59042.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 224

 Score =  247 bits (631), Expect = 2e-63,   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|150036764|emb|CAM98032.1| DNA-directed RNA polymerase alpha chain [Leuconostoc lactis]
          Length = 227

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 94/218 (43%), Positives = 139/218 (63%), Gaps = 2/218 (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 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           +GSI   D+++L ++IL + L +F++      E    +
Sbjct: 181 NGSIKPSDALSLGAKILAEHLNLFMDISPVAAEANVMV 218


>gi|295809868|emb|CBL85110.1| alpha subunit of RNA polymerase [Vibrio tapetis]
          Length = 263

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 112/263 (42%), Positives = 172/263 (65%), 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-AVVRMELTVSKGHGYVPAK---HHRTENDPIG 169
           V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  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++  + +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDIRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADMLRMANFGRKSLVEIKGVLGT 312
            ++L+  N G KSL EIK VL +
Sbjct: 238 VELLKTPNLGNKSLTEIKDVLAS 260


>gi|332144694|dbj|BAK19507.1| RNA polymerase alpha subunit [Lactobacillus parafarraginis]
          Length = 236

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 111/236 (47%), 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 VSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
            +KG GYV A     R+   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|119668291|emb|CAK95501.1| RNA polymerase alpha subunit [Lactobacillus collinoides]
          Length = 209

 Score =  247 bits (630), Expect = 3e-63,   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|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 =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 103/337 (30%), Positives = 171/337 (50%), Gaps = 13/337 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+ + 
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSD 127

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IE++NP+  +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIK 
Sbjct: 128 H-IEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKN 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             EI   L  +G  +G  L     ES+++  +K EDK
Sbjct: 304 YDEIAEKLNDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|72534416|emb|CAH59044.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 217

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 104/215 (48%), Positives = 148/215 (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 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
             ++++L+++I+ + L +F+N  +  K  +  +  
Sbjct: 181 PLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEK 215


>gi|317009976|gb|ADU80556.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           India7]
          Length = 344

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 104/337 (30%), Positives = 172/337 (51%), Gaps = 13/337 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKESNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+ + 
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSE 127

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IE++NP+  +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKK
Sbjct: 128 H-IEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKK 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSTKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             EI   L  +G  +G  L     ES+++  +K EDK
Sbjct: 304 YDEIAEKLNDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|119662313|emb|CAJ33144.1| RNA polymerase alpha subunit [Lactobacillus hilgardii]
          Length = 227

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 106/226 (46%), Positives = 151/226 (66%), 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 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 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
            T+GSIT  ++V+LA++IL + L MF++  +  K  +  +  +   
Sbjct: 181 WTNGSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMVEKEETH 226


>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 =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 79/313 (25%), Positives = 152/313 (48%), Gaps = 25/313 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G  +RR+L+  + G  IT  + + + HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLMKGQADTIGITMRRILLGEIEGTCITRAKSEKIPHEYSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I L+ +    +  +I  +GPG VTA DI   + +EV++    I NL 
Sbjct: 81  QESIHEILMNLKEIVLRSNLYGTREASICFKGPGYVTAQDIILPS-VEVIDNTQHIANLT 139

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + +  GY     +  ++       IDA++ P++  ++++ S   G     
Sbjct: 140 EPINLCIELQIERKRGYRIKTLNNIQDGSYT---IDAVFMPVRNANHSIHSYVNGNQ-KQ 195

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     + + +  +LP       
Sbjct: 196 EILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEENLNFENNQHKMTLPLFTFHDH 255

Query: 259 K--------------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
                                +++LEL  R  NCL+  NI  + +L+ +++ D++++ +F
Sbjct: 256 DRFVKDKLRKNQKEITLKSIFIDQLELPPRIYNCLKKSNIHTVLELLNKSQEDLMKIEHF 315

Query: 299 GRKSLVEIKGVLG 311
             + L  I  +L 
Sbjct: 316 RVEDLKFILNILQ 328


>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 =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 98/321 (30%), Positives = 168/321 (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+ GDS+K  V    +G   +   D+     +EV+N D  +  +
Sbjct: 75  LEDVALFIINLKKLRFKIKGDSNKEIVEFSFKGSKEIYGKDLNND-QVEVVNKDAYLATI 133

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           + DA ++  L V KG GYVP++  +   +    I +DA ++P+++ +Y +E        D
Sbjct: 134 NEDAELKFTLIVEKGIGYVPSEEIKELINDPKFIALDAFFTPVREATYDIEKVLFEDNPD 193

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           Y+K+ +T+ TDG IT  ++   A   +  QL +F      +  +K       L  N  LL
Sbjct: 194 YEKVVLTVTTDGQITPNEAFQNALEAMYKQLSVFDKITNVRSVIKNQATSNELE-NTKLL 252

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + + +L LS RS NCL    +VY+G+L   + +++  + N G+KSL EIK ++ ++G  +
Sbjct: 253 QNITDLNLSARSYNCLEKAGVVYIGELALMSVSELAGLKNLGKKSLDEIKNIMESIGFPV 312

Query: 318 GMNLPDWPPESIEELAKKYED 338
           G +      ++ E L  K  +
Sbjct: 313 GTS---KLSDNKEILKNKIAE 330


>gi|86438812|emb|CAJ43371.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 213

 Score =  246 bits (629), Expect = 3e-63,   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|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 =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 103/337 (30%), Positives = 170/337 (50%), Gaps = 13/337 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPIGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +G   + A D+ + 
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGSMELRARDLNSD 127

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IE++NP+  +  ++ DA +   L + KG GYVP++  R E  P G + +D  ++PIKK
Sbjct: 128 H-IEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSETTR-ELMPEGYMPLDGSFTPIKK 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             EI   L  +G  +G  L     ES+++  +K EDK
Sbjct: 304 YDEIAEKLNDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|218680479|ref|ZP_03528376.1| DNA-directed RNA polymerase subunit alpha [Rhizobium etli CIAT 894]
          Length = 208

 Score =  246 bits (628), Expect = 4e-63,   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|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 =  246 bits (628), Expect = 4e-63,   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|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 =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 108/324 (33%), Positives = 176/324 (54%), Gaps = 9/324 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  N  +L    NI+             +   P+ +G AH LGN++RRVL+SSL GA+I 
Sbjct: 1   MSNNNSKLEFVPNIQLK--EDLGAFSYKVQLSPVEKGMAHILGNSIRRVLLSSLSGASII 58

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQ 120
            V I  VLHE S+++ V ED+ +I+ N+K + +K+     +  + +     GVV AGD +
Sbjct: 59  KVNIANVLHEYSTLEDVKEDVVEIVSNLKKVAIKLDTGIDRLDLELSVNKSGVVRAGDFK 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T   +E++N D  I  L       +  TVS G          TE + +G I +DA ++PI
Sbjct: 119 TTQGVEIINKDQPIATLTNQRAFSLTATVSVGRNVGILSAIPTELERVGDIAVDADFNPI 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+V++ V         D + L + + T+G+I    +V  A     +Q+ +F++   P   
Sbjct: 179 KRVAFEVF-----DNGDSETLEVFVKTNGTIGPLAAVTKALEYFCEQISVFVSLRVP-SN 232

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            K    +     +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ ++++ N G+
Sbjct: 233 GKTGDVLIDSNIDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMKIPNLGK 292

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDW 324
           KSL EIK +L    L LG+ + ++
Sbjct: 293 KSLNEIKQILIDNNLSLGVQIDNF 316


>gi|317013080|gb|ADU83688.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           Lithuania75]
          Length = 344

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 104/337 (30%), Positives = 172/337 (51%), Gaps = 13/337 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+ + 
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSE 127

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IE++NP+  +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKK
Sbjct: 128 H-IEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKK 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             EI   L  +G  +G  L     ES+++  +K EDK
Sbjct: 304 YDEIAEKLNDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|308062578|gb|ADO04466.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           Cuz20]
          Length = 344

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 104/337 (30%), Positives = 172/337 (51%), Gaps = 13/337 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRIKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+ + 
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVNYSFKGPMELRARDLNSE 127

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IE++NP+  +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKK
Sbjct: 128 H-IEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKK 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             EI   L  +G  +G  L     ES+++  +K EDK
Sbjct: 304 YDEIAEKLNDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|332144666|dbj|BAK19493.1| RNA polymerase alpha subunit [Lactobacillus sp. YIT 12364]
          Length = 239

 Score =  246 bits (628), Expect = 4e-63,   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|317181015|dbj|BAJ58801.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori F32]
          Length = 344

 Score =  246 bits (627), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 102/337 (30%), Positives = 172/337 (51%), Gaps = 13/337 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+ + 
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSE 127

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IE++NP+  +  ++ +A +   L + KG GYVP+++ R E  P G + +D  ++PIKK
Sbjct: 128 H-IEIVNPEMPLATINENAQLNFSLIICKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKK 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             EI   L  +G  +G  L     E++++  +K EDK
Sbjct: 304 YDEIAEKLNDLGYPVGTELNPEQRENLKKRLEKLEDK 340


>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 =  246 bits (627), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 85/321 (26%), Positives = 153/321 (47%), Gaps = 25/321 (7%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID--GVLHEISSIKGV 78
             +  +       P  +G A T+GNALRR L+  ++GAAIT       G++HE  ++ G+
Sbjct: 209 ENDHRHYARFAVSPFRQGQAITVGNALRRALLGEVQGAAITCATFKDMGIVHEYQAVDGI 268

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + DI+LN++ + +  +    ++  I   GP  V AGDI     + V +P   I  + 
Sbjct: 269 QETVQDILLNVRDVAIGSNTHEPQKAFISVMGPRQVIAGDILCPPSLVVPDPSQNIALVT 328

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +E+ V K  GY      ++ N   G   ID+++ P+ + +Y+V S     V   
Sbjct: 329 AAIPFNVEIEVEKDVGYRIVDPGKSTN---GRFYIDSVFMPVVQANYSVHSFEVEDVT-R 384

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQ---------DQLGMFINFEEPKKEVKEDINVKS 249
           + L + I T+GSI+ E+++  A+R L          + + +    E+        +    
Sbjct: 385 EILFLEIYTNGSISPEEALIEAARSLIDLLLPLLESEVIEVTNTTEKENGSRNISMLSSF 444

Query: 250 LPFNPALLKK-------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           L  +  + K+       +++L+L  R+ NCL+  NI  + DL+  T+ D++R+ NFG+KS
Sbjct: 445 LSSSDQITKEVTYKHVFIDQLKLPARAYNCLKRANIHTVSDLLDYTQDDLMRIKNFGKKS 504

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + E+   L        ++LP 
Sbjct: 505 VEEVLEALRA---QFNISLPK 522


>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 =  246 bits (627), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 104/337 (30%), Positives = 172/337 (51%), Gaps = 13/337 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+ + 
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLSSE 127

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IE++NP+  +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKK
Sbjct: 128 H-IEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKK 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             EI   L  +G  +G  L     ES+++  +K EDK
Sbjct: 304 YDEIAEKLNDLGYPVGTELSHEQRESLKKRLEKLEDK 340


>gi|117575075|emb|CAJ84777.1| RNA polymerase alpha subunit [Lactobacillus amylotrophicus]
          Length = 225

 Score =  246 bits (627), Expect = 5e-63,   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|323925214|gb|ADY11800.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 240

 Score =  246 bits (627), Expect = 5e-63,   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|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 =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 104/337 (30%), Positives = 170/337 (50%), Gaps = 13/337 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKESNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+   
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDL-NS 126

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
             IE++NP+  +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKK
Sbjct: 127 EQIEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKK 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             EI   L  +G  +G  L     ES+++  +K EDK
Sbjct: 304 YDEIAEKLNDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|119662295|emb|CAJ33134.1| RNA polymerase alpha subunit [Lactobacillus crispatus]
          Length = 212

 Score =  246 bits (627), Expect = 5e-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|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 =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 85/321 (26%), Positives = 153/321 (47%), Gaps = 25/321 (7%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID--GVLHEISSIKGV 78
             +  +       P  +G A T+GNALRR L+  ++GAAIT       G++HE  ++ G+
Sbjct: 122 ENDHRHYARFAVSPFRQGQAITVGNALRRALLGEVQGAAITCATFKDMGIVHEYQAVDGI 181

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + DI+LN++ + +  +    ++  I   GP  V AGDI     + V +P   I  + 
Sbjct: 182 QETVQDILLNVRDVAIGSNTHEPQKAFISVMGPRQVIAGDILCPPSLVVPDPSQNIALVT 241

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +E+ V K  GY      ++ N   G   ID+++ P+ + +Y+V S     V   
Sbjct: 242 AAIPFNVEIEVEKDVGYRIVDPGKSTN---GRFYIDSVFMPVVQANYSVHSFEVEDVT-R 297

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQ---------DQLGMFINFEEPKKEVKEDINVKS 249
           + L + I T+GSI+ E+++  A+R L          + + +    E+        +    
Sbjct: 298 EILFLEIYTNGSISPEEALIEAARSLIDLLLPLLESEVIEVTNTTEKENGSRNISMLSSF 357

Query: 250 LPFNPALLKK-------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
           L  +  + K+       +++L+L  R+ NCL+  NI  + DL+  T+ D++R+ NFG+KS
Sbjct: 358 LSSSDQITKEVTYKHVFIDQLKLPARAYNCLKRANIHTVSDLLDYTQDDLMRIKNFGKKS 417

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + E+   L        ++LP 
Sbjct: 418 VEEVLEALRA---QFNISLPK 435


>gi|119662303|emb|CAJ33139.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           indicus]
          Length = 223

 Score =  246 bits (627), Expect = 5e-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|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 =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 104/337 (30%), Positives = 170/337 (50%), Gaps = 13/337 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+   
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDL-NS 126

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
             IE++NP+  +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKK
Sbjct: 127 EQIEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKK 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             EI   L  +G  +G  L     ES+++  +K EDK
Sbjct: 304 YDEIAEKLNDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>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 =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 108/324 (33%), Positives = 177/324 (54%), Gaps = 9/324 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +  N  +L    NI+             +   P+ +G AH LGN++RRVL+SSL GA+I 
Sbjct: 1   MSNNNSKLEFVPNIQLK--EDLGAFSYKVQLSPVEKGMAHILGNSIRRVLLSSLSGASII 58

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQ 120
            V I  VLHE S+++ V ED+ +I+ N+K + +K+     +  + +     GVV+AGD +
Sbjct: 59  KVNIANVLHEYSTLEDVKEDVVEIVSNLKKVAIKLDTGIDRLDLELSVNKSGVVSAGDFK 118

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           T   +E++N D  I  L       +  TVS G          TE + +G I +DA ++PI
Sbjct: 119 TTQGVEIINKDQPIATLTNQRAFSLTATVSVGRNVGILSAIPTELERVGDIAVDADFNPI 178

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           K+V++ V         D + L + + T+G+I    +V  A     +Q+ +F++   P   
Sbjct: 179 KRVAFEVF-----DNGDSETLEVFVKTNGTIEPLAAVTKALEYFCEQISVFVSLRVP-SN 232

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            K    +     +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ ++++ N G+
Sbjct: 233 GKTGDVLIDSNIDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMKIPNLGK 292

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDW 324
           KSL EIK +L    L LG+ + ++
Sbjct: 293 KSLNEIKQILIDNNLSLGVQIDNF 316


>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 =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 99/237 (41%), Positives = 150/237 (63%), Gaps = 8/237 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E ++P  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLRPRLVDIEQIST---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 HDGDVEIANPEHVICHLTDDNAEISMRIKVERGRGYVPASARIHTEEDERPIGRLLVDAT 177

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           Y P+ K++Y VE+AR  Q  D DKL + ++T G++  E++V  A+ IL +QL  F++
Sbjct: 178 YRPVDKIAYAVEAARVEQRTDLDKLVIDMETSGTLEPEEAVRRAATILAEQLDAFVD 234


>gi|119662351|emb|CAJ33164.1| RNA polymerase alpha subunit [Lactobacillus ruminis]
          Length = 203

 Score =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 99/202 (49%), Positives = 145/202 (71%), Gaps = 2/202 (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 GYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GYV A     + ++ PIG++ ID++Y+PI++V+Y VE  R GQ  DYDKL++ + T+GSI
Sbjct: 121 GYVSANENKAKADDMPIGVLAIDSIYTPIERVNYQVEKTRVGQKNDYDKLTLDVWTNGSI 180

Query: 212 TGEDSVALASRILQDQLGMFIN 233
           T  ++++L+++IL + L +F+N
Sbjct: 181 TPSEAISLSAKILTEHLALFVN 202


>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 =  246 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 97/321 (30%), Positives = 168/321 (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+ G+S+K  V    +G   +   D+     +EV+N D  +  +
Sbjct: 75  LEDVALFIINLKKLRFKIKGESNKEIVEFSFKGSKEIYGKDLNND-QVEVVNKDAYLATI 133

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           + DA ++  L V KG GYVP++  +   +    I +DA ++P+++ +Y +E        D
Sbjct: 134 NEDAELKFTLIVEKGIGYVPSEEIKELINDPKFIALDAFFTPVREATYDIEKVLFEDNPD 193

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           Y+K+ +T+ TDG IT  ++   A   +  QL +F      +  +K       L  N  LL
Sbjct: 194 YEKVVLTVTTDGQITPNEAFQNALEAMYKQLSVFDKITNVRSVIKNQATSNELE-NTKLL 252

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + + +L LS RS NCL    +VY+G+L   + +++  + N G+KSL EIK ++ ++G  +
Sbjct: 253 QNITDLNLSARSYNCLEKAGVVYIGELALMSVSELAGLKNLGKKSLDEIKNIMESIGFPV 312

Query: 318 GMNLPDWPPESIEELAKKYED 338
           G +      ++ E L  K  +
Sbjct: 313 GTS---KLSDNKEILKNKIAE 330


>gi|295809862|emb|CBL85107.1| alpha subunit of RNA polymerase [Vibrio tapetis]
          Length = 260

 Score =  245 bits (626), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 112/263 (42%), Positives = 172/263 (65%), 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-AVVRMELTVSKGHGYVPAK---HHRTENDPIG 169
           V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  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++  + +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDIRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADMLRMANFGRKSLVEIKGVLGT 312
            ++L+  N G KSL EIK VL +
Sbjct: 238 VELLKTPNLGNKSLTEIKDVLAS 260


>gi|71056953|emb|CAH59037.1| DNA-directed RNA polymerase alpha chain [Enterococcus sp. LMG
           14595]
          Length = 224

 Score =  245 bits (626), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 104/224 (46%), Positives = 149/224 (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 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           +++++LA++IL + L +F+N  +  K  +  +  +       L 
Sbjct: 181 QEALSLAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLE 224


>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 =  245 bits (626), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 103/337 (30%), Positives = 169/337 (50%), Gaps = 13/337 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+   
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMEIRARDL-NS 126

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
             IE++NP+  +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIK 
Sbjct: 127 EQIEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKN 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             EI   L  +G  +G  L     ES+++  +K EDK
Sbjct: 304 YDEIAEKLNDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|71056902|emb|CAH59008.1| DNA-directed RNA polymerase alpha chain [Enterococcus hirae]
          Length = 224

 Score =  245 bits (626), Expect = 6e-63,   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|261838612|gb|ACX98378.1| alpha subunit of the DNA-dependent RNA polymerase core enzyme
           [Helicobacter pylori 51]
          Length = 344

 Score =  245 bits (626), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 102/337 (30%), Positives = 171/337 (50%), Gaps = 13/337 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+ + 
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALIGQDSSLENQSVVVDYSFKGPMEIRARDLSSE 127

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IE++NP+  +  ++ DA +   L + KG G+VP+++ R E  P G + +D  ++PIK 
Sbjct: 128 H-IEIVNPEMPLATINEDAQLNFSLIIYKGMGHVPSENTR-ELMPEGYMPLDGSFTPIKN 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             EI   L  +G  +G  L     ES+++  +K EDK
Sbjct: 304 YDEIAEKLNDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>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 =  245 bits (626), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 97/321 (30%), Positives = 168/321 (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+ G+S+K  V    +G   +   D+     +EV+N D  +  +
Sbjct: 75  LEDVALFIINLKKLRFKIKGESNKEIVEFSFKGSKEIYGKDLNND-QVEVVNKDTYLATI 133

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           + DA ++  L V KG GYVP++  +   +    I +DA ++P+++ +Y +E        D
Sbjct: 134 NEDAELKFTLIVEKGIGYVPSEEIKELINDPKFIALDAFFTPVREATYDIEKVLFEDNPD 193

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           Y+K+ +T+ TDG IT  ++   A   +  QL +F      +  +K       L  N  LL
Sbjct: 194 YEKVVLTVTTDGQITPNEAFQNALEAMYKQLSVFDKITNVRSVIKNQATSNELE-NTKLL 252

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + + +L LS RS NCL    +VY+G+L   + +++  + N G+KSL EIK ++ ++G  +
Sbjct: 253 QNITDLNLSARSYNCLEKAGVVYIGELALMSVSELAGLKNLGKKSLDEIKNIMESIGFPV 312

Query: 318 GMNLPDWPPESIEELAKKYED 338
           G +      ++ E L  K  +
Sbjct: 313 GTS---KLSDNKEILKNKIAE 330


>gi|71056874|emb|CAH58992.1| DNA-directed RNA polymerase alpha chain [Enterococcus ratti]
          Length = 227

 Score =  245 bits (626), Expect = 6e-63,   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|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 =  245 bits (626), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 96/321 (29%), Positives = 165/321 (51%), Gaps = 6/321 (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  HEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
            ED+   I+N+K +  K+  DS+K  V    +G   +   D+     +EV+N D  +  +
Sbjct: 75  LEDVALFIINLKKLRFKIKSDSNKEIVEFSFKGSKEIYGKDLNND-QVEVVNKDAYLATI 133

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           + DA +   L V KG GY+P++  +   +    I +DA ++P+++ +Y +E        D
Sbjct: 134 NEDAELEFTLIVEKGIGYIPSEEIKEFLNDPKFIALDAFFTPVREATYDIEKVLFEDNPD 193

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           Y+K+ +T+ TDG IT  ++   A   +  QL +F      +  +K       L  N  LL
Sbjct: 194 YEKVVLTVTTDGQITPNEAFQNALEAMYKQLSVFDKITNVRSVIKNQATSNELE-NTKLL 252

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + + +L LS RS NCL    +VY+G+L   + +++  + N G+KSL EIK ++  +G  +
Sbjct: 253 QNITDLNLSARSYNCLEKAGVVYIGELALMSVSELAGLKNLGKKSLDEIKNIMENIGFPV 312

Query: 318 GMNLPDWPPESIEELAKKYED 338
           G +      ++ E L  K  +
Sbjct: 313 GTS---KLSDNKEILKNKIAE 330


>gi|332144692|dbj|BAK19506.1| RNA polymerase alpha subunit [Lactobacillus otakiensis]
          Length = 233

 Score =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 109/232 (46%), Positives = 151/232 (65%), Gaps = 4/232 (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 TDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           TDGSIT  ++V+LA++IL + L MF++  +  K  +  +  +       L  
Sbjct: 181 TDGSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMVEKEETHKEKMLEM 232


>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 =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 95/320 (29%), Positives = 168/320 (52%), Gaps = 3/320 (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  HEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
            ED+   I+N+K +  K+ G+S+K  V    +G   +   D+     +EV+N D  +  +
Sbjct: 75  LEDVALFIINLKKLRFKIKGESNKEIVEFSFKGSKEIYGKDLNND-QVEVVNKDAYLATI 133

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           + DA ++  L V KG GYVP++  +   +    I +DA ++P+++ +Y +E        D
Sbjct: 134 NEDAELKFTLIVEKGIGYVPSEEIKELINDPKFIALDAFFTPVREATYDIEKVLFEDNPD 193

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           Y+K+ +T+ TDG IT  ++   A   +  QL +F      +  +K       L  N  LL
Sbjct: 194 YEKVVLTVTTDGQITPNEAFQNALEAMYKQLSVFDKITNVRSVIKNQATSNELE-NTKLL 252

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + + +L LS RS NCL    +VY+G+L   + +++  + N G+KSL EIK ++ ++G  +
Sbjct: 253 QNITDLNLSARSYNCLEKAGVVYIGELALMSVSELAGLKNLGKKSLDEIKNIMESIGFPV 312

Query: 318 GMNLPDWPPESIEELAKKYE 337
           G +      E ++   ++ +
Sbjct: 313 GTSKLSDNKEILKNKNRRIK 332


>gi|71056846|emb|CAH58978.1| DNA-directed RNA polymerase alpha chain [Enterococcus moraviensis]
          Length = 225

 Score =  245 bits (626), Expect = 7e-63,   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|332144696|dbj|BAK19508.1| RNA polymerase alpha subunit [Lactobacillus rapi]
          Length = 230

 Score =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 107/230 (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 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 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
            TDGSIT  ++V+LA++IL + L MF++  +  K  +  +  +       
Sbjct: 181 WTDGSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMVEKEETHKEKM 230


>gi|71056904|emb|CAH59009.1| DNA-directed RNA polymerase alpha chain [Enterococcus durans]
          Length = 226

 Score =  245 bits (626), Expect = 7e-63,   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|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 =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 108/325 (33%), Positives = 177/325 (54%), Gaps = 10/325 (3%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M   N ++   PN     +          +   P+ +G AH LGN++RRVL+SSL GA+I
Sbjct: 1   MSNNNSKQEFVPN---IQLKEDLGAFSYKVQLSPVEKGMAHILGNSIRRVLLSSLSGASI 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDI 119
             V I  VLHE S+++ V ED+ +I+ N+K + +K+     +  + +     GVV+AGD 
Sbjct: 58  IKVNIANVLHEYSTLEDVKEDVVEIVSNLKKVAIKLDTAIDRLDLELSVNKSGVVSAGDF 117

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
           +T   +E++N D  I  L       +  TVS G          TE + +G I +DA ++P
Sbjct: 118 KTTQGVEIINKDQPIATLTNQRAFSLTATVSVGRNVGILSAIPTELERVGDIAVDADFNP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           IK+V++ V         D + L + + T+G+I    +V  A     +Q+ +F++   P  
Sbjct: 178 IKRVAFEVF-----DNGDSETLEVFVKTNGTIEPLAAVTKALEYFCEQISVFVSLRVP-S 231

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
             K    +     +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ ++++ N G
Sbjct: 232 NGKTGDVLIDSNIDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMKIPNLG 291

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDW 324
           +KSL EIK +L    L LG+ + ++
Sbjct: 292 KKSLNEIKQILIDNNLSLGVQIDNF 316


>gi|69215820|gb|AAZ03866.1| RNA polymerase alpha chain [Ginkgo biloba]
          Length = 337

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 81/321 (25%), Positives = 142/321 (44%), Gaps = 23/321 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +  +       PL +G A+T+G A+RR L+  + G  IT  + + + HE S+I G+
Sbjct: 21  RVNGKRLHYGRFALSPLQKGQANTIGIAMRRALLGEVEGTCITHAKFENMTHEYSAIMGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + DI +N++GI L+      +  +I+  GP  VTA DI     + +++    I +L 
Sbjct: 81  EESVHDISINLRGIVLQSDPYGIREASIYSVGPRDVTAQDIILPPSVRIIDTTQHIASLK 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +   + K  GY         N   G+ + DA+  P++  +Y++ S   G  +  
Sbjct: 141 ESITSDIRSQIGKDRGYRI---QSPNNSRDGIFSTDAVSMPVRNANYSIHSYGNGNEM-Q 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED-------------- 244
           + L   I T+GS+   +++  ASR L D    F+  EE   +  ++              
Sbjct: 197 EILFSEIWTNGSLAPGEALYEASRNLIDLFIPFMRAEEQNIDGIDNWNGYNMSLFPFSHI 256

Query: 245 --INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                K           +++ EL  R  NCL+  NI  + DL+  +  D  R+ NFG +S
Sbjct: 257 STDTEKMEEEIAFKHIFIDQSELPPRVYNCLKRVNIHTLSDLLNYSRDDPTRIENFGNQS 316

Query: 303 LVEIKGVLGTMGLFLGMNLPD 323
           + +I  VL        ++LP 
Sbjct: 317 VEQILEVL---QKRFAIDLPK 334


>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 =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 108/325 (33%), Positives = 177/325 (54%), Gaps = 10/325 (3%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M   N ++   PN     +          +   P+ +G AH LGN++RRVL+SSL GA+I
Sbjct: 1   MSNNNSKQEFVPN---IQLKEDLGAFSYKVQLSPVEKGMAHILGNSIRRVLLSSLSGASI 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDI 119
             V I  VLHE S+++ V ED+ +I+ N+K + +K+     +  + +     GVV+AGD 
Sbjct: 58  IKVNIANVLHEYSTLEDVKEDVVEIVSNLKKVAIKLDAGIDRLDLELSVNKSGVVSAGDF 117

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
           +T   +E++N D  I  L       +  TVS G          TE + +G I +DA ++P
Sbjct: 118 KTTQGVEIINKDQPIATLTNQRAFSLTATVSVGRNVGILSAIPTELERVGDIAVDADFNP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           IK+V++ V         D + L + + T+G+I    +V  A     +Q+ +F++   P  
Sbjct: 178 IKRVAFEVF-----DNGDSETLEVFVKTNGTIEPLAAVTKALEYFCEQISVFVSLRVP-S 231

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
             K    +     +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ ++++ N G
Sbjct: 232 NGKTGDVLIDSNIDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMKIPNLG 291

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDW 324
           +KSL EIK +L    L LG+ + ++
Sbjct: 292 KKSLNEIKQILIDNNLSLGVQIDNF 316


>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 =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 108/325 (33%), Positives = 177/325 (54%), Gaps = 10/325 (3%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M   N ++   PN     +          +   P+ +G AH LGN++RRVL+SSL GA+I
Sbjct: 1   MSNNNSKQEFVPN---IQLKEDLGAFSYKVQLSPVEKGMAHILGNSIRRVLLSSLSGASI 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDI 119
             V I  VLHE S+++ V ED+ +I+ N+K + +K+     +  + +     GVV+AGD 
Sbjct: 58  IKVNISNVLHEYSTLEDVKEDVVEIVSNLKKVAIKLDTGIDRLDLELSVNKSGVVSAGDF 117

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
           +T   +E++N D  I  L       +  TVS G          TE + +G I +DA ++P
Sbjct: 118 KTTQGVEIINKDQPIATLTNQRAFSLTATVSVGRNVGILSAIPTELERVGDIAVDADFNP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           IK+V++ V         D + L + + T+G+I    +V  A     +Q+ +F++   P  
Sbjct: 178 IKRVAFEVF-----DNGDSETLEVFVKTNGTIEPLAAVTKALEYFCEQISVFVSLRVP-S 231

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
             K    +     +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ ++++ N G
Sbjct: 232 NGKTGDVLIDSNIDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMKIPNLG 291

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDW 324
           +KSL EIK +L    L LG+ + ++
Sbjct: 292 KKSLNEIKQILIDNNLSLGVQIDNF 316


>gi|161511765|emb|CAP16893.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           acidilactici]
          Length = 215

 Score =  245 bits (625), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 103/215 (47%), Positives = 141/215 (65%), 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 GYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A     R  + 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|317014684|gb|ADU82120.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           Gambia94/24]
          Length = 344

 Score =  245 bits (625), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 103/337 (30%), Positives = 171/337 (50%), Gaps = 13/337 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+ + 
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSE 127

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IE++NP+  +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIK 
Sbjct: 128 H-IEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKN 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             EI   L  +G  +G  L     ES+++  +K EDK
Sbjct: 304 YDEIAEKLNDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>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 =  245 bits (625), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 96/329 (29%), Positives = 170/329 (51%), Gaps = 7/329 (2%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P   +  V+ Q   N   +IA P   GFA +L + +RR L+SS  G A   ++I+G  HE
Sbjct: 8   PLLPKEFVVEQISANEANIIAYPFETGFAVSLAHPIRRFLLSSSVGFAPIGIKIEGAKHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
             S++G+ ED++D I+N+KGI  K+      K +T    GP  +   D+    D+EV+ P
Sbjct: 68  FDSVRGMLEDISDFIINLKGIRFKLKNGLKEKEITYSFAGPCEIHGSDLDND-DVEVVTP 126

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           +  +  L+ DA +   + + +G GY P++  R +    G I +DA ++P+++ +Y +E+ 
Sbjct: 127 NAFLATLNEDATLNFSVKIHQGIGYAPSEDVR-DILGDGYIALDAYFTPVRRATYAIENV 185

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
                 +++K+ + I TDG I+  D+   A  ++  Q+ +F +    K     +   +  
Sbjct: 186 LVEDNPNFEKVVINIATDGQISPVDAFKNALEVMYAQMAVFNSEVSIKAPAAAERGDEHP 245

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                  + +E+L LS RS NCL   NI Y+G+++  ++ D+  + N G+KS  EI   +
Sbjct: 246 ELKRLGAR-IEDLGLSARSFNCLDRSNIKYIGEIVMMSQNDLKEVKNLGKKSFEEILEKI 304

Query: 311 GTMGLFLGMNLPDWPPESIEELAKKYEDK 339
              G  +G +L D   + I  + KK E +
Sbjct: 305 TEYGYTVGQDLAD---DLISAIKKKIEAE 330


>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 =  244 bits (624), Expect = 1e-62,   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|332144688|dbj|BAK19504.1| RNA polymerase alpha subunit [Lactobacillus farraginis]
          Length = 218

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 105/218 (48%), Positives = 148/218 (67%), 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 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 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           GSIT  ++V+LA++IL + L MF++  +  K  +  + 
Sbjct: 181 GSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMVE 218


>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 =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 93/329 (28%), Positives = 167/329 (50%), Gaps = 9/329 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
            P     + +    E    + A P   GFA TL + LRR+L+SS  G +  AV+I+G  H
Sbjct: 7   TPFLPTEVEIEAISETEAKISAYPFESGFAITLAHPLRRLLLSSSVGYSPIAVKIEGASH 66

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           E  S++G+ ED+   I+N+K I  K+  D ++  V     GP  +   D+   +D+E+++
Sbjct: 67  EFDSLRGMLEDIAIFIINLKNIKFKILSDENQVEVEYSFNGPKEIKGSDLV-NSDVEIVS 125

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  +  ++ D  +   + + KG GY+P++  R +      I +DA ++P+KKV Y +E 
Sbjct: 126 PEAHLATINADCNLTFSVIIQKGIGYMPSEDIR-DMVSSDYIPLDAFFTPVKKVVYDIEK 184

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                  +++K   T+ T+G IT  ++   A  ++  Q+ +F    +   EV    + + 
Sbjct: 185 MLVEDNPNFEKAVFTVQTNGQITPINAFKEAVSVMYSQMSVFNKVFDL-SEVTVSDSTEE 243

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 L+ K+++L LS RS N L    + Y+G+L+  +E ++  + N G+KS  EI   
Sbjct: 244 PVELKDLIVKIDDLNLSARSFNSLDRAGLKYLGELVLMSEVEVKNIKNLGKKSYDEIADK 303

Query: 310 LGTMGLFLGMNLPDWPPESIEE-LAKKYE 337
           L ++G      + +  PE+I   L +K E
Sbjct: 304 LASLGFP----VENTLPENIASALRRKLE 328


>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 =  244 bits (624), Expect = 1e-62,   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|119668343|emb|CAK95510.1| RNA polymerase alpha subunit [Lactobacillus paracasei subsp.
           paracasei]
          Length = 214

 Score =  244 bits (624), Expect = 1e-62,   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|328675432|gb|AEB28107.1| DNA-directed RNA polymerase alpha subunit [Francisella cf. novicida
           3523]
          Length = 323

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 108/325 (33%), Positives = 177/325 (54%), Gaps = 10/325 (3%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M   N ++   PN     +          +   P+ +G AH LGN++RRVL+SSL GA+I
Sbjct: 1   MSNNNSKQEFVPN---IQLKEDLGAFSYKVELSPVEKGMAHILGNSIRRVLLSSLSGASI 57

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDI 119
             V I  VLHE S+++ V ED+ +I+ N+K + +K+     +  + +     GVV+AGD 
Sbjct: 58  IKVNIANVLHEYSTLEDVKEDVVEIVSNLKKVAIKLDKGIDRLDLELSVNKSGVVSAGDF 117

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
           +T   +E++N D  I  L       +  TVS G          TE + +G I +DA ++P
Sbjct: 118 KTTQGVEIINKDQPIATLTNQRAFNLTATVSIGRNVGILSAIPTELERVGDIAVDADFNP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           IK+V++ V         D + L + + T+G+I    +V  A     +Q+ +F++   P  
Sbjct: 178 IKRVAFEVF-----DNGDSETLEVFVKTNGTIEPLAAVTKALEYFCEQISVFVSLRVP-S 231

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
             K    +     +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ ++++ N G
Sbjct: 232 NGKTGDVLIDSNIDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMKIPNLG 291

Query: 300 RKSLVEIKGVLGTMGLFLGMNLPDW 324
           +KSL EIK +L    L LG+ + ++
Sbjct: 292 KKSLNEIKQILIDNNLSLGVQIDNF 316


>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 =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 90/334 (26%), Positives = 167/334 (50%), Gaps = 7/334 (2%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
           ++P   E + + +   N   + A P    +A T+ + +RR+L+SS  G A   ++I+GV 
Sbjct: 6   VRPYIPEKLEIEEIAPNHIRLHAYPFEPHYAVTIAHPVRRLLLSSSVGYAPIGIKIEGVR 65

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR----VTIFKRGPGVVTAGDIQTVNDI 125
           HE  +++GV ED+   I+NIK +  K++ D  +     +     GP  +  G+  +  +I
Sbjct: 66  HEFDTVRGVAEDVAPFIVNIKNLKFKVNEDMQQHEKFELHYEFNGPMELR-GEHLSNENI 124

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
            VL+ D  + N++ DA ++  + + KG G+V ++  R E      I +DA ++P+K+  Y
Sbjct: 125 TVLSTDSHLANINSDAKLKFSILIHKGLGFVASETIREEI-GSEYIPLDADFTPVKRAVY 183

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            +E+       +++K+   ++T+G I   ++   A  I+  Q+ +F   E          
Sbjct: 184 DIENVLHESNPNFEKIVFEVETNGQIEPMEAFKEAVAIMHSQMSVF-GAELSDVPTSNGR 242

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                P    LL  VE L L  R +NCL+  NI Y+G+L+   E+D+  + N G++S  E
Sbjct: 243 LNDDSPELKVLLSSVEILNLEHRPSNCLQKSNIKYIGELVLMNESDLKNIKNLGKRSFDE 302

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           I   L  +G  +G +LP     ++ +   K + +
Sbjct: 303 ITAKLNEVGYAVGADLPHELATTLSKRLAKLKGQ 336


>gi|317178416|dbj|BAJ56204.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori F30]
          Length = 344

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 103/335 (30%), Positives = 168/335 (50%), Gaps = 16/335 (4%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+ + 
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLSSE 127

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IE++NP+  +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIK 
Sbjct: 128 H-IEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKN 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMGKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKSVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337
             EI   L  +G  +G  L    PE  E L K+ E
Sbjct: 304 YDEIAEKLNDLGYPVGTEL---NPEQRESLKKRLE 335


>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 =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 103/337 (30%), Positives = 171/337 (50%), Gaps = 13/337 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+ + 
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALIGQDSSLENQSVVVDYSFKGPMELKARDLSSE 127

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IE++NP+  +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIK 
Sbjct: 128 H-IEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKN 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMGKQLGVF--GERPITNTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             EI   L  +G  +G  L     ES+++  +K EDK
Sbjct: 304 YDEIAEKLNDLGYPVGTELSSEQRESLKKRLEKLEDK 340


>gi|71056943|emb|CAH59030.1| DNA-directed RNA polymerase alpha chain [Enterococcus hirae]
          Length = 225

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 104/225 (46%), Positives = 150/225 (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 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
             ++++L+++I+ + L +F+N  +  K  +  +  +       L 
Sbjct: 181 PLEAMSLSAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLE 225


>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 =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 105/305 (34%), Positives = 173/305 (56%), Gaps = 7/305 (2%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
            +       +   P+ +G AH LGN++RR L+SSL GA+I  V IDGVLHE S+++ V E
Sbjct: 18  EELGAFGYKIQVSPVEKGMAHILGNSIRRFLLSSLSGASIIKVNIDGVLHEYSTLEDVKE 77

Query: 81  DLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           D+ +I+ N+K + +K+  +  K  + +     GVVTAGD +T   IE++N D  I  L  
Sbjct: 78  DVVEIVSNLKKVAIKLDKNVSKVELELSVTKSGVVTAGDFKTTQGIEIINKDQPIATLTN 137

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           +    +  TVS G          TE + +G I +D+ ++PIK+V++ +           +
Sbjct: 138 ERKFSLTATVSVGRNVGILSALPTELEKVGDIAVDSDFNPIKRVAFEIF-----DNGTNE 192

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
            L + + T+G+I    +V  A     +Q+ +F++   P    K    +     +P LLK 
Sbjct: 193 TLEVFVKTNGTIEPLVAVTKALEYFCEQISVFVSLRVP-SNGKTGDALLDSNIDPILLKP 251

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
           +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L    L LG+
Sbjct: 252 IDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQILIDNNLSLGV 311

Query: 320 NLPDW 324
            + ++
Sbjct: 312 QIDNF 316


>gi|51859691|gb|AAU11125.1| RNA polymerase alpha subunit [Psathyrostachys caduca]
          Length = 339

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 83/289 (28%), Positives = 141/289 (48%), Gaps = 20/289 (6%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGSVPHEYSTIAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+++    I NL 
Sbjct: 81  EESVQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIVDXAQPIANLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 ++L + +  GY        +N   G   IDA+  P++ V+Y++ S   G    +
Sbjct: 141 EPIDFCIDLQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  + P      +
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRFTPPLFTFQKR 256

Query: 259 ----------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
                            +++LEL+ R+ NCL+  NI  + DL+ +TE D
Sbjct: 257 LTNLKKNKKGIPLNCIFIDQLELTSRTYNCLKRANIHTLLDLLSKTEED 305


>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 =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 104/337 (30%), Positives = 170/337 (50%), Gaps = 13/337 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKESNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPIGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+   
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDL-NS 126

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
             IE++NP+  +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKK
Sbjct: 127 EQIEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKK 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYTQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             EI   L  +G  +G  L     ES+++  +K EDK
Sbjct: 304 YDEIAEKLNDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|150036790|emb|CAM98272.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 223

 Score =  244 bits (623), Expect = 2e-62,   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|323925205|gb|ADY11797.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 240

 Score =  244 bits (623), Expect = 2e-62,   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|332144690|dbj|BAK19505.1| RNA polymerase alpha subunit [Lactobacillus kisonensis]
          Length = 232

 Score =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 108/231 (46%), Positives = 151/231 (65%), Gaps = 4/231 (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 SKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           +KG GYV A     R+   PIG++ +D++Y+PI++V+Y VES R GQ  D+DKL++ + T
Sbjct: 121 NKGRGYVSAVENKKRSSEMPIGVLPVDSIYTPIERVNYQVESTRVGQRDDFDKLTLDVWT 180

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           DGSIT  ++V+LA++IL + L MF++  +  K  +  +  +       L  
Sbjct: 181 DGSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMVEKEETHKEKMLEM 231


>gi|317182539|dbj|BAJ60323.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori F57]
          Length = 344

 Score =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 103/337 (30%), Positives = 171/337 (50%), Gaps = 13/337 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+ + 
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSE 127

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IE++NP+  +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIK 
Sbjct: 128 H-IEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKN 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             EI   L  +G  +G  L     ES+++  +K EDK
Sbjct: 304 YDEIAEKLNDLGYPVGTELSPDQRESLKKRLEKLEDK 340


>gi|323925187|gb|ADY11791.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
          Length = 240

 Score =  244 bits (623), Expect = 2e-62,   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|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 =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 91/330 (27%), Positives = 166/330 (50%), Gaps = 9/330 (2%)

Query: 10  IKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL 69
             P     + +    +N   + A P   GFA TL + LRR+L+SS  G A  AV+I+G  
Sbjct: 6   ETPFLPTEVEIEAISDNEAKISAYPFEDGFAITLAHPLRRLLLSSSVGCAPIAVKIEGAS 65

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT-IFKRGPGVVTAGDIQTVNDIEVL 128
           HE  S++G+ ED+   ++N+K I  K++GD  + V      GP  +   D+   ++++V+
Sbjct: 66  HEFDSLRGMLEDVAIFVINLKNIKFKINGDKEQVVVEYSFNGPRDIKGEDLI-NSEVDVV 124

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           + D  +  ++ D  +   + + KG GY+P++  R +      I IDA ++P+KKV Y +E
Sbjct: 125 SKDAHLATINSDCNLTFSVILQKGIGYMPSEDIR-DIVGADYIPIDAFFTPVKKVVYDIE 183

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
                   +Y+K    + T+G I+   +   A  ++  Q+ +F    +   EV    + +
Sbjct: 184 KMLVEDNPNYEKAVFRVQTNGQISPVTAFKEAVSVMYSQMSVFNKVFDL-SEVAVSDSGE 242

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                  L+ ++++L LS RS N L    + Y+G+L+  +E ++  + N G+KS  EI  
Sbjct: 243 EPVELKELVIRIDDLNLSARSFNSLDRAGLKYLGELVLMSEVEVKNIKNLGKKSYDEIAE 302

Query: 309 VLGTMGLFLGMNLPDWPPESIEE-LAKKYE 337
            L ++G      + +  PE++   L +K E
Sbjct: 303 KLESLGYP----VENTLPENVASALRRKLE 328


>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 =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 106/322 (32%), Positives = 164/322 (50%), Gaps = 8/322 (2%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +    +    + A P   G+A TL + LRR+L SS  G A T V+I GV HE  S++G+
Sbjct: 15  SIENISDTVAKVSAWPFEIGYAITLAHPLRRLLYSSTVGFAPTGVKIKGVAHEFDSMRGM 74

Query: 79  HEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
            ED+   I+N+K +  K+  DS K  VT   +GP  +   D+     +EV+N D  +  +
Sbjct: 75  LEDVALFIINLKKLRFKLKTDSEKEIVTFSFKGPKEICGKDLDNDV-VEVVNADSYLATI 133

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           + DA +   L + KG GYVP++  +   DP   I +DA ++P+K   Y +E        D
Sbjct: 134 NEDADLEFTLIIEKGIGYVPSEEVQNFLDP-EFIALDAFFTPVKHAVYDIEKVLFEDNPD 192

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           Y+K+  TI TDG I+  D+   A   +  QL +F       + V       +   +  LL
Sbjct: 193 YEKVVFTITTDGQISPSDAFKNALEAMYKQLSVFDKITN-AQSVVRSQTQNNEVEHVKLL 251

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + + EL L  RS NCL   N+VY+G+L     +++  + N G+KSL EIK V+ ++G  +
Sbjct: 252 QNITELNLGARSFNCLEKANVVYIGELALMNASELADLKNLGKKSLDEIKSVMESIGFPI 311

Query: 318 G-MNLPDWPPESIEELAKKYED 338
           G   L D    + E L KK  +
Sbjct: 312 GNSKLSD---SAKETLKKKITE 330


>gi|317178032|dbj|BAJ55821.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori F16]
          Length = 344

 Score =  244 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 102/337 (30%), Positives = 171/337 (50%), Gaps = 13/337 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+ + 
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSE 127

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IE++NP+  +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIK 
Sbjct: 128 H-IEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKN 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             EI   L  +G  +G  L     E++++  +K EDK
Sbjct: 304 YDEITEKLNDLGYPVGTELNPEQRENLKKRLEKLEDK 340


>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 =  244 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 103/336 (30%), Positives = 169/336 (50%), Gaps = 16/336 (4%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+ + 
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSE 127

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IE++NP+  +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKK
Sbjct: 128 H-IEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKK 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
             EI   L  +G  +G  L     E  E L K+ E+
Sbjct: 304 YDEIAEKLNDLGYPVGTELS---HEQRESLKKRLEN 336


>gi|119668283|emb|CAK95498.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
          Length = 220

 Score =  244 bits (622), Expect = 2e-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|297380475|gb|ADI35362.1| DNA-directed RNA polymerase, alpha subunit [Helicobacter pylori
           v225d]
          Length = 344

 Score =  244 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 104/335 (31%), Positives = 168/335 (50%), Gaps = 16/335 (4%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRIKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+ + 
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDL-SS 126

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
             IE++NP+  +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKK
Sbjct: 127 EYIEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKK 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLNAKIENMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337
             EI   L  +G  +G  L    PE  E L K+ E
Sbjct: 304 YDEIAEKLNDLGYPVGTEL---NPEQRESLKKRLE 335


>gi|315587182|gb|ADU41563.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori 35A]
          Length = 344

 Score =  244 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 103/335 (30%), Positives = 168/335 (50%), Gaps = 16/335 (4%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+ + 
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSE 127

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IE++NP+  +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIK 
Sbjct: 128 H-IEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKN 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337
             EI   L  +G  +G  L    PE  E L K+ E
Sbjct: 304 YDEIAEKLNDLGYPVGTEL---NPEQRESLKKRLE 335


>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 =  244 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 97/329 (29%), Positives = 157/329 (47%), Gaps = 11/329 (3%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
            P  +E   +     NR  ++A P   G+A TL + LRR+++ S  G A  +V+I+G  H
Sbjct: 10  MPTEVEVNEI---SANRAEIVAYPFESGYAVTLAHPLRRLILGSSIGYAPISVKIEGAAH 66

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           E  +I+G+HED+   I+N+K I  K+  G     +     G   VTA D+     IEV+N
Sbjct: 67  EFDNIRGMHEDVAVFIINLKNIRFKIKDGSDRVELKYSFSGYKEVTAQDLNND-QIEVVN 125

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
            D  +  L+ DA +   + ++KG GYVP++  R E  P   I +DA ++P++K +Y +E 
Sbjct: 126 GDLPLATLNEDAELNFTMVIAKGIGYVPSEDLRDEVAPDS-IALDAFFTPVRKANYKIEP 184

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                  +++K++  I+TD  I   ++   A  ++  QL +F    +             
Sbjct: 185 VLVEDNPNFEKITFDIETDAQIGPVEAFTNALEVMNKQLSVFNGVLDVDISTTLPKRTND 244

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                  L  V+ L LS RS N L    I ++G+L+  +E ++  + N G+KSL E    
Sbjct: 245 DNELKPFLAAVDALGLSARSFNSLDRAGIKFLGELVLMSENEIKNIKNLGKKSLDETNEC 304

Query: 310 LGTMGLFLGMNLPDWPPESI-EELAKKYE 337
           L   G   G        E+    L KK E
Sbjct: 305 LVEHG--FGPEFE--LKENTRANLVKKLE 329


>gi|150036806|emb|CAM98276.1| DNA-directed RNA polymerase alpha chain [Fructobacillus
           pseudoficulneus]
          Length = 242

 Score =  244 bits (622), Expect = 2e-62,   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|58761465|gb|AAW82426.1| RNA polymerase alpha subunit [Takakia lepidozioides]
          Length = 382

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 76/322 (23%), Positives = 142/322 (44%), Gaps = 24/322 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +     + +     P   G A T+G A+RR  +  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSARLHYSRFAIPPFRSGQASTVGIAMRRASLGEVEGTCITCAESKRVTHEYSTILGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + D+ +N   I L+      ++  I   GP  VTA DI +   +++++       + 
Sbjct: 81  QESVHDVSINSGEIVLRSDSYETQKAFISILGPKKVTAQDIISPPSVKIIDTTQYTATVT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + K  GY      ++ +   G    DA++ PI+  +Y+V S   G     
Sbjct: 141 KAIHSDIELKIEKDFGYRIEDPIKSAD---GNSPADAVFMPIRNANYSVHSFENGNET-Q 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP----------KKEVKEDINVK 248
           + L + I T+GS+T ++++  ASR L +    F++ E+           +  +    +  
Sbjct: 197 EILFLEIWTNGSVTPKEALYEASRSLINLFIPFLHAEKKEFIYGLKNTYESNMSYFSSPS 256

Query: 249 SLPFNPALLK-------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
                  + K        +++LEL  R+ NC +  N   + D +  ++ D++++ NFG+K
Sbjct: 257 LSADIDEMTKGVTFKHIFIDQLELPARAYNCPKRVNAHTISDPLNYSQDDLMKIKNFGKK 316

Query: 302 SLVEIKGVLGTMGLFLGMNLPD 323
           S   ++ VL        +NLP 
Sbjct: 317 S---VEQVLEASQKRFSINLPK 335


>gi|161513426|emb|CAP16856.1| DNA-directed RNA polymerase subunit alpha [Pediococcus parvulus]
          Length = 223

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 98/223 (43%), Positives = 147/223 (65%), 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 --KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
                R ++ 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|332144684|dbj|BAK19502.1| RNA polymerase alpha subunit [Lactobacillus diolivorans]
          Length = 216

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 107/216 (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 GHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
           G GYV A     R+   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|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 =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 80/326 (24%), Positives = 143/326 (43%), Gaps = 25/326 (7%)

Query: 15  IEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           I++  +  + E    +    +  P  RG  +T+G A+RR L+  + GA+IT  + +GV+H
Sbjct: 13  IQWKCVESKTESKRLHHGRSVISPFKRGQVNTVGIAMRRALLEEVGGASITCAKFEGVIH 72

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           E S+I G+ E + DI +N+K    +   +  K   +   GP  VTAGD      +++++ 
Sbjct: 73  EYSTITGIQETIHDISVNLKETVPRSDSNDSKEAFLSVTGPKRVTAGDTSLPPSVKIIDD 132

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
              I  +     V +E  + K  GY             G   +DA+  P++ V+Y+V   
Sbjct: 133 SQYIVTITQPISVNIESRIEKDCGYRI---EEFNGYRDGEFPVDAVPMPVRNVNYSVHPF 189

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK-- 248
             G     +   + I T+GS T  +++  AS+ L D L  F++ +       ED      
Sbjct: 190 GSG-REMREISFIEIWTNGSPTPNEALCEASKNLIDLLIPFLHMKHEDVPHFEDEQDSSD 248

Query: 249 ------------SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
                                  +++LE   R+ NCL+   I  + DL+  +  D+L++ 
Sbjct: 249 LTILSSQLIGVGESEGEVLRNTFIDQLESPARAFNCLKRAEIHTITDLLNHSREDLLKIK 308

Query: 297 NFGRKSLVEIKGVLGTMGLFLGMNLP 322
           +FG+KS+ ++   L          LP
Sbjct: 309 SFGKKSVDQVSRALWER---FATELP 331


>gi|150187102|emb|CAK30171.1| RNA polymerase alpha subunit [Streptococcus agalactiae]
          Length = 219

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 94/218 (43%), Positives = 147/218 (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 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           +I  ED++ L++R+L + L +F +  E  K  +     
Sbjct: 181 TIIPEDALGLSARVLIEHLNLFTDLTEVAKATEVMKET 218


>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 =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 82/319 (25%), Positives = 154/319 (48%), Gaps = 22/319 (6%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +  +       P  +G A+T+G A+RR L+  + G +IT+ +  G  HE S++ G+
Sbjct: 21  RIESKRLHYGRFAISPFQKGQANTVGIAIRRALLGEVGGTSITSAKFQGAAHEYSTMAGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + DI++N+K I L+ +    ++  I   GP  + AGDIQ  + +++++P   I  + 
Sbjct: 81  QESIHDILMNLKEIVLENNSYEVQKGFIQVIGPKKILAGDIQVCSSVKIIDPSQYIATIT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + K  GY        EN+      IDA++ PI+  +Y+V S ++ + L Y
Sbjct: 141 KSISLNIELKIEKDRGYRIKNTDLKENE----FPIDAIFMPIRNANYSVHSFQKNKQL-Y 195

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK---------- 248
           + L + I T+GS+T E +++ A+R L D +   I+  +   E   +              
Sbjct: 196 EILFLEIWTNGSLTPEKAISEATRNLIDLVVPLIHIGDKLTENPINGTSDINFPSVSGTN 255

Query: 249 ----SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
                          +++LEL  R+ N L+  N+  + DL+  TE D+  + + G+KS+ 
Sbjct: 256 DLNKIAQEVAFKNIFIDQLELPARAYNGLKKVNVHTVSDLLMYTETDLRNIRSLGKKSVE 315

Query: 305 EIKGVLGTMGLFLGMNLPD 323
           +I   L  +     + L +
Sbjct: 316 QI---LEALQKKFAIKLSE 331


>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 =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 88/344 (25%), Positives = 167/344 (48%), Gaps = 31/344 (9%)

Query: 1   MIQKNWQELIKP-NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSL 55
           MIQ    E+  P   +++  +  ++E    +       P  +G A T+G A+RR L+  +
Sbjct: 1   MIQ---DEIPIPVQTLQWKCIESKKEGKRLHYGRFAVSPFRKGQASTVGVAMRRALLGEV 57

Query: 56  RGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVT 115
            G +IT  +   V+HE S++ G+ E + DI++N+K I L+      ++ +I   GP  VT
Sbjct: 58  EGTSITYAKFKNVVHEYSTLVGIKESIHDILINLKEIVLQSDSYETQKASISILGPRDVT 117

Query: 116 AGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDA 175
           AGDI     +++++    I  +     + +EL + +  GY   +    +    G   IDA
Sbjct: 118 AGDILLPTSVKIIDASQHIATITTAIPLDVELRIERDCGY---RTLNLKESQSGEFFIDA 174

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           L++PI+  +Y++ S  E      + L + + T+GS+T   +++ ASR L D   +F+N E
Sbjct: 175 LFTPIRNANYSIHSF-ESNNKVREILFLEVWTNGSLTPGAALSEASRDLIDLFIIFLNME 233

Query: 236 EPKKEVKEDINVKSLPFNPALLKK----------------VEELELSVRSTNCLRGENIV 279
           + +   + + N  ++   P+                    +++LEL  R+ NCL+   + 
Sbjct: 234 KEESIKEIENNELNIKNFPSTSISVDIDRMAKEVAFKQIFIDQLELPARAYNCLKKMQVH 293

Query: 280 YMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            + DL++ T+ D+ ++ NFG KS+ ++   L        + LP 
Sbjct: 294 TVSDLLKYTQYDLKKVKNFGNKSVEQVVEALQER---FAIQLPK 334


>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 =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 96/321 (29%), Positives = 167/321 (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+ GDS+K  V    +G   +   D+     +EV+N D  +  +
Sbjct: 75  LEDVALFIINLKKLRFKIKGDSNKEIVEFNFKGSKEIYGKDLNND-QVEVVNKDAYLATI 133

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
           + D  ++  L + KG GYVP++  +   +    I +DA ++P+++ +Y +E        D
Sbjct: 134 NEDTELKFTLIIEKGIGYVPSEEIKELLNDPKFIALDAFFTPVREATYDIEKVLFEDNPD 193

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           Y+K+ +T+ TDG IT  ++   A   +  QL +F      +  +K       L  N  LL
Sbjct: 194 YEKVVLTVTTDGQITPNEAFQNALEAMYKQLSVFDKITNVRSAIKNQATSNELE-NTKLL 252

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           + + +L LS RS NCL    +VY+G+L   + +++  + N G+KSL EIK ++ ++G  +
Sbjct: 253 QNITDLNLSARSYNCLEKAGVVYIGELALMSVSELAGLKNLGKKSLDEIKNIMESIGFPV 312

Query: 318 GMNLPDWPPESIEELAKKYED 338
           G +      ++ E L  K  +
Sbjct: 313 GTS---KLSDNKEILKNKIVE 330


>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 =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 106/321 (33%), Positives = 179/321 (55%), Gaps = 11/321 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DG 67
           L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+V+I DG
Sbjct: 6   LLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGYALKQTMLYSIHGACVTSVKINDG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
            +  +  +    E + DIILN+K + + +  G     +T    G       +   +++  
Sbjct: 63  KVTSLEDVIPCDETVADIILNVKSLPVTLAEGVDTGVITFELSGSEEEVFSEEAKLSEGL 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
            +  +  IC+ +    +++E  V KG GY  A+    EN       +DA +SP+    Y 
Sbjct: 123 AITEEVFICSYNGGKKLKIEAKVEKGIGYRQAQ----ENFKNEEFLLDAAFSPVSFCDYE 178

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           ++ AR G+  D DKL + I T+G+++ E+++ +A+  +Q+QL   ++ EE  K +   + 
Sbjct: 179 IKDARVGRRTDLDKLELNIKTNGNVSCEEALRIAATKIQNQLRNIVDVEEINKGI--FVE 236

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
             +   NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL EI
Sbjct: 237 DPTKDINPLLLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLTEI 296

Query: 307 KGVLGTMGLFLGMNLPDWPPE 327
           K  L  +GL LG  + +WP +
Sbjct: 297 KDKLSELGLSLGTMIDNWPED 317


>gi|317011493|gb|ADU85240.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           SouthAfrica7]
          Length = 344

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 103/337 (30%), Positives = 169/337 (50%), Gaps = 13/337 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPIGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+   
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDL-NS 126

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
             IE++NP+  +  ++ DA +   L + KG GYVP++  R E  P G + +D  ++PIK 
Sbjct: 127 EQIEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSEITR-ELMPEGYMPLDGSFTPIKN 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E+P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GEKPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             EI   L  +G  +G  L     ES+++  +K EDK
Sbjct: 304 YDEIAEKLSDLGYPVGTELSPEQRESLKKRLEKLEDK 340


>gi|119662849|emb|CAJ33217.1| RNA polymerase alpha subunit [Lactobacillus suebicus]
          Length = 219

 Score =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 101/219 (46%), Positives = 152/219 (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 PA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A     R ++ 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|119668289|emb|CAK95500.1| RNA polymerase alpha subunit [Lactobacillus buchneri]
          Length = 227

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 108/227 (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 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 GSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           GSIT  ++V+LA++IL + L MF++  +  K  +  +  +       
Sbjct: 181 GSITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMVEKEETHKEKM 227


>gi|119668285|emb|CAK95451.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
          Length = 217

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 94/216 (43%), Positives = 138/216 (63%)

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 SVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           +++ A++IL +   +F + +   +  +  +  +   
Sbjct: 181 ALSFAAKILVEHFKVFESADANTQFSEVMVEKEDDK 216


>gi|154424845|emb|CAL18525.1| RNA polymerase alpha subunit [Streptococcus pyogenes]
          Length = 219

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 96/218 (44%), Positives = 147/218 (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 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           +I  ED++ L++R+L + L +F +  E  K  +     
Sbjct: 181 TIIPEDALGLSARVLIEHLNLFTDLTEVAKATEVMKET 218


>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 =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 103/338 (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   MRKITTSAYMPTEIEVKSV---SENVANITAYPFEAGYAVTLAHPLRRLLYTSTVGFAPI 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKRGPGVVTAGDIQ 120
            V+I GV HE  S++G+ ED+   I+N+K I  K+   S  + +    +GP  +T  D+ 
Sbjct: 58  GVKIKGVSHEFDSMRGMLEDVAFFIINLKKIRFKLKSGSEREVIEYSFKGPKEITGADLN 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
               +E++NPD  +  ++ DA +   + + KG GYVP++  R E +   +  +DA ++P+
Sbjct: 118 NDL-VEIVNPDAYLATINEDAELNFSVIIQKGIGYVPSEEIREEIEDEYI-ALDAFFTPV 175

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KK  Y +++       DY+K+  TI TDG +   ++       +  Q+ +F    +    
Sbjct: 176 KKAVYEIQNVLVEDDPDYEKIVFTITTDGQVGPVEAFKNCLEAMYQQMSVFKGILDIDVS 235

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                +  S  F+  LL  VE+L LS RS NCL    I ++G+L    E ++  + N G+
Sbjct: 236 APVASSSASGEFSK-LLSSVEDLNLSARSFNCLDKAEIRFIGELALMDENELKELKNLGK 294

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           KSL EIK V+  +G  +G+++     +S E+L KK  +
Sbjct: 295 KSLEEIKAVMEEIGYPVGVDV---LKDSKEQLRKKITE 329


>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 =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 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|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 =  242 bits (618), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 103/337 (30%), Positives = 169/337 (50%), Gaps = 13/337 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPIGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+   
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDL-NS 126

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
             IE++NP+  +  ++ DA +   L + KG GYVP+++ R E    G + +D  ++PIKK
Sbjct: 127 EQIEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMSEGYMPLDGSFTPIKK 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             EI   L  +G  +G  L     ES+++  +K EDK
Sbjct: 304 YDEIAEKLNDLGYPVGTELSHEQRESLKKRLEKLEDK 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 =  242 bits (618), Expect = 5e-62,   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|161513442|emb|CAP16864.1| DNA-directed RNA polymerase subunit alpha [Pediococcus inopinatus]
          Length = 223

 Score =  242 bits (618), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 99/223 (44%), Positives = 147/223 (65%), 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 --KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
                R ++ 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|119668359|emb|CAK95474.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
          Length = 221

 Score =  242 bits (618), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 99/220 (45%), Positives = 152/220 (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 GYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY+ A     R ++  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|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 =  242 bits (618), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 102/337 (30%), Positives = 171/337 (50%), Gaps = 13/337 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+ + 
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLSSE 127

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IE++N +  +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKK
Sbjct: 128 H-IEIVNLEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKK 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             EI   L  +G  +G  L     E++++  +K EDK
Sbjct: 304 YDEIAEKLNDLGYPVGTELSPEQRENLKKRLEKLEDK 340


>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 =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 96/328 (29%), Positives = 173/328 (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  EISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLN 129
           E  S++G+ ED++D ILN+K I  K+  ++ + +++    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|308064070|gb|ADO05957.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           Sat464]
          Length = 344

 Score =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 102/337 (30%), Positives = 171/337 (50%), Gaps = 13/337 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+ + 
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKVLVGQDSSLENQSVVVDYSFKGPMELRARDLSSE 127

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IE++N +  +  ++ DA +   L + KG GYVP+++ R E  P G + +D  ++PIKK
Sbjct: 128 H-IEIVNLEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMPEGYMPLDGSFTPIKK 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             EI   L  +G  +G  L     E++++  +K EDK
Sbjct: 304 YDEIAEKLNDLGYPVGTELSPEQRENLKKRLEKLEDK 340


>gi|261840008|gb|ACX99773.1| DNA-directed RNA polymerase alpha subunit [Helicobacter pylori 52]
          Length = 344

 Score =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 102/335 (30%), Positives = 167/335 (49%), Gaps = 16/335 (4%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+ + 
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSE 127

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IE++NP+  +  ++ DA +   L + KG GYVP+++ R E    G + +D  ++PIK 
Sbjct: 128 H-IEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELMHEGYMPLDGSFTPIKN 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GERPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337
             EI   L  +G  +G  L    PE  E L K+ E
Sbjct: 304 YDEIAEKLNDLGYPVGTEL---NPEQRESLKKRLE 335


>gi|150036766|emb|CAM98264.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides KCTC 3652]
          Length = 229

 Score =  242 bits (617), Expect = 7e-62,   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|161513422|emb|CAP16854.1| DNA-directed RNA polymerase subunit alpha [Pediococcus damnosus]
          Length = 222

 Score =  242 bits (617), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 101/222 (45%), Positives = 147/222 (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 --KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
                R ++ 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|161511727|emb|CAP16874.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 235

 Score =  242 bits (617), Expect = 7e-62,   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|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 =  242 bits (617), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 106/307 (34%), Positives = 175/307 (57%), Gaps = 9/307 (2%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
            +       +   P+ +G AH LGN++RR L+SSL GA+I  V IDGVLHE S+++ V E
Sbjct: 18  EELGAFGYKIQVSPVEKGMAHILGNSIRRFLLSSLSGASIIKVNIDGVLHEYSTLEDVKE 77

Query: 81  DLTDIILNIKGINLKMSGDSHK---RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           D+ +I+ N+K + +K+  +  K    +++ K G  VVTAGD +T   IE++N D  I  L
Sbjct: 78  DVVEIVSNLKKVAIKLDKNVSKVELELSVTKSGVVVVTAGDFKTTQGIEIINKDQPIATL 137

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
             +    +  TVS G          TE + +G I +D+ ++PIK+V++ +          
Sbjct: 138 TNEREFSLTATVSVGRNVGILSALPTELEKVGDIAVDSDFNPIKRVAFEIF-----DNGT 192

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
            + L + + T+G+I    +V  A     +Q+ +F++   P    K    +     +P LL
Sbjct: 193 NETLEVFVKTNGTIEPLVAVTKALEYFCEQISVFVSLRVP-SNGKTGDALLDSNIDPILL 251

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           K +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L    L L
Sbjct: 252 KPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQILIDNNLSL 311

Query: 318 GMNLPDW 324
           G+ + ++
Sbjct: 312 GVQIDNF 318


>gi|119662301|emb|CAJ33138.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           delbrueckii]
          Length = 215

 Score =  242 bits (617), Expect = 8e-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|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 =  241 bits (616), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 88/293 (30%), Positives = 149/293 (50%), Gaps = 7/293 (2%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
               E  +  + + L +G   T+GN LRRVL++ L G AITAV+I+G+ +E ++I GV E
Sbjct: 14  NDLGEQSSRFLLKELTQGQGLTIGNTLRRVLLTELEGTAITAVRINGINNEFATIPGVRE 73

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
           D+ +I+LN+K I             +  +GP +VTA +I   + + +LN +H I  +   
Sbjct: 74  DVLEILLNLKQIKFTGLVTEPFFTHVSVQGPQLVTAANISLPDGLSLLNSNHYIAAVAEQ 133

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
               +EL +  G GY               +++D++++P+K V+Y ++ + +      + 
Sbjct: 134 TNFEIELKIESGTGY-NFTDEENRICSGDFLSLDSIFTPVKNVNYQIKDSYKIDEKITEI 192

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L + I T+GSIT  D++  A+ +LQ   G  +  E     V              L   +
Sbjct: 193 LDLEIITNGSITPNDALNKAALVLQTLFGSLVIDELQTNPV------LPEQTETELDILI 246

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           EEL+LSVR+ NCL+  NI  + DL+Q +  ++  + NFG+KS  E+   L   
Sbjct: 247 EELQLSVRAYNCLKRVNIKTIADLVQYSVKELKDIKNFGQKSANEVVEKLQDR 299


>gi|150187156|emb|CAK30183.1| RNA polymerase alpha subunit [Streptococcus halichoeri]
          Length = 223

 Score =  241 bits (616), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 95/218 (43%), Positives = 146/218 (66%)

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 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           +I  ED++ L++R+L + L +F +  E  K        
Sbjct: 181 TIIPEDALGLSARVLIEHLNLFTDLTEVAKATDVMKET 218


>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 =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 106/307 (34%), Positives = 170/307 (55%), Gaps = 9/307 (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  LTDIILNIKGINLKMSG---DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL- 137
           +  I+LN+K + + +     D  + + +F  G   VTA   + V  I+++NP+  I NL 
Sbjct: 77  VMSIVLNLKQVVISVDSIDDDFEQEMELFVTGKQKVTASCFEQVEGIKIINPEQEIANLV 136

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
             +A ++M + + +G GYV A+ ++       GLI+ID LY+P+ KVSY +E     ++ 
Sbjct: 137 SENASLKMTVLIKRGIGYVSAEENKIYTKKKKGLISIDTLYTPVSKVSYDIEK----KLG 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 LGMNLPD 323
              +L  
Sbjct: 313 FQNDLEK 319


>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 =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 89/332 (26%), Positives = 165/332 (49%), Gaps = 8/332 (2%)

Query: 11  KPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
            P     + + +   N+  ++A P   G+A TL + LRR+L+SS  G A  A++I+GV H
Sbjct: 7   TPYIPTTVDVEELGPNKVRVMAYPFESGYAVTLAHPLRRLLLSSSVGLAPIALKIEGVAH 66

Query: 71  EISSIKGVHEDLTDIILNIKGINLKMS-----GDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           E  SI+G+ ED++  I+N+K I           +    +    +GP V++ G +     I
Sbjct: 67  EFDSIRGIVEDVSPFIVNLKNIRFLGKEGGFLEEEKVELHYSFQGPMVLSGGHLAND-QI 125

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           +++N +  +  ++ DAV+   + V KG GYVP++  R        I +DA ++P++K  Y
Sbjct: 126 DIVNKEAPLATINEDAVLNFSIIVQKGIGYVPSEDIRGLISE-DYIPLDAYFTPVRKAVY 184

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
            +E+        Y+K+   ++TDG +   ++   A  I+  Q+ +F N +       +  
Sbjct: 185 EIENVLVEDNPTYEKIIFDVETDGQVDPYEAFKQAIAIMYSQMSIF-NADISSISTTQKQ 243

Query: 246 NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            ++       LL K++ L L+ R  NCL    I Y+G+L+  +E+++  + N G+ S  E
Sbjct: 244 AIEDNFDFKDLLMKIDSLNLNARCFNCLDRIGIRYVGELVLMSESEIKGVKNLGKTSYNE 303

Query: 306 IKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337
           I   L  +G  +G  L +    ++ +   K +
Sbjct: 304 IVEKLQEIGYPIGTELEEDKKIALTKKISKLK 335


>gi|332144682|dbj|BAK19501.1| RNA polymerase alpha subunit [Lactobacillus buchneri]
          Length = 226

 Score =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 107/226 (47%), 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 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 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           SIT  ++V+LA++IL + L MF++  +  K  +  +  +       
Sbjct: 181 SITPSEAVSLAAKILTEHLEMFVDLTDEAKNTEIMVEKEETHKEKM 226


>gi|72534403|emb|CAH59034.1| DNA-directed RNA polymerase alpha chain [Enterococcus sp. LMG
           13603]
          Length = 226

 Score =  241 bits (616), Expect = 1e-61,   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|72534407|emb|CAH59040.1| DNA-directed RNA polymerase alpha chain [Enterococcus gallinarum]
          Length = 219

 Score =  241 bits (616), Expect = 1e-61,   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|161511771|emb|CAP16896.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 229

 Score =  241 bits (615), Expect = 1e-61,   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|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 =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 105/250 (42%), Positives = 163/250 (65%), 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++  + +   +++   +  P    LL+ V+
Sbjct: 121 VIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVD 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|119672807|emb|CAK95484.1| RNA polymerase alpha subunit [Lactobacillus fermentum]
          Length = 196

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 92/196 (46%), Positives = 137/196 (69%), 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 SKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
            KG GY  A     R 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|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 =  241 bits (615), Expect = 1e-61,   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 ENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
            ++   +I    +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 ARILVDQLSVFAAL-EGTESAAEAAAARAPQIDPILLRPVDDLELTVRSANCLKAENIYY 179

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +GDLIQRTE ++L+  N GRKSL EIK VL + GL LGM L +WPP  +E+
Sbjct: 180 IGDLIQRTENELLKTPNLGRKSLNEIKEVLASRGLTLGMKLENWPPAGLEK 230


>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 =  241 bits (615), Expect = 1e-61,   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|150036812|emb|CAM98039.1| DNA-directed RNA polymerase alpha chain [Fructobacillus
           pseudoficulneus]
          Length = 240

 Score =  241 bits (615), Expect = 1e-61,   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|71056951|emb|CAH59036.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           casseliflavus]
          Length = 219

 Score =  241 bits (614), Expect = 1e-61,   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|197941213|gb|ACH78326.1| RNA polymerase [Streptococcus equi subsp. zooepidemicus]
          Length = 226

 Score =  241 bits (614), Expect = 1e-61,   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|151416838|emb|CAO78490.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gelidum]
          Length = 220

 Score =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 93/219 (42%), Positives = 139/219 (63%), Gaps = 2/219 (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 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           +GSI   D+++L S+IL + L +F++      E    + 
Sbjct: 181 NGSIKPSDALSLGSKILAEHLNLFMDISPVAAEANVMVE 219


>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 =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 103/337 (30%), Positives = 172/337 (51%), Gaps = 13/337 (3%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRIKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPVGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMS---------GDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+ + 
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSPLENQSVVVDYSFKGPMELRARDLNSE 127

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + IE++NP+ ++  ++ DA +   L + KG GYVP++  R E  P G + +D  ++PIK 
Sbjct: 128 H-IEIINPEMLLATINEDAQLNFSLIIYKGMGYVPSEITR-ELMPEGYMPLDGSFTPIKN 185

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V Y +E+       +Y+K+   I+TDG I    +   A +++  QLG+F   E+P    +
Sbjct: 186 VVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSKQLGVF--GEKPIANTE 243

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
              +         L  K+E + LS R  NCL    I Y+G+L+  +E ++  + N G+KS
Sbjct: 244 YSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVLMSEEELKGVKNMGKKS 303

Query: 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             EI   L  +G  +G  L     ES+++  +K EDK
Sbjct: 304 YDEIAEKLNDLGYPVGTELSLEQRESLKKRLEKLEDK 340


>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 =  241 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 94/328 (28%), Positives = 167/328 (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  EISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLN 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 ++    E    G I +DA ++P++  +Y +E+
Sbjct: 126 PNTHLATLNEDSTLNFSIRIAQGIGYVASEDTYDE-LQDGYIALDAYFTPVRSATYKIEN 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|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 =  241 bits (614), Expect = 2e-61,   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 GHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           G GYVP    +  ++   +I    +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|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 =  240 bits (613), Expect = 2e-61,   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  PTKIEVKEVG---VNKVQITAYPFENGYAITLAHPLRRLLLGSSVGFAPVALHIAGVAHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
             S++GV ED++  I+N+K I  K+  DS    V     GP V+T  D+     +EV+ P
Sbjct: 68  FDSVRGVTEDVSQFIVNLKTIRFKIKDDSDSVSVDYTFNGPKVITGADLSNDL-VEVVTP 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|119668309|emb|CAK95455.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           delbrueckii]
          Length = 200

 Score =  240 bits (613), Expect = 2e-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|154424745|emb|CAL18475.1| RNA polymerase alpha subunit [Streptococcus salivarius]
          Length = 214

 Score =  240 bits (613), Expect = 2e-61,   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|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 =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 97/329 (29%), Positives = 169/329 (51%), Gaps = 12/329 (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  PTKIEVKEVG---ANKIEITAYPFEAGYAITLAHPLRRLLLGSSVGFAPVALRIEGVAHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR--GPGVVTAGDIQTVNDIEVLN 129
             S++GV ED++  I+N+K I  K+  D  + V+I  +  GP V+T  D++    ++++ 
Sbjct: 68  FDSVRGVVEDVSHFIVNLKTIRFKVKDD-SESVSIDYKFIGPKVITGEDLKNDL-VDIVT 125

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES 189
           P+  +  ++ DA++   + V KG GYVP++  R       +  +DA ++P+  V+Y  E+
Sbjct: 126 PNIHLATINEDAILNFSIIVRKGIGYVPSEDIRNLISEGYM-PLDAYFTPVTSVTYDTEN 184

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
                  +Y+K+   I TDG I    +   A  ++  Q+ +F N E   +  +  +  + 
Sbjct: 185 VLVEDDPNYEKVVFNIQTDGQIEPLTAFKNALSVMHKQMAIF-NSELNIEVPEVSLGEED 243

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
            P    L + ++ L  S R  NCL    I Y+G+L+  +E  +  + N G+KSL EI   
Sbjct: 244 SPEIRVLSQSIDSLNFSARCFNCLDRSGIKYLGELVLLSEDQIKNIKNLGKKSLDEITVK 303

Query: 310 LGTMGLFLGMNLPDWPPESIEELAKKYED 338
           L  +G  +G  + +   +    L KK+ +
Sbjct: 304 LEELGYPIGKVIAE---DLAALLKKKFSN 329


>gi|119668299|emb|CAK95504.1| RNA polymerase alpha subunit [Lactobacillus curvatus]
          Length = 212

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 91/210 (43%), Positives = 144/210 (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 ALASRILQDQLGMFINFEEPKKEVKEDINV 247
           +LA++I+ + L +F++  +  K  +  +  
Sbjct: 181 SLAAKIMTEHLAIFVDLTDEAKNAEIMVEK 210


>gi|150036744|emb|CAM98026.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. mesenteroides]
          Length = 226

 Score =  240 bits (612), Expect = 3e-61,   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|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 =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 105/321 (32%), Positives = 180/321 (56%), Gaps = 11/321 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DG 67
           L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I DG
Sbjct: 6   LLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKINDG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
            +  +  +    E + DIILN+K + + +  G     +T    G       +   +++  
Sbjct: 63  KVTSLEDVIPCDETVADIILNVKSLPVTLAEGVETGTITFELSGSEEEIFSEEAKLSEGL 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
            +  +  IC+ +    +++E  V KG G+ PA+    +N   G   +DA +SP+    + 
Sbjct: 123 AITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQ----DNFKNGEFLLDATFSPVVFCDFE 178

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +   + 
Sbjct: 179 IKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGI--FVE 236

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
             +   NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL EI
Sbjct: 237 DPTKDINPILLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLTEI 296

Query: 307 KGVLGTMGLFLGMNLPDWPPE 327
           K  L  +GL LG  + +WP +
Sbjct: 297 KDKLSELGLSLGTLIENWPQD 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 =  239 bits (611), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 105/321 (32%), Positives = 180/321 (56%), Gaps = 11/321 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DG 67
           L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I DG
Sbjct: 6   LLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKINDG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
            +  +  +    E + DIILN+K + + +  G     +T    G       +   +++  
Sbjct: 63  KVTSLEDVIPCDETVADIILNVKSLPVTLAEGVETGTITFELSGSEEEIFSEEAKLSEGL 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
            +  +  IC+ +    +++E  V KG G+ PA+    +N   G   +DA +SP+    + 
Sbjct: 123 AITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQ----DNFKDGEFLLDATFSPVVFCDFE 178

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +   + 
Sbjct: 179 IKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGI--FVE 236

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
             +   NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL EI
Sbjct: 237 DPTKDINPILLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLTEI 296

Query: 307 KGVLGTMGLFLGMNLPDWPPE 327
           K  L  +GL LG  + +WP +
Sbjct: 297 KDKLSELGLSLGTLIENWPQD 317


>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 =  239 bits (611), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 98/337 (29%), Positives = 171/337 (50%), Gaps = 8/337 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + K   E++ P+++ +     EE N+  +   P   GF  ++ + +RR L++S  G A  
Sbjct: 1   MNKIKTEVLIPSDVSFK----EEGNKATIEVYPFEAGFGVSVAHPIRRTLIASTPGFAPI 56

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           A++I+GV HE  S+KG+ ED+   I+N+K I  K+       V     GP  +   D+  
Sbjct: 57  ALKIEGVKHEFDSLKGMLEDVASFIINLKNIRFKIKEGDEAVVDYVFVGPKEIKGSDLAN 116

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
              ++++ P+  I  L+ +A +++ L + KG G+V  ++ R E  P G I +DA +SPIK
Sbjct: 117 DL-VDIVTPNEYIATLNEEAELKLTLIIRKGMGFVAVENFRDEI-PEGFIGLDAYFSPIK 174

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           KV Y +E+       +++K+   ++TDG I+  D+   A     +Q  +F   +E K E 
Sbjct: 175 KVVYNIENILVEDDPNFEKVIFEVETDGQISPIDAFKNAVNNYLNQFSVF--SKEFKLEQ 232

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           K   +V+       L + +E L L  RS N L    I ++G+L+   +  +  + N G K
Sbjct: 233 KTSQSVELDEVYNVLFEPIENLNLRSRSFNALDRAGIRFVGELVLMGKEKISNIKNLGTK 292

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           SL EI   L  +G  L   LP    ++IE+   + ++
Sbjct: 293 SLEEIFDKLEEIGFPLNKTLPLDIKKAIEDKLSQLKE 329


>gi|161511749|emb|CAP16885.1| DNA-directed RNA polymerase subunit alpha [Pediococcus parvulus]
          Length = 214

 Score =  239 bits (611), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 97/214 (45%), Positives = 145/214 (67%), 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 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA- 158
             K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A 
Sbjct: 61  DEKSLEINVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAVLTADTGRGYVSAD 120

Query: 159 -KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
               R ++ PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSI+  ++ 
Sbjct: 121 ENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSISPSEAT 180

Query: 218 ALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           +L+++IL + L +F+N  +  ++ +  +  +   
Sbjct: 181 SLSAKILTEHLALFVNLTDEAQDAEIMVEKEETN 214


>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 =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 105/321 (32%), Positives = 180/321 (56%), Gaps = 12/321 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DG 67
           L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I DG
Sbjct: 6   LLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKINDG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIE 126
            +  +  +    E + DIILN+K + + ++ D     +T    G       +   +++  
Sbjct: 63  KVTSLEDVIPCDETVADIILNVKSLPVTLAEDVEMGTITFELSGSEEEIFSEEAKLSEGL 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
            +  +  IC+ +    +++E  V KG G+ PA+    +N   G   +DA +SP+    + 
Sbjct: 123 AITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQ----DNFKDGEFLLDATFSPVVFCDFE 178

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +  +  
Sbjct: 179 IKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGIFVEDP 238

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
                 NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL EI
Sbjct: 239 K---DINPILLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLTEI 295

Query: 307 KGVLGTMGLFLGMNLPDWPPE 327
           K  L  +GL LG  + +WP +
Sbjct: 296 KDKLSELGLSLGTLIENWPQD 316


>gi|119668365|emb|CAK95514.1| RNA polymerase alpha subunit [Lactobacillus rhamnosus]
          Length = 205

 Score =  239 bits (611), Expect = 4e-61,   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|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 =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 105/321 (32%), Positives = 180/321 (56%), Gaps = 11/321 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DG 67
           L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I DG
Sbjct: 6   LLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKINDG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
            +  +  +    E + DIILN+K + + +  G     +T    G       +   +++  
Sbjct: 63  KVTSLEDVIPCDETVADIILNVKSLPVTLAEGVETGTITFELSGSEEEIFSEEAKLSEGL 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
            +  +  IC+ +    +++E  V KG G+ PA+    +N   G   +DA +SP+    + 
Sbjct: 123 AITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQ----DNFKDGEFLLDATFSPVVFCDFE 178

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +   + 
Sbjct: 179 IKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNILDIEEINKGI--FVE 236

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
             +   NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL EI
Sbjct: 237 DPTKDINPILLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLTEI 296

Query: 307 KGVLGTMGLFLGMNLPDWPPE 327
           K  L  +GL LG  + +WP +
Sbjct: 297 KDKLSELGLSLGTLIENWPQD 317


>gi|150036818|emb|CAM98041.1| DNA-directed RNA polymerase alpha chain [Leuconostoc fallax]
          Length = 222

 Score =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 94/221 (42%), Positives = 142/221 (64%), Gaps = 2/221 (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 SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           SI   D+++L ++IL + L +F +      E +  ++V+  
Sbjct: 181 SIKPSDALSLGAKILSEHLNLFTDISSVAAETEVMVDVEQT 221


>gi|317016853|gb|ADU85967.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 228

 Score =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 92/218 (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  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 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
              D+++L ++IL + L +F++      E    +  + 
Sbjct: 181 KPSDALSLGAKILAEHLNLFMDISPVAAEASVMVEAEP 218


>gi|161513436|emb|CAP16861.1| DNA-directed RNA polymerase subunit alpha [Pediococcus inopinatus]
          Length = 214

 Score =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 98/214 (45%), Positives = 145/214 (67%), 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 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA- 158
             K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A 
Sbjct: 61  DEKSLEIDVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAILTADTGRGYVSAD 120

Query: 159 -KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
               R ++ 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|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 =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 105/321 (32%), Positives = 180/321 (56%), Gaps = 11/321 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DG 67
           L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I DG
Sbjct: 6   LLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKINDG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
            +  +  +    E + DIILN+K + + +  G     +T    G       +   +++  
Sbjct: 63  KVTSLEDVIPCDETVADIILNVKSLPVTLAEGVETGTITFELSGSEEEIFSEEAKLSEGL 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
            +  +  IC+ +    +++E  V KG G+ PA+    +N   G   +DA +SP+    + 
Sbjct: 123 AITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQ----DNFKEGEFLLDATFSPVVFCDFE 178

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +   + 
Sbjct: 179 IKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGI--FVE 236

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
             +   NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL EI
Sbjct: 237 DPTKDINPILLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLTEI 296

Query: 307 KGVLGTMGLFLGMNLPDWPPE 327
           K  L  +GL LG  + +WP +
Sbjct: 297 KDKLSELGLSLGTLIENWPQD 317


>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 =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 105/321 (32%), Positives = 181/321 (56%), Gaps = 12/321 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DG 67
           L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I DG
Sbjct: 6   LLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKINDG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIE 126
            +  +  +    E + DIILN+K +++ ++ D     +T    G       +   +++  
Sbjct: 63  KVTSLEDVIPCDETVADIILNVKSLSVTLAEDVETGTITFELSGSEEEIFSEEAKLSEGL 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
            +  +  IC+ +    +++E  V KG G+ PA+    +N   G   +DA +SP+    + 
Sbjct: 123 AITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQ----DNFKDGEFLLDATFSPVVFCDFE 178

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +  +  
Sbjct: 179 IKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGIFVEDP 238

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
                 NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL EI
Sbjct: 239 K---DINPILLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLTEI 295

Query: 307 KGVLGTMGLFLGMNLPDWPPE 327
           K  L  +GL LG  + +WP +
Sbjct: 296 KDKLSELGLSLGTLIENWPQD 316


>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 =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 103/321 (32%), Positives = 179/321 (55%), Gaps = 11/321 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DG 67
           L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I DG
Sbjct: 6   LLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKINDG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIE 126
            +  +  +    E + DIILN+K + + ++       +T    G       +   +++  
Sbjct: 63  KVTSLEDVIPCDETVADIILNVKSLPVTLTEGVETGTITFELSGSEEEIFSEEAKLSEGL 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
            +  +  IC+ +    +++E  V KG G+ PA+    +N   G   +DA +SP+    + 
Sbjct: 123 AITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQ----DNFKDGEFLLDATFSPVVFCDFE 178

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +   + 
Sbjct: 179 IKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGI--FVE 236

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
             +   NP LLK  EEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL EI
Sbjct: 237 DPTKDINPILLKHAEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLTEI 296

Query: 307 KGVLGTMGLFLGMNLPDWPPE 327
           K  L  +GL LG  + +WP +
Sbjct: 297 KDKLSELGLSLGTLIENWPQD 317


>gi|328813985|gb|AEB52108.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 228

 Score =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 106/228 (46%), Positives = 152/228 (66%), 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 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA- 158
             K + I  +GP  VTAGDI    D+EVLNPD  IC +   A   M +T + G GYV A 
Sbjct: 61  ETKTLEIDVKGPANVTAGDIIGDADVEVLNPDLPICTVADGAHFHMRMTANTGRGYVSAE 120

Query: 159 -KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
              HR ++ 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|290489672|gb|ADD31220.1| RNA polymerase alpha subunit protein [Phoradendron serotinum]
          Length = 326

 Score =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 80/307 (26%), Positives = 154/307 (50%), Gaps = 21/307 (6%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RR L+  + G  IT  + D + HE S+I+G+
Sbjct: 21  RVDNKRFYYGRFILSPLIKGQADTIGIAMRRALLGEIEGTCITRAKSDQIPHEYSTIRGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + DI++N+K I L+ +       +I+ +GP  +TA DI     +E+++   +I +L 
Sbjct: 81  QESVHDILINLKEIVLRSNLYGTCNASIYIKGPRYITAQDIILPPYVEIIDHTQIIASLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 + L + K  GY        +N   G  +I+A++ P++  ++++ +         
Sbjct: 141 EQIDFGIGLQIEKNRGYRIIT---PKNLQEGNFSIEAIFMPVRNANHSIHNY----NEKL 193

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  A+R L D    F++ ++ K  V+++ +  SL      L+
Sbjct: 194 EILFLEIWTNGSLTPKEALHEAARNLIDLFIPFLHVKKEKLHVEDNQHKLSLFTFHDRLQ 253

Query: 259 K--------------VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
           K              +++ ELS R  NCL+  NI  + DL+ +   D++++ +F  + L 
Sbjct: 254 KLRKTKEKIALKSIFIDQSELSPRIYNCLKSSNIQNILDLLNKNREDLMKIEHFRIEDLK 313

Query: 305 EIKGVLG 311
            I G+L 
Sbjct: 314 HIWGILE 320


>gi|12467|emb|CAA30670.1| RNA polymerase alpha-subunit (AA 1-341) [Zea mays]
          Length = 341

 Score =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 89/323 (27%), Positives = 155/323 (47%), Gaps = 25/323 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G ALRR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  RVDSKRLYYGRFILSPLRKGQADTVGIALRRALLGEIEGTCITRAKFGNVPHEYSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E+ +    I NL 
Sbjct: 81  EESIQEILLNLKEIVLRSNLYGVRDASICVKGPRYITAQDIILPPSVEIDDTTQPIANLR 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
                 +EL + +   Y        +N   G   IDA++ P++ V+Y++ S   G    +
Sbjct: 141 EPVDFCIELQIKRDRAYHTELR---KNSQDGSYPIDAVFMPVRNVNYSIFSCGNGNE-KH 196

Query: 199 DKLSMTIDTDGSITGED-SVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           + L + I T+G +T ++  +  ASR L D    F++ EE     +E+ N  + P      
Sbjct: 197 EILFLEIWTNGKLTPKEGGIYEASRNLIDLFLPFLHTEEEGTSFEENKNRLTPPLLTFQK 256

Query: 258 K----------------KVEELELSVRSTNCLRGENIVY-MGDLIQRTEADMLRMANFGR 300
           +                 +++LEL  R+ NCL+  NI   + DL+ +TE D++++ +FG 
Sbjct: 257 RFTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIPSALLDLLVKTEEDLIKINSFG- 315

Query: 301 KSLVEIKGVLGTMGLFLGMNLPD 323
             + + K +  T+   L ++LP 
Sbjct: 316 --MEDGKLIWDTLEKHLPIDLPK 336


>gi|197131692|gb|ACH47364.1| RNA polymerase alpha subunit [Geranium macrorrhizum]
          Length = 329

 Score =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 70/297 (23%), Positives = 136/297 (45%), Gaps = 8/297 (2%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
             +       I  PL +G A  +G A+RR L+  + G  IT  + D + HE +++ G+ E
Sbjct: 23  DSKRLYYGRFILSPLKKGQADMIGIAMRRALLGEIEGTCITHAKFDKIPHEYTTLVGIQE 82

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
            + +I++N+K I L+      +  +I  RGP  VT+ DI       +++    I  L   
Sbjct: 83  SIYEILMNLKEIVLRSHLYGTRDASICVRGPRDVTSQDIILPTFATIVDNTQHIVTLTEP 142

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDK 200
               + L + +  GY       +         IDA++ P+K V++++ S   G    +  
Sbjct: 143 IDFCVGLQIERNRGYFIQIPMLSNLHDDRGYPIDAVFMPVKNVNHSIHSYENG---IHAM 199

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L + I T+GS+T ++++  ASR L +    F++ EE     + + N  +   +       
Sbjct: 200 LFLEIWTNGSLTPKEALRGASRKLINLFIPFLHAEEQNCHFENNQNEHTDELSIDFCALK 259

Query: 261 EE-----LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +      +EL  R   CL+G  I  + DL+ +   D++++  F ++ + ++  +L  
Sbjct: 260 DIYIDQLVELPARFYKCLKGSGIDTVMDLLNKNTDDLIKITQFCQQDVEKVMNILNN 316


>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 =  239 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 95/328 (28%), Positives = 168/328 (51%), Gaps = 7/328 (2%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P+    I + +   N+  + A P   G+A TL + LRR+L+ S  G A  A++I GV HE
Sbjct: 8   PHIPTKIEVRETGNNKVQITAYPFENGYAITLAHPLRRLLLGSSVGFAPIALRISGVAHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSH-KRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
             S++GV ED++  I+N+K I  ++  +S    V     G  V+T  D+ +   +EV+ P
Sbjct: 68  FDSVRGVVEDVSQFIVNLKAIRFRIKDNSDNVSVDYKFNGSKVITGADL-SNELVEVVTP 126

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           D  +  ++ DA +   + + KG GYVP++  R  + P G + +DA ++P+   +YT E+ 
Sbjct: 127 DIHLATINEDATLAFSIIIYKGIGYVPSEEIRA-SVPEGFMPLDAYFTPVTSATYTTENM 185

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
                 +Y+K+   I TDG +    +   A  ++  Q+ +F N E   +  +  ++ +  
Sbjct: 186 LLEDDPNYEKIIFDIQTDGQVDPLTAFKNALSVMHKQMSIF-NSELNIEMPETTVSEEER 244

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           P    L + ++ L  S R  NCL    I Y+G+L+   E  +  + N G+KSL EI   L
Sbjct: 245 PELKVLSQTIDSLNFSARCFNCLDRSGIRYLGELVLLNEDQIKNIKNLGKKSLDEITAKL 304

Query: 311 GTMGLFLGMNLPDWPPESIEELAKKYED 338
             +G  +   +P+   + ++ L KK+ +
Sbjct: 305 DELGYPVNREIPE---DLLQILKKKFSN 329


>gi|150036746|emb|CAM98260.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. mesenteroides]
          Length = 226

 Score =  239 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 94/216 (43%), Positives = 139/216 (64%), Gaps = 2/216 (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 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           I   D+++L ++IL + LG+F++      E    + 
Sbjct: 181 IKPSDALSLGAKILAEHLGLFMDISPVAAEASVMVE 216


>gi|190411115|gb|ACE78312.1| RpoA [Vibrio parahaemolyticus]
          Length = 252

 Score =  239 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 107/255 (41%), Positives = 169/255 (66%), 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++  + +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GD
Sbjct: 181 LAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGD 237

Query: 284 LIQRTEADMLRMANF 298
           L+QRTE ++L+  N 
Sbjct: 238 LVQRTEVELLKTPNL 252


>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 =  238 bits (608), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 103/321 (32%), Positives = 181/321 (56%), Gaps = 12/321 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DG 67
           L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I DG
Sbjct: 6   LLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKINDG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIE 126
            +  +  +    E + DIILN+K +++ ++ D     +T    G       +   +++  
Sbjct: 63  KVTSLEDVIPCDETVADIILNVKSLSVTLAEDVETGTITFELSGSEEEIFSEEAKLSEGL 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
            +  +  IC+ +    +++E  V KG G+ PA+ +  + +      +DA +SP+    + 
Sbjct: 123 AITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQDNFKDCE----FLLDATFSPVVFCDFE 178

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +  +  
Sbjct: 179 IKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGIFVEDP 238

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
                 NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL EI
Sbjct: 239 K---DINPILLKHVEELNLTARSSNCLKAVNIRLIGELVQKTENELLKAPNFGKKSLTEI 295

Query: 307 KGVLGTMGLFLGMNLPDWPPE 327
           K  L  +GL LG  + +WP +
Sbjct: 296 KDKLSELGLSLGTLIENWPQD 316


>gi|119668361|emb|CAK95513.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
          Length = 211

 Score =  238 bits (608), Expect = 7e-61,   Method: Composition-based stats.
 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 YVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           Y+ A     R ++  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|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 =  238 bits (608), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 78/310 (25%), Positives = 143/310 (46%), Gaps = 22/310 (7%)

Query: 15  IEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           I++  +  + E    +    +  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 SQYVVTITQPISVNIESKIEKDCGYRIENSH---GYGGGEFPVDAVSMPVRNVNYSVHLF 189

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN--------------FEE 236
             G+ +  + L + I T+GS+T ++++  AS+ L D L  F++              F  
Sbjct: 190 GSGKAM-RETLFIEIWTNGSLTPDEAICEASKKLIDLLTPFLHVKCEDVPHSGDNQDFSA 248

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
                    +V  L    +    +++LEL  R+ NCL+   I  + DL+  +  D  R+ 
Sbjct: 249 STGSPSHFDDVSELEGKISKNTFIDQLELPARAFNCLKRAEIHTISDLLNYSREDSSRIK 308

Query: 297 NFGRKSLVEI 306
           +FG+KS+ ++
Sbjct: 309 SFGQKSVDQV 318


>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 =  238 bits (608), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 107/322 (33%), Positives = 180/322 (55%), Gaps = 12/322 (3%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
              E +++ +          EPL  G+  T+GN+LRRVL+SSL G AI++V+I+GV +E 
Sbjct: 7   TKNENLIILKLTPEEGSFKIEPLYPGWGLTIGNSLRRVLLSSLEGYAISSVKIEGVNNEY 66

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRV-----TIFKRGPGVVTAGDI-QTVNDIE 126
           S+IKGV ED+T+IILN+K I  K   +           I       +TAGD+ + +N  E
Sbjct: 67  STIKGVIEDMTEIILNLKKIRFKKKIEDEDFESEEFHIIINNNKKEITAGDLGEFLNLFE 126

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
           ++NPD +I N +    + + L + +G GY+P++ ++   + IG I ID +++PIKKV Y 
Sbjct: 127 IINPDLIILNKEKLISLNITLVIKRGIGYLPSEKNKDMPNMIGTIPIDTIFTPIKKVKYK 186

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL------GMFINFEEPKKE 240
           +++    +   Y+ + + I TDGSI    ++  AS +L           + + +++PKK 
Sbjct: 187 IDNCSINKNPFYESIILKIKTDGSINPRKALTRASNLLIRHFQCLSNEKILLEYKKPKKR 246

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            K D N+  +        + E   LSVR+ NCL+   I   GDL++  ++D+L++ NFGR
Sbjct: 247 NKYDKNILKMRNLLKSSLEEEIDYLSVRTLNCLKSAKIFTWGDLVKSNKSDLLKLKNFGR 306

Query: 301 KSLVEIKGVLGTMGLFLGMNLP 322
           KSL E+   +  + ++ GM++ 
Sbjct: 307 KSLSELDKRMKKLNIYSGMDIS 328


>gi|150036820|emb|CAM98279.1| DNA-directed RNA polymerase alpha chain [Fructobacillus ficulneus]
          Length = 238

 Score =  238 bits (608), Expect = 9e-61,   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|150187107|emb|CAK30172.1| RNA polymerase alpha subunit [Streptococcus downei MFe28]
          Length = 219

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 96/215 (44%), Positives = 146/215 (67%)

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 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
            ED++ L++R+L + L +F +  E  K  +     
Sbjct: 181 PEDALGLSARVLIEHLNLFTDLTEIAKTTEVMKET 215


>gi|161367356|gb|ABX71083.1| DNA-directed RNA polymerase alpha subunit [Vibrio cholerae O1]
          Length = 244

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 105/247 (42%), Positives = 165/247 (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++  + +   +++   +  P    LL+ V++LEL+VRS NC
Sbjct: 181 PEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANC 237

Query: 273 LRGENIV 279
           L+ E I 
Sbjct: 238 LKAEAIH 244


>gi|150036736|emb|CAM98023.1| DNA-directed RNA polymerase alpha chain [Leuconostoc citreum]
          Length = 223

 Score =  238 bits (607), Expect = 1e-60,   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|119668297|emb|CAK95503.1| RNA polymerase alpha subunit [Lactobacillus curvatus]
          Length = 207

 Score =  238 bits (607), Expect = 1e-60,   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|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 =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 102/239 (42%), Positives = 154/239 (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++  + +   +++   +  P    LL+ V++LEL+VRS NC
Sbjct: 128 PEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANC 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|150036762|emb|CAM98031.1| DNA-directed RNA polymerase alpha chain [Leuconostoc carnosum]
          Length = 221

 Score =  237 bits (606), Expect = 1e-60,   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|86438810|emb|CAJ43370.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 208

 Score =  237 bits (606), Expect = 2e-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|119662355|emb|CAJ33166.1| RNA polymerase alpha subunit [Lactobacillus salivarius]
          Length = 199

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 94/197 (47%), Positives = 141/197 (71%), Gaps = 2/197 (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 VALASRILQDQLGMFIN 233
           ++L+++IL + L +F++
Sbjct: 181 ISLSAKILTEHLALFVD 197


>gi|150036814|emb|CAM98040.1| DNA-directed RNA polymerase alpha chain [Leuconostoc kimchii]
          Length = 226

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 92/222 (41%), Positives = 140/222 (63%), Gaps = 2/222 (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 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
              D+++L S+IL + L +F++      E    +  + +  N
Sbjct: 181 KPSDALSLGSKILAEHLNLFMDISPVAAEASVMVEAEPVATN 222


>gi|162955842|gb|ABY25296.1| RNA polymerase alpha subunit [Vibrio sp. MSSRF7]
          Length = 240

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 101/235 (42%), Positives = 154/235 (65%), Gaps = 5/235 (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 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + +   +++   +  P
Sbjct: 181 DLDKLVIDMETNGTIEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP 235


>gi|193795085|gb|ACF21672.1| RpoA [Rhizobium tropici]
 gi|193795087|gb|ACF21673.1| RpoA [Rhizobium tropici]
          Length = 212

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 152/213 (71%), 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 RILQDQLGVFVNFDEPQKEAEE-EAVTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           GDLIQ+TEA+MLR  NFGRKSL EIK VL +MG
Sbjct: 180 GDLIQKTEAEMLRTPNFGRKSLNEIKEVLASMG 212


>gi|119662383|emb|CAJ33180.1| RNA polymerase alpha subunit [Lactobacillus sakei subsp. carnosus]
          Length = 212

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 90/212 (42%), Positives = 144/212 (67%)

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 LASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           LA++I+ + L +F++  +  K  +  +  +  
Sbjct: 181 LAAKIMTEHLAIFVDLTDEAKNAEIMVEKEET 212


>gi|161513434|emb|CAP16860.1| DNA-directed RNA polymerase subunit alpha [Pediococcus cellicola]
          Length = 214

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 97/210 (46%), Positives = 143/210 (68%), Gaps = 2/210 (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 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA- 158
             K + I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A 
Sbjct: 61  EEKSLEINVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAVLTADTGRGYVSAD 120

Query: 159 -KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
               R ++ PIG++ ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSI+  ++ 
Sbjct: 121 ENKARKDDMPIGVLPIDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSISPSEAT 180

Query: 218 ALASRILQDQLGMFINFEEPKKEVKEDINV 247
           +L+++IL + L +F+N  +  + ++     
Sbjct: 181 SLSAKILTEHLALFVNLTDEAQRLRSWSKR 210


>gi|119662343|emb|CAJ33160.1| RNA polymerase alpha subunit [Lactobacillus plantarum]
          Length = 204

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 101/204 (49%), Positives = 144/204 (70%), 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 --KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
               HR ++ 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|119668353|emb|CAK95471.1| RNA polymerase alpha subunit [Lactobacillus plantarum]
          Length = 219

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 101/219 (46%), Positives = 146/219 (66%), 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 --KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
               HR ++ 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|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 =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 92/218 (42%), Positives = 141/218 (64%), Gaps = 8/218 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQIST---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 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|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 = 91/197 (46%), Positives = 132/197 (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 LASRILQDQLGMFINFE 235
            A++IL +   +F + +
Sbjct: 181 FAAKILVEHFKVFESAD 197


>gi|119668281|emb|CAK95497.1| RNA polymerase alpha subunit [Lactobacillus amylolyticus]
          Length = 217

 Score =  237 bits (604), Expect = 3e-60,   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|119662279|emb|CAJ33126.1| RNA polymerase alpha subunit [Lactobacillus amylovorus]
          Length = 210

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 92/209 (44%), Positives = 135/209 (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 LASRILQDQLGMFINFEEPKKEVKEDINV 247
            A++IL +   +F + +   +  +  +  
Sbjct: 181 FAAKILVEHFKVFESADANTQFSEVMVEK 209


>gi|119668319|emb|CAK95460.1| RNA polymerase alpha subunit [Lactobacillus gasseri]
          Length = 198

 Score =  236 bits (603), Expect = 3e-60,   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|150187161|emb|CAK30184.1| RNA polymerase alpha subunit [Streptococcus equi subsp.
           ruminatorum]
          Length = 225

 Score =  236 bits (603), Expect = 3e-60,   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|193795063|gb|ACF21663.1| RpoA [Rhizobium giardinii]
          Length = 212

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 150/213 (70%), 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   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 RILQDQLGVFVNFDEPQKEAEE-EAVTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           GDLIQ+TEA+MLR  N GRKSL EIK VL +MG
Sbjct: 180 GDLIQKTEAEMLRTPNLGRKSLNEIKEVLASMG 212


>gi|332184519|gb|AEE26773.1| DNA-directed RNA polymerase alpha subunit [Francisella cf. novicida
           3523]
          Length = 318

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 104/321 (32%), Positives = 179/321 (55%), Gaps = 11/321 (3%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DG 67
           L+ P NI+   + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I DG
Sbjct: 6   LLHPTNIK---IDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKINDG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKM-SGDSHKRVTIFKRGPGVVTAGDIQTVNDIE 126
            +  +  +    E + DIILN+K + + +  G     +T    G       +   +++  
Sbjct: 63  KVTSLEDVIPCDETVADIILNVKSLPVTLAEGVETGIITFELSGSEEEIFSEEAKLSEGL 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
            +  +  IC+ +    +++E  V KG G+ PA+    +N   G   +DA +SP+    + 
Sbjct: 123 AITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQ----DNFKDGEFLLDATFSPVVFCDFE 178

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL   ++ EE  K +   + 
Sbjct: 179 IKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLRNIVDIEEINKGI--FVE 236

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
             +   NP LLK VEEL L+ RS+NCL+  NI  +G+L+Q+TE ++L+  NFG+KSL EI
Sbjct: 237 DPTKDINPILLKHVEELNLTARSSNCLKAVNIKLIGELVQKTENELLKAPNFGKKSLTEI 296

Query: 307 KGVLGTMGLFLGMNLPDWPPE 327
           K  L  + L LG  + +WP +
Sbjct: 297 KDKLSELSLSLGTIIENWPQD 317


>gi|71056933|emb|CAH59025.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
          Length = 221

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 99/220 (45%), Positives = 147/220 (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 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           LA++I+ + L +F+N  +  K  +  +  +       L  
Sbjct: 181 LAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEM 220


>gi|119668317|emb|CAK95459.1| RNA polymerase alpha subunit [Lactobacillus gallinarum]
          Length = 214

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 92/213 (43%), Positives = 136/213 (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 +     + 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 LASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
            A++IL +   +F + +   K  +  +  +   
Sbjct: 181 FAAKILVEHFKVFESADADTKFSEVMVEKEDDK 213


>gi|119668321|emb|CAK95507.1| RNA polymerase alpha subunit [Lactobacillus gasseri]
          Length = 214

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 98/214 (45%), Positives = 143/214 (66%)

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 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            A++IL +   +F++ +   +     +  +    
Sbjct: 181 FAAKILVEHFKVFMSTDMDAQFDDVMVEKEDDKN 214


>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 =  236 bits (602), Expect = 4e-60,   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|119662317|emb|CAJ33146.1| RNA polymerase alpha subunit [Lactobacillus johnsonii]
          Length = 214

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 98/214 (45%), Positives = 143/214 (66%)

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 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
            A++IL +   +F++ +   +     +  +    
Sbjct: 181 FAAKILVEHFKVFMSTDMDAQFDDVMVEKEDDKN 214


>gi|119662367|emb|CAJ33172.1| RNA polymerase alpha subunit [Lactobacillus ultunensis]
          Length = 212

 Score =  236 bits (601), Expect = 5e-60,   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|193795090|gb|ACF21674.1| RpoA [Rhizobium tropici]
          Length = 212

 Score =  236 bits (601), Expect = 5e-60,   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|317447066|emb|CBX24362.1| DNA-directed RNA polymerase subunit alpha [Thiomonas perometabolis]
          Length = 201

 Score =  236 bits (601), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 94/201 (46%), Positives = 133/201 (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 TVSKGHGYVPA---KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 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|193795092|gb|ACF21675.1| RpoA [Sinorhizobium sp. 206]
          Length = 212

 Score =  236 bits (601), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 150/212 (70%), Positives = 180/212 (84%), 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 RILQDQLGVFVNFDEPQKEAEE-ESVTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           GDLIQ+TEA+MLR  NFGRKSL EIK VL +M
Sbjct: 180 GDLIQKTEAEMLRTPNFGRKSLNEIKEVLASM 211


>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 =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 97/332 (29%), Positives = 158/332 (47%), Gaps = 36/332 (10%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           +     +E  +  L IA PL  G A TLG A+RR L+ S++G AI A +I G  HE S++
Sbjct: 20  KIDSTKEECLDYMLFIASPLLAGQATTLGVAIRRTLLESIQGTAIVAAKIYGAAHEYSTL 79

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
           +G+ E + DI+LN+K + +K      ++  I   GP  VTA DI+   +I + NP H I 
Sbjct: 80  EGIQESIHDILLNLKQVIIKNKICEFQKCLISIIGPKKVTAADIELSQNITISNPYHHIA 139

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
            +      ++EL ++KG GY         +   G   +DAL++P++ V++++ +  E Q 
Sbjct: 140 TITKPIRFQVELIINKGRGY---LIQDGNDVQDGYFPVDALFNPVRNVNFSIHNLAEQQ- 195

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQL--------------------------G 229
              + L + I T+G+IT  D++   S  L                               
Sbjct: 196 ---EALILEIWTNGAITPLDALRQGSENLIHLFLPPFGLEDDTYMTSLGSQDYNIHIKNS 252

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
           +   FE    E  ED ++    F       +E LELS R   CL+  NI  + DL++ ++
Sbjct: 253 LKEKFELHSIERIEDSHLIKDQFLEYSKTPIELLELSTRPFKCLKNANIYTINDLLKLSQ 312

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
            D+L+++N G  S+ +I   L       G+NL
Sbjct: 313 QDLLKISNMGPSSVKQIVEALD---KRFGINL 341


>gi|119668301|emb|CAK95453.1| RNA polymerase alpha subunit [Lactobacillus curvatus]
          Length = 212

 Score =  235 bits (600), Expect = 7e-60,   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|193795065|gb|ACF21664.1| RpoA [Sinorhizobium sp. 72]
          Length = 212

 Score =  235 bits (599), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 147/213 (69%), 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   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 RILQDQLSVFVNFDEPQKEAEE-EAVTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           GDLIQ+TEA+MLR  NFGRKSL EIK VL + G
Sbjct: 180 GDLIQKTEAEMLRTPNFGRKSLNEIKEVLASSG 212


>gi|150036794|emb|CAM98273.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. mesenteroides]
          Length = 213

 Score =  235 bits (599), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 93/212 (43%), 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 HGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
            GY  A  ++   +  PIG++ +D++Y+PI++V+Y VE+ R G   DYDKL+  I T+GS
Sbjct: 121 RGYTSADENKKLRDEMPIGVLAVDSIYTPIERVNYQVENTRIGARDDYDKLTFDIWTNGS 180

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           +   D+++L ++IL + LG+F++      E  
Sbjct: 181 VKPSDALSLGAKILAEHLGLFMDISPVAAEAS 212


>gi|193795067|gb|ACF21665.1| RpoA [Rhizobium tropici]
          Length = 212

 Score =  235 bits (599), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 151/212 (71%), Positives = 181/212 (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 RILQDQLGVFVNFDEPQKEAEE-EAVTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           GDLIQ+TEA+MLR  NFGRKSL EIK VL +M
Sbjct: 180 GDLIQKTEAEMLRTPNFGRKSLNEIKEVLASM 211


>gi|150036796|emb|CAM98274.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. mesenteroides]
          Length = 214

 Score =  235 bits (599), Expect = 9e-60,   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|150036808|emb|CAM98277.1| DNA-directed RNA polymerase alpha chain [Fructobacillus
           pseudoficulneus]
          Length = 235

 Score =  235 bits (599), Expect = 9e-60,   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|71056900|emb|CAH59007.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
          Length = 219

 Score =  235 bits (599), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 99/219 (45%), Positives = 147/219 (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 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           LA++I+ + L +F+N  +  K  +  +  +       L 
Sbjct: 181 LAAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLE 219


>gi|119662321|emb|CAJ33148.1| RNA polymerase alpha subunit [Lactobacillus kefiranofaciens subsp.
           kefirgranum]
          Length = 215

 Score =  235 bits (599), Expect = 9e-60,   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|193795070|gb|ACF21666.1| RpoA [Rhizobium tropici CIAT 899]
 gi|193795078|gb|ACF21669.1| RpoA [Rhizobium tropici]
          Length = 212

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 150/212 (70%), Positives = 181/212 (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 RILQDQLGVFVNFDEPQKEAEE-EAVTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           GDLIQ+TEA+MLR  NFGRKSL EIK VL +M
Sbjct: 180 GDLIQKTEAEMLRTPNFGRKSLNEIKEVLASM 211


>gi|119662363|emb|CAJ33170.1| RNA polymerase alpha subunit [Lactobacillus spicheri]
          Length = 210

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 98/210 (46%), Positives = 143/210 (68%), 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 PA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A     R    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|161511723|emb|CAP16872.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           acidilactici]
          Length = 229

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 105/229 (45%), Positives = 145/229 (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 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA- 158
             K + I   GP  VTAGDI    D+ VLNPD  IC +         LT   G GY  A 
Sbjct: 61  DEKTLDINVVGPANVTAGDIMGDGDVTVLNPDSPICTVAEGTTFHAVLTADTGRGYTSAD 120

Query: 159 -KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
               R  + 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|193795075|gb|ACF21668.1| RpoA [Rhizobium tropici]
 gi|193795083|gb|ACF21671.1| RpoA [Rhizobium tropici]
          Length = 212

 Score =  234 bits (597), Expect = 1e-59,   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|193795081|gb|ACF21670.1| RpoA [Rhizobium gallicum]
          Length = 212

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 149/212 (70%), Positives = 181/212 (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 RILQDQLGVFVNFDEPQKEAEE-EAVTELAFNPALLKKVDELELSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           GDLIQ+TEA+MLR  NFGRKSL EIK VL +M
Sbjct: 180 GDLIQKTEAEMLRTPNFGRKSLNEIKEVLASM 211


>gi|71056937|emb|CAH59027.1| DNA-directed RNA polymerase alpha chain [Enterococcus malodoratus]
          Length = 221

 Score =  234 bits (597), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 100/220 (45%), Positives = 145/220 (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 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           LA++IL + L +F+N  +  K  +  +  +       L  
Sbjct: 181 LAAKILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEM 220


>gi|71056864|emb|CAH58987.1| DNA-directed RNA polymerase alpha chain [Enterococcus canis]
          Length = 217

 Score =  234 bits (597), Expect = 2e-59,   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|117575079|emb|CAJ84779.1| RNA polymerase alpha subunit [Lactobacillus amylotrophicus]
          Length = 202

 Score =  234 bits (596), Expect = 2e-59,   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|119662825|emb|CAJ33205.1| RNA polymerase alpha subunit [Lactobacillus fermentum]
          Length = 190

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 90/190 (47%), Positives = 133/190 (70%), 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 GYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           GY  A     R 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|193795072|gb|ACF21667.1| RpoA [Rhizobium tropici]
          Length = 212

 Score =  234 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 149/213 (69%), Positives = 179/213 (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 RILQDQLGVFVNFDEPQKEAEE-EAVTELAFNPALLKKVDERERSVRSANCLKNDNIVYI 179

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           GDLIQ+TEA+MLR  N GRKSL EIK VL +MG
Sbjct: 180 GDLIQKTEAEMLRTPNLGRKSLNEIKEVLASMG 212


>gi|119668341|emb|CAK95468.1| RNA polymerase alpha subunit [Lactobacillus paracasei subsp.
           paracasei]
          Length = 209

 Score =  234 bits (596), Expect = 2e-59,   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|71056939|emb|CAH59028.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecalis]
          Length = 220

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 99/219 (45%), Positives = 146/219 (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 ASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           A++I+ + L +F+N  +  K  +  +  +       L  
Sbjct: 181 AAKIMTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEM 219


>gi|195973794|gb|ACG63462.1| DNA-directed RNA polymerase subunit alpha [Francisella philomiragia
           subsp. philomiragia ATCC 25015]
          Length = 290

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 102/291 (35%), Positives = 166/291 (57%), Gaps = 7/291 (2%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
            +       +   P+ +G AH LGN++RR L+SSL GA+I  V IDGVLHE S+++ V E
Sbjct: 5   EELGAFGYKIQVSPVEKGMAHILGNSIRRFLLSSLSGASIIKVNIDGVLHEYSTLEDVKE 64

Query: 81  DLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           D+ +I+ N+K + +K+  +  K  + +     GVVTAGD +T   IE++N D  I  L  
Sbjct: 65  DVVEIVSNLKKVAIKLDKNVSKVELELSVTKSGVVTAGDFKTTQGIEIINKDQPIATLTN 124

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           +    +  TVS G          TE + +G I +D+ ++PIK+V++ +           +
Sbjct: 125 ERKFSLTATVSVGRNVGILSALPTELEKVGDIAVDSDFNPIKRVAFEIF-----DNGTNE 179

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
            L + + T+G+I    +V  A     +Q+ +F++   P    K    +     +P LLK 
Sbjct: 180 TLEVFVKTNGTIEPLVAVTKALEYFCEQISVFVSLRVP-SNGKTGDALLDSNIDPILLKP 238

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L
Sbjct: 239 IDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQIL 289


>gi|255027946|ref|ZP_05299932.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL J2-003]
          Length = 219

 Score =  233 bits (595), Expect = 3e-59,   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|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 =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 100/321 (31%), Positives = 162/321 (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  LTDIILNIKGINLKMS--GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           +   I+N+K I  K+         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 KVIFEVETDGQIDPIDAFKNAVNNYLNQFGVF--SKEFKLETKKVENVELPDEYNILFKP 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|119662845|emb|CAJ33215.1| RNA polymerase alpha subunit [Lactobacillus hamsteri]
          Length = 212

 Score =  233 bits (594), Expect = 3e-59,   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|86438806|emb|CAJ43368.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 192

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 90/192 (46%), Positives = 129/192 (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 LASRILQDQLGM 230
            A++IL +   +
Sbjct: 181 FATKILVEHFKV 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 =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 102/291 (35%), Positives = 166/291 (57%), Gaps = 7/291 (2%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
            +       +   P+ +G AH LGN++RR L+SSL GA+I  V IDGVLHE S+++ V E
Sbjct: 5   EELGAFGYKIQVSPVEKGMAHILGNSIRRFLLSSLSGASIIKVNIDGVLHEYSTLEDVKE 64

Query: 81  DLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           D+ +I+ N+K + +K+  +  K  + +     GVVTAGD +T   IE++N D  I  L  
Sbjct: 65  DVVEIVSNLKKVAIKLDKNVSKVELELSVTKSGVVTAGDFKTTQGIEIINKDQPIATLTN 124

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           +    +  TVS G          TE + +G I +D+ ++PIK+V++ +           +
Sbjct: 125 EREFSLTATVSVGRNVGILSALPTELEKVGDIAVDSDFNPIKRVAFEIF-----DNGTNE 179

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
            L + + T+G+I    +V  A     +Q+ +F++   P    K    +     +P LLK 
Sbjct: 180 TLEVFVKTNGTIEPLVAVTKALEYFCEQISVFVSLRVP-SNGKTGDALLDSNIDPILLKP 238

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L
Sbjct: 239 IDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQIL 289


>gi|71056866|emb|CAH58988.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           hermanniensis]
          Length = 214

 Score =  232 bits (593), Expect = 4e-59,   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|150036822|emb|CAM98042.1| DNA-directed RNA polymerase alpha chain [Leuconostoc fallax KCTC
           3537]
          Length = 204

 Score =  232 bits (593), Expect = 4e-59,   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|151416840|emb|CAO78491.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gelidum]
          Length = 233

 Score =  232 bits (592), Expect = 6e-59,   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|195973802|gb|ACG63466.1| DNA-directed RNA polymerase subunit alpha [Francisella
           philomiragia]
          Length = 290

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 101/291 (34%), Positives = 165/291 (56%), Gaps = 7/291 (2%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
            +       +   P+ +G AH LGN++RR L+SSL GA+I  V IDGVLHE S+++ V E
Sbjct: 5   EELGAFGYKIQVSPVEKGMAHILGNSIRRFLLSSLSGASIIKVNIDGVLHEYSTLEDVKE 64

Query: 81  DLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           D+ +I+ N+K + +K+  +  K  + +     G VTAGD +T   IE++N D  I  L  
Sbjct: 65  DVVEIVSNLKKVAIKLDKNVSKVELELSVTKSGAVTAGDFKTTQGIEIINKDQPIATLTN 124

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           +    +  TVS G          TE + +G I +D+ ++PIK+V++ +           +
Sbjct: 125 EREFSLTATVSVGRNVGILSALPTELEKVGDIAVDSDFNPIKRVAFEIF-----DNGTNE 179

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
            L + + T+G+I    +V  A     +Q+ +F++   P    K    +     +P LLK 
Sbjct: 180 TLEVFVKTNGTIEPLVAVTKALEYFCEQISVFVSLRVP-SNGKTGDALLDSNIDPILLKP 238

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L
Sbjct: 239 IDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQIL 289


>gi|154424803|emb|CAL18504.1| RNA polymerase alpha subunit [Streptococcus hyovaginalis]
          Length = 212

 Score =  232 bits (591), Expect = 8e-59,   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|150036778|emb|CAM98268.1| DNA-directed RNA polymerase alpha chain [Fructobacillus fructosus
           KCTC 3544]
          Length = 206

 Score =  232 bits (591), Expect = 8e-59,   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|161511729|emb|CAP16875.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 229

 Score =  232 bits (591), Expect = 8e-59,   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|195973808|gb|ACG63469.1| DNA-directed RNA polymerase subunit alpha [Francisella noatunensis]
          Length = 290

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 101/291 (34%), Positives = 165/291 (56%), Gaps = 7/291 (2%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
            +       +   P+ +G AH LGN++RR L+SSL GA+I  V I GVLHE S+++ V E
Sbjct: 5   EELGAFGYKIQVSPVEKGMAHILGNSIRRFLLSSLSGASIIKVNISGVLHEYSTLEDVKE 64

Query: 81  DLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           D+ +I+ N+K + +K+  +  K  + +     GVVTAGD +T   IE++N D  I  L  
Sbjct: 65  DVVEIVSNLKKVAIKLDKNVSKVELELSVTKSGVVTAGDFKTTQGIEIINKDQPIATLTN 124

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           +    +  TVS G           E + +G I +DA ++PIK+V++ +           +
Sbjct: 125 EREFSLVATVSVGRNVGILSALPIELEKVGDIAVDADFNPIKRVAFEIFDNGAS-----E 179

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
            L + + T+G+I    +V  A     +Q+ +F++ + P    K    +     +P LLK 
Sbjct: 180 TLEVFVKTNGTIEPLAAVTKALEYFCEQISVFVSLKVP-SNGKTGDALLDSNIDPILLKP 238

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L
Sbjct: 239 IDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQIL 289


>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 =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 108/337 (32%), Positives = 176/337 (52%), 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 NFE-----EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 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|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 =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 89/322 (27%), Positives = 153/322 (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 VNDIEVLNPDHVICNLDVDA-VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              +EV+NP+  +C +  +   + ++L      G+  +  +R     + LI ID  +SP+
Sbjct: 128 FAGVEVVNPELKLCEITEEGTSLEIDLYCMVDRGHRSSNENRERLSTLSLIPIDTTFSPV 187

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP--- 237
             V + V   +  +    D+L + + T+GSI   D+V  A++IL          +     
Sbjct: 188 LLVDWKVSEEKTTKYGISDRLRLNVSTNGSIKALDAVWYAAKILISMFTKIAEHDVELFK 247

Query: 238 --KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 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|161511721|emb|CAP16871.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           acidilactici]
          Length = 225

 Score =  231 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 102/225 (45%), Positives = 141/225 (62%), 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 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA- 158
             K + I   GP  VTAGDI    D+ VLNPD  IC +         LT   G GY  A 
Sbjct: 61  DEKTLDINVVGPANVTAGDIMGDGDVTVLNPDSPICTVAEGTTFHAVLTADTGRGYTSAD 120

Query: 159 -KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
               R  + 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|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 =  231 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 89/322 (27%), Positives = 153/322 (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 VNDIEVLNPDHVICNLDVDA-VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
              +EV+NP+  +C +  +   + ++L      G+  +  +R     + LI ID  +SP+
Sbjct: 131 FAGVEVVNPELKLCEITEEGTSLEIDLYCMVDRGHRSSNENRERLSTLSLIPIDTTFSPV 190

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP--- 237
             V + V   +  +    D+L + + T+GSI   D+V  A++IL          +     
Sbjct: 191 LLVDWKVSEEKTTKYGISDRLRLNVSTNGSIKALDAVWYAAKILISMFTKIAEHDVELFK 250

Query: 238 --KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 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|161511755|emb|CAP16888.1| DNA-directed RNA polymerase subunit alpha [Pediococcus damnosus]
          Length = 187

 Score =  231 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 94/186 (50%), Positives = 132/186 (70%), 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 --KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
                R ++ 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|119662841|emb|CAJ33213.1| RNA polymerase alpha subunit [Lactobacillus fructivorans KCTC 3543]
          Length = 220

 Score =  231 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 102/220 (46%), Positives = 149/220 (67%), 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 S--HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 157
               K ++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|158148899|dbj|BAF81984.1| RNA polymerase alpha subunit [Lactobacillus senmaizukei]
          Length = 199

 Score =  231 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 98/198 (49%), Positives = 141/198 (71%), Gaps = 4/198 (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 A--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
           A     R  + PIG++ +D++Y+PI++V+Y VE+AR GQ  DYDKL++ + T+GSI   +
Sbjct: 121 ADENKARNTDMPIGVLAVDSIYTPIERVNYQVENARVGQRADYDKLTLDVWTNGSINPSE 180

Query: 216 SVALASRILQDQLGMFIN 233
           ++ALA++IL + L MF++
Sbjct: 181 AIALAAKILTEHLAMFVD 198


>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 =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 104/295 (35%), Positives = 168/295 (56%), Gaps = 8/295 (2%)

Query: 18  IVLGQEEENRT-LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
           I L +E       +   P+ +G AH LGN++RR L+SSL GA+I  V I G+LHE S+++
Sbjct: 1   IQLKEELGTFGYKIQVSPVEKGMAHILGNSIRRFLLSSLSGASIIKVNISGILHEYSTLE 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
            V ED+ +I+ N+K + +K+  +  K  + +     GVVTAGD +T   IE++N D  I 
Sbjct: 61  DVKEDVVEIVSNLKKVAIKLDKNVSKVELELSVTKSGVVTAGDFKTTQGIEIINKDQPIA 120

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
            L  +    +  TVS G          TE + +G I +DA ++PIK+V++ +        
Sbjct: 121 TLTNEREFSLVATVSVGRNVGILSALPTELEKVGDIAVDADFNPIKRVAFEIFDNGAS-- 178

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
              + L + + T+G+I    +V  A     +Q+ +F++   P    K    +     +P 
Sbjct: 179 ---ETLEVFVKTNGTIEPLAAVTKALEYFCEQISVFVSLRVP-SNGKTGDALLDSNIDPI 234

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L
Sbjct: 235 LLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMKIPNLGKKSLNEIKQIL 289


>gi|150036754|emb|CAM98262.1| DNA-directed RNA polymerase alpha chain [Fructobacillus durionis]
          Length = 220

 Score =  230 bits (587), Expect = 2e-58,   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|119668355|emb|CAK95472.1| RNA polymerase alpha subunit [Lactobacillus plantarum]
          Length = 214

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 100/214 (46%), Positives = 144/214 (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 KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--K 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 ASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
           +++IL D L +F+N  +  K     +  +     
Sbjct: 181 SAKILTDHLSIFVNLTDEAKNTDVMVEKEETHKE 214


>gi|154424747|emb|CAL18476.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
          Length = 216

 Score =  229 bits (585), Expect = 4e-58,   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|150187035|emb|CAK30156.1| RNA polymerase alpha subunit [Streptococcus entericus]
          Length = 222

 Score =  229 bits (585), Expect = 4e-58,   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|150036760|emb|CAM98030.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 223

 Score =  229 bits (585), Expect = 4e-58,   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|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 =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 102/291 (35%), Positives = 166/291 (57%), Gaps = 7/291 (2%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
            +       +   P+ +G AH LGN++RR L+SSL GA+I  V I GVLHE S+++ V E
Sbjct: 5   EELGAFGYKIQVSPVEKGMAHILGNSIRRFLLSSLSGASIIKVNISGVLHEYSTLEDVKE 64

Query: 81  DLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           D+ +I+ N+K + +K+  +  K  + +     GVVTAGD +T   IE++N D  I  L  
Sbjct: 65  DVVEIVSNLKKVAIKLDKNVSKVELELSVTKSGVVTAGDFKTTQGIEIINKDQPIATLTN 124

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
           +    +  TVS G          TE + +G I +DA ++PIK+V++ +           +
Sbjct: 125 EREFSLVATVSVGRNVGILSALPTELEKVGDIAVDADFNPIKRVAFEIFDNGAS-----E 179

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
            L + + T+G+I    +V  A +   +Q+ +F++   P    K    +     +P LLK 
Sbjct: 180 TLEVFVKTNGTIESLAAVTKALKYFCEQISVFVSLRVP-SNGKTGDALLDSNIDPILLKP 238

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
           +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ ++++ N G+KSL EIK +L
Sbjct: 239 IDDLELTVRSSNCLRAENIKYLGDLVQYSESQLIKIPNLGKKSLNEIKQIL 289


>gi|150036838|emb|CAM98284.1| DNA-directed RNA polymerase alpha chain [Leuconostoc lactis]
          Length = 228

 Score =  229 bits (584), Expect = 4e-58,   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|228017206|gb|ACP52026.1| RNA polymerase alpha subunit [Pinus leiophylla var. chihuahuana]
          Length = 335

 Score =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 75/317 (23%), Positives = 143/317 (45%), Gaps = 23/317 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            +  +               T+G A+RR L+  + G  IT V+++ + HE S+I G+ E 
Sbjct: 24  SKRLHYGRFXXXXXXXXXXDTIGIAMRRALLGEVEGTCITRVKLENIKHEYSAIIGIEES 83

Query: 82  LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDA 141
           + DI++N+K I L+      +  +I+  GP  VTA DI     +++++    I  L    
Sbjct: 84  VHDILMNLKEIVLRSDSYGIREASIYIVGPRNVTAQDIILPPSVKIIDTTQHIARLTKSI 143

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
              + L + K  GY+    H   N   G+  IDA++ P++  +Y++ S   G  +  + L
Sbjct: 144 TSDIRLQIEKNRGYII---HSPNNYQDGIFPIDAVFMPVRDANYSIHSYGSGNEI-REVL 199

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL----------- 250
            + I T+G +T  +++  ASR L D    F++ EE   +   +    ++           
Sbjct: 200 FLEIWTNGGLTPREALYEASRNLIDLFIPFLHGEEQNIDGMNNKKGSNMLPFPLSHLLTD 259

Query: 251 -----PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
                      L  +++L         LR  NI  + DL+  +  D++R+ +FG++S+ +
Sbjct: 260 TGETKEKIAFQLIFIDQLXXXXXXXXXLRRANIHTLLDLLNYSREDLMRIEHFGKESVEQ 319

Query: 306 IKGVLGTMGLFLGMNLP 322
           +  VL  +     ++ P
Sbjct: 320 VLEVLQKL---FAIDPP 333


>gi|190411125|gb|ACE78317.1| RpoA [Vibrio parahaemolyticus]
          Length = 244

 Score =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 106/247 (42%), Positives = 165/247 (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++  + +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+
Sbjct: 181 TILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYI 237

Query: 282 GDLIQRT 288
           GDL+QRT
Sbjct: 238 GDLVQRT 244


>gi|119668307|emb|CAK95506.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           delbrueckii]
          Length = 209

 Score =  229 bits (584), Expect = 5e-58,   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|119668339|emb|CAK95509.1| RNA polymerase alpha subunit [Lactobacillus kefiri]
          Length = 218

 Score =  229 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 103/217 (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 PA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A     R+   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|150187048|emb|CAK30159.1| RNA polymerase alpha subunit [Streptococcus australis ATCC 700641]
          Length = 217

 Score =  229 bits (583), Expect = 6e-58,   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|72534420|emb|CAH59046.1| DNA-directed RNA polymerase alpha chain [Enterococcus canis]
          Length = 218

 Score =  229 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 97/217 (44%), Positives = 143/217 (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 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           +IL + L +F+N  +  K  +  +  +       L  
Sbjct: 181 KILTEHLDIFVNLTDEAKNAEIMVEKEETQKEKMLEM 217


>gi|119662811|emb|CAJ33197.1| RNA polymerase alpha subunit [Lactobacillus psittaci]
          Length = 205

 Score =  229 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 92/194 (47%), Positives = 134/194 (69%)

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 LQDQLGMFINFEEP 237
           L +   +F   +  
Sbjct: 181 LVEHFKVFEFSDAE 194


>gi|154424781|emb|CAL18493.1| RNA polymerase alpha subunit [Streptococcus dysgalactiae subsp.
           equisimilis]
          Length = 205

 Score =  229 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 92/205 (44%), Positives = 142/205 (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 SVALASRILQDQLGMFINFEEPKKE 240
           ++ L++R+L + L +F +  +  K 
Sbjct: 181 ALGLSARVLIEHLNLFTDLTDVAKA 205


>gi|119668303|emb|CAK95505.1| RNA polymerase alpha subunit [Lactobacillus curvatus]
          Length = 217

 Score =  228 bits (582), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 90/216 (41%), Positives = 143/216 (66%)

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 ILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           I+ + L +F++  +  K  +  +  +       L  
Sbjct: 181 IMTEHLAIFVDLTDEAKNAEIMVEKEETHKEKMLEM 216


>gi|161511709|emb|CAP16865.1| DNA-directed RNA polymerase subunit alpha [Pediococcus inopinatus]
          Length = 204

 Score =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 95/204 (46%), Positives = 141/204 (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 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHR 162
            I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A     R
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|150036810|emb|CAM98038.1| DNA-directed RNA polymerase alpha chain [Fructobacillus
           pseudoficulneus]
          Length = 235

 Score =  228 bits (581), Expect = 1e-57,   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|71056858|emb|CAH58984.1| DNA-directed RNA polymerase alpha chain [Enterococcus villorum]
          Length = 208

 Score =  228 bits (581), Expect = 1e-57,   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|119668279|emb|CAK95450.1| RNA polymerase alpha subunit [Lactobacillus amylolyticus]
          Length = 213

 Score =  228 bits (581), Expect = 1e-57,   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|119662833|emb|CAJ33209.1| RNA polymerase alpha subunit [Lactobacillus ingluviei]
          Length = 180

 Score =  227 bits (580), Expect = 1e-57,   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 GYVPAKHHR-TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           GY  A  ++   +  IG++ ID++Y+PI++V+YTVE+ R GQ  DYDKL++ + TDGS+T
Sbjct: 121 GYNSADVNKARMDLAIGVLPIDSIYTPIERVNYTVENTRVGQSNDYDKLTLDVWTDGSLT 180


>gi|71056856|emb|CAH58983.1| DNA-directed RNA polymerase alpha chain [Enterococcus villorum]
          Length = 219

 Score =  227 bits (579), Expect = 2e-57,   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|190411123|gb|ACE78316.1| RpoA [Vibrio parahaemolyticus]
          Length = 243

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 105/246 (42%), Positives = 164/246 (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++  + +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+
Sbjct: 181 TILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYI 237

Query: 282 GDLIQR 287
           GDL+QR
Sbjct: 238 GDLVQR 243


>gi|119662371|emb|CAJ33174.1| RNA polymerase alpha subunit [Lactobacillus amylolyticus DSM 11664]
          Length = 208

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 91/205 (44%), Positives = 134/205 (65%)

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 ILQDQLGMFINFEEPKKEVKEDINV 247
           IL +   +F + +   K  +  +  
Sbjct: 181 ILVEHFKVFESADADNKFSEVMVEK 205


>gi|119662361|emb|CAJ33169.1| RNA polymerase alpha subunit [Lactobacillus zymae]
          Length = 202

 Score =  227 bits (579), Expect = 2e-57,   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|150187071|emb|CAK30164.1| RNA polymerase alpha subunit [Streptococcus equi subsp. equi]
          Length = 215

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 91/210 (43%), Positives = 143/210 (68%)

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 VALASRILQDQLGMFINFEEPKKEVKEDIN 246
           + L++R+L + L +F +  +  K  +    
Sbjct: 181 LGLSARVLIEHLNLFTDLTDVAKATEVMKE 210


>gi|119668325|emb|CAK95462.1| RNA polymerase alpha subunit [Lactobacillus hilgardii]
          Length = 200

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 100/199 (50%), Positives = 139/199 (69%), Gaps = 4/199 (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 DSVALASRILQDQLGMFIN 233
           ++V+LA++IL + L MF++
Sbjct: 181 EAVSLAAKILTEHLEMFVD 199


>gi|119668273|emb|CAK95495.1| RNA polymerase alpha subunit [Lactobacillus kefiri]
          Length = 203

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 102/203 (50%), 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 PA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
            A     R+   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|295809866|emb|CBL85109.1| alpha subunit of RNA polymerase [Vibrio tapetis]
          Length = 247

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 104/250 (41%), Positives = 163/250 (65%), 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-AVVRMELTVSKGHGYVPAK---HHRTENDPIG 169
           V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  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++  + +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDIRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADMLRMANFG 299
            ++L+  N G
Sbjct: 238 VELLKTPNLG 247


>gi|308125193|gb|ADO14945.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           saccharolyticus]
          Length = 204

 Score =  227 bits (578), Expect = 2e-57,   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|161511747|emb|CAP16884.1| DNA-directed RNA polymerase subunit alpha [Pediococcus inopinatus]
          Length = 215

 Score =  227 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 96/215 (44%), Positives = 143/215 (66%), Gaps = 2/215 (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 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHR 162
            I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A     R
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 ILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           IL + L +F+N  +  K+ +  +  +       L 
Sbjct: 181 ILTEHLALFVNLTDEAKDAEIMVEKEETHKEKMLE 215


>gi|119672813|emb|CAK95487.1| RNA polymerase alpha subunit [Lactobacillus gasseri]
          Length = 195

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 94/195 (48%), Positives = 137/195 (70%)

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 LQDQLGMFINFEEPK 238
           L +   +F++ +   
Sbjct: 181 LVEHFKVFMSTDMDA 195


>gi|150036834|emb|CAM98282.1| DNA-directed RNA polymerase alpha chain [Leuconostoc fallax]
          Length = 228

 Score =  226 bits (577), Expect = 3e-57,   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|150036784|emb|CAM98269.1| DNA-directed RNA polymerase alpha chain [Leuconostoc lactis]
          Length = 211

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 89/210 (42%), Positives = 133/210 (63%), Gaps = 2/210 (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 VALASRILQDQLGMFINFEEPKKEVKEDIN 246
           ++L ++IL + L +F++      E    + 
Sbjct: 181 LSLGAKILAEHLNLFMDISPVAAEANVMVE 210


>gi|308125189|gb|ADO14943.1| DNA-directed RNA polymerase alpha chain [Enterococcus pallens]
          Length = 204

 Score =  226 bits (576), Expect = 4e-57,   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|119662299|emb|CAJ33137.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           bulgaricus]
          Length = 214

 Score =  226 bits (576), Expect = 4e-57,   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|119662815|emb|CAJ33199.1| RNA polymerase alpha subunit [Lactobacillus kefiranofaciens subsp.
           kefiranofaciens]
          Length = 203

 Score =  226 bits (576), Expect = 4e-57,   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|119668295|emb|CAK95502.1| RNA polymerase alpha subunit [Lactobacillus crispatus]
          Length = 203

 Score =  226 bits (576), Expect = 4e-57,   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|119662323|emb|CAJ33149.1| RNA polymerase alpha subunit [Lactobacillus kimchii]
          Length = 213

 Score =  226 bits (576), Expect = 4e-57,   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|161511715|emb|CAP16868.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           acidilactici]
          Length = 225

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 103/225 (45%), Positives = 143/225 (63%), 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 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHH 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|119662305|emb|CAJ33140.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           lactis]
          Length = 214

 Score =  226 bits (576), Expect = 4e-57,   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|308125183|gb|ADO14940.1| DNA-directed RNA polymerase alpha chain [Enterococcus aquimarinus]
          Length = 204

 Score =  226 bits (576), Expect = 5e-57,   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|154424751|emb|CAL18478.1| RNA polymerase alpha subunit [Streptococcus salivarius]
          Length = 216

 Score =  226 bits (575), Expect = 5e-57,   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|119662375|emb|CAJ33176.1| RNA polymerase alpha subunit [Lactobacillus parabuchneri]
          Length = 201

 Score =  226 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 100/199 (50%), Positives = 140/199 (70%), Gaps = 4/199 (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 DSVALASRILQDQLGMFIN 233
           ++V+LA++IL + L MF++
Sbjct: 181 EAVSLAAKILTEHLEMFVD 199


>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 =  226 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 78/308 (25%), Positives = 146/308 (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 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI-----------GLITIDALYSPIKKVS 184
           +L     +  +L +  G GY+  + ++T                  + 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|71056862|emb|CAH58986.1| DNA-directed RNA polymerase alpha chain [Enterococcus malodoratus]
          Length = 205

 Score =  226 bits (575), Expect = 5e-57,   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|71056860|emb|CAH58985.1| DNA-directed RNA polymerase alpha chain [Enterococcus gilvus]
          Length = 205

 Score =  226 bits (575), Expect = 5e-57,   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|119668293|emb|CAK95452.1| RNA polymerase alpha subunit [Lactobacillus collinoides]
          Length = 191

 Score =  225 bits (574), Expect = 6e-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|289803215|ref|ZP_06533844.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. AG3]
          Length = 222

 Score =  225 bits (574), Expect = 7e-57,   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|71056854|emb|CAH58982.1| DNA-directed RNA polymerase alpha chain [Enterococcus asini]
          Length = 204

 Score =  225 bits (573), Expect = 8e-57,   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|154424851|emb|CAL18528.1| RNA polymerase alpha subunit [Streptococcus ratti]
          Length = 212

 Score =  225 bits (573), Expect = 9e-57,   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|119662847|emb|CAJ33216.1| RNA polymerase alpha subunit [Lactobacillus kunkeei]
          Length = 202

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 96/202 (47%), Positives = 139/202 (68%), Gaps = 4/202 (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 HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA-- 158
            K + I   GP  VTAGDIQ   D+ VLNPD  I  +   +   M +T +KG GYV A  
Sbjct: 61  DKEMEINVTGPAQVTAGDIQADGDVTVLNPDLHIATVAEGSTFHMRMTANKGRGYVSADE 120

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
              R +  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|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 =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 81/346 (23%), Positives = 155/346 (44%), Gaps = 51/346 (14%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
               +    +   P+  G   T+GN LRR+L++ L G  +   +I+GV  E S++ G+ E
Sbjct: 16  NSLTDCYGRLSFGPVNPGQGLTIGNTLRRILLNDLPGIGVIGAEINGVQSEFSTLPGIRE 75

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFK--------------RGPGVVTAGDIQTVNDIE 126
            + +I LN++ +    +    ++V   K                P VVTA D+    + E
Sbjct: 76  SVIEIFLNLRELIFTPTATCAQKVKQTKPFVYAKLNSELKIDNFPYVVTAKDLHIP-EYE 134

Query: 127 VLNPDHVICNL---DVDAVVRMELTVSKGHGYV-----------------PAKHHRTEND 166
            ++P+  I  +         ++ L + +G GY                          N 
Sbjct: 135 FVDPNQQIATILSPTAAENFKLTLLIGQGRGYQSWKKLPGVPQLMDQRFFEQFDSTQTNS 194

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
                 IDA++ PI++V++TV+       +D + +   + T+GSI   D+V  A+++   
Sbjct: 195 KSVTFPIDAIFMPIRQVNFTVQ----EHSVDGEYIYFEVWTNGSINPFDAVKSAAKVGMK 250

Query: 227 QLGMFINFEE------PKKEVKEDINVKSLPFNPALLKK------VEELELSVRSTNCLR 274
            +   +   +       + ++ E  N   + +N    +       +E+LELS+R+ NCL+
Sbjct: 251 LMTACLTTLQDQQVYLDESKLPETPNFVQVNYNKMESESNFDQIFIEQLELSLRAYNCLK 310

Query: 275 GENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
             NI+ + DL Q++  D++++ NFG+KS  E++  L T G+ L  +
Sbjct: 311 RANILTLADLSQQSFRDLMKLRNFGQKSADEVRAALSTYGIELKED 356


>gi|119668373|emb|CAK95478.1| RNA polymerase alpha subunit [Lactobacillus sakei subsp. carnosus]
          Length = 203

 Score =  224 bits (572), Expect = 1e-56,   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|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 (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 90/332 (27%), Positives = 159/332 (47%), Gaps = 9/332 (2%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P+    I + +  +    +       G+A TL + LRR+L+ S  G A  A++I+GV HE
Sbjct: 9   PHVPTDIRVERLGDRGIRVSVSAFESGYAITLAHPLRRLLLQSSVGFAPIAIKIEGVAHE 68

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSG----DSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
             S++G+ ED+   I N+K I L        +    V     GP  ++  D+ T  ++EV
Sbjct: 69  FDSVRGMAEDVALFIANLKNIRLVAKNLENAEDQLVVHYSFNGPAKLSGKDLAT-EEVEV 127

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           ++ +  +  ++ D  +   L + KG GYVP++  R        I +DA ++PIKK  Y +
Sbjct: 128 VDTETYLATINEDGQLGFSLIIQKGMGYVPSESIRGFISS-DYIPLDACFTPIKKAIYHI 186

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+       +++K+   I++DG +  + +   A + +  Q+ +F       K      N 
Sbjct: 187 ENILVDGNPNFEKVIFEIESDGQVDPKQAFQEAIKTMHAQMHIFSTNLSDSKNAYHLENN 246

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
             +     L+KKVE+L+LS R  NCL    I Y+G+L+     ++  + N G+KS  EI 
Sbjct: 247 LEI---KELIKKVEDLDLSARCLNCLDKVGIKYIGELVLMDVYELKGIKNLGKKSYDEIA 303

Query: 308 GVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
             L  +   +G  LP+    S++    K + +
Sbjct: 304 EKLEQLKYPVGQELPEGFKASLKARIDKLKSE 335


>gi|119672805|emb|CAK95518.1| RNA polymerase alpha subunit [Lactobacillus vaccinostercus]
          Length = 197

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 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 RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KH 160
            + I  +GP  VTAGDI+   D+EVLNP+  I  +   A + +++T + G GYV A    
Sbjct: 61  TLEIDVKGPAAVTAGDIEADGDVEVLNPELHIATVADGAELHIQMTANTGRGYVSADDNK 120

Query: 161 HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALA 220
            R ++ 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|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 =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 94/316 (29%), Positives = 161/316 (50%), Gaps = 5/316 (1%)

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  HEISSIKGVHEDLTDIILNIKGINL--KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           HE  SI+G+ ED++  I N+K I    K       +V    +GP V++A ++   + ++V
Sbjct: 66  HEFDSIRGIVEDVSHFISNLKNIRFLIKDETLDSVQVHYEFKGPMVLSANELANES-VDV 124

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +NP+  +  ++ +A +   L V KG GYVP++  R +      I +DA ++P+KK  Y +
Sbjct: 125 VNPEAYLATINENASISFSLIVQKGIGYVPSESIRGKIAE-DYIPLDAYFTPVKKAIYEI 183

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+       +Y+K+   I+TDG I    +   A  ++  Q+ +F           + I  
Sbjct: 184 ENVLVEDNPNYEKIIFDIETDGQIEPLTAFKEAISVMHKQMSIFGVDLSATPNGSKSIAE 243

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            S      ++K ++ L LS R  NCL    + Y+G+L+  +E ++  + N G+KS  EI 
Sbjct: 244 DSGELKTLMIK-IDTLNLSARCFNCLDRSGLKYVGELVIMSENELKNIKNMGKKSYDEIT 302

Query: 308 GVLGTMGLFLGMNLPD 323
             L  +G  +G  + +
Sbjct: 303 EKLEELGYPVGGEIAE 318


>gi|308125187|gb|ADO14942.1| DNA-directed RNA polymerase alpha chain [Enterococcus devriesei]
          Length = 204

 Score =  224 bits (570), Expect = 2e-56,   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|150036786|emb|CAM98270.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 221

 Score =  224 bits (570), Expect = 2e-56,   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|308125199|gb|ADO14948.1| DNA-directed RNA polymerase alpha chain [Enterococcus termitis]
          Length = 204

 Score =  224 bits (570), Expect = 2e-56,   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|119668345|emb|CAK95469.1| RNA polymerase alpha subunit [Lactobacillus paracasei subsp.
           paracasei]
          Length = 186

 Score =  224 bits (570), Expect = 2e-56,   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|150036830|emb|CAM98044.1| DNA-directed RNA polymerase alpha chain [Leuconostoc kimchii]
          Length = 216

 Score =  223 bits (569), Expect = 2e-56,   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|150036798|emb|CAM98035.1| DNA-directed RNA polymerase alpha chain [Leuconostoc fallax]
          Length = 208

 Score =  223 bits (569), Expect = 3e-56,   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|168805077|gb|ACA28617.1| DNA-directed RNA polymerase subunit alpha [Thiomonas arsenivorans]
          Length = 228

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 98/228 (42%), Positives = 152/228 (66%), 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 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREG 193
           L     + M++ V KG GYVP    R  ++    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|308125195|gb|ADO14946.1| DNA-directed RNA polymerase alpha chain [Enterococcus sanguinicola]
          Length = 204

 Score =  223 bits (568), Expect = 3e-56,   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|150036816|emb|CAM98278.1| DNA-directed RNA polymerase alpha chain [Leuconostoc fallax]
          Length = 220

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 89/213 (41%), Positives = 136/213 (63%), Gaps = 2/213 (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 ALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           +L ++IL + L +F +      E +  ++V+  
Sbjct: 181 SLGAKILSEHLNLFTDISSVAAETEVMVDVEQT 213


>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 =  222 bits (567), Expect = 5e-56,   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|311990468|gb|ADQ26364.1| RNA polymerase alpha subunit [Lactobacillus fermentum]
          Length = 220

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 94/220 (42%), Positives = 144/220 (65%), 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 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHH 161
           + I  +GP  VTA DIQ   D+ +LN D  I  +   A + +++T  KG GY  A     
Sbjct: 61  LEIDVKGPAEVTAADIQGDGDVTILNSDLHIATVSDGAELHVKMTADKGRGYSSADDNKT 120

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           R 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|150036802|emb|CAM98037.1| DNA-directed RNA polymerase alpha chain [Fructobacillus
           pseudoficulneus]
          Length = 231

 Score =  222 bits (566), Expect = 5e-56,   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|150036804|emb|CAM98275.1| DNA-directed RNA polymerase alpha chain [Fructobacillus
           pseudoficulneus]
          Length = 230

 Score =  222 bits (566), Expect = 6e-56,   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|119662837|emb|CAJ33211.1| RNA polymerase alpha subunit [Lactobacillus satsumensis]
          Length = 210

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 87/210 (41%), Positives = 141/210 (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 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHH 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|119668313|emb|CAK95457.1| RNA polymerase alpha subunit [Lactobacillus fructivorans KCTC 3543]
          Length = 192

 Score =  222 bits (565), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 98/192 (51%), Positives = 141/192 (73%), Gaps = 4/192 (2%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS--H 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|150036774|emb|CAN89786.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gasicomitatum]
          Length = 219

 Score =  222 bits (565), Expect = 7e-56,   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|328814011|gb|AEB52121.1| DNA-directed RNA polymerase alpha chain [Lactobacillus rhamnosus]
          Length = 218

 Score =  222 bits (565), Expect = 8e-56,   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|154424867|emb|CAL18536.1| RNA polymerase alpha subunit [Streptococcus uberis]
          Length = 210

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 90/209 (43%), Positives = 139/209 (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 LASRILQDQLGMFINFEEPKKEVKEDINV 247
           L++R+L + L +F +  E  K        
Sbjct: 181 LSARVLIEHLNLFTDLTEVAKATDVMKET 209


>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 = 93/177 (52%), Positives = 126/177 (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 --KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
               HR ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D+DKL++ + T+GSIT 
Sbjct: 121 EDNKHREDDMPIGVLAVDSLYSPIERVNYQVENTRVGQRDDFDKLTLDVWTNGSITP 177


>gi|269784298|emb|CBH50794.1| alpha subunit of RNA polymerase [Vibrio sp. C 15.19]
          Length = 244

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 102/247 (41%), Positives = 161/247 (65%), 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++  + +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADMLRMA 296
            ++L+  
Sbjct: 238 VELLKTP 244


>gi|119662369|emb|CAJ33173.1| RNA polymerase alpha subunit [Lactobacillus versmoldensis]
          Length = 215

 Score =  221 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 86/214 (40%), Positives = 141/214 (65%), Gaps = 1/214 (0%)

Query: 39  FAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS- 97
           +  TLGN+LRRVL++SL G A++ +QIDGVLHE  +I GV ED+T I+LNIK ++LK   
Sbjct: 1   YGTTLGNSLRRVLLASLPGTAVSDIQIDGVLHEFFAIDGVIEDVTQIVLNIKKLSLKSYA 60

Query: 98  GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP 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|119672791|emb|CAK95479.1| RNA polymerase alpha subunit [Lactobacillus sakei subsp. sakei]
          Length = 176

 Score =  221 bits (562), Expect = 2e-55,   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|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 =  221 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 88/328 (26%), Positives = 157/328 (47%), Gaps = 19/328 (5%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           +  K + +E        +     I +PL RGF  TLG ALRRVL+S++   A   V+I+G
Sbjct: 3   KFQKLDYLEVPSNSNTSDFENKFIIQPLERGFGTTLGVALRRVLLSNITSLAPFCVRIEG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLK-----MSGDSHKRVTIFKRGPGVVTAGDIQTV 122
           V HE   I+GV ED+  +I+N++ +        +  D   RV +     G + +  ++ V
Sbjct: 63  VTHEFRGIEGVVEDVPSLIMNLRKVRFSYDPELVKDDDIIRVELKADQVGEINSRYLEVV 122

Query: 123 N--DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK-----------HHRTENDPIG 169
           +  ++EV++ +  I  +  +  +R+EL +  G G+V ++              T+     
Sbjct: 123 DNLNVEVIDHNVHIAEVSQENALRLELYLRPGRGFVSSEENKALVSKLEAQLETKIKKGK 182

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            I +D+ +SP++KV+Y V       +   +KL   + TDG++  +D++  A+ IL     
Sbjct: 183 FIAVDSNFSPVEKVNYVVSELNSSSIKIEEKLEFNVYTDGTVKPKDAIKQAADILIAHFK 242

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE 289
              N +E + ++ E  + K    N      + +L LSVRS N LR      + D+ + + 
Sbjct: 243 EIGNVDEIRNDIFETADDKITD-NQETDIDITQLGLSVRSLNALRRIGRTKVSDISKMSY 301

Query: 290 ADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            ++ +  N G+KSL EI   +   G  L
Sbjct: 302 EELEQTKNLGKKSLDEIVQKIKEHGFEL 329


>gi|119662817|emb|CAJ33200.1| RNA polymerase alpha subunit [Lactobacillus homohiochii]
          Length = 205

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 99/205 (48%), Positives = 145/205 (70%), Gaps = 4/205 (1%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HK 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 SRILQDQLGMFINFEEPKKEVKEDI 245
           ++IL     +FI+  +  K     +
Sbjct: 181 AKILNQHFQLFIDLTDRAKNANVMV 205


>gi|119662357|emb|CAJ33167.1| RNA polymerase alpha subunit [Lactobacillus salivarius]
          Length = 194

 Score =  220 bits (561), Expect = 2e-55,   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|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 =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 90/333 (27%), Positives = 153/333 (45%), 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  ISSIKGVHEDLTDIILNIKGINLKMSG-----DSHKRVTIFKRGPGVVTAGDIQTVNDIE 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 VVNHDAYLATINEDAHLEFSLIVQKGMGYVPSESIRGYISS-DYIPLDAYFTPIKKVVYN 185

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
           +E+       +++KL   I++DG +  + +   A R +  Q+ +F       K       
Sbjct: 186 IENMLVDGNPNFEKLIFEIESDGQVDPQRAFQEAIRTMNAQMHIFNTNIADYKGNAHLEE 245

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
                    LL ++E L LS R  NCL    + Y+G+L+     ++  + N G+KS  EI
Sbjct: 246 G----LERDLLMEIEGLNLSARCFNCLDKIGLKYVGELVLMDAYELKNIKNLGKKSYDEI 301

Query: 307 KGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
              L  +G  +G  +      S+E    K +++
Sbjct: 302 AEKLEGLGYPVGSEISAEFRASLETKLDKIKNQ 334


>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 =  220 bits (561), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 81/328 (24%), Positives = 151/328 (46%), Gaps = 17/328 (5%)

Query: 6   WQEL-IKPNNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           W +L I  + +++  L  + E    +       PL +G A+T+  A+RR L+  + G +I
Sbjct: 3   WDKLEISKSPLQWKCLDSKTESKRYHYGRFSLSPLLKGQANTIAIAIRRTLLGEVEGTSI 62

Query: 61  TAVQIDGV-LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           T  +I+   +H+ S++ G+ E + DI+LN+K I LK       + +I   GP  VTA DI
Sbjct: 63  TYAKIEKTTVHDYSTMSGIKESVHDILLNLKEIVLKSELYGIHKASICTVGPRNVTAQDI 122

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
              + I++++    I +L       + LT+ +  GY         +   GL  IDA   P
Sbjct: 123 ILPSSIKIIDGTQHIASLTKSVPFNVMLTIERNQGYAIPSQSSRRHK-NGLFPIDAPCMP 181

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           ++ V++++ S +    +  + L   I T+G +T  ++   A   L D +   ++ EE   
Sbjct: 182 VRNVNFSIHSYKSENDI-REMLIFEIWTNGGLTPREAFYEACWKLIDLIVPLLHMEEDMN 240

Query: 240 EVKEDINVKSLPFNPALLK------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
             K+   +  L     L K       + +LELS ++++C +   I  + D +  +  +  
Sbjct: 241 GAKDFFALPILTRMDKLGKALFQHLFMNQLELSSKNSSCFQQTFIYRLSDFLNYSRQNSK 300

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNL 321
              +  +KS   IK ++       G+NL
Sbjct: 301 TFEDLDKKS---IKKIMEFFQKRFGINL 325


>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 =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 80/350 (22%), Positives = 141/350 (40%), Gaps = 45/350 (12%)

Query: 9   LIKPN---NIEYIVLGQEE--ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            I PN    +E +   +    ++   ++  PL  G   TLGN  RR+L++ L G AITA 
Sbjct: 3   FIVPNSSAKLECVEFRENNPRDHYARLVLGPLAPGQGVTLGNTFRRLLLNDLPGVAITAA 62

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS-----------HKRVTIFKRGPG 112
           +++    E  ++ G+ E + +I LN++ I    +               +  T   +   
Sbjct: 63  KLNETRTEFMTLPGIRESVVEIFLNLRDIVFFNTFPDVLAPQGTITISPRPQTDESKSFH 122

Query: 113 ---VVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS--------------KGHG 154
              V+ AGD+Q    I  ++P   I  L + D    +   +                G G
Sbjct: 123 TPRVICAGDMQLPEGITCVDPTQPIATLMNGDTAFNLTFILEQSTGYRVWKKPTQSYGTG 182

Query: 155 YVPAKHHR----TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
           + P+         +        ID  + P+K V++ V           + +   I T+GS
Sbjct: 183 FYPSPQIESVQIEQVKSGVFQPIDGNFMPVKNVNFAVHEV----QPHGEYIHFEITTNGS 238

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPK---KEVKEDINVKSLPFNPALLKKVEELELSV 267
           I   ++   A  IL +     +    P     E    ++             +E+LELS+
Sbjct: 239 IHPHNAFKHAGAILTEITRATLQDPRPVVGIDEASTPVDTAVAQKAYFENIAIEQLELSL 298

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           R+ NCL+   I+ + DL + + + +L + NFG+KS  E+   L T G+ L
Sbjct: 299 RAYNCLKRAQILTLADLSRESYSSLLALRNFGQKSAEEVAKALETYGIEL 348


>gi|295809864|emb|CBL85108.1| alpha subunit of RNA polymerase [Vibrio tapetis]
          Length = 244

 Score =  219 bits (559), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 102/247 (41%), Positives = 161/247 (65%), 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-AVVRMELTVSKGHGYVPAK---HHRTENDPIG 169
           V AGDI    D+E+ NP+HVIC+L  D A + M + V +G GYVPA    H   +  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++  + +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDIRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADMLRMA 296
            ++L+  
Sbjct: 238 VELLKTP 244


>gi|154424821|emb|CAL18513.1| RNA polymerase alpha subunit [Streptococcus mutans]
          Length = 200

 Score =  219 bits (559), Expect = 4e-55,   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|150036842|emb|CAM98286.1| DNA-directed RNA polymerase alpha chain [Leuconostoc carnosum]
          Length = 179

 Score =  219 bits (559), Expect = 4e-55,   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|150036756|emb|CAM98263.1| DNA-directed RNA polymerase alpha chain [Leuconostoc inhae KCTC
           3774]
          Length = 214

 Score =  219 bits (557), Expect = 6e-55,   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|150186982|emb|CAK30141.1| RNA polymerase alpha subunit [Streptococcus suis]
          Length = 205

 Score =  219 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 93/204 (45%), Positives = 142/204 (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 ILQDQLGMFINFEEPKKEVKEDIN 246
           IL + LG+F +  E  K  +    
Sbjct: 181 ILMEHLGLFTDLTEVAKSAEVMKE 204


>gi|119662329|emb|CAJ33152.1| RNA polymerase alpha subunit [Lactobacillus mindensis]
          Length = 197

 Score =  219 bits (557), Expect = 6e-55,   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|150036772|emb|CAN89785.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gasicomitatum
           LMG 18811]
          Length = 203

 Score =  219 bits (557), Expect = 6e-55,   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|119668275|emb|CAK95496.1| RNA polymerase alpha subunit [Lactobacillus parabuchneri]
          Length = 216

 Score =  219 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 100/216 (46%), 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 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 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
           LA++IL + L MF++  +  K  +  +  +      
Sbjct: 181 LAAKILTEHLEMFVDLTDEAKNTEIMVEKEETHKEK 216


>gi|168805075|gb|ACA28616.1| DNA-directed RNA polymerase subunit alpha [Thiomonas perometabolis]
          Length = 228

 Score =  219 bits (557), Expect = 7e-55,   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 LDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 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 =  219 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 100/228 (43%), Positives = 147/228 (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 LDVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALYSPIKKVSYTVESAREG 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|150036740|emb|CAM98259.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. dextranicum]
          Length = 195

 Score =  219 bits (557), Expect = 7e-55,   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|119668335|emb|CAK95508.1| RNA polymerase alpha subunit [Lactobacillus johnsonii]
          Length = 185

 Score =  218 bits (556), Expect = 8e-55,   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|255645616|gb|ACU23302.1| unknown [Glycine max]
          Length = 269

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 68/239 (28%), Positives = 123/239 (51%), Gaps = 4/239 (1%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +       I  PL +G A T+G A+RRVL+  + G  IT V+++ + HE S+I G+
Sbjct: 21  RIDSKRLYYGRFILSPLMKGQADTIGIAMRRVLLGEIEGTCITRVKLEKIPHEYSTIIGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I L+ +    +  +I  +GPG VTA DI     +E+++    I N+ 
Sbjct: 81  EESVHEILMNLKEIVLRSNLYGTRDASICFKGPGYVTAQDIILPPSVEIVDNTQHIANVT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + +EL + +  GY        +N   G   IDA + P++ V++++ S   G     
Sbjct: 141 EPVNLCIELKIERNRGYRIKT---LKNFQDGSYPIDATFMPVRNVNHSIHSYVNGNE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL 257
           + L + I T+GS+T ++++  ASR L D    F++ EE    ++ + +  +LP      
Sbjct: 197 EILFLEIWTNGSLTPKEALYEASRNLIDLFIPFLHAEEDNFNLENNQHKVTLPLFTFHD 255


>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 =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 91/376 (24%), Positives = 149/376 (39%), 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 EVLNPDHVICNLDVDAVVRMELTVSKGHGY------------------------------ 155
           +V++P   I  L   A +  E+ +S+G GY                              
Sbjct: 124 KVVDPSQYIATLASGASLEFEIQLSQGSGYRLRRTSLVPPGFTLPPPRDPLEPENDSKSE 183

Query: 156 -------------VPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY---- 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++    A L  +E L+LSVRS NCL+  NI  +G LI  T  ++L++ N
Sbjct: 304 LIEPEKKPTTKTIAKEIA-LTPIESLDLSVRSFNCLKRANITNVGKLIAYTRQELLQLKN 362

Query: 298 FGRKSLVEIKGVLGTM 313
           FG KS  E+  VL + 
Sbjct: 363 FGTKSASEVVDVLNSR 378


>gi|119668347|emb|CAK95470.1| RNA polymerase alpha subunit [Lactobacillus paracasei subsp.
           paracasei]
          Length = 180

 Score =  218 bits (555), Expect = 1e-54,   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|150036728|emb|CAM98255.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 194

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 87/194 (44%), 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 KHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
             ++   +  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|150036844|emb|CAM98287.1| DNA-directed RNA polymerase alpha chain [Leuconostoc holzapfelii]
          Length = 199

 Score =  218 bits (555), Expect = 1e-54,   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|328813999|gb|AEB52115.1| DNA-directed RNA polymerase alpha chain [Lactobacillus plantarum]
          Length = 215

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 97/215 (45%), Positives = 141/215 (65%), 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 KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTEN 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 DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           D L +F+N  +  K     +  +       L   +
Sbjct: 181 DHLSIFVNLTDEAKNTDVMVEKEETHKEKMLEMTI 215


>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 =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 118/250 (47%), Gaps = 8/250 (3%)

Query: 13  NNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 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         N   G   IDA++ P++  ++++ 
Sbjct: 131 DNTQHIASLTEPIDLCIGLQIERNRGY---LMKMPHNSQDGSYPIDAVFMPVRNANHSIH 187

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G    ++ L + I T+GS+T ++++  A R L D    F++ EE    ++++ +  
Sbjct: 188 SYGSGNE-KHEILFLEIWTNGSLTPKEALHEACRNLIDLFIPFLHKEEETSPLEDNHHTV 246

Query: 249 SLPFNPALLK 258
            L       K
Sbjct: 247 PLSPLTFHDK 256


>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 =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 81/311 (26%), Positives = 150/311 (48%), 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  EDLTDIILNIKGINL-----KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           ED+  I+ N+K +         S +S    +   +  G + A DI++ + ++++NPD  I
Sbjct: 74  EDVVTILNNLKRVRFFYNPSVFSQNSIHVASFLGQKAGQIYARDIESHSGLKIVNPDLYI 133

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI----------GLITIDALYSPIKKVS 184
            ++     ++ EL ++ G G+V  + ++   + +           ++ +D+ +SP+   +
Sbjct: 134 ADVSKVGALKFELFITNGKGFVDFETNKKYVNEVISRLESQIEGSVLAVDSDFSPVLNAN 193

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE- 243
           Y          +  +KL+ +I TDGSI  +D+++  ++IL   L +  + E   K   + 
Sbjct: 194 YQAVEINSASPIIEEKLNFSIKTDGSIFAKDALSQGAKILIAHLNLLADVENLNKFSADF 253

Query: 244 -DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            ++ 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 (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 81/311 (26%), Positives = 150/311 (48%), 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  EDLTDIILNIKGINL-----KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           ED+  I+ N+K +         S +S    +   +  G + A DI++ + ++++NPD  I
Sbjct: 74  EDVVTILNNLKRVRFFYNPSVFSQNSIHVASFLGQKAGQIYARDIESHSGLKIVNPDLYI 133

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI----------GLITIDALYSPIKKVS 184
            ++     ++ EL ++ G G+V  + ++   + +           ++ +D+ +SP+   +
Sbjct: 134 ADVSKVGALKFELFITNGKGFVDFETNKKYVNEVISLLESQIEGSVLAVDSDFSPVLNAN 193

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE- 243
           Y          +  +KL+ +I TDGSI  +D+++  ++IL   L +  + E   K   + 
Sbjct: 194 YQAVEINSASPIIEEKLNFSIKTDGSIFAKDALSQGAKILIAHLNLLADVENLNKFSADF 253

Query: 244 -DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302
                            ++ L+LSVRS N LR      + D+ + ++ D   + N GRKS
Sbjct: 254 FGDQEIKEEPIRRFSNSIDALDLSVRSLNALRRAQYYKISDIEKLSQDDFENIKNLGRKS 313

Query: 303 LVEIKGVLGTM 313
           + EI   L   
Sbjct: 314 VQEIMEKLQNY 324


>gi|86438816|emb|CAJ43373.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 203

 Score =  217 bits (553), Expect = 2e-54,   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|168805061|gb|ACA28609.1| DNA-directed RNA polymerase subunit alpha [Thiomonas sp. Ynys1]
          Length = 228

 Score =  217 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 99/228 (43%), Positives = 149/228 (65%), Gaps = 3/228 (1%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           G+ ED+  ++LN+KG+ LK+       +++ K G GVVTA DIQT +D+E++NP+HVI +
Sbjct: 1   GLQEDVIGVLLNLKGVVLKLHNRDEVTLSLRKDGEGVVTAADIQTPHDVEIINPEHVIAH 60

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTEN---DPIGLITIDALYSPIKKVSYTVESAREG 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|154424871|emb|CAL18538.1| RNA polymerase alpha subunit [Streptococcus vestibularis]
          Length = 211

 Score =  217 bits (552), Expect = 2e-54,   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|90567617|emb|CAJ31076.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
 gi|119662365|emb|CAJ33171.1| RNA polymerase alpha subunit [Lactobacillus helveticus]
          Length = 193

 Score =  217 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 85/188 (45%), Positives = 125/188 (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 LGMFINFE 235
             +F + +
Sbjct: 181 FKVFESAD 188


>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 =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 66/243 (27%), Positives = 122/243 (50%), Gaps = 4/243 (1%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +  +    +  PL +G A T+G A+RR L+  + G  IT  + + V HE S+I G+
Sbjct: 21  RVDSKRLHYGRFVLSPLMKGQADTIGIAMRRALLEEMEGTCITRAKSEKVPHEYSTIVGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + +I++N+K I L+ +    +  +I  +GP  +TA DI     +E+++    I  L 
Sbjct: 81  EESVHEILMNLKEIVLRSNLYGTREASICVKGPKTITAEDIILPASVEIVDTTQHIATLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
               + + L + +  GY   +   T N   G   IDA++ P++  ++++ S   G     
Sbjct: 141 EPLDLYIGLQIQRDRGY---RMRPTNNSQDGSYPIDAVFMPVRNANHSIYSYGNGNE-KQ 196

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLK 258
           + L + I T+GS+T ++++  ASR L D    F++ EE    ++E+ +  +LP      K
Sbjct: 197 EILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEKDINLEENKSRFTLPLFTFHDK 256

Query: 259 KVE 261
            V 
Sbjct: 257 LVN 259


>gi|150187066|emb|CAK30163.1| RNA polymerase alpha subunit [Streptococcus dysgalactiae subsp.
           equisimilis]
          Length = 208

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 90/206 (43%), Positives = 140/206 (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 RILQDQLGMFINFEEPKKEVKEDINV 247
           R+L + L +F +  +  K  +     
Sbjct: 181 RVLIEHLNLFTDLTDVAKATEVMKET 206


>gi|290489664|gb|ADD31216.1| RNA polymerase alpha subunit protein [Lonicera japonica]
          Length = 264

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 66/262 (25%), Positives = 127/262 (48%), Gaps = 10/262 (3%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLR 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 FMPVRNANHSIHSYGNENE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHTEE 234

Query: 237 PKKEVKEDINVKSLPFNPALLK 258
               ++++ +   L       K
Sbjct: 235 ENLHLEDNQHTVPLTPFTFHEK 256


>gi|150186939|emb|CAK30132.1| RNA polymerase alpha subunit [Streptococcus equinus]
          Length = 185

 Score =  216 bits (551), Expect = 4e-54,   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|119662347|emb|CAJ33162.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
          Length = 203

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 92/203 (45%), Positives = 143/203 (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 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHR 162
            +  +GP  VTA DIQ  N++ +LNPD  I  +   A + ++LT  KG GY+ A     R
Sbjct: 61  ELDVKGPAEVTASDIQGDNEVTILNPDLHIATVADGAELHIKLTADKGRGYLSANDNKAR 120

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 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|150036828|emb|CAM98281.1| DNA-directed RNA polymerase alpha chain [Leuconostoc lactis]
          Length = 208

 Score =  215 bits (548), Expect = 7e-54,   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|289524824|emb|CBJ94468.1| alpha subunit of RNA polymerase [Vibrio sp. Cmf 6.5]
          Length = 241

 Score =  215 bits (548), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 102/244 (41%), Positives = 158/244 (64%), Gaps = 8/244 (3%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINL-KMSGDSHKRVTIFKRGPGV 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++  + +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 181 AFVDLRDVRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 237

Query: 290 ADML 293
            ++L
Sbjct: 238 VELL 241


>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 =  215 bits (547), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 80/356 (22%), Positives = 140/356 (39%), Gaps = 51/356 (14%)

Query: 9   LIKPN---NIEYIVLGQEEEN--RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
            I PN    +E +   ++        ++  P+  G   TLGN  RR+L++ L G AITA 
Sbjct: 3   FIVPNSSAKLECVEFREKNPRTQYARLVLGPVAPGQGVTLGNTFRRLLLNDLPGVAITAA 62

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD----SHKRVTIF------------ 107
           +++    E  ++ G+ E + +I LN++ I    +          +TI             
Sbjct: 63  KLNDARTEFVTLPGIRESVVEIFLNLRDIVFFNTFPDVLAPQGTITIDPSVHEGPTDAGE 122

Query: 108 ----KRGPGVVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVS------------ 150
                  P V+ AGD+Q    +  ++P   I  L +      +   +             
Sbjct: 123 GFELSTSPRVICAGDMQLPEGVYCVDPTQPIATLMNAHTPFHLSFILEQATGYRVWKKPT 182

Query: 151 --KGHGYVPAKHHRTENDPIG----LITIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
              G G+ P +                 ID  + P++ V++ V           + +   
Sbjct: 183 QPYGRGFYPPRQTAAPQMEQVKSGLFQPIDGNFMPVRTVNFKVH----DGPPHGEYIHFE 238

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEP---KKEVKEDINVKSLPFNPALLKKVE 261
           I T+GSI    +   A  IL +     +    P     EV +  +V +          +E
Sbjct: 239 ITTNGSIHPHAAFKHAGAILTEITRATLQEPRPLVGMDEVSQPADVPNNQMAYFETIAIE 298

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +LELS+R+ NCL+   I+ + DL + +   +L + NFG+KS  E+   L T G+ L
Sbjct: 299 QLELSLRAYNCLKRAQILTLADLSRESYQSLLALRNFGQKSAEEVAKALETYGIEL 354


>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 =  215 bits (547), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 118/241 (48%), Gaps = 8/241 (3%)

Query: 16  EYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           ++  +    +         I  PL +G A T+G A+RR L+  L G  IT  + + + HE
Sbjct: 16  QWKCVESRTDSKRLYYGRFILSPLMKGQADTIGIAMRRALLGELEGTCITRAKSEKIPHE 75

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            S+I G+ E + +I++N+K I L+ +    +   I  +GPG VTA DI     +E+++  
Sbjct: 76  YSTIVGIQESVHEILMNLKEIVLRGNLYGTRNAFICAKGPGYVTAQDIILPPSVEIVDNT 135

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
             + +L     + + L + +  GY        +N   G   IDA++ P++  ++++    
Sbjct: 136 QHVASLTEPIDLCIGLQIERNRGYGIKT---PKNFHDGSYPIDAVFMPVRNANHSIHCYG 192

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                  + L + I T+GS+T ++++  ASR L D    F++ +E    ++ + +  +L 
Sbjct: 193 NDNE-KQEILFLEIWTNGSLTPKEALHEASRNLIDLFIHFLHAKEENLHLENNQHDVTLH 251

Query: 252 F 252
           F
Sbjct: 252 F 252


>gi|150036748|emb|CAM98027.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 210

 Score =  215 bits (547), Expect = 1e-53,   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|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 =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 89/254 (35%), Positives = 142/254 (55%), Gaps = 12/254 (4%)

Query: 4   KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           KN +  IKP  +E I    E       I +PL RG+  T+GNALRRVL+SSL G AI  V
Sbjct: 2   KNIK-FIKPFFVEEI---DENPISGKFIIKPLERGYGITVGNALRRVLLSSLPGTAIVNV 57

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMS---GDSHKRVTIFKRGPGVVTAGDIQ 120
           +I GV  E ++I GV+ED+  IILN+K I   +     D  +++ +  +GP  +TA   +
Sbjct: 58  KIQGVEQEFTTIPGVYEDVMTIILNLKKIVFAVDDESDDFEEKLELIAKGPQRLTASSFE 117

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE-NDPIGLITIDALYSP 179
               ++++NPDH I  L  D    M +T+ KG GYV AK ++    + +G+I ID+L++P
Sbjct: 118 LPAGVKIINPDHYITTLSDDVCFHMTVTLKKGIGYVGAKDNKVHGENQVGVIAIDSLFTP 177

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +  VSY VE     ++ + D+L++ I T+G++  ++++A A+ IL D   + +   +   
Sbjct: 178 VVNVSYQVEK----KLGNKDELTIEITTNGALLAKEALATAASILVDHFNVLVELSQKPA 233

Query: 240 EVKEDINVKSLPFN 253
            V+     K    N
Sbjct: 234 HVEFVSESKKEAHN 247


>gi|154424847|emb|CAL18526.1| RNA polymerase alpha subunit [Streptococcus pyogenes]
          Length = 202

 Score =  214 bits (546), Expect = 1e-53,   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 =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 90/205 (43%), Positives = 138/205 (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 ILQDQLGMFINFEEPKKEVKEDINV 247
           +L + L +F +  E  K        
Sbjct: 181 VLIEHLNLFTDLTEVAKATDVMKET 205


>gi|154424753|emb|CAL18479.1| RNA polymerase alpha subunit [Streptococcus agalactiae]
          Length = 213

 Score =  214 bits (545), Expect = 2e-53,   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|150036792|emb|CAN89787.1| DNA-directed RNA polymerase alpha chain [Leuconostoc lactis]
          Length = 198

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 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|154424859|emb|CAL18532.1| RNA polymerase alpha subunit [Streptococcus sobrinus]
          Length = 203

 Score =  214 bits (544), Expect = 2e-53,   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|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 =  214 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 92/334 (27%), Positives = 154/334 (46%), Gaps = 26/334 (7%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
            I+ NW E             +  +  T  I +PL +G A TLG A+RRVL+SS+   A 
Sbjct: 4   FIKINWTE---------NKTKRINDFSTSFIVQPLEKGLATTLGTAIRRVLLSSISSVAP 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|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 =  213 bits (543), Expect = 3e-53,   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|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 =  213 bits (542), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 76/343 (22%), Positives = 146/343 (42%), Gaps = 47/343 (13%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +     +       PL  G A T+G A+RR L+  +    IT+  + G  HE S++KG+
Sbjct: 18  EIQNARLHYGRFAVYPLFPGQAITIGTAIRRALLGEVHSTCITSAYVVGASHEYSTLKGI 77

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + DI+LN+K I  K      +   +   GPG+VTA  I+    ++V++    I  L+
Sbjct: 78  RESIHDILLNLKDIVFKSDTLERQEGILLFNGPGIVTAQHIKLPPVVQVVDNTQYIARLE 137

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
           +   + + +T+             T     G   +DA   P++ ++Y++ S  EG  +  
Sbjct: 138 MPTSIEIHITLE---NTKTCTSLNTMPTTKGRFILDAALKPVRNMNYSIHSLGEGD-MRQ 193

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL- 257
           + L + + T+GS+T ++ ++ AS+ L D L   +  E   +  +     +      +   
Sbjct: 194 EMLVLEVWTNGSLTPQEVISQASQNLNDLLKPLLKVERYFQAKQNIHKKRMFTPTQSENL 253

Query: 258 -----------------------------------------KKVEELELSVRSTNCLRGE 276
                                                      +++L++SVR++NCL+  
Sbjct: 254 NMDQIEMIGGNKLIDQPLLPADSHLNSSLSLNIDNLVHLEGISIDDLQISVRASNCLKKV 313

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEI-KGVLGTMGLFLG 318
            I  +  L+  T+ D+ ++ N G+KS+ +I   +  + G  LG
Sbjct: 314 GIYTIRQLLSYTQQDLFQIKNLGKKSVEQIVIAIRKSYGHILG 356


>gi|150187022|emb|CAK30153.1| RNA polymerase alpha subunit [Streptococcus thoraltensis]
          Length = 184

 Score =  212 bits (541), Expect = 4e-53,   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|150036722|emb|CAM98252.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. dextranicum]
          Length = 189

 Score =  212 bits (541), Expect = 5e-53,   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|119662831|emb|CAJ33208.1| RNA polymerase alpha subunit [Lactobacillus mucosae]
          Length = 180

 Score =  212 bits (540), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 86/176 (48%), Positives = 124/176 (70%), Gaps = 2/176 (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 HHR--TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
            ++       IG + ID++Y+PI++V+YTVE+ R GQ  D+DKL++ + TDGS+T 
Sbjct: 121 QNKLRLSGLEIGTLPIDSIYTPIERVNYTVENTRVGQSNDFDKLTLDVWTDGSLTP 176


>gi|119662851|emb|CAJ33218.1| RNA polymerase alpha subunit [Lactobacillus fuchuensis]
          Length = 202

 Score =  212 bits (540), Expect = 5e-53,   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|151416836|emb|CAO78489.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gelidum]
          Length = 193

 Score =  212 bits (540), Expect = 7e-53,   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|119662823|emb|CAJ33204.1| RNA polymerase alpha subunit [Lactobacillus coleohominis DSM 14060]
          Length = 173

 Score =  212 bits (539), Expect = 9e-53,   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 GYVPAKHHR-TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
           GY  A  ++   +  IG++ ID++Y+PI++V+YTVE+ R GQ  DY+KL++ +
Sbjct: 121 GYSSADDNKARMDLAIGVLPIDSIYTPIERVNYTVENTRVGQNNDYNKLTLDV 173


>gi|150186952|emb|CAK30135.1| RNA polymerase alpha subunit [Streptococcus equi subsp.
           zooepidemicus]
          Length = 205

 Score =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 87/203 (42%), Positives = 138/203 (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 LQDQLGMFINFEEPKKEVKEDIN 246
           L + L +F +  +  K  +    
Sbjct: 181 LIEHLNLFTDLTDVAKATEVMKE 203


>gi|119668371|emb|CAK95515.1| RNA polymerase alpha subunit [Lactobacillus sakei subsp. carnosus]
          Length = 196

 Score =  211 bits (538), Expect = 1e-52,   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|150036788|emb|CAM98271.1| DNA-directed RNA polymerase alpha chain [Leuconostoc
           pseudomesenteroides]
          Length = 205

 Score =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 85/204 (41%), Positives = 129/204 (63%), Gaps = 2/204 (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 ILQDQLGMFINFEEPKKEVKEDIN 246
           IL + L +F++      E    + 
Sbjct: 181 ILAEHLNLFMDISPVAAEASVMVE 204


>gi|154424839|emb|CAL18522.1| RNA polymerase alpha subunit [Streptococcus pluranimalium]
          Length = 203

 Score =  211 bits (537), Expect = 1e-52,   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|119662393|emb|CAJ33186.1| RNA polymerase alpha subunit [Lactobacillus plantarum]
          Length = 204

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 94/204 (46%), Positives = 137/204 (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 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDP 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 LGMFINFEEPKKEVKEDINVKSLP 251
           L +F+N  +  K     +  +   
Sbjct: 181 LSIFVNLTDEAKNTDVMVEKEETH 204


>gi|119662315|emb|CAJ33145.1| RNA polymerase alpha subunit [Lactobacillus iners DSM 13335]
          Length = 209

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 92/205 (44%), Positives = 140/205 (68%)

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 ILQDQLGMFINFEEPKKEVKEDINV 247
           IL++   +F++ +   +     I  
Sbjct: 181 ILEEHFKVFMSADMSDQFANVMIEK 205


>gi|150036732|emb|CAM98257.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. mesenteroides]
          Length = 186

 Score =  211 bits (537), Expect = 1e-52,   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|168805063|gb|ACA28610.1| DNA-directed RNA polymerase subunit alpha [Thiomonas sp. WJ68]
          Length = 228

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 96/227 (42%), Positives = 146/227 (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 LDVDAVVRMELTVSKGHGYVPAKHHRTEN---DPIGLITIDALYSPIKKVSYTVESAREG 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|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 =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 83/317 (26%), Positives = 148/317 (46%), Gaps = 18/317 (5%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
                 +  T    +PL RGFA+TLGN+LRR ++SS+   A+  V+I+GV HE S I  V
Sbjct: 13  KAEHLSDFETTFELQPLERGFANTLGNSLRRTILSSVPSVAVFGVKIEGVEHEFSVIDKV 72

Query: 79  HEDLTDIILNIKGINLKMSGD-----SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
            ED+  I+ N+K +      +       +  +   R  G +T  DI   + +E++N D V
Sbjct: 73  REDVVTILNNLKKLRFSFKKEVFLQNEIQVASFDGRKVGKITGADILVNSALEIVNKDQV 132

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP-----------IGLITIDALYSPIKK 182
           + N      ++ E+ ++ G G+V  + ++ +                +I +D+ +S ++ 
Sbjct: 133 VANTSEVGALKFEMFLTYGRGFVDFETNKRKIQELGPALESKLGYGQIIAVDSDFSAVEN 192

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           V ++         +  +KL+ ++ TDG+I  +D++A A++IL   L +  +      EV 
Sbjct: 193 VKFSSTELNSSNPIVEEKLTFSVKTDGTILAKDALAEAAKILIAHLKLVSDTANLDAEVD 252

Query: 243 EDINVKSLPFNPALLKKVE--ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
                             +   L+L+VRS N LR      + DL++ T  ++  + N G+
Sbjct: 253 SFFEEVKQKEEAPKKNSADLTTLDLTVRSLNALRRAQYYKISDLLELTLEELENIKNLGK 312

Query: 301 KSLVEIKGVLGTMGLFL 317
           KS+ EI   L    L L
Sbjct: 313 KSVEEIVEKLKEHNLEL 329


>gi|150187019|emb|CAK30152.1| RNA polymerase alpha subunit [Streptococcus sobrinus]
          Length = 202

 Score =  210 bits (536), Expect = 2e-52,   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|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 =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 71/318 (22%), Positives = 133/318 (41%), Gaps = 18/318 (5%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI--DGVLHEIS--S 74
            +  +  +       PL RG   T+G+ALRR L+  + G  +T V+     V H  S  +
Sbjct: 21  RVESKRSHYGRFSLSPLLRGQGGTIGSALRRTLLRDVEGTNVTHVKFFNKRVKHLFSSST 80

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           I G+ E + DII+N++ I  +       +  I+  GP  VTA DI     I++++    I
Sbjct: 81  ILGIEESVHDIIMNLREIVFRCELHGIHKAYIYTVGPKNVTAQDIILPPFIQIVDGTQHI 140

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG- 193
            ++     + + L + K  G      H         I  +  Y P++ V+Y V   ++  
Sbjct: 141 ASITKPIHLHVTLKIEKNWGETTESIHPITKYFTRYIPTEIFYMPVRSVTYNVYFYKDEY 200

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
            +  YD L   + T+G +T ++++  A   L D +   ++      E         LP  
Sbjct: 201 DIHIYDILIFELWTNGELTPKEALYEACWRLIDLIIPLLDVPLLHVEGSGVKESIPLPIV 260

Query: 254 PALLKKVEE----------LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             + +  E+          L L  + +  LR  +I  + D +  ++ D+  +    ++S 
Sbjct: 261 SNMNRTQEDLFVQHLFIDQLGLPSKISKSLRESHIYRVSDFMNYSQQDLKNLEYSKKES- 319

Query: 304 VEIKGVLGTMGLFLGMNL 321
             I+  L  +  + G+NL
Sbjct: 320 --IEQTLEILHKYFGINL 335


>gi|315451273|gb|ADU24721.1| RNA polymerase alpha subunit [Lactobacillus sp. YM 0097]
          Length = 212

 Score =  210 bits (535), Expect = 2e-52,   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|150186989|emb|CAK30143.1| RNA polymerase alpha subunit [Streptococcus gordonii]
          Length = 202

 Score =  209 bits (533), Expect = 4e-52,   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|119668357|emb|CAK95473.1| RNA polymerase alpha subunit [Lactobacillus pontis]
          Length = 179

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 85/178 (47%), Positives = 127/178 (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 A--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           A     R E+  IG++ ID++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T 
Sbjct: 121 ANDNKARMEDLAIGVLPIDSIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSLTP 178


>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 =  209 bits (532), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 85/331 (25%), Positives = 152/331 (45%), Gaps = 40/331 (12%)

Query: 19  VLGQEEENRTLMI-AEPLPRGFAHTLGNALRRVL-------MSSLRGAAI--TAVQIDGV 68
            +  +       I    L +G A       RRVL       +  + G  +  T  +   V
Sbjct: 21  RVDSKRLYYGRFISVLRLGKGQAE-----HRRVLALGRGFNLEKIEGNNVLATRAKFGSV 75

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVL 128
            HE S+I G+ E + +I+LN+K I L+ +    +  +I  +GP  +TA DI     +E++
Sbjct: 76  PHEYSTIAGIEESVQEILLNLKEIVLRSNLYGVRDASISVKGPRYITAQDIILPPSVEIV 135

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           +    I NL       +EL + +  GY        +N   G   IDA+  P++ V+Y++ 
Sbjct: 136 DTSQPIANLTEPIDFCIELQIKRDRGYQTELR---KNYQDGSYPIDAVSMPVRNVNYSIF 192

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248
           S   G    ++ L + I T+GS+T ++++  ASR L D    F++ EE     +E+ N  
Sbjct: 193 SCGNGNE-KHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLHAEEEGTSFEENKNRF 251

Query: 249 SLPFNPALLK------------------KVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
           + P      +                   +++LEL  R+ NCL+  NI  + DL+ +TE 
Sbjct: 252 TPPLFTFQKRLTNLNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRANIHTLLDLLSKTEE 311

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           D++R+ +F    + + K +  T+  +L ++L
Sbjct: 312 DLMRIDSF---HMEDGKQIWDTLEKYLPIDL 339


>gi|150036768|emb|CAM98265.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. cremoris]
          Length = 212

 Score =  209 bits (531), Expect = 6e-52,   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|150187125|emb|CAK30176.1| RNA polymerase alpha subunit [Streptococcus intermedius]
          Length = 202

 Score =  209 bits (531), Expect = 7e-52,   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|150187122|emb|CAK30175.1| RNA polymerase alpha subunit [Streptococcus lutetiensis]
          Length = 201

 Score =  208 bits (530), Expect = 8e-52,   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|150186960|emb|CAK30137.1| RNA polymerase alpha subunit [Streptococcus infantis ATCC 700779]
          Length = 173

 Score =  208 bits (530), Expect = 8e-52,   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|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 =  208 bits (530), Expect = 9e-52,   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|154424797|emb|CAL18501.1| RNA polymerase alpha subunit [Streptococcus gordonii]
          Length = 194

 Score =  208 bits (530), Expect = 9e-52,   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|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 =  208 bits (530), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 87/323 (26%), Positives = 151/323 (46%), Gaps = 22/323 (6%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           +   L     N T    +PL RG   TLG ALRR+L+S++   A+ A++I+ V HE   +
Sbjct: 11  KVTKLNNSTSNVTAFTLQPLERGMGQTLGVALRRILLSNITSLALFAIKIEDVNHEFQVV 70

Query: 76  KGVHEDLTDIILNIKGINLKMS-----GDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLN 129
            G  ED+  II+N++ +  + +      D   +VT+    PG VT+  ++   + IE+LN
Sbjct: 71  DGCVEDVATIIMNLRKVKFQYNPEFVKDDEIIKVTLKADQPGEVTSRLLEVNNSSIEILN 130

Query: 130 PDHVICNLDVDA--VVRMELTVSKGHGYVP-------------AKHHRTENDPIGLITID 174
               I +L  +    + +EL +  G G++                   ++      I  D
Sbjct: 131 KSLEIAHLSANGKHKLNIELYLRPGRGFISNEENKKLLNNSSITTRMESKIKNGIFIATD 190

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           + +SPI+KV+YTVE          ++L+ +  TDG++  + ++  A  IL     +  N 
Sbjct: 191 SNFSPIEKVNYTVEELNSSSNKIEERLTFSFQTDGTVDPKSALQQACEILVGHFKLIGNV 250

Query: 235 EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           +E K  V  + + ++   N      +  L LSVRS N L+      +  + + +  ++ +
Sbjct: 251 DEMKVNVFAEESEQTQETND-NDVDINSLNLSVRSLNALKRIGKTKISQVAEMSLEELEQ 309

Query: 295 MANFGRKSLVEIKGVLGTMGLFL 317
           + N GRKSL EI+  L   G  L
Sbjct: 310 VKNLGRKSLDEIQQRLKEYGYEL 332


>gi|119668333|emb|CAK95466.1| RNA polymerase alpha subunit [Lactobacillus intestinalis]
          Length = 191

 Score =  208 bits (530), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 83/186 (44%), Positives = 125/186 (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 MFINFE 235
           +F + +
Sbjct: 181 VFESAD 186


>gi|150036776|emb|CAM98267.1| DNA-directed RNA polymerase alpha chain [Weissella viridescens]
          Length = 175

 Score =  208 bits (529), Expect = 1e-51,   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|119668337|emb|CAK95467.1| RNA polymerase alpha subunit [Lactobacillus johnsonii]
          Length = 187

 Score =  208 bits (529), Expect = 1e-51,   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|238810271|dbj|BAH70061.1| hypothetical protein [Mycoplasma fermentans PG18]
          Length = 339

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 87/323 (26%), Positives = 151/323 (46%), Gaps = 22/323 (6%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           +   L     N T    +PL RG   TLG ALRR+L+S++   A+ A++I+ V HE   +
Sbjct: 13  KVTKLNNSTSNVTAFTLQPLERGMGQTLGVALRRILLSNITSLALFAIKIEDVNHEFQVV 72

Query: 76  KGVHEDLTDIILNIKGINLKMS-----GDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLN 129
            G  ED+  II+N++ +  + +      D   +VT+    PG VT+  ++   + IE+LN
Sbjct: 73  DGCVEDVATIIMNLRKVKFQYNPEFVKDDEIIKVTLKADQPGEVTSRLLEVNNSSIEILN 132

Query: 130 PDHVICNLDVDA--VVRMELTVSKGHGYVP-------------AKHHRTENDPIGLITID 174
               I +L  +    + +EL +  G G++                   ++      I  D
Sbjct: 133 KSLEIAHLSANGKHKLNIELYLRPGRGFISNEENKKLLNNSSITTRMESKIKNGIFIATD 192

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           + +SPI+KV+YTVE          ++L+ +  TDG++  + ++  A  IL     +  N 
Sbjct: 193 SNFSPIEKVNYTVEELNSSSNKIEERLTFSFQTDGTVDPKSALQQACEILVGHFKLIGNV 252

Query: 235 EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           +E K  V  + + ++   N      +  L LSVRS N L+      +  + + +  ++ +
Sbjct: 253 DEMKVNVFAEESEQTQETND-NDVDINSLNLSVRSLNALKRIGKTKISQVAEMSLEELEQ 311

Query: 295 MANFGRKSLVEIKGVLGTMGLFL 317
           + N GRKSL EI+  L   G  L
Sbjct: 312 VKNLGRKSLDEIQQRLKEYGYEL 334


>gi|150036770|emb|CAM98266.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gasicomitatum]
          Length = 210

 Score =  207 bits (528), Expect = 1e-51,   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|119662391|emb|CAJ33185.1| RNA polymerase alpha subunit [Lactobacillus amylophilus]
          Length = 174

 Score =  207 bits (528), Expect = 2e-51,   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|150187039|emb|CAK30157.1| RNA polymerase alpha subunit [Streptococcus agalactiae ATCC 13813]
          Length = 188

 Score =  207 bits (528), Expect = 2e-51,   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|150036836|emb|CAM98283.1| DNA-directed RNA polymerase alpha chain [Leuconostoc fallax]
          Length = 215

 Score =  207 bits (528), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 85/206 (41%), Positives = 131/206 (63%), Gaps = 2/206 (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 QDQLGMFINFEEPKKEVKEDINVKSL 250
            + L +F +      E +  ++V+  
Sbjct: 181 SEHLNLFTDISSVAAETEVMVDVEQT 206


>gi|150187098|emb|CAK30170.1| RNA polymerase alpha subunit [Streptococcus criceti]
          Length = 181

 Score =  207 bits (527), Expect = 2e-51,   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|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 =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 71/309 (22%), Positives = 150/309 (48%), Gaps = 16/309 (5%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           + +V  +  +  T  + EPL RG+ +T+G  +RR L+SS+   A  A++I  V HE ++I
Sbjct: 10  KELVAEKVSDFNTTFVIEPLMRGYGNTIGTVIRRTLLSSITSVAPFAIKISHVEHEFTAI 69

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKR-----VTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           +G+ ED   ++ NI+ I      +  ++     ++      G V A DI+T+  ++++N 
Sbjct: 70  EGLREDAITLVANIRKIRFAYDPELFEKDNLAKISFKSTKEGEVHASDIETIPGLDIVNK 129

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI-----------GLITIDALYSP 179
           D  I  +  +  +  EL +  G GYV  + ++                   + +D+ +SP
Sbjct: 130 DQYIATISKNGSLEFELYLRTGRGYVSFEDNKKTILEYGPKLESKIKNGQFLAMDSDFSP 189

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           IKKV+   E       +  ++L + ++TDG++  ++ +  A++I+     +  N +    
Sbjct: 190 IKKVAILFEELNSTSNIIEERLKIKVETDGTVEAKNVMEEAAKIIVAHFQIIGNIDALGT 249

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
               D   +     P +   +++L L++RS N LR      + ++++ ++ ++  + N G
Sbjct: 250 IDLFDDQKEKHEKTPKVSVSIDKLNLTIRSLNALRRAGFNNVDEIMKLSDEELSNIKNLG 309

Query: 300 RKSLVEIKG 308
           +KS+ +I  
Sbjct: 310 KKSVQDIID 318


>gi|255023418|ref|ZP_05295404.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
           FSL J1-208]
          Length = 195

 Score =  207 bits (527), Expect = 2e-51,   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|150186968|emb|CAK30138.1| RNA polymerase alpha subunit [Streptococcus mutans]
          Length = 192

 Score =  207 bits (527), Expect = 2e-51,   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|150187089|emb|CAK30168.1| RNA polymerase alpha subunit [Streptococcus alactolyticus]
          Length = 202

 Score =  207 bits (527), Expect = 2e-51,   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|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 =  207 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 89/329 (27%), Positives = 158/329 (48%), Gaps = 21/329 (6%)

Query: 9   LIKPNNIEYIVLGQ--EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           + K   ++Y+ +      +       +PL RGFA TLG ALRRVL+S++   A   V+I+
Sbjct: 1   MEKFQKLDYLEVPSSTTSDFEGTFNLQPLERGFATTLGVALRRVLLSNITSLAPFCVRIE 60

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLK-----MSGDSHKRVTIFKRGPGVVTAGDIQT 121
           GV HE   I GV ED+  +I+N++ +        +  D   +V +     G + +  ++ 
Sbjct: 61  GVTHEFQGITGVIEDVPSLIMNLRKVRFSYDPELVKDDEIIKVELKADQIGEINSRYLEV 120

Query: 122 VN--DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK-----------HHRTENDPI 168
           V+  ++EV++ +  I ++ ++  +R+EL +  G G+V ++              T+    
Sbjct: 121 VDNLNVEVIDHNIHIADVALENSLRLELYLRPGRGFVSSEENKALVSKLETQLETKIKKG 180

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
             I +D+ +SP++KV+Y V       V   +KL   + TDG++  +D++  A+ IL    
Sbjct: 181 KFIAVDSNFSPVEKVNYVVSELNSSSVKIEEKLEFNVITDGTVKPKDAIKQAAEILISHF 240

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
            +  N +E K  + E    K L         + +L LSVRS N LR        ++ + T
Sbjct: 241 KVIGNVDEIKDSIFETSEDKVLDV-QEQDIDINQLGLSVRSLNALRRIGKTKASEVAKMT 299

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             ++ +  N G+KSL EI   +   G  L
Sbjct: 300 YDELEQTKNLGKKSLDEIITKIKEHGFEL 328


>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 =  206 bits (524), Expect = 4e-51,   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|154424761|emb|CAL18483.1| RNA polymerase alpha subunit [Streptococcus equinus]
          Length = 183

 Score =  206 bits (524), Expect = 4e-51,   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|150186942|emb|CAK30133.1| RNA polymerase alpha subunit [Streptococcus canis]
          Length = 204

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 86/202 (42%), Positives = 136/202 (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 DQLGMFINFEEPKKEVKEDINV 247
           + L +F +  +  K  +     
Sbjct: 181 EHLNLFTDLTDVAKATEVMKET 202


>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 =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 86/375 (22%), Positives = 151/375 (40%), Gaps = 77/375 (20%)

Query: 16  EYIVLGQEEEN-----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH 70
           E+  +  + ++      +     PL    A T+G A+RR L+S + G +I +  I G +H
Sbjct: 13  EWKCVDDQPDHNRRLHYSRFALSPLLVDQAMTIGVAIRRALLSEVEGISIISANIVGAVH 72

Query: 71  EISSIKGVHEDLTDIILNIKGINLK--------MSGDSHKRVTIFKRGPGVVTAGDIQTV 122
           E S++ GV E + +I+LN+K I +K               R +IF +GPGVVTA  I+  
Sbjct: 73  EYSTLDGVRESVDEILLNLKQIVIKGAKGASITPLDHKEYRASIFAQGPGVVTAEHIKFP 132

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           + I  ++PD  I  L  +  + +EL + +G     AK             IDA ++P++K
Sbjct: 133 SSILAVDPDQSIATLLNETQLCIELFIRQG----IAKQLTRTKKNHQGFFIDANFTPVQK 188

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL-------------- 228
            ++++ S  + + L    L + I T+ ++T  +++  A   L +                
Sbjct: 189 ANFSIHSVGDPKGL-QQLLLLEIWTNKTLTPAEALYQAHASLLNLFHQISPPLLHKELSP 247

Query: 229 --------------------GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL--- 265
                                +             + ++         LK   +  L   
Sbjct: 248 SKNILNQNSDSNSLGGSSFGRVVSLETRRDSTQTNNSSIPKEIQPSVRLKSYTDTNLSID 307

Query: 266 -------------------SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
                              S R +NCL+  NI  + DL+  T+ D+L++ NFGRKS+ ++
Sbjct: 308 KQMNDSVNKENLSIDELELSPRISNCLKKANINTIADLLNYTQEDLLKIKNFGRKSVEQV 367

Query: 307 KGVLGTMGLFLGMNL 321
             VL        M L
Sbjct: 368 SLVLR---KRFNMEL 379


>gi|290489674|gb|ADD31221.1| RNA polymerase alpha subunit protein [Rhododendron simsii]
          Length = 262

 Score =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 75/263 (28%), Positives = 122/263 (46%), Gaps = 11/263 (4%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEE----NRTLMIAEPLPRGFAHTLGNALRRVLMSSLR 56
           M QKN +    P  +++  +    +            PL RG A TLG A+RR L+  + 
Sbjct: 1   MSQKNRRGF--PRRLQWKCVESRVDSKRLYYGRFSLFPLRRGEAETLGIAMRRALLGEIE 58

Query: 57  GAAITAVQIDGVL--HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 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             G    D
Sbjct: 119 TARDIMVAPYVEIIDNTQHIASLTKRIDLYMKLEIQKNRGYQI--KSPKNTLQDGSYPTD 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 EEPKKEVKEDINVKSLPFNPALL 257
           EE    + E+ +  +LP      
Sbjct: 236 EEENVHLDENQHKINLPLFTFHE 258


>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 =  205 bits (522), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 108/219 (49%), Positives = 150/219 (68%), Gaps = 10/219 (4%)

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--------ENDPIGLITIDALYSPIKK 182
           D +IC L  +  + M + V+ G GY+P   ++         E D IG I ++ALYSP+ +
Sbjct: 1   DLLICTLGQNVELNMTIYVASGKGYLPVTKYKENELLKLMSEQDLIGFIPVNALYSPVNR 60

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE--EPKKE 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|639724|gb|AAA61684.1| RNA polymerase alpha subunit [Chlamydia muridarum]
          Length = 322

 Score =  205 bits (522), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 72/310 (23%), Positives = 149/310 (48%), Gaps = 16/310 (5%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           + +V  +  +  T  + EPL RG+A+T+G  LRR L+SS+   A  A++I+ V HE  +I
Sbjct: 10  KELVAEKVNDFNTTFVIEPLARGYANTMGTVLRRTLLSSITSVAPFAIKINNVEHEFQTI 69

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKR-----VTIFKRGPGVVTAGDIQTVNDIEVLNP 130
            G+ ED   ++ NI+ I    + +  ++     ++      G + A DI  V+ +E++N 
Sbjct: 70  SGLKEDAITLVRNIRNIRFVYNEEIFEKENLAKISFKTNKEGEIFASDIPEVSGLEIVNK 129

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI-----------GLITIDALYSP 179
           D  I N+     +  +L + KG G++  + ++                   + +D+ +SP
Sbjct: 130 DQYIANIAKGGSLEFDLFLRKGRGFIDFEENKNVISQYGSRLESSIKNGQFLAMDSDFSP 189

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +KK + + E       L  ++L + I+TD +++ ++++  A++I+     +  N    + 
Sbjct: 190 VKKCAISFEELNSSSKLIEERLKIKIETDCTVSAKEAIEQAAKIIVAHFQIIGNINALET 249

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
               + N +           + +L LSVRS N LR      + +++  ++ ++  + N G
Sbjct: 250 IELFEENKEKKEREIKSTTPITKLGLSVRSENALRRAKYNTVEEVLGLSDEELSNIKNLG 309

Query: 300 RKSLVEIKGV 309
           +KS+ +I   
Sbjct: 310 KKSIQDIIEK 319


>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 =  205 bits (522), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 77/343 (22%), Positives = 162/343 (47%), Gaps = 19/343 (5%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           + +V  +  +  T  + EPL RG+A+T+G  LRR L+SS+   A  A++I+ V HE  +I
Sbjct: 10  KELVAEKVNDFNTTFVIEPLARGYANTMGTVLRRTLLSSITSVAPFAIKINNVEHEFQTI 69

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKR-----VTIFKRGPGVVTAGDIQTVNDIEVLNP 130
            G+ ED   ++ NI+ I    + +  ++     ++      G + A DI  V+ +E++N 
Sbjct: 70  SGLKEDAITLVRNIRNIRFVYNEEIFEKENLAKISFKTNKEGEIFASDIPEVSGLEIVNK 129

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI-----------GLITIDALYSP 179
           D  I N+     +  +L + KG G++  + ++                   + +D+ +SP
Sbjct: 130 DQYIANIAKGGSLEFDLFLRKGRGFIDFEENKNVISQYGSRLESSIKNGQFLAMDSDFSP 189

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +KK + + E       L  ++L + I+TD +++ ++++  A++I+     +  N    + 
Sbjct: 190 VKKCAISFEELNSSSKLIEERLKIKIETDCTVSAKEAIEQAAKIIVAHFQIIGNINALET 249

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
               + N +           + +L LSVRS N LR      + +++  ++ ++  + N G
Sbjct: 250 IELFEENKEKKEREIKSTTPITKLGLSVRSENALRRAKYNTVEEVLGLSDEELSNIKNLG 309

Query: 300 RKSLVEIKGVLGTMGLFLGMNL---PDWPPESIEELAKKYEDK 339
           +KS+ +I          +G +     ++  ES+++L    E +
Sbjct: 310 KKSIQDIIEKRNEWKERIGYDDGQSDNFIIESLDQLNNSEEGE 352


>gi|150036708|emb|CAM98019.1| DNA-directed RNA polymerase alpha chain [Leuconostoc carnosum]
          Length = 199

 Score =  205 bits (521), Expect = 1e-50,   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|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 =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 83/211 (39%), Positives = 136/211 (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 ADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
            +M+++ N GRKSL E+K  L  +GL L  +
Sbjct: 181 PEMMKVRNLGRKSLEEVKIKLADLGLGLKND 211


>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 =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 85/322 (26%), Positives = 148/322 (45%), Gaps = 29/322 (9%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------VL 69
              QE     L    P   G   T+ N LRR L++++ G  IT+V+ +           +
Sbjct: 39  ETDQELLLYALFQLGPFSHGQGLTIANGLRRTLLNNIIGFGITSVKFEPKWVDISKEVFI 98

Query: 70  HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR-----VTIFKRGPGVVTAGDIQTVND 124
           HE S+I G+ E + +II N+K I ++      +      + I +  PGV+ A  I+    
Sbjct: 99  HEYSTIPGIWESIFEIIENLKKIKIRRENSPFEPFEKQVIRITQDKPGVLRADSIKLPPF 158

Query: 125 IEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           +++LN +  I ++   + ++ + +T+    G                I +  +  PIK V
Sbjct: 159 LKILNQNQPIVSMMSSNLILDIIITIEAQTGNHLCN--------NQFIHVSEVCLPIKWV 210

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ---LGMFINFEEPKKE 240
           +Y +++         + L   I TDG+IT +++++ A+ I  D            E K  
Sbjct: 211 NYVIKTDPLLGSKSPESLFFEISTDGTITPQEALSKAADICIDLYSCFSTAQKELEVKSI 270

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           VKE +  +           +E L LSVR+ NCL+  NI  + DL+ ++++D+L M NFG+
Sbjct: 271 VKEKVTEEVKEEIITNKVTIENLGLSVRAYNCLKRANIYTVTDLLTKSKSDLLAMKNFGK 330

Query: 301 KSLVEIKGVLGTMGLFLGMNLP 322
           KS  E+   L      LG++LP
Sbjct: 331 KSADEVYEALQNR---LGIDLP 349


>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 =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 82/316 (25%), Positives = 149/316 (47%), Gaps = 17/316 (5%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            + Q  +  T    +PL RG  +T+GNALRR ++SS+  A++ A++I  + HE S +  V
Sbjct: 13  SIQQVSDFETTFELKPLERGLGNTIGNALRRTILSSVSSASVFAIKIANIDHEFSVLDNV 72

Query: 79  HEDLTDIILNIKGINLKMS-----GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHV 133
            ED+  I+ N+K I  +        D  ++V+      G + A DI     +E++N D  
Sbjct: 73  VEDVVSILNNLKKIRFRYHEELFDNDQIQKVSFSGDKAGNIYAKDIDNTGGLEIVNQDQY 132

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRT----------ENDPIGLITIDALYSPIKKV 183
           I ++     ++ E+ +  G G+   + ++            +    +I +D+ +SP+ KV
Sbjct: 133 IASVGKVGALKFEMFIIGGKGFTDFETNKKRVSDLAGKLQSDLLGTIIAVDSDFSPVVKV 192

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
            Y          +  ++L + + TDG+I  +D++A A++IL   L +  N E   +    
Sbjct: 193 HYEANELNSSNPIVEERLVLNLKTDGTIFAKDALAEAAKILIAHLQLVSNTENLDQIADN 252

Query: 244 --DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
             + +          L  +  L+LSVRS N LR      + D+   T+ ++  + N G+K
Sbjct: 253 FFEESRYHEEQPKKNLIDLSALDLSVRSLNALRRAQYYKVSDIQDLTQEELENIKNLGKK 312

Query: 302 SLVEIKGVLGTMGLFL 317
           S+ EI   L   G+ L
Sbjct: 313 SVQEILDKLKEQGIEL 328


>gi|150036716|emb|CAM98021.1| DNA-directed RNA polymerase alpha chain [Fructobacillus durionis]
          Length = 197

 Score =  204 bits (520), Expect = 1e-50,   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|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 =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 93/330 (28%), Positives = 155/330 (46%), Gaps = 26/330 (7%)

Query: 13  NNIEYIVLGQ----EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           + ++Y+ +         N      +PL RGF +T+  ALRRVL+S++   A+ A++I GV
Sbjct: 5   SKLDYLQVSNSAINNNLNEVTFSLKPLERGFGNTVAVALRRVLLSNVTSLALFAIKISGV 64

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR-----VTIFKRGPGVVTAGDIQ-TV 122
            HE  +I G+ ED+T II+N++ +  K + +  K       TI    PG+VT+  I+ T 
Sbjct: 65  SHEFQTIPGIVEDVTAIIMNLRKVKFKYNPEFVKDGEIIKATIKAEQPGIVTSKSIEITN 124

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV--------------PAKHHRTENDPI 168
             +E++N    I N+     + +EL +  G G++               A    +     
Sbjct: 125 PSVEIINKSQEIANIQKG-SLVIELFLRPGRGFISNESNKKFIQNDSLFASKIESNIKKG 183

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
             I +D+ +SP++K SYTV           ++L  TI TDG+I  + ++  A +IL    
Sbjct: 184 LFIAVDSNFSPVEKCSYTVRELNTSSNKIEEELLFTIKTDGTIDAKSAINQACKILVAHF 243

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
               + +  K +V E+  VK+          + +L LSVRS N L+        ++   T
Sbjct: 244 MAVGDVDSMKLDVFEEEKVKNDEP-IENDVDINQLGLSVRSLNALKRIGKTKASEVAAMT 302

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
             ++ +  N GRKSL EI+  L   G  L 
Sbjct: 303 WEELEQTKNLGRKSLDEIQECLKVNGFTLN 332


>gi|154424857|emb|CAL18531.1| RNA polymerase alpha subunit [Streptococcus sanguinis]
          Length = 194

 Score =  204 bits (520), Expect = 1e-50,   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|119672795|emb|CAK95481.1| RNA polymerase alpha subunit [Lactobacillus saerimneri]
          Length = 170

 Score =  204 bits (519), Expect = 2e-50,   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|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 =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 92/330 (27%), Positives = 157/330 (47%), Gaps = 26/330 (7%)

Query: 13  NNIEYIVLGQ----EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           + ++Y+ +         N      +PL RGFA+T+  ALRRVL+S++   A+ A++I GV
Sbjct: 5   SKLDYLQVSNSAINNNLNEVTFSLKPLERGFANTVAVALRRVLLSNITSLALFAIKISGV 64

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR-----VTIFKRGPGVVTAGDIQ-TV 122
            HE  +I G+ ED+T II+N++ +  K + +  K       TI    PGVVT+  I+ + 
Sbjct: 65  SHEFQTIPGIVEDVTAIIMNLRKVKFKYNPEFVKDGEIIKATIKAEQPGVVTSKSIEISN 124

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV--------------PAKHHRTENDPI 168
             +E++N    I N+   A + +EL +  G G++               A    +     
Sbjct: 125 PSVEIINKSQEIANIQKGA-LVIELFLRPGRGFISNESNKRFIQNDSLFASKIESNIKKG 183

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
             I +D+ +SP++K SYTV+          ++L  TI TDG++  + ++  A +IL    
Sbjct: 184 LFIAVDSNFSPVEKCSYTVKELNTSSNKIEEELLFTIKTDGTVDAKSAINQACKILVAHF 243

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
               + +  K +V E+  + +          + +L LSVRS N L+        ++   T
Sbjct: 244 MTVGDVDTMKIDVFEEERINNDEP-IENDVDINQLGLSVRSLNALKRIGKTKASEVAAMT 302

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
             ++ +  N GRKSL EI+  L   G  L 
Sbjct: 303 WEELEQTKNLGRKSLDEIQECLKLNGFTLN 332


>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 =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 92/330 (27%), Positives = 157/330 (47%), Gaps = 26/330 (7%)

Query: 13  NNIEYIVLGQ----EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
           + ++Y+ +         N      +PL RGFA+T+  ALRRVL+S++   A+ A++I GV
Sbjct: 5   SKLDYLQVSNSAINNNLNEVTFSLKPLERGFANTVAVALRRVLLSNITSLALFAIKISGV 64

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR-----VTIFKRGPGVVTAGDIQ-TV 122
            HE  +I G+ ED+T II+N++ +  K + +  K       TI    PGVVT+  I+ + 
Sbjct: 65  SHEFQTIPGIVEDVTAIIMNLRKVKFKYNPEFVKDGEIIKATIKAEQPGVVTSKSIEISN 124

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV--------------PAKHHRTENDPI 168
             +E++N    I N+   A + +EL +  G G++               A    +     
Sbjct: 125 PSVEIINKSQEIANIQKGA-LVIELFLRPGRGFISNESNKKFIQNDSLFASKIESNIKKG 183

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
             I +D+ +SP++K SYTV+          ++L  TI TDG++  + ++  A +IL    
Sbjct: 184 LFIAVDSNFSPVEKCSYTVKELNTSSNKIEEELLFTIKTDGTVDAKSAINQACKILVAHF 243

Query: 229 GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRT 288
               + +  K +V E+  + +          + +L LSVRS N L+        ++   T
Sbjct: 244 MTVGDVDAMKIDVFEEEKINNDEP-IENDVDINQLGLSVRSLNALKRIGKTKASEVAAMT 302

Query: 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
             ++ +  N GRKSL EI+  L   G  L 
Sbjct: 303 WEELEQTKNLGRKSLDEIQECLKLNGFTLN 332


>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 = 77/343 (22%), Positives = 162/343 (47%), Gaps = 19/343 (5%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           + +V  +  +  T  + EPL RG+A+T+G  LRR L+SS+   A  A++I+ V HE  +I
Sbjct: 10  KELVAEKVNDFNTTFVIEPLARGYANTMGTVLRRTLLSSITSVAPFAIKINNVEHEFETI 69

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKR-----VTIFKRGPGVVTAGDIQTVNDIEVLNP 130
            G+ ED   ++ NI+ I    + +  ++     ++      G + A DI  V+ +E++N 
Sbjct: 70  SGLKEDAITLVRNIRNIRFVYNEEIFEKENLAKISFKTNKEGEIFASDIPEVSGLEIVNK 129

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI-----------GLITIDALYSP 179
           D  I N+     +  +L + KG G++  + ++                   + +D+ +SP
Sbjct: 130 DQYIANIAKGGSLEFDLFLRKGRGFIDFEENKNVISQYGSRLESSIKNGQFLAMDSDFSP 189

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +KK + + E       L  ++L + I+TD +++ ++++  A++I+     +  N    + 
Sbjct: 190 VKKCAISFEELNSSSKLIEERLKIKIETDCTVSAKEAIEQAAKIIVAHFQIIGNINALET 249

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
               + N +           + +L LSVRS N LR      + +++  ++ ++  + N G
Sbjct: 250 IELFEENKEKKEREIKSTTPITKLGLSVRSENALRRAKYNTVEEVLGLSDEELSNIKNLG 309

Query: 300 RKSLVEIKGVLGTMGLFLGMNL---PDWPPESIEELAKKYEDK 339
           +KS+ +I          +G +     ++  ES+++L    E +
Sbjct: 310 KKSIQDIIEKRNEWKERIGYDDGQSDNFIIESLDQLNNSEEGE 352


>gi|154424837|emb|CAL18521.1| RNA polymerase alpha subunit [Streptococcus pluranimalium]
          Length = 204

 Score =  204 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 83/201 (41%), Positives = 132/201 (65%)

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 QLGMFINFEEPKKEVKEDINV 247
            L +F +  E  K        
Sbjct: 181 HLNLFTDLTEVAKATDVMKET 201


>gi|161511725|emb|CAP16873.1| DNA-directed RNA polymerase subunit alpha [Pediococcus
           acidilactici]
          Length = 199

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 90/191 (47%), Positives = 124/191 (64%), 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 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDP 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 LGMFINFEEPK 238
           L +F+N  +  
Sbjct: 189 LAIFVNLNDQA 199


>gi|119668331|emb|CAK95465.1| RNA polymerase alpha subunit [Lactobacillus iners]
          Length = 201

 Score =  203 bits (517), Expect = 3e-50,   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|161511753|emb|CAP16887.1| DNA-directed RNA polymerase subunit alpha [Pediococcus damnosus]
          Length = 211

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 89/199 (44%), Positives = 132/199 (66%), Gaps = 2/199 (1%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           + GAA+T++QIDGVLHE SSI+GV ED+T IILNIK ++LK+  D  K + I  +GP  V
Sbjct: 13  ITGAAVTSIQIDGVLHEFSSIEGVVEDVTQIILNIKKVSLKIESDDEKSLEIDVKGPATV 72

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLIT 172
           TAGDIQ  +D+E+LNPD  IC +         LT   G GYV A     R ++ PIG++ 
Sbjct: 73  TAGDIQGDSDVEILNPDQYICTVADGVTFHAILTADTGRGYVSADENKARKDDMPIGVLP 132

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           ID++Y+PI++V+Y VE+ R GQ  DYDKL++ + TDGSIT  ++ +L+++IL + L +F+
Sbjct: 133 IDSIYTPIERVNYQVENTRVGQRDDYDKLTLDVWTDGSITPSEATSLSAKILTEHLALFV 192

Query: 233 NFEEPKKEVKEDINVKSLP 251
           N  +  K+ +  +  +   
Sbjct: 193 NLTDEAKDAEIMVEKEETH 211


>gi|154424829|emb|CAL18517.1| RNA polymerase alpha subunit [Streptococcus alactolyticus]
          Length = 200

 Score =  203 bits (516), Expect = 3e-50,   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|150187139|emb|CAK30179.1| RNA polymerase alpha subunit [Streptococcus peroris ATCC 700780]
          Length = 181

 Score =  203 bits (516), Expect = 4e-50,   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|119668327|emb|CAK95463.1| RNA polymerase alpha subunit [Lactobacillus hilgardii]
          Length = 198

 Score =  202 bits (514), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 94/198 (47%), Positives = 133/198 (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 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 QLGMFINFEEPKKEVKED 244
            L MF++  +  K  +  
Sbjct: 181 HLEMFVDLTDEAKNTEIM 198


>gi|154424833|emb|CAL18519.1| RNA polymerase alpha subunit [Streptococcus parauberis]
          Length = 194

 Score =  202 bits (513), Expect = 7e-50,   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|150187166|emb|CAK30185.1| RNA polymerase alpha subunit [Streptococcus marimammalium]
          Length = 210

 Score =  202 bits (513), Expect = 8e-50,   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|150187043|emb|CAK30158.1| RNA polymerase alpha subunit [Streptococcus anginosus]
          Length = 203

 Score =  202 bits (513), Expect = 8e-50,   Method: Composition-based stats.
 Identities = 86/200 (43%), Positives = 132/200 (66%)

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 LGMFINFEEPKKEVKEDINV 247
           L +F N  E  K        
Sbjct: 181 LDLFTNLTEVAKSTDVMKET 200


>gi|119672793|emb|CAK95480.1| RNA polymerase alpha subunit [Lactobacillus salivarius]
          Length = 199

 Score =  201 bits (512), Expect = 1e-49,   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|119662285|emb|CAJ33129.1| RNA polymerase alpha subunit [Lactobacillus brevis]
          Length = 190

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 87/190 (45%), Positives = 131/190 (68%), 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 GPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDP 167
           GP  +TAGDI    D+++LNPD  I  +   A   M +T  KG GYV A     R  + 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|72534426|emb|CAH59048.1| DNA-directed RNA polymerase alpha chain [Enterococcus sp. LMG
           22681]
          Length = 213

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 89/204 (43%), Positives = 130/204 (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 EEPKKEVKEDINVKSLPFNPALLK 258
            +  K  +  +  +       L  
Sbjct: 189 TDEAKNAEIMVEKEETQKEKMLEM 212


>gi|119662283|emb|CAJ33128.1| RNA polymerase alpha subunit [Lactobacillus antri]
          Length = 203

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 90/200 (45%), Positives = 136/200 (68%), Gaps = 2/200 (1%)

Query: 54  SLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGV 113
           SL GAAIT +QIDGVLHE S++KGV ED+T IILN+K ++LK++ +  K + +  +GP  
Sbjct: 3   SLPGAAITTMQIDGVLHEFSTVKGVTEDVTQIILNLKKVSLKINSEDQKDLELDVKGPAE 62

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLI 171
           VTAGDIQ  +++ VLNPD  I  +   A + +++T  KG GY+ A     R E+  IG++
Sbjct: 63  VTAGDIQGDSEVSVLNPDLHIATVADGAELHIKMTADKGRGYLSANDNKARMEDLAIGVL 122

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            ID++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGSIT  ++V+L ++IL + L MF
Sbjct: 123 PIDSIYTPIERVNYTVENARVGQRSDYDKLTLDVWTDGSITPTEAVSLGAKILTEHLAMF 182

Query: 232 INFEEPKKEVKEDINVKSLP 251
           +N  E  +  +  +  +   
Sbjct: 183 VNLTETAQNAQVMVEKEETH 202


>gi|161511717|emb|CAP16869.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           dextrinicus]
          Length = 205

 Score =  201 bits (511), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 88/205 (42%), Positives = 135/205 (65%)

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 FEEPKKEVKEDINVKSLPFNPALLK 258
             +  K  +  +  +       L  
Sbjct: 181 LSDEAKNTEIMVEKEETQKEKKLEM 205


>gi|119662377|emb|CAJ33177.1| RNA polymerase alpha subunit [Lactobacillus paraplantarum]
          Length = 176

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 89/176 (50%), Positives = 126/176 (71%), 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 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPI 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|119662827|emb|CAJ33206.1| RNA polymerase alpha subunit [Lactobacillus gastricus]
          Length = 172

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 81/172 (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 T--ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
           +  +   IG++ ID++Y+PI +V+YTVE+ R GQ  DYDKL++ + T+GS+T
Sbjct: 121 SNMDMSAIGVLPIDSIYTPIDRVNYTVENTRVGQSNDYDKLTLDVWTNGSLT 172


>gi|150187174|emb|CAK30187.1| RNA polymerase alpha subunit [Streptococcus devriesei]
          Length = 161

 Score =  200 bits (508), Expect = 3e-49,   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|119672815|emb|CAK95519.1| RNA polymerase alpha subunit [Lactobacillus gasseri]
          Length = 165

 Score =  199 bits (507), Expect = 4e-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|119668367|emb|CAK95476.1| RNA polymerase alpha subunit [Lactobacillus rhamnosus]
          Length = 198

 Score =  199 bits (507), Expect = 4e-49,   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|154424861|emb|CAL18533.1| RNA polymerase alpha subunit [Streptococcus suis]
          Length = 203

 Score =  199 bits (507), Expect = 4e-49,   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|119662821|emb|CAJ33203.1| RNA polymerase alpha subunit [Lactobacillus parakefiri]
          Length = 203

 Score =  199 bits (506), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 95/203 (46%), Positives = 135/203 (66%), Gaps = 4/203 (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 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 LGMFINFEEPKKEVKEDINVKSL 250
           L MF++  +  K  +  +  +  
Sbjct: 181 LEMFVDLTDEAKNTEIMVEKEET 203


>gi|119662381|emb|CAJ33179.1| RNA polymerase alpha subunit [Lactobacillus sakei subsp. sakei]
          Length = 184

 Score =  199 bits (505), Expect = 7e-49,   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|296044726|gb|ADG85772.1| RpoA [Vibrio sp. WH134]
          Length = 200

 Score =  199 bits (505), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 87/194 (44%), Positives = 132/194 (68%), Gaps = 5/194 (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 ASRILQDQLGMFIN 233
           A+ IL +QL  F++
Sbjct: 181 AATILAEQLDAFVD 194


>gi|119663530|emb|CAK22336.1| RNA polymerase alpha subunit [Lactobacillus kitasatonis]
          Length = 171

 Score =  198 bits (504), Expect = 1e-48,   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|150036800|emb|CAM98036.1| DNA-directed RNA polymerase alpha chain [Leuconostoc fallax]
          Length = 196

 Score =  198 bits (503), Expect = 1e-48,   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|119662373|emb|CAJ33175.1| RNA polymerase alpha subunit [Lactobacillus panis]
          Length = 190

 Score =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 87/190 (45%), Positives = 133/190 (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 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLIT 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|119662397|emb|CAJ33188.1| RNA polymerase alpha subunit [Lactobacillus vaccinostercus]
          Length = 174

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 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 PGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPI 168
           P  VTAGDI+   D+EVLNP+  I  +   A + +++T + G GYV A     R ++ 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|154424827|emb|CAL18516.1| RNA polymerase alpha subunit [Streptococcus parasanguinis]
          Length = 194

 Score =  197 bits (501), Expect = 2e-48,   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|150036832|emb|CAO03476.1| DNA-directed RNA polymerase alpha chain [Leuconostoc carnosum]
          Length = 174

 Score =  197 bits (500), Expect = 2e-48,   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|150036824|emb|CAM98043.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gasicomitatum]
          Length = 179

 Score =  196 bits (498), Expect = 4e-48,   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|154424855|emb|CAL18530.1| RNA polymerase alpha subunit [Streptococcus sanguinis]
          Length = 198

 Score =  196 bits (498), Expect = 4e-48,   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|291533601|emb|CBL06714.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Megamonas
           hypermegale ART12/1]
          Length = 179

 Score =  195 bits (497), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 71/158 (44%), Positives = 101/158 (63%), Gaps = 2/158 (1%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E+ KP  IE + +  E+      + EPL RG+  TLGN+LRR+L+SSL GAAIT+++IDG
Sbjct: 3   EIEKP-KIEIVEI-SEDNRYGKFVCEPLERGYGTTLGNSLRRILLSSLEGAAITSIKIDG 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 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
           LN D  I  +D    ++ME+ V +G GY PA  ++ + 
Sbjct: 121 LNKDLHIATVDETGSLKMEMVVERGRGYTPADKNKNQI 158


>gi|150187144|emb|CAK30180.1| RNA polymerase alpha subunit [Streptococcus phocae]
          Length = 204

 Score =  195 bits (496), Expect = 7e-48,   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|119662333|emb|CAJ33155.1| RNA polymerase alpha subunit [Lactobacillus oris]
          Length = 200

 Score =  195 bits (496), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 87/199 (43%), Positives = 135/199 (67%), 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 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLIT 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 NFEEPKKEVKEDINVKSLP 251
           N  E  +  +  +  +   
Sbjct: 181 NLTETAQNAQVMVEKEETH 199


>gi|154424863|emb|CAL18534.1| RNA polymerase alpha subunit [Streptococcus thoraltensis]
          Length = 200

 Score =  195 bits (496), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 80/198 (40%), Positives = 129/198 (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 MFINFEEPKKEVKEDINV 247
           +F +  E  K        
Sbjct: 181 LFTDLTEVAKATDVMKET 198


>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 (496), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 83/196 (42%), Positives = 128/196 (65%), Gaps = 6/196 (3%)

Query: 139 VDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQV 195
               + M + V +G GYVPA    H   +  PIG + +DA YSP+++++Y VE+AR  Q 
Sbjct: 2   KTTSISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQR 61

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
            D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++    ++  +   F+P 
Sbjct: 62  TDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP---EVKEEKPEFDPI 118

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
           LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL + GL
Sbjct: 119 LLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGL 178

Query: 316 FLGMNLPDWPPESIEE 331
            LGM L +WPP SI +
Sbjct: 179 SLGMRLENWPPASIAD 194


>gi|154424865|emb|CAL18535.1| RNA polymerase alpha subunit [Streptococcus thoraltensis]
          Length = 203

 Score =  195 bits (496), Expect = 9e-48,   Method: Composition-based stats.
 Identities = 80/198 (40%), Positives = 129/198 (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 MFINFEEPKKEVKEDINV 247
           +F +  E  K        
Sbjct: 181 LFTDLTEVAKATDVMKET 198


>gi|23012374|ref|ZP_00052476.1| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Magnetospirillum magnetotacticum MS-1]
          Length = 146

 Score =  195 bits (495), Expect = 9e-48,   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|161511713|emb|CAP16867.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 207

 Score =  195 bits (495), Expect = 1e-47,   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|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 =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 78/298 (26%), Positives = 127/298 (42%), 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                +  
Sbjct: 194 GTFESLELIVYTNLAVDPVEVIRQAANFLSEEFRKVAEAKEAAAGEVVVEEQAIS--DEK 251

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           L   VE L LS      L   NI  + DL+   E +   +   G   L EI+  L   
Sbjct: 252 LDASVEMLNLSRAVLTHLEKANINTIRDLVDVLEHN-ESIPGIGAVRLEEIRNKLAAY 308


>gi|150036710|emb|CAM98249.1| DNA-directed RNA polymerase alpha chain [Leuconostoc carnosum]
          Length = 189

 Score =  194 bits (493), Expect = 2e-47,   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|150187007|emb|CAK30149.1| RNA polymerase alpha subunit [Streptococcus pluranimalium]
          Length = 200

 Score =  194 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 79/197 (40%), Positives = 128/197 (64%)

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 FINFEEPKKEVKEDINV 247
           F +  E  K        
Sbjct: 181 FTDLTEVAKATDVMKET 197


>gi|161511731|emb|CAP16876.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 199

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 87/199 (43%), Positives = 127/199 (63%), Gaps = 2/199 (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 INFEEPKKEVKEDINVKSL 250
           +N  +  KE +  +  +  
Sbjct: 181 VNLNDQAKETEIMVEKEET 199


>gi|151416842|emb|CAO78492.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gelidum]
          Length = 164

 Score =  192 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 75/164 (45%), 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 HGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
            GY  A  ++   +  PIG++ +D++Y+PI++V+Y VE+ R G 
Sbjct: 121 RGYSSADENKQLRDEMPIGVLAVDSIYTPIERVNYHVENTRVGS 164


>gi|154424755|emb|CAL18480.1| RNA polymerase alpha subunit [Streptococcus alactolyticus]
          Length = 196

 Score =  192 bits (489), Expect = 5e-47,   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|150036726|emb|CAM98254.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. dextranicum]
          Length = 189

 Score =  192 bits (487), Expect = 7e-47,   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|150187056|emb|CAK30161.1| RNA polymerase alpha subunit [Streptococcus cristatus ATCC 51100]
          Length = 172

 Score =  192 bits (487), Expect = 8e-47,   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|119662281|emb|CAJ33127.1| RNA polymerase alpha subunit [Lactobacillus animalis KCTC 3501]
          Length = 167

 Score =  192 bits (487), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 83/167 (49%), Positives = 115/167 (68%), 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 VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGL 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|42906|emb|CAA23646.1| unnamed protein product [Escherichia coli]
          Length = 159

 Score =  192 bits (487), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 71/158 (44%), Positives = 103/158 (65%), Gaps = 4/158 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|119668323|emb|CAK95461.1| RNA polymerase alpha subunit [Lactobacillus gasseri]
          Length = 166

 Score =  191 bits (486), Expect = 1e-46,   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|121489391|emb|CAJ44676.1| RNA polymerase alpha subunit [Carnobacterium maltaromaticum]
 gi|145586275|emb|CAM91232.1| RNA polymerase alpha-subunit [Carnobacterium maltaromaticum]
          Length = 199

 Score =  191 bits (485), Expect = 1e-46,   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|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 =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 78/322 (24%), Positives = 146/322 (45%), Gaps = 17/322 (5%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEIS 73
             + +   +  +  T    EPL RGF  T+G ALRR L+SS+      A++I  V  E  
Sbjct: 8   KYKEVKTKRVNDYETTFKIEPLERGFGSTIGTALRRTLLSSITSVVPFAIKIKDVDQEFD 67

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFK----RGPGVVTAGDIQTV--NDIEV 127
           +I  + ED+  I+LN+K I+L    +  +   I++         +T+ D++     +IE+
Sbjct: 68  TISDIVEDVQMIMLNVKNIHLVYDENIFEDNKIYRGVIETKNEKITSSDLKFPENPEIEI 127

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI-----------GLITIDAL 176
           +N D  I   +      ME+    G GY+  + ++   +               + ID+ 
Sbjct: 128 VNKDLEIATNNGQKPFVMEVYFHVGRGYISFEDNKKLIEEKVALLNSTIKRGKFLAIDSD 187

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           +SP++KV   V+      +   ++L + I T G+I  ++ ++ A++IL   L +  + + 
Sbjct: 188 FSPVEKVKVKVQEINSSSLNIEEELEIEIKTKGTIDTKNILSQAAQILIAHLQVIGDVKN 247

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
                  +   +           +  L+LSVRS N L+ +    + D++  TE D++ + 
Sbjct: 248 LDAVDVFEQKKQEKVEPSIHSVDITSLDLSVRSINALKRQGYTKLADILTLTEDDLVAVK 307

Query: 297 NFGRKSLVEIKGVLGTMGLFLG 318
           N G+KS+ EI   L    + L 
Sbjct: 308 NLGKKSVEEIIQKLKEYNVTLN 329


>gi|154424721|emb|CAL18463.1| RNA polymerase alpha subunit [Streptococcus thermophilus]
          Length = 169

 Score =  190 bits (484), Expect = 2e-46,   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|161511775|emb|CAP16898.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 193

 Score =  190 bits (484), Expect = 2e-46,   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|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 =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 62/224 (27%), Positives = 100/224 (44%), Gaps = 7/224 (3%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI--DGVLHEISSIK 76
            +  E       I  P   G A+TLG A+RR L+  L GA IT      + + HE ++I 
Sbjct: 19  KVDNERSYYGRFIISPPKIGQANTLGIAMRRALLGELEGACITPAGSPPERINHEYTAIA 78

Query: 77  GVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
           GV E + DI++N+K I LK +   + +   I   GP  VTA DI     +  ++P   I 
Sbjct: 79  GVRESVHDILMNLKEIVLKTNPFSAAQEAHIPIVGPRKVTAQDIVLPPSVGTMDPTQHIA 138

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR-EGQ 194
            +       + L V +G G+             G +  DA++ PI+  +Y++      G 
Sbjct: 139 TITRKIHSSIGLRVERGCGFRKRNMI---EYQKGSLPPDAVFMPIRHANYSIHRLGSHGG 195

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
            +  + L +   TDGS T  +++  ASR L +    F +    +
Sbjct: 196 GIMKEMLLLEARTDGSPTPREAIYEASRNLANLFSPFPHNNIHE 239


>gi|72534423|emb|CAH59047.1| DNA-directed RNA polymerase alpha chain [Enterococcus faecium]
          Length = 190

 Score =  190 bits (482), Expect = 3e-46,   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|269991336|emb|CAX12520.1| DNA-directed RNA polymerase alpha chain [Fucus vesiculosus]
          Length = 368

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 78/347 (22%), Positives = 145/347 (41%), 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  LTDIILNIKGINL--KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           L +IILN+K I +      D      +   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 ESLIEIEVKIEAGKSYILAKDQKLEG-ALDFIPIDSNFAPVLKVNWYIISLPQDGESINE 194

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE------------------------ 235
           +L + I T+G++    ++  A  ++   L      E                        
Sbjct: 195 ELHLEIYTNGTLLPHQALLQARTMIGYMLSPISTIEFSCLDTYEKEEIHDTNHIKSLTYI 254

Query: 236 -----------------------------EPKKEVKEDINVKSLPFNPALLKKVEELELS 266
                                        +   +V  D             + ++ L LS
Sbjct: 255 TDPISRDQNKTVLRSNLIKNKSKFEKINLDKINQVSIDEQKLIKNIVDLEYESLKNLGLS 314

Query: 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
            R  N L   NI ++ DLI    + ++ +   G KS+ EIK  L   
Sbjct: 315 NRIINALNKVNINFISDLIHYPSSSLINIVGLGPKSVEEIKNKLNQF 361


>gi|150186935|emb|CAK30131.1| RNA polymerase alpha subunit [Streptococcus macedonicus]
          Length = 203

 Score =  189 bits (481), Expect = 4e-46,   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|150187001|emb|CAK30147.1| RNA polymerase alpha subunit [Streptococcus ovis]
          Length = 202

 Score =  189 bits (481), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 82/202 (40%), Positives = 129/202 (63%)

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 EPKKEVKEDINVKSLPFNPALL 257
           +  K  +     ++   +  L 
Sbjct: 181 DVAKAAEVMKETETASDDRMLD 202


>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 =  189 bits (481), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 71/172 (41%), Positives = 106/172 (61%), Gaps = 5/172 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQIST---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 TVNDIEVLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI 171
              D+E++NP+HVIC+L   +A + M + V +G GYVPA       +    I
Sbjct: 118 HDGDVEIVNPEHVICHLTSDNAAIAMRIKVERGRGYVPASARIHTEEDERPI 169


>gi|119662389|emb|CAJ33184.1| RNA polymerase alpha subunit [Lactobacillus alimentarius]
          Length = 165

 Score =  189 bits (480), Expect = 5e-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|150036724|emb|CAM98253.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. mesenteroides]
          Length = 181

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 79/180 (43%), Positives = 117/180 (65%), Gaps = 2/180 (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


>gi|150186996|emb|CAK30145.1| RNA polymerase alpha subunit [Streptococcus mitis]
          Length = 160

 Score =  187 bits (476), Expect = 1e-45,   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|150036714|emb|CAM98250.1| DNA-directed RNA polymerase alpha chain [Leuconostoc citreum]
          Length = 186

 Score =  187 bits (476), Expect = 2e-45,   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|119662341|emb|CAJ33159.1| RNA polymerase alpha subunit [Lactobacillus parabuchneri]
          Length = 200

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 90/199 (45%), 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 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 NFEEPKKEVKEDINVKSLP 251
           +  +  K  +  +  +   
Sbjct: 181 DLTDEAKNTEIMVEKEETH 199


>gi|119662835|emb|CAJ33210.1| RNA polymerase alpha subunit [Lactobacillus rossiae]
          Length = 173

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 87/172 (50%), Positives = 124/172 (72%), Gaps = 2/172 (1%)

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVN 123
           QIDGVLHE S+++GV ED+T IILN+K ++LKM+ D  K + I  +GP  VTAGDIQT  
Sbjct: 1   QIDGVLHEFSTVEGVVEDVTQIILNMKKVSLKMATDEEKGMDIDVKGPATVTAGDIQTDA 60

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIK 181
           D+EV+NPD  IC +   A   M LT +KG GYV A     R ++ PIG++ ID++Y+PI+
Sbjct: 61  DVEVMNPDLYICTVADGATFHMHLTANKGRGYVSADENKARQDDMPIGVLPIDSIYTPIE 120

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           +V+Y VE+ R GQ  DYDKL++ + TDGSIT  ++++LA++IL + L MF++
Sbjct: 121 RVNYQVENTRVGQRDDYDKLTLDVWTDGSITPSEAISLAAKILTEHLAMFVD 172


>gi|270265493|emb|CBI68383.1| RNA polymerase alpha-subunit [Vibrio tapetis]
          Length = 200

 Score =  187 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 86/203 (42%), Positives = 131/203 (64%), Gaps = 7/203 (3%)

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAK---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++  + +   +++   +  P    LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE
Sbjct: 121 AFVDLRDIRVPEEKEEKPEFDP---ILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTE 177

Query: 290 ADMLRMANFGRKSLVEIKGVLGT 312
            ++L+  N G KSL EIK VL +
Sbjct: 178 VELLKTPNLGNKSLTEIKDVLAS 200


>gi|150186978|emb|CAK30140.1| RNA polymerase alpha subunit [Streptococcus sanguinis SK1]
          Length = 194

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 81/193 (41%), Positives = 122/193 (63%)

Query: 54  SLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGV 113
           SL GAA+T++ I+GVLHE  +I GV ED+  IILN+KGI +K      K + +   GP  
Sbjct: 2   SLPGAAVTSINIEGVLHEFDTISGVREDVMQIILNVKGIAVKSYVQDEKIIELDVEGPAE 61

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITI 173
           VTAGDI T +DIE++NPDH +  +   A  +  +TV+ G GYVPA  ++ ++ P+G + +
Sbjct: 62  VTAGDILTDSDIEIINPDHYLFTIGEGASFKATMTVNSGRGYVPADENKKDDAPVGTLAV 121

Query: 174 DALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           D++Y+P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N
Sbjct: 122 DSIYTPVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLNLFTN 181

Query: 234 FEEPKKEVKEDIN 246
             E          
Sbjct: 182 LTEVAIAADVMKE 194


>gi|161511711|emb|CAP16866.1| DNA-directed RNA polymerase subunit alpha [Pediococcus pentosaceus]
          Length = 209

 Score =  186 bits (472), Expect = 4e-45,   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|23013214|ref|ZP_00053138.1| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Magnetospirillum magnetotacticum MS-1]
          Length = 159

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 99/153 (64%), Positives = 124/153 (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   KVENTRVGQVTDYDKLNMTVETNGAVTPDDAVALAARILQDQLQLFINFEEPTAVVEE-E 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|229915533|gb|ACQ90877.1| alpha subunit of RNA polymerase [Pedinomonas minor]
          Length = 365

 Score =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 72/355 (20%), Positives = 139/355 (39%), Gaps = 58/355 (16%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            + QE    +     P   G A T+ N+LRR L+S  +G  + AV+IDG +HE S ++G+
Sbjct: 13  RMEQETSWYSRFEIGPFQAGQALTVANSLRRTLLSDQQGVFLAAVEIDGAIHEYSRLEGL 72

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFK-----------RGPGVVTAGDIQTVNDIEV 127
            E + DI+LN++ +++ ++ D+ K  + F            +GP  V A D++    IE 
Sbjct: 73  KESILDILLNLRQVSVLLTDDTSKTASEFANQETFVGYFDLQGPMEVKAKDLKFPKQIEC 132

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE----------------NDPIGLI 171
            NP+  I  L  +   +    +    G         +                      +
Sbjct: 133 GNPNQHIATLTRNCTFQGRFLILTNPGLTFKNQSIGDPLLFTKQVAKLEIGNRLLEKNWL 192

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDY-DKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
            ++ + + I++V+Y VE    G V +  + + + + T+G+I  + ++  A   L      
Sbjct: 193 YVNPITNAIRRVNYVVEQF--GDVWEQKEVVVLEVWTNGTIHPKQAIHSACTKLSTLFSS 250

Query: 231 FINFE----------------------------EPKKEVKEDINVKSLPFNPALLKKVEE 262
             +                              +P  E     +             +  
Sbjct: 251 LSSVNTTAFKFPASVARFKKVKTDSGADGNLTVKPMTEFSGQESPAGDKLTILFDLDIAN 310

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L+LS+++   L+   I  +G+L+Q  ++D+ R+ N     + EI+  L   GL  
Sbjct: 311 LQLSLKTYLVLKNAKIQNIGNLLQYNKSDLTRLLNLANSQIEEIETALNVFGLAF 365


>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 =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 71/159 (44%), Positives = 104/159 (65%), Gaps = 5/159 (3%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQINS---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  EVEIEGVLHEYSTKEGVQEDILEILLNLKGLSVRVAEGKDEVFITLNKSGSGPVVAGDIT 117

Query: 121 TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPA 158
              D+E+ NP+HVIC+L  D A + M + V +G GYVPA
Sbjct: 118 HDGDVEIANPEHVICHLTDDNAEIAMRIKVERGRGYVPA 156


>gi|150186985|emb|CAK30142.1| RNA polymerase alpha subunit [Streptococcus gallolyticus subsp.
           gallolyticus]
          Length = 204

 Score =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 81/203 (39%), Positives = 129/203 (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 EPKKEVKEDINVKSLPFNPALLK 258
           E  K        + +     L +
Sbjct: 181 EVAKNTDVMKETEKVNDEKVLDR 203


>gi|154424835|emb|CAL18520.1| RNA polymerase alpha subunit [Streptococcus phocae]
          Length = 153

 Score =  185 bits (470), Expect = 7e-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|150187178|emb|CAK30188.1| RNA polymerase alpha subunit [Streptococcus acidominimus]
          Length = 174

 Score =  185 bits (470), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 77/173 (44%), Positives = 120/173 (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 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           +Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L
Sbjct: 121 IYTPVKKVNYQVEPARVGSNDGFDKLTLEIMTNGTIIPEDALGLSARILMEHL 173


>gi|119668311|emb|CAK95456.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           lactis]
          Length = 191

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 72/190 (37%), Positives = 114/190 (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 KKEVKEDINV 247
            +  +  +  
Sbjct: 181 AEIGEVMVEQ 190


>gi|71056848|emb|CAH58979.1| DNA-directed RNA polymerase alpha chain [Enterococcus
           haemoperoxidus]
          Length = 199

 Score =  185 bits (469), Expect = 1e-44,   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|119672797|emb|CAK95482.1| RNA polymerase alpha subunit [Lactobacillus animalis]
          Length = 190

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 79/189 (41%), Positives = 123/189 (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 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKK 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|119662359|emb|CAJ33168.1| RNA polymerase alpha subunit [Lactobacillus sanfranciscensis]
          Length = 186

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 84/186 (45%), Positives = 128/186 (68%), 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 KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTEN 165
             GP  VTA DI T ++  +LNPD  I  +   A + M +T +KG G+V A     R ++
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|154424853|emb|CAL18529.1| RNA polymerase alpha subunit [Streptococcus salivarius]
          Length = 199

 Score =  184 bits (466), Expect = 2e-44,   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|150036780|emb|CAM98033.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. cremoris]
          Length = 153

 Score =  184 bits (466), Expect = 2e-44,   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|154424731|emb|CAL18468.1| RNA polymerase alpha subunit [Streptococcus thermophilus]
          Length = 179

 Score =  184 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 78/177 (44%), Positives = 123/177 (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 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           Y+P+KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F +
Sbjct: 121 YTPVKKVNYQVEPARVGSNDGFDKLTIEIVTNGTIIPEDALGLSARILIEHLNLFTD 177


>gi|154424727|emb|CAL18466.1| RNA polymerase alpha subunit [Streptococcus gallolyticus]
          Length = 184

 Score =  184 bits (466), Expect = 2e-44,   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|119662803|emb|CAJ33193.1| RNA polymerase alpha subunit [Lactobacillus mali]
          Length = 196

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 80/195 (41%), Positives = 129/195 (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 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDAL 176
           IQ  +D+EVLN D  IC +   A   + +T + G GYV A     R ++ 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|150187112|emb|CAK30173.1| RNA polymerase alpha subunit [Streptococcus equinus]
          Length = 191

 Score =  182 bits (463), Expect = 5e-44,   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|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 =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 69/164 (42%), Positives = 102/164 (62%), Gaps = 4/164 (2%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN  +      E ++    + EPL RG+  TLGN+LRRVL++SL GAA+T++ IDG
Sbjct: 3   EFEKPNITKI----DENKDYGKFVIEPLERGYGTTLGNSLRRVLLASLPGAAVTSINIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE  ++ GV ED+  IILNIKGI +K   +  K + +   GP  +TAGDI T +DIE+
Sbjct: 59  VLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKIIELDVEGPAEITAGDILTDSDIEI 118

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI 171
           +NPDH +  +   + ++  +TV+ G GYVPA  ++     +  +
Sbjct: 119 VNPDHYLFTIGEGSSLKATMTVNSGRGYVPADENKKIMHQLEHL 162


>gi|119668305|emb|CAK95454.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii subsp.
           bulgaricus]
          Length = 173

 Score =  182 bits (461), Expect = 8e-44,   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|71056955|emb|CAH59038.1| DNA-directed RNA polymerase alpha chain [Enterococcus avium]
          Length = 177

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 83/177 (46%), Positives = 121/177 (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 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           +KV+Y VE+ R G+  D+DKL+M I TDGSI  +++++LA++IL + L +F+N  + 
Sbjct: 121 RKVNYQVENTRVGRRDDFDKLTMEIWTDGSIIAQEALSLAAKILTEHLDIFVNLTDE 177


>gi|269929683|gb|ACZ53737.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
          Length = 166

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 78/165 (47%), Positives = 119/165 (72%), Gaps = 2/165 (1%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAAIT++QIDGVLHE S+++GV ED+T IILN+K ++LK+  ++ K + +  +GP  VTA
Sbjct: 1   GAAITSMQIDGVLHEFSTVEGVTEDVTQIILNLKKVSLKLDSENQKNLELDVKGPAEVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITID 174
            DIQ  N++ +LNPD  I  +   A + ++LT  KG GY+ A     R ++  IG++ ID
Sbjct: 61  SDIQGDNEVTILNPDLHIATVADGAELHIKLTADKGRGYLSANDNKARMDDLAIGVLPID 120

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           ++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T  ++V+L
Sbjct: 121 SIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSLTPTEAVSL 165


>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 =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 78/165 (47%), Positives = 118/165 (71%), Gaps = 2/165 (1%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAAIT++QIDGVLHE S+++GV ED+T IILN+K ++LK+  +  K + +  +GP  VTA
Sbjct: 1   GAAITSMQIDGVLHEFSTVEGVTEDVTQIILNLKKVSLKLDSEDQKNLELDVKGPAEVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITID 174
            DIQ  N++ +LNPD  I  +   A + ++LT  KG GY+ A     R ++  IG++ ID
Sbjct: 61  SDIQGDNEVTILNPDLHIATVADGAELHIKLTADKGRGYLSANDNKARMDDLAIGVLPID 120

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           ++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T  ++V+L
Sbjct: 121 SIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSLTPTEAVSL 165


>gi|154424805|emb|CAL18505.1| RNA polymerase alpha subunit [Streptococcus hyovaginalis]
          Length = 183

 Score =  180 bits (456), Expect = 3e-43,   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|269929659|gb|ACZ53725.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
 gi|269929703|gb|ACZ53747.1| RNA polymerase alpha subunit [Lactobacillus reuteri]
          Length = 166

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 79/165 (47%), Positives = 118/165 (71%), Gaps = 2/165 (1%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAAIT++QIDGVLHE S++KGV ED+T IILN+K ++LK+  +  K + +  +GP  VTA
Sbjct: 1   GAAITSMQIDGVLHEFSTVKGVTEDVTQIILNLKKVSLKLDSEDQKNLELDVKGPAEVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITID 174
            DIQ  N++ +LNPD  I  +   A + ++LT  KG GY+ A     R ++  IG++ ID
Sbjct: 61  SDIQGDNEVTILNPDLHIATVADGAELHIKLTADKGRGYLSANDNKARMDDLAIGVLPID 120

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           ++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T  ++V+L
Sbjct: 121 SIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSLTPTEAVSL 165


>gi|154424795|emb|CAL18500.1| RNA polymerase alpha subunit [Streptococcus gordonii]
          Length = 183

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 78/183 (42%), Positives = 120/183 (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 KKE 240
            K 
Sbjct: 181 AKA 183


>gi|150186992|emb|CAK30144.1| RNA polymerase alpha subunit [Streptococcus minor]
          Length = 189

 Score =  179 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 77/188 (40%), Positives = 124/188 (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 KEVKEDIN 246
           K  +    
Sbjct: 181 KSAEVMKE 188


>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 =  179 bits (453), Expect = 7e-43,   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|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 =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 74/170 (43%), Positives = 115/170 (67%), Gaps = 3/170 (1%)

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
             +  PIG + +DA +SP+++++Y+VESAR  Q  D DKL + ++T+G++  E+++  AS
Sbjct: 7   DDDERPIGRLLLDASFSPVERIAYSVESARVEQRTDLDKLIIDMETNGTLDREEAIRRAS 66

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYM 281
            IL +QL  F++  +     + +   +   F+P LL+ V++LEL+VRS NCL+ E I Y+
Sbjct: 67  TILAEQLDAFVDLRDV---TEPEEKEEKPEFDPILLRPVDDLELTVRSANCLKAEQIQYI 123

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           GDL+QRTE ++L+  N G+KSL EIK VL + GL LGM L +WPP S+ E
Sbjct: 124 GDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASLAE 173


>gi|300379501|gb|ADK08381.1| DNA-directed RNA polymerase alpha subunit [Lactobacillus reuteri]
          Length = 166

 Score =  179 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 78/165 (47%), Positives = 118/165 (71%), Gaps = 2/165 (1%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAA+T++QIDGVLHE S++KGV ED+T IILN+K ++LK+  +  K + +  +GP  VTA
Sbjct: 1   GAAVTSMQIDGVLHEFSTVKGVTEDVTQIILNLKKVSLKIDSEDQKDLELDVKGPAEVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITID 174
            DIQ  N++ +LNPD  I  +   A + ++LT  KG GY+ A     R ++  IG++ ID
Sbjct: 61  SDIQGDNEVTILNPDLHIATVADGAELHIKLTADKGRGYLSANDNKARMDDLAIGVLPID 120

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           ++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T  ++V+L
Sbjct: 121 SIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSLTPTEAVSL 165


>gi|269929829|gb|ACZ53810.1| RNA polymerase alpha subunit [Lactobacillus reuteri mlc3]
          Length = 166

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 78/165 (47%), Positives = 118/165 (71%), Gaps = 2/165 (1%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           GAAIT++QIDGVLHE S+++GV ED+T IILN+K ++LK+  +  K + +  +GP  VTA
Sbjct: 1   GAAITSMQIDGVLHEFSTVEGVTEDVTQIILNLKKVSLKLDSEDQKNLELDVKGPAEVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITID 174
            DIQ  N++ +LNPD  I  +   A + ++LT  KG GY+ A     R ++  IG++ ID
Sbjct: 61  SDIQGDNEVTILNPDLHITTVADGAELHIKLTADKGRGYLSANDNKARMDDLAIGVLPID 120

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           ++Y+PI++V+YTVE+AR GQ  DYDKL++ + TDGS+T  ++V+L
Sbjct: 121 SIYTPIERVNYTVENARVGQRNDYDKLTLDVWTDGSLTPTEAVSL 165


>gi|154424813|emb|CAL18509.1| RNA polymerase alpha subunit [Streptococcus intermedius]
          Length = 177

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 78/176 (44%), Positives = 121/176 (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 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           +P+KKV+Y VE AR G    +DKL++ I TDG+I  ED++ L++RIL + L +F N
Sbjct: 121 TPVKKVNYQVEPARVGSNDSFDKLTLEIMTDGTIIPEDALGLSARILTEHLDLFTN 176


>gi|145586271|emb|CAM91230.1| RNA polymerase alpha-subunit [Lactobacillus plantarum subsp.
           argentoratensis]
          Length = 176

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 84/176 (47%), Positives = 120/176 (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 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKV 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|254751247|ref|ZP_05203285.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis str.
           Vollum]
          Length = 136

 Score =  178 bits (451), Expect = 1e-42,   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-KIETVEL-NEDAKYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDG 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|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 =  177 bits (450), Expect = 2e-42,   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|154424743|emb|CAL18474.1| RNA polymerase alpha subunit [Streptococcus salivarius]
          Length = 201

 Score =  177 bits (448), Expect = 3e-42,   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|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 =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 85/237 (35%), Positives = 133/237 (56%), Gaps = 6/237 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +K    + + + +      L   EPL  G+  T+GN LRRVL+SSL G AI++V+I+GV
Sbjct: 3   FLKFKQSKNLRVLKLTPEEGLFKIEPLFPGWGVTIGNTLRRVLLSSLEGYAISSVKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT-----IFKRGPGVVTAGDI-QTV 122
            HE S+IKGV ED+T+IILN+K +  K +       +     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 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           V Y +++    +  +Y+ L + I TDGSI   D++  AS IL   L MFI     KK
Sbjct: 183 VKYKIDNCSINKNSNYESLLLEIKTDGSINPRDALTNASNILIQHLKMFIYETRKKK 239


>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 =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 85/237 (35%), Positives = 133/237 (56%), Gaps = 6/237 (2%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
            +K    + + + +      L   EPL  G+  T+GN LRRVL+SSL G AI++V+I+GV
Sbjct: 3   FLKFKQSKNLRVLKLTPEEGLFKIEPLFPGWGVTIGNTLRRVLLSSLEGYAISSVKIEGV 62

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT-----IFKRGPGVVTAGDI-QTV 122
            HE S+IKGV ED+T+IILN+K +  K +       +     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 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           V Y +++    +  +Y+ L + I TDGSI   D++  AS IL   L MFI     KK
Sbjct: 183 VKYKIDNCSINKNSNYESLLLEIKTDGSINPRDALTNASNILIQHLKMFIYETRKKK 239


>gi|119668329|emb|CAK95464.1| RNA polymerase alpha subunit [Lactobacillus iners]
          Length = 188

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 81/183 (44%), Positives = 122/183 (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 INV 247
           I  
Sbjct: 182 IEK 184


>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|150186909|emb|CAK30125.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
          Length = 171

 Score =  176 bits (446), Expect = 5e-42,   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|162751067|gb|ABY19888.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  175 bits (445), Expect = 6e-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|150187170|emb|CAK30186.1| RNA polymerase alpha subunit [Streptococcus iniae]
          Length = 183

 Score =  175 bits (444), Expect = 8e-42,   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|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|154424809|emb|CAL18507.1| RNA polymerase alpha subunit [Streptococcus iniae]
          Length = 174

 Score =  175 bits (444), Expect = 9e-42,   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|150187076|emb|CAK30165.1| RNA polymerase alpha subunit [Streptococcus ferus]
          Length = 191

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 78/187 (41%), Positives = 123/187 (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 VKEDINV 247
            +     
Sbjct: 181 TEVMKET 187


>gi|108792431|emb|CAJ44678.1| RNA polymerase alpha subunit [Lactobacillus acidipiscis]
          Length = 196

 Score =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 79/196 (40%), Positives = 124/196 (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 LNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSY 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|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|162751111|gb|ABY19910.1| 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 YGYVPADENKVDGWPIGTIAVDSIYT 146


>gi|150187135|emb|CAK30178.1| RNA polymerase alpha subunit [Streptococcus oralis ATCC 35037]
          Length = 177

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 76/175 (43%), Positives = 119/175 (68%)

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 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           P+ KV+Y VE AR G    +DKL++ I T+G+I  ED++ L++RIL + L +F N
Sbjct: 121 PVTKVNYQVEPARVGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLDLFTN 175


>gi|150187117|emb|CAK30174.1| RNA polymerase alpha subunit [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 187

 Score =  175 bits (443), Expect = 1e-41,   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|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 =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 76/331 (22%), Positives = 146/331 (44%), Gaps = 25/331 (7%)

Query: 9   LIKPNNIEYIVL---GQEEENRTLMI-AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           + K   I++ ++     +  +   ++  + L RGF +TL  ALRR+L+S++ G A   V+
Sbjct: 1   MEKLTKIKHRIIPAKDSQNNSYKKVLKIKGLERGFGNTLAVALRRILLSNITGIAPFCVR 60

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR-----VTIFKRGPGVVTAGDI 119
           I+GV HE ++++ V ED+  I+ N+K + L    D  K      +++       +T+  +
Sbjct: 61  IEGVEHEFTALEKVSEDIVTILSNLKKVVLNYDEDYVKDNQIIKLSLNANEDNRITSNHL 120

Query: 120 QTV--NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI--------- 168
                  +EV N D  I  L    V+++E+ +  G GYV  + ++   +           
Sbjct: 121 TVTNAPRVEVQNKDVEIATLSKPGVLKLEMFLRAGRGYVDFEDNKKFIEEKEKELKELSS 180

Query: 169 ----GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
                 I +D+++SP+  V++ V       +   ++L + ++T   +T E ++ LA +IL
Sbjct: 181 LSKGAFIAMDSVFSPVVNVAWKVTELNTASLKIEEQLELELETKLGVTPESAIKLACKIL 240

Query: 225 QDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDL 284
                   +  +   + +   + K          ++  L LS+RS N L    I  + +L
Sbjct: 241 VAHFQTIGDLTDLDSD-EIFQSEKQSLEKEEDDMEIRLLNLSMRSQNALAKSGIKTLNEL 299

Query: 285 IQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
                  +  + N G KS  EI   L   G 
Sbjct: 300 ASYPIEKLKEIKNLGEKSREEIIRKLNEYGK 330


>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 =  174 bits (442), 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|154424783|emb|CAL18494.1| RNA polymerase alpha subunit [Streptococcus equi subsp. equi]
          Length = 171

 Score =  174 bits (442), Expect = 2e-41,   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|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|108792433|emb|CAJ44679.1| RNA polymerase alpha subunit [Lactobacillus acidipiscis]
          Length = 194

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 78/193 (40%), Positives = 122/193 (63%), Gaps = 2/193 (1%)

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           VLHE SSI GV ED+T IILN+K + LK++ +  + + I   GP  VTAGDIQ  +++EV
Sbjct: 1   VLHEFSSIDGVLEDVTTIILNLKKVALKLNSEDVQTLEIDVTGPMEVTAGDIQGSSEVEV 60

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSY 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 NVKSLPFNPALLK 258
             +       L  
Sbjct: 181 EKEETHKEKMLEM 193


>gi|150186998|emb|CAK30146.1| RNA polymerase alpha subunit [Streptococcus orisratti]
          Length = 199

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 75/199 (37%), Positives = 126/199 (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 KEVKEDINVKSLPFNPALL 257
           K       V+ +     L 
Sbjct: 181 KATDVMKEVEKVNDEKVLD 199


>gi|162751135|gb|ABY19922.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 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|150187052|emb|CAK30160.1| RNA polymerase alpha subunit [Streptococcus constellatus subsp.
           pharyngis]
          Length = 150

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 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|108792429|emb|CAJ44677.1| RNA polymerase alpha subunit [Lactobacillus acidipiscis]
          Length = 187

 Score =  174 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 77/186 (41%), Positives = 121/186 (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 LNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSY 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|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 =  174 bits (440), Expect = 3e-41,   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  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV---TIFKRGPGVVTAG--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 = 77.7 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 24/79 (30%), Positives = 40/79 (50%)

Query: 235 EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
            + +  ++E     +          +EEL LSVR+ N L+  NI  + DL+Q +  D+  
Sbjct: 318 SKSEPSIEEKRENVTSNERNLSQMPIEELILSVRAYNGLKRANIHSVSDLVQYSIKDLKD 377

Query: 295 MANFGRKSLVEIKGVLGTM 313
           + NFG+KSL E+   L  +
Sbjct: 378 IKNFGKKSLDEVVASLKNL 396


>gi|162751167|gb|ABY19938.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
          Length = 146

 Score =  174 bits (440), Expect = 3e-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|154424757|emb|CAL18481.1| RNA polymerase alpha subunit [Streptococcus anginosus]
          Length = 184

 Score =  173 bits (439), Expect = 3e-41,   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|162751121|gb|ABY19915.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          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++ 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|162751006|gb|ABY19858.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  173 bits (438), Expect = 4e-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|162751051|gb|ABY19880.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  172 bits (437), Expect = 5e-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|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 =  172 bits (437), Expect = 5e-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|154424773|emb|CAL18489.1| RNA polymerase alpha subunit [Streptococcus cristatus]
          Length = 182

 Score =  172 bits (436), Expect = 6e-41,   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|154424785|emb|CAL18495.1| RNA polymerase alpha subunit [Streptococcus ferus]
          Length = 175

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 76/173 (43%), Positives = 120/173 (69%)

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 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           KKV+Y VE AR G   +YDKL++ I T+G+I  ED++ L++R+L + L +F +
Sbjct: 121 KKVNYQVEPARVGSKDNYDKLTIEIMTNGTIIPEDALGLSARVLMEHLNLFTD 173


>gi|119672811|emb|CAK95486.1| RNA polymerase alpha subunit [Lactobacillus farciminis]
          Length = 172

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 69/170 (40%), Positives = 116/170 (68%)

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 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           +Y VE+ R G+  D+DKL++ I T+GSI   ++++L+++IL + L  F+N
Sbjct: 121 NYQVENTRVGKRNDFDKLTIDIWTNGSIGPREAISLSAKILTEHLNSFVN 170


>gi|150036712|emb|CAM98020.1| DNA-directed RNA polymerase alpha chain [Leuconostoc citreum]
          Length = 181

 Score =  172 bits (435), Expect = 9e-41,   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|154424779|emb|CAL18492.1| RNA polymerase alpha subunit [Streptococcus dysgalactiae subsp.
           equisimilis]
          Length = 179

 Score =  172 bits (435), Expect = 1e-40,   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|154424765|emb|CAL18485.1| RNA polymerase alpha subunit [Streptococcus canis]
          Length = 188

 Score =  172 bits (435), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 75/187 (40%), Positives = 122/187 (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 VKEDINV 247
            +     
Sbjct: 181 TEVMKET 187


>gi|162751171|gb|ABY19940.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  171 bits (434), Expect = 1e-40,   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|162751155|gb|ABY19932.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. cremoris]
          Length = 146

 Score =  171 bits (434), Expect = 1e-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|162751022|gb|ABY19866.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  171 bits (433), Expect = 1e-40,   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|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 =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 64/260 (24%), Positives = 113/260 (43%), Gaps = 10/260 (3%)

Query: 6   WQELIK----PN-NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           W EL      P           +  +       PL +G A+TL  A+R+ L+  ++G  I
Sbjct: 3   WNELKTAESSPRWKCLESRTDSKRSHYGRFSISPLFKGQANTLAIAIRKTLLQEVKGTYI 62

Query: 61  TAVQID-GVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDI 119
           T  +    +LHE SSI G+ E + DI++N+K I L+         +I   GP  VTA DI
Sbjct: 63  TYARFQKNILHEYSSIIGIKESVHDILMNLKQIVLRSELYGIHEASICTVGPKNVTAQDI 122

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
              + I++++    I +L       + L + K   Y      + ++       ID +  P
Sbjct: 123 ILPSSIQIIDDTQHIASLTKRIPFNVTLKIEKKKRYTIENMKQPKDI---FFPIDGVSLP 179

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           ++ V++++ S +    +  + L   I T+G +T  +++  A   L D +   +  E+  K
Sbjct: 180 VQNVNFSIHSYKSSDNI-QEMLIFEIWTNGGLTPRETIYEACWSLLDLIIPLLCVEQNIK 238

Query: 240 EVKEDINVKSLPFNPALLKK 259
             ++  N  SL       KK
Sbjct: 239 NSQKKPNPLSLVTKDRNKKK 258


>gi|162751026|gb|ABY19868.1| DNA-directed RNA polymerase alpha subunit [Lactococcus lactis
           subsp. lactis]
          Length = 146

 Score =  171 bits (433), Expect = 2e-40,   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|154424723|emb|CAL18464.1| RNA polymerase alpha subunit [Streptococcus gallolyticus]
          Length = 175

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 74/173 (42%), Positives = 118/173 (68%)

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 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           KKV+Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +
Sbjct: 121 KKVNYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTD 173


>gi|119662839|emb|CAJ33212.1| RNA polymerase alpha subunit [Lactobacillus acidophilus]
          Length = 151

 Score =  170 bits (432), Expect = 2e-40,   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|154424771|emb|CAL18488.1| RNA polymerase alpha subunit [Streptococcus cristatus]
          Length = 181

 Score =  170 bits (432), Expect = 2e-40,   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|150186920|emb|CAK30128.1| RNA polymerase alpha subunit [Streptococcus pasteurianus]
          Length = 177

 Score =  170 bits (430), Expect = 3e-40,   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|119662331|emb|CAJ33154.1| RNA polymerase alpha subunit [Lactobacillus nagelii]
          Length = 175

 Score =  169 bits (429), Expect = 5e-40,   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|150036742|emb|CAM98025.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. dextranicum]
          Length = 178

 Score =  169 bits (429), Expect = 5e-40,   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|117575081|emb|CAJ84780.1| RNA polymerase alpha subunit [Lactobacillus amylophilus]
          Length = 159

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 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|154424787|emb|CAL18496.1| RNA polymerase alpha subunit [Streptococcus ferus]
          Length = 177

 Score =  169 bits (427), Expect = 8e-40,   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|289524820|emb|CBJ94466.1| alpha subunit of RNA polymerase [Vibrio sp. C15.18]
          Length = 173

 Score =  169 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 74/176 (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++  + +   +++   +  P    LL+ V+
Sbjct: 61  VIDMETNGTLEPEEAIRRAATILAEQLDAFVDLRDVRVPEEKEEKPEFDP---ILLRPVD 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|154424735|emb|CAL18470.1| RNA polymerase alpha subunit [Streptococcus pasteurianus]
          Length = 168

 Score =  169 bits (427), Expect = 9e-40,   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|150187014|emb|CAK30151.1| RNA polymerase alpha subunit [Streptococcus sinensis]
          Length = 171

 Score =  169 bits (427), Expect = 9e-40,   Method: Composition-based stats.
 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|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 =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 53/116 (45%), Positives = 78/116 (67%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLT 83
            +NR+  + EPL  GF +TLGN+LRR L+SS+ GAA+T+++IDGVLHE +++ GV ED+T
Sbjct: 15  TDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVT 74

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV 139
           +IILN+K + +    D    + + K+GPG VTAGDI     + V NP   I + + 
Sbjct: 75  EIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPGMHIAHAER 130


>gi|154424799|emb|CAL18502.1| RNA polymerase alpha subunit [Streptococcus hyointestinalis]
          Length = 167

 Score =  168 bits (426), Expect = 1e-39,   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|119662327|emb|CAJ33151.1| RNA polymerase alpha subunit [Lactobacillus lindneri]
          Length = 191

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 79/191 (41%), Positives = 118/191 (61%), 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 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKV 183
            +LNPD  I  +   A + M +T +KG GYV A     R ++ 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|154424811|emb|CAL18508.1| RNA polymerase alpha subunit [Streptococcus intermedius]
          Length = 168

 Score =  168 bits (425), Expect = 1e-39,   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|150036720|emb|CAM98251.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. cremoris]
          Length = 176

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 74/173 (42%), Positives = 113/173 (65%), Gaps = 2/173 (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 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPI 180
            D+EVLNPD  I  +     + M +T  KG GY  A  ++   +  PIG++ +D++Y+PI
Sbjct: 63  ADVEVLNPDLHIATVAAGKSLHMTVTAVKGRGYTSADENKKLRDEMPIGVLAVDSIYTPI 122

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           ++V+Y VE+ R G   DYDKL+  I T+GSI   D+++L ++IL + LG+F++
Sbjct: 123 ERVNYQVENTRIGARDDYDKLTFDIWTNGSIKPSDALSLGAKILAEHLGLFMD 175


>gi|154424807|emb|CAL18506.1| RNA polymerase alpha subunit [Streptococcus lutetiensis]
          Length = 167

 Score =  168 bits (425), Expect = 1e-39,   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|154424823|emb|CAL18514.1| RNA polymerase alpha subunit [Streptococcus mutans]
          Length = 176

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 76/176 (43%), Positives = 118/176 (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 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           Y VE AR G   ++DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K 
Sbjct: 121 YQVEPARVGSNDNFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKA 176


>gi|119663532|emb|CAK22337.1| RNA polymerase alpha subunit [Lactobacillus sharpeae]
          Length = 164

 Score =  167 bits (424), Expect = 2e-39,   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|154424791|emb|CAL18498.1| RNA polymerase alpha subunit [Streptococcus gallolyticus subsp.
           gallolyticus]
          Length = 172

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 74/170 (43%), Positives = 116/170 (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 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           +Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +
Sbjct: 121 NYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTD 170


>gi|154424789|emb|CAL18497.1| RNA polymerase alpha subunit [Streptococcus gallolyticus subsp.
           gallolyticus]
          Length = 169

 Score =  167 bits (423), Expect = 2e-39,   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|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 =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 74/170 (43%), Positives = 116/170 (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 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           +Y VE AR G    +DKL++ I T+G+I  ED++ L++R+L + L +F +
Sbjct: 121 NYQVEPARVGSNDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTD 170


>gi|119668277|emb|CAK95449.1| RNA polymerase alpha subunit [Lactobacillus acidophilus]
          Length = 150

 Score =  167 bits (423), Expect = 2e-39,   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|13560647|gb|AAK30140.1|AF346704_1 DNA-directed RNA polymerase [Fucus vesiculosus]
          Length = 226

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 58/227 (25%), Positives = 118/227 (51%), Gaps = 5/227 (2%)

Query: 9   LIKPNNIEYIVLG--QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           ++  +  + + L      E     +   L +   +T+GN LRR L+S+L G  I  V+  
Sbjct: 1   MLMSSKCKCVDLDLLNTNEFYGHFVFTALKKSQGNTIGNVLRRTLLSNLYGFRIVGVRFA 60

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINL--KMSGDSHKRVTIFKRGPGVVTAGDIQTVND 124
           G+ +E + ++GV EDL +IILN+K I +      D      +   GP V+TAG ++  N+
Sbjct: 61  GINNEFALLEGVREDLFEIILNLKEIIILNSNRIDQTCYGRLKVYGPAVITAGSLELPNN 120

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           +++LNP++ +  +  ++++ +E+ +  G  Y+ AK  + E   +  I ID+ ++P+ KV+
Sbjct: 121 VKILNPNNHLLTISDESLIEIEVKIEAGKSYILAKDQKLEG-ALDFIPIDSNFAPVLKVN 179

Query: 185 YTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           + + S  +      ++L + I T+G++    ++  A  ++   L   
Sbjct: 180 WYIISLPQDGESINEELHLEIYTNGTLLPHQALLQARTMIGYMLSPI 226


>gi|154424825|emb|CAL18515.1| RNA polymerase alpha subunit [Streptococcus parasanguinis]
          Length = 167

 Score =  167 bits (422), Expect = 3e-39,   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|58758774|gb|AAW81778.1| RNA polymerase alpha subunit [Andreaea rupestris]
          Length = 195

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 48/178 (26%), Positives = 84/178 (47%), Gaps = 3/178 (1%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  E  + +     P   G A+T+G A+RR L+  + G  IT  +   V HE S+I G+
Sbjct: 21  KVDSERLHYSRFAISPFRCGQANTVGIAMRRALLGEIEGTCITCAKFKKVTHEYSTILGI 80

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
            E + DI++N K I LK +    ++  I   GP  +TA DI     +++++    I  L 
Sbjct: 81  QESVHDILINSKEIVLKSNSYETQKAFISILGPKKITAQDIILPPSVKIIDTTQYIATLT 140

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
               + +E  + K  GY      ++ +   GL  +DA++ PI+  +Y++ S       
Sbjct: 141 KAIHLDIESEIEKDCGYRIQDSKKSTD---GLFFVDAVFMPIRNANYSIHSFENKNKT 195


>gi|119662853|emb|CAJ33219.1| RNA polymerase alpha subunit [Lactobacillus farciminis KCTC 3681]
          Length = 164

 Score =  167 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 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|150187152|emb|CAK30182.1| RNA polymerase alpha subunit [Streptococcus vestibularis ATCC
           49124]
          Length = 190

 Score =  166 bits (420), Expect = 5e-39,   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|207092984|ref|ZP_03240771.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           HPKX_438_AG0C1]
          Length = 235

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 73/233 (31%), Positives = 123/233 (52%), Gaps = 4/233 (1%)

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
             +GP  + A D+ + + IE++NP+  +  ++ DA +   L + KG GYVP+++ R E  
Sbjct: 3   SFKGPMELRARDLNSEH-IEIVNPEMPLATINEDAQLNFSLIIYKGMGYVPSENTR-ELM 60

Query: 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           P G + +D  ++PIKKV Y +E+       +Y+K+   I+TDG I    +   A +++  
Sbjct: 61  PEGYMPLDGSFTPIKKVVYEIENVLVEGDPNYEKIIFDIETDGQIDPYKAFLSAVKVMSK 120

Query: 227 QLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQ 286
           QLG+F   E P   ++   +         L  K+E + LS R  NCL    I Y+G+L+ 
Sbjct: 121 QLGVF--GERPIANMEYSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIKYVGELVL 178

Query: 287 RTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            +E ++  + N G+KS  EI   L  +G  +G  L     ES+++  +K EDK
Sbjct: 179 MSEEELKGVKNMGKKSYDEIAEKLNDLGYPVGTELSLEQRESLKKRLEKLEDK 231


>gi|154424775|emb|CAL18490.1| RNA polymerase alpha subunit [Streptococcus dysgalactiae subsp.
           dysgalactiae]
          Length = 169

 Score =  165 bits (419), Expect = 7e-39,   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|119668351|emb|CAK95512.1| RNA polymerase alpha subunit [Lactobacillus pentosus]
          Length = 160

 Score =  165 bits (419), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 75/160 (46%), Positives = 109/160 (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 DHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVE 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|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 =  165 bits (418), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 68/177 (38%), Positives = 114/177 (64%)

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 203
           +  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++
Sbjct: 2   KATMTVAKNRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTI 61

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            I T+G+I  ED++ L++R+L + L +F +  E  K  +     + +     L + +EEL
Sbjct: 62  EIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKATEVMKETEKVNDEKVLDRTIEEL 121

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           +LSVRS NCL+   I  + DL ++TE +M+++ N GRKSL E+K  L  +GL L  +
Sbjct: 122 DLSVRSYNCLKRAGINTIFDLTEKTEPEMMKVRNLGRKSLEEVKIKLADLGLGLKND 178


>gi|311990456|gb|ADQ26358.1| RNA polymerase alpha subunit [Lactobacillus delbrueckii]
          Length = 185

 Score =  164 bits (416), Expect = 2e-38,   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|119663524|emb|CAK22333.1| RNA polymerase alpha subunit [Lactobacillus graminis]
          Length = 160

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 67/159 (42%), Positives = 109/159 (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 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
             D+DKL++ + T+GSI+  ++++LA++I+ + L +F++
Sbjct: 121 RNDFDKLTLDVWTNGSISPREAISLAAKIMTEHLAIFVD 159


>gi|161511745|emb|CAP16883.1| DNA-directed RNA polymerase subunit alpha [Pediococcus inopinatus]
          Length = 141

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 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 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRT 163
           I  +GP  VTAGDIQ  +D+E+LNPD  IC +         LT   G GYV A     R 
Sbjct: 61  IDVKGPATVTAGDIQGDSDVEILNPDQYICTVADGVTFHAILTADTGRGYVSADENKARK 120

Query: 164 ENDPIGLITIDALYSPIKKVS 184
           ++ PIG++ ID++Y+PI++V+
Sbjct: 121 DDMPIGVLPIDSIYTPIERVN 141


>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 =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 83/339 (24%), Positives = 138/339 (40%), Gaps = 51/339 (15%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLH-EISSIKGVHE 80
              E     +   L +    T+GN LRRVL+S+L G  IT V++  V H E + + GV E
Sbjct: 16  SPSELYGHFVFTSLEQSEGSTIGNMLRRVLLSNLYGLKITGVRLPDVTHNEFNLLDGVRE 75

Query: 81  DLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
           D  ++ILN+K I LK            +  +GP VVTAG I+    I+VLNP++ +  + 
Sbjct: 76  DFLEVILNLKEIILKDENKYGQSYHGLLKIQGPAVVTAGSIKFSKGIKVLNPNNYLLTIS 135

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
            D+ V + L +  G  YV AK  + E      + ID+ ++P+ KV+  V++  +      
Sbjct: 136 DDSFVEIHLKLEHGKAYVLAKDQKLEGS-TYFLPIDSNFAPVLKVNSYVKTLPQHIENTD 194

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP--------------------- 237
            +L + I T+GS+    ++  A  ++   L      E P                     
Sbjct: 195 VELHLEIFTNGSLLPHQALLQAKNMIGYMLSTVNKMEFPCLSQVVSEETKSIVKIENIQK 254

Query: 238 -----------------------KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLR 274
                                    E      +     N      ++ L+LS R    L+
Sbjct: 255 KIYKKKEKTVQAKIFQSGEKKAKCIEEPTPEELLLKRVNEMDSGSLDCLKLSDRIVKALK 314

Query: 275 GENIVYMGDLIQRTEA---DMLRMANFGRKSLVEIKGVL 310
             NI +  +L+    +    ++ +   G KS+ EI+  L
Sbjct: 315 KANINFTWELMDYDSSGPPYLIDIKGLGPKSVAEIEKSL 353


>gi|254755535|ref|ZP_05207569.1| DNA-directed RNA polymerase subunit alpha [Bacillus anthracis str.
           Vollum]
          Length = 150

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 56/146 (38%), Positives = 92/146 (63%)

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 MLRMANFGRKSLVEIKGVLGTMGLFL 317
           M+++ N GRKSL E+K  L  +GL L
Sbjct: 121 MMKVRNLGRKSLEEVKHKLEELGLGL 146


>gi|150187130|emb|CAK30177.1| RNA polymerase alpha subunit [Streptococcus macacae NCTC 11558]
          Length = 178

 Score =  163 bits (412), Expect = 4e-38,   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|119662807|emb|CAJ33195.1| RNA polymerase alpha subunit [Lactobacillus pantheris]
          Length = 165

 Score =  162 bits (411), Expect = 5e-38,   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|150036752|emb|CAM98261.1| DNA-directed RNA polymerase alpha chain [Leuconostoc lactis]
          Length = 187

 Score =  162 bits (411), Expect = 6e-38,   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|119672803|emb|CAK95517.1| RNA polymerase alpha subunit [Lactobacillus alimentarius]
          Length = 149

 Score =  162 bits (409), Expect = 1e-37,   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|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 =  162 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 62/304 (20%), Positives = 122/304 (40%), Gaps = 32/304 (10%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             I+   +    +          P+    T+ NALRR L++     +IT V I+ + HE 
Sbjct: 21  TRIDENTVDHTPQLYACFQLGLFPKNQGLTIANALRRTLLTESTECSITGVLIEDIKHEY 80

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
           S++KG+ E + DI++N+K I           +   + ++GP V+ A +++  + +  +NP
Sbjct: 81  SNLKGIKETVFDILMNLKKIIFFSGQSFFKTQVSFLSEKGPIVLKAKNLKLPSFLFCINP 140

Query: 131 DHVICNLDVDAVVRMEL-------------------TVSKGHGYVPAKHHRTENDPIGLI 171
           D  I  L+ ++ + M +                     S        K + T+N     +
Sbjct: 141 DQYITTLETNSKINMTIFIDQSTPKNFSYFTHCYYSNFSNNFFPFKLKKNFTQNQQSNFL 200

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
            +D  + PI  ++Y ++     +    + L   I T+GS+     +  A + L   L  F
Sbjct: 201 FLDTQFCPISNLNYKIKK----KESQKEILFFEIWTNGSVHPNFILKKAIKNLLLNLIPF 256

Query: 232 INFEEPKKEVKEDINVKSLP-------FNPALLKKVEELELSVRSTNCLRGENIVYMGDL 284
            +    K E ++  N K              +   +    +S+ +   L+  NI+ +GDL
Sbjct: 257 HSLRNSKIEFEDYENKKIQKIVSQKKFIQKLIKLDLTNFPISLETYQSLKKLNILTIGDL 316

Query: 285 IQRT 288
            +  
Sbjct: 317 YRLK 320


>gi|161511737|emb|CAP16879.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 171

 Score =  161 bits (408), Expect = 1e-37,   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|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 =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 83/313 (26%), Positives = 148/313 (47%), Gaps = 8/313 (2%)

Query: 15  IEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISS 74
           ++ I +      R+++  E     F  +LGN ++RV+  +     I  ++I  +  E   
Sbjct: 10  LKKISIKNISFFRSIIRIETFNNSFCDSLGNFIKRVIFLTTNSYKIIYLKIYKIKSEFYD 69

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           + G+ E+   I+ N+  I +K++ D+   + I K+GP ++TA DI +  +I + NP+ +I
Sbjct: 70  LPGIIENTQTILKNLDNIIIKINNDNVANLIIKKKGPCIITAKDIFSDKNITIFNPNKII 129

Query: 135 CNLDVDAVVR--MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            N+  + V    M+   S    Y      + +     +I ++   SPI  ++Y +     
Sbjct: 130 ANVSNNIVFYCIMKCVNSLFKNYTDEF-FQFKIFKENIIFLNNFKSPIISLNYYINKKIF 188

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM---FINFEEPKKEVKEDINVKS 249
                  KL   I+T+GSI   D        ++    +   FI F++ KK   E  N  +
Sbjct: 189 --NKKLKKLFFDIETNGSIKPVDCFKNCIFYIKKYFDLIFSFIGFKKYKKINVEKKNNLN 246

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           L  N   L  +  L+LS+RS NCL+  NI  +GDLI+ ++ +++ + N G+KS  EI   
Sbjct: 247 LKINSVYLNSINNLKLSIRSLNCLKNNNIFLIGDLIKISKNNLINIPNLGKKSYNEILNS 306

Query: 310 LGTMGLFLGMNLP 322
           L   GL L   + 
Sbjct: 307 LKNFGLNLNSKIE 319


>gi|119662401|emb|CAJ33190.1| RNA polymerase alpha subunit [Lactobacillus frumenti]
          Length = 162

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 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 HVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVES 189
             I  +   A + +++T  KG GY+ A     R ++  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|154424759|emb|CAL18482.1| RNA polymerase alpha subunit [Streptococcus anginosus]
          Length = 184

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 73/179 (40%), Positives = 113/179 (63%)

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 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
            AR G    +DKL++ I TDG+I  ED++ L++RIL + L +F N  E  K        
Sbjct: 121 PARVGSNDGFDKLTLEIMTDGTIIPEDALGLSARILTEHLDLFTNLTEVAKSTDVMKET 179


>gi|154424843|emb|CAL18524.1| RNA polymerase alpha subunit [Streptococcus porcinus]
          Length = 148

 Score =  160 bits (405), Expect = 2e-37,   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|119663528|emb|CAK22335.1| RNA polymerase alpha subunit [Lactobacillus malefermentans]
          Length = 175

 Score =  160 bits (405), Expect = 2e-37,   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|119662293|emb|CAJ33133.1| RNA polymerase alpha subunit [Lactobacillus coryniformis subsp.
           torquens KCTC 3535]
          Length = 161

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 62/160 (38%), Positives = 102/160 (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 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           +GSI+  ++++LA++IL + L +F+N  +  K  +  +  
Sbjct: 121 NGSISPREAISLAAKILTEHLDIFVNLTDEAKNAEIMVEK 160


>gi|154424869|emb|CAL18537.1| RNA polymerase alpha subunit [Streptococcus uberis]
          Length = 170

 Score =  160 bits (404), Expect = 3e-37,   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|150036718|emb|CAM98022.1| DNA-directed RNA polymerase alpha chain [Fructobacillus durionis]
          Length = 178

 Score =  160 bits (404), Expect = 3e-37,   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|150036738|emb|CAM98024.1| DNA-directed RNA polymerase alpha chain [Leuconostoc mesenteroides
           subsp. dextranicum]
          Length = 171

 Score =  159 bits (403), Expect = 5e-37,   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|117575083|emb|CAJ84781.1| RNA polymerase alpha subunit [Lactobacillus amylophilus]
          Length = 171

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 65/171 (38%), Positives = 107/171 (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 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           KL+M + TDGSIT  D+++  ++IL + L +F+N     +     +  +  
Sbjct: 121 KLTMEVWTDGSITPNDALSFGAKILTEHLNVFMNTNLETEFTDVMVEKEDT 171


>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 =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 54/158 (34%), Positives = 86/158 (54%), Gaps = 2/158 (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  HEDLTDIILNIKGINLKMS--GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
            E + DI+LN+K I LK        +   I+ +GPGV+ AGDI   + I+ ++P+  I  
Sbjct: 87  RESVLDILLNLKQIVLKSKKSVKRAQTAYIYCQGPGVIRAGDIILPSSIQCVDPEQYIAT 146

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITID 174
           L  D +++M++ + +G  Y+    +    D +    +D
Sbjct: 147 LSSDGILKMKVIIRQGKNYLVQTPNSLFFDEVSEFVLD 184



 Score = 36.5 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 13/65 (20%), Positives = 23/65 (35%)

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFN 253
                D + + I T+GSI    ++  A++ L +    F N +  K    E     +    
Sbjct: 449 NQSPKDIIILEIWTNGSILPRTALKHATQNLSNLFIKFQNAKMMKNSFFETNKTYTQTIR 508

Query: 254 PALLK 258
               K
Sbjct: 509 QLYEK 513


>gi|154424725|emb|CAL18465.1| RNA polymerase alpha subunit [Streptococcus gallolyticus]
          Length = 158

 Score =  157 bits (397), Expect = 2e-36,   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|119662345|emb|CAJ33161.1| RNA polymerase alpha subunit [Lactobacillus pontis]
          Length = 160

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 67/159 (42%), Positives = 109/159 (68%), Gaps = 2/159 (1%)

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           GV ED+T IILN+K ++LK++ +  K + +  +GP  VTA DIQ   ++ +LNPD  I  
Sbjct: 1   GVTEDVTQIILNLKKVSLKINSEDQKDLELDVKGPAEVTAADIQGDGEVTILNPDLHIAT 60

Query: 137 LDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
           +   A + +++T  KG GY+ A     R E+  IG++ ID++Y+PI++V+YTVE+AR GQ
Sbjct: 61  VADGAELHIKMTADKGRGYLSANDNKARMEDLAIGVLPIDSIYTPIERVNYTVENARVGQ 120

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
             DYDKL++ + TDGS+T  ++V+L ++IL + L +F++
Sbjct: 121 RNDYDKLTLDVWTDGSLTPTEAVSLGAKILTEHLAIFVD 159


>gi|161511741|emb|CAP16881.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 179

 Score =  157 bits (397), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 69/178 (38%), Positives = 112/178 (62%), Gaps = 2/178 (1%)

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           I+GV ED+T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  I
Sbjct: 2   IEGVVEDVTQIILNLKKVSLKVESDEEKSLEINVMGPANVTAGDIVGDGDVTILNPELPI 61

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESARE 192
           C +         LT  KG GY  A  ++    + PIG++ ID++Y+PI++V+Y VE+ R 
Sbjct: 62  CTVAEGTTFHAVLTAEKGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTRV 121

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           GQ  DYDKL++ + TDGS+   ++++L+++IL + L +F+N ++  K+ +  +  K+ 
Sbjct: 122 GQRDDYDKLTLDVWTDGSLAASEAISLSAKILTEHLTIFVNLDDQAKDTEIMVEKKNS 179


>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 =  157 bits (396), Expect = 3e-36,   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|119662843|emb|CAJ33214.1| RNA polymerase alpha subunit [Lactobacillus bifermentans]
          Length = 142

 Score =  157 bits (396), Expect = 3e-36,   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|154424841|emb|CAL18523.1| RNA polymerase alpha subunit [Streptococcus pneumoniae]
          Length = 150

 Score =  156 bits (394), Expect = 5e-36,   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|119662379|emb|CAJ33178.1| RNA polymerase alpha subunit [Lactobacillus pentosus]
          Length = 158

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 73/156 (46%), Positives = 106/156 (67%), Gaps = 2/156 (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 DAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLD 197
            A   M +T + G GYV A    HR ++ PIG++ +D+LYSPI++V+Y VE+ R GQ  D
Sbjct: 62  GAHFHMRMTANTGRGYVSAEDNKHREDDMPIGVLAVDSLYSPIERVNYQVETTRVGQRDD 121

Query: 198 YDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           +DKL++ + T+GSIT  ++++L+++IL D L +F+N
Sbjct: 122 FDKLTLDVWTNGSITPSEAISLSAKILTDHLSIFVN 157


>gi|165932201|emb|CAP66258.1| RNA polymerase alpha subunit [Lactobacillus oligofermentans]
          Length = 151

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 70/151 (46%), Positives = 102/151 (67%), 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 PDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSPIKKVSYTV 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|150036840|emb|CAM98285.1| DNA-directed RNA polymerase alpha chain [Leuconostoc argentinum
           KCTC 3773]
          Length = 190

 Score =  155 bits (392), Expect = 8e-36,   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|150036826|emb|CAM98280.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gasicomitatum]
          Length = 186

 Score =  155 bits (392), Expect = 9e-36,   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|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 =  155 bits (392), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 68/251 (27%), Positives = 100/251 (39%), Gaps = 43/251 (17%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  + E           RG A T+ NALRR L+  L    +T V IDGV+HE SSI GV
Sbjct: 15  RIQSQGEMYARFHLGTFFRGQALTVANALRRTLLGELPYLIVTKVHIDGVVHEFSSIPGV 74

Query: 79  HEDLTDIILNIKGINLKMSGDSH---------KRVTIFKRGPGVVTAGDIQTVNDIEVLN 129
            E + DI+LN+K +   +S              +V +  RGP  VTA D++    +  + 
Sbjct: 75  QESVLDILLNLKRLTFTISNKKFNIFSNSWLKTKVFLKIRGPAKVTAADLKLPPHLACVW 134

Query: 130 PDHVICNLDVDAVVRMELT-------------------------------VSKGHGYVPA 158
           P+H I  L  +A +   L                                  KG G    
Sbjct: 135 PNHYIATLSSNAELACVLELAVVHPKQKISIAKNEVGSKNKIFGKVTNDVFEKGKGTESK 194

Query: 159 KHHRTENDPIGLIT-IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
           K      +    I  +D  YSPI+KV+Y +         + + L + I TDGSI  + ++
Sbjct: 195 KILTDSIEKNKKIFSLDTNYSPIRKVNYVI--YELDSKKNSEYLVLEIVTDGSIEPKQAL 252

Query: 218 ALASRILQDQL 228
             A + L    
Sbjct: 253 RFAFKQLTKLF 263


>gi|213612396|ref|ZP_03370222.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. E98-2068]
          Length = 117

 Score =  155 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 53/120 (44%), Positives = 77/120 (64%), Gaps = 3/120 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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|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 =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 66/143 (46%), Positives = 94/143 (65%), Gaps = 1/143 (0%)

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE-P 237
           PIK+V++ VE+AR G+V DYDKL++ + TDGS+T  ++V+ ++ IL++ L + I  EE  
Sbjct: 1   PIKRVNFHVENARVGRVTDYDKLNLEVWTDGSVTPLEAVSSSASILREHLAICIPSEEMK 60

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           + E            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|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 =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 65/230 (28%), Positives = 117/230 (50%), Gaps = 13/230 (5%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q+N  E I  N +E       +EN    I +PL  G   ++GN  RR+L++ +    IT
Sbjct: 1   MQENL-EFI--NLLEVP-----DENFGKYIIKPLNLGMGVSIGNLFRRILLTQMPRTNIT 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 ALPDEITLVNPSQYIATITNDSTLEFELKIESEKKSNLANNQAIFESS-DFLEVDKITSP 171

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           I+++ + V   ++ +    ++L + I TDGSIT  D++  + +++Q+   
Sbjct: 172 IRQILFDV--YKKSETETQEELVLQIWTDGSITPIDALITSVKLVQNLFT 219


>gi|150187149|emb|CAK30181.1| RNA polymerase alpha subunit [Streptococcus ratti]
          Length = 178

 Score =  153 bits (387), Expect = 3e-35,   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|119662801|emb|CAJ33192.1| RNA polymerase alpha subunit [Lactobacillus kefiri]
          Length = 153

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 77/152 (50%), Positives = 100/152 (65%), Gaps = 4/152 (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 KVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           +V+Y VES R GQ  D+DKL++ I TDGSIT 
Sbjct: 121 RVNYQVESTRVGQRDDFDKLTLDIWTDGSITP 152


>gi|161511733|emb|CAP16877.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 180

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 67/177 (37%), Positives = 110/177 (62%), Gaps = 2/177 (1%)

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           I+GV ED+T IILN+K ++LK+  D  K + I   GP  VTAGDI    D+ +LNP+  I
Sbjct: 2   IEGVVEDVTQIILNLKKVSLKVESDEEKSLEINVMGPANVTAGDIVGDGDVTILNPELPI 61

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYSPIKKVSYTVESARE 192
           C +         LT  KG GY  A  ++    + PIG++ ID++Y+PI++V+Y VE+ R 
Sbjct: 62  CTVAEGTTFHAVLTAEKGRGYTSADENKARKVDMPIGVLPIDSIYTPIERVNYQVENTRV 121

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKS 249
           GQ  DYDKL++ + TD S+   ++++L+++IL + L +F+N ++  K+ +  +  + 
Sbjct: 122 GQRDDYDKLTLDVWTDXSLAASEAISLSAKILTEHLTIFVNLDDQVKDTEIMVETRR 178


>gi|119663526|emb|CAK22334.1| RNA polymerase alpha subunit [Lactobacillus paracollinoides]
          Length = 154

 Score =  153 bits (386), Expect = 5e-35,   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|218755235|ref|ZP_03534031.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis GM 1503]
          Length = 118

 Score =  153 bits (386), Expect = 5e-35,   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|150186916|emb|CAK30127.1| RNA polymerase alpha subunit [Streptococcus oligofermentans]
          Length = 170

 Score =  152 bits (385), Expect = 6e-35,   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|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 =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 55/265 (20%), Positives = 100/265 (37%), Gaps = 47/265 (17%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +             RG A T GN++RR L+S + G  +T V+I G  HE + +  V
Sbjct: 15  RVQDQGSLYARFHIGTFFRGQALTFGNSIRRALLSEMPGFLMTDVRIQGATHEFAVLPDV 74

Query: 79  HEDLTDIILNIKGINLKMSGDSHK-------RVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            E + +I+LN+K          ++          +   GPG V A DI+    ++ ++P+
Sbjct: 75  EETVLEILLNLKKTVFVPRIPKNQKFETFQGFGFLKNNGPGKVRAADIRLPETVQCVSPE 134

Query: 132 HVICNLDVDAVVRMEL-------------------------TVSKG-------------H 153
             I  L   A + +                               G              
Sbjct: 135 VHIATLTSGAELSLRFNLQFRNFSQLEKREGTFKSKTVAQAKTEDGNVQDTTNELPTLEK 194

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
             +  +  + + +    + +D +  P++KV+Y ++S       +Y  + + I TDGS+  
Sbjct: 195 NSLFFQQLQNKRNSKDQLFLDTVPMPVQKVNYVIKSLNAKNGSEY--IILEIWTDGSLYP 252

Query: 214 EDSVALASRILQDQLGMFINFEEPK 238
           ++SV  A R L D    F N  +  
Sbjct: 253 QESVEFALRNLTDLFFQFANISKKS 277


>gi|154424819|emb|CAL18512.1| RNA polymerase alpha subunit [Streptococcus mitis]
          Length = 171

 Score =  152 bits (384), Expect = 8e-35,   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|117575077|emb|CAJ84778.1| RNA polymerase alpha subunit [Lactobacillus amylophilus]
          Length = 138

 Score =  152 bits (384), Expect = 8e-35,   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|154424767|emb|CAL18486.1| RNA polymerase alpha subunit [Streptococcus constellatus subsp.
           constellatus]
          Length = 171

 Score =  152 bits (384), Expect = 8e-35,   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|154424737|emb|CAL18471.1| RNA polymerase alpha subunit [Streptococcus oligofermentans]
          Length = 168

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 68/168 (40%), Positives = 106/168 (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 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
            G    +DKL++ I T+G+I  ED++ L++RIL + L +F +  E   
Sbjct: 121 VGSNDGFDKLTLEILTNGTIIPEDALGLSARILTEHLNLFTDLTEVAI 168


>gi|154424801|emb|CAL18503.1| RNA polymerase alpha subunit [Streptococcus hyointestinalis]
          Length = 162

 Score =  151 bits (381), Expect = 2e-34,   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|119663522|emb|CAK22332.1| RNA polymerase alpha subunit [Lactobacillus acetotolerans]
          Length = 140

 Score =  151 bits (381), Expect = 2e-34,   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|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 =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 48/155 (30%), Positives = 73/155 (47%), Gaps = 2/155 (1%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +       +     P   G   T+GNA RR L+S L G  IT ++IDGV HE S++ GV
Sbjct: 12  RIEHNRSFYSRFQLGPFDLGQGLTVGNAFRRTLLSELSGVGITLIEIDGVCHEYSTLPGV 71

Query: 79  HEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
            E + DI+LN+K + L         +   +   GPGVVTA D++    +  ++PD  I  
Sbjct: 72  RESVLDILLNLKQLVLTSDTTFTVPQVGYLNFTGPGVVTAKDLKLPVSVYCVDPDQPIAT 131

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI 171
           L  DA +  +  V +G  Y+        ++    I
Sbjct: 132 LSADATLNFKFLVCQGKNYIIQTPVDKFHEYQKKI 166



 Score = 70.4 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 35/188 (18%), Positives = 62/188 (32%), Gaps = 61/188 (32%)

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           + +D L+ PIKKV+Y ++        D + + + I T+GSI    +V  A++ L      
Sbjct: 318 LPVDTLFMPIKKVNYMIDIDPAE--PDRESVVLEIWTNGSIHPRQAVHEAAKQLIHLFSP 375

Query: 231 FINFEEPKKEVKEDI---------------------------------------NVKSLP 251
           F+        ++                                          N +   
Sbjct: 376 FLQTHLVPTTLQSTPYSKAASKTQEFSLNETSTEKVKDELGKVAFGSENNTAALNQQKNL 435

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLI-----QRTEAD-----------MLRM 295
                   +  L  S+R+   L+ ENI  + +L+     Q+TEA            +L +
Sbjct: 436 VTAIQTLDIANLNFSLRTFTFLKKENINTVSELVEFWTRQKTEAKDSIQSNVQSSVLLEI 495

Query: 296 ----ANFG 299
                NFG
Sbjct: 496 SNNLKNFG 503


>gi|154424777|emb|CAL18491.1| RNA polymerase alpha subunit [Streptococcus dysgalactiae subsp.
           dysgalactiae]
          Length = 185

 Score =  150 bits (379), Expect = 3e-34,   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|154424815|emb|CAL18510.1| RNA polymerase alpha subunit [Streptococcus minor]
          Length = 174

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 68/172 (39%), Positives = 110/172 (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 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN 246
              +DKL++ I T+G+   ED++ L++RIL + LG+F +  +  K  +    
Sbjct: 121 NDGFDKLTLEIMTNGTTNPEDALGLSARILMEHLGLFTDLTDVAKSAEVMKE 172


>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 =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 62/330 (18%), Positives = 122/330 (36%), Gaps = 60/330 (18%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           IV              P   G   T+ NALRR L+S L   A+T++QI  V+H+  +I+G
Sbjct: 100 IVKKNLRNIYGQFYIGPFFIGQGLTIANALRRTLLSELSSLAVTSIQIQDVVHQYQTIQG 159

Query: 78  VHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVIC 135
           + E + D++LN+K I LK        +   +  +GP ++ A D+     I+ ++P+  I 
Sbjct: 160 LQESVFDLLLNMKDIVLKSKTTIPVPQIGYLQVQGPCIIKAKDLLLPPFIQCVDPEQYIA 219

Query: 136 NLDVDAVVRMELTVSKGH--------GYVPAKHHRTE----------------------- 164
            L  D ++ M+  + +G         GY        +                       
Sbjct: 220 TLSEDGILNMKFVIRQGKHSLTHVTPGYDSFTQKYDQHSYNSTCDTNVHSNKNRNSLSLL 279

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQ-VLDYDKLSMT------------------- 204
           N     + IDA ++P+ KV+Y +E     Q   + D + +                    
Sbjct: 280 NTYSKHLIIDASFNPVIKVNYIIEVLDFDQLFFEKDSVKLESNDSNNFYCNEEKTLIKKE 339

Query: 205 -----IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK 259
                I T+GSI+   ++ ++ + L          +    ++ +        F     + 
Sbjct: 340 IIILEIWTNGSISPITALKVSIQKLISVFLKIQKSKILNIQLIDSEIFYRDIFEKLTNQF 399

Query: 260 VEELELSVRSTNCLRGENIVYMGD--LIQR 287
                   ++ +  +   +  + +  L+Q+
Sbjct: 400 YILKFKQCQTLSDFKDSKVRPISEKFLVQK 429


>gi|161511735|emb|CAP16878.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 161

 Score =  148 bits (374), Expect = 1e-33,   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|154424763|emb|CAL18484.1| RNA polymerase alpha subunit [Streptococcus canis]
          Length = 173

 Score =  148 bits (374), Expect = 1e-33,   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|167010108|ref|ZP_02275039.1| DNA-directed RNA polymerase subunit alpha [Francisella tularensis
           subsp. holarctica FSC200]
          Length = 224

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 63/223 (28%), Positives = 119/223 (53%), Gaps = 9/223 (4%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DG 67
           L+ P NI    + +  +N T    E L RG  +TLG AL++ ++ S+ GA +T+++I DG
Sbjct: 6   LLHPTNI---KIDEYAKNATKFSFEALERGVGYTLGFALKQTMLYSIAGACVTSIKINDG 62

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK-RVTIFKRGPGVVTAGDIQTVNDIE 126
            +  +  +    E + DIILN+K +++ ++ D     +T    G       +   +++  
Sbjct: 63  KVTSLEDVIPCDETVADIILNVKSLSVTLAEDVETGTITFELSGSEEEIFSEEAKLSEGL 122

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT 186
            +  +  IC+ +    +++E  V KG G+ PA+    +N   G   +DA +SP+    + 
Sbjct: 123 AITEEVFICSYNGGKKLKIEAKVEKGVGFRPAQ----DNFKDGEFLLDATFSPVVFCDFE 178

Query: 187 VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           ++ AR G+  D DKL + I T+G++  E+++ LA+  +Q+QL 
Sbjct: 179 IKDARVGRRTDLDKLELNIKTNGNVNCEEALRLAATKIQNQLR 221


>gi|48374282|gb|AAT41971.1| putative RNA polymerase alpha subunit [Fremyella diplosiphon Fd33]
          Length = 155

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 48/155 (30%), Positives = 86/155 (55%), 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
                        ++       +P +P     +EEL+LSVR+ NCL+   +  + DL+  
Sbjct: 61  FNPL-----KDISLEPTDTGSDIPDDPTAQIPIEELQLSVRAYNCLKRAQVNSVADLLDY 115

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322
           T+ D+L + NFG+KS  E+   L      LG+ LP
Sbjct: 116 TQEDLLEIKNFGQKSAEEVVEALQRR---LGITLP 147


>gi|150187010|emb|CAK30150.1| RNA polymerase alpha subunit [Streptococcus pyogenes]
          Length = 184

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 69/183 (37%), Positives = 113/183 (61%)

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           I GV ED+  IILN+KG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +
Sbjct: 2   IPGVREDVMQIILNVKGLAVKSYVEDEKIIELEVEGPAEVTAGDILTDSDIELVNPDHYL 61

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
             +     +R  +TV+K  GYVPA+ ++ ++ P+G + +D++Y+P+KKV+Y VE AR G 
Sbjct: 62  FTIAEGHSLRATMTVAKKRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPARVGS 121

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
              +DKL++ I T+G+I  ED++ L++R+L + L +F +  E  K  +     + +    
Sbjct: 122 NDGFDKLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKATEVMKETEKVNDEK 181

Query: 255 ALL 257
            L 
Sbjct: 182 VLD 184


>gi|119662809|emb|CAJ33196.1| RNA polymerase alpha subunit [Lactobacillus perolens]
          Length = 138

 Score =  147 bits (372), Expect = 2e-33,   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|161511739|emb|CAP16880.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 166

 Score =  147 bits (372), Expect = 2e-33,   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|154424741|emb|CAL18473.1| RNA polymerase alpha subunit [Streptococcus thermophilus]
          Length = 155

 Score =  147 bits (370), Expect = 3e-33,   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|119662399|emb|CAJ33189.1| RNA polymerase alpha subunit [Lactobacillus equi]
          Length = 170

 Score =  147 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 62/170 (36%), Positives = 103/170 (60%), Gaps = 2/170 (1%)

Query: 86  ILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRM 145
           ILN+K + LKM  +  + + I   GP  VTAGDI+  +D+EVLN D  I  +     + +
Sbjct: 1   ILNLKKVALKMDSEESQTLEIDVVGPLEVTAGDIKGPSDVEVLNDDLYIATVAEGHSLHV 60

Query: 146 ELTVSKGHGYVPAK--HHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSM 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|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 =  145 bits (367), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 45/193 (23%), Positives = 82/193 (42%), Gaps = 3/193 (1%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M  +N  E I   +     +             P   G   T+ N LRR L+S L G AI
Sbjct: 1   MDHENLNESIS-ISSIISRIETNRSFYGRFEIGPFAHGQGITVANMLRRTLLSELSGLAI 59

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGD 118
           TAV+I    HE  ++ G+ E + DIILN+K +  + + D    +   +  +GP ++ A  
Sbjct: 60  TAVEIKEASHEYMTLPGISESVQDIILNLKQLIFRSNFDLKQPEFGFLSIQGPAIIKASH 119

Query: 119 IQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178
            +  + I+ ++P+  I  L  +  + +++ + +G  Y             G ++     +
Sbjct: 120 FRLPSFIKCVDPNQYIATLAFNGQLNLKVQICQGKNYKFQTPLDLNWPGSGFLSSIHNSN 179

Query: 179 PIKKVSYTVESAR 191
             +K  Y   + R
Sbjct: 180 SKQKSFYIKNNTR 192



 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 16/68 (23%), Positives = 38/68 (55%), Gaps = 3/68 (4%)

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDY-DKLSMTIDTDGSITGEDSVALASRI 223
                ++ +DA+++P+ KV+Y +    + +V  + +++ + I T+GSIT + ++  A+  
Sbjct: 466 IKTDNILPVDAIFTPVTKVNYLI--CLDEKVKPFKEQILLEIWTNGSITPKTAIYKAADC 523

Query: 224 LQDQLGMF 231
           + D L   
Sbjct: 524 ILDLLLPL 531


>gi|2951864|gb|AAC05400.1| RNA polymerase alpha subunit [Buchnera aphidicola]
 gi|448401|prf||1917188B RNA polymerase:SUBUNIT=alpha
          Length = 113

 Score =  145 bits (366), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 51/116 (43%), Positives = 74/116 (63%), Gaps = 3/116 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +    +KP  +E   +       T +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQNSIIGFLKPRLVEIEQI---TATHTKVTLEPLERGFGHTLGNALRRILLSSMPGYAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
            V+IDGVLHE S+ +GV ED+ +I+LN+K + +K+ G     +++ K G G VTA 
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKELAVKVHGKDEVFMSLNKSGIGSVTAS 113


>gi|156619301|gb|ABU88330.1| RNA polymerase alpha subunit [Chlamydomonas moewusii]
          Length = 633

 Score =  145 bits (366), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 45/147 (30%), Positives = 73/147 (49%), Gaps = 2/147 (1%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +             P     + T+ N LRR L+S + G AI +V+I+G  HE SS+ GV
Sbjct: 12  RIENNRSFYGCFELGPFEPSQSLTIANTLRRTLLSEIYGLAIVSVEIEGASHEYSSLPGV 71

Query: 79  HEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           HE + DI+LN+K I LK S  +   +   +  RGPGVVT   ++    I+ ++PD  I  
Sbjct: 72  HESVLDILLNLKEIVLKKSIKNFTPQIGYLRARGPGVVTGSHLRLPPFIQCVDPDQYIAT 131

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRT 163
           L  +  + ++  V  G+ ++ +     
Sbjct: 132 LSHNGFLNIKFVVQYGNKWLASGRMPD 158


>gi|150187084|emb|CAK30167.1| RNA polymerase alpha subunit [Streptococcus hyovaginalis]
          Length = 165

 Score =  144 bits (364), Expect = 2e-32,   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|150186957|emb|CAK30136.1| RNA polymerase alpha subunit [Streptococcus hyointestinalis]
          Length = 171

 Score =  144 bits (363), Expect = 2e-32,   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|222446775|gb|ACM51431.1| RNA polymerase alpha subunit [Caulerpa filiformis]
          Length = 301

 Score =  143 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 52/235 (22%), Positives = 89/235 (37%), Gaps = 28/235 (11%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            + +  +        P       T  N+LRR L+          +QI GV HE SS+ GV
Sbjct: 9   KIEKTGQFYGCFKIGPFQTHSGMTFANSLRRTLLEDNSRYIFDTIQISGVEHEYSSLIGV 68

Query: 79  HEDLTDIILNIK--------GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP 130
            E + DII N++         ++L       +   +   GPG++ A  I    D   + P
Sbjct: 69  RESVIDIIFNLQKLIFEVSDKVHLVGKDPKPQIAFLNFTGPGILRAQHIHLPKDFHFVYP 128

Query: 131 DHVICNLDVDAVVRME--------------LTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
           D  I  L+VD  +  +              L    G G         EN     + +D+ 
Sbjct: 129 DQYIATLEVDGKLNFKLFFSPKIFQKKYKSLHSKSGSGRQMPPSVLLEN----YLFLDSD 184

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           +  I++V+YT++S    Q    + +   I T+GSI  + ++      +      +
Sbjct: 185 FCSIERVNYTIQSGN--QNPKEEFILFEIWTNGSIHPQKAIYQGINEILLDFFPY 237


>gi|150187031|emb|CAK30155.1| RNA polymerase alpha subunit [Streptococcus urinalis 2285-97]
          Length = 169

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 65/168 (38%), Positives = 107/168 (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 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           KL++ I T+G+I  ED++ L++R+L + L +F +  E  K  +     
Sbjct: 121 KLTIEIMTNGTIIPEDALGLSARVLIEHLNLFTDLTEVAKATEVMKET 168


>gi|154424733|emb|CAL18469.1| RNA polymerase alpha subunit [Streptococcus pasteurianus]
          Length = 173

 Score =  143 bits (360), Expect = 4e-32,   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|161511743|emb|CAP16882.1| DNA-directed RNA polymerase subunit alpha [Pediococcus claussenii]
          Length = 158

 Score =  142 bits (359), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 61/152 (40%), Positives = 96/152 (63%), Gaps = 2/152 (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 LSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           L++ + TDGS+   ++++L+++IL + L +F+
Sbjct: 121 LTLDVWTDGSLAASEAISLSAKILTEHLXIFV 152


>gi|67968322|dbj|BAE00222.1| RNA polymerase alpha chain like [Selaginella uncinata]
          Length = 245

 Score =  142 bits (359), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 51/215 (23%), Positives = 77/215 (35%), Gaps = 5/215 (2%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSIKG 77
            +  E    +  I  P   G A TLG A+RR       GA  T     + + HE  +I G
Sbjct: 19  KVDNERPCHSRSIIPPPKIGQASTLGIAMRRAPPGESEGACTTPAGSPERINHEYPAIAG 78

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
           V E + +  +N+K I L     + +   I   GPG V A D    + I ++ P      +
Sbjct: 79  VRESVHETSMNLKEIALTAHPSAAQEAHIPIVGPGKVAARDTVPPSSIGIIYPAQHAATV 138

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR-EGQVL 196
                      V  G GY             G    DA+  PI+  +Y++         +
Sbjct: 139 TRKIRSSTGSRVEGGCGYRRRNMV---EYQKGSPPPDAVSMPIRNANYSIHRLESHSGGI 195

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
             +       TDGS T  ++   ASR   +     
Sbjct: 196 MKEMPPPEARTDGSPTPGEATYEASRDSANLFSPV 230


>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 =  142 bits (359), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 46/151 (30%), Positives = 69/151 (45%), Gaps = 2/151 (1%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
                  +         P   G + T+ NALRR L+S + G  +T+V+I+GV HE S+I 
Sbjct: 28  KEEKENNQTFYGRFYIGPFEIGQSLTMANALRRSLLSEVPGLGLTSVEIEGVAHEYSTIP 87

Query: 77  GVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           GV E + DI+LNIK I  K +      +       GP  + A D+     I+ +NPD  I
Sbjct: 88  GVQETVFDILLNIKNIVFKSTTYLKKAEIGYCRASGPKTLRAKDLLLPAHIQCVNPDQYI 147

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
             L  D  + M+L + +G  Y+         
Sbjct: 148 ATLKSDGTLNMKLKIRQGTHYLVNTPFEQSE 178



 Score = 50.0 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 28/60 (46%)

Query: 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
             + +D ++ P+ K +Y +E          + + + I T+GSI+   ++  A + L   L
Sbjct: 247 KPLLLDPVFMPVTKANYVLELDERVHNSPKELIVLEIWTNGSISPHGALQTAIKKLVRLL 306


>gi|154424849|emb|CAL18527.1| RNA polymerase alpha subunit [Streptococcus ratti]
          Length = 170

 Score =  142 bits (359), Expect = 6e-32,   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|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 =  142 bits (357), Expect = 1e-31,   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-KIETVEL-NEDAKYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVTAIQIDG 60

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           VLHE S+++GV ED+T IILN+K + LK+  +  K + I  +G G+V
Sbjct: 61  VLHEFSTVEGVVEDVTTIILNLKKLALKIYSEEEKTLEIDVQGEGIV 107


>gi|56807381|ref|ZP_00365362.1| COG0202: DNA-directed RNA polymerase, alpha subunit/40 kD subunit
           [Streptococcus pyogenes M49 591]
          Length = 145

 Score =  142 bits (357), Expect = 1e-31,   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|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 =  142 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 49/228 (21%), Positives = 97/228 (42%), Gaps = 13/228 (5%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +  +             +G A T  NALRR L+S + G  +T + ++G  HE + + GV
Sbjct: 15  RIQDQGSMYARFHLGTFIQGQALTFANALRRTLLSEIPGIIMTDILVEGASHEFAILPGV 74

Query: 79  HEDLTDIILNIKGINLKMS-------GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPD 131
            E + DIILN+K +    S        +      +   GP  ++  D++    ++ + P 
Sbjct: 75  EETVLDIILNLKKLVFAPSTSKLINLENFQATGFLKSCGPRKLSGADVKLPLTLKCVEPK 134

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE---NDPIGLITIDALYSPIKKVSYTVE 188
             I  +   A   +   +        +  ++      +    + +D +  PI+KV+Y ++
Sbjct: 135 AHIATITNGAEFALRFNLEL-RNPQQSVTNKIYYPVENKTRKLVLDNVPMPIQKVNYVIK 193

Query: 189 SAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           +    Q L+Y  + + + TDGS+  ++SV  A + L +    F    +
Sbjct: 194 ALNGKQGLEY--IVLEVWTDGSVLPQESVQFALKNLTNFFFQFAEMSK 239


>gi|154424729|emb|CAL18467.1| RNA polymerase alpha subunit [Streptococcus gallolyticus]
          Length = 167

 Score =  141 bits (356), Expect = 1e-31,   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|119029438|gb|ABL59935.1| DNA-directed RNA polymerase alpha subunit [uncultured bacterium]
          Length = 219

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 72/193 (37%), Positives = 115/193 (59%), Gaps = 4/193 (2%)

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQ 120
            ++IDGVLH+ S++ G+ ED+ +++LN+K +   ++ D +   +   K  PG V A D  
Sbjct: 18  RIKIDGVLHDYSALDGLQEDVVEVLLNLKELAFNIASDENTVAINFEKSSPGPVLASDFA 77

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITIDALYS 178
             ++IEV NP+ VICN+     ++MELT  +G GY  A +   +     IG++ +DA YS
Sbjct: 78  DQSNIEVFNPNLVICNVTSGV-LKMELTAQRGRGYELAVNRDVDRNEKSIGVLQLDASYS 136

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           P+KKVSY VE AR G   D DKL + ++T+G+I+ ED++ ++S ILQ QL  F+N +   
Sbjct: 137 PVKKVSYNVEVARFGGRADLDKLVIDLETNGAISPEDAIRISSTILQQQLLAFVNLDSKL 196

Query: 239 KEVKEDINVKSLP 251
            +       +  P
Sbjct: 197 LKEPTKKEEEFDP 209


>gi|21039418|gb|AAM33638.1| RpoA [Pseudomonas putida]
          Length = 127

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 58/130 (44%), Positives = 85/130 (65%), Gaps = 3/130 (2%)

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
             Q  D DKL + ++T+G++  E+++  A+ ILQ QL  F++ +   + V  +       
Sbjct: 1   VEQRTDLDKLVIDLETNGTLDPEEAIRRAATILQQQLAAFVDLKGDSEPVVVEQE---DE 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|150036750|emb|CAM98028.1| DNA-directed RNA polymerase alpha chain [Leuconostoc gelidum KCTC
           3527]
          Length = 153

 Score =  140 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 62/152 (40%), Positives = 95/152 (62%), Gaps = 2/152 (1%)

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           + GV ED+T IILN+K + L +  D  + + +  +GP  VTA D+Q   D+EVLNPD  I
Sbjct: 2   VDGVVEDVTQIILNLKKVVLAIDSDEERSLEVDIQGPADVTAADLQAGADVEVLNPDLHI 61

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALYSPIKKVSYTVESARE 192
             +     + M +T  KG GY  A  ++   +  PIG++ +D++Y+PI++V+Y VE+ R 
Sbjct: 62  ATVAAGKSLHMTITAFKGRGYSSADENKQLRDEMPIGVLAVDSIYTPIERVNYHVENTRV 121

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
           G   DYDKL+  I T+GSI   D+++L S+IL
Sbjct: 122 GSRDDYDKLTFDIWTNGSIKPSDALSLGSKIL 153


>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 =  140 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 59/319 (18%), Positives = 119/319 (37%), Gaps = 46/319 (14%)

Query: 8   ELIKPNNI----EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAV 63
           +L  P  +    + I++             P P     TLG+ L+ + +S   G  + AV
Sbjct: 234 DLDLPTKVKTASDLIMIPDTGRLYQKFYMGPYPITMGWTLGSLLKVLALSRSPGHGVVAV 293

Query: 64  QIDGVLHEISSIKGVHEDLTDIILNIKGINL-KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
           ++  + +E ++I GV +DL +I LN+  + L  +      RV    +GP  V AG I+  
Sbjct: 294 KVHNM-NEDTTIDGVTDDLMNIALNLNEVALETLEPGGEARVRTVIKGPAQVCAGSIEWP 352

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA------------------KHHRTE 164
           + +++  PD  I N++    + +E+ +  G G   A                  +    E
Sbjct: 353 SFVKIATPDAYITNVEEGGTLDIEIKIEWGRGLWLADYKGLYRHEDAADAVCMRRRRIKE 412

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLD---------YDKLSMTIDTDGSITG-- 213
            D      I   +   + V   V     G+  D          ++L + + TD S T   
Sbjct: 413 VDEEDFHPITTFFGGCRMVRLAVHKL-IGERWDLITSSCPDPREQLVVEVWTDRSTTPKA 471

Query: 214 --EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTN 271
             E  ++ +   +++     I   +   E ++  +          L++ +++     + N
Sbjct: 472 ALEFGLSESIAWIRELKRQLIQDADFDGEDEQLRDTWEKIDKYKSLQQRQQMMGGPPTYN 531

Query: 272 C--------LRGENIVYMG 282
                    L+  +  Y+G
Sbjct: 532 LHDTNAIPGLKESDCQYVG 550


>gi|150036734|emb|CAM98258.1| DNA-directed RNA polymerase alpha chain [Leuconostoc citreum]
          Length = 145

 Score =  139 bits (351), Expect = 5e-31,   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|161511777|emb|CAP16899.1| DNA-directed RNA polymerase subunit alpha [Pediococcus stilesii]
          Length = 141

 Score =  139 bits (351), Expect = 5e-31,   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|21039420|gb|AAM33639.1| RpoA [Escherichia coli]
          Length = 127

 Score =  139 bits (350), Expect = 7e-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|150186949|emb|CAK30134.1| RNA polymerase alpha subunit [Streptococcus dysgalactiae subsp.
           dysgalactiae]
          Length = 161

 Score =  138 bits (349), Expect = 9e-31,   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|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 =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 55/288 (19%), Positives = 99/288 (34%), Gaps = 34/288 (11%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           + I   Q           PL     HT G  L+ V  + L G AI A++I  + +E + I
Sbjct: 426 DIIKYPQNGRLYQKFYIGPLNITDGHTFGTLLKYVCQTQLYGYAIVAIKIHNM-NEDTRI 484

Query: 76  KGVHEDLTDIILNIKGINLKMSG-DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
             V EDL +I LN+  + +     +    + +  +GP ++ AG I   + ++V+N +  I
Sbjct: 485 DNVQEDLLEIALNLSDVCIYSKEVNIETNIRLIFKGPLMLVAGMIPLPSHLQVVNKEQYI 544

Query: 135 CNLDVDAVVRMELTVSKGHGYV------------------PAKHHRTENDPIGLITIDAL 176
           C L  D  + + + +  G G+                     K    E      + I A 
Sbjct: 545 CTLKEDGHLDISIKIEYGKGHWLTYEKGLYKRELGSDNECMKKRQVKEVVEKNYMPISAS 604

Query: 177 YSPIKKVSYTVESA--------REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           +   + V   V           R         L M I TD  +  ++ +    + ++  L
Sbjct: 605 FGTCRMVRMAVHKIATKYWCEDRCEFTDPKQMLVMEIWTDCRMLPKNVLLYGIKNIKKIL 664

Query: 229 GMFINF------EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
             F              E +E   +         L+  +++E      
Sbjct: 665 RKFREMIISDSDFPSDAEDEEMKKLWPAIDRYKFLQTKQKMEGGPPIH 712


>gi|154424817|emb|CAL18511.1| RNA polymerase alpha subunit [Streptococcus minor]
          Length = 167

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 61/167 (36%), Positives = 103/167 (61%)

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 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
           +G+   ED++ L++RIL + LG+F +  +  K  +     +    + 
Sbjct: 121 NGTTNPEDALGLSARILMEHLGLFTDLTDVAKSAEVMKEAEPASDDR 167


>gi|313622252|gb|EFR92762.1| DNA-directed RNA polymerase subunit alpha [Listeria innocua FSL
           J1-023]
          Length = 129

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 53/124 (42%), Positives = 82/124 (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 SRIL 224
           +   
Sbjct: 121 ANSS 124


>gi|154424769|emb|CAL18487.1| RNA polymerase alpha subunit [Streptococcus criceti]
          Length = 168

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 59/167 (35%), Positives = 107/167 (64%)

Query: 88  NIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMEL 147
           N+KG+ +K   +  K + +  +GP  VTAGD+ T +DIE++NPDH +  +     ++  +
Sbjct: 2   NVKGLAVKSYVEDEKTIELDVQGPAEVTAGDVLTDSDIEIINPDHYLFTIAEGHSLKATM 61

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
           TV+K  GYVPA+ +++++ P+G + +D++Y+P+KKV+Y VE AR G    +DKL++ I T
Sbjct: 62  TVAKNRGYVPAEGNKSDSAPVGTLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTIEIMT 121

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNP 254
           +G+I  ED++ L++R+L + L +F +  E  K  +     +S+  + 
Sbjct: 122 NGTIIPEDALGLSARVLIEHLNLFTDLTEIAKTTEVMKETESVSNDQ 168


>gi|161511751|emb|CAP16886.1| DNA-directed RNA polymerase subunit alpha [Lactobacillus
           dextrinicus]
          Length = 138

 Score =  137 bits (344), Expect = 4e-30,   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|150186925|emb|CAK30129.1| RNA polymerase alpha subunit [Streptococcus thermophilus]
          Length = 145

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 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|213517416|gb|ACJ50122.1| RNA polymerase alpha subunit [Chlamydomonas reinhardtii]
          Length = 737

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 40/157 (25%), Positives = 73/157 (46%), Gaps = 11/157 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +             P     + TL N LRR L+S L G AIT+++I+GVLH+ S++ G+
Sbjct: 27  RIENNTNFYGCFYLGPFDESLSQTLANDLRRTLLSELTGLAITSIEIEGVLHKFSTLTGM 86

Query: 79  HEDLTDIILNIKGINLKMS-----------GDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
            E + D+I N++ I L+                     +   GP V+ A D++    ++ 
Sbjct: 87  KEPVLDLICNLQNIVLRKETISSTNMNYRATKKTYIGFLSVNGPRVIKAADLKLPAGLQC 146

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
           ++P+  I  L  D  + M+  +++G  Y+  K +  +
Sbjct: 147 VDPNQYIATLAEDGFLNMKFNINEGKNYIKQKPYNLD 183



 Score = 68.9 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 20/58 (34%), Positives = 35/58 (60%)

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           L++S+RS   L+   I  + DLI+ ++ D+  + N G+KS+ EI+  L  +GL L  +
Sbjct: 680 LKISLRSYTALKKAGITTLKDLIKYSKKDLFAIKNLGQKSVFEIEQNLALLGLTLVTD 737


>gi|119662829|emb|CAJ33207.1| RNA polymerase alpha subunit [Lactobacillus ingluviei]
          Length = 132

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 54/128 (42%), Positives = 83/128 (64%), Gaps = 1/128 (0%)

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR-TEN 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 DQLGMFIN 233
             L MF+N
Sbjct: 121 SHLTMFVN 128


>gi|61676006|gb|AAX51668.1| DNA dependent RNA polymerase alpha subunit [Waddlia chondrophila
           WSU 86-1044]
          Length = 174

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 67/174 (38%), Positives = 96/174 (55%), Gaps = 17/174 (9%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINL--- 94
           G  HTLGN+LRR++++SL   AI  V+I+GV HE  +I  + ED+T+IILNIKG  L   
Sbjct: 1   GMGHTLGNSLRRLMLTSLEAPAIIGVRIEGVAHEYMAIDSIVEDMTNIILNIKGAKLRKL 60

Query: 95  --------KMSGDSHKRVTI------FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
                   +  G   K + I        +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|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 =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 40/157 (25%), Positives = 73/157 (46%), Gaps = 11/157 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +             P     + TL N LRR L+S L G AIT+++I+GVLH+ S++ G+
Sbjct: 27  RIENNTNFYGCFYLGPFDESLSQTLANDLRRTLLSELTGLAITSIEIEGVLHKFSTLTGM 86

Query: 79  HEDLTDIILNIKGINLKMS-----------GDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
            E + D+I N++ I L+                     +   GP V+ A D++    ++ 
Sbjct: 87  KEPVLDLICNLQNIVLRKETISSTNMNYRATKKTYIGFLSVNGPRVIKAADLKLPAGLQC 146

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
           ++P+  I  L  D  + M+  +++G  Y+  K +  +
Sbjct: 147 VDPNQYIATLAEDGFLNMKFNINEGKNYIKQKPYNLD 183


>gi|119662339|emb|CAJ33158.1| RNA polymerase alpha subunit [Lactobacillus paralimentarius]
          Length = 134

 Score =  135 bits (340), Expect = 9e-30,   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|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 =  135 bits (340), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 55/199 (27%), Positives = 90/199 (45%), Gaps = 12/199 (6%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +    +        P   G A T+ NALRR L+S L G +IT V++ G  +E   I GV
Sbjct: 48  RVENLTKFYGRFELGPFAPGQALTVANALRRSLLSQLPGTSITLVEVRGASNEYEIITGV 107

Query: 79  HEDLTDIILNIKGINLKMSGD--SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
            E + DI+LN+K I L    +  S +   +   GPGV+ A D++  + I  ++P+  I  
Sbjct: 108 RESILDILLNLKQIVLTSDFEIFSPQIGFLSVEGPGVIRANDLKLPSFIYAVDPNQYIAT 167

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           L     + M+  +  G  Y+        ND      +    S +KK    ++S      L
Sbjct: 168 LSNSGRLNMKFLICCGKNYIT----YNPNDSQYFEWL----SLLKKSKPLIKS--NSPKL 217

Query: 197 DYDKLSMTIDTDGSITGED 215
           +   ++  ID+D SI  ++
Sbjct: 218 NKGNINSEIDSDISIDKKN 236



 Score =  117 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 43/189 (22%), Positives = 79/189 (41%), Gaps = 33/189 (17%)

Query: 162 RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
             ++  IG   IDA++ PI +V+Y +ES  + ++   D++ + + T+GSI    ++  A+
Sbjct: 388 DHKSTKIGYFPIDAIFMPINRVNYLIESTEDIKLKIKDRVILEVWTNGSIHPRHAIHKAA 447

Query: 222 RILQDQLGMFINFEE------PKKEVKEDINVKSLPFNPALLK----------------- 258
           + L                       +E  +      +    +                 
Sbjct: 448 KALIQLFLPLQQIRTNLFLISDNSHFEEGQDKIKKRIDNFKKEALLKANPQIQANPQLKK 507

Query: 259 ----------KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
                      +  LEL+ R  +CL+  NI  + DLI  ++ D+L + NFGR+SL+E++ 
Sbjct: 508 RNFDHRLLELDIANLELTARPYSCLKLANINTIEDLISYSQEDLLSIKNFGRRSLIEVQK 567

Query: 309 VLGTMGLFL 317
            L  M L L
Sbjct: 568 ALQLMKLTL 576


>gi|324533916|gb|ADY49343.1| DNA-directed RNA polymerase subunit alpha [Ascaris suum]
          Length = 179

 Score =  134 bits (338), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 52/178 (29%), Positives = 98/178 (55%), 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 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK----- 259
           I+T+G+I+ E++++ ++ I+++ + +  N EE   + +  I  K       + +      
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|150186930|emb|CAK30130.1| RNA polymerase alpha subunit [Streptococcus salivarius]
          Length = 141

 Score =  134 bits (338), Expect = 1e-29,   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|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 =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 44/144 (30%), Positives = 66/144 (45%), Gaps = 2/144 (1%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
                     +  P   G   T+  ALRR L+S L+G AI+AV+I G  H+ SSI GV E
Sbjct: 14  EGNGSIYGRFLLGPFKVGQGTTVATALRRTLLSELQGIAISAVEIKGATHQYSSIAGVRE 73

Query: 81  DLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD 138
              DI+LN+K I L     +       +  +GP    A D++  N I  ++ D  I ++ 
Sbjct: 74  STLDIVLNLKQIVLTGDVRNGLPAVGYLAVQGPKAARARDLKLPNGIRCVDGDQYIASVS 133

Query: 139 VDAVVRMELTVSKGHGYVPAKHHR 162
            +  + M+  +S G  YV      
Sbjct: 134 ANGSLTMKFVISAGKNYVSPHSPS 157



 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 24/199 (12%), Positives = 63/199 (31%), Gaps = 54/199 (27%)

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
                 + IDA++ P+ KV+++++   + Q    +++ + I T+GS+    ++  A+  L
Sbjct: 427 EMDSSPLPIDAVFMPVNKVNFSLQIDDQWQE-PRERVILEIWTNGSLHPRQAIGEAASYL 485

Query: 225 QDQLGMFINFEEPK---------------------------------------------- 238
                +    +                                                 
Sbjct: 486 VYLFSLLRQGDASPAATVQPSPQLRGLGWGTADQRGRTNLQSVEGGGREGEGSSGGMSSY 545

Query: 239 -KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
              +K                 + +L+LS+++   L+   +    D++  +   +  +  
Sbjct: 546 RATIKHPSPRALPGPGRDRSTDIADLDLSIQAYALLKRAGVHTFRDVMSLS---LNSIKG 602

Query: 298 FGRKS---LVEIKGVLGTM 313
            G  S   L+EI  ++  +
Sbjct: 603 GGLASPAILLEIDALIKRL 621


>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 =  134 bits (338), Expect = 2e-29,   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|262286213|gb|ACY41680.1| RNA polymerase alpha subunit [Streptococcus anginosus SK52]
          Length = 140

 Score =  134 bits (337), Expect = 2e-29,   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|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 =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 47/155 (30%), Positives = 78/155 (50%), Gaps = 4/155 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + K  Q+     + +  +L             P     + T+ NALRR L++ L   AIT
Sbjct: 1   MNKKIQDFFL--SCKECILENPRSFYGSFSLGPFKNSQSLTVANALRRTLLAELSNIAIT 58

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV--TIFKRGPGVVTAGDI 119
            ++I+GV HE S++ GV E + D++LN KGI LK +    K +   +  RGPGVV A D+
Sbjct: 59  HLEIEGVTHEYSTLVGVRESVLDLLLNFKGIALKNTSPVTKPLFGYLQVRGPGVVRASDL 118

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHG 154
           +    I+ ++PD  I  L+ +  + ++  +S    
Sbjct: 119 KFPPMIQCVDPDQYIATLNENGKLILKFRISDFKN 153



 Score = 62.7 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 35/216 (16%), Positives = 71/216 (32%), Gaps = 53/216 (24%)

Query: 161 HRTENDPIGLITIDALYSPIKKVSYTVESAREGQ-VLDYDKLSMTIDTDGSITGEDSVAL 219
             ++ +    + +D L++PI KV+Y +E+    Q  +  + + + + T+GSI    +   
Sbjct: 261 FDSQKNKTNSLWVDPLFNPILKVNYIIETIEPMQKNIPNEIVFIELWTNGSIHPRKAFYT 320

Query: 220 ASRILQDQL--------------------------------------------------- 228
           A   L+                                                      
Sbjct: 321 ALLYLKTMFDKLDCMRLLNYEFSNTMLESEKTSTKFFKTFEYDFRFYNSREDKTMKSFTP 380

Query: 229 -GMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
              F+  E    E    +N+K+   N      +  L L  R T  L   N   +GDL++ 
Sbjct: 381 EKFFLPEEIEDVEKDYLLNLKNQADNTWNDLPLTNLNLPYRITKILAKNNFFVVGDLLKI 440

Query: 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           +  ++ +++  G   +  ++     +GL LG     
Sbjct: 441 SPNELKKLSGIGNYCVFILQKRFEKLGLKLGSRNEK 476


>gi|262286211|gb|ACY41679.1| RNA polymerase alpha subunit [Streptococcus intermedius]
          Length = 140

 Score =  133 bits (336), Expect = 3e-29,   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|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 =  133 bits (335), Expect = 3e-29,   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|150036846|emb|CAM98288.1| DNA-directed RNA polymerase alpha chain [Fructobacillus
           pseudoficulneus]
          Length = 169

 Score =  133 bits (334), Expect = 5e-29,   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|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 =  132 bits (332), Expect = 7e-29,   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|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 =  132 bits (332), Expect = 9e-29,   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|207109275|ref|ZP_03243437.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           HPKX_438_CA4C1]
          Length = 176

 Score =  132 bits (331), Expect = 9e-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  AVKVMSKQLGVF--GERPIANMEYSGDYAQRDDAKDLSAKIESMNLSARCFNCLDKIGIK 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|119662291|emb|CAJ33132.1| RNA polymerase alpha subunit [Lactobacillus collinoides]
          Length = 135

 Score =  132 bits (331), Expect = 1e-28,   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|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 =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 40/157 (25%), Positives = 76/157 (48%), Gaps = 11/157 (7%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +             P     + T+ N +RR L+S L   AIT+++I+G+LH+ SS+ G+
Sbjct: 27  RIENNTSFYGCFYLGPFDDSLSQTIANDIRRTLLSELTSLAITSIEIEGILHKYSSLPGM 86

Query: 79  HEDLTDIILNIKGINLKMSG-----------DSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
            E + D+I N++ I LK                  R  +   GP V+ A D++  + ++ 
Sbjct: 87  KETVLDLICNLQSIVLKKQEISFTNITLRSTKKTYRGFLNVSGPRVIKAMDLKLPSGLQC 146

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
           ++P+  I  L  D ++ M+L +++G  ++  K H  +
Sbjct: 147 VDPNQYIATLAEDGLLNMKLNINEGKNFIKQKPHNLD 183



 Score = 69.6 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 30/136 (22%), Positives = 64/136 (47%), Gaps = 6/136 (4%)

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           + +Y   +A   + +++DK       +  +  E S   ++     ++ + +         
Sbjct: 635 RNNYNFYNADHIKKINFDKK------NRRLHRETSEQTSTSFAFGKIKLLLEQPGNTSTR 688

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           K  +N        AL   +  L++S+R+   L+   I+ + DL++ ++ D+L++ N G+K
Sbjct: 689 KTYLNQMKFYSQAALKAPIGILKISLRAYTALKKAGILTINDLVKCSKNDLLKINNLGKK 748

Query: 302 SLVEIKGVLGTMGLFL 317
           SLV I+  L  +GL L
Sbjct: 749 SLVLIETSLSYLGLTL 764


>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 =  132 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 54/288 (18%), Positives = 99/288 (34%), Gaps = 34/288 (11%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           + I   Q           PL     HT G  L+ V  + + G AI A+++  + +E + I
Sbjct: 403 DIIKYPQNGRLYQKFYIGPLNITDGHTFGTLLKYVCQTQVYGYAIVAIKVHNM-NEDTRI 461

Query: 76  KGVHEDLTDIILNIKGINLKMSG-DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
             V EDL +I LN+  + +     +    V +  +GP +V AG I   + ++V+N +  I
Sbjct: 462 DNVQEDLLEIALNLSDVCIYSKEINIETNVRLIFKGPLMVVAGMIPLPSHLQVVNKEQYI 521

Query: 135 CNLDVDAVVRMELTVSKGHGYV------------------PAKHHRTENDPIGLITIDAL 176
           C L  D  + + + +  G G+                     K    E      + I A 
Sbjct: 522 CTLKEDGYLDISIKIEYGKGHWLTYEKGLYKREVGSDNECMKKRQVKEVVEKNYMPISAS 581

Query: 177 YSPIKKVSYTVESA--------REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           +   + V   V           R         L M I +D  +  ++ +    + ++  L
Sbjct: 582 FGSCRMVRMAVHKIATKYWCEDRCEFTDPKQMLVMEIWSDCRMLPKNVLLYGIKNIKKIL 641

Query: 229 GMFINF------EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRST 270
             F              E +E   +         L+  +++E      
Sbjct: 642 RKFREMIISDTDFPSDVEDEEIKKLWPAIDRYKFLQTKQKMEGGPPIY 689


>gi|150187079|emb|CAK30166.1| RNA polymerase alpha subunit [Streptococcus parasanguinis ATCC
           15912]
          Length = 150

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 58/150 (38%), Positives = 92/150 (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 SRILQDQLGMFINFEEPKKEVKEDINVKSL 250
           +RIL + L +F N  E          V + 
Sbjct: 121 ARILTEHLNLFTNLTEIAIATDVMKEVDTT 150


>gi|246880788|gb|ACS95100.1| alpha subunit of RNA polymerase [Dunaliella salina]
          Length = 547

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 42/162 (25%), Positives = 70/162 (43%), Gaps = 25/162 (15%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +   +             G + T+ NALRR L+S   G AI +V+ID V HE S++ GV
Sbjct: 5   RIENNKSFYGCFYLGSFDSGQSITVANALRRSLLSDCTGLAIISVKIDAVQHEYSTLPGV 64

Query: 79  HEDLTDIILNIKGINLK-------------------------MSGDSHKRVTIFKRGPGV 113
            + + DI+LN K I LK                          +        +  +GPG+
Sbjct: 65  RDSVLDILLNFKEIVLKKVKNPFGGPNGYKNKGLSSVYDKVGSTFFKPVVGYLKVKGPGI 124

Query: 114 VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY 155
           + A D++    I+ ++P+  I  L  D V+ ++  + +G  Y
Sbjct: 125 IRAKDLRLPPFIQCVDPNQYIATLAEDGVLNVKFVIMEGKSY 166


>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 =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 63/340 (18%), Positives = 125/340 (36%), Gaps = 49/340 (14%)

Query: 23  EEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL 82
           +    +     P  +  A    N LRRVL+S      ITAV I G  HE S + GV E  
Sbjct: 16  KRNYYSRFYIGPFLKNQAFLYSNVLRRVLLSDSSNIVITAVNIVGAKHEYSLLPGVRESS 75

Query: 83  TDIILNIKGINLK----MSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL- 137
            D++LN+K +          +      +   GP ++   DI   N I  ++    I  + 
Sbjct: 76  LDLLLNLKELVFVKDIYTKFNKSYFAYLKSNGPKIIRCSDIILPNTIYAVDSTQYIATIS 135

Query: 138 -DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL-----------ITIDALYSPIKKVSY 185
            +   +++M+LT +  + +    ++   +                + ID  +S + KV+ 
Sbjct: 136 NNKSLILKMKLTANLLNNFYSNLNYELNSLLSYYTNDILEKTNFSLIIDPNFSCVNKVNS 195

Query: 186 TVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           ++ S    +  + D +S+ + T+ S +    +  + + + +      +      +++   
Sbjct: 196 SLISLDNLENYN-DSISLEVWTNSSYSPRIIIQNSIKSMVNLFLSIYDTSFIDIKLENSD 254

Query: 246 NVKSLP-------------------------------FNPALLKKVEELELSVRSTNCLR 274
           N                                         L  ++EL+LS+ S   L+
Sbjct: 255 NFLENHLVSLSNRATFFKKSFFNICTEFNTVKYKTSFDKNLTLISIDELDLSIYSKFLLK 314

Query: 275 GENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
             NI+ + DL +  +  + R  N   K+L  I+  +   G
Sbjct: 315 RHNILTLYDLFKIDKRVLERFYNISYKTLQSIERKMVKYG 354


>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 =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 62/235 (26%), Positives = 117/235 (49%), Gaps = 18/235 (7%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           M+ K       P+    I + + + N   ++  PL + F+ +  N LR+++     G +I
Sbjct: 1   MVHK------TPSFRPIIHVLKHDFNSIQVLIGPLEKNFSGSFANLLRKIIFRYTSGVSI 54

Query: 61  TAVQIDGV--LHEISSIKGVHEDLTDIILNIKGINLKM--SGDSHKRVTIFKRGPGVVTA 116
             ++I+G+  LH  S I GV ED+ +++ N+K + +++         +TI K+GP ++ +
Sbjct: 55  IGLKINGIDSLHSYSLIPGVKEDVLNVLNNLKHLLIQIDDYDYKPILLTIQKKGPYIIKS 114

Query: 117 GDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176
            DI   ++I++LN D  IC L+ D+ + + L    G GYV + +     +   ++  D  
Sbjct: 115 KDIICPSNIKILNDDLYICTLENDSQIDLTLIGDIGCGYVLSTYF---GNRKSIVYSDTN 171

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           + PIK VSY V S        Y++L   I T+G+      +  A   L+D++ + 
Sbjct: 172 FCPIKHVSYYVRSY-----TTYEELIFYIKTNGTCNPLFVMKNAFSFLKDKINIT 221


>gi|150186973|emb|CAK30139.1| RNA polymerase alpha subunit [Streptococcus porcinus]
          Length = 161

 Score =  130 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 57/157 (36%), Positives = 97/157 (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 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           I  ED++ L++R+L + L +F +  E  K        
Sbjct: 121 IIPEDALGLSARVLIEHLNLFTDLTEVAKATDVMKET 157


>gi|55274199|gb|AAV48981.1| DNA-directed RNA polymerase [Leuconostoc pseudomesenteroides]
          Length = 101

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 47/102 (46%), Positives = 65/102 (63%), Gaps = 4/102 (3%)

Query: 8   ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67
           E  KPN    I   +E+      + EPL RG+  TLGN+LRR+L+SSL GAA+  VQIDG
Sbjct: 3   EFEKPN----IHNIEEDARYGKFVIEPLERGYGTTLGNSLRRILLSSLPGAAVNTVQIDG 58

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR 109
           V+HE S++ GV ED+T IILN+K + L +  D  + + I  +
Sbjct: 59  VVHEFSTVDGVVEDVTQIILNLKKVVLAIDSDDERSLEIDVQ 100


>gi|108792413|emb|CAJ33201.1| RNA polymerase alpha subunit [Lactobacillus acidipiscis]
          Length = 133

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 53/133 (39%), Positives = 88/133 (66%), Gaps = 2/133 (1%)

Query: 116 AGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK--HHRTENDPIGLITI 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|119662799|emb|CAJ33191.1| RNA polymerase alpha subunit [Lactobacillus jensenii]
          Length = 117

 Score =  129 bits (324), Expect = 7e-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|218755234|ref|ZP_03534030.1| DNA-directed RNA polymerase subunit alpha [Mycobacterium
           tuberculosis GM 1503]
          Length = 153

 Score =  129 bits (324), Expect = 7e-28,   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|119662387|emb|CAJ33182.1| RNA polymerase alpha subunit [Lactobacillus acidifarinae]
          Length = 132

 Score =  128 bits (323), Expect = 8e-28,   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|225466312|ref|XP_002271159.1| PREDICTED: similar to Os04g0237300, partial [Vitis vinifera]
          Length = 274

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 37/119 (31%), Positives = 63/119 (52%), Gaps = 4/119 (3%)

Query: 13  NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGV 68
             +++  +    +N        I  PL +G A T+G A+RR L+  + G  IT  + + +
Sbjct: 156 RTLQWKCVESRVDNKRLCYGRFILSPLIKGQADTIGIAMRRALLGEIEGTCITRAKSEKI 215

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
            HE S+I G+ E + +I++N+K I L+ +    +   I  RGPG VTA DI +   +E+
Sbjct: 216 PHEYSTIVGIQESVHEILMNLKEIVLRSNLYGTRGAFICARGPGYVTAQDIISPPSVEI 274


>gi|154424739|emb|CAL18472.1| RNA polymerase alpha subunit [Streptococcus oligofermentans]
          Length = 136

 Score =  128 bits (322), Expect = 1e-27,   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|119672817|emb|CAK95488.1| RNA polymerase alpha subunit [Lactobacillus johnsonii]
          Length = 115

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 57/113 (50%), Positives = 78/113 (69%)

Query: 101 HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
            K   I   GP +VTA D++  +DIEVLNPD  IC++     + M + +  G GYVPA  
Sbjct: 2   EKIAEIDVTGPAIVTAADLKVDSDIEVLNPDQYICSIADGGHLHMNVAIKTGRGYVPASE 61

Query: 161 HRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           ++T++ PIG+I +D+L+SPIKKV+Y VESAR G+  DYDKL++ I TDGSIT 
Sbjct: 62  NKTDDMPIGVIPVDSLFSPIKKVNYQVESARVGKRDDYDKLTLEIWTDGSITP 114


>gi|150036730|emb|CAM98256.1| DNA-directed RNA polymerase alpha chain [Leuconostoc citreum]
          Length = 133

 Score =  127 bits (320), Expect = 2e-27,   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|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 =  127 bits (320), Expect = 2e-27,   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|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 =  127 bits (318), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 52/303 (17%), Positives = 107/303 (35%), Gaps = 39/303 (12%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           + ++  Q           PL     HT G+ ++ V  S + G AI  ++I  + +E + I
Sbjct: 325 DVLIYPQNGRLYQKFYIGPLNITDGHTFGSLIKYVCQSQIYGYAIVGIKIHNM-NEDTKI 383

Query: 76  KGVHEDLTDIILNIKGINLKMSG-DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           +   EDL +I LN+  + +     +    + +  +GP ++ AG I   + ++V+N +  I
Sbjct: 384 ENTQEDLLEIALNLSDVCIYSKEINIETNIRLIFKGPLMLVAGMIPLPSHLKVVNKEQYI 443

Query: 135 CNLDVDAVVRMELTVSKGHGYV------------------PAKHHRTENDPIGLITIDAL 176
           C +  +  + + + +  G G+                     K    E        + A 
Sbjct: 444 CTIKENGYIDISIKIEYGKGHWITYDKGLYKREIGSDNECMKKRQIKEVVNNNYTPLTAS 503

Query: 177 YSPIKKVSYTVESA--------REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           +SP + V  TV           R         L + I TD  +  ++ +    + ++  L
Sbjct: 504 FSPCRMVRITVHKIATKYWCEDRCEFTDPKQMLVVEIWTDPRMLPKNVLLYGIKNIKKIL 563

Query: 229 GMFINFEEP------KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC-----LRGEN 277
             F             +E +E   +         L+  +++E      N       +  N
Sbjct: 564 NKFREMIINDTDFPCDQEDREIKKLWPFIDRYKYLQTKQKMEGGPPIVNVDEELNTKNTN 623

Query: 278 IVY 280
           +  
Sbjct: 624 VNT 626


>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 =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 51/278 (18%), Positives = 97/278 (34%), Gaps = 34/278 (12%)

Query: 11  KPNNI----EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            P  +    + I +             P P     T+G+ L+ +  S   G A+ AV+I 
Sbjct: 242 TPTKVKEASDLIRIPDTGRLYQKFYMGPYPVTMGWTIGSLLKVMTQSRCPGHAVVAVKIH 301

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-SHKRVTIFKRGPGVVTAGDIQTVNDI 125
            +  + +++ GV +DL +I LN K + L+        RV    +GP +V AG ++    +
Sbjct: 302 NMNKD-TTVDGVADDLLNIALNFKMVALQTLEPGKEARVRTKIKGPAMVCAGALEWPPFV 360

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA------------------KHHRTENDP 167
           ++ NP+  I  L+  A + +E+ +  G G+  A                  +    E   
Sbjct: 361 KICNPESYITKLEEGAELDLEIKIEWGRGFWMADSKGLYRVEEGANSLCQKRRDIKEVKE 420

Query: 168 IGLITIDALYSPIKKVSYTVESAREGQVL---------DYDKLSMTIDTDGSITGEDSVA 218
            G      ++   + +   V     GQ             D+L + I TD S T +  + 
Sbjct: 421 EGFYPTSCVFGGCRMIRLAVHKL-MGQRWCSLTYTCPDPMDQLVVEIWTDVSTTPKHVLE 479

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAL 256
                +   L           + + +       +    
Sbjct: 480 FGLCEVIAWLTELKRQVSHDVDFENEDEQLKDIWEKID 517


>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 =  126 bits (316), Expect = 6e-27,   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|254701950|ref|ZP_05163778.1| DNA-directed RNA polymerase subunit alpha [Brucella suis bv. 5
          str. 513]
          Length = 70

 Score =  126 bits (316), Expect = 6e-27,   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  MIQKNWQELIKPNKVDFITHGSRT--HATVVAEPLERGFGLTLGNALRRVLLSSLRGAAV 58

Query: 61 TAVQIDGVLHEI 72
          TAVQIDGVLHE 
Sbjct: 59 TAVQIDGVLHEF 70


>gi|150186905|emb|CAK30124.1| RNA polymerase alpha subunit [Streptococcus gallinaceus]
          Length = 138

 Score =  125 bits (313), Expect = 1e-26,   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|150187003|emb|CAK30148.1| RNA polymerase alpha subunit [Streptococcus parauberis]
          Length = 161

 Score =  125 bits (313), Expect = 1e-26,   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|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 =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 52/303 (17%), Positives = 107/303 (35%), Gaps = 39/303 (12%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           + ++  Q           PL     HT G+ ++ V  S + G AI  ++I  + +E + I
Sbjct: 401 DVLIYPQNGRLYQKFYIGPLNITDGHTFGSLIKYVCQSQIYGYAIVGIKIHNM-NEDTKI 459

Query: 76  KGVHEDLTDIILNIKGINLKMSG-DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           +   EDL +I LN+  + +     +    + +  +GP ++ AG I   + ++V+N +  I
Sbjct: 460 ENTQEDLLEIALNLSDVCIYSKEINIETNIRLIFKGPLMLVAGMIPLPSHLKVVNKEQYI 519

Query: 135 CNLDVDAVVRMELTVSKGHGYV------------------PAKHHRTENDPIGLITIDAL 176
           C +  +  + + + +  G G+                     K    E        + A 
Sbjct: 520 CTIKENGYIDISIKIEYGKGHWITYDKGLYKREIGSDNECMKKRQIKEVVNNNYTPLTAS 579

Query: 177 YSPIKKVSYTVESA--------REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           +SP + V  TV           R         L + I TD  +  ++ +    + ++  L
Sbjct: 580 FSPCRMVRTTVHKIATKYWCEDRCEFTDPKQMLVVEIWTDPRMLPKNVLLYGIKNIKKIL 639

Query: 229 GMFINFEEP------KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC-----LRGEN 277
             F             +E +E   +         L+  +++E      N       +  N
Sbjct: 640 KKFREMIINDTDFPCDQEDREIKKLWPFIDRYKYLQTKQKMEGGPPIVNIDEELNTKNNN 699

Query: 278 IVY 280
           +  
Sbjct: 700 VNT 702


>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 =  123 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 56/326 (17%), Positives = 120/326 (36%), Gaps = 44/326 (13%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           + I   Q  +        PL     HT G+ ++ V  + + G AI  +++  + +E + I
Sbjct: 468 DIIKYPQNGKLYQKFYIGPLNITDGHTFGSLIKYVCQTQIYGYAIVGIKVHNM-NEDTKI 526

Query: 76  KGVHEDLTDIILNIKGINLKMSG-DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
             V EDL +I LNI  + +     +    + +  +GP ++ AG I   + ++++N +H I
Sbjct: 527 NNVQEDLLEIALNISDVCIYSKEINLESNIRLIFKGPLMLVAGMIPLPSHLKIINKEHYI 586

Query: 135 CNLDVDAVVRMELTVSKGHGYV------------------PAKHHRTENDPIGLITIDAL 176
           C +  D  + + + +  G G+                     K    E      + I + 
Sbjct: 587 CTIKEDGFIDISIKIEYGKGHWLTYDKGLYKRERGSDNDCMKKREIKEVVHKNYMPISSS 646

Query: 177 YSPIKKVSYTVESA--------REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228
           +   + +  TV           R         L + I TD  +  ++ +    + ++  L
Sbjct: 647 FGACRMIRLTVHKIATKFWCEDRCEFTDPKQMLVVEIWTDCRMLPKNVLLYGIKNIKKIL 706

Query: 229 GMFINFEEP------KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMG 282
             F            ++E +E  N+         L+  +++E      N         + 
Sbjct: 707 RKFREMIVKDTDFTFQEEEQEIKNLWPAIDKYKFLQTRQKMEGGPPIHNIDEDV----LS 762

Query: 283 DLIQRTEA------DMLRMANFGRKS 302
           + IQ+ ++      +++   NF + S
Sbjct: 763 EQIQKNKSLDPFSQELMNPDNFPKHS 788


>gi|289804411|ref|ZP_06535040.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
          subsp. enterica serovar Typhi str. AG3]
          Length = 74

 Score =  122 bits (306), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 36/77 (46%), Positives = 50/77 (64%), Gaps = 3/77 (3%)

Query: 2  IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
          +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1  MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62 AVQIDGVLHEISSIKGV 78
           V+IDGVLHE S+ +GV
Sbjct: 58 EVEIDGVLHEYSTKEGV 74


>gi|58618634|gb|AAW80815.1| RNA polymerase alpha subunit [Polytrichadelphus purpureus]
          Length = 165

 Score =  122 bits (306), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 46/163 (28%), Positives = 82/163 (50%), Gaps = 20/163 (12%)

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
           + PI+  +Y+V S      +  + L + I T+GSIT ++++  ASR L D    F++ E+
Sbjct: 1   FMPIRNANYSVHSFENNNKI-QEILFIEIWTNGSITPKEALYEASRSLXDLFIPFLHTEK 59

Query: 237 PKK------EVKEDINVKSLPFNPALLKKVEEL----------ELSVRSTNCLRGENIVY 280
            +       E K +       F+P   K  +E+          ELS R+ NCL+  N+  
Sbjct: 60  KETIDGLKTEYKSNDMSDFSSFSPLANKSTKEITFKHIFIDQLELSARAYNCLKRVNVHT 119

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           + DL+  ++ D++++ NFG+KS   ++ VL  +     +NLP 
Sbjct: 120 ISDLLNYSQDDLMKIKNFGKKS---VEQVLEALXKXFSINLPK 159


>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 =  120 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 50/226 (22%), Positives = 95/226 (42%), Gaps = 9/226 (3%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM---SGDSH 101
           NA RRV M  L+G  +TA++I  + HE   I GV E+  D+  N++ I  K    + D  
Sbjct: 322 NAFRRVAMKHLKGGRVTALRIPNMKHEFYCIVGVRENFFDLAQNLRQITFKNVPENIDMD 381

Query: 102 KRVT--IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP-- 157
             +T     +GP +V AG +Q    IE++N +  IC++   + + M++ +     YV   
Sbjct: 382 NYITGKFRIKGPMIVVAGHMQLPKGIEIVNKNQYICSVSAGSYLEMDVKIESIEEYVMPE 441

Query: 158 --AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
             ++    +      I   +  +P++   +  +          +   + + TDGSIT + 
Sbjct: 442 YGSQSRNRDICKDNFIHFSSSCTPVEYFGFMGQRRGINLDTLGEINIVEMHTDGSITPKS 501

Query: 216 SVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           ++      + +      N         +D +V+    NP      +
Sbjct: 502 ALLKTIDYISENFQYMENALYNNCHTCDDGSVEEEFRNPEFYMDKD 547


>gi|119672809|emb|CAK95485.1| RNA polymerase alpha subunit [Lactobacillus mucosae]
          Length = 121

 Score =  119 bits (299), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 49/121 (40%), Positives = 77/121 (63%), Gaps = 2/121 (1%)

Query: 120 QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT--ENDPIGLITIDALY 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|154424749|emb|CAL18477.1| RNA polymerase alpha subunit [Streptococcus pyogenes]
          Length = 128

 Score =  118 bits (297), Expect = 1e-24,   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|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 =  118 bits (297), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 46/82 (56%), Positives = 61/82 (74%)

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
             F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK V
Sbjct: 2   SHFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDV 61

Query: 310 LGTMGLFLGMNLPDWPPESIEE 331
           L + GL LGM L +WPP SI +
Sbjct: 62  LASRGLSLGMRLENWPPASIAD 83


>gi|228311784|pdb|2JZB|A Chain A, Solution Structure Of The Complex Between E.Coli Nusa-Ar2
           And Rnap-Actd
          Length = 99

 Score =  118 bits (297), Expect = 1e-24,   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|156102625|ref|XP_001617005.1| hypothetical protein [Plasmodium vivax SaI-1]
 gi|148805879|gb|EDL47278.1| hypothetical protein, conserved [Plasmodium vivax]
          Length = 668

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 48/226 (21%), Positives = 93/226 (41%), Gaps = 9/226 (3%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-----SGD 99
           NA RRV +  L+G  +TA++I  + HE   I GV E+  D+  N++ I  K        D
Sbjct: 316 NAFRRVAIKHLKGGRVTALRIPNMKHEFYCIVGVRENFFDLAQNLRHITFKNVPEEADID 375

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP-- 157
           ++       +GP +V AG +Q    IE++N +  IC++   + + M++ +     YV   
Sbjct: 376 NYITGKFRIKGPMIVVAGHMQLPKGIEIVNKNQYICSVSAGSYLEMDVKIESIEEYVMPE 435

Query: 158 --AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
             ++    +      I   +  +P++   +  +          +   + + TDGSIT + 
Sbjct: 436 YGSQSRNRDICKDNFIHFSSSCTPVEYFGFMGQRRGINLDTLGEINIVEMHTDGSITPKS 495

Query: 216 SVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           ++      + +      N         +D  V+    NP      +
Sbjct: 496 ALLKTIDYISENFQYMENALYNNCHTCDDGTVQEEFRNPEFYMDKD 541


>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 =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 46/82 (56%), Positives = 61/82 (74%)

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
             F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK V
Sbjct: 2   PEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDV 61

Query: 310 LGTMGLFLGMNLPDWPPESIEE 331
           L + GL LGM L +WPP SI +
Sbjct: 62  LASRGLSLGMRLENWPPASIAD 83


>gi|81301|pir||S05342 DNA-directed RNA polymerase (EC 2.7.7.6) alpha chain - green alga
           KS3/2 chloroplast (fragment)
          Length = 129

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 41/114 (35%), Positives = 62/114 (54%), Gaps = 2/114 (1%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
           +L             P     + T+ NALRR L++ L   AIT ++I+GV HE S++ GV
Sbjct: 16  ILENPRSFYGSFSLGPFKNSQSLTVANALRRTLLAELSNIAITHLEIEGVTHEYSTLVGV 75

Query: 79  HEDLTDIILNIKGINLKMSGDSHKRV--TIFKRGPGVVTAGDIQTVNDIEVLNP 130
            E + D++LN KGI LK +    K +   +  RGPGVV A D++    I+ ++P
Sbjct: 76  RESVLDLLLNFKGIALKNTSPVTKPLFGYLQVRGPGVVRASDLKFPPMIQCVDP 129


>gi|157830665|pdb|1COO|A Chain A, The Cooh-Terminal Domain Of Rna Polymerase Alpha Subunit
          Length = 98

 Score =  117 bits (293), Expect = 3e-24,   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|119662855|emb|CAJ33220.1| RNA polymerase alpha subunit [Lactobacillus vaginalis]
          Length = 120

 Score =  116 bits (291), Expect = 4e-24,   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|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 =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 64/195 (32%), Positives = 99/195 (50%), Gaps = 6/195 (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 KHHRTENDPI--GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDS 216
              R     +  G   +DA +SP+K+VSY V SA + +  D  +L   I+T+G + G  +
Sbjct: 145 AQARARWSRVLAGYTVVDAHFSPVKRVSYKVSSAEDDRSCDRAQLV--IETNG-VDGAHA 201

Query: 217 VALASRILQDQLGMF 231
           V  A R L     + 
Sbjct: 202 VVDACRELSRCFQLV 216


>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 =  116 bits (290), Expect = 6e-24,   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|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 =  116 bits (290), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 51/226 (22%), Positives = 95/226 (42%), Gaps = 9/226 (3%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR- 103
           NA RRV +  L+G  +TA++I G+ HE   I GV E+  D+  N++ I  K   +     
Sbjct: 304 NAFRRVAIKHLKGGRVTALRIPGMKHEYYCIVGVRENFFDLSQNLRQITFKNVPEDADMN 363

Query: 104 ----VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP-- 157
                    +GP +V AG +Q   +IE++N +  IC +   + + M++ +     YV   
Sbjct: 364 NYIIGKFRIKGPMIVVAGHMQLPKNIEIINKNQYICYVAAGSYLEMDVKIESIEEYVMPE 423

Query: 158 --AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
             ++    +      I   +  +P++   +T +       +  +   + + TDGSIT + 
Sbjct: 424 YGSQSRNRDICKDNFIHFCSSCTPVEYFGFTGQRRGINLDILGEINIVEMHTDGSITPKT 483

Query: 216 SVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           ++      + +      N         ED +V+    NP      E
Sbjct: 484 ALLKTIDYMSENFQYIENALHNNCHSCEDGSVEEEFRNPEFYMDKE 529


>gi|300431274|gb|ADK12602.1| RNA polymerase alpha subunit [Pappostipa vaginata]
          Length = 167

 Score =  116 bits (290), Expect = 6e-24,   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   DAVSMPVRNVNYSIFSCGNGNE-KHEILFLEIWTNGSLTPKEALYEASRNLIDLFLPFLH 59

Query: 234 FEEPKKEVKEDINVKSLPFNPALLKK----------------VEELELSVRSTNCLRGEN 277
            EE     +E+ N  + P      K                 +++LEL  R+ NCL+  N
Sbjct: 60  AEEEGTSFEENKNRFTPPLFTFQKKLTNLKKNKKGIPLNCIFIDQLELPSRTYNCLKRAN 119

Query: 278 IVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           I  + DL+ +TE D++R+ +F    + + K +   +   L +NL
Sbjct: 120 IHTLLDLLSKTEEDLMRIDSF---RMEDGKQIWDNLEKHLPINL 160


>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 =  115 bits (287), Expect = 1e-23,   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|119662287|emb|CAJ33130.1| RNA polymerase alpha subunit [Lactobacillus buchneri]
          Length = 125

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 49/124 (39%), Positives = 76/124 (61%), Gaps = 2/124 (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 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|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 =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 52/226 (23%), Positives = 98/226 (43%), Gaps = 9/226 (3%)

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--IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP-- 157
             +T     +GP +V AG +Q   +IE++N +  IC +   + + M++ +     YV   
Sbjct: 315 NYITGKFRIKGPMIVVAGHMQLPKNIEIINKNQYICYVAAGSYLEMDVKIESIEEYVMPE 374

Query: 158 --AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
             ++    +      I   +  +P++   +T +       +  +   + + TDGSIT + 
Sbjct: 375 YGSQSRNRDICKDNFIHFCSSCTPVEHFGFTGQRRGINLDVLGEINIVEMHTDGSITPKT 434

Query: 216 SVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           ++      + +      N         ED +++    NP      E
Sbjct: 435 ALLKTIDYMSENFQYMENALHNNCHSCEDGSLEEEFRNPEFYMDKE 480


>gi|169835538|ref|ZP_02868726.1| hypothetical protein cdivTM_00193 [candidate division TM7
           single-cell isolate TM7a]
          Length = 96

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 36/91 (39%), Positives = 55/91 (60%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
           +            EPL  G+ +TLGN+LRRVLMSS+ GAA+ + +I+G  HE +++ G+ 
Sbjct: 6   IEDYSSTSAAFTVEPLRGGYGNTLGNSLRRVLMSSIHGAAVISFKIEGATHEFTTVPGIK 65

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKRG 110
           ED+ DI LN+K + +KM  D    + + K G
Sbjct: 66  EDVVDISLNLKSVKIKMHTDDPIELRLEKHG 96


>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 =  113 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 47/226 (20%), Positives = 97/226 (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 SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP-- 157
           ++       +GP +V AG +Q   ++E++N +  IC++   + + M++ +     YV   
Sbjct: 327 NYMIGKFRIKGPMIVVAGHMQLPKNVEIVNRNQYICSVAAGSYLSMDVKIESIEEYVMPE 386

Query: 158 --AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
             ++    +      I   +  +P++   +T +          +   + + TDGSIT + 
Sbjct: 387 YGSQSRNRDICKDNFIHFSSSCTPVEHFVFTGQRRGINLDTLGEINIVEMHTDGSITPKS 446

Query: 216 SVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           ++      + +      N       + +D ++     NP      +
Sbjct: 447 ALLKTIDYISENFQYIENALYNNCHICDDGSLDEEFRNPEFYMDKD 492


>gi|119662813|emb|CAJ33198.1| RNA polymerase alpha subunit [Lactobacillus vaccinostercus]
          Length = 114

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 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 LNPDHVICNLDVDAVVRMELTVSKGHGYVPA--KHHRTENDPIGLITIDALYSP 179
           LNP+  I  +   A + +++T + G GYV A     R ++ PIG++ ID++Y+P
Sbjct: 61  LNPELHIATVADGAELHIQMTANTGRGYVSADDNKARMDDLPIGVLPIDSIYTP 114


>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 =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 51/226 (22%), Positives = 96/226 (42%), Gaps = 10/226 (4%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR- 103
           NA RRV +  L+G  +TA++I G+ HE   I GV E+  D+  N++ I  K   ++    
Sbjct: 222 NAFRRVAIKHLKGGRVTALRIPGMKHEYYCIVGVRENFFDLSQNLRQITFKNVPENADMN 281

Query: 104 ----VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP-- 157
                    +GP +V AG +Q   +IE++N +  IC +   + + M++ +     YV   
Sbjct: 282 NYIIGKFRIKGPMIVVAGHMQLPKNIEIINKNQYICYVAAGSYLEMDVKIESIEEYVMPE 341

Query: 158 --AKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED 215
             ++    +      I   +  +P++   +T +       +  +   + + TDGSIT + 
Sbjct: 342 YGSQSRNRDICKDNFI-FCSSCTPVEYFGFTGQRRGINLDILGEINIVEMHTDGSITPKT 400

Query: 216 SVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
           ++      + +      N         ED +V+    NP      E
Sbjct: 401 ALLKTIDYMSENFQYIENALHNNCHSCEDGSVEEEFRNPEFYMDKE 446


>gi|62361814|gb|AAX81443.1| RNA polymerase alpha subunit [Simkania negevensis]
          Length = 159

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 51/159 (32%), Positives = 82/159 (51%), Gaps = 17/159 (10%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLK-----------------MS 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|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 =  110 bits (276), Expect = 3e-22,   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|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 =  108 bits (269), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 39/76 (51%), Positives = 55/76 (72%)

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
                 LL++V++LELSVRS NCL+ + I ++G+L+Q++E +MLR  NFGR+SL EIK +
Sbjct: 234 SQQAGKLLERVDDLELSVRSANCLKKDGINHVGELVQKSEDEMLRTPNFGRRSLNEIKDL 293

Query: 310 LGTMGLFLGMNLPDWP 325
           L   GL LGM+L  WP
Sbjct: 294 LAASGLHLGMDLSGWP 309



 Score =  103 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 40/102 (39%), Positives = 69/102 (67%)

Query: 234 FEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           +E P       +    +P    L + ++ELELSVR++ CL+ +++  +GD  + +EA++L
Sbjct: 135 WEPPPSPPPPYVPPVGIPPTVHLYRSIDELELSVRTSLCLKNDDVRLVGDFARNSEAELL 194

Query: 294 RMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKK 335
           R+ NFGRKSL E+K +LG +GL LG+ LP+WPP +++ L+++
Sbjct: 195 RIPNFGRKSLNELKEILGQVGLQLGLALPEWPPPNVDFLSQQ 236


>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 =  108 bits (269), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 53/173 (30%), Positives = 91/173 (52%), Gaps = 6/173 (3%)

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
              IE++N D  I  L  +    +  TVS G          TE + +G I +DA ++PIK
Sbjct: 1   TQGIEIINKDQPIATLTNEREFSLVATVSVGRNVGILSALPTELEKVGDIAVDADFNPIK 60

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +V++ +           + L + + T+G+I    +V  A     +Q+ +F++   P    
Sbjct: 61  RVAFEIFDNGAS-----ETLEVFVKTNGTIEPLAAVTKALEYFCEQISVFVSLRVP-SNG 114

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           K    +     +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ +++
Sbjct: 115 KTGDALLDSNIDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMK 167


>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 =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 32/123 (26%), Positives = 58/123 (47%), Gaps = 11/123 (8%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            +             P     + T+ N +RR L+S L   AIT+++I+G+LH+ SS+ G+
Sbjct: 14  RIENNTSFYGCFYLGPFDDSLSQTIANDIRRTLLSELTSLAITSIEIEGILHKYSSLPGM 73

Query: 79  HEDLTDIILNIKGINLKMSG-----------DSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
            E + D+I N++ I LK                  R  +   GP V+ A D++  + ++ 
Sbjct: 74  KETVLDLICNLQSIVLKKQEISFTNITLRSTKKTYRGFLNVSGPRVIKAMDLKLPSGLQC 133

Query: 128 LNP 130
           ++P
Sbjct: 134 VDP 136


>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 =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 49/323 (15%), Positives = 100/323 (30%), Gaps = 79/323 (24%)

Query: 11  KPNNI----EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
            P  +    + I +             P P     T+G+ L+ +  S   G A+ AV+I 
Sbjct: 264 TPTKVKEASDLIRIPDTGRLYQKFYMGPYPVTMGWTIGSLLKVMTQSRCPGHAVVAVKIH 323

Query: 67  GVLHEISSIKGVHEDLTDIILNIKGI---NLKMSGDSHKRVTIF---------------- 107
            +  + +++ GV +DL +I LN+K +   +          + I+                
Sbjct: 324 NMNKD-TTVNGVADDLLNIALNLKMVSYTHFYTIYTHFTHLHIYTFTHLHIYTFTHLHTY 382

Query: 108 ---------------------------KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
                                       +GP ++ AG ++  + +++ NP+  I  L+  
Sbjct: 383 TFLQIFTQFIVSLQTLEYGKEARVRTVIKGPAMLCAGALEWPSFVKLCNPECYITKLEEG 442

Query: 141 AVVRMELTVSKGHGYVPA------------------KHHRTENDPIGLITIDALYSPIKK 182
           A + +E+ +  G G+  A                  +    E    G      ++   + 
Sbjct: 443 AELDLEIKIEWGRGFWMADSKGLYRLEEGANSLCHKRRDIKEVKEEGFYPTSCVFGGCRM 502

Query: 183 VSYTVESAREGQVL---------DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           +   V     GQ             D+L + I TD S T +  +      +   L  F  
Sbjct: 503 IRLAVHKL-MGQRWCSLTYTCPDPMDQLVVEIWTDVSTTPKHVLEFGLSEVIAWLTEFKR 561

Query: 234 FEEPKKEVKEDINVKSLPFNPAL 256
                 + + +       +    
Sbjct: 562 QVSHDVDFEHEDEQLKDIWEKID 584



 Score = 40.7 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 16/89 (17%), Positives = 31/89 (34%), Gaps = 1/89 (1%)

Query: 226 DQLGMFINFEEPKKEVKEDINVKSLP-FNPALLKKVEELELSVRSTNCLRGENIVYMGDL 284
           ++L      E+ +   K        P  +    K ++ L ++    + LR      M DL
Sbjct: 654 EELQAEEYNEKSEINAKNFEKFIPKPVEDTFENKDIDLLPVNSDIISSLRMSGFNVMADL 713

Query: 285 IQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           +  +  ++    N   +S   IK  L   
Sbjct: 714 MDYSVEELSHFPNLSIESAKIIKNFLTEH 742


>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 =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 52/173 (30%), Positives = 91/173 (52%), Gaps = 6/173 (3%)

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
              IE++N D  I  L  +    +  TVS G          TE + +G I +D+ ++PIK
Sbjct: 1   TQGIEIINKDQPIATLTNEREFSLTATVSVGRNVGILSALPTELEKVGDIAVDSDFNPIK 60

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           +V++ +           + L + + T+G+I    +V  A     +Q+ +F++   P    
Sbjct: 61  RVAFEIF-----DNGTNETLEVFVKTNGTIEPLVAVTKALEYFCEQISVFVSLRVP-SNG 114

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           K    +     +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ +++
Sbjct: 115 KTGDALLDSNIDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMK 167


>gi|152218448|gb|ABS31658.1| RpoA [Francisella philomiragia subsp. philomiragia ATCC 25015]
          Length = 167

 Score =  106 bits (266), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 52/170 (30%), Positives = 91/170 (53%), 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    K  
Sbjct: 64  FEIF-----DNGTNETLEVFVKTNGTIEPLVAVTKALEYFCEQISVFVSLRVP-SNGKTG 117

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
             +     +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ +++
Sbjct: 118 DALLDSNIDPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQLMK 167


>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 =  106 bits (264), Expect = 5e-21,   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|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 =  106 bits (264), Expect = 5e-21,   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|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 =  105 bits (261), Expect = 1e-20,   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|143452|gb|AAA22708.1| RNA polymerase alpha subunit [Bacillus subtilis]
          Length = 65

 Score =  104 bits (260), Expect = 2e-20,   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|156089709|ref|XP_001612261.1| hypothetical protein [Babesia bovis T2Bo]
 gi|154799515|gb|EDO08693.1| hypothetical protein BBOV_III011410 [Babesia bovis]
          Length = 610

 Score =  103 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 44/211 (20%), Positives = 85/211 (40%), Gaps = 26/211 (12%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-----SGD 99
           N+LRRV    L    ITA++I G+ +E  SI G+ ED  D+  N+  +  +      +  
Sbjct: 239 NSLRRVAKRHLGAGRITALRIPGMKNEFYSIVGLREDFFDLSRNLTKVIFRNVPMTATFH 298

Query: 100 SHKRVTIFKRGPGVVTAGDIQTVNDIE-----------------VLNPDHVICNLDVDAV 142
                 +  +GP +  AG I+     +                 ++N +  IC L  DA 
Sbjct: 299 RPLIGRLRLKGPIIAVAGHIELDQTFQKEGVGSSSGSKDDRRIEIVNKNQYICALSRDAY 358

Query: 143 VRMELTVSKGHGYVPAKHH----RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDY 198
           + ME+ +     YV  +        +  P G I   +  +PI+  ++  +     +    
Sbjct: 359 LDMEVKIEYIANYVMPEKGPESLNRDITPDGFIHFSSSCTPIEVFAFDGDRRGIDEESTS 418

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           + +++ + TDGS T   ++   +  ++    
Sbjct: 419 EIVTLELHTDGSTTPRLALLNCATFIETWFE 449


>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 =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 27/65 (41%), Positives = 40/65 (61%), Gaps = 3/65 (4%)

Query: 2  IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
          +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1  MQGSVTEFLKPRLVDIEQINT---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62 AVQID 66
           V+I+
Sbjct: 58 EVEIE 62


>gi|221487600|gb|EEE25832.1| hypothetical protein TGGT1_089410 [Toxoplasma gondii GT1]
          Length = 1082

 Score =  100 bits (248), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 47/293 (16%), Positives = 100/293 (34%), Gaps = 54/293 (18%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI----------- 65
             ++ +       +   P+P     T+G+ ++        G AI A+++           
Sbjct: 602 VTIIPETGHLYQKLYIGPVPVTTGWTMGSLIKAFAAQRCPGHAIVALKLHAPRKPNAGGR 661

Query: 66  -------DGVLH---------EISSIKGVHEDLTDIILNIKGINL-KMSGDSHKRVTIFK 108
                  +G             ++ +  V EDL +I LN+KG+    +       V +  
Sbjct: 662 RGRKKTGEGEPQSAGGEAEAPMVTQLPNVREDLLEIALNLKGVAFETLRPRESACVRVKA 721

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA---------- 158
            GP ++ AG I   + + V NP+H I  ++   V+ +E+ +  G G   A          
Sbjct: 722 VGPQLLVAGMIDWPSFVRVGNPEHFIAKVEEGGVLDLEMKLEWGRGAWLADLHGLYREEE 781

Query: 159 --------KHHRTENDPIGLITIDALY---SPIKKVSYTVESAREGQV-----LDYDKLS 202
                   +    E D  G      ++   + ++   + +   R  Q         ++L 
Sbjct: 782 GVDTRCYKRRRIWEVDHRGFYPTSCIFGACTMMRLAVHKLMGTRFCQDRQASTNPTEQLV 841

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           + I TD S + ++ +A A + +               + K +    +  +   
Sbjct: 842 LEIWTDASKSPKEVLAFALQDMLAWFVDLRRQLVEDVDWKTEDEDLTAAWKHV 894


>gi|218672329|ref|ZP_03521998.1| DNA-directed RNA polymerase subunit alpha [Rhizobium etli GR56]
          Length = 57

 Score = 99.3 bits (246), Expect = 7e-19,   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|20451756|emb|CAD30546.1| DNA-directed RNA polymerase alpha subunit [Listonella
          anguillarum]
          Length = 61

 Score = 99.3 bits (246), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 27/64 (42%), Positives = 38/64 (59%), Gaps = 3/64 (4%)

Query: 2  IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
          +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1  MQGSVTEFLKPRLVDIEQIST---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62 AVQI 65
           V I
Sbjct: 58 EVVI 61


>gi|221507397|gb|EEE33001.1| RNA polymerase Rpb3/Rpb11 dimerisation domain-containing protein,
           putative [Toxoplasma gondii VEG]
          Length = 1084

 Score = 98.9 bits (245), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 47/293 (16%), Positives = 101/293 (34%), Gaps = 54/293 (18%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI----------- 65
             ++ +       +   P+P     T+G+ ++        G A+ A+++           
Sbjct: 604 VTIIPETGHLYQKLYIGPVPVTTGWTMGSLIKAFAAQRCPGHAVVALKLHAPRKPNAGGR 663

Query: 66  -------DGVLH---------EISSIKGVHEDLTDIILNIKGINL-KMSGDSHKRVTIFK 108
                  +G             ++ +  V EDL +I LN+KG+    +       V +  
Sbjct: 664 RGRKKTGEGEPQSAGGEAEAPMVTQLPNVREDLLEIALNLKGVAFETLRPRESACVRVKA 723

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA---------- 158
            GP ++ AG I   + + V NP+H I  ++   V+ +E+ +  G G   A          
Sbjct: 724 VGPQLLVAGMIDWPSFVRVGNPEHFIAKVEEGGVLDLEMKLEWGRGAWLADLHGLYREEE 783

Query: 159 --------KHHRTENDPIGLITIDALY---SPIKKVSYTVESAREGQV-----LDYDKLS 202
                   +    E D  G      ++   + ++   + +   R  Q         ++L 
Sbjct: 784 GVDTRCYKRRRIWEVDHRGFYPTSCIFGACTMMRLAVHKLMGTRFCQDRQASTNPTEQLV 843

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           + I TD S + ++ +A A + +   L           + K +    +  +   
Sbjct: 844 LEIWTDASKSPKEVLAFALQDMLAWLVDLRRQLVEDVDWKTEDEDLTAAWKHV 896


>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 = 98.9 bits (245), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 47/293 (16%), Positives = 101/293 (34%), Gaps = 54/293 (18%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI----------- 65
             ++ +       +   P+P     T+G+ ++        G A+ A+++           
Sbjct: 143 VTIIPETGHLYQKLYIGPVPVTTGWTMGSLIKAFAAQRCPGHAVVALKLHAPRKPNAGGR 202

Query: 66  -------DGVLH---------EISSIKGVHEDLTDIILNIKGINL-KMSGDSHKRVTIFK 108
                  +G             ++ +  V EDL +I LN+KG+    +       V +  
Sbjct: 203 RGRKKTGEGEPQSAGGEAEAPMVTQLPNVREDLLEIALNLKGVAFETLRPRESACVRVKA 262

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA---------- 158
            GP ++ AG I   + + V NP+H I  ++   V+ +E+ +  G G   A          
Sbjct: 263 VGPQLLVAGMIDWPSFVRVGNPEHFIAKVEEGGVLDLEMKLEWGRGAWLADLHGLYREEE 322

Query: 159 --------KHHRTENDPIGLITIDALY---SPIKKVSYTVESAREGQV-----LDYDKLS 202
                   +    E D  G      ++   + ++   + +   R  Q         ++L 
Sbjct: 323 GVDTRCYKRRRIWEVDHRGFYPTSCIFGACTMMRLAVHKLMGTRFCQDRQASTNPTEQLV 382

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           + I TD S + ++ +A A + +   L           + K +    +  +   
Sbjct: 383 LEIWTDASKSPKEVLAFALQDMLAWLVDLRRQLVEDVDWKTEDEDLTAAWKHV 435


>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 = 97.4 bits (241), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 25/61 (40%), Positives = 36/61 (59%), Gaps = 3/61 (4%)

Query: 2  IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
          +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1  MQGSVTEFLKPRLVDIEQISS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62 A 62
           
Sbjct: 58 E 58


>gi|213420797|ref|ZP_03353863.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. E01-6750]
          Length = 56

 Score = 97.0 bits (240), Expect = 4e-18,   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|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 = 97.0 bits (240), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 26/65 (40%), Positives = 39/65 (60%), Gaps = 3/65 (4%)

Query: 2  IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
          +Q +  E +KP  ++   +         +  EPL RGF +TL NALRR+L+SS+ G A+T
Sbjct: 1  MQGSVTEFLKPRLVDIEQIST---THAKVTLEPLERGFGYTLRNALRRILLSSMPGCAVT 57

Query: 62 AVQID 66
           V+ID
Sbjct: 58 EVEID 62


>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 = 96.2 bits (238), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 55/279 (19%), Positives = 102/279 (36%), Gaps = 63/279 (22%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKM-----SGD 99
           N+LRRV    L    ITA++I G+ +E  S+ G+ ED  +++ N++G+  K      +  
Sbjct: 183 NSLRRVAKRHLGSGRITALRIPGMENEFYSVVGLREDFFELVRNLRGVIFKNVPKTATFH 242

Query: 100 SHKRVTIFKRGPGVVTAGDIQTV------------------------------------- 122
                T+  +GP +  AG ++                                       
Sbjct: 243 RPVIATLRLKGPIIAVAGHLKFDNKRSTKTASDIDNKTENKNDNTDTKADNEEGVINDYV 302

Query: 123 ------NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP----AKHHRTENDPIGLIT 172
                  +IEV+N +H IC+L     + M++ +     YV      +    +  P G I 
Sbjct: 303 YDKKYTGEIEVINKNHYICSLSQGCYLTMDVKIEYISNYVIPEFGPESLNRDITPDGFIH 362

Query: 173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
             +  +P++   +T E     +    + +S+ + TDGS T   ++  ++  L +     +
Sbjct: 363 FCSSCNPVEIFGFTGERRGLDEQSTSEIVSLELHTDGSATPRVALLRSATFLLNWFDRTL 422

Query: 233 NFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTN 271
                           +L  +   LKKV     S    N
Sbjct: 423 Y-----------ALRTNLTRDYYALKKVNTFNTSQLIHN 450


>gi|119662819|emb|CAJ33202.1| RNA polymerase alpha subunit [Lactobacillus diolivorans]
          Length = 98

 Score = 96.2 bits (238), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 50/98 (51%), Positives = 62/98 (63%), Gaps = 2/98 (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 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           D+ VLNPD  I  +   A   M LT +KG GYV A  +
Sbjct: 61  DVTVLNPDLHIATVAEGATFHMRLTANKGRGYVSAVEN 98


>gi|166714704|gb|ABY88077.1| RpoA [Stenotrophomonas sp. ICB220]
          Length = 122

 Score = 95.0 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 40/112 (35%), Positives = 63/112 (56%), Gaps = 3/112 (2%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R  +D    I    +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   LNMRLKIERGFGYQPAAARRHPDDETRTIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           KL + I+T+G+I  E++V  A+ IL DQL +F +F   ++   +       P
Sbjct: 62  KLVLDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRQRGEAKPSKTGVDP 113


>gi|166714638|gb|ABY88044.1| RpoA [Pseudoxanthomonas dokdonensis]
          Length = 122

 Score = 95.0 bits (235), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 40/112 (35%), Positives = 63/112 (56%), Gaps = 3/112 (2%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R  +D    I    +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   LNMRLKIERGFGYQPAAARRHPDDETRTIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           KL + I+T+G+I  E++V  A+ IL DQL +F +F   ++   +       P
Sbjct: 62  KLVLDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRQRGEAKPSPTGVDP 113


>gi|119662805|emb|CAJ33194.1| RNA polymerase alpha subunit [Lactobacillus manihotivorans]
          Length = 89

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 36/88 (40%), Positives = 55/88 (62%)

Query: 101 HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
            K V I   GP  VTA DI + +D+EVLNP+  IC +       + +TV  G GYV A  
Sbjct: 2   DKTVEIDVAGPATVTAADIVSDSDVEVLNPEQYICTVAEGGRFHVRMTVKTGRGYVAADQ 61

Query: 161 HRTENDPIGLITIDALYSPIKKVSYTVE 188
           ++ ++ PIG++ ID++++PI +V+Y VE
Sbjct: 62  NKVDDMPIGVLPIDSIFTPISRVNYQVE 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 = 94.7 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 30/84 (35%), Positives = 46/84 (54%)

Query: 234 FEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
             +  +  +  +  +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+
Sbjct: 1   MTDEAQHAEIMVEKEEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMM 60

Query: 294 RMANFGRKSLVEIKGVLGTMGLFL 317
           ++ N GRKSL E+K  L  +GL L
Sbjct: 61  KVRNLGRKSLEEVKAKLEELGLGL 84


>gi|213585431|ref|ZP_03367257.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. E98-0664]
          Length = 54

 Score = 93.9 bits (232), Expect = 3e-17,   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|183397281|gb|ACC62187.1| RpoA1 [Francisella noatunensis]
          Length = 154

 Score = 93.9 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 48/160 (30%), Positives = 83/160 (51%), Gaps = 6/160 (3%)

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  L  +    +  TVS G           E + +G I +DA ++PIK+V++ +     
Sbjct: 1   PIATLTNEREFSLVATVSVGRNVGILSALPIELEKVGDIAVDADFNPIKRVAFEIF---- 56

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
                 + L + + T+G+I    +V  A     +Q+ +F++ + P    K    +     
Sbjct: 57  -DNSASETLEVFVKTNGTIEPLAAVTKALEYFCEQISVFVSLKVP-SNGKTGDALLDSNI 114

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ +
Sbjct: 115 DPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQL 154


>gi|166714628|gb|ABY88039.1| RpoA [Stenotrophomonas maltophilia]
          Length = 122

 Score = 93.5 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 39/112 (34%), Positives = 65/112 (58%), Gaps = 3/112 (2%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M + + +G+GY PA   R+ ++    I    +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMAVKIERGYGYQPAAARRSPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N    P
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFNHRDRGAAKPANNGVDP 113


>gi|166714682|gb|ABY88066.1| RpoA [Stenotrophomonas sp. LMG 981]
          Length = 122

 Score = 93.5 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 40/113 (35%), Positives = 64/113 (56%), Gaps = 3/113 (2%)

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDY 198
            + M L + +G GY PA   R  ++    I    +DA +SP+++V+Y+VE+AR  Q  D 
Sbjct: 1   SINMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYSVEAARVEQRTDL 60

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           DKL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N    P
Sbjct: 61  DKLVIEIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNGVDP 113


>gi|183397279|gb|ACC62186.1| RpoA1 [Francisella noatunensis]
          Length = 154

 Score = 93.5 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 49/160 (30%), Positives = 83/160 (51%), 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    K    +     
Sbjct: 61  S-----ETLEVFVKTNGTIEPLAAVTKALEYFCEQISVFVSLRVP-SNGKTGDALLDSNI 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 = 93.5 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 48/160 (30%), Positives = 83/160 (51%), Gaps = 6/160 (3%)

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESARE 192
            I  L  +    +  TVS G          TE + +G I +D+ ++PIK+V++ +     
Sbjct: 1   PIATLTNEREFSLTATVSVGRNVGILSALPTELEKVGDIAVDSDFNPIKRVAFEIF---- 56

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
                 + L + + T+G+I    +V  A     +Q+ +F++   P    K    +     
Sbjct: 57  -DNGTNETLEVFVKTNGTIEPLVAVTKALEYFCEQISVFVSLRVP-SNGKTGDALLDSNI 114

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ +
Sbjct: 115 DPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQL 154


>gi|71904766|gb|AAZ52664.1| DNA-dependent RNA polymerase alpha chain [Mycoplasma hominis ATCC
           23114]
          Length = 180

 Score = 93.1 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 29/150 (19%), Positives = 72/150 (48%)

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
               ++      + +D+ +SPIKKV+   E       +  ++L + ++TDG++  ++ + 
Sbjct: 5   PKLESKIKNGQFLAMDSDFSPIKKVAILFEELNSTSNIIEERLKIKVETDGTVEAKNVME 64

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENI 278
            A++I+     +  N +        D   +     P +   +++L L++RS N LR    
Sbjct: 65  EAAKIIVAHFQIIGNIDALGTIDLFDDQKEKHEKTPKVSVSIDKLNLTIRSLNALRRAGF 124

Query: 279 VYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
             + ++++ ++ ++  + N G+KS+ +I  
Sbjct: 125 NNVDEIMKLSDEELSNIKNLGKKSVQDIID 154


>gi|166714644|gb|ABY88047.1| RpoA [Stenotrophomonas sp. LMG 10857]
          Length = 122

 Score = 93.1 bits (230), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 41/112 (36%), Positives = 64/112 (57%), Gaps = 3/112 (2%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R  ++    I    +DA +SP+++V+Y+VE+AR  Q  D D
Sbjct: 2   INMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYSVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           KL M I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N    P
Sbjct: 62  KLVMDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNGVDP 113


>gi|183397277|gb|ACC62185.1| RpoA1 [Francisella sp. PQ1104]
 gi|183397283|gb|ACC62188.1| RpoA1 [Francisella sp. PQ1105]
          Length = 154

 Score = 93.1 bits (230), Expect = 6e-17,   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 +DA ++PIK+V++ +     
Sbjct: 1   PIATLTNEREFSLVATVSVGRNVGILSALPTELEKVGDIAVDADFNPIKRVAFEIFDNGA 60

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
                 + L + + T+G+I    +V  A +   +Q+ +F++   P    K    +     
Sbjct: 61  S-----ETLEVFVKTNGTIESLAAVTKALKYFCEQISVFVSLRVP-SNGKTGDALLDSNI 114

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM 292
           +P LLK +++LEL+VRS+NCLR ENI Y+GDL+Q +E+ +
Sbjct: 115 DPILLKPIDDLELTVRSSNCLRAENIKYLGDLVQYSESQL 154


>gi|166714680|gb|ABY88065.1| RpoA [Stenotrophomonas sp. ICB207]
          Length = 122

 Score = 92.7 bits (229), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 39/112 (34%), Positives = 62/112 (55%), Gaps = 3/112 (2%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R  ++    I    +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   LNMRLKIERGFGYQPAAARRRPDEETRTIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +       P
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAPKPATGGVDP 113


>gi|166714634|gb|ABY88042.1| RpoA [Stenotrophomonas nitritireducens]
          Length = 122

 Score = 92.3 bits (228), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 41/112 (36%), Positives = 63/112 (56%), Gaps = 3/112 (2%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L V +G GY PA   R  ++    I    +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKVERGFGYQPAASRRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N    P
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNGVDP 113


>gi|207108315|ref|ZP_03242477.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
           HPKX_438_CA4C1]
          Length = 130

 Score = 92.3 bits (228), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 35/121 (28%), Positives = 59/121 (48%), Gaps = 9/121 (7%)

Query: 12  PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
           P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8   PLIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPIGLKIEGVHHE 67

Query: 72  ISSIKGVHEDLTDIILNIKGINL---------KMSGDSHKRVTIFKRGPGVVTAGDIQTV 122
             S++GV ED++  I+N+K I               +    V    +GP  + A D+ + 
Sbjct: 68  FDSLRGVTEDVSLFIMNLKNIRFIAKALVGQDSSLENQSVVVDYSFKGPMELRARDLNSE 127

Query: 123 N 123
           +
Sbjct: 128 H 128


>gi|166714630|gb|ABY88040.1| RpoA [Stenotrophomonas maltophilia]
          Length = 107

 Score = 92.3 bits (228), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 38/105 (36%), Positives = 62/105 (59%), Gaps = 3/105 (2%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G+GY PA   R  ++    I    +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKIERGYGYQPAAARRCPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   + 
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKP 106


>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 = 92.3 bits (228), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 40/112 (35%), Positives = 63/112 (56%), Gaps = 3/112 (2%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R  ++    I    +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N    P
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRARGAAKPANNGVDP 113


>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 = 92.0 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 40/112 (35%), Positives = 63/112 (56%), Gaps = 3/112 (2%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R  ++    I    +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N    P
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNGVDP 113


>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 = 92.0 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 41/112 (36%), Positives = 63/112 (56%), Gaps = 3/112 (2%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L V +G GY PA   R  ++    I    +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKVERGFGYQPAAARRRPDEESRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N    P
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNGVDP 113


>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 = 92.0 bits (227), Expect = 1e-16,   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|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 = 92.0 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 53/264 (20%), Positives = 87/264 (32%), Gaps = 13/264 (4%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
             +E   L             PL    A  L   L   L++ +     T  +I      +
Sbjct: 11  QQVEADQLDS-GLYYGRFALSPLTAKQASLLKKGLPEALLTEILCLRFTHAKIQNECVNL 69

Query: 73  SSIKGVHEDLTDIILNIKGINLKMS-----GDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
            +I G+ E L +I+ N   I L        G       +  RGP    A DI+    I+V
Sbjct: 70  MNIVGIQESLDEILKNFGKIILTGKLEEFVGKGPFVAILDVRGPLNAMAVDIELPPGIKV 129

Query: 128 LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
                 I  +       +EL +             T        +ID    PI+KV  ++
Sbjct: 130 EIETQHIATITEPIPFVVELKIEL---VSSTSKGETGITDEEGFSIDPN-PPIQKVDTSI 185

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           +   + Q   +  L + I TD +I   +++A ASR +   L +    E  +    E  N 
Sbjct: 186 QCY-DYQGEPFQTLFLDIWTDRTIHPHEALAQASRKIFGLLSLVFQAEYFQYN--ELENG 242

Query: 248 KSLPFNPALLKKVEELELSVRSTN 271
                        E+ +    + N
Sbjct: 243 LRYGKFCLYPMTKEQFQWIQTALN 266


>gi|166714642|gb|ABY88046.1| RpoA [Stenotrophomonas sp. LMG 10992]
          Length = 122

 Score = 91.6 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 39/112 (34%), Positives = 64/112 (57%), Gaps = 3/112 (2%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M + + +G GY PA   R+ ++    I    +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMAVKIERGFGYQPAAARRSPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N    P
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFNHRDRGAAKPANNGVDP 113


>gi|166714636|gb|ABY88043.1| RpoA [Stenotrophomonas koreensis]
          Length = 122

 Score = 91.6 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 42/112 (37%), Positives = 63/112 (56%), Gaps = 3/112 (2%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L V +G GY PA   R  ++    I    +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   LNMRLKVERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           KL + IDT+G+I  E++V  A+ IL DQL +F +F    +   +  N    P
Sbjct: 62  KLVLDIDTNGTIDAEEAVRTAADILTDQLSVFGDFTHRDRGAAKPTNNGVDP 113


>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 = 91.2 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 29/133 (21%), Positives = 62/133 (46%), Gaps = 2/133 (1%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           + ++  Q           PL     HT G+ ++ V  S + G AI  ++I  + +E + I
Sbjct: 81  DVLIYPQNGRLYQKFYIGPLNITDGHTFGSLIKYVCQSQIYGYAIVGIKIHNM-NEDTKI 139

Query: 76  KGVHEDLTDIILNIKGINLKMSG-DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           +   EDL +I LN+  + +     +    + +  +GP ++ AG I   + ++V+N +  I
Sbjct: 140 ENTQEDLLEIALNLSDVCIYSKEINIETNIRLIFKGPLMLVAGMIPLPSHLKVVNKEQYI 199

Query: 135 CNLDVDAVVRMEL 147
           C +  +  + + +
Sbjct: 200 CTIKENGYIDISI 212


>gi|166714648|gb|ABY88049.1| RpoA [Stenotrophomonas sp. LMG 10887]
          Length = 122

 Score = 91.2 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 39/112 (34%), Positives = 62/112 (55%), Gaps = 3/112 (2%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY P    R  ++    I    +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKIERGFGYQPVAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N    P
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNGVDP 113


>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 = 91.2 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 41/112 (36%), Positives = 63/112 (56%), Gaps = 3/112 (2%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           V M L + +G GY PA   R  ++    I    +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   VNMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N    P
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNGVDP 113


>gi|166714664|gb|ABY88057.1| RpoA [Stenotrophomonas sp. LMG 10853]
          Length = 122

 Score = 91.2 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 39/112 (34%), Positives = 62/112 (55%), Gaps = 3/112 (2%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R  ++    I    +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           KL + I+T+G+I  E++V  A+ I  DQL +F +F    +   +  N    P
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADIPSDQLSVFGDFTHRDRGAAKPANNGVDP 113


>gi|166714646|gb|ABY88048.1| RpoA [Stenotrophomonas sp. LMG 10881]
          Length = 122

 Score = 90.8 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 41/113 (36%), Positives = 62/113 (54%), Gaps = 3/113 (2%)

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDY 198
            + M L V +G GY PA   R  ++    I    +DA +SP+++V+Y VE+AR  Q  D 
Sbjct: 1   DINMRLKVERGFGYQPAASRRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDL 60

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           DKL + I+T+G+I  E++V  A  IL DQL +F +F    +   +  N    P
Sbjct: 61  DKLVIDIETNGTIDAEEAVRTAGDILSDQLSVFGDFTHRDRGAAKPANNGVDP 113


>gi|166714678|gb|ABY88064.1| RpoA [Stenotrophomonas sp. ICB128]
          Length = 122

 Score = 90.4 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 39/112 (34%), Positives = 63/112 (56%), Gaps = 3/112 (2%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           ++M L + +G GY P    R  ++    I    +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   IKMRLKIERGFGYQPGAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N    P
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNGVDP 113


>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 = 90.4 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 30/67 (44%), Positives = 41/67 (61%)

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L
Sbjct: 4   MKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKL 63

Query: 311 GTMGLFL 317
             +GL L
Sbjct: 64  EELGLGL 70


>gi|166714632|gb|ABY88041.1| RpoA [Stenotrophomonas acidaminiphila]
          Length = 119

 Score = 90.0 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 41/110 (37%), Positives = 62/110 (56%), Gaps = 3/110 (2%)

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYDKL 201
           M L V +G GY PA   R  ++    I    +DA +SP+++V+Y VE+AR  Q  D DKL
Sbjct: 1   MRLKVERGFGYQPAASRRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLDKL 60

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
            + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N    P
Sbjct: 61  VIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNGVDP 110


>gi|150187027|emb|CAK30154.1| RNA polymerase alpha subunit [Streptococcus uberis]
          Length = 101

 Score = 90.0 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 41/100 (41%), Positives = 64/100 (64%)

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           I GV ED+  IILNIKG+ +K   +  K + +   GP  VTAGDI T +DIE++NPDH +
Sbjct: 2   IPGVREDVMQIILNIKGLAVKSYVEDEKMIELDVEGPAEVTAGDILTDSDIELVNPDHYL 61

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITID 174
             +     ++  +TV+K  GYVPA+ ++ ++ P+G + +D
Sbjct: 62  FTIAEGHSLKATMTVAKKRGYVPAEGNKKDDAPVGTLAVD 101


>gi|166714652|gb|ABY88051.1| RpoA [Stenotrophomonas sp. LMG 11004]
          Length = 98

 Score = 90.0 bits (222), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 37/97 (38%), Positives = 58/97 (59%), Gaps = 3/97 (3%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA      ++    I    +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|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 = 89.7 bits (221), Expect = 5e-16,   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 = 78.5 bits (192), Expect = 2e-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|119662857|emb|CAJ33221.1| RNA polymerase alpha subunit [Lactobacillus coryniformis subsp.
           coryniformis KCTC 3167]
          Length = 98

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Composition-based stats.
 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|224983719|pdb|3GFK|B Chain B, Crystal Structure Of Bacillus Subtilis SpxRNA POLYMERASE
           Alpha Subunit C-Terminal Domain Complex
          Length = 79

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 30/71 (42%), Positives = 42/71 (59%)

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+
Sbjct: 5   KEEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEV 64

Query: 307 KGVLGTMGLFL 317
           K  L  +GL L
Sbjct: 65  KAKLEELGLGL 75


>gi|166714666|gb|ABY88058.1| RpoA [Stenotrophomonas sp. LMG 10991]
          Length = 122

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 39/112 (34%), Positives = 62/112 (55%), Gaps = 3/112 (2%)

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 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N    P
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNGVDP 113


>gi|166714656|gb|ABY88053.1| RpoA [Stenotrophomonas sp. LMG 11114]
          Length = 122

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 40/112 (35%), Positives = 62/112 (55%), Gaps = 3/112 (2%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R  ++    I    +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           KL + I+T+G+I  ED+V   + IL DQL +F +F    +   +  N    P
Sbjct: 62  KLVIDIETNGTIDAEDAVRTGADILSDQLSVFGDFTHRDRGAAKPANNGVDP 113


>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 = 89.3 bits (220), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 30/68 (44%), Positives = 42/68 (61%)

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           +     L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K  
Sbjct: 1   MEKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAK 60

Query: 310 LGTMGLFL 317
           L  +GL L
Sbjct: 61  LEELGLGL 68


>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 = 89.3 bits (220), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 30/74 (40%), Positives = 43/74 (58%)

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
            +  +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL
Sbjct: 1   MVEKEEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSL 60

Query: 304 VEIKGVLGTMGLFL 317
            E+K  L  +GL L
Sbjct: 61  EEVKHKLEELGLGL 74


>gi|325119669|emb|CBZ55222.1| putative RNA polymerase Rpb3/Rpb11 dimerisation domain-containing
           protein [Neospora caninum Liverpool]
          Length = 980

 Score = 89.3 bits (220), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 46/310 (14%), Positives = 100/310 (32%), Gaps = 71/310 (22%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID--------GV 68
             V+ +       +   P+P     T+G+ ++        G A+ A+++         G 
Sbjct: 453 VTVIPETGHLYQKLYIGPIPVTTGWTMGSLIKAFAAQRCPGHAVVALKLHAPPQAAKKGA 512

Query: 69  LH------------------------------------EISSIKGVHEDLTDIILNIKGI 92
                                                  ++ +  V ED+ +I LN+KG+
Sbjct: 513 RKGRLKTREKRSEAHMHGAVASEGEGEPGGGDGEQTQPMVTKLPSVREDILEIALNLKGV 572

Query: 93  NLKMSGDSH-KRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
             +         + +   GP ++ AG I   + + V NP+H I  ++   V+ +E+ +  
Sbjct: 573 AFETLAPRESACIRVKVVGPQLLVAGMIGWPSFVRVANPEHFIAKVEEGGVLDLEIKLEW 632

Query: 152 GHGYVPA------------------KHHRTENDPIGLITIDALY---SPIKKVSYTVESA 190
           G G   A                  +    E D  G      ++   + ++   + +   
Sbjct: 633 GRGAWLADLHGLYREEEGVDTRCYKRRRIWEVDNRGFYPTSCVFGACTMMRLAVHKLMGT 692

Query: 191 REGQV-----LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDI 245
           R  Q         ++L + I TD S + ++ +A A + +   L           + K + 
Sbjct: 693 RFCQDRQVSTNPTEQLVVEIWTDASKSPKEVLAFALQDMLAWLLDLRRQLVQDVDWKTED 752

Query: 246 NVKSLPFNPA 255
              +  +   
Sbjct: 753 EDLNASWKHV 762


>gi|207092544|ref|ZP_03240331.1| DNA-directed RNA polymerase subunit alpha [Helicobacter pylori
          HPKX_438_AG0C1]
          Length = 126

 Score = 89.3 bits (220), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 30/83 (36%), Positives = 48/83 (57%)

Query: 12 PNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE 71
          P     I + ++E NR  +   P   G+A TL + +RR+L+ S  G A   ++I+GV HE
Sbjct: 8  PLIPSEIKVLEKEGNRVKISLAPFEFGYAVTLAHPIRRLLLLSSVGYAPIGLKIEGVHHE 67

Query: 72 ISSIKGVHEDLTDIILNIKGINL 94
            S++GV ED++  I+N+K I  
Sbjct: 68 FDSLRGVTEDVSLFIMNLKNIRF 90


>gi|166714650|gb|ABY88050.1| RpoA [Stenotrophomonas sp. LMG 10890]
          Length = 122

 Score = 88.9 bits (219), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 41/112 (36%), Positives = 63/112 (56%), Gaps = 3/112 (2%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           V M L + +G GY PA   R  ++    I    +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   VNMRLKIDRGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N    P
Sbjct: 62  KLVIDIETNGTIDAEEAVQTAADILSDQLSVFGDFTHRDRGAAKPANNGVDP 113


>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|166714692|gb|ABY88071.1| RpoA [Stenotrophomonas sp. LMG 11000]
          Length = 122

 Score = 88.1 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 39/112 (34%), Positives = 62/112 (55%), Gaps = 3/112 (2%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G  Y PA   R  ++    I    +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKIERGFAYQPAALRRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           KL + I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N    P
Sbjct: 62  KLVIDIETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNGVDP 113


>gi|166714706|gb|ABY88078.1| RpoA [Stenotrophomonas sp. LMG 11108]
          Length = 122

 Score = 88.1 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 40/112 (35%), Positives = 60/112 (53%), Gaps = 3/112 (2%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L   +G GY PA   R  ++    I    +DA +SP+++V+Y+VE+AR  Q  D D
Sbjct: 2   INMRLKSERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYSVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           KL M I+T+G+I  +++V  A  IL DQL  F +F    +      N    P
Sbjct: 62  KLVMDIETNGTIDAQEAVRTAPDILNDQLSAFGDFPHRHRGAPIPANNGMDP 113


>gi|255027531|ref|ZP_05299517.1| DNA-directed RNA polymerase subunit alpha [Listeria monocytogenes
          FSL J2-003]
          Length = 55

 Score = 88.1 bits (217), Expect = 2e-15,   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-KIETIEISDDAK-YGKFVVEPLERGYGTTLGNSLRRILLSSLPGAAVTS 55


>gi|166714660|gb|ABY88055.1| RpoA [Stenotrophomonas sp. LMG 957]
          Length = 97

 Score = 87.7 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 37/92 (40%), Positives = 56/92 (60%), Gaps = 3/92 (3%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R  ++    I    +DA +SP+++V+Y VE+AR  Q  D D
Sbjct: 2   INMRLKIERGFGYQPAAWRRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLD 61

Query: 200 KLSMTIDTDGSITGEDSVALASRILQDQLGMF 231
           KL + I+T+G+I  E++V  A  IL DQL +F
Sbjct: 62  KLVIDIETNGTIDAEEAVRTADDILSDQLSVF 93


>gi|166714708|gb|ABY88079.1| RpoA [Stenotrophomonas sp. LMG 10878]
          Length = 116

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 38/107 (35%), Positives = 60/107 (56%), Gaps = 3/107 (2%)

Query: 148 TVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYDKLSMT 204
            + +G GY PA   R  ++    I    +DA +SP+++V+Y VE+AR  Q  D DKL + 
Sbjct: 1   KIERGFGYQPAAARRRPDEETRAIGRLVLDASFSPVRRVAYAVEAARVEQRTDLDKLVID 60

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           I+T+G+I  E++V  A+ IL DQL +F +F    +   +  N    P
Sbjct: 61  IETNGTIDAEEAVRTAADILSDQLSVFGDFTHRDRGAAKPANNGVDP 107


>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 = 1e-14,   Method: Composition-based stats.
 Identities = 32/80 (40%), Positives = 45/80 (56%)

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+           L + V + ELSVRS NCL   +I  +GDL + +E D+L   NFG+ 
Sbjct: 249 DEETARNEARMKQLLDRPVTDFELSVRSRNCLHAMDIHTLGDLTRVSENDLLAGKNFGQT 308

Query: 302 SLVEIKGVLGTMGLFLGMNL 321
           SL EI+ +L + GL +G NL
Sbjct: 309 SLDEIREMLSSFGLHIGQNL 328



 Score = 78.5 bits (192), Expect = 1e-12,   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|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 = 85.0 bits (209), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 51/202 (25%), Positives = 100/202 (49%), 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  YIKGIKEDIIDIVLNIKNVIFKIKNNKTTF-FLKNYFLGPIYAYNIKTLNKNIKILNPSH 120

Query: 133 VICNLDVDAVVRMELTVSKGHGY-----VPAKHHRTENDPIGLITIDALYSPIKKVSYTV 187
           +I N  +   + + + V KG GY          +  +     +I +D  Y+P+KK  + +
Sbjct: 121 LIANAIIKTKLNILIKVKKGKGYINNNEKKKFKYYNKEKKKIVIYLDTNYTPVKKFFFKI 180

Query: 188 ESAREGQVLDYDKLSMTIDTDG 209
           +         Y+ L + I T+G
Sbjct: 181 KKKII--KKKYEDLKIYIKTNG 200


>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 = 84.3 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 31/86 (36%), Positives = 41/86 (47%)

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+   +       L   + + ELS RS NCL    I  + DL + +E  +L   NFG  
Sbjct: 271 DEEAARRDKQLEQILSIPMSDFELSARSRNCLERAGIDRLEDLTKMSEEQLLAGKNFGET 330

Query: 302 SLVEIKGVLGTMGLFLGMNLPDWPPE 327
           SL EIK +L   GL LG N+    PE
Sbjct: 331 SLKEIKAILEMHGLKLGQNVHKKQPE 356



 Score = 83.5 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 27/97 (27%), Positives = 44/97 (45%)

Query: 221 SRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVY 280
           + +    L +  N  + + E        +          V +LELSVR+  CL    I  
Sbjct: 337 AILEMHGLKLGQNVHKKQPEPLYKPEELTPEERMIHEMTVSDLELSVRARKCLARLGINT 396

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           +G+L+ R+  ++L + NFG  SL EI+  LG   + L
Sbjct: 397 VGELVSRSADELLSVRNFGVTSLNEIREKLGEKNIRL 433


>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 = 84.3 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 31/77 (40%), Positives = 42/77 (54%)

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+   ++      L   V   ELSVRS NCL+   I  +GDL + +E ++L   NFG  
Sbjct: 334 DEEAQRRNDRLAQTLNMPVANFELSVRSRNCLQKMGIETIGDLTRHSEQELLSSKNFGET 393

Query: 302 SLVEIKGVLGTMGLFLG 318
           SLVEI+ +L   GL LG
Sbjct: 394 SLVEIREMLSQKGLSLG 410



 Score = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 28/82 (34%), Positives = 43/82 (52%)

Query: 235 EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           E+   +   D +  S      L + + +L LSVR+  C+    I  +G+LI++T  DML 
Sbjct: 415 EKKSNDPPVDTSHMSPDEQALLERPIADLNLSVRARKCMTRLQINSIGELIRKTGDDMLE 474

Query: 295 MANFGRKSLVEIKGVLGTMGLF 316
             NFG  SL E++  LG +GL 
Sbjct: 475 CKNFGVTSLNEVREKLGDLGLK 496


>gi|91203075|emb|CAJ72714.1| hypothetical protein kustd1969 [Candidatus Kuenenia
           stuttgartiensis]
          Length = 380

 Score = 82.7 bits (203), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 40/169 (23%), Positives = 62/169 (36%), Gaps = 11/169 (6%)

Query: 163 TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASR 222
            ++  I          P  K +Y            YD      +   ++   + +   + 
Sbjct: 209 EDDLAIEYYERCTNLRPAHKNAYMNLGILYEDNGKYDDAIFCYE---AVLDVEPMHERAS 265

Query: 223 ILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMG 282
                               E+ + K       L   + + ELSVRS NCL   NI  + 
Sbjct: 266 FCLKSAKASSEM-----VFDEEASKKQGHEGDVLNIPISDFELSVRSRNCLEKMNIHTLR 320

Query: 283 DLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           DL + +E D+L   NFG  SL EIK +L   GL LG +   +   +IE+
Sbjct: 321 DLTRISEPDLLTFKNFGETSLNEIKAILIQKGLQLGQS---YDGHNIEK 366


>gi|168704678|ref|ZP_02736955.1| probable DNA-directed RNA polymerase alpha chain [Gemmata
           obscuriglobus UQM 2246]
          Length = 458

 Score = 81.9 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 30/83 (36%), Positives = 43/83 (51%)

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
               +    +      L   + + ELSVRS NCL+  NI  +GDL + TE  +L   NFG
Sbjct: 289 HYSPEDEQLTQANRVVLEIPITDFELSVRSRNCLKRMNIRTLGDLTRVTEPQLLASKNFG 348

Query: 300 RKSLVEIKGVLGTMGLFLGMNLP 322
             SL EI+ ++ T GL +G +L 
Sbjct: 349 ETSLDEIRAIMVTKGLRIGQSLD 371



 Score = 74.2 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 38/74 (51%)

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
                S      L K V +L LSVR+  C+   NI  +G+L+QRT  ++L   NFG+ SL
Sbjct: 382 PQQNLSPEEQATLGKPVSDLNLSVRARKCMNRLNIGTLGELVQRTADELLEAKNFGQTSL 441

Query: 304 VEIKGVLGTMGLFL 317
            E++  L    L L
Sbjct: 442 TEVRERLQQFNLKL 455


>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 = 81.6 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 32/77 (41%), Positives = 43/77 (55%)

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+   K       L   V + ELSVRS NCL+   I  +GDL + +E ++L   NFG  
Sbjct: 289 DEEAQKKRDRIAQVLSIPVTDFELSVRSRNCLQKMGIQTLGDLSRCSEQELLSSKNFGET 348

Query: 302 SLVEIKGVLGTMGLFLG 318
           SLVEI+ +L + GL LG
Sbjct: 349 SLVEIREMLNSKGLELG 365



 Score = 73.5 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 25/83 (30%), Positives = 42/83 (50%)

Query: 235 EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           ++ + E   ++   S      L + + EL LSVR+  C+    I  +G+L++RT  ++L 
Sbjct: 370 DKGQPEPTIEVAGLSPDEQALLDRPISELNLSVRARKCMVRLGISTIGELVRRTGDELLE 429

Query: 295 MANFGRKSLVEIKGVLGTMGLFL 317
             NFG  SL E++  L    L L
Sbjct: 430 CKNFGVTSLNEVREKLTASNLKL 452


>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 = 81.2 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 30/100 (30%), Positives = 52/100 (52%), Gaps = 4/100 (4%)

Query: 226 DQLGMFINFEEPKKEVKEDINVKSLPFNPAL----LKKVEELELSVRSTNCLRGENIVYM 281
           + +   +  ++ +   +   +         +     + V + ELSVRS NCL   +I  +
Sbjct: 255 NHVRARMYMKDIEATQEMYYDDDMARNEARMAQLLSRPVTDFELSVRSRNCLASMDIHTL 314

Query: 282 GDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
           GDL + +E+D+L+  NFG  SLVEI+ ++   GL +G NL
Sbjct: 315 GDLTRVSESDLLQGKNFGETSLVEIRDLMQQHGLKVGQNL 354



 Score = 72.7 bits (177), Expect = 8e-11,   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|110004169|emb|CAK98507.1| hypothetical protein with alpha rna polymerase domain pd001179
           [Spiroplasma citri]
          Length = 111

 Score = 79.6 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 23/83 (27%), Positives = 43/83 (51%)

Query: 235 EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
            E ++++   + +     N  L   +++LE++ R+  CL    I  + DL+ +TE ++  
Sbjct: 27  NEIQEQITIWLEMDETERNQLLNHSIDDLEITQRTQICLEKAKIYRLSDLVSKTENEIKN 86

Query: 295 MANFGRKSLVEIKGVLGTMGLFL 317
           + N G KSL EIK  +  +GL  
Sbjct: 87  IKNLGEKSLTEIKEKMHELGLHF 109


>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 = 79.3 bits (194), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 30/77 (38%), Positives = 44/77 (57%)

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
            E+   ++      L   V + ELSVRS NCL+   +  +GDL + +E ++L   NFG  
Sbjct: 274 DEEAQRRNDRLAQVLSIPVTDFELSVRSRNCLQKMGVRTLGDLTRTSEQELLASKNFGET 333

Query: 302 SLVEIKGVLGTMGLFLG 318
           SLVEI+ +L + GL LG
Sbjct: 334 SLVEIRDMLHSKGLELG 350



 Score = 70.0 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 27/83 (32%), Positives = 44/83 (53%)

Query: 235 EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           E+   E   D+   S      L + + EL LSVR+  C+    +  +G+L+++T  D+L 
Sbjct: 355 EKAVAEPVLDLASMSPDEQALLERPISELNLSVRARKCMARLGLTLIGELVRKTGDDLLE 414

Query: 295 MANFGRKSLVEIKGVLGTMGLFL 317
             NFG  SL E++  L T+G+ L
Sbjct: 415 CKNFGVTSLNEVREKLTTLGIKL 437


>gi|166714710|gb|ABY88080.1| RpoA [Stenotrophomonas sp. LMG 10851]
 gi|166714712|gb|ABY88081.1| RpoA [Stenotrophomonas sp. LMG 10877]
          Length = 93

 Score = 78.9 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 31/81 (38%), Positives = 50/81 (61%)

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           + +DA +SP+++V+Y VE+AR  Q  D DKL + I+T+G+I  E++V  A+ IL DQL +
Sbjct: 4   LVLDASFSPVRRVAYAVEAARVEQRTDLDKLVIDIETNGTIDAEEAVRTAADILSDQLSV 63

Query: 231 FINFEEPKKEVKEDINVKSLP 251
           F +F    +   +  N    P
Sbjct: 64  FGDFTHRDRGAAKPANNGVDP 84


>gi|291533600|emb|CBL06713.1| DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Megamonas
           hypermegale ART12/1]
          Length = 85

 Score = 78.9 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 43/74 (58%)

Query: 235 EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           E+   +       +    +  +   +E+L+LSVRS NCL+   I  + DL+Q++E DM++
Sbjct: 6   EDIPADEGIFNVPEEDNTSKVMEMTIEDLDLSVRSYNCLKRAEINTVADLMQKSEDDMIK 65

Query: 295 MANFGRKSLVEIKG 308
           + N GRKSL E+K 
Sbjct: 66  VRNLGRKSLEEVKK 79


>gi|166714662|gb|ABY88056.1| RpoA [Stenotrophomonas sp. LMG 978]
          Length = 81

 Score = 75.0 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 29/79 (36%), Positives = 47/79 (59%), Gaps = 3/79 (3%)

Query: 143 VRMELTVSKGHGYVPAKHHRTENDPIGLI---TIDALYSPIKKVSYTVESAREGQVLDYD 199
           + M L + +G GY PA   R  ++    I    +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|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 = 73.5 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 43/250 (17%), Positives = 88/250 (35%), Gaps = 53/250 (21%)

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 264
           + L    EL 
Sbjct: 241 SPLMLNHELN 250


>gi|213580698|ref|ZP_03362524.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
          subsp. enterica serovar Typhi str. E98-0664]
          Length = 46

 Score = 73.5 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 3/49 (6%)

Query: 2  IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRV 50
          +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+
Sbjct: 1  MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRI 46


>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 = 72.3 bits (176), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 30/159 (18%), Positives = 63/159 (39%), Gaps = 4/159 (2%)

Query: 107 FKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVP----AKHHR 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|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 = 71.5 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 35/182 (19%), Positives = 73/182 (40%), Gaps = 41/182 (22%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGV-------------LHEISSIKGVHEDLTDIILNI 89
             N LRR+L+    G     ++I G              ++E S  + ++E +  + LNI
Sbjct: 35  FANQLRRILLGKSEGLRF--LKISGFIANKNSKFSVYQKINEFSEFEEINESVFQLFLNI 92

Query: 90  KGINLKMSG---DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRME 146
           K I+L       +     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------------------IGSFFTPVKRVNYIIE----ENKLSFSRVVLELE 189

Query: 207 TD 208
           TD
Sbjct: 190 TD 191


>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 = 71.2 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 9/71 (12%)

Query: 21  GQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------VLHE 71
                +        L +G   T+ NALRRVL+  + G  IT V+ +           LHE
Sbjct: 36  ENSSLHYGKFYLSGLKKGQGITVANALRRVLLYDIMGLGITKVKFNSKNNENLSSQKLHE 95

Query: 72  ISSIKGVHEDL 82
            S+I G+ E +
Sbjct: 96  FSTISGIRESI 106



 Score = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 28/151 (18%), Positives = 52/151 (34%), Gaps = 19/151 (12%)

Query: 95  KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN----------LDVDAVVR 144
           K   +      +  +          Q  N  +++NP+  +            L       
Sbjct: 174 KNKNNQSSVFVLRGKHLISADQRTNQNPNFAQLINPEQYLATILPIQKTATGLSKFPEFE 233

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREG------QVLDY 198
           +E  +  G G +        N+    +     + P+KKV+YTVE  +        +    
Sbjct: 234 IEYKI--GKGNLFENLDLQSNNE-EFLLNSGPFFPVKKVNYTVEDIKNSTNNFLWERGFS 290

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           + +   I TDGS+  E +++ A  IL D   
Sbjct: 291 ECVFFEIWTDGSLHPEKALSQAFDILLDFFQ 321


>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 = 71.2 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 41/217 (18%), Positives = 77/217 (35%), Gaps = 10/217 (4%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED 81
            ++         PL    +  L   L   L++ +     T  +I      + +I G+ E 
Sbjct: 28  HKDFAYGRFALSPLTAKESRLLKKGLFEALLTEILCLRFTHAKIQNECVNLMNIVGIQES 87

Query: 82  LTDIILNIKGINLKMS-----GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN 136
           L +I+ N   I L        G       +  RGP    A DI+    I+V      I  
Sbjct: 88  LDEILKNFGKIILTGKLEEFVGKGPFVAILDVRGPLNAMAVDIELPPGIKVEIETQHIAT 147

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           +       +EL +             T        +ID    PI+KV+ +++    G   
Sbjct: 148 ITEPIPFVVELRIEL---VSSTSKGETGITDEEGFSIDPN-PPIRKVNSSIQGYEYGGQT 203

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
            +++LS+ + T   I   +++ L S  + +   + + 
Sbjct: 204 -FERLSIEMLTSLPIIPNEALLLGSMKIMNLFQIVLQ 239



 Score = 50.4 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 15/86 (17%), Positives = 35/86 (40%), Gaps = 5/86 (5%)

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           G         E D      ID+ ++P++ +   +ES  E     + +L + I T      
Sbjct: 283 GRKHQGPLTDEEDDS----IDSNFTPVQNLDCRIESYEEEGQT-FQRLFLEIWTKSPTEP 337

Query: 214 EDSVALASRILQDQLGMFINFEEPKK 239
           ++++  AS  + +   +F+   +  +
Sbjct: 338 QEALWEASAKILELFSLFLQTSKENE 363


>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 = 68.1 bits (165), Expect = 2e-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|239933877|ref|ZP_04690830.1| DNA-directed RNA polymerase subunit alpha [Streptomyces ghanaensis
           ATCC 14672]
          Length = 88

 Score = 67.3 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 24/88 (27%), Positives = 46/88 (52%)

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
             ++     IG I +D++YSP+ KV+Y VE+ R  Q  D+DKL + ++T  ++   D++A
Sbjct: 1   MQNKQVGQEIGRIPVDSIYSPVLKVTYKVEATRVEQRTDFDKLIVDVETKQAMRPRDAMA 60

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDIN 246
            A + L +  G+        + +    +
Sbjct: 61  SAGKTLVELFGLARELNIGAEGIDMGPS 88


>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 = 66.9 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 23/59 (38%), Positives = 35/59 (59%)

Query: 257 LKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
                E+ L+VR+TNCL    I  + DL+  T AD+L ++NFG K+L E+   L ++G 
Sbjct: 21  EMSTAEIGLTVRTTNCLEERGIFTVRDLLNCTRADLLSISNFGEKTLDEVYSSLESIGF 79


>gi|221484912|gb|EEE23202.1| DNA-directed RNA polymerase alpha chain, putative [Toxoplasma
           gondii GT1]
          Length = 837

 Score = 65.8 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 23/52 (44%), Positives = 32/52 (61%), Gaps = 1/52 (1%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED-LTDIILNIKGINLK 95
           NALRR  +S L   AI+AV+I+G  HE  S+ G+ ED + DI  N+  I  +
Sbjct: 74  NALRRTSLSRLESLAISAVKIEGAKHEFYSLPGIREDIVDDIFNNLGKIVFR 125



 Score = 48.8 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 23/109 (21%), Positives = 42/109 (38%), Gaps = 4/109 (3%)

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
           +     R  +  RGP V  AG IQ    +EV+N +  +  ++    V M+  + +   YV
Sbjct: 277 NFTHPLRAKLRVRGPLVAVAGHIQLPEGVEVVNKNQYLFTVNAGYYVNMDFKIERIREYV 336

Query: 157 PA----KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
                      + D  G +      +P+   +Y  E   E     +D++
Sbjct: 337 MPEFGYDSLERDRDKEGFMYFTNYVAPVPIFAYAAERRGEAVHTKWDEV 385


>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 = 65.8 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 23/52 (44%), Positives = 32/52 (61%), Gaps = 1/52 (1%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED-LTDIILNIKGINLK 95
           NALRR  +S L   AI+AV+I+G  HE  S+ G+ ED + DI  N+  I  +
Sbjct: 74  NALRRTSLSRLESLAISAVKIEGAKHEFYSLPGIREDIVDDIFNNLGKIVFR 125



 Score = 48.8 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 23/109 (21%), Positives = 42/109 (38%), Gaps = 4/109 (3%)

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
           +     R  +  RGP V  AG IQ    +EV+N +  +  ++    V M+  + +   YV
Sbjct: 277 NFTHPLRAKLRVRGPLVAVAGHIQLPEGVEVVNKNQYLFTVNAGYYVNMDFKIERIREYV 336

Query: 157 PA----KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
                      + D  G +      +P+   +Y  E   E     +D++
Sbjct: 337 MPEFGYDSLERDRDKEGFMYFTNYVAPVPIFAYAAERRGEAVHTKWDEV 385


>gi|295106723|emb|CBL04266.1| DNA-directed RNA polymerase subunit beta' [Gordonibacter pamelaeae
            7-10-1-b]
          Length = 1473

 Score = 65.4 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 19/56 (33%), Positives = 29/56 (51%)

Query: 261  EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
            ++L +S R  N      I  + DL+  TE D+LR+   G K++ E+K  L   GL 
Sbjct: 1322 DDLGVSQRWANKFSEAGIETVADLVGHTEEDLLRIEGIGVKAIEELKEGLAERGLS 1377


>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 = 65.0 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 20/56 (35%), Positives = 30/56 (53%)

Query: 261  EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
            ++L +S R  N      I  +GDL+  TE ++LR+   G K+L E+K  L   GL 
Sbjct: 1311 DDLGVSQRWANKFSEAGIETVGDLVGYTEDELLRIEGIGAKALEELKAGLQDHGLE 1366


>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 = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 19/56 (33%), Positives = 29/56 (51%)

Query: 261  EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
            ++L +S R  N      I  +GDL+  TE ++LR+   G K+L E+K  L    L 
Sbjct: 1310 DDLGVSQRWANKFSEAGIDTVGDLVGYTEDELLRIEGIGAKALEELKAGLEEHELS 1365


>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 = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 40/219 (18%), Positives = 72/219 (32%), Gaps = 12/219 (5%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI--SSIKGVH 79
             +         PL    +  L   LR  L++ +     T  +I      +   +I G+ 
Sbjct: 19  HNDLLYGRFALSPLTAKESRLLKKGLREALLTGILCLRFTHAKIQNACKNLNLMNIVGIQ 78

Query: 80  EDLTDIILNIKGINLKMS-----GDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVI 134
           E L +I+ N   I L        G       +  RGP    A DI+    I+V      I
Sbjct: 79  ESLDEILKNFGKIILTGKLEEFVGKGPFVAILDVRGPLNAMAVDIELPPGIKVEIETQHI 138

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQ 194
             +       +EL +             T        +ID    PI+KV+ +++    G 
Sbjct: 139 ATITEPIPFVVELRIEL---VSSTSKGETGITDEEGFSIDPN-PPIQKVNSSIQGYEYGG 194

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
              +  L + I +        ++ L S  + +   + + 
Sbjct: 195 QT-FQTLFIEILSTSPTVPNKALLLVSMKIMNLFQIVLQ 232



 Score = 50.4 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 20/115 (17%), Positives = 43/115 (37%), Gaps = 10/115 (8%)

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           G         E D      ID+ ++P++ +   +ES  E     + +L + I T      
Sbjct: 276 GRKHQGPLTDEEDDS----IDSNFTPVQNLDCRIESYEEEGQT-FQRLFLEIWTKSPTEP 330

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE-----VKEDINVKSLPFNPALLKKVEEL 263
           ++++  AS  + +   +F+   +  ++     +K+    K        L   EE 
Sbjct: 331 QEALWEASAKILELFSLFLQTSKENEKDLKQIIKDWTENKRKHQEVLRLLDSEES 385


>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 = 65.0 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 21/58 (36%), Positives = 33/58 (56%)

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
            ++ + LS RSTN L  E I  +GD++  TE  +L++ N G+KS+ EI   +    L 
Sbjct: 7   SIDTIGLSARSTNALHREEIHTVGDMLGFTEESLLQVKNLGKKSVEEIVEKIKKYKLN 64


>gi|297745992|emb|CBI16048.3| unnamed protein product [Vitis vinifera]
          Length = 110

 Score = 64.2 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 20/54 (37%), Gaps = 4/54 (7%)

Query: 13 NNIEYIVLGQEEEN----RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
            +++  +     N        I  P   G A T+G  +RR L   + G  IT 
Sbjct: 11 RTLQWKCVESRVNNKRLCYGRFILSPFIIGQADTIGIVMRRTLFGEIEGTCITR 64


>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 = 64.2 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 33/192 (17%), Positives = 72/192 (37%), Gaps = 36/192 (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  GINLKMSGDSHK--RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
            +  K      K     +   G G + + DI   +++ +L    +   +     + + L 
Sbjct: 95  NLRFKEKFSLSKRYYARLLTYGSGEINSKDIIVPSNLSLLENKSLFTLITDSLCIDVILQ 154

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           +   +G                    + ++ +++V+Y +E++  G  ++Y+KL + I T 
Sbjct: 155 ILSKNG--------------------SPFNGVERVNYILENSNSGN-INYNKLYLDISTR 193

Query: 209 GSITGEDSVALA 220
             ++  +++   
Sbjct: 194 YFLSPMEALFEC 205


>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 = 63.8 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 41/235 (17%), Positives = 80/235 (34%), Gaps = 31/235 (13%)

Query: 21  GQEEENRT-LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVH 79
            +   N     +  PLP G A +LG  +R VL+      A+  ++ +   +   +  G  
Sbjct: 11  NEYNNNYAASFLIGPLPEGIAQSLGFNIRSVLLKEFPYFAVKNIRFNPENNNYKTHIGTK 70

Query: 80  EDLTDIILNIKGINLKMSGDSHKRVTIFKR----------------------GPGVVTAG 117
           E +  II  I GI+   S D +K + ++K                       G G++ A 
Sbjct: 71  ESIETIINTILGIDFNYSFDFYKAMGLYKSKPKALFQENLSKAKFLCSAKQVGEGILYAK 130

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
           D+     I+   P  +I ++     +     +    G         +   I    I  + 
Sbjct: 131 DLMLPVGIKCTTPYKIIAHVTKQNFLGFTFELGFLFGLNNNIKFENKLYSIKTYPIQNIN 190

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA-LASRILQDQLGMF 231
             I     +         L+ + + ++  T  S+   D +  L+  +L   L + 
Sbjct: 191 IEIINSKKSF-------NLNSESIILSFTTKSSLQPIDVIKILSYLLLNKHLILI 238


>gi|166714640|gb|ABY88045.1| RpoA [Stenotrophomonas rhizophila]
          Length = 79

 Score = 63.8 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 27/70 (38%), Positives = 41/70 (58%)

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 KEDINVKSLP 251
            +  N    P
Sbjct: 61  AKPANNGVDP 70


>gi|325120592|emb|CBZ56146.1| putative DNA-directed RNA polymerase alpha chain [Neospora caninum
           Liverpool]
          Length = 941

 Score = 63.8 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 21/52 (40%), Positives = 31/52 (59%), Gaps = 1/52 (1%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED-LTDIILNIKGINLK 95
           NALRR  +S +   A+ AV+I+G  HE  S+ G+ ED + DI  N+  I  +
Sbjct: 183 NALRRTSLSRIESLAVAAVKIEGAKHEFYSLPGIREDIVDDIFNNLGKIVFR 234



 Score = 50.4 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 23/109 (21%), Positives = 43/109 (39%), Gaps = 4/109 (3%)

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
           +     R  +  RGP V  AG IQ    +EV+N +  +  ++    V M+  + +   YV
Sbjct: 384 NFTHPLRAKLRVRGPLVAVAGHIQLPEGVEVVNKNQYLFTVNSGYYVNMDFKIERIREYV 443

Query: 157 PAKHHRT----ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
             +        + D  G +      +P+   +Y  E   E     +D++
Sbjct: 444 MPEFGYDSLERDRDEEGFMYFTNHVAPVPIFAYAAERRGEAVHTKWDEV 492


>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 = 63.8 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 31/86 (36%), Positives = 49/86 (56%)

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           GYVP++ ++      G I +D++++PIK V Y +++    +  +Y+ L + I TDGSI  
Sbjct: 2   GYVPSEENKENLIGSGSIPMDSIFTPIKNVKYKIDNCSINKNSNYESLLLEIKTDGSINP 61

Query: 214 EDSVALASRILQDQLGMFINFEEPKK 239
            D++  AS IL   L MFI     KK
Sbjct: 62  RDALTNASNILIQHLKMFIYETRKKK 87


>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 = 63.8 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 19/55 (34%), Positives = 29/55 (52%)

Query: 261  EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
            ++L +S R  N      I  +GDLI  +E D+LR+   G K++ E+K  L    L
Sbjct: 1320 DDLGVSQRWANKFSEAGIETVGDLIGYSEEDLLRIEGIGAKAIEELKEGLEKHDL 1374


>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 = 63.8 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 24/90 (26%), Positives = 42/90 (46%)

Query: 226  DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLI 285
             QL      E    +     N +++  + A L   ++L +S R TN      I  +GDL+
Sbjct: 1308 QQLDWAGFDEFGVGDGSFTRNGRTISADDAKLYLFDDLGVSQRWTNKFSEVGIETVGDLV 1367

Query: 286  QRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
             ++E D+LR+   G K++ E++  L    L
Sbjct: 1368 GKSEEDLLRIDGIGAKAIEELRDGLEAHNL 1397


>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 = 63.5 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 30/131 (22%), Positives = 56/131 (42%), Gaps = 12/131 (9%)

Query: 211 ITGEDSVALASRILQDQLGMFINFEE---PKKEVKEDINVKSLPFNPALLKKVEELELSV 267
           IT    +A AS      +  ++   +    +   +  + +  L  +  +   +E L+LS 
Sbjct: 110 ITTVQDLASASTFYIRAILGYVGRSQALVKQYTEEYLMKLLRLSKSHEVDNSLENLQLSP 169

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
           R    LR   I     L + T+ ++L++   G+ +L EIK V       LG +  +    
Sbjct: 170 RIRGILRRAGIFTADQLYRLTDEELLKLKGIGKAALEEIKAV------KLG-DADN--KR 220

Query: 328 SIEELAKKYED 338
           SIEE  ++ +D
Sbjct: 221 SIEEEKQRLDD 231


>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 = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 261  EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
            ++L +S R TN      I  +GDLI +TE D+LR+   G K++ E++  L    L L + 
Sbjct: 1336 DDLGVSQRWTNKFSEVGIETVGDLIGKTEEDLLRIDGIGSKAIEELRQGLDARNL-LYIL 1394

Query: 321  LPDWPPESIEELAKKY 336
             PD      E+L++  
Sbjct: 1395 EPDEDEADAEDLSQLL 1410


>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 = 63.5 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 19/65 (29%), Positives = 31/65 (47%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
            E  EL+      L    +  +GDL+Q +   ++R+  F   ++  I+  L   GL +GM
Sbjct: 146 SEIYELTDPVIALLVAAGVHRLGDLVQMSPTALMRIRGFDVLAMERIEEGLTIFGLKVGM 205

Query: 320 NLPDW 324
            LP W
Sbjct: 206 ALPGW 210


>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 = 63.1 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 261  EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
            ++L +S R TN      I  +GDLI +TE D+LR+   G K++ E++  L    L L + 
Sbjct: 1334 DDLGVSQRWTNKFSEVGIETVGDLIGKTEEDLLRIDGIGAKAIEELRDGLEARNL-LYIL 1392

Query: 321  LPDWPPESIEELAKKY 336
             P+      E+L++  
Sbjct: 1393 EPEEDEADSEDLSQLL 1408


>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 = 63.1 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 30/102 (29%), Positives = 48/102 (47%), Gaps = 1/102 (0%)

Query: 235  EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
            E+         N +SL    A L   ++L +S R TN      I  +GDLI +TE ++LR
Sbjct: 1311 EDYSNNGVYSKNGRSLSTEDAKLYLFDDLGVSQRWTNKFSEVGIETVGDLIGKTEDELLR 1370

Query: 295  MANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKY 336
            +   G K++ E++  L    L L +  PD      E+L++  
Sbjct: 1371 IDGIGAKAIEELREGLEARNL-LYILEPDEDEADSEDLSQLL 1411


>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 = 62.7 bits (151), Expect = 8e-08,   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|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 = 62.7 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 18/55 (32%), Positives = 31/55 (56%)

Query: 261  EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
            ++L +S R TN      I  +GDL+ ++E D+LR+   G K++ E++  L    L
Sbjct: 1346 DDLGVSQRWTNKFSEVGIETVGDLVGKSEEDLLRIDGIGAKAIEELRDGLEEHNL 1400


>gi|166714718|gb|ABY88084.1| RpoA [Stenotrophomonas sp. LMG 11002]
          Length = 65

 Score = 62.7 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 27/61 (44%), Positives = 43/61 (70%)

Query: 171 ITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230
           + +DA +SP+++V+Y VE+A   Q  D DKL + I+T+G+I  E++V  A+ IL DQL +
Sbjct: 3   LVLDASFSPVRRVAYAVEAAAVEQRTDLDKLVIDIETNGTIDAEEAVRTAADILSDQLSV 62

Query: 231 F 231
           F
Sbjct: 63  F 63


>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 = 62.3 bits (150), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 24/90 (26%), Positives = 40/90 (44%)

Query: 226  DQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLI 285
             QL      E    +     N  ++    A L   ++L +S R TN      I  +GDL+
Sbjct: 1189 QQLDWAGYDEFGGADGSFTRNGHTISAEKARLYLFDDLGVSQRWTNKFSEVGIETVGDLV 1248

Query: 286  QRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
             ++E D+LR+   G K++ E++  L    L
Sbjct: 1249 GKSEEDLLRIDGIGAKAIEELRDGLEAHDL 1278


>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 = 62.3 bits (150), Expect = 1e-07,   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|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 = 62.3 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 261  EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
            ++L +S R TN      I  +GDLI +TE D+LR+   G K++ E++  L    L L + 
Sbjct: 1335 DDLGVSQRWTNKFSEVGIETVGDLIGKTEDDLLRIDGIGAKAIEELRDGLEARNL-LYIL 1393

Query: 321  LPDWPPESIEELAKKY 336
             PD      E+L++  
Sbjct: 1394 EPDDDEADSEDLSQLL 1409


>gi|4140424|gb|AAD04047.1| DNA-directed RNA polymerase [Chlamydia trachomatis]
          Length = 62

 Score = 62.3 bits (150), Expect = 1e-07,   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|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 = 61.9 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 28/91 (30%), Positives = 45/91 (49%), Gaps = 1/91 (1%)

Query: 246  NVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305
            N + L    A L   ++L +S R TN      I  +GDLI +TE ++LR+   G K++ E
Sbjct: 1321 NGRCLSSEDAKLYLFDDLGVSQRWTNKFSEVGIETVGDLIGKTEDELLRIDGIGAKAIEE 1380

Query: 306  IKGVLGTMGLFLGMNLPDWPPESIEELAKKY 336
            ++  L    L L +  PD      E+L++  
Sbjct: 1381 LREGLEARNL-LYLLEPDEDEADSEDLSQLL 1410


>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 = 61.5 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 43/180 (23%), Positives = 67/180 (37%), Gaps = 41/180 (22%)

Query: 44  GNALRRVLMSSLRGAAI---------TAVQID--GVLHEISSIKGVHEDLTDIILNIKGI 92
           GN LRR L+  L G            +  +I     ++E S I+ V+  L  +  N + +
Sbjct: 38  GNLLRRTLLKDLEGLRFGNSSIFISRSFSKIPYYHRVNEYSDIEQVNPSLLQVFSNFRNL 97

Query: 93  NL---KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN-LDVDAVVRMELT 148
           ++   K          I         + DI   N++ V+NPD  +   L     +R+   
Sbjct: 98  HIFSSKPFYRKTSYSMIKVLTSRSYFSKDILLPNNLYVVNPDVQLFEFLSKRYKLRIISE 157

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
           + KG G                      +SPIKKV+Y VE       + Y  L + I TD
Sbjct: 158 ICKGSGK--------------------SFSPIKKVNYVVE------GIPYASLLLEIYTD 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 = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 28/109 (25%), Positives = 51/109 (46%), Gaps = 3/109 (2%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEI--SSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           NA+RR L+S      +  V+I+   +        G  +   D+I  ++ +++++   S  
Sbjct: 36  NAVRRTLLSFSTQLKLVGVKINSSRNTYPWCMFSGCRDSYLDLISRLQRLSVRIRETSLC 95

Query: 103 RV-TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
            V  +   GP VV AG + T   +E+L P+  + +L     + MEL  S
Sbjct: 96  YVLQLKSSGPLVVVAGHMITPPTLEILTPNKYLTSLAAKCALDMELIFS 144


>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 = 61.1 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 30/151 (19%), Positives = 59/151 (39%), Gaps = 9/151 (5%)

Query: 15  IEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEIS 73
           IE  +L ++E++    +     +G   +  NALRR ++  +   A+  V+  +       
Sbjct: 4   IEVQILEKKEDS-IKFVL----KGVHVSFANALRRTILGEVPTFAVDEVEFYENDSALFD 58

Query: 74  SIKGVHEDLTDIILNIKGINLKM--SGDSHKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNP 130
            I      +  +   +    L      D    +++   GPG+V +GD++    D++ +NP
Sbjct: 59  EIIAHRLAMIPLTTPVDRFELDALELDDYTVTLSLEAEGPGIVYSGDLKSDDPDVKPVNP 118

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           +  I  L     +        G G   AK  
Sbjct: 119 NIPIVKLAEGQRLVFNAYAKLGRGKDHAKWQ 149


>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 = 61.1 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 18/56 (32%), Positives = 28/56 (50%)

Query: 261  EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
            ++L +S R  N      I  + DL+  TE D+LR+   G K++ E+K  L    L 
Sbjct: 1322 DDLGVSQRWANKFSEAGIETVADLVGHTEEDLLRIEGIGVKAIEELKEGLEAHDLT 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 = 61.1 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 18/56 (32%), Positives = 28/56 (50%)

Query: 261  EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
            ++L +S R  N      I  + DL+  TE D+LR+   G K++ E+K  L    L 
Sbjct: 1322 DDLGVSQRWANKFSEAGIETVADLVGHTEEDLLRIEGIGVKAIEELKEGLEAHDLT 1377


>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 = 60.8 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 26/86 (30%), Positives = 42/86 (48%)

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           I  E    +V    N         L  ++E+L LSVR+ NCL+ + I Y   L+ +   +
Sbjct: 70  IYCEIKDTQVVPKKNFIGNDGQKYLDVEIEKLCLSVRAYNCLKSDGIEYYSQLVDKLVEE 129

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFL 317
           ++ + N G+KSLVEI+    +    L
Sbjct: 130 LITIPNMGQKSLVEIEEKRASFQPEL 155



 Score = 54.6 bits (130), Expect = 2e-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|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 = 60.8 bits (146), Expect = 3e-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|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 = 4e-07,   Method: Composition-based stats.
 Identities = 24/120 (20%), Positives = 51/120 (42%), Gaps = 7/120 (5%)

Query: 199 DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK-----EVKEDINVKSLPFN 253
            K    +   G ++ E+     +     Q G  +  E  ++     E   + +  S    
Sbjct: 133 QKDIFELRNVGVLSREEITK--AIESIVQSGKIVYHEREEESKTIIETAPESSRLSELLP 190

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
                +++++  SVR+ N L+  NI    +L+Q +E D++ + N G ++  EI  V+  +
Sbjct: 191 EIESIRLDDVPFSVRARNALKRANIQTADELVQMSEKDIMGLRNVGAQTRDEILAVINAI 250



 Score = 54.6 bits (130), Expect = 2e-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|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 = 60.0 bits (144), Expect = 5e-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 = 46.9 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 22/108 (20%), Positives = 49/108 (45%), Gaps = 2/108 (1%)

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            +   + G  + E+ V   +    ++  + +  E    + +             +   +E
Sbjct: 42  IINFRSVGVKSLEEIVN--AIDSLNKYKLEMYSENMLNKKRNHKTFVGHDGLKYIDIAIE 99

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
            L LSVR+ NCL+  ++ Y   LI   + +++ + N GRK+L+E++ +
Sbjct: 100 NLNLSVRAFNCLKSTSVDYYSQLIDVLDEELIAIPNMGRKTLLELEHI 147


>gi|1491730|emb|CAA67855.1| orf [Musa balbisiana]
          Length = 67

 Score = 60.0 bits (144), Expect = 5e-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|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 = 60.0 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 22/59 (37%), Positives = 33/59 (55%)

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            ++ L+L+ R TN L    I  +GDL   + +D+L+M  FG KSL E++  L   G  L
Sbjct: 13  PLDLLDLNFRVTNRLASAGIFRVGDLCVCSASDLLKMPGFGVKSLQEVERSLQRAGRSL 71


>gi|13124813|sp|O59303|RPOD_PYRHO RecName: Full=DNA-directed RNA polymerase subunit D
          Length = 259

 Score = 59.6 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 40/246 (16%), Positives = 81/246 (32%), Gaps = 41/246 (16%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSI 75
            I + ++ E+    I E    G +    NALRR ++  +   A+  V+  +        I
Sbjct: 3   KIKILKKTEDSITFILE----GVSVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEI 58

Query: 76  KGVHEDLTDIILNIKGINLKM--SGDSHKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPDH 132
                 +  +        L      D    +++   GPG+V +GD++    D++ + PD 
Sbjct: 59  IAHRLAMIPLKTPTDRFELDALELDDYTVTLSLEAEGPGIVYSGDLKSDDPDVKPVTPDI 118

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL--ITIDALYSPIKKVSYTVESA 190
            I  L     +        G G   AK             + I    +  +K++   +  
Sbjct: 119 PIVKLAKGQRLVFNAYAKLGRGKDHAKWQPGFTYYKYFTRVHISKKINGWEKLAKLAKKR 178

Query: 191 REGQVLDYDKLSMT-------------------------------IDTDGSITGEDSVAL 219
                 + +++ +                                ++T+G +  E+ V +
Sbjct: 179 GLPTKENEEEVIVETIKPFYIPKEFEEYEGKEIWEEIVPDTYVFVVETNGELPVEEIVKI 238

Query: 220 ASRILQ 225
           A RIL 
Sbjct: 239 ALRILM 244


>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 = 59.6 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 19/84 (22%), Positives = 41/84 (48%)

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           K+ ++  ++         L + +  ++++    + L    I+Y+GDLIQ  E  ++ +  
Sbjct: 148 KEGLEIALDNIQAEEVHYLSQPIFSMKMTPIVRSKLESHGILYVGDLIQLNEEYLMEIWG 207

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNL 321
            G  +L  IK  L   G++ GM++
Sbjct: 208 LGPVALERIKTKLNENGVWFGMDV 231


>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 = 59.6 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 40/246 (16%), Positives = 81/246 (32%), Gaps = 41/246 (16%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSI 75
            I + ++ E+    I E    G +    NALRR ++  +   A+  V+  +        I
Sbjct: 5   KIKILKKTEDSITFILE----GVSVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEI 60

Query: 76  KGVHEDLTDIILNIKGINLKM--SGDSHKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPDH 132
                 +  +        L      D    +++   GPG+V +GD++    D++ + PD 
Sbjct: 61  IAHRLAMIPLKTPTDRFELDALELDDYTVTLSLEAEGPGIVYSGDLKSDDPDVKPVTPDI 120

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL--ITIDALYSPIKKVSYTVESA 190
            I  L     +        G G   AK             + I    +  +K++   +  
Sbjct: 121 PIVKLAKGQRLVFNAYAKLGRGKDHAKWQPGFTYYKYFTRVHISKKINGWEKLAKLAKKR 180

Query: 191 REGQVLDYDKLSMT-------------------------------IDTDGSITGEDSVAL 219
                 + +++ +                                ++T+G +  E+ V +
Sbjct: 181 GLPTKENEEEVIVETIKPFYIPKEFEEYEGKEIWEEIVPDTYVFVVETNGELPVEEIVKI 240

Query: 220 ASRILQ 225
           A RIL 
Sbjct: 241 ALRILM 246


>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 = 59.2 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 18/55 (32%), Positives = 31/55 (56%)

Query: 261  EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
            ++L +S R TN      I  +GDL+ ++E D+LR+   G K++ E++  L    L
Sbjct: 1346 DDLGVSQRWTNKFSEVGIEVVGDLVGKSEEDLLRIDGIGAKAIEELRDGLEEHNL 1400


>gi|255560816|ref|XP_002521421.1| conserved hypothetical protein [Ricinus communis]
 gi|223539320|gb|EEF40911.1| conserved hypothetical protein [Ricinus communis]
          Length = 111

 Score = 59.2 bits (142), Expect = 9e-07,   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|224088404|ref|XP_002335097.1| predicted protein [Populus trichocarpa]
 gi|222832850|gb|EEE71327.1| predicted protein [Populus trichocarpa]
          Length = 54

 Score = 59.2 bits (142), Expect = 1e-06,   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|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 = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 29/161 (18%), Positives = 57/161 (35%), Gaps = 8/161 (4%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSI 75
            I + ++ E+    + E    G +    N+LRR ++  +   A+  V+  +        I
Sbjct: 3   KIKILKKTEDSITFLLE----GVSVAFANSLRRTILGEVPTFAVDEVEFYENDSALFDEI 58

Query: 76  KGVHEDLTDIILNIKGINLKMS--GDSHKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPDH 132
                 +  +   +    L      D    +++   GPG+V +GD++    D++ +NP+ 
Sbjct: 59  IAHRLAMIPLKTPVDRFELDALELDDYTVTLSLKAEGPGIVYSGDLESDDPDVKPVNPNI 118

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITI 173
            I  L     +        G G   AK             I
Sbjct: 119 PIVKLAKGQKLVFNAYARLGRGKDHAKWQPGFTYYKYYTKI 159


>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 = 58.8 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 32/193 (16%), Positives = 76/193 (39%), Gaps = 42/193 (21%)

Query: 45  NALRRVLMSSLRGAAITAV--------QIDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
           N +RR+L+  +    ++ +        +    +HE + ++ V  +L   ++ +K I  + 
Sbjct: 38  NLIRRILLKEIYNFKVSTISIFLFNSNKFCYKIHEFTKVEEVKNNLVSFLILLKEIKFRS 97

Query: 97  SGD---SHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDV-DAVVRMELTVSKG 152
                       +  +    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--------------------NFNPVKKVNYIEE----------NNVYFEIYTNQTST 187

Query: 213 GEDSVALASRILQ 225
             + +  + +I++
Sbjct: 188 PLEVLVKSLKIIK 200


>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 = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 30/148 (20%), Positives = 54/148 (36%), Gaps = 8/148 (5%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSIK 76
           I + ++ ++    I E    G      NALRR ++  +   AI  V+  +        I 
Sbjct: 16  IKILEKRDDAIRFILE----GMDIAFANALRRTIIGEVPTFAIDEVEFYENDSALFDEII 71

Query: 77  GVHEDLTDIILNIKGINLKMSG--DSHKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPDHV 133
                L  +        L+     D    +++   GP +V +GD++    D++ +NP+  
Sbjct: 72  AHRLSLIPLTTPFDRFELESMELEDYTVTLSLEAEGPAIVYSGDLKSDDPDVKPVNPNIP 131

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           I  L     +        G G   AK  
Sbjct: 132 IVKLAEGQRLVFNAYAKMGKGKDHAKWQ 159


>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 = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 42/254 (16%), Positives = 73/254 (28%), Gaps = 55/254 (21%)

Query: 24  EENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSIKGVHEDL 82
           +E            G + +  N LRR ++S +   AI  V+I D        +      L
Sbjct: 9   DERVAKFTLS----GVSMSFANMLRRAMISEVPTLAIEDVRIYDNTSVLFDEMLAHRLGL 64

Query: 83  TDIILNIKGINLKMSGDSHKRV--------TIFKRGPGVVTAGDIQT-VNDIEVLNPDHV 133
             +  ++K    +                 T+   GP  V + D+     D    +    
Sbjct: 65  IPLRTDLKRYKPRSECTCEDAGCPVCTATYTLSVEGPKTVYSSDLIPQDPDAAPADEKIP 124

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTE---NDPIGLITIDALY----SPIKKVSYT 186
           I  L  D  + +E     G G   AK   T         +I ID         I +   +
Sbjct: 125 IIELARDQKLVLEAQAIVGTGKEHAKWQATTACGYKNYPVIAIDERCDGCGMCIDECPRS 184

Query: 187 VESAREGQ----------------------------------VLDYDKLSMTIDTDGSIT 212
           V    +G+                                    D ++    ++ DGSI 
Sbjct: 185 VLETAQGKIRVVEERQELCSLCRLCERACLAGGIGTEPAIHIGTDAERFIFVVEGDGSIP 244

Query: 213 GEDSVALASRILQD 226
             + +  A + +Q 
Sbjct: 245 VREIIERALQYIQK 258


>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 = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 5/80 (6%)

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM--- 319
            +   R     R  +I  + DL Q    D++R+ + GRKS+ EI+ VL    L LGM   
Sbjct: 17  SKYEARIQRIFREFDIKTIRDLCQWPGKDLVRVRDMGRKSIEEIEDVLERYNLRLGMLGK 76

Query: 320 NLPDWPPESIEELAKKYEDK 339
            L ++    IE   +  E++
Sbjct: 77  ELDEY--AGIENSVQDEEEE 94


>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 = 58.5 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 5/80 (6%)

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM--- 319
            +   R     R  +I  + DL Q    D++R+ + GRKS+ EI+ VL    L LGM   
Sbjct: 17  SKYEARIQRIFREFDIKTIRDLCQWPGKDLVRVRDMGRKSIEEIEEVLERYNLRLGMLGK 76

Query: 320 NLPDWPPESIEELAKKYEDK 339
            L ++    IE   +  E++
Sbjct: 77  ELDEY--AGIENSVQDEEEE 94


>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 = 19/83 (22%), Positives = 37/83 (44%), Gaps = 4/83 (4%)

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI---KGVL 310
                 ++ L LS RS N L+  NI+ + DL+  ++ D+      G KS+ EI     +L
Sbjct: 1   MKKDTSIQILHLSKRSYNVLKKFNIITIQDLLTISKEDIKNFRGIGEKSIQEILSKIEIL 60

Query: 311 GTMGLFLGMNLPDWPPESIEELA 333
                   +++ +   E++ +  
Sbjct: 61  KDYNFD-DIDISEVNVENLSKNK 82



 Score = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/128 (21%), Positives = 51/128 (39%), Gaps = 5/128 (3%)

Query: 215 DSVALASRILQDQLGMFINFEE---PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTN 271
           +  +      + +       EE    + +            N      ++ L LSVR+ N
Sbjct: 116 ECYSELLTKTEKEFESIKYSEEIIQKEIKSIRKKPNIETAINLEKDIPIDFLGLSVRAKN 175

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           CL+  NI Y   LI +TE +++ + + G  +L E+   L  + +F     P    E+ E 
Sbjct: 176 CLKSANIEYYSQLISKTEEELMTIKHMGVTTLKEL-QRLKFL-IFFYFGFPVVDTENKES 233

Query: 332 LAKKYEDK 339
             +K  ++
Sbjct: 234 KEEKISNE 241


>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 = 57.7 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGEN-IVYMGDLIQRTEADMLRMANF 298
           E    I  K L  +     K+E++ LS R+ + L  +  +  +GD++  T  D+L + NF
Sbjct: 123 ERFHQITAKDLHPDFQGAVKLEDIRLSHRTFHTLLNQGQMETIGDVMLTTCTDLLSLKNF 182

Query: 299 GRKSLVEIKGVLGTM 313
           GRKSL EIK V+ ++
Sbjct: 183 GRKSLNEIKEVIRSL 197


>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 = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 88/246 (35%), Gaps = 45/246 (18%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ-IDGVLHEISSIKG 77
            + +  E+    I     RG      NALRR +++ +   A+  V+  +        I  
Sbjct: 6   EIFERREDAIKFIL----RGVDVPFANALRRTILAEVPTFAVDEVEFFENDSALFDEIIA 61

Query: 78  VHEDLTDIILNIKGINLKM--SGDSHKRVTIFKRGPGVVTAGDIQTVN-DIEVLNPDHVI 134
               +  +   ++  +L      D    +++   GPG+V +GD+++ +  ++  NP+  I
Sbjct: 62  HRLAMIPLTTPVERFSLDALELDDYTVTLSLQAEGPGMVYSGDLKSDDEGVKPANPNIPI 121

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHH--------------------------------- 161
             L     +        G G   AK                                   
Sbjct: 122 VKLAEGQKLTFNAYAKLGRGKDHAKWQPGFVYYKYLTEIHVSKEVPDWEELKELAERRGL 181

Query: 162 --RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
               + D I + TI A Y P K  +Y  +  R  + +       T++T+G +  E+ V++
Sbjct: 182 PVEEKKDEIIIKTIKAFYLPRKFEAYEGDKIR--EEIIPGAFVFTVETNGELPVEEIVSI 239

Query: 220 ASRILQ 225
           A +IL 
Sbjct: 240 ALKILM 245


>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 = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 31/160 (19%), Positives = 55/160 (34%), Gaps = 8/160 (5%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSIK 76
           I + ++ ++    I E    G      NALRR ++  +   A+  V+  +        I 
Sbjct: 4   IKILKKTDDSITFILE----GVDVAFANALRRTILGEVPTFAVDEVEFYENDSALFDEII 59

Query: 77  GVHEDLTDIILNIKGINLKM--SGDSHKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPDHV 133
                +  +   +    L      D    +++   GPG+V +GD++    D++  NPD  
Sbjct: 60  AHRLAMIPLKTPVDRFELDALELDDYTVTLSLEAEGPGIVYSGDLKSDDPDVKPANPDIP 119

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITI 173
           I  L     +        G G   AK             I
Sbjct: 120 IVKLAKGQRLVFNAFAKLGRGKDHAKWQPGFTYYKYFTRI 159


>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 = 57.7 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 44/248 (17%), Positives = 87/248 (35%), Gaps = 49/248 (19%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGV 78
            + ++  +    I      G      NALRR ++S +   A+  V+   + ++ +    +
Sbjct: 5   KILEKRPDSIKFIVS----GVDVPFANALRRTILSEVPTFAVDEVEF--LENDSALFDEI 58

Query: 79  HEDLTDII-LNIKGINLKMS----GDSHKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPDH 132
                 +I L        +      D    +++   GPG+V +GD++ +  D++  NP+ 
Sbjct: 59  IAHRLAMIPLTTPHERFSLDALELDDYTVTLSLEAEGPGMVYSGDLKSSDGDVKPANPNI 118

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHH------------------------------- 161
            I  L     +        G G   AK                                 
Sbjct: 119 PIVKLAEGQRLTFNAYARLGRGKDHAKWQPGFVYYKYLTKIHVSKDVPDWEELKELAERR 178

Query: 162 ----RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSV 217
                  ++ I + TI A Y P K   +  +  R  + +       T++T+G +  E+ V
Sbjct: 179 GLPVEESDEEIVITTIKAFYLPRKFEEHMGKGIR--EEIVPGSFVFTVETNGELPVEEIV 236

Query: 218 ALASRILQ 225
           ++A +IL 
Sbjct: 237 SIALKILM 244


>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 = 57.3 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 85/246 (34%), Gaps = 45/246 (18%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ-IDGVLHEISSIKG 77
            + +   +    I     RG      NALRR +++ +   A+  V+  +        I  
Sbjct: 6   EILERRGDAIKFIL----RGVDVPFANALRRTILAEVPTFAVDEVEFFENDSALFDEIIA 61

Query: 78  VHEDLTDIILNIKGINLKM--SGDSHKRVTIFKRGPGVVTAGDIQTVN-DIEVLNPDHVI 134
               +  +   ++  +L      D    +++   GPG+V +GD+++ +  ++  NP+  I
Sbjct: 62  HRLAMIPLTTPVERFSLDSLDLDDYTVTLSLQAEGPGMVYSGDLKSDDEGVKPANPNIPI 121

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHH--------------------------------- 161
             L     +        G G   AK                                   
Sbjct: 122 VKLAEGQKLTFNAYARLGRGKDHAKWQPGFVYYKYLTEIHVSKEVPDWEELKELAERRGL 181

Query: 162 --RTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
               + D I + T  A Y P K   Y  +  R  + +       T++T+G +  E+ V++
Sbjct: 182 PVEEKEDEIVIKTTKAFYLPRKFEEYEGDKIR--EEIIPGAFVFTVETNGELPVEEIVSI 239

Query: 220 ASRILQ 225
           A +IL 
Sbjct: 240 ALKILM 245


>gi|145308100|gb|AAR05652.2| hypothetical protein bst011 [Bacteroides uniformis]
          Length = 137

 Score = 57.3 bits (137), Expect = 3e-06,   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 P------PESIEELAKKYE 337
                  PE  EE AK  +
Sbjct: 82  AGIGNTTPEDKEEEAKWEQ 100


>gi|218508353|ref|ZP_03506231.1| DNA-directed RNA polymerase subunit alpha [Rhizobium etli Brasil
          5]
          Length = 37

 Score = 57.3 bits (137), Expect = 3e-06,   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|31580946|dbj|BAC77576.1| RNA polymerase alpha subunit [Nicotiana tomentosiformis]
          Length = 77

 Score = 56.9 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 14/47 (29%), Positives = 30/47 (63%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           +++LEL  R  NCL+  NI  + DL+  ++ D++++ +F  + + +I
Sbjct: 29  IDQLELPSRIYNCLKMSNIYTLLDLLNNSQEDLMKIEHFRSEDVKQI 75


>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 = 56.9 bits (136), Expect = 4e-06,   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|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 = 56.5 bits (135), Expect = 6e-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|31580902|dbj|BAC77553.1| RNA polymerase alpha subunit [Nicotiana sylvestris]
          Length = 79

 Score = 56.5 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 14/47 (29%), Positives = 29/47 (61%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
           +++LEL  R  NCL+  NI  + DL+  ++ D++++ +F  + +  I
Sbjct: 31  IDQLELPSRIYNCLKMSNIYTLLDLLNNSQEDLMKIEHFRSEDVKRI 77


>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 = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 5/80 (6%)

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM--- 319
            +   R     R  +I  + DL Q    D++R+ + GRKS+ EI+ VL    L LGM   
Sbjct: 17  SKYEARIQRIFREFDIKTIRDLCQWPGKDLVRVRDMGRKSIEEIEDVLERYNLRLGMPGK 76

Query: 320 NLPDWPPESIEELAKKYEDK 339
            L ++    I    +  E++
Sbjct: 77  ELDEY--AGIGNSVQDEEEE 94


>gi|282164928|ref|YP_003357313.1| DNA-directed RNA polymerase subunit D [Methanocella paludicola
           SANAE]
 gi|282157242|dbj|BAI62330.1| DNA-directed RNA polymerase subunit D [Methanocella paludicola
           SANAE]
          Length = 262

 Score = 56.1 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 39/252 (15%), Positives = 78/252 (30%), Gaps = 47/252 (18%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSI 75
            + + +  + +   +   +   FA    NA+RR +++ +   AI  V I D        +
Sbjct: 2   KLEILELGDRKAKFVLSEVTPAFA----NAVRRAMLADIPKMAIDYVDIYDNTSVMFDEM 57

Query: 76  KGVHEDLTDIILNIKGINLKMSGD--------SHKRVTIFKRGPGVVTAGDIQ-TVNDIE 126
                 L  I  N+    L+   D             T+   GP +V + D++ +  D  
Sbjct: 58  LAHRMGLIPIKTNLDMYKLREECDCKGEGCALCQVSFTLSAEGPCMVHSRDMKSSDPDTV 117

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK------------------------HHR 162
             + +  I  L     V +      G G   +K                           
Sbjct: 118 PADDNVPIIELKERQKVVLTAVARLGRGKEHSKFQPVCPPGYKYVPIIEISDKCDSCKQC 177

Query: 163 TENDPIGLITIDA---------LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
            E  P G+  +D            S  ++     +       +D       ++TDGS + 
Sbjct: 178 VEQCPRGVFAVDKNKVVVDNPYNCSMCEECLEACDLKAIKLSIDNTAFIFMVETDGSYSA 237

Query: 214 EDSVALASRILQ 225
           ++ +  A   ++
Sbjct: 238 QEIITRAVESIR 249


>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 = 56.1 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 24/64 (37%), Positives = 31/64 (48%)

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEEL 332
           +  E IV +G  +Q T  D+LR    G+KS  E +  L  +GL LGM L  W  E   E 
Sbjct: 1   MAKEGIVLVGSFVQLTAGDILRKQGLGKKSYREARATLEALGLSLGMELCGWDEELAFEA 60

Query: 333 AKKY 336
            K  
Sbjct: 61  RKAL 64


>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 = 55.4 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 31/149 (20%), Positives = 57/149 (38%), Gaps = 8/149 (5%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSI 75
            I + ++ E+    I E +   FA    NALRRV++  +   A+  V+  +        I
Sbjct: 2   KIKVLEKREDAIRFILEGVDAAFA----NALRRVIIGEVPTFAVDEVEFYENDSALFDEI 57

Query: 76  KGVHEDLTDIILNIKGINLKMS--GDSHKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPDH 132
                 +  +        L      +    +++   GPGVV +GD++    D++ + P+ 
Sbjct: 58  IAHRLAMIPLTTPYDRFELDALELDEYTVTLSLEAEGPGVVYSGDLKSDDPDVKPVTPNI 117

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHH 161
            I  L     + +      G G   AK  
Sbjct: 118 PIVKLAEGQKLTLNAYAKLGRGKDHAKWQ 146


>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 = 55.0 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 21/84 (25%), Positives = 38/84 (45%)

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           K  ++  +N         L + V  L ++    + L    I+Y+GDLI   E  ++ +  
Sbjct: 145 KVGLEIALNNIQAEEVHYLSEPVFSLGITPSIKSHLESHGILYIGDLIHLNEQYLMEIWG 204

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNL 321
            G  +L +IK  L   G + GM++
Sbjct: 205 IGPVTLDKIKTKLNENGAWFGMDV 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 = 55.0 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 21/84 (25%), Positives = 38/84 (45%)

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           K  ++  +N         L + V  L ++    + L    I+Y+GDLI   E  ++ +  
Sbjct: 145 KVGLEIALNNIQAEEVHYLSEPVFSLGITPSIKSHLESHGILYIGDLIHLNEQYLMEIWG 204

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNL 321
            G  +L +IK  L   G + GM++
Sbjct: 205 IGPVTLDKIKTKLNENGAWFGMDV 228


>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 = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 38/242 (15%), Positives = 82/242 (33%), Gaps = 44/242 (18%)

Query: 15  IEYIVLGQEEENRTLMIAEPLPRGFAHT--LGNALRRVLMSSLRGAAITAVQI-DGVLHE 71
           +E++   + +      +          T    N +RR +++ +   AI  V+  +     
Sbjct: 7   VEFVEREERD---ARFLV------QGITPAFANGIRRAMLADVPTMAIDTVRFVENSSVM 57

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND-IEVLNP 130
                 +   L  +     G  +    D    ++I   GP    +GD+ + +D ++  + 
Sbjct: 58  FDEQLALRLGLVPLTTPPVGEFV---EDDTVTLSIDVEGPATAYSGDLVSSDDLVQPADE 114

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHH--------------RTENDP--------- 167
           +  I +L     +  E       G   AKH                 E+ P         
Sbjct: 115 NVPIIDLKDGQRLEAEADAVLDRGKDHAKHQGGVAVGYRHLQRVAAVEDLPEFEDPDRRI 174

Query: 168 -IGLITIDALYSPIKKVSYTVESAREGQVLDYDKL----SMTIDTDGSITGEDSVALASR 222
             G+I  D    P  +  + + +   G+ +  + +       ++TDGS + E+ V  A+ 
Sbjct: 175 VRGVIEEDGELVPTSEFDHDLSNRYPGKEVTLEDVPNSFVFHVETDGSFSVEELVTRAAD 234

Query: 223 IL 224
            +
Sbjct: 235 TI 236


>gi|224126651|ref|XP_002319890.1| predicted protein [Populus trichocarpa]
 gi|222858266|gb|EEE95813.1| predicted protein [Populus trichocarpa]
          Length = 62

 Score = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 31/52 (59%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
           +++LEL+ +  NCL+   I  + D ++ ++ D+++  +F  + +  I G+L 
Sbjct: 10  IDQLELAPKIYNCLKRSVIHTLWDFLKNSQEDLMKTEHFRIEDVKHIFGILK 61


>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 = 54.6 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 21/84 (25%), Positives = 39/84 (46%)

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           K  ++  +N         L + V  L ++    + L    I+Y+GDLI   E  ++ + +
Sbjct: 145 KVGLEIALNNIQAEEVHYLSEPVFSLGITPSIKSHLESHGILYIGDLIHLNEQYLMEIWD 204

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNL 321
            G  +L +IK  L   G + GM++
Sbjct: 205 IGPVTLDKIKTKLNENGAWFGMDV 228


>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 = 54.2 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 17/57 (29%), Positives = 28/57 (49%)

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
           + V++L L  R+   LR   I  +G L++  E  + R+   G +SL EI   L  + 
Sbjct: 165 RPVDDLGLGQRAYRALRRAGIQTVGQLLELGEPGLQRLRGLGPRSLAEICHRLDALQ 221



 Score = 42.7 bits (99), Expect = 0.084,   Method: Composition-based stats.
 Identities = 16/80 (20%), Positives = 26/80 (32%), Gaps = 6/80 (7%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF------LG 318
           L  R    L+   +  +G L   T+  + R+   G   +  +   L              
Sbjct: 253 LPRRVVTALQRAGLHTVGALAGFTQEGLRRLRGLGESGVAAVLQSLHQYRQECSRRGAFP 312

Query: 319 MNLPDWPPESIEELAKKYED 338
             L DW  E IE L  +  +
Sbjct: 313 RRLEDWLQELIEPLPDRERE 332


>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 = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 21/84 (25%), Positives = 38/84 (45%)

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           K  ++  +N         L + V  L ++    + L    I+Y+GDLI   E  ++ +  
Sbjct: 145 KVGLEIALNNIQAEEVHYLSEPVFSLGITPSIKSHLESHGILYIGDLIHLNEQYLMEIWG 204

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNL 321
            G  +L +IK  L   G + GM++
Sbjct: 205 VGPVTLEKIKTKLNENGAWFGMDV 228


>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 = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/82 (30%), Positives = 44/82 (53%), Gaps = 3/82 (3%)

Query: 235 EEPKKEVKEDINVKSLPFNPALLKKVEEL---ELSVRSTNCLRGENIVYMGDLIQRTEAD 291
            E ++ V+  I      FN +  K   ++   +L +RSTNCLR   I  + DL++ ++ +
Sbjct: 116 NEIEQNVEFPIGSLGSRFNMSNNKLELDVVVLDLDIRSTNCLRSRGIDKIEDLLKLSDTE 175

Query: 292 MLRMANFGRKSLVEIKGVLGTM 313
           +LR+ N GR+SL  I   +  +
Sbjct: 176 LLRIDNLGRRSLKLIIDSISKL 197


>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 = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 26/116 (22%), Positives = 44/116 (37%), Gaps = 8/116 (6%)

Query: 222 RILQDQLGMFINFEEPKKEVKEDINVKSLPF------NPALLKKVEELELSVRSTNCLRG 275
              ++ L  + N  E   E     +            +     ++ EL L  RS N L  
Sbjct: 773 DNAEEMLRAWRNCFEGIDEPGALSDHADETRLQELLADAEFETQIPELGLGSRSANALDR 832

Query: 276 ENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            NI+ + DL+      ++R+   G K+  EI   +  +   LG   PD  P S+ +
Sbjct: 833 ANILTVEDLLTVPMRRLMRLRGVGNKTRREITSAVKILRDRLG--KPDRDPSSLSD 886


>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 = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 28/147 (19%), Positives = 58/147 (39%), Gaps = 8/147 (5%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ-IDGVLHEISSIKG 77
            + ++ E+    I E    G      NALRR +++ +   A+  V+  +        I  
Sbjct: 6   RILEKREDSIKFIVE----GIDIPFANALRRTILAEVPTFAVDEVEFFENDSALFDEIIA 61

Query: 78  VHEDLTDIILNIKGINLKM--SGDSHKRVTIFKRGPGVVTAGDIQTVN-DIEVLNPDHVI 134
               +  +   ++  +L      D    +++   GPG+V +GD+++ +  ++  NP+  I
Sbjct: 62  HRLAMIPLTTPVERFSLDALELDDYTVTLSLEAEGPGMVYSGDLKSDDEGVKPANPNIPI 121

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHH 161
             L     + +      G G   AK  
Sbjct: 122 VKLAEGQNLTLNAYAKLGRGKDHAKWQ 148


>gi|6633993|dbj|BAA88567.1| C-terminal domain of the RNA polymerase alpha subunit [synthetic
           construct]
          Length = 85

 Score = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 21/80 (26%), Positives = 30/80 (37%)

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
               +             L   +EEL LS R  + L+ E I  +  L+     D+  +  
Sbjct: 4   AAPEEAKEPEAPPEQEEELDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPG 63

Query: 298 FGRKSLVEIKGVLGTMGLFL 317
            G +SL EIK  L   G  L
Sbjct: 64  IGERSLEEIKEALEKKGFTL 83


>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 = 54.2 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 21/84 (25%), Positives = 37/84 (44%)

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           K  ++  +N         L + V  L ++      L    I+Y+GDLI   E  ++ +  
Sbjct: 145 KVGLEIALNNIQAEEVHYLSEPVFSLGITPSIKRHLESHGILYIGDLIHLNEQYLMEIWG 204

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNL 321
            G  +L +IK  L   G + GM++
Sbjct: 205 IGPVTLDKIKTKLNENGTWFGMDV 228


>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 = 53.8 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 26/53 (49%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  + N L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 42  LSSPARNALENHGIHTIEELSKYSEKEILKLHGMGPASLPKLRKALEENGLSF 94


>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 = 53.4 bits (127), Expect = 5e-05,   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|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 = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 20/84 (23%), Positives = 39/84 (46%)

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           K+ ++  +  K     P L + +  L +   + N L    + Y+GDL++R E  ++ +  
Sbjct: 147 KEGLEIAVENKPAEEVPYLSQPLFSLGIQPSAQNHLTAYGLRYVGDLVRRDEQYLMEIWG 206

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNL 321
            G  ++  IK  L   G  L M++
Sbjct: 207 IGPATVERIKTKLNENGACLDMDV 230


>gi|159162213|pdb|1DOQ|A Chain A, The C-Terminal Domain Of The Rna Polymerase Alpha Subunit
           From Thermus Thermophilus
          Length = 69

 Score = 52.7 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 23/52 (44%)

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           S R  + L+ E I  +  L+     D+  +   G +SL EIK  L   G  L
Sbjct: 16  STRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALEKKGFTL 67


>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 = 52.3 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 26/53 (49%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  + N L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 42  LSSPARNALEQHGIHTIEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSF 94


>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 = 51.9 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/62 (30%), Positives = 30/62 (48%)

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL 315
               + +L L  R  N LR   +  +G+L      D+L   N G +SL +++ VLG +G 
Sbjct: 77  NHTPIRDLPLPTRIANGLRRMGVRTLGELTALHAEDILLSPNLGERSLDQLRHVLGLIGR 136

Query: 316 FL 317
            L
Sbjct: 137 SL 138


>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 = 51.9 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 26/53 (49%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  + N L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 42  LSSPARNALEHHGIHTIEELSKYSEKEILKLHGMGPASLPKLRKALEEQGLSF 94


>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 = 51.9 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 27/53 (50%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  + N L+   I  + +L + +E ++L++   G  S+ +++  L   GL  
Sbjct: 42  LSSPARNALQHHGIHTIEELSKYSEKEILKLHGMGPASMPKLRKALEERGLSF 94


>gi|296412916|ref|XP_002836165.1| hypothetical protein [Tuber melanosporum Mel28]
 gi|295629972|emb|CAZ80356.1| unnamed protein product [Tuber melanosporum]
          Length = 340

 Score = 51.9 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 54/265 (20%), Positives = 95/265 (35%), Gaps = 43/265 (16%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG----VLHEIS 73
           I + + +     ++       FA    NALRR++++ +   AI  V+I      +  E  
Sbjct: 16  ITIKEADSRHAQIVLSNCDLAFA----NALRRIMLAEIPTIAIDIVEIQTNTSVIPDEFL 71

Query: 74  SIK-GVHE-DLTDIILNI--KGINLKMSGDSHKRVTIFK------RGPGVVTAGDIQTVN 123
             + G+   D T+I   +                VT+             V A D+    
Sbjct: 72  CHRLGMVPLDSTNIDDKLIYTRDCFCDQYCERCSVTLSLHARCTGEDNVTVYARDLVIAE 131

Query: 124 DIE-----VLNPD---HVICNLDVDAVVRMELTVSKGHGYVPAKHHRT-----ENDPIGL 170
             +     + +P+    VIC L     +R++    KG     AK   T     E DP   
Sbjct: 132 GAQLGSPVINDPEGQGTVICKLRKGQELRLKCIAKKGIAKEHAKWAPTAAVGFEYDPWNK 191

Query: 171 I-TIDALYSPIKKVSY-------TVESAREGQVLDYD----KLSMTIDTDGSITGEDSVA 218
           +  ID  Y    K  +         E   EG+  +YD    +  + I++ GS+  ++ + 
Sbjct: 192 LRHIDYWYEEDAKEEWPKSKYADWEEPPIEGEPFNYDAVPSRFYLDIESAGSLPPDEILQ 251

Query: 219 LASRILQDQLGMFINFEEPKKEVKE 243
              + LQ++L   I     K E  +
Sbjct: 252 QGIKYLQEKLAAVIETFSNKNETGD 276


>gi|15678067|ref|NP_275181.1| DNA-directed RNA polymerase subunit D [Methanothermobacter
           thermautotrophicus str. Delta H]
 gi|3122766|sp|O26144|RPOD_METTH RecName: Full=DNA-directed RNA polymerase subunit D
 gi|2621073|gb|AAB84545.1| DNA-dependent RNA polymerase, subunit D [Methanothermobacter
           thermautotrophicus str. Delta H]
          Length = 264

 Score = 51.9 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 50/268 (18%), Positives = 86/268 (32%), Gaps = 57/268 (21%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLG--NALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           I L ++ +   + +          T+   NA+RR+ M  +   AI  V +    ++    
Sbjct: 3   IALKEKTDTEMVFVVS------GVTVPFINAIRRICMMEVPKLAIEYVNMY--RNDAKMF 54

Query: 76  KGVHEDLTDIILNIKGINLKMS-------------GDSHKRVTIFKRGPGVVTAGDIQT- 121
             V      ++          S              +    +T+ K+GPGVV +GD+ + 
Sbjct: 55  DEVLAHRLGLVPLAADPEFAESLKMPEECDCEEYCSECSVSLTLRKKGPGVVYSGDLVSE 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT--------- 172
              ++ + PD  +  L  D  + +E     G G   AK   T                  
Sbjct: 115 TPAVKPVYPDIPLVKLGDDDELELEAVAQLGVGREHAKWEPTTACAYKYYPRIEFSEDCD 174

Query: 173 -----IDA-------------------LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
                I+A                     S  K      +        +  K    I+TD
Sbjct: 175 ECLECIEACPRDVLGEESGKPVVVDLENCSMCKSCVRACDKRAIDVGYEEGKFIFRIETD 234

Query: 209 GSITGEDSVALASRILQDQLGMFINFEE 236
           GS+  +D +  A  IL+D+    I F E
Sbjct: 235 GSVDPKDVLLKACDILRDKAEQVITFCE 262


>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 = 51.9 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 27/53 (50%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  + N L+   I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 42  LSSPARNALQHHGIHTIEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSF 94


>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 = 51.5 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 34/206 (16%), Positives = 67/206 (32%), Gaps = 20/206 (9%)

Query: 24  EENRTLMIAEPLPRGFAHT--LGNALRRVLMSSLRGAAITAVQI-DGVLHEISSIKGVHE 80
           +++               T    NALRR ++  +   AI  ++I D        +     
Sbjct: 9   DDSVARFTI------HGATPAFANALRRSMIGEVPTLAIEDIRIYDNTSVLFDEMLAHRL 62

Query: 81  DLTDIILNIKGINLKMSGD--------SHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPD 131
            L  I  ++     +                 T+   GP +VT+GD+ +   ++  ++ +
Sbjct: 63  GLIPIKTDLSQYVPRSECSCGGEGCPHCTVMFTLSVEGPKMVTSGDLISMDENVVPVHNN 122

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV-SYTVESA 190
             I  L  +  V +E      +G   AK   T         +  +            E  
Sbjct: 123 IPIVKLWENQKVVLEAVAEVNYGKEHAKWQPTLACGYSEYPVITIKDTCDGCGKCVAECP 182

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDS 216
           R+   L  D +S+ +  +G    +D 
Sbjct: 183 RDVLELTKDTVSIRV-VNGESKEKDC 207


>gi|154151761|ref|YP_001405379.1| DNA-directed RNA polymerase subunit D [Candidatus Methanoregula
           boonei 6A8]
 gi|154000313|gb|ABS56736.1| DNA-directed RNA polymerase [Methanoregula boonei 6A8]
          Length = 276

 Score = 51.5 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 45/278 (16%), Positives = 85/278 (30%), Gaps = 57/278 (20%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSI- 75
           I     ++            GFA    N+ RR ++  +   AI  V+I D        + 
Sbjct: 3   IEFASLDDTVARFTLSGAQPGFA----NSFRRAMIGEVPTLAIEDVRIYDNTSALFDEML 58

Query: 76  ------KGVHEDLTDIILNIKGINLKMSGDSHKRV--TIFKRGPGVVTAGDIQT-VNDIE 126
                   +  DLT         +   +G     V  T+   GP +VT+ D+        
Sbjct: 59  AHRLGLIPIRTDLTSYSTQ-GDCSCGGAGCPSCTVTYTLSVEGPKLVTSSDLIPQDPQAA 117

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT-----ENDPIGLITI--DALYSP 179
            ++ +  I  L     + +E       G V AK   T     +N P+  I+   DA    
Sbjct: 118 PVSDNIPIVKLIKGQKLVIEARAVLNKGKVHAKWQPTLVCGYKNYPVITISPTCDACGMC 177

Query: 180 IKKV--------SYTVESA--------------------REGQVL------DYDKLSMTI 205
           + +            VE                        G+        + D+   ++
Sbjct: 178 VDECPRTILALKGKKVEVIEGRLPDCSMCKLCERACLASGIGEEPAIRISAEPDRYIFSV 237

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           ++DGS+  ++ +  A   ++ Q              ++
Sbjct: 238 ESDGSLPVKEIMVQALGFVKAQAEELEKQTSEISGEEK 275


>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 = 51.5 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 26/53 (49%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  + N L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 42  LSSPARNALEHHGIHTIEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSF 94


>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 = 51.5 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 26/53 (49%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  + N L    I  + +L + +E ++L++   G  S+ +++  L   GL  
Sbjct: 42  LSSPARNALEHHGIHTIEELSKYSEKEILKLHGMGPASMPKLRKALEERGLSF 94


>gi|312137109|ref|YP_004004446.1| RNA polymerase insert [Methanothermus fervidus DSM 2088]
 gi|311224828|gb|ADP77684.1| RNA polymerase insert [Methanothermus fervidus DSM 2088]
          Length = 264

 Score = 51.1 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 46/267 (17%), Positives = 82/267 (30%), Gaps = 51/267 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSIK 76
           +V+ +E         +    G   +  NALRR  M+ +   AI  ++I          + 
Sbjct: 3   VVVNKENNTEIKFTID----GVDTSFVNALRRASMTEVPKLAIEYIRIVTNTSRMYDEML 58

Query: 77  GVHEDLTDIILNIKGI----------NLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDI 125
                L  +  N K +            K         T+ K+GP VV +GD+     +I
Sbjct: 59  AHRLGLIPLRSNEKIVGNLLMPEECDCDKYCAKCSVSFTLKKQGPCVVYSGDLVPSDPEI 118

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY 185
           + +  +  I  L+ D  + +E     G G   AK   T            +         
Sbjct: 119 KPVYENIPIIKLEEDEKIELEAIAQLGLGKKHAKWRPTTACGYKYYPKIIIKDTCDNCQA 178

Query: 186 TVESAREG----------------------------------QVLDYDKLSMTIDTDGSI 211
            +E   +                                   Q +D +K    ++TDGS+
Sbjct: 179 CIEECPKDVLKANKDTIKIENIEACSLCRACERICENESISVQYID-NKFIFKMETDGSM 237

Query: 212 TGEDSVALASRILQDQLGMFINFEEPK 238
              + +  A   +  +    I F E +
Sbjct: 238 PPREILNKACDSIIKKADEIIKFCEGE 264


>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 = 51.1 bits (121), Expect = 3e-04,   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|4140450|gb|AAD04060.1| DNA-directed RNA polymerase alpha chain [Chlamydia trachomatis]
          Length = 46

 Score = 51.1 bits (121), Expect = 3e-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|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 = 50.4 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 47/243 (19%), Positives = 85/243 (34%), Gaps = 42/243 (17%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIILNIKG 91
            +L N+LRR +++ +   AI  V+I         + + H +  I  V ED+ ++  +   
Sbjct: 26  LSLANSLRRTMLAEVPTLAIDLVEIKMNTSVLADEFISHRLGLIPLVSEDVEEMKYSRDC 85

Query: 92  INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP--------------DHVI--C 135
                  +    + +  R  G     D+ + + I+V  P              D  I  C
Sbjct: 86  TCEDYCDECSVVLELSARHEGEEGTTDVYSSSLIKVSGPGNLNVGEPVRRDDYDQGILLC 145

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKH------------HRTENDPIGLITIDALYS-PIKK 182
            L     + +     KG     AK             H           +DA    P  K
Sbjct: 146 KLRNHQELNIRCIAKKGIAKEHAKWSPCSAIAFEYDPHNKLKHTDFWFEVDAKKEWPDSK 205

Query: 183 VSYTVESAREGQVLDY----DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
            +   E  + G+V DY    ++  MT++T GS+      +   + LQ++L   +   E  
Sbjct: 206 YATWEEPPKPGEVFDYKAKPNRFYMTVETTGSLKANQVFSRGIKTLQEKLANVLFELENS 265

Query: 239 KEV 241
           +  
Sbjct: 266 RPA 268


>gi|255316715|ref|ZP_05358298.1| hypothetical protein CdifQCD-7_20312 [Clostridium difficile
           QCD-76w55]
          Length = 70

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 19/54 (35%), Positives = 28/54 (51%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
           + +L+LS +  N L   NI  +  L   T  D+L++   G KSL EIK  L  +
Sbjct: 1   MNQLKLSKKIVNHLIKANIDSIESLKTMTSNDLLKINGIGPKSLEEIKQALSLL 54


>gi|147919298|ref|YP_686966.1| DNA-directed RNA polymerase subunit D [uncultured methanogenic
           archaeon RC-I]
 gi|110622362|emb|CAJ37640.1| DNA-directed RNA polymerase, subunit D [uncultured methanogenic
           archaeon RC-I]
          Length = 262

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 42/256 (16%), Positives = 83/256 (32%), Gaps = 50/256 (19%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEI 72
            +E I L    + +   +   +   FA    N LRR +++ +   AI  V I D      
Sbjct: 2   KLEIIELK---DRKAKFVLTDVTPAFA----NGLRRAMIADVPKMAIDYVDIYDNTSVLF 54

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGD--------SHKRVTIFKRGPGVVTAGDIQ-TVN 123
             +  +   L  +  N+    L+   +            +++   GP VV + D++ +  
Sbjct: 55  DEMLALRLGLIPLKTNLDMYQLQSECECKGAGCSLCQVTLSVSAEGPCVVHSSDMKSSDP 114

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGH-------------GYVPAK----------- 159
           +   ++ +  I  L     V    T   G              GY               
Sbjct: 115 ETVPVDNNIPIIELKQGQKVVASGTARLGFTKEHAKYQPVCAAGYKNVPIVTVSDKCDQC 174

Query: 160 HHRTENDPIGLITIDAL---------YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
               +  P G+  I+            S  K      ++       D      T++TDGS
Sbjct: 175 KACIDECPRGVFKIEKNKLVVTDQYKCSMCKLCVDVCDAGAIDVSADKKAFIFTVETDGS 234

Query: 211 ITGEDSVALASRILQD 226
            + ++ +  A++ ++D
Sbjct: 235 YSAQEIITRAAKSMKD 250


>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 = 50.4 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 3/77 (3%)

Query: 244 DINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGD---LIQRTEADMLRMANFGR 300
           +          +L + +  L L  R T  L    I  +G    L+++ EA +L +  FGR
Sbjct: 73  EQKKAREEARTSLERPIASLNLGTRPTEALAKAGITTVGQVIALLEQGEAALLNVEGFGR 132

Query: 301 KSLVEIKGVLGTMGLFL 317
           K+L+++K  L  +G  L
Sbjct: 133 KALIDLKKTLRGLGYQL 149


>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 = 50.0 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 26/53 (49%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  + N L    I  + +L + +E ++L++   G  S+ +++  L   GL  
Sbjct: 42  LSSPARNALEHHGIHTIEELSKYSEKEILKLHGMGPASMPKLRKALEEAGLSF 94


>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 = 49.6 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 16/55 (29%), Positives = 26/55 (47%)

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
               L    IV + DL ++TE ++  +     K+L  IK +L   GL  GM+  +
Sbjct: 23  IRKALMQAGIVTVEDLCRKTEEELSSIPFIKGKNLQAIKDMLAEKGLHTGMSQEE 77


>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 = 49.6 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 23/115 (20%), Positives = 44/115 (38%), Gaps = 9/115 (7%)

Query: 218 ALASRILQDQLGMFINF---------EEPKKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           + A   L+ QL + + +              E++              L  ++ L+L+ R
Sbjct: 273 SKALYFLKRQLNILVPWGATFINLSDYLSSSELEVIKKAIQTLPGAIYLIPIQFLDLTNR 332

Query: 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           + NC     I  +G   + T  D+    NFG+KSL E++     +  +  +   D
Sbjct: 333 ANNCCLNAEITTVGMFSKMTLFDIASSRNFGKKSLEELQSKTKNLIDYFNITGED 387


>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 = 49.6 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 17/74 (22%), Positives = 28/74 (37%)

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
           EVK         +       +  L L  +  N L    I  +GDL   T  D+L + N G
Sbjct: 38  EVKSQRRELCDEYALPREVPLARLNLEPQILNALEYCEINTVGDLQGVTYEDLLSVPNLG 97

Query: 300 RKSLVEIKGVLGTM 313
           +    E++  +  +
Sbjct: 98  QSRASEVRDSVRQL 111


>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 = 49.6 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 21/88 (23%), Positives = 34/88 (38%), Gaps = 1/88 (1%)

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
                  E+IN  + P        +E L L   +   L+   +  + DL +     +  +
Sbjct: 165 NSNVHPVEEINGDNKPNGVVDENSIESLNLKRNTYTALKDAKVNTIEDLNKYGVTGLRTL 224

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            N G KS+ +I   L   G+ L   LPD
Sbjct: 225 KNLGNKSVSQIVEALLFRGIELP-ELPD 251


>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 = 49.2 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 30/165 (18%), Positives = 55/165 (33%), Gaps = 26/165 (15%)

Query: 16  EYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSI 75
           + + + +   +R  +  E  P  +    GNALRR+ +S +   A+  V      +E S  
Sbjct: 4   QKVSIVELGNSRITVSMEGFPVAY----GNALRRLALSEVPTMAVDFVYFY--DNESSVY 57

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKR-------------VTIFKRGPGV------VTA 116
             +      +++      L+  G   +              V +    P        V A
Sbjct: 58  DEIIAHRLGLLVLRSDEALRKYGSPEECSNASENDSHCFAQVYLEYEVPQDAASGVYVKA 117

Query: 117 GDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
            D++    DI  + P+  I  L     + +      G GY   K 
Sbjct: 118 SDLKFSDPDIRPIYPETPIVYLAPGQRIHLVGYARLGRGYEHGKW 162


>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 = 49.2 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 1/66 (1%)

Query: 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTE-ADMLRMANFGRKSLVEIK 307
                      ++ LELS R+ NCLR   +  +G LI+  +  D+  +   GR S+ E++
Sbjct: 1   MEMKFITKDDFIDVLELSTRTNNCLRRAEVHTIGSLIEYAKNNDLSMIYGMGRLSVEEVE 60

Query: 308 GVLGTM 313
            VL  +
Sbjct: 61  RVLKEL 66


>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 = 49.2 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 19/55 (34%), Positives = 32/55 (58%), Gaps = 1/55 (1%)

Query: 260 VEELELSVRSTNCLRGENIVYMGDLIQRTE-ADMLRMANFGRKSLVEIKGVLGTM 313
           ++ LELS R+ NCLR   +  +G LI+  +  D+  +   GR S+ E++ VL  +
Sbjct: 10  IDVLELSTRTNNCLRRAEVHTIGSLIEYAKNNDLSMIYGMGRLSVEEVERVLKEL 64


>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 = 49.2 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/53 (28%), Positives = 27/53 (50%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  + N L+   I  + +L + +E ++L+M   G  SL +++  L   GL  
Sbjct: 42  LSSPARNALQHHGIQTIEELSKYSEKEILKMHGMGPASLPKLRRALEESGLSF 94


>gi|50307587|ref|XP_453773.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|49642907|emb|CAH00869.1| KLLA0D16170p [Kluyveromyces lactis]
          Length = 307

 Score = 48.8 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 47/262 (17%), Positives = 91/262 (34%), Gaps = 41/262 (15%)

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 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT------IDALYSPIKKVSY------- 185
               +R++    KG     AK   +                D  Y    +  +       
Sbjct: 149 KGQEIRVKCIAKKGISKEHAKWSPSAAIEFEYDPWNKLKHTDYWYEQDARDEWPQSKNCE 208

Query: 186 TVESAREGQVLDY----DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
             +   E +  DY    +   + +++ GSIT E  V    + LQD++   +   +   + 
Sbjct: 209 FEDPPNEDEDFDYRAKPNTFYINVESVGSITSEQVVVRGIKTLQDKVADILFSLKKMDQE 268

Query: 242 KEDINVKSLPFNPALLKKVEEL 263
           K +    ++  + +    +EE 
Sbjct: 269 KVNFAAGAVSTHVSQQVPMEED 290


>gi|166714716|gb|ABY88083.1| RpoA [Stenotrophomonas sp. LMG 980]
          Length = 66

 Score = 48.8 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 19/57 (33%), Positives = 30/57 (52%)

Query: 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
             D DKL + I+T+G+I  E++V  A+ I  DQL +F +F    +   +  N    P
Sbjct: 1   RTDLDKLVIDIETNGTIDAEEAVRTAADITSDQLSVFGDFTHRDRGAAKPANNGVDP 57


>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 = 48.8 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 42  LSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRAALEKKGLSF 94


>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 = 48.8 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 39  LSAPARRALEHHGIHTLEELSKYSEKEILKLHGIGPASLPKLRAALEDKGLSF 91


>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 = 48.8 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 42  LSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSF 94


>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 = 48.8 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 27/158 (17%), Positives = 56/158 (35%), Gaps = 19/158 (12%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSIK 76
           + + Q  ++    + E +      +L N+LRR+L++ +   AI  V + D        + 
Sbjct: 7   VKVLQYSDDYLKFVVEGVKP----SLINSLRRILITDVPVLAIDRVIVLDNTTVMYDEVL 62

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRV---------TIFKRGPGVVT---AGDIQT-VN 123
                +  +  N++ +  K+     + V          +  +    V    A D+     
Sbjct: 63  AHRLSMIPLKTNLEKLP-KIEECEDELVDPSLCQVRYQLSIKANDQVVSVYAKDLIPDDP 121

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           D   + PD +I  +    V+ +E     G     AK  
Sbjct: 122 DFAPVYPDTLIVKMSKGQVLSIEAYAKLGRARDHAKWQ 159


>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 = 48.4 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 39  LSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKALEECGLSF 91


>gi|324325259|gb|ADY20519.1| hypothetical protein YBT020_06365 [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 95

 Score = 48.4 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 26/53 (49%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  + N L    I  + +L + +E ++L++   G  S+ +++  L   GL  
Sbjct: 42  LSSPARNALEHHGIQTIEELSKYSEKEILKLHGMGPTSMPKLRKALEESGLSF 94


>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 = 48.4 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 39  LSAPARRALEHHGIHTLEELSKYSEKEILKLHGIGPASLPKLRTALEDKGLSF 91


>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 = 48.4 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 36/217 (16%), Positives = 76/217 (35%), Gaps = 35/217 (16%)

Query: 40  AHT--LGNALRRVLMSSLRGAAITAVQI-DGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
             T    N +RR +++ +   AI  V+  +           +   L  +    +G     
Sbjct: 23  GVTPGFANGIRRAMLADVPTMAIDTVRFVENSSVMFDEQLALRLGLVPLTTPPEGEF--- 79

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQTVND-IEVLNPDHVICNLDVDAVVRMELTVSKGHGY 155
             D    ++I   GP    +GD+ + +D ++  + +  I +L  D  +  E      +G 
Sbjct: 80  GEDETVTLSIDVEGPATAYSGDLVSSDDLVQPADENVPIIDLKDDQRLEAEADAVLDYGK 139

Query: 156 VPAKHH--------------------RTENDPIG----LITIDALYSPIKKVSYTVESAR 191
             AKH                       E +       +I  D    P  +  + + +  
Sbjct: 140 DHAKHQGGVAVGYRHLQRVEVVGDLPEFEEEESRIVRGVIEDDGELVPTSEFDHDLSNRY 199

Query: 192 EGQVLDYDKL----SMTIDTDGSITGEDSVALASRIL 224
            G+ ++ + +       ++TDGS + E+ V  A+  +
Sbjct: 200 PGKEVEIEDVPNAFVFHVETDGSFSVEELVTRAADSI 236


>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 = 48.1 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 42  LSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSF 94


>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 = 48.1 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 24/53 (45%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L +   G  SL +++  L   GL  
Sbjct: 39  LSAPARRALEHHGIHTVEELSKYSEKEILNLHGMGPASLPKLRKALEENGLSF 91


>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 = 48.1 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 29/146 (19%), Positives = 55/146 (37%), Gaps = 10/146 (6%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSIK 76
           +   + E+ R   +A    RG    L N +RR +++ +   +I  V+  +        + 
Sbjct: 7   VEFIEREDRRARFVA----RGLTPALANGIRRAMVADVPTFSIDTVRFVENTSVMFDEMI 62

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV-LNPDHVIC 135
           G+   L  +   +              V +   GP    +GDI++ +D+ V  + +  I 
Sbjct: 63  GLRLGLVPLTTPLDD----FEPGDTVTVALEVDGPATAYSGDIESADDMVVPADENIPII 118

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHH 161
            L     +  E     GHG   AK+ 
Sbjct: 119 ELKEGQRLEFEADAVLGHGKDHAKNQ 144


>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 = 48.1 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 42  LSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSF 94


>gi|166714714|gb|ABY88082.1| RpoA [Stenotrophomonas sp. LMG 10996]
          Length = 67

 Score = 48.1 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 19/58 (32%), Positives = 30/58 (51%)

Query: 194 QVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
              D DKL + I+T+G+I  E++V  A+ I  DQL +F +F    +   +  N    P
Sbjct: 1   HRTDLDKLVIDIETNGTIDAEEAVRTAADIPSDQLSVFGDFTHRDRGAAKPANNGVDP 58


>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 = 48.1 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 39  LSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKALEEGGLSF 91


>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 = 48.1 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 42  LSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSF 94


>gi|310794498|gb|EFQ29959.1| RNA polymerase Rpb3/RpoA insert domain-containing protein
           [Glomerella graminicola M1.001]
          Length = 339

 Score = 48.1 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 43/234 (18%), Positives = 87/234 (37%), Gaps = 41/234 (17%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTDIILNIKG 91
            +  N+LRRV+ + +   AI  V+I+          + H +  I    +D+  ++     
Sbjct: 36  LSFANSLRRVIQAEVPVIAIDLVEIEANTSVLADEFIAHRLGLIPLQSKDVNSLLYTRDC 95

Query: 92  INLKMSGDSHKRVTIFKRG----PGVVTAGDIQTVN--------DIEVLNPD---HVICN 136
              +   +   ++T+  R        V A D+   +        +  +L+P+    +IC 
Sbjct: 96  DCEQYCDNCSVKLTLHARCSSDDTMKVYASDLIVDSFRQNGTVGNPVILDPEGQGSLICK 155

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHR------TENDPIGLITIDALYS-------PIKKV 183
           L     +++     KG     AK           +    L  +D  Y        P  K 
Sbjct: 156 LRKGQELKISCIAKKGIAKEHAKWMPTSAVGFEYDPHNKLHHLDMWYEEDAKAEWPDSKY 215

Query: 184 SYTVESAREGQVLDYD----KLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           +   +  +EG   DYD    K    ++  GS+  +  +    +ILQ++L + ++
Sbjct: 216 AKMEDPPQEGDPFDYDAVPGKFYFEVEGVGSLEPDQIIQEGIKILQEKLALTLH 269


>gi|19075824|ref|NP_588324.1| RNA polymerase II subunit 3 [Schizosaccharomyces pombe 972h-]
 gi|13124820|sp|P37382|RPB3_SCHPO RecName: Full=DNA-directed RNA polymerase II subunit RPB3;
           Short=RNA polymerase II subunit 3; Short=RNA polymerase
           II subunit B3; AltName: Full=DNA-directed RNA polymerase
           II 33 kDa polypeptide
 gi|256599717|pdb|3H0G|C Chain C, Rna Polymerase Ii From Schizosaccharomyces Pombe
 gi|256599729|pdb|3H0G|O Chain O, Rna Polymerase Ii From Schizosaccharomyces Pombe
 gi|2465184|dbj|BAA22566.1| polymerase II third largest subunit (subunit 3)
           [Schizosaccharomyces pombe]
 gi|3790255|emb|CAA21444.1| RNA polymerase II subunit 3 [Schizosaccharomyces pombe]
          Length = 297

 Score = 48.1 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 46/271 (16%), Positives = 89/271 (32%), Gaps = 54/271 (19%)

Query: 43  LGNALRRVLMSSLRGAAITAVQID----GVLHEI---------------SSIKGVHEDLT 83
           + N+LRRV+++ +   AI  V+I+     +  E                     V  + T
Sbjct: 28  VANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFLAHRLGMIPLDSSNIDEPPPVGLEYT 87

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH--------VIC 135
                      K S +          G   + A D+   ++  + +P          +IC
Sbjct: 88  RNCD-CDQYCPKCSVELFLNAKCTGEGTMEIYARDLVVSSNSSLGHPILADPKSRGPLIC 146

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT--------------IDALYSPIK 181
            L  +  + +     KG     AK   T                        DA +   K
Sbjct: 147 KLRKEQEISLRCIAKKGIAKEHAKWSPTSAVAFEYDPWNKLQHTDYWFENDADAEWPKSK 206

Query: 182 KVSYTVESAREGQVLDYD----KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
              +  E  REG+  ++     +  M +++ GSI   + +    RILQ++L + +   + 
Sbjct: 207 NADWE-EPPREGEPFNFQEEPRRFYMDVESVGSIPPNEIMVQGLRILQEKLAVLVRDLDE 265

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           ++  +   N  ++  N        E+  S  
Sbjct: 266 EQPTQLSANELNMEEN-------AEMNWSPY 289


>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 = 48.1 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 38/167 (22%), Positives = 59/167 (35%), Gaps = 14/167 (8%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG-----VLHE 71
            I     EEN    +    P  FA    NALRR ++S +   AI  V+I           
Sbjct: 2   KIEFSSLEENAASFVLSDAPIAFA----NALRRAMVSEVMTFAIEDVKIYDNTSALFDEI 57

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSG----DSHKRVTIFKRGPGVVTAGDIQT-VNDIE 126
           ++   G+   +TD    +       +G         +T+   GPGVV +GD+ +    + 
Sbjct: 58  LTHRLGLIPLVTDPDSFVPRSQCSCNGAGCPRCTVTLTMSVEGPGVVMSGDLISQDAVVR 117

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITI 173
               +  I  L+ +  V +E       G   AK   T         I
Sbjct: 118 PAEDNIPIVKLEKNQKVVIEAQAYMERGMEHAKWSPTTVCGYKNYPI 164


>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 = 48.1 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 37/244 (15%), Positives = 79/244 (32%), Gaps = 48/244 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ-IDGVLHEISSIK 76
           + + + ++     +     RG      N +RR +++ +   +I +V+ I+      +   
Sbjct: 7   VEIIERDDRSARFLV----RGATPAFANGIRRAMLADVPTLSIDSVRFIENSSVMFNE-- 60

Query: 77  GVHEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTA---GDIQTVNDIEVLNPD 131
                   + L +  + L    D    + VT+     G  TA     + +   +E  + +
Sbjct: 61  -------QLALRLGLVPLSTPEDYELGEDVTLALDVEGPATAYSGDLVSSDEQVEPADRN 113

Query: 132 HVICNLDVDAVVRMEL--TVSKGH-----------GYVPAKHHRTENDPIGLITIDAL-- 176
             I  L     + +E    +  G            GY        E D       +A   
Sbjct: 114 VPIIELKEGQRLELEADAVLDVGREHAKHQGGVAVGYRHLVRVNIEGDREEFADEEANIV 173

Query: 177 ----------YSPIKKVSYTVESAREGQVLDYDKL----SMTIDTDGSITGEDSVALASR 222
                          +  + + +   G+ L  + +       ++TDGS+T  + V  A+ 
Sbjct: 174 RGVVETDEGELVLTDEFDHDLTNRYPGKELRLEDVPDAFVFHVETDGSMTASELVDRAAA 233

Query: 223 ILQD 226
            L D
Sbjct: 234 SLGD 237


>gi|13541396|ref|NP_111084.1| DNA-directed RNA polymerase subunit D [Thermoplasma volcanium GSS1]
 gi|20978715|sp|Q97B93|RPOD_THEVO RecName: Full=DNA-directed RNA polymerase subunit D
 gi|14324779|dbj|BAB59706.1| DNA-directed RNA polymerase D [Thermoplasma volcanium GSS1]
          Length = 271

 Score = 48.1 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 52/271 (19%), Positives = 91/271 (33%), Gaps = 61/271 (22%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + +  +       + +    A    NALRR L++ +   AI  V       EI   +G
Sbjct: 3   VKIFKLSDKYMSFEIDGITPSQA----NALRRTLINDIPKLAIENVTFH--HGEIRDAEG 56

Query: 78  VHEDLT------DIILNIKGINLKMS----------------GDSHKRVTIFKRGPGVVT 115
              D +       +   +  I LK                         +I K GP  V 
Sbjct: 57  NVYDSSLPLFDEMVAHRLGLIPLKTDLSLNFRDQCSCGGKGCSLCTVTYSINKIGPASVM 116

Query: 116 AGDIQTVN--DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---------- 163
           +GDIQ ++  D+  ++PD  I  L     + +      G     AK   T          
Sbjct: 117 SGDIQAISHPDLVPVDPDIPIVKLGAKQAILITAEAILGTAKEHAKWQVTSGVAYKYHRE 176

Query: 164 ---------------ENDPIGLITIDA---LYS---PIKKVSYTVESAREGQVLDYDKLS 202
                          E  P  +++ D    +++       +S   ES       D  +  
Sbjct: 177 FEVNKKLFEDWAKIKERCPKSVLSEDENTIVFTDDYGCNDLSILFESDGVQIKEDDSRFI 236

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFIN 233
              +TDGS+T E++++ A   L D+ G+ + 
Sbjct: 237 FHFETDGSLTAEETLSYALNRLMDRWGILVE 267


>gi|1834323|dbj|BAA09316.1| RNA polymerase II subunit 3 [Schizosaccharomyces pombe]
          Length = 296

 Score = 48.1 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 46/271 (16%), Positives = 89/271 (32%), Gaps = 54/271 (19%)

Query: 43  LGNALRRVLMSSLRGAAITAVQID----GVLHEI---------------SSIKGVHEDLT 83
           + N+LRRV+++ +   AI  V+I+     +  E                     V  + T
Sbjct: 28  VANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFLAHRLGMIPLDSSNIDEPPPVGLEYT 87

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH--------VIC 135
                      K S +          G   + A D+   ++  + +P          +IC
Sbjct: 88  RNCD-CDQYCPKCSVELFLNAKCTGEGTMEIYARDLVVSSNSSLGHPILADPKSRGPLIC 146

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT--------------IDALYSPIK 181
            L  +  + +     KG     AK   T                        DA +   K
Sbjct: 147 KLRKEQEISLRCIAKKGIAKEHAKWSPTSAVAFEYDPWNKLQHTDYWFENDADAEWPKSK 206

Query: 182 KVSYTVESAREGQVLDYD----KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
              +  E  REG+  ++     +  M +++ GSI   + +    RILQ++L + +   + 
Sbjct: 207 NADWE-EPPREGEPFNFQEEPRRFYMDVESVGSIPPNEIMVQGLRILQEKLAVLVRDLDE 265

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           ++  +   N  ++  N        E+  S  
Sbjct: 266 EQPTQLSANELNMEEN-------AEMNWSPY 289


>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 = 48.1 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 40/219 (18%), Positives = 75/219 (34%), Gaps = 25/219 (11%)

Query: 45  NALRRVLMSSLRGAAI--------TAVQIDGVL-HEISSIKGVHEDLTDI--ILNIKGIN 93
           N+LRRVL+S +   AI        T+V  D VL H +S +  +  DL  +  I   +   
Sbjct: 27  NSLRRVLISDVPVLAIDEVIILDNTSVLYDEVLAHRLSMMP-IKTDLRKLPKIEECEQEL 85

Query: 94  LKMSGDSHKR-VTIFKRGPGVVTAGDIQ-TVNDIEVLNPDHVICNLDVDAVVRMELTVSK 151
           +  S    +  + +  + P +V + D++    ++  +  D  I  L     + +E     
Sbjct: 86  VDPSLCQVRFELNVEAKEPMIVYSRDLKSDDPEVRPVYEDIPIVKLVPGQKIVLEAYAKL 145

Query: 152 GHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
           G     AK             +  +     K    +E             ++ I  DGSI
Sbjct: 146 GRARNHAKWQAGLASYYYYPKVSVVGKADDKCRVCLEVCNG---------ALEIKEDGSI 196

Query: 212 TGEDSVALA--SRILQDQLGMFINFEEPKKEVKEDINVK 248
              D +          +QL   +  +  + +    +   
Sbjct: 197 IINDVLKCTFNKWKTCEQLCPALKVDWDENKYVFWVESF 235


>gi|1834322|dbj|BAA09315.1| RNA polymerase II subunit 3 [Schizosaccharomyces pombe]
          Length = 296

 Score = 47.7 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 46/271 (16%), Positives = 89/271 (32%), Gaps = 54/271 (19%)

Query: 43  LGNALRRVLMSSLRGAAITAVQID----GVLHEI---------------SSIKGVHEDLT 83
           + N+LRRV+++ +   AI  V+I+     +  E                     V  + T
Sbjct: 28  VANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFLAHRLDMIPLDSSNIDEPPPVGLEYT 87

Query: 84  DIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH--------VIC 135
                      K S +          G   + A D+   ++  + +P          +IC
Sbjct: 88  RNCD-CDQYCPKCSVELFLNAKCTGEGTMEIYARDLVVSSNSSLGHPILADPKSRGPLIC 146

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT--------------IDALYSPIK 181
            L  +  + +     KG     AK   T                        DA +   K
Sbjct: 147 KLRKEQEISLRCIAKKGIAKEHAKWSPTSAVAFEYDPWNKLQHTDYWFENDADAEWPKSK 206

Query: 182 KVSYTVESAREGQVLDYD----KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
              +  E  REG+  ++     +  M +++ GSI   + +    RILQ++L + +   + 
Sbjct: 207 NADWE-EPPREGEPFNFQEEPRRFYMDVESVGSIPPNEIMVQGLRILQEKLAVLVRDLDE 265

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVR 268
           ++  +   N  ++  N        E+  S  
Sbjct: 266 EQPTQLSANELNMEEN-------AEMNWSPY 289


>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 = 47.7 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 31/151 (20%), Positives = 57/151 (37%), Gaps = 16/151 (10%)

Query: 38  GFAHTLGNALRRVLMSSLRGAAITAVQID---GV------LHEISSIK-GVHEDLTDIIL 87
           G   +L NALRR+L+S +   A+  VQI    GV       H +  I   +  DL +   
Sbjct: 51  GLDVSLANALRRILISEVPTLAVETVQIYQNTGVIQDELLAHRLGLIPFAIDPDLFNFKS 110

Query: 88  NIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP------DHVICNLDVDA 141
           N K    +++  +     +  +      +  + + + +   NP      D +I  L    
Sbjct: 111 NFKTNCEEINDKNSVCFKLKVKYNKFDQSDYLSSNSLMFKDNPPKPVYDDILITKLAPGQ 170

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLIT 172
            + + + + KG G V +K           + 
Sbjct: 171 EIDLNMYLEKGIGKVHSKWSPVSTAVYKFMP 201


>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 = 47.7 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 42  LSAPARRALEHHGIQTVEELSKYSEKEILKLHGMGPASLPKLRKALEERGLSF 94


>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 = 47.7 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 49/259 (18%), Positives = 92/259 (35%), Gaps = 57/259 (22%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHT---LGNALRRVLMSSLRGAAITAVQIDG------- 67
           + + +  +     + E       +T   + N++RRV MS +   AI  VQID        
Sbjct: 9   VKITELSDENVKFVIE-------NTDLAVANSIRRVFMSEVPTIAIDWVQIDANSSVLHD 61

Query: 68  --VLHEISSIKGVHEDLTDIILNIKG---------------INLKMSGDSHKRVT---IF 107
             V H +  I    +D+ D +   +                ++++ + D  + VT   + 
Sbjct: 62  EFVAHRVGLIPLTSDDIVDKMQYSRDCTCDDFCPECSVELTLDVRCTEDQTRHVTSRDLL 121

Query: 108 KRGPGV--VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
              P V  VT+       +  V   D ++  L     +R+     KG G   AK + T  
Sbjct: 122 SNNPRVIPVTSRSRDNDPNDYVEQDDILLVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181

Query: 166 DPIGLITIDAL---------------YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
                   +AL               YS I++     +    G+    ++    +++ GS
Sbjct: 182 VAFEYDPDNALRHTVYPIPQEWPKSEYSEIEEDGVQAQYDPNGKP---ERFYYNVESCGS 238

Query: 211 ITGEDSVALASRILQDQLG 229
           +  E  V  A  +L+ +L 
Sbjct: 239 LRPETIVMSALAMLKKKLS 257


>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 = 47.3 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 42  LSAPARRALEYHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSF 94


>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 = 47.3 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 15/44 (34%), Positives = 23/44 (52%)

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
             LS R+ N L   NI+ +  L + +E ++  M   G K+L EI
Sbjct: 9   TNLSTRAINILARNNILTLSQLKECSEKELRSMRGLGGKTLDEI 52



 Score = 41.9 bits (97), Expect = 0.13,   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


>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 = 19/78 (24%), Positives = 36/78 (46%), Gaps = 1/78 (1%)

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQ-RTEADMLRMA 296
           +++ +          +      +EEL LSVR+ N  R  NI  +  LI+     D+  + 
Sbjct: 72  EEDFEITEADLIEEKDVQEDFPIEELGLSVRALNAFRRVNIHTLNSLIEFLATNDISEIK 131

Query: 297 NFGRKSLVEIKGVLGTMG 314
           N G K++ E + ++  +G
Sbjct: 132 NVGAKTIQETEELMRRVG 149


>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 = 0.004,   Method: Composition-based stats.
 Identities = 16/55 (29%), Positives = 26/55 (47%)

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
           EL LS+R+ N LR   I  + DL   ++  + +    G  SL +I+  L    + 
Sbjct: 11  ELNLSIRAYNSLRNMGINTLEDLSTYSKKQLYQFKGIGIVSLRKIEKGLDKKNMK 65


>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 = 46.9 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 26/57 (45%)

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
            +  VR     +   I  + DL  +++ ++       +KS+  I+ +LG   L LGM
Sbjct: 17  KQYGVRVQRIFQTNGIFTVRDLCSQSKQELRHTRYLSKKSISMIEKILGKYALRLGM 73


>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 = 46.9 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 47/276 (17%), Positives = 92/276 (33%), Gaps = 45/276 (16%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG--------- 67
            + + Q +  R           FA    N+LRRV+++ +   AI  V+I+          
Sbjct: 17  VVKISQADNTRVKFELSNTELSFA----NSLRRVMLAEIPTIAIDLVEIEANSSVLADEF 72

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG----VVTAGDIQTVN 123
           + H +  I    E +  ++ +      +        + +  +  G     V A D+  V 
Sbjct: 73  IAHRLGLIPLNAEGIEQLLYSRDCDCDEYCEHCSVTLNLHAKCTGDDIMQVCARDLVPVG 132

Query: 124 D-IE------VLNPDH----VICNLDVDAVVRMELTVSKGHGYVPAKHHR------TEND 166
           D +       ++N       +I  L     ++++    KG     +K           + 
Sbjct: 133 DRVNQVLGSPIINDPEGQGPLILKLRHGQEIKLQCIAKKGIAKEHSKWAPSAAIGFEYDP 192

Query: 167 PIGLITIDALYSPIKKVSY-------TVESAREGQVLDYD----KLSMTIDTDGSITGED 215
              L  +D  Y    K  +         E  +EG+  DYD    +    ++T G I  + 
Sbjct: 193 HNKLHHLDLWYEQDPKKEWPPSEYADWEEPPQEGEPFDYDAVPQRFYYNVETAGPIPPDA 252

Query: 216 SVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
            V    +++Q +L   I+        +   N    P
Sbjct: 253 IVTEGIKVIQQKLAGLIHELTESDGGENGYNGPRSP 288


>gi|167517689|ref|XP_001743185.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163778284|gb|EDQ91899.1| predicted protein [Monosiga brevicollis MX1]
          Length = 276

 Score = 46.9 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 47/229 (20%), Positives = 79/229 (34%), Gaps = 45/229 (19%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDG---VLH-EISSIK----GVHEDLTDIILNIKGINL 94
           L N+ RRV+++ +   AI AV I     VLH E  + +     +  +  D     +   L
Sbjct: 34  LANSFRRVMIAEVPTMAIDAVHIAKNTSVLHDEFLAHRLGLIPLTSEAADKFYYPRDCTL 93

Query: 95  KMSG--DSHKRVTIFKRGPGV----VTAGDI--QTVNDIEVLNP-----------DHVIC 135
              G       +T+   G       VT  D+  Q   D   + P             VIC
Sbjct: 94  CEMGCDHCQVMLTLDVEGHTEEPTHVTTDDLISQAAGDFMAVKPISAREESNIRNPIVIC 153

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL---------------YSPI 180
            L     +++     KG G   AK   T          +AL               +S +
Sbjct: 154 KLAKGQRIQLTAFAKKGFGKEHAKWCPTAGIAFEYDPDNALRHTFFEVPSMWPKSEFSTL 213

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            +  +  E   +G+   Y    MT+++ G++     +  A   L ++L 
Sbjct: 214 PEGEHEAEYDYKGKPSTY---FMTVESTGALPAPLILFSALESLHEKLS 259


>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 = 46.9 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 18/61 (29%), Positives = 34/61 (55%)

Query: 201 LSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV 260
           L + I T+GS+T ++++  ASR L +    F++ EE    ++ + +  +LPF P   + V
Sbjct: 4   LFLEIWTNGSLTPKEALHEASRNLINLFIPFLHVEEETFYLENNQHQVTLPFFPFHNRLV 63

Query: 261 E 261
            
Sbjct: 64  N 64


>gi|218931178|ref|NP_001135345.1| DNA-directed RNA polymerase II subunit RPB3 [Salmo salar]
 gi|209734758|gb|ACI68248.1| DNA-directed RNA polymerase II subunit RPB3 [Salmo salar]
 gi|223647266|gb|ACN10391.1| DNA-directed RNA polymerase II subunit RPB3 [Salmo salar]
 gi|223673145|gb|ACN12754.1| DNA-directed RNA polymerase II subunit RPB3 [Salmo salar]
          Length = 275

 Score = 46.5 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 46/254 (18%), Positives = 88/254 (34%), Gaps = 45/254 (17%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG--------- 67
            + + +  +     + E        ++ N++RRV MS +   AI  +QID          
Sbjct: 8   IVKITELTDENVKFVIENTD----LSVANSIRRVFMSEVATIAIDWIQIDANSSVIHDEF 63

Query: 68  VLHEISSIKGVHEDLTDIILNIKG---------------INLKMSGDSHKRVT---IFKR 109
           + H +  I    +D+ D +   +                ++++ + D  + VT   +   
Sbjct: 64  IAHRVGLIPLTSDDVVDKMQYSRDCTCDDFCPECSVELTLDVRCTEDQTRHVTSRDLLSN 123

Query: 110 GPGV--VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
            P V  VT+       +  V   D ++  L     +R+     KG G   AK + T    
Sbjct: 124 HPRVIPVTSKSRDNDPNDYVEQDDILLVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVS 183

Query: 168 IGLITIDALYSPIK-------KVSYT-----VESAREGQVLDYDKLSMTIDTDGSITGED 215
                 +AL   +        K  Y+        A        ++    ++T GS+  E 
Sbjct: 184 FEYDPDNALRHTVYPRPEEWPKSEYSEIEEDEVQAPFDPNGKPERFYYNVETCGSLRPET 243

Query: 216 SVALASRILQDQLG 229
            V  A  +L+ +L 
Sbjct: 244 IVMSALAVLKKKLS 257


>gi|225716034|gb|ACO13863.1| DNA-directed RNA polymerase II subunit RPB3 [Esox lucius]
          Length = 275

 Score = 46.5 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 46/254 (18%), Positives = 88/254 (34%), Gaps = 45/254 (17%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG--------- 67
            + + +  +     + E        ++ N++RRV MS +   AI  +QID          
Sbjct: 8   IVKITELTDENVKFVIENTD----LSVANSIRRVFMSEVATIAIDWIQIDANSSVIHDEF 63

Query: 68  VLHEISSIKGVHEDLTDIILNIKG---------------INLKMSGDSHKRVT---IFKR 109
           + H +  I    +D+ D +   +                ++++ + D  + VT   +   
Sbjct: 64  IAHRVGLIPLTSDDVVDKMQYSRDCTCDDFCPECSVELTLDVRCTEDQTRHVTSRDLLSN 123

Query: 110 GPGV--VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
            P V  VT+       +  V   D ++  L     +R+     KG G   AK + T    
Sbjct: 124 HPRVIPVTSKSRDNDPNDYVEQDDILLVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVS 183

Query: 168 IGLITIDALYSPIK-------KVSYT-----VESAREGQVLDYDKLSMTIDTDGSITGED 215
                 +AL   +        K  Y+        A        ++    ++T GS+  E 
Sbjct: 184 FEYDPDNALRHTVYPRPEEWPKSEYSEIEEDEVQAPFDPNGKPERFYYNVETCGSLRPET 243

Query: 216 SVALASRILQDQLG 229
            V  A  +L+ +L 
Sbjct: 244 IVMSALAVLKKKLS 257


>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 = 46.5 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 26/53 (49%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LSV +   L    I  + +L + +E ++L++   G  S+ +++  L   GL  
Sbjct: 42  LSVPARRALEHHGIHTVEELSKYSEKEVLKLHGMGPASMPKLRKALEEQGLSF 94


>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 = 16/55 (29%), Positives = 26/55 (47%)

Query: 262 ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLF 316
           EL LS+R+ N LR   I  + DL   ++  + +    G  SL +I+  L    + 
Sbjct: 11  ELNLSIRAYNSLRNMGINTLEDLSMYSKKQLYQFKGIGIVSLRKIEKGLDKKNMK 65


>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 = 46.5 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 36/178 (20%), Positives = 59/178 (33%), Gaps = 19/178 (10%)

Query: 29  LMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88
                    G   +  +ALRR+++SS+   AI  V      +  S    +      +I  
Sbjct: 17  KFTIG----GAPISFSSALRRIMVSSVPTYAIENVYFY--ENSSSMYDEILAHRLALIPI 70

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
                +    D   R +I K GP  V + D+++ +D  V   +  I  L     + +E  
Sbjct: 71  TGKPVI---SDEVVRFSIMKEGPCTVYSADLESESDSMVAFDNIPIVKLKEGQKLELECE 127

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTID 206
              G G           +       +A Y  IK           GQ+   D L   I+
Sbjct: 128 ALVGVG----------KNHAKWQPCNASYKLIKDNEVEFSVESHGQMDSEDILISAIE 175


>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 = 46.5 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 28/57 (49%)

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
              ++R  N     +I  + +L   +  D++   + G +S+  ++ +LG  GL LGM
Sbjct: 17  EPYALRIRNVCNSHDIATIRELCLHSNWDLIHFRHLGERSIAHMEEMLGNFGLRLGM 73


>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 = 46.1 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 4/67 (5%)

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD----MLRMANFGRKSLVEIK 307
            N   L  V + +L  R+ N LR   I  + DL++ T+      +L+   FG  SL  +K
Sbjct: 112 MNVLSLSLVSDFDLDTRTINMLRKMEIYTLEDLLRYTKDKGLQVLLKYRGFGAHSLALLK 171

Query: 308 GVLGTMG 314
             L   G
Sbjct: 172 ESLIKKG 178


>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 = 46.1 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 42  LSAPARRALEHHGIQTVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSF 94


>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 = 46.1 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 42  LSAPARRALEHHGIQTVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSF 94


>gi|328853564|gb|EGG02702.1| hypothetical protein MELLADRAFT_72730 [Melampsora larici-populina
           98AG31]
          Length = 359

 Score = 46.1 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 43/273 (15%), Positives = 83/273 (30%), Gaps = 60/273 (21%)

Query: 9   LIKPNNIE----YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           L  P +I+     + + + +E     + E    G    L N+LRR +M+ L   AI +V+
Sbjct: 8   LEPPQSIDGSNLQVKVTELDERHAAFVVE----GVDLALANSLRRTIMADLTTVAIHSVE 63

Query: 65  IDG---------VLHEISSIKGVHEDLTDIILNIKG--INLKMSGDSHKRVTIFKRG--- 110
            +          + H +  +  + EDL   + N +     L    D    + +  +    
Sbjct: 64  FEENTSVLPDEMIAHRLGLMPLMSEDLDKYLKNWQRDCTCLSFCDDCSIELVLSVKSTLP 123

Query: 111 --PGVVTAGDIQTVN--------------DIEVLNPDHV---ICNLDVDAVVRMELTVSK 151
                VT+ D+                     + N +     I  L     V+++    K
Sbjct: 124 GETLEVTSKDLVITPREDGGDRGDVGKPVQFTLPNGEQPGVLITKLRKGQEVKLKCRAIK 183

Query: 152 GHGYVPAKHHR------TENDPIGLITID----------ALYSPIKKVSYT---VESARE 192
           G     AK           +    L   D          A +   K   +    ++    
Sbjct: 184 GIAQEHAKWSAVSTIGFEYDPHNRLGHTDLWYEVGTDARAEWPLTKNAKFERPPLDDEPV 243

Query: 193 GQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
                  +    +++ G++  ED V      L 
Sbjct: 244 DFTTKPSRFYFDVESAGNLRPEDIVVKGIESLI 276


>gi|304314287|ref|YP_003849434.1| DNA-directed RNA polymerase, subunit D [Methanothermobacter
           marburgensis str. Marburg]
 gi|302587746|gb|ADL58121.1| DNA-directed RNA polymerase, subunit D [Methanothermobacter
           marburgensis str. Marburg]
          Length = 264

 Score = 46.1 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 53/260 (20%), Positives = 87/260 (33%), Gaps = 61/260 (23%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLG--NALRRVLMSSLRGAAITAVQ--------IDG 67
           I L ++ +   + +          T+   NA+RR+ M  +   AI  V          D 
Sbjct: 3   IALKEKTDTEMVFVVT------GVTVPFINAIRRICMMEVPKLAIEYVNMYRNDARMFDE 56

Query: 68  VL-HEISSIKGVHEDLTDIILNIK---GINLKMS-GDSHKRVTIFKRGPGVVTAGD-IQT 121
           VL H +  +  +  D  + I  +K     + +    +     T+ K+GPGVV + D +  
Sbjct: 57  VLAHRLGLVP-LKAD-PEFIEGLKMPEECDCEEYCSECSVSFTLKKKGPGVVYSRDLLSE 114

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT--------- 172
              +E + PD  +  L  +  V +E     G G   AK   T                  
Sbjct: 115 TPAVEPVYPDIPLVKLGDEDEVELEAVAQLGVGRDHAKWEPTTACAYKYYPMITFTEECD 174

Query: 173 -----IDA-------------------LYSPIKKV--SYTVESAREGQVLDYDKLSMTID 206
                +DA                     S  K    +    +   G      K    I+
Sbjct: 175 ECLECVDACPRGVLGDESGKPEVLDVENCSMCKSCVRACDKGAIIVGYEE--GKFIFRIE 232

Query: 207 TDGSITGEDSVALASRILQD 226
           TDGS+  +D +  A  IL+D
Sbjct: 233 TDGSVDPQDVLLKACDILRD 252


>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 = 46.1 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 26/53 (49%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L++   G  SL +++ VL   GL  
Sbjct: 42  LSAPARRALEHRGIQTVEELSKYSEKEILKLHGMGPASLPKLRKVLEESGLSF 94


>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 = 46.1 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 42  LSAPARRALEHHGIQTVEELSKYSEKEILKLHGMGPASLPKLRRALEESGLSF 94


>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 = 45.7 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 42  LSAPARRALEQRGIQTVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSF 94


>gi|226287322|gb|EEH42835.1| DNA-directed RNA polymerases I and III subunit RPAC1
           [Paracoccidioides brasiliensis Pb18]
          Length = 380

 Score = 45.7 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 37/193 (19%), Positives = 61/193 (31%), Gaps = 53/193 (27%)

Query: 33  EPLPRGFAH-----TLGNALRRVLMSSLRGAAITAVQIDG----VLHEI----------- 72
           EP    F+      ++ NA RR+L+S +   AI  V I      +  E+           
Sbjct: 60  EPYEASFSLIGVDASIANAFRRILISEIPSLAIETVYIHNNTSVIQDEVLAHRLGLVPLT 119

Query: 73  SSIKGVH-------------------EDLTDIILNIK-------------GINLKMSGDS 100
            S +G++                    D   I+L++                 LK+   +
Sbjct: 120 GSPEGINWLRWFRQPNEGDPSSGSELADYNTIVLHLNVECKKNPKASPDEQDPLKLYSHA 179

Query: 101 HKRVT-IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
           H     I  +  G   A   +    I   NPD ++  L     + +E+   KG G   AK
Sbjct: 180 HVYAKDITFQPVGRQEAYFPEPDGGIRPTNPDILLAKLRPGQKIDIEMHCVKGIGADHAK 239

Query: 160 HHRTENDPIGLIT 172
                     L+ 
Sbjct: 240 FSPVATASYRLLP 252


>gi|257388632|ref|YP_003178405.1| RNA polymerase insert [Halomicrobium mukohataei DSM 12286]
 gi|257170939|gb|ACV48698.1| RNA polymerase insert [Halomicrobium mukohataei DSM 12286]
          Length = 259

 Score = 45.7 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 32/249 (12%), Positives = 79/249 (31%), Gaps = 49/249 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ-IDGVLHEISSIK 76
           +   +  +     +     RG +    N +RR +++ +   ++  V+ I+          
Sbjct: 7   VEFVERSDREARFLV----RGISPAFANGIRRAMIADVPTFSVDTVRVIENSSVMFDEQI 62

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPDHVIC 135
           G+   L  +  ++    +         ++I   GP    +GD+  + + +   + +  I 
Sbjct: 63  GLRLGLVPLTTDLDDFEV----GDEVTLSIDVSGPETAYSGDLVSSDSLVGPADDNIPII 118

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHH--------------------RTENDPIGLI---- 171
           +L     + +E       G   AKH                       E+D   ++    
Sbjct: 119 DLKDGQRLEVEADAVLDRGREHAKHQGGVAVGYRHLQRVEVVGDKGEFEDDETHILRGVI 178

Query: 172 -----------TIDALYSPIKKVSYTVESAREGQVLD----YDKLSMTIDTDGSITGEDS 216
                        D      ++    +     G+ L+     +     ++TDGS++ E+ 
Sbjct: 179 EEQAAEHVDGDADDGDLVLTEEFDSDLTKRYPGKELEVHDVENAFVFHVETDGSLSVEEL 238

Query: 217 VALASRILQ 225
              A   ++
Sbjct: 239 TLRAVDSIR 247


>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 = 45.7 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 17/60 (28%), Positives = 29/60 (48%)

Query: 202 SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVE 261
            + I T+GS+T ++++   SR L D    FI+ EE     +E+ N  + PF     +   
Sbjct: 7   FLEIWTNGSLTPKEALYETSRNLIDLFLPFIHTEEEGTNFEENKNRLTPPFLTFQKRFTN 66


>gi|254167082|ref|ZP_04873935.1| RNA polymerase Rpb3/Rpb11 dimerisation domain [Aciduliprofundum
           boonei T469]
 gi|197623938|gb|EDY36500.1| RNA polymerase Rpb3/Rpb11 dimerisation domain [Aciduliprofundum
           boonei T469]
          Length = 273

 Score = 45.7 bits (107), Expect = 0.011,   Method: Composition-based stats.
 Identities = 44/271 (16%), Positives = 86/271 (31%), Gaps = 62/271 (22%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHT--LGNALRRVLMSSLRGAAITAVQI--------DGVL 69
           + + ++       +        T  + NALRR L++ +   AI  V          +G +
Sbjct: 5   ILEVQDRYIKFEIK------GITPSVANALRRTLINDIPKLAIHKVIFHHGQIRDMEGNV 58

Query: 70  HEISS--IKGVHEDLTDIILNIKGINLKMSGDSHKRV-----------TIFKRGPGVVTA 116
           ++ S+     +      +I     +N+K   +                T+ K GP  V +
Sbjct: 59  YDSSTPLFDEIIAHRLGLIPLPTDLNMKFRDECDHPPDEGCPLCTVTYTLNKHGPATVYS 118

Query: 117 GDIQTVND--IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH------------- 161
           GD+  V D   + ++P   I  L     + +E     G     AK               
Sbjct: 119 GDLIPVGDEKFKPVDPLIPIVKLKEHQAILLEAEAIMGTAKEHAKWQVTSGVSYKYHREI 178

Query: 162 ------------RTENDPIGLITIDALY------SPIKKVSYTVESAREGQVLDYDKLSM 203
                         ++ P  +I  D  +       P K+++  +         D      
Sbjct: 179 KVNKKDSELWEKVKKSCPKNVIKEDDKFIIFTDDMPCKEIAEILSFENPEITEDDSWFIF 238

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINF 234
             +TDGS+   D++  A + L+ +       
Sbjct: 239 EFETDGSLKAIDTLEYAIKRLKTRFNTLREH 269


>gi|303389576|ref|XP_003073020.1| DNA-directed RNA polymerase II subunit Rpb3 [Encephalitozoon
           intestinalis ATCC 50506]
 gi|303302164|gb|ADM11660.1| DNA-directed RNA polymerase II subunit Rpb3 [Encephalitozoon
           intestinalis ATCC 50506]
          Length = 240

 Score = 45.4 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 36/190 (18%), Positives = 60/190 (31%), Gaps = 23/190 (12%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + +    R          G+A    NALRR+L+S +   AI  V+I+     +     
Sbjct: 4   LSIEELTPERIRFTLSNTTVGYA----NALRRILISEVPTIAIDMVEIERNNTVL--PDE 57

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVT---------IFKRGPG----VVTAGDIQTVND 124
           V      +I       LK   +               I          VV+  DI    +
Sbjct: 58  VLAHRLGLIPVYSKRELKYKDECSCSGFCSECSVVFEIDVVHTEDALRVVSTRDIICDEE 117

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
             V+    +I  L  D  ++      KG G   AK              +A     ++ +
Sbjct: 118 DVVVKSGPIITKLARDQGLKARCIGRKGIGRTHAKWSPVSAISFEYDKDNAR----RETN 173

Query: 185 YTVESAREGQ 194
           Y  E + E +
Sbjct: 174 YWFEESIEEE 183


>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 = 45.4 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 42  LSAPARRALEHHGIHNVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSF 94


>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 = 45.4 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 41/243 (16%), Positives = 81/243 (33%), Gaps = 47/243 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSIK 76
           +     ++     +   +   FA    N +RR ++  +   +I  V+  +          
Sbjct: 8   VEFVDRDDREARFVVRNITPAFA----NGIRRAILVDVPTLSIDTVRFVENSSVMFDEQL 63

Query: 77  GVHEDLTDIILNIKGINLKMSGDS----HKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPD 131
           G+          +  + L    D        + +   GPG   +GD+     ++E  + +
Sbjct: 64  GLR---------LGLVPLTTPEDYAAGEAVTLALDVEGPGTAYSGDLVSNDPEVEAADEN 114

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHH---------------------RTENDPI-- 168
             I  L  D  + +E     GHG   AKH                        ++DP   
Sbjct: 115 IPIIELKDDQRLELEADAVMGHGRDHAKHQGGVAVGYRHLQRVHVVGDSPEYADDDPQML 174

Query: 169 -GLITIDALYSPIKKVSYTVESAREGQVLDYDKL----SMTIDTDGSITGEDSVALASRI 223
            G+I  D    P       + +   G+ ++ + +       +++DGS+  E+ V  A   
Sbjct: 175 RGVIEEDDELVPTDDFDNDLTTRYPGKEVEIEDVDGAFVFHVESDGSMPVEELVLRAVDT 234

Query: 224 LQD 226
           L D
Sbjct: 235 LVD 237


>gi|169836384|ref|ZP_02869572.1| DNA-directed RNA polymerase alpha chain [candidate division TM7
           single-cell isolate TM7a]
          Length = 74

 Score = 45.4 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 3/71 (4%)

Query: 117 GDIQTVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAKHHRTE--NDPIGLITI 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|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 = 45.4 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 44  LSAPARRALEHHGIHNVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSF 96


>gi|219852957|ref|YP_002467389.1| DNA-directed RNA polymerase subunit D [Methanosphaerula palustris
           E1-9c]
 gi|219547216|gb|ACL17666.1| RNA polymerase insert [Methanosphaerula palustris E1-9c]
          Length = 273

 Score = 45.4 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 33/192 (17%), Positives = 61/192 (31%), Gaps = 21/192 (10%)

Query: 45  NALRRVLMSSLRGAAITAVQI-DGVLHEISSIKGVHEDLTDIILNIKGINLKMS------ 97
           NA+RR + S +   AI  ++I D        +      L  +  N   + +         
Sbjct: 26  NAIRRAMCSEVPKLAIEDIKIYDNTSALFDEMLAHRIGLVPLKTN-SDLYVSADRCTCEG 84

Query: 98  ---GDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
                     T+   GPG+V + D+     +   ++    I  L+    V +E       
Sbjct: 85  AGCDRCSTMYTLSVEGPGMVYSRDLIPSDPEAVPVDEKIPIVKLEKGQKVVIEARAEMNL 144

Query: 154 GYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
           G V AK   T N       +  + +        V+          D L +     G +T 
Sbjct: 145 GKVHAKWQPTINCGYKNYPVITVETHCDACGTCVDQCP------RDVLVLK---GGVLTV 195

Query: 214 EDSVALASRILQ 225
           E+    +  + +
Sbjct: 196 EEGKLESCSLCK 207


>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 = 45.4 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 44/197 (22%), Positives = 79/197 (40%), Gaps = 34/197 (17%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR- 103
           NA+RR+++S +   AI  V I        +   + +++    L +  I  K   D+    
Sbjct: 28  NAIRRIMISEVPTFAIEDVYI------YENSSSMDDEILAHRLGLIPIKGKPLLDTEIIT 81

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
            T+ K GP  V + D+++ N  EV   +  I  L     +++E     G G V AK    
Sbjct: 82  FTLEKEGPCTVYSSDLKSENG-EVAFKNIPIVKLGKGQRIKIECEAVPGIGKVHAKWQ-- 138

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
                     +A+Y                + L  D++   ++T G I  E  +  A +I
Sbjct: 139 --------PCNAVY----------------KQLSEDEVEFFVETFGQIDAEQILKEAVKI 174

Query: 224 LQDQLGMFINFEEPKKE 240
           L+D+   F+   E  ++
Sbjct: 175 LRDKADSFLQQLETIEQ 191


>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 = 45.4 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 42  LSAPARRALEHRGIQTVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSF 94


>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 = 45.4 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 42  LSAPARRALEHHGIQTVEELSKYSEKEILKLHGMGHASLPKLRRALEESGLSF 94


>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 = 45.4 bits (106), Expect = 0.014,   Method: Composition-based stats.
 Identities = 45/272 (16%), Positives = 83/272 (30%), Gaps = 54/272 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSIK 76
           I + ++++ R + + E    G   T  N +RR+ +  +   AI  V I          + 
Sbjct: 3   IEIREKDDERAVFVVE----GVDDTFINTIRRICLVEIPTLAIEDVNIYKNDAKMFDEVL 58

Query: 77  GVHEDLTDIILNIKGINLKMSGDSH---KRVTIFK---------RGPGVVTAGDIQ-TVN 123
                L  I+ ++    +    D     +   +               +V + D++    
Sbjct: 59  AHRLGLIPIVTDLDSYVMPSECDCESGCQHCRVSFLLKEKCEEGNDSKIVYSKDLKSDDP 118

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT---IDA----- 175
            ++ +     I  L     V +E     G G   AK   T            ID      
Sbjct: 119 AVKPVYDTIPIVRLREGEEVELEAIAELGLGSEHAKWQATTTCGYKYYPKIEIDTEKVND 178

Query: 176 --------------------------LYSPIKKVSYTVESAREGQVLDYD--KLSMTIDT 207
                                       S  +      E      V+D++  K    I+T
Sbjct: 179 LEEYVEECPRNVLQIEDDTLVVGNIENCSTCRTCQRLSEKDDNAIVVDFEESKYIFKIET 238

Query: 208 DGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           DGS+   D + +A  IL ++    INF   ++
Sbjct: 239 DGSLKPFDVLTIACDILSEKADNIINFVNEEE 270


>gi|320166369|gb|EFW43268.1| polymerase II polypeptide C [Capsaspora owczarzaki ATCC 30864]
          Length = 270

 Score = 45.4 bits (106), Expect = 0.014,   Method: Composition-based stats.
 Identities = 48/269 (17%), Positives = 90/269 (33%), Gaps = 40/269 (14%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID---GVLH-EI 72
            + + +   +    +          ++ N+LRRV ++ +   AI  VQ D    VLH E 
Sbjct: 8   VVQILELTPDNVRFVLSKTE----LSVANSLRRVCIAEVPTMAIDLVQFDENSSVLHDEF 63

Query: 73  SSIK----GVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
            + +     +  +       +   +           +T+   GP  V A D+++ ++   
Sbjct: 64  VAHRLGLLPLASETAGEFDYLAECDCDGGCNRCTVSLTLEAEGPCSVVARDLRSSDE--S 121

Query: 128 LNP------------DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT-----ENDPIGL 170
           + P            D V+  L     +++     KG G   AK + T     E DP   
Sbjct: 122 VVPISQRDASGSEQHDVVLVKLGAGQRIKLTAIAKKGIGKEHAKWNPTCGVSMEYDPDNK 181

Query: 171 ITIDALYSPIKKVSYTVESAREGQ-------VLDYDKLSMTIDTDGSITGEDSVALASRI 223
           +     Y P       +     GQ           DK  + ++  G I   D V  A  +
Sbjct: 182 LRHTTYYDPQNWPQSHLSELPAGQCEAPFDINAKADKFWLNVEASGVIPPADIVLNAISV 241

Query: 224 LQDQLG-MFINFEEPKKEVKEDINVKSLP 251
           L+ +L  +   F     +  +    +  P
Sbjct: 242 LKQKLKTLADAFSTEVSQQSDWTQPQHQP 270


>gi|325187132|emb|CCA21673.1| DNAdirected RNA polymerase I and III subunit RPAC1 p [Albugo
           laibachii Nc14]
          Length = 343

 Score = 45.4 bits (106), Expect = 0.015,   Method: Composition-based stats.
 Identities = 36/190 (18%), Positives = 61/190 (32%), Gaps = 38/190 (20%)

Query: 14  NIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-------- 65
            I+   L  +E    L+  +P       ++ NALRR+L+S +   AI  V I        
Sbjct: 42  QIQIKHLDDQEMEFDLIGVDP-------SIANALRRILLSEVPTMAIEHVYIWNNSSIIQ 94

Query: 66  -DGVLH------------EISSIKGVHEDLTDIILNIK-GINLKMSGDSHKRVTIFKRGP 111
            + + H            E        E        I   +++    D ++     K   
Sbjct: 95  DEVLAHRLGLIPLLVDPREFQHFPEDEEAEATDENTIVFKLDVTCRSDPNEPENSSKASH 154

Query: 112 GVVTAGDIQTVND---------IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR 162
             V + D++ V           I  ++ D +I  L     + +E    KG G   AK   
Sbjct: 155 SSVYSRDLEWVPQGNQEERFTSIRPVSEDILIAKLRPGQSIALEAHCRKGIGRDHAKFSP 214

Query: 163 TENDPIGLIT 172
                  L+ 
Sbjct: 215 VSTASYRLLP 224


>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 = 45.0 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 42  LSAPARRALEHHGIHNVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSF 94


>gi|322369534|ref|ZP_08044099.1| DNA-directed RNA polymerase subunit D [Haladaptatus paucihalophilus
           DX253]
 gi|320551266|gb|EFW92915.1| DNA-directed RNA polymerase subunit D [Haladaptatus paucihalophilus
           DX253]
          Length = 248

 Score = 45.0 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 38/239 (15%), Positives = 81/239 (33%), Gaps = 38/239 (15%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ-IDGVLHEISSIK 76
           +      E +   +   +   FA    N +RR +++ +   +I  ++ I+          
Sbjct: 7   VEFIDRGERKARFLVRNVTPAFA----NGIRRAMIADVPTLSIDTLRVIENSSVMFDEQI 62

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND-IEVLNPDHVIC 135
           G+   L  +                  +++   GPG   +GD+ + ++ ++  + +  I 
Sbjct: 63  GLRLGLVPLTTPPGE----FEEGDTVTLSLDVSGPGTAFSGDLISSDEMVQPADDNIPII 118

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRT---------------------ENDPI---GLI 171
           +L     + +E     G G   AKH                        E +P    G I
Sbjct: 119 DLKEGQRLELEADAVLGSGKDHAKHQGGVAVGYRHLQRVEVVGDRDEFGEEEPRILRGTI 178

Query: 172 TIDALYSPIKKVSYTVESAREGQVLD----YDKLSMTIDTDGSITGEDSVALASRILQD 226
             D    P +   + +     G+ ++     +     +++DGS T E+ V  A   L +
Sbjct: 179 EDDGELVPTETFDHDLSQRFPGKEVEVHDVPNAFVFDVESDGSFTVEELVTQAVDSLTE 237


>gi|302908578|ref|XP_003049900.1| predicted protein [Nectria haematococca mpVI 77-13-4]
 gi|256730836|gb|EEU44187.1| predicted protein [Nectria haematococca mpVI 77-13-4]
          Length = 335

 Score = 45.0 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 40/227 (17%), Positives = 76/227 (33%), Gaps = 44/227 (19%)

Query: 43  LGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIILNIKGIN 93
             NALRRV+ + +   AI  V+I         + + H +  I  +       + N +  +
Sbjct: 38  FANALRRVIQAEVPTIAIDLVEIEINSSVLADEFIAHRLGLIP-LDSKGVGELNNSRDCD 96

Query: 94  LKMSGD-SHKRVTIFKRGP----GVVTAGDIQTVNDI-------EVLNPDHV---ICNLD 138
            +   +     + +  +        V A D+              + +P+     I  L 
Sbjct: 97  CEQYCEQCSVTLNLHAKCTSDEIMKVYARDLVVDGRHANSVGSPVITDPEGYGCLIAKLR 156

Query: 139 VDAVVRMELTVSKGHGYVPAKHHR------TENDPIGLITIDALYS---------PIKKV 183
            D  +++     KG     AK           +    L  +D  +          P  K 
Sbjct: 157 KDQELKITCIAKKGIAKEHAKWMPTSAVGFEYDPHNKLHHLDMWFENDTDPEVEWPKSKY 216

Query: 184 SYTVESAREGQVLDYD----KLSMTIDTDGSITGEDSVALASRILQD 226
           +   +  +EG+  DYD    +    ++T GS+  +  V    R+LQ 
Sbjct: 217 AQWEDPPQEGEPFDYDAVPNRFYFEVETSGSMEPDQIVQSGIRVLQQ 263


>gi|168697904|ref|ZP_02730181.1| protein kinase [Gemmata obscuriglobus UQM 2246]
          Length = 1390

 Score = 45.0 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 22/106 (20%), Positives = 41/106 (38%)

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNC 272
             +    A  +L+     F     P      +  +++          V EL L  R+TN 
Sbjct: 756 ARERHDNADEMLRAWRDCFAAIGPPDAGELNEEELRARLEGATFDSSVHELGLGTRATNA 815

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           L   N++ + D++  +   +LR+   G K+  EI   +  +   LG
Sbjct: 816 LDRANMLTVEDMLSVSMRRLLRLRGVGNKTRREIASAVKILRARLG 861


>gi|19074310|ref|NP_585816.1| DNA-DIRECTED RNA POLYMERASE II THIRD CHAIN [Encephalitozoon
           cuniculi GB-M1]
 gi|19068952|emb|CAD25420.1| DNA-DIRECTED RNA POLYMERASE II THIRD CHAIN [Encephalitozoon
           cuniculi GB-M1]
          Length = 240

 Score = 45.0 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 30/156 (19%), Positives = 48/156 (30%), Gaps = 19/156 (12%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + +               G+A    NALRR+L+S +   AI  V+I+     +     
Sbjct: 4   LTVEELTPEHIRFTLSNTTVGYA----NALRRILISEVPTIAIDMVEIERNNTVL--PDE 57

Query: 78  VHEDLTDIILNIKGINLKMSGDSHKRVT---------IFKRGPG----VVTAGDIQTVND 124
           V      +I       LK   +               I           V+  DI    +
Sbjct: 58  VLAHRLGLIPIYSKRELKYKEECSCSGFCSECSVVFEIDVVHTDDTLRTVSTRDIVCDEE 117

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
             ++    VI  L  D  ++      KG G   AK 
Sbjct: 118 DVIIKSGPVITKLARDQGLKARCIGRKGVGKTHAKW 153


>gi|257076683|ref|ZP_05571044.1| DNA-directed RNA polymerase subunit D [Ferroplasma acidarmanus
           fer1]
          Length = 269

 Score = 45.0 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 45/270 (16%), Positives = 88/270 (32%), Gaps = 61/270 (22%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHT--LGNALRRVLMSSLRGAAITAV-----QI---DGV 68
            + + ++N      +        T  + N++RR L++ +   AI  V     +I   DG 
Sbjct: 2   KILELKDNFIRFSID------GITPAIANSIRRTLINDIPKLAIENVIYHHGEIRDADGN 55

Query: 69  LHEISS--IKGVHEDLTDIILNIKGINLKMSGDSHKRV----------TIFKRGPGVVTA 116
           +++ S      +      +I     +++    +               +I K GPG+V +
Sbjct: 56  VYDSSLPLFDEILASRIGLIPLKTDLSMNFRDECSCGGKGCDLCTVTYSINKLGPGMVYS 115

Query: 117 GDI--QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL---- 170
            DI      ++ V +P   I  L  +  + +      G G   AK   T           
Sbjct: 116 SDIMPVNNPELTVTDPLIPIVELKKNQAMLVTCEAILGRGKEHAKWQATSGVSYKYHRNF 175

Query: 171 ----ITIDA--------------------LYS---PIKKVSYTVESAREGQVLDYDKLSM 203
                 +D                     L++   P   +S  +E        D  K   
Sbjct: 176 HVNKAALDNWQFYKDTCPKSVLSENDTTILFTDDIPCSYLSQLMERDGVVVEEDSTKFIF 235

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFIN 233
             +TDGS+   D ++ A   L+++    + 
Sbjct: 236 KFETDGSLKASDVLSYALHRLENRFTALME 265


>gi|291390190|ref|XP_002711589.1| PREDICTED: DNA directed RNA polymerase II polypeptide C
           [Oryctolagus cuniculus]
          Length = 275

 Score = 45.0 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 48/256 (18%), Positives = 90/256 (35%), Gaps = 51/256 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHT---LGNALRRVLMSSLRGAAITAVQIDG------- 67
           + + +  +     I E       +T   + N++RRV ++ +   AI  VQID        
Sbjct: 9   VRITELTDENVKFIIE-------NTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHD 61

Query: 68  --VLHEISSIKGVHEDLTDIILNIKG---------------INLKMSGDSHKRVT---IF 107
             + H +  I    +D+ D + N +                ++++ + D  + VT   + 
Sbjct: 62  EFIAHRLGLIPLTSDDIVDKLQNSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDLI 121

Query: 108 KRGPGV--VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
              P V  VT+ +     +  V   D +I  L     +R+     KG G   AK + T  
Sbjct: 122 SNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181

Query: 166 DPIGLITIDALYSPIK-------KVSYT-----VESAREGQVLDYDKLSMTIDTDGSITG 213
                   +AL   +        K  Y+        A        ++    +++ GS+  
Sbjct: 182 VAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLRP 241

Query: 214 EDSVALASRILQDQLG 229
           E  V  A   L+ +L 
Sbjct: 242 ETIVLSALSGLKKKLS 257


>gi|225677934|gb|EEH16218.1| DNA-directed RNA polymerases I and III subunit RPAC1
           [Paracoccidioides brasiliensis Pb03]
          Length = 345

 Score = 45.0 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 37/215 (17%), Positives = 64/215 (29%), Gaps = 54/215 (25%)

Query: 12  PNNIEYIVLGQEEENRTLMIA-EPLPRGFAH-----TLGNALRRVLMSSLRGAAITAVQI 65
           P       +   +         EP    F+      ++ NA RR+L++ +   AI  V I
Sbjct: 3   PRIASLEEINDRKNLIVTFHKNEPYEASFSLIGVDASIANAFRRILIAEIPSLAIETVYI 62

Query: 66  DG----VLHEI-----------SSIKGVH-------------------EDLTDIILNIK- 90
                 +  E+            S +G++                    D   I+L++  
Sbjct: 63  HNNTSVIQDEVLAHRLGLVPLTGSPEGINWLRWFRQPNEGDPSSGSELADYNTIVLHLNV 122

Query: 91  ------------GINLKMSGDSHKRVT-IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNL 137
                          LK+   +H     I  +  G   A   +    I   NPD ++  L
Sbjct: 123 KCKKNPKASPDEQDPLKLYSHAHVYAKDITFQPVGRQEAYFPEPDGGIRPTNPDILLAKL 182

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT 172
                + +E+   KG G   AK          L+ 
Sbjct: 183 RPGQKIDIEMHCVKGIGADHAKFSPVATASYRLLP 217


>gi|325103580|ref|YP_004273234.1| hypothetical protein Pedsa_0840 [Pedobacter saltans DSM 12145]
 gi|324972428|gb|ADY51412.1| hypothetical protein Pedsa_0840 [Pedobacter saltans DSM 12145]
          Length = 93

 Score = 45.0 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 12/56 (21%), Positives = 27/56 (48%)

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           ++L+  +   L    I  +  L   +E ++L++   G+ ++ ++K  L T GL   
Sbjct: 37  IQLAAPARRALENAGIDTLNKLSLYSEKEILKLHGIGKTAIPKLKEALLTKGLTFN 92


>gi|209730678|gb|ACI66208.1| DNA-directed RNA polymerase II subunit RPB3 [Salmo salar]
          Length = 275

 Score = 45.0 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 46/254 (18%), Positives = 85/254 (33%), Gaps = 45/254 (17%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG--------- 67
            + + +  +     + E        ++ N++RRV MS +   AI  +QID          
Sbjct: 8   IVKITELTDENVKFVIENTD----LSVANSIRRVFMSEVATIAIDWIQIDANSSVIHDEF 63

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINL---------------KMSGDSHKRVT---IFKR 109
           + H +  I    +D+ D +   +                   + + D  + VT   +   
Sbjct: 64  IAHRVGLIPLTSDDVVDKMQYSRDCTCDDFCPECSVELTLDARCTEDQTRHVTSRDLLSN 123

Query: 110 GPGV--VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
            P V  VT+       +  V   D ++  L     +R+     KG G   AK + T    
Sbjct: 124 HPRVIPVTSKSRDNDPNDYVEQDDILLVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVS 183

Query: 168 IGLITIDALYSPIK-------KVSYT-----VESAREGQVLDYDKLSMTIDTDGSITGED 215
                 +AL   +        K  Y+        A        ++    ++T GS+  E 
Sbjct: 184 FEYDPDNALRHTVYPRPEEWPKSEYSEIEEDEVQAPFDPNGKPERFYYNVETCGSLRPET 243

Query: 216 SVALASRILQDQLG 229
            V  A  +L+ +L 
Sbjct: 244 IVMSALAVLKKKLS 257


>gi|6172230|dbj|BAA85898.1| RNA-polymerase D [Halobacterium salinarum]
          Length = 249

 Score = 45.0 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 41/244 (16%), Positives = 80/244 (32%), Gaps = 48/244 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSIK 76
           +     ++     +   +   FA    N +RR ++  +   +I  V+  +          
Sbjct: 8   VEFVDRDDREARFVVRNITPAFA----NGIRRAILVDVPTLSIDTVRFVENSSVMFDEQL 63

Query: 77  GVHEDLTDIILNIKGINLKMSGDSH---KRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPDH 132
           G+          +  + L    D       + +   GPG    GD+     ++E  + + 
Sbjct: 64  GLR---------LGLVPLTTPEDYPAGEVTLALDVEGPGTAYPGDLVSNDPEVEAADENI 114

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAKHH-----------------------RTENDPI- 168
            I  L  D  + +E     GHG   AKH                          ++DP  
Sbjct: 115 PIIELKDDQRLELEADAVDGHGRDHAKHQGGVAVGYRHLQLQRVHVVGDSPEYADDDPQM 174

Query: 169 --GLITIDALYSPIKKVSYTVESAREGQVLDYDKL----SMTIDTDGSITGEDSVALASR 222
             G+I  D    P       + +   G+ ++ + +       +++DGS+  E+ V  A  
Sbjct: 175 LRGVIEEDDELVPTDDFDNDLTTRYPGKEVEIEDVDGAFVFHVESDGSMPVEELVLRAVD 234

Query: 223 ILQD 226
            L D
Sbjct: 235 TLVD 238


>gi|48478294|ref|YP_024000.1| DNA-directed RNA polymerase subunit D [Picrophilus torridus DSM
           9790]
 gi|55976419|sp|Q6KZP5|RPOD_PICTO RecName: Full=DNA-directed RNA polymerase subunit D
 gi|48430942|gb|AAT43807.1| DNA-directed RNA polymerase subunit D [Picrophilus torridus DSM
           9790]
          Length = 271

 Score = 45.0 bits (105), Expect = 0.019,   Method: Composition-based stats.
 Identities = 40/267 (14%), Positives = 88/267 (32%), Gaps = 64/267 (23%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHT--LGNALRRVLMSSLRGAAITAVQI--------DGVL 69
           + + ++N               T  + N++RR L++ +   AI  V          +G +
Sbjct: 4   IIELKDNYIKFSIS------GITPAIANSIRRTLINDIPKLAIENVVFHHGEIRDSEGNV 57

Query: 70  HE-----ISSIKGVHEDLTDIILNIKGINLKMSGD--------SHKRVTIFKRGPGVVTA 116
           ++        +  +   L  +  ++K +N +               + +I K GP  V +
Sbjct: 58  YDSSLPLFDEVVALRLGLIPLKTDLK-MNFRDQCSCNGEGCDLCTVKYSINKLGPADVFS 116

Query: 117 GDIQT--VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH------------- 161
            D+      D++ ++P   I  L     + +      G G   AK               
Sbjct: 117 SDLIPINNPDLKPVDPMIPIVKLKKGQAMLVTCEAIMGRGKDHAKWQVTSGVSYKYHREF 176

Query: 162 ------------RTENDPIGLITIDAL---YSPIKKVSY----TVESAREGQVLDYDKLS 202
                         +  P  +I+ +     ++   +  Y      E +      D  K  
Sbjct: 177 KINKNELENWSFYKDKCPKSVISENENEITFTDDVECRYLQQLFDEKSGVTITEDDTKFI 236

Query: 203 MTIDTDGSITGEDSVALASRILQDQLG 229
              +TDGS+T  +++  A + L+++  
Sbjct: 237 FQFETDGSLTAIETLDYALKRLKERFN 263


>gi|300681098|sp|P0CG28|RPOD_METAC RecName: Full=DNA-directed RNA polymerase subunit D
          Length = 266

 Score = 44.6 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 40/253 (15%), Positives = 84/253 (33%), Gaps = 49/253 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSIK 76
           + + +  +     +   +   FA    N +RR +++ +   AI  V + D          
Sbjct: 5   VDILELSDRSAKFVLSNVSTAFA----NGIRRAMVADVPTLAIEYVNLYDNTSVLYDEQL 60

Query: 77  GVHEDLTDIILNIKGINLKMSGD---------SHKRVTIFKRGPGVVTAGDIQT-VNDIE 126
            +   L  +  +I+    +   D             +T+   GPG V + D+ +    I+
Sbjct: 61  ALRLSLIPLATDIETYLPQAECDVCGGEGCPACEVSLTLSAEGPGTVYSRDLISSDPKIQ 120

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP------- 179
             +P+  I  L     + +E     G+G    K           + +  + +        
Sbjct: 121 PADPNVPIVELKKGQKLVLEAIAHMGYGRDSVKWQAGVACGYKNMPVITIENCDACGHCA 180

Query: 180 --IKKVSYTVESARE----------------GQVLDYDKLSMT---------IDTDGSIT 212
               K   +VE A                   QV D + + +          +++DGS T
Sbjct: 181 AECPKGIISVEEAGAKIAEEDIMKCSICRLCEQVCDINAIKVDFYENSFVFTMESDGSYT 240

Query: 213 GEDSVALASRILQ 225
            +D V  A+ +++
Sbjct: 241 AKDLVLNAANVIK 253


>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 = 44.6 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 42/275 (15%), Positives = 81/275 (29%), Gaps = 38/275 (13%)

Query: 15  IEYIVLGQEEENRTLMIAEPLPRGFAHT--LGNALRRVLMSSLRGAAITAVQI-DGVLHE 71
           +  + + ++ +     + +        T  L NALRRV +S +   AI  V I D     
Sbjct: 18  VVLVKVIEKSDLYMKAVVD------GITPPLINALRRVFISDVPVLAIDEVIILDNTSVL 71

Query: 72  ISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV-----------TIFKRGPGVVTAGDIQ 120
              +      +  I  ++K +  K+     + V            +  + P VV   D++
Sbjct: 72  YDEVLAHRLSMIPIKTDLKKLP-KIEECEQELVDPSLCQVRFELNVEAKEPVVVYGRDLK 130

Query: 121 -TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSP 179
               ++  +  D  I  L     + +E     G     AK             +  +   
Sbjct: 131 SDDPEVRPVYEDVPIVKLVPGQKIVLEAYAKLGRARNHAKWQAGLAAYYYYPKVSVVDKA 190

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
             K     E             ++ I  DGSI   D +             +   E+   
Sbjct: 191 NDKCMTCTEICNG---------ALEIKDDGSIMIHDVLKCT-------FNKWKTCEQVCS 234

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLR 274
            +K D +     F       +   ++       L+
Sbjct: 235 ALKVDWDENKYVFWVESFGNMPVEDMVREGFRILK 269


>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 = 44.6 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 27/129 (20%), Positives = 47/129 (36%), Gaps = 12/129 (9%)

Query: 45  NALRRVLMSSLRGAAI-TAVQIDGVLHEISSIKGVHEDLTDIILNIK--------GINLK 95
           N+LRRV++S L   AI T + ++        +      L  +   ++           L 
Sbjct: 27  NSLRRVIISELPVMAIDTVIVVNNTSVMYDEMLAHRLGLIPLTTPLQSLPPIEDCESGLA 86

Query: 96  MSGDSHKRVTIFKRGPGVVT--AGDIQTV-NDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
              +   R T+     G VT  +GD+ +   D+  ++ D  I  L     + +E     G
Sbjct: 87  DPSECTVRFTLQVNADGEVTVYSGDLVSERPDVVPVHKDIPIVKLVKGQSIVLEAYAKLG 146

Query: 153 HGYVPAKHH 161
                AK  
Sbjct: 147 RARGHAKWQ 155


>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 = 44.6 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 26/90 (28%), Positives = 45/90 (50%), Gaps = 1/90 (1%)

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
            +  +E  +E +  +   +      L   V+ L LSVR+ N L    I   G++ +   A
Sbjct: 377 SVVKDESLRETRNQVVDINSHVAELLNTPVQNLNLSVRAINVLNVIGISTFGEIPKIDAA 436

Query: 291 -DMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
             +L++ N GRK++ +I+  +G  GL LGM
Sbjct: 437 VTLLKVRNSGRKTVHDIEVFIGKFGLQLGM 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 = 44.6 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 26/90 (28%), Positives = 45/90 (50%), Gaps = 1/90 (1%)

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
            +  +E  +E +  +   +      L   V+ L LSVR+ N L    I   G++ +   A
Sbjct: 377 SVVKDESLRETRNQVVDINSHVAELLNTPVQNLNLSVRAINVLNVIGISTFGEIPKIDAA 436

Query: 291 -DMLRMANFGRKSLVEIKGVLGTMGLFLGM 319
             +L++ N GRK++ +I+  +G  GL LGM
Sbjct: 437 VTLLKVRNSGRKTVHDIEVFIGKFGLQLGM 466


>gi|221043080|dbj|BAH13217.1| unnamed protein product [Homo sapiens]
          Length = 424

 Score = 44.6 bits (104), Expect = 0.025,   Method: Composition-based stats.
 Identities = 50/291 (17%), Positives = 100/291 (34%), Gaps = 51/291 (17%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHT---LGNALRRVLMSSLRGAAITAVQIDG------- 67
           + + +  +     I E       +T   + N++RRV ++ +   AI  VQID        
Sbjct: 9   VRITELTDENVKFIIE-------NTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHD 61

Query: 68  --VLHEISSIKGVHEDLTDIILNIKG---------------INLKMSGDSHKRVT---IF 107
             + H +  I  + +D+ D +   +                ++++ + D  + VT   + 
Sbjct: 62  EFIAHRLGLIPLISDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDLI 121

Query: 108 KRGPGV--VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
              P V  VT+ +     +  V   D +I  L     +R+     KG G   AK + T  
Sbjct: 122 SNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181

Query: 166 DPIGLITIDALYSPIK-------KVSY-----TVESAREGQVLDYDKLSMTIDTDGSITG 213
                   +AL   +        K  Y         A        ++    +++ GS+  
Sbjct: 182 VAFEYDPDNALRHTVYPKPEEWPKSEYLELDEDESQAPYDPNGKPERFYYNVESCGSLRP 241

Query: 214 EDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           E  V  A   L+ +L       +     ++ ++  S   +      VE+ +
Sbjct: 242 ETIVLSALSGLKKKLTNKEAERDMLPSPEQTLSPLSKMPHSVPQPLVEKTD 292


>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 = 44.2 bits (103), Expect = 0.025,   Method: Composition-based stats.
 Identities = 40/237 (16%), Positives = 82/237 (34%), Gaps = 47/237 (19%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSIKGVHE 80
             +E     +     RG      N LRR +++ +   +I  +++ +              
Sbjct: 11  DRDERSARFLV----RGVTPAFANGLRRAMIADVPTLSIDTLRVVENSSVMFDE------ 60

Query: 81  DLTDIILNIKGINLKMSGDSH--KRVTIFKRGPGVVTA--GDIQTVND-IEVLNPDHVIC 135
               + L +  + L    D    + VT+     G  TA  GD+ + +D ++  + +  I 
Sbjct: 61  ---QLALRLGLVPLTTPDDYEPGETVTLAIDVEGPATAYSGDLVSSDDKVQPADENIPII 117

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHH--------------------RTENDPIG----LI 171
            L  D  + +E   + G G   AKH                       E+D       +I
Sbjct: 118 ELKDDQQLELEADATLGRGKDHAKHQGGVAVGYRHLQRVEVVGEKGEFEDDEPEILRGVI 177

Query: 172 TIDALYSPIKKVSYTVESAREGQVLDYDKL----SMTIDTDGSITGEDSVALASRIL 224
             D       +    +     G+ ++ +++       ++TDGS+  E+ V  A+  +
Sbjct: 178 EEDGDLIETGEFDNDLSQRYPGKEVEVEEVPNAFVFDVETDGSMPVEELVLKAAESI 234


>gi|42780320|ref|NP_977567.1| hypothetical protein BCE_1246 [Bacillus cereus ATCC 10987]
 gi|42736239|gb|AAS40175.1| conserved domain protein [Bacillus cereus ATCC 10987]
          Length = 95

 Score = 44.2 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 12/53 (22%), Positives = 24/53 (45%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  +  L + +E ++L++   G  S+ +++  L   GL  
Sbjct: 42  LSAPARRALEHHGIYTVEKLSKYSEKEILKLHGMGPASMPKLRKALEESGLSF 94


>gi|73667627|ref|YP_303642.1| DNA-directed RNA polymerase subunit D [Methanosarcina barkeri str.
           Fusaro]
 gi|72394789|gb|AAZ69062.1| DNA-directed RNA polymerase, subunit D [Methanosarcina barkeri str.
           Fusaro]
          Length = 266

 Score = 44.2 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 37/255 (14%), Positives = 81/255 (31%), Gaps = 53/255 (20%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSIK 76
           + + +  +     +   +   FA    N +RR +++ +   AI  V + +          
Sbjct: 5   VDILELSDRSAKFVLSKVSTSFA----NGIRRAMIADVPTLAIEYVNLYENTSVLYDEQL 60

Query: 77  GVHEDLTDIILNIKGINLKMSGD---------SHKRVTIFKRGPGVVTAGDIQT-VNDIE 126
            +   L  ++ +++    +   D             +T+   GP  V + D+ +    I+
Sbjct: 61  ALRLSLIPLVTDVETYVPQAECDVCGGEGCPACEVSLTLSAEGPCTVYSRDLISSDPKIQ 120

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITI------DAL---- 176
             +P+  I  L     + +E     G+G    K           + +      DA     
Sbjct: 121 PADPNIPIVELKKGQKLVLEALAHMGYGRDSVKWQAGVACGYKNVPVITIENCDACGHCA 180

Query: 177 ------------------------YSPIKKVS--YTVESAREGQVLDYDKLSMTIDTDGS 210
                                    S  K       + + + G   D +    T+++DGS
Sbjct: 181 AECPKGIIRFEESGAKVSSEDVLKCSLCKLCEQVCDIHAIKIG--FDENAFVFTMESDGS 238

Query: 211 ITGEDSVALASRILQ 225
            T +D    AS +++
Sbjct: 239 YTAKDLALNASNVIK 253


>gi|47221930|emb|CAF98942.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 275

 Score = 44.2 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 47/259 (18%), Positives = 91/259 (35%), Gaps = 57/259 (22%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHT---LGNALRRVLMSSLRGAAITAVQIDG------- 67
           + + +  +     + E       +T   + N++RRV MS +   AI  +QID        
Sbjct: 9   VKITELTDENVKFVIE-------NTDLAVANSIRRVFMSEVPTIAIDWIQIDANSSVLHD 61

Query: 68  --VLHEISSIKGVHEDLTDIILNIKG---------------INLKMSGDSHKRVT---IF 107
             V H +  I    +D+ D +   +                ++++ + D  + VT   + 
Sbjct: 62  EFVAHRVGLIPLTSDDIVDKLQYSRDCTCDDFCPECSVELTLDVRCTEDQTRHVTSRDLL 121

Query: 108 KRGPGV--VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
              P V  VT+       +  V   D ++  L     +R+     KG G   AK + T  
Sbjct: 122 SNNPRVIPVTSRSRDNDPNDYVEQDDILVVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181

Query: 166 DPIGLITID---------------ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
                   +               + YS I++          G+    +K    +++ GS
Sbjct: 182 VSFEYDPDNVLRHTVYPRPEEWPKSEYSEIEEDEIQAPFDPNGKP---EKFFYNVESCGS 238

Query: 211 ITGEDSVALASRILQDQLG 229
           +  E+ V  A  +L+ +L 
Sbjct: 239 LRPENIVMSALAVLKKKLS 257


>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 = 44.2 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 35/236 (14%), Positives = 78/236 (33%), Gaps = 39/236 (16%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSIKGVHE 80
           + ++    ++   L   FA    N +RR +++ +   +I  V+  +        + G+  
Sbjct: 12  ERDDRSARVLIRGLTPAFA----NGIRRAMIADVPTFSIDTVRFVENSSVMFDEMIGLRL 67

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPDHVICNLDV 139
            L  +   +    +         + +   GP    +GDI+     +EV + +  I  L  
Sbjct: 68  GLIPLKTPLDDFEV----GDEVTLALDVEGPATAYSGDIESADPLVEVADDNIPIIELKE 123

Query: 140 DAVVRMELTVSKGHGYVPAKHH--------------------RTENDPIGLI-----TID 174
              +  E       G   AKH                       ++D   ++     T D
Sbjct: 124 GQRLEFEADAVLDTGKEHAKHQGGVSVGYRHLQRVSVEGDLGEFDDDEPRILRGVIETPD 183

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKL----SMTIDTDGSITGEDSVALASRILQD 226
                  +    +     G+ +  + +       I+TDGS + E+ +  A   +++
Sbjct: 184 GEIELTDEFDNDLSERFPGKEVSVEDVPGAFVFHIETDGSFSVEELLLRAIDSIEE 239


>gi|213405883|ref|XP_002173713.1| DNA-directed RNA polymerase II subunit RPB3 [Schizosaccharomyces
           japonicus yFS275]
 gi|212001760|gb|EEB07420.1| DNA-directed RNA polymerase II subunit RPB3 [Schizosaccharomyces
           japonicus yFS275]
          Length = 308

 Score = 44.2 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 44/269 (16%), Positives = 88/269 (32%), Gaps = 55/269 (20%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI---------DGV 68
           + +    +N    +          +L N+LRRV++  +   AI  V+I         + +
Sbjct: 7   VTIKNIGKNSVEFVLSNTD----LSLANSLRRVVLGEIPTVAIDLVEISVNTSVMPDEFL 62

Query: 69  LHEISSIK----GVHEDLTDIILNIKGINLKMS-GDSHKRVTIFKRGPG----VVTAGDI 119
            H +  I      + E     +   +  +           +++  +  G     V A D+
Sbjct: 63  AHRLGMIPLNSNNIDEPPPVGLEYTRNCDCDQYCNKCSVELSLNAKCTGDGTMEVYARDL 122

Query: 120 QTVNDIEVLNPDH--------VICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLI 171
              ++  +  P          +I  L  +  V +     KG     AK   T        
Sbjct: 123 VVDSNSTLGQPVLADARSHGPLILKLRKEQEVSLRCIAKKGIAKEHAKWSPTAAVSFEYD 182

Query: 172 TIDALYSPIKKVSYTV-----------------ESAREGQVLDYD----KLSMTIDTDGS 210
                ++ +K   Y                   E  REG+  DY+    K  M ++  GS
Sbjct: 183 P----WNKLKHTDYWFETDADEEWPKSKNADWEEPPREGETFDYNAQPRKFYMEVEGVGS 238

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKK 239
           I     +    R+LQ++L + +   + ++
Sbjct: 239 IPPNQIILQGIRVLQEKLAVLVRDLDEEQ 267


>gi|229010531|ref|ZP_04167733.1| hypothetical protein bmyco0001_9890 [Bacillus mycoides DSM 2048]
 gi|229166076|ref|ZP_04293838.1| hypothetical protein bcere0007_10500 [Bacillus cereus AH621]
 gi|228617385|gb|EEK74448.1| hypothetical protein bcere0007_10500 [Bacillus cereus AH621]
 gi|228750729|gb|EEM00553.1| hypothetical protein bmyco0001_9890 [Bacillus mycoides DSM 2048]
          Length = 92

 Score = 44.2 bits (103), Expect = 0.031,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 24/53 (45%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I    +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 39  LSAPARRALEHHGITTEAELSKYSEKEILKLHGIGPASLPKLRAALEDKGLSF 91


>gi|225874866|ref|YP_002756325.1| transcription termination factor NusA [Acidobacterium capsulatum
           ATCC 51196]
 gi|225794228|gb|ACO34318.1| transcription termination factor NusA [Acidobacterium capsulatum
           ATCC 51196]
          Length = 548

 Score = 43.8 bits (102), Expect = 0.033,   Method: Composition-based stats.
 Identities = 17/90 (18%), Positives = 32/90 (35%), Gaps = 3/90 (3%)

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGE 276
           V LA+++L  ++ +     E +K  + +  +             E  EL       L   
Sbjct: 328 VRLAAKLLGWKIDI---KSEEEKRQEVEQQMGGFAQGGTATAIEEVKELGESIIQKLVAA 384

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            I  +  L   T   +  +   G K+L +I
Sbjct: 385 GITTVESLADMTPEQLEEIPGIGEKTLEKI 414


>gi|241667733|ref|ZP_04755311.1| transcription elongation factor NusA [Francisella philomiragia
           subsp. philomiragia ATCC 25015]
 gi|254876277|ref|ZP_05248987.1| transcription elongation factor nusA [Francisella philomiragia
           subsp. philomiragia ATCC 25015]
 gi|254842298|gb|EET20712.1| transcription elongation factor nusA [Francisella philomiragia
           subsp. philomiragia ATCC 25015]
          Length = 489

 Score = 43.8 bits (102), Expect = 0.033,   Method: Composition-based stats.
 Identities = 27/166 (16%), Positives = 61/166 (36%), Gaps = 11/166 (6%)

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDG--SITGEDSVALASR---ILQDQLGMFINFE 235
             V Y + S       D  ++++  +T+    +  ++S++ A     +        I ++
Sbjct: 284 DMVQYAINSLSPVDSEDILEVNVDEETNSMDIVVKQESLSKAIGKNGVNVRLASALIGWK 343

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
                  E    +       + K VE L++       L  E I  + DL      ++L +
Sbjct: 344 INVLSDTEQEEKQMS----IVEKFVEALDIDHDFALVLIEEGIETLEDLAYLDRDELLEI 399

Query: 296 ANFGRKSLVEIKGVLGTMGLF--LGMNLPDWPPESIEELAKKYEDK 339
             F  + + E++     + L   LG   P     +++ + ++  DK
Sbjct: 400 EGFDEEIVDELQERAKAVILSQALGGKKPAEDLLNMQGMNQELADK 445


>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 = 43.8 bits (102), Expect = 0.033,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 25/53 (47%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L++   G  SL ++K VL    L  
Sbjct: 42  LSAPARRALEHRGIQTVEELSKYSEKEILKLHGMGPASLPKLKKVLEESWLSF 94


>gi|221114057|ref|XP_002158521.1| PREDICTED: similar to predicted protein [Hydra magnipapillata]
          Length = 273

 Score = 43.8 bits (102), Expect = 0.033,   Method: Composition-based stats.
 Identities = 45/270 (16%), Positives = 88/270 (32%), Gaps = 54/270 (20%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---VLH-EI- 72
           + + +  ++    I E        ++ N+LRR+ ++ +   AI  VQI+    VLH E  
Sbjct: 9   VKILEWTDDNLKFILENTD----LSVANSLRRIFIAEVPTIAIDWVQIENNTSVLHDEFI 64

Query: 73  SSIKGVH-----EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           +   G+      E +  +  +      +   +   + T+  +  G  T     T  D+  
Sbjct: 65  AHRIGLIPLTSDEKVDKMCYSRDCTCSEFCDECSVKFTLDVKCTGETTR--HVTSRDLIS 122

Query: 128 LNP--------------------DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
            +P                    + VI  L     +++     KG G   AK + T    
Sbjct: 123 EDPKVIPVTSRIKDDDTGYGETDEIVIVKLRKGQELKLHAFAKKGFGKEHAKWNPTAGVS 182

Query: 168 IGLITIDAL---------------YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSIT 212
                 +AL               YS + +  Y        +    DK    +++ GS+ 
Sbjct: 183 FEYDPDNALRHTTFARPDQWPKSEYSQLDEDQYEAPYDIHAKA---DKFYFNVESCGSLK 239

Query: 213 GEDSVALASRILQDQLGMFINFEEPKKEVK 242
            E+ V     +L+ +L         +    
Sbjct: 240 PENIVMTGISVLKKKLSELQTHHSHEIAAD 269


>gi|257053585|ref|YP_003131418.1| RNA polymerase insert [Halorhabdus utahensis DSM 12940]
 gi|256692348|gb|ACV12685.1| RNA polymerase insert [Halorhabdus utahensis DSM 12940]
          Length = 247

 Score = 43.8 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 26/142 (18%), Positives = 48/142 (33%), Gaps = 10/142 (7%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ-IDGVLHEISSIKGVHE 80
           +  E     +     RG      N +RR +++ +   +I  V+ I+          G+  
Sbjct: 10  ERGEREARFLV----RGVTPAFANGVRRAMIADVPTFSIDNVRVIENSSVMFDEQIGLRL 65

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPDHVICNLDV 139
            L  +   +    +         + +  +GP    +GD+      +E   PD  I  L  
Sbjct: 66  GLVPLTTPVGEFEI----GDEVTLALDVQGPDTAYSGDLVGNDEMVEPAEPDVPIIELKD 121

Query: 140 DAVVRMELTVSKGHGYVPAKHH 161
           D  + +E       G   AKH 
Sbjct: 122 DQRLELEADAVLDKGREHAKHQ 143


>gi|229016491|ref|ZP_04173432.1| hypothetical protein bcere0030_10650 [Bacillus cereus AH1273]
 gi|229022700|ref|ZP_04179224.1| hypothetical protein bcere0029_10490 [Bacillus cereus AH1272]
 gi|228738512|gb|EEL88984.1| hypothetical protein bcere0029_10490 [Bacillus cereus AH1272]
 gi|228744758|gb|EEL94819.1| hypothetical protein bcere0030_10650 [Bacillus cereus AH1273]
          Length = 92

 Score = 43.8 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 24/53 (45%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I    +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 39  LSAPARRALEHHGITTEAELSKYSEKEILKLHGIGPASLPKLRAALADKGLSF 91


>gi|229132032|ref|ZP_04260895.1| hypothetical protein bcere0014_9750 [Bacillus cereus BDRD-ST196]
 gi|228651432|gb|EEL07404.1| hypothetical protein bcere0014_9750 [Bacillus cereus BDRD-ST196]
          Length = 92

 Score = 43.8 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 24/53 (45%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I    +L + +E ++L++   G  SL +++  L   GL  
Sbjct: 39  LSAPARRALEHHGITTEAELSKYSEKEILKLHGIGPASLPKLRAALEDKGLSF 91


>gi|326797608|ref|YP_004315427.1| hypothetical protein Sph21_0174 [Sphingobacterium sp. 21]
 gi|326548372|gb|ADZ76757.1| hypothetical protein Sph21_0174 [Sphingobacterium sp. 21]
          Length = 97

 Score = 43.8 bits (102), Expect = 0.035,   Method: Composition-based stats.
 Identities = 11/45 (24%), Positives = 20/45 (44%)

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           L  + I  +  L   +E ++L +   G  S+ ++K  L   GL  
Sbjct: 51  LENQGITTLRKLASFSEKEILSLHGMGPGSIPKLKQKLEEKGLAF 95


>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 = 43.8 bits (102), Expect = 0.035,   Method: Composition-based stats.
 Identities = 12/55 (21%), Positives = 24/55 (43%)

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             LS  +   L    I  + +L + +E ++ ++   G  SL +++  L   GL  
Sbjct: 40  SPLSAPARRALEHHGIQTVEELSKYSEKEISKLHGMGPASLPKLRKALEESGLSF 94


>gi|167627171|ref|YP_001677671.1| transcription elongation factor NusA [Francisella philomiragia
           subsp. philomiragia ATCC 25017]
 gi|167597172|gb|ABZ87170.1| transcription elongation factor [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
          Length = 489

 Score = 43.8 bits (102), Expect = 0.036,   Method: Composition-based stats.
 Identities = 27/166 (16%), Positives = 61/166 (36%), Gaps = 11/166 (6%)

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDG--SITGEDSVALASR---ILQDQLGMFINFE 235
             V Y + S       D  ++++  +T+    +  ++S++ A     +        I ++
Sbjct: 284 DMVQYAINSLSPVDSEDILEVNVDEETNSMDIVVKQESLSKAIGKNGVNVRLASALIGWK 343

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
                  E    +       + K VE L++       L  E I  + DL      ++L +
Sbjct: 344 INVLSDTEQEEKQMS----IVEKFVEALDIDHDFALVLIEEGIETLEDLAYLDRDELLEI 399

Query: 296 ANFGRKSLVEIKGVLGTMGLF--LGMNLPDWPPESIEELAKKYEDK 339
             F  + + E++     + L   LG   P     +++ + ++  DK
Sbjct: 400 EGFDEEIVDELQERAKAVILSQALGGKKPAEDLLNMQGMNQELADK 445


>gi|55376999|ref|YP_134849.1| DNA-directed RNA polymerase subunit D [Haloarcula marismortui ATCC
           43049]
 gi|1350858|sp|Q00813|RPOD_HALMA RecName: Full=DNA-directed RNA polymerase subunit D
 gi|148773|gb|AAA73212.1| ribosomal protein HmaRp-alpha subunit [Haloarcula marismortui]
 gi|55229724|gb|AAV45143.1| DNA-directed RNA polymerase subunit D [Haloarcula marismortui ATCC
           43049]
          Length = 259

 Score = 43.8 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 35/232 (15%), Positives = 69/232 (29%), Gaps = 51/232 (21%)

Query: 40  AHT--LGNALRRVLMSSLRGAAITAVQ-IDGVLHEISSIKGVHEDLTDIILNIKGINLKM 96
             T    N +RR +++ +   +I  V+ I+      +   G+   L  +  ++    +  
Sbjct: 23  GITPAFANGIRRAMVADVPTFSIDTVRVIENTSVMFNEQIGLRLGLVPLTTDLDDFEI-- 80

Query: 97  SGDSHKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY 155
                  +++   GP    + D+  +   +E  + +  I +L     + +E       G 
Sbjct: 81  --GDEVTLSLSVDGPSTAYSSDLVSSDPMVEAADDNIPIIDLKEGQRLEVEADAVLDTGR 138

Query: 156 VPAKHHR--------------------------------TENDPIGLITIDAL------- 176
             AKH                                   E         DA        
Sbjct: 139 EHAKHQGGVAVGYRHLQQVEVVGDLGEFEDDDPNILRGVIEEQAAEHAAGDATNGELVAT 198

Query: 177 --YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD 226
             +    +  Y  +      V +       ++TDGS T E+ V  A   L+D
Sbjct: 199 DEFDNDLRNRYPGKDVEVSDVPN--AFVFHVETDGSFTTEELVLRAVETLRD 248


>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 = 43.8 bits (102), Expect = 0.040,   Method: Composition-based stats.
 Identities = 12/53 (22%), Positives = 24/53 (45%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++ ++   G  SL +++  L   GL  
Sbjct: 42  LSAPARRALEHHGIQTVEELSKYSEKEISKLHGMGPASLPKLRKALEESGLSF 94


>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 = 43.8 bits (102), Expect = 0.041,   Method: Composition-based stats.
 Identities = 15/59 (25%), Positives = 27/59 (45%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
           L+  +   L G     + DL + TE  +L++   G K+L +++  L   GL    +  D
Sbjct: 14  LAQPARRALLGAGYTRLEDLTRVTEDQLLQLHGIGPKALAQLREALAARGLAFAADTDD 72


>gi|337497|gb|AAA36586.1| RNA polymerase subunit hRPB 33 [Homo sapiens]
 gi|2920709|emb|CAA11842.1| RNA polymerase II subunit [Homo sapiens]
 gi|2920711|emb|CAA11843.1| RNA polymerase subunit [Homo sapiens]
          Length = 275

 Score = 43.8 bits (102), Expect = 0.042,   Method: Composition-based stats.
 Identities = 47/256 (18%), Positives = 91/256 (35%), Gaps = 51/256 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHT---LGNALRRVLMSSLRGAAITAVQIDG------- 67
           + + +  +     I E       +T   + N++RRV ++ +   AI  VQID        
Sbjct: 9   VRITELTDENVKFIIE-------NTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHD 61

Query: 68  --VLHEISSIKGVHEDLTDIILNIKG---------------INLKMSGDSHKRVT---IF 107
             + H +  I  + +D+ D +   +                ++++ + D  + VT   + 
Sbjct: 62  EFIAHRLGLIPLISDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDLI 121

Query: 108 KRGPGV--VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
              P V  VT+ +     +  V   D +I  L     +R+     KG G   AK + T  
Sbjct: 122 SNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181

Query: 166 DPIGLITIDALYSPIK-------KVSYT-----VESAREGQVLDYDKLSMTIDTDGSITG 213
                   +AL + +        K  Y+        A        ++    +++ GS+  
Sbjct: 182 VAFEYDPDNALRTTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLRP 241

Query: 214 EDSVALASRILQDQLG 229
           E  V  A   L+ +L 
Sbjct: 242 ETIVLSALSGLKKKLS 257


>gi|307352912|ref|YP_003893963.1| DNA-directed RNA polymerase [Methanoplanus petrolearius DSM 11571]
 gi|307156145|gb|ADN35525.1| DNA-directed RNA polymerase [Methanoplanus petrolearius DSM 11571]
          Length = 274

 Score = 43.4 bits (101), Expect = 0.044,   Method: Composition-based stats.
 Identities = 39/235 (16%), Positives = 69/235 (29%), Gaps = 51/235 (21%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDG-----VLHEISSIKGVHEDLTDIILNIKGINLKMS 97
             N  RR ++  +   AI  V I           ++   G+    TD+   +K       
Sbjct: 24  FANTFRRTMIGEVPTLAIEDVLIYDNNSALFDEMLAHRLGLIPIKTDLSEYVKKSECSCG 83

Query: 98  GD----SHKRVTIFKRGPGVVTAGDIQ-TVNDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
           G+         T+   GPG V + D+         +N D  +  L+ D  V +E      
Sbjct: 84  GEGCSSCQAIFTLSVEGPGTVHSSDLIPADPRATPVNMDIPVVKLEKDQKVVLEARAELN 143

Query: 153 HGYVPAKHHRTENDPIGLITI-------DAL----------------------------Y 177
            G   AK   T         +       DA                              
Sbjct: 144 IGDEHAKWEPTLACGYKAYPVITIDDRCDACGNCVEECPRNVLRVGKKSVEIADGKLEDC 203

Query: 178 SPIKKVSYTVESAREGQV------LDYDKLSMTIDTDGSITGEDSVALASRILQD 226
           S  +       ++  G         D  +    +++DGS+  ++ +  A  I++D
Sbjct: 204 SMCRLCEKACMASGIGDRPAISVKPDNTRFLFVVESDGSLPVKEIMTCALGIMKD 258


>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 = 43.4 bits (101), Expect = 0.045,   Method: Composition-based stats.
 Identities = 43/192 (22%), Positives = 77/192 (40%), Gaps = 32/192 (16%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           NA+RR+++S +   AI  V I    +  S    +      +I  IKG  L    +     
Sbjct: 28  NAIRRIMISEVPTYAIEDVYI--FENSSSMDDEIIAHRLGLIP-IKGKPL--LENEIITF 82

Query: 105 TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
           T+ K GP  V + D+++ N  EV   +  I  L     +++E     G G V AK     
Sbjct: 83  TLEKEGPCTVYSSDLKSENG-EVAFKNIPIVKLGNGQKIQIECEAVPGIGKVHAKWQ--- 138

Query: 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRIL 224
                    +A+Y                + +  D++   ++T G +  E+ +  A +IL
Sbjct: 139 -------PCNAVY----------------KQISEDEVEFFVETFGQMEAEEILEEAVKIL 175

Query: 225 QDQLGMFINFEE 236
           +++   F+   E
Sbjct: 176 KNKAESFLQQLE 187


>gi|255714803|ref|XP_002553683.1| KLTH0E04598p [Lachancea thermotolerans]
 gi|238935065|emb|CAR23246.1| KLTH0E04598p [Lachancea thermotolerans]
          Length = 328

 Score = 43.4 bits (101), Expect = 0.045,   Method: Composition-based stats.
 Identities = 44/232 (18%), Positives = 81/232 (34%), Gaps = 51/232 (21%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTDIILNIKG 91
            T+ N+LRRV+++ +   AI +V+++          + H +  I     D+ D+I   + 
Sbjct: 27  ITMANSLRRVMIAEIPTLAIDSVEVETNTSVLADEFISHRLGLIPLQSSDINDLIY-CRD 85

Query: 92  INLKMSGD-SHKRVTIFKRGPGV----VTAGDIQTVNDIEVLNPDHV-----------IC 135
              +   D     +T+   G       V A D+  V+++   N  H            IC
Sbjct: 86  CYCEDHCDRCSVVLTLQAVGESESTTNVYAKDLVIVSNLMGRNIGHPIIQDKDGNGVLIC 145

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYT--------- 186
            L     ++++    KG     AK                 ++ +K   Y          
Sbjct: 146 KLRKGQELKLKCVAKKGISKEHAKWSPAAAIEFEYDP----WNKLKHTDYWHETDAAAEW 201

Query: 187 --------VESAREGQVLDYD----KLSMTIDTDGSITGEDSVALASRILQD 226
                    +   E +  DY+       M ++T GS+T +  V    + LQD
Sbjct: 202 PQSKNCEYEDPPNEDEAFDYNAKPTTFYMNVETVGSLTVDQVVIRGMKTLQD 253


>gi|145231693|ref|XP_001399321.1| DNA-directed RNA polymerase II subunit RPB3 [Aspergillus niger CBS
           513.88]
 gi|134056224|emb|CAK37482.1| unnamed protein product [Aspergillus niger]
          Length = 338

 Score = 43.4 bits (101), Expect = 0.047,   Method: Composition-based stats.
 Identities = 40/265 (15%), Positives = 88/265 (33%), Gaps = 50/265 (18%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTDIILNIKGIN 93
             N+LRRV++S +   AI  V+++          + H +  I  + ++    +   +   
Sbjct: 35  FANSLRRVMLSEIPTMAIDLVEVEKNTSVLPDEFLAHRLGLIPLISKNCDQDVEYTRDCE 94

Query: 94  LKMSG-DSHKRVTIFKRGPGV----VTAGDIQTVND-----I---EVLNPDHV---ICNL 137
            +         +++  R  G     V A D+    +     +    +L+P+     IC L
Sbjct: 95  CEDHCARCSVTLSLHARCTGDDIMRVYARDLVVSGERANEWVGNPVILDPEGNGPLICKL 154

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE--------- 188
                ++M     KG     AK   T             ++ ++ V Y  E         
Sbjct: 155 RRGQELKMTCIAKKGIAKEHAKWMPTSAIGFEYDP----HNNLRHVDYWYEEDPAKEWPV 210

Query: 189 --------SAREGQVLDYD----KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
                    A   Q  DYD       + +++ G++  +  +     +LQ +L   I+   
Sbjct: 211 SANAGWEQPAPPDQPFDYDAQPNSFYIDVESIGTLEPDMIIQQGITVLQRKLASVISSLS 270

Query: 237 PKKEVKEDINVKSLPFNPALLKKVE 261
             +    +  +     +   ++  +
Sbjct: 271 GTEGADRNGVMGGDDEDMMGVRSPD 295


>gi|325958565|ref|YP_004290031.1| DNA-directed RNA polymerase subunit D [Methanobacterium sp. AL-21]
 gi|325329997|gb|ADZ09059.1| DNA-directed RNA polymerase subunit D [Methanobacterium sp. AL-21]
          Length = 262

 Score = 43.4 bits (101), Expect = 0.048,   Method: Composition-based stats.
 Identities = 48/252 (19%), Positives = 83/252 (32%), Gaps = 49/252 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSIK 76
           I + Q++E   L   E    G      NA+RR+    +   AI  V+I            
Sbjct: 3   IDIKQKDETHLLFAIE----GVDDAFINAIRRISTVEVPTMAIETVEILKNDAKIFDEAL 58

Query: 77  GVHEDLTDIILNIKGINLKMSGDSH-------KRVTIFKRGPGVVTAGDIQT-VNDIEVL 128
                L  +  +++ + L    D           + + ++GP  V +GD+Q+   D+  +
Sbjct: 59  AHRLGLVPLKTDLESMVLASDCDCEDYCPTCSVTLLLKEKGPKTVYSGDLQSQDPDVVPV 118

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT---IDALY-------- 177
           +    +  L     V +      G G   +K   T            ID+          
Sbjct: 119 HDTIPLLKLKEGQEVELIAVAKLGIGLEHSKWQPTTTCAYKYYPKITIDSDKCESCGLCA 178

Query: 178 SPIKKVSYTV-ESAREGQVLDYD------------------------KLSMTIDTDGSIT 212
           S   +  Y   E A   +++D +                        K   TI+TDGS++
Sbjct: 179 SECPRAVYEFDEKANTLEIVDIENCSMCKTCVRGCEAGAITVEGEKGKYLFTIETDGSLS 238

Query: 213 GEDSVALASRIL 224
            E  +  A  IL
Sbjct: 239 PEKVLTTACEIL 250


>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 = 43.4 bits (101), Expect = 0.048,   Method: Composition-based stats.
 Identities = 11/57 (19%), Positives = 23/57 (40%)

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320
           +LS  +   L       +G L Q +  ++ ++   G K + +++  L   GL     
Sbjct: 14  KLSQPALRALHNAGYHSLGQLTQVSARELGKLHGMGPKGIRQLREALAAKGLAFADE 70


>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 = 43.4 bits (101), Expect = 0.049,   Method: Composition-based stats.
 Identities = 40/267 (14%), Positives = 86/267 (32%), Gaps = 51/267 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------V 68
           + +          I E        ++ N+LRR+ ++++   AI  VQ            +
Sbjct: 9   VTIPDLTNENVKFILENTD----LSVANSLRRIFIANVPTLAIDWVQFVNNTSVLSDEFI 64

Query: 69  LHEISSIKGVHEDLTDIILNIKG---------------INLKMSGDSHKRVTI-----FK 108
            H +  I    +++ D +   +                ++++ + D  + VT        
Sbjct: 65  AHRLGLIPLTCDEVIDRLQYSRDCNCVEHCPECSVEFTLDVRCNDDQTRHVTTRDLISSD 124

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
                VT    +          D +I  L     ++++    KG G   AK + T +   
Sbjct: 125 SRVVPVTTRYGEDDTVYGDQEDDILIAKLRRGQEIKIKAYAKKGLGTEHAKWNPTASVAF 184

Query: 169 GLITIDAL---------------YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
                +A+               YS + + +Y             DK  + ++T GS+  
Sbjct: 185 EYDPDNAMRHTTYPKPEEWPKSEYSNLPEDNYEASYDP---QTVADKFYLNVETSGSLRP 241

Query: 214 EDSVALASRILQDQLGMFINFEEPKKE 240
           E+ V      L+++L         ++ 
Sbjct: 242 ENIVLSGISTLKNKLSELQLHFSHEQS 268


>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 = 43.4 bits (101), Expect = 0.050,   Method: Composition-based stats.
 Identities = 21/115 (18%), Positives = 40/115 (34%), Gaps = 4/115 (3%)

Query: 225 QDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDL 284
                      +    + + I      +   +L  +    +   + N L    I  + DL
Sbjct: 510 IKFFAGKSQENKKINNILQSIEKAKDAYLRNVLAALGIKGIGNIAANLLTN-KITKLSDL 568

Query: 285 IQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
              T+ D+L +  FG KS+  +K  L +       +L  +  E++  L  K   K
Sbjct: 569 NNLTDEDLLSIDTFGEKSIENLKEFLSS---EKNQDLIKFLDENLNYLNSKKSSK 620


>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 = 43.4 bits (101), Expect = 0.050,   Method: Composition-based stats.
 Identities = 48/264 (18%), Positives = 86/264 (32%), Gaps = 47/264 (17%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI-TAVQIDGVLHEISSI 75
            + + ++ +     + E +P     +L N+LRRV++S L   AI + V ++        +
Sbjct: 3   KVSIVEKSQFFAKAVVEGVPP----SLINSLRRVIISELPVLAIDSVVVVNNTSVMYDEM 58

Query: 76  KGVHEDLTDIILNIK--------GINLKMSGDSHKRVTI--FKRGPGVVTAGDIQTV-ND 124
                 L  +   +K           L    +   R+T+     G  VV AGD+     D
Sbjct: 59  LAHRLGLIPLTTPLKDLPPIEDCESGLVDPSECTVRLTLQVNATGDVVVYAGDLVADRPD 118

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVS 184
           +  +  D  I  L     V +E     G     AK             +      +K+  
Sbjct: 119 VAPVYKDIPIVKLVEGQSVVVEAYAKLGRARDHAKWQAALASYYYYPKV-----VVKREE 173

Query: 185 YTVESAREGQVL--------------------------DYDKLSMTIDTDGSITGEDSVA 218
                    + L                          + DK    I++ G+   E ++ 
Sbjct: 174 CREMCKEVCRNLENPLECTFNKATTCKEMCGGGIVVEWEKDKYVFWIESFGNYDAETALR 233

Query: 219 LASRILQDQLGMFINFEEPKKEVK 242
            A RIL+ +   F++    K E K
Sbjct: 234 EAFRILKKKFEDFLDALSRKAEAK 257


>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 = 43.4 bits (101), Expect = 0.055,   Method: Composition-based stats.
 Identities = 16/55 (29%), Positives = 28/55 (50%)

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            +LS  + N L  E I  + +L + TE D+L++   G  S+  ++ +L   GL  
Sbjct: 47  SKLSSPARNALIHEGIDTLHELSKYTEKDVLKIHGIGPASIPMMRALLEEEGLSF 101


>gi|327438397|dbj|BAK14762.1| hypothetical protein SSIL_0339 [Solibacillus silvestris StLB046]
          Length = 97

 Score = 43.0 bits (100), Expect = 0.059,   Method: Composition-based stats.
 Identities = 15/53 (28%), Positives = 23/53 (43%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  + N L    I  +  L   TE ++L++   G  +L  +K  L   GL  
Sbjct: 43  LSSPACNALINAGITELAQLADYTEKEILKLHGIGPATLPTLKHALLEKGLDF 95


>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 = 43.0 bits (100), Expect = 0.059,   Method: Composition-based stats.
 Identities = 40/160 (25%), Positives = 64/160 (40%), Gaps = 14/160 (8%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
           ALRR+++S +   AI  V      +  S    V      +I  IKG+ +  SGD    +T
Sbjct: 14  ALRRIMISEVPTYAIENVYFY--ENTSSMYDEVLAHRLGLIP-IKGVPV--SGDEVIVLT 68

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
           I K GP  V + D+++ +       +  I  L  D  + +E     G G + AK     N
Sbjct: 69  ISKEGPCTVYSSDLKSESGEPAF-ENIPIVKLAEDQKLELETEALVGTGKIHAKWQPC-N 126

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
                I+ D +        + +ES       D  + S+ I
Sbjct: 127 ASYKQISNDEV-------EFKIESFGNMDAEDIIRSSLEI 159


>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 = 43.0 bits (100), Expect = 0.066,   Method: Composition-based stats.
 Identities = 30/155 (19%), Positives = 55/155 (35%), Gaps = 14/155 (9%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE-ISSI 75
            + + +  E     +       FA    N++RR +++ +   AI  + I           
Sbjct: 4   KVDMLELSERSARFVLSNTTPAFA----NSIRRAMLADVPTFAIDDLNIYNNTSVLYDEQ 59

Query: 76  KGVHEDLTDI-ILNIKGINLKMSGDSHK-------RVTIFKRGPGVVTAGDIQ-TVNDIE 126
            G+   L  +   NI     +      +        +T+   GP +V +GD+  +   I+
Sbjct: 60  LGLRLALIPLATENIDDYTTQDECTCEEGCPSCEVSITLSAEGPKMVYSGDLISSDPGIQ 119

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
             + +  I  L  D  V +E    KG G   AK  
Sbjct: 120 PADTNIPIIELKEDQRVVLEALAHKGLGKDNAKWQ 154


>gi|328768461|gb|EGF78507.1| hypothetical protein BATDEDRAFT_20338 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 285

 Score = 43.0 bits (100), Expect = 0.067,   Method: Composition-based stats.
 Identities = 40/258 (15%), Positives = 86/258 (33%), Gaps = 47/258 (18%)

Query: 40  AHT---LGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTDIIL 87
            +T   + NALRR +++ +   AI  V+ +          + H +  I    E +  I  
Sbjct: 32  GNTDLSVANALRRTMIAEVPTVAIDLVEFESNSSVLTDEFLAHRLGLIPLNSEQVGTITY 91

Query: 88  NIKGINLKMSGDSHKRVTIFK----RGPGVVTAGDIQTVND--IEVLNPD----HVICNL 137
                  +        + +           VT+ D+ + +   + +++ D     +I  L
Sbjct: 92  TRDCSCTQYCPQCSVELHLNVRCDEEFTREVTSRDLISSHSSIMPIIHGDDDSGIMIAKL 151

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES-------- 189
                + +     KG     AK                 ++ ++  +Y VE         
Sbjct: 152 RKGQEINLRCIAKKGTAKEHAKWSPCAGIAFEYDP----HNRLRHTTYWVEDDIKSEWPV 207

Query: 190 ---------AREGQVLDY----DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
                      + +  D+    DK  MT++  G+I  ++ V  A RI+Q +L +     +
Sbjct: 208 SANGLLEPEVVDDEPFDFNAKPDKFYMTVEGTGAIDPKEIVTTALRIMQTKLSLVQMLIK 267

Query: 237 PKKEVKEDINVKSLPFNP 254
              +  +D +   +    
Sbjct: 268 EISDDNDDSSRAQMNGMY 285


>gi|226311725|ref|YP_002771619.1| hypothetical protein BBR47_21380 [Brevibacillus brevis NBRC 100599]
 gi|226094673|dbj|BAH43115.1| conserved hypothetical protein [Brevibacillus brevis NBRC 100599]
          Length = 70

 Score = 43.0 bits (100), Expect = 0.070,   Method: Composition-based stats.
 Identities = 12/53 (22%), Positives = 22/53 (41%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  +  L   +E ++L+    G  S+ +++  L   GL  
Sbjct: 15  LSAPARRALEHNGITSLEQLASYSEKEILKFHGMGPASMPKLRTALKEKGLSF 67


>gi|118431575|ref|NP_148137.2| DNA-directed RNA polymerase subunit D [Aeropyrum pernix K1]
 gi|150421654|sp|Q9YB53|RPOD_AERPE RecName: Full=DNA-directed RNA polymerase subunit D
 gi|116062900|dbj|BAA80745.2| DNA-directed RNA polymerase subunit D [Aeropyrum pernix K1]
          Length = 286

 Score = 43.0 bits (100), Expect = 0.070,   Method: Composition-based stats.
 Identities = 24/155 (15%), Positives = 51/155 (32%), Gaps = 18/155 (11%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAI---------TAVQIDGVLHEISSIKGVHEDLTDIIL 87
           RG+     NA+RR ++S +   A+         TAV  + V H +  +     +  +   
Sbjct: 24  RGYPVVFVNAIRRTVLSDVPTMAVDYAYIFDNTTAVYDEMVAHRLGLVVLDSNEAVEKYR 83

Query: 88  NIKGINLKMSGDSHKRVTIFK--------RGPGVVTAGDI-QTVNDIEVLNPDHVICNLD 138
             +    K   +    V +               +TAGD+  +   ++ + P+  +  + 
Sbjct: 84  RPEECAGKEPSEEDCFVEVSLEAEVDAEGETGRYITAGDLSISDPQVKPVYPETPLIYVA 143

Query: 139 VDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITI 173
               + ++     G G    K        +    I
Sbjct: 144 PGQRIHVQAFARLGRGKEHTKWSPASLSVLRYTPI 178


>gi|154310335|ref|XP_001554499.1| RNA polymerase II subunit 3 [Botryotinia fuckeliana B05.10]
 gi|150851419|gb|EDN26612.1| RNA polymerase II subunit 3 [Botryotinia fuckeliana B05.10]
          Length = 336

 Score = 43.0 bits (100), Expect = 0.070,   Method: Composition-based stats.
 Identities = 49/264 (18%), Positives = 88/264 (33%), Gaps = 51/264 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG----VLHEI- 72
           + + +   +        +   FA    N+LRR ++S +   AI  VQI+     +  E  
Sbjct: 17  VKITEAGSHHVDFELSNVDLSFA----NSLRRTVLSEVPTIAIDRVQIEANTSVLADEFI 72

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSH-------KRVTIFKRGPG----VVTAGDIQT 121
           +   G+   +     N   +      D           +T+  R  G     V A D+  
Sbjct: 73  AHRLGL---IPLNSKNCDDVIYTRDCDCEGNCELCSVTLTLHARCTGDEIMKVYARDLVV 129

Query: 122 VND-----I---EVLNPD---HVICNLDVDAVVRMELTVSKGHGYVPAKHHR------TE 164
                   +    + +PD    VI  L     +RM+    KG     AK           
Sbjct: 130 DPQRANKWVGNPVITDPDGLGPVIAKLRKGQELRMKCIALKGIAKEHAKWAPTAAVGFEY 189

Query: 165 NDPIGLITIDALYS-------PIKKVSYTVESAREGQVLDYDKL----SMTIDTDGSITG 213
           +    L  ID  Y        P  K +   E A+EG   DYD +       +++ G++  
Sbjct: 190 DPHNKLKHIDLWYEHDAAKEWPKSKYADWEEPAQEGAPFDYDAVPNNFYFEVESIGNLEP 249

Query: 214 EDSVALASRILQDQLGMFINFEEP 237
           +  +    +++Q +L   +     
Sbjct: 250 DAIIQQGIKVMQQKLAAVLQDLTE 273


>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 = 43.0 bits (100), Expect = 0.072,   Method: Composition-based stats.
 Identities = 24/107 (22%), Positives = 46/107 (42%), Gaps = 1/107 (0%)

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALL-KKVEELELSVRST 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|50555259|ref|XP_505038.1| YALI0F05566p [Yarrowia lipolytica]
 gi|49650908|emb|CAG77845.1| YALI0F05566p [Yarrowia lipolytica]
          Length = 314

 Score = 42.7 bits (99), Expect = 0.073,   Method: Composition-based stats.
 Identities = 44/235 (18%), Positives = 83/235 (35%), Gaps = 41/235 (17%)

Query: 40  AHTLGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIILNIK 90
             TL N+LRRV+++ +   AI  V+I         + + H +  I    +D+ D+  +  
Sbjct: 19  GITLANSLRRVMLAEIPTLAIDLVEISTNTSVLADEFISHRLGLIPLDSQDVNDLEYSRD 78

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIE------------VLNPDHV---IC 135
            +  +        + +     G  T         +               +P      IC
Sbjct: 79  CVCDEYCDKCSVVLMLDATCTGDDTMDIYSRDLMVHTTPERPELGKPIYTDPAKKGILIC 138

Query: 136 NLDVDAVVRMELTVSKGHGYVPAKHHR-----TENDPIGLI-TIDALYS-------PIKK 182
            L  +  +R++    KG     AK         E DP   +   D  Y        P+ K
Sbjct: 139 KLRKNQSLRIKCIAKKGIAKEHAKWSPCAAIGFEYDPWNKLKHTDYWYEENAEEEWPLSK 198

Query: 183 VSYTVESAREGQVLDY----DKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
            +   E  +E +  DY    +K  + ++  G++T  + V    ++LQ +L   + 
Sbjct: 199 NADWEEPPKENEPFDYNAKPNKFYINVEATGALTQYEVVLRGMQVLQKKLAEVVM 253


>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 = 42.7 bits (99), Expect = 0.074,   Method: Composition-based stats.
 Identities = 36/192 (18%), Positives = 56/192 (29%), Gaps = 54/192 (28%)

Query: 34  PLPRGFAHT-----LGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIK--- 76
           PL   F+       + NA RR+L++ +   AI  V I           + H +  I    
Sbjct: 61  PLEASFSLIGVDAAIANAFRRILLAEIPALAIEYVYIQNNTSVIQDEVLAHRLGLIPLKG 120

Query: 77  ----------------------GVHEDLTDIILNIKGINLKMSGDSH--KRVTIFKRGPG 112
                                   HED   I+L +     K        +  TI      
Sbjct: 121 SLEGLNWLRWFKAPKEGDPDSGSTHEDSNTIVLRLVKECTKNRSAPPGEEDPTILYNNAH 180

Query: 113 VVTAGDIQTVND------------IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
            + A D+                 I+  NPD ++  L     + +E+   KG G   AK 
Sbjct: 181 -IYAKDLVFEPQGRQEKYFHGDGAIQSCNPDILLAKLRPGQKIDIEMHCIKGIGADHAKF 239

Query: 161 HRTENDPIGLIT 172
                    L+ 
Sbjct: 240 SPVATASYRLLP 251


>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 = 42.7 bits (99), Expect = 0.074,   Method: Composition-based stats.
 Identities = 36/241 (14%), Positives = 81/241 (33%), Gaps = 43/241 (17%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ-IDGVLHEISSI 75
            + + +  + RTL++ E +   FA    N++RR +++ +   AI  V   +         
Sbjct: 2   KVRVIELSDQRTLLVLEGVSPSFA----NSIRRAIIAEVPTFAIDEVIFFENTTPFFDEY 57

Query: 76  KGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG---VVTAGDIQ-TVNDIEVLNPD 131
                 +  +  ++    L++  +    + + K+      VV +G+++ +   I   N  
Sbjct: 58  IAHRLAMIPLRTSLD--VLRVDPNRTVVLELSKKAKDPIEVVYSGELKSSDPLIYPANDK 115

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITI-------------DALY- 177
             I  +     +R +     G G   +K           + I              +   
Sbjct: 116 IPIIKMRKGQKLRFQAIARIGRGKDHSKWSPAAAVGYSYMPIYELKDPVECDLSQCSNCI 175

Query: 178 ---SPIKKVSYTV---------ESAREGQ------VLDYDKLSMTIDTDGSITGEDSVAL 219
                I +V Y V         E  R           D  ++ ++ ++ GS+  E+  + 
Sbjct: 176 ESDGGISRVDYPVLCEGCLEALERCRVRNPDKIIRRWDESRIIISYESTGSLRPEEIFSE 235

Query: 220 A 220
           A
Sbjct: 236 A 236


>gi|156055988|ref|XP_001593918.1| hypothetical protein SS1G_05346 [Sclerotinia sclerotiorum 1980]
 gi|154703130|gb|EDO02869.1| hypothetical protein SS1G_05346 [Sclerotinia sclerotiorum 1980
           UF-70]
          Length = 335

 Score = 42.7 bits (99), Expect = 0.076,   Method: Composition-based stats.
 Identities = 48/264 (18%), Positives = 87/264 (32%), Gaps = 51/264 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG----VLHEI- 72
           + + +   +        +   FA    N+LRR ++S +   AI  VQI+     +  E  
Sbjct: 17  VKITEAGSHHVDFELSNVDLSFA----NSLRRTILSEVPTIAIDRVQIEANTSVLADEFI 72

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSH-------KRVTIFKRGPG----VVTAGDIQT 121
           +   G+   +     N   +      D           +T+  R  G     V A D+  
Sbjct: 73  AHRLGL---IPLNSKNCDDVIYTRDCDCDGNCELCSVTLTLHARCTGDEIMKVYARDLVV 129

Query: 122 VND-----I---EVLNPD---HVICNLDVDAVVRMELTVSKGHGYVPAKHHR------TE 164
                   +    + +PD    VI  L     +RM+    KG     AK           
Sbjct: 130 DPQRANKWVGNPVITDPDGLGPVIAKLRKGQELRMKCIALKGIAKEHAKWAPTAAVGFEY 189

Query: 165 NDPIGLITIDALYS-------PIKKVSYTVESAREGQVLDYDKL----SMTIDTDGSITG 213
           +    L  ID  Y        P  K +   E  +EG   DYD +       +++ G++  
Sbjct: 190 DPHNKLKHIDLWYEHDAAKEWPKSKYADWEEPPQEGAPFDYDAVPNNFYFEVESIGNLEP 249

Query: 214 EDSVALASRILQDQLGMFINFEEP 237
           +  +    +++Q +L   +     
Sbjct: 250 DAIIQQGIKVMQQKLAAVLQDLTE 273


>gi|284161974|ref|YP_003400597.1| hypothetical protein Arcpr_0861 [Archaeoglobus profundus DSM 5631]
 gi|284011971|gb|ADB57924.1| hypothetical protein Arcpr_0861 [Archaeoglobus profundus DSM 5631]
          Length = 261

 Score = 42.7 bits (99), Expect = 0.077,   Method: Composition-based stats.
 Identities = 14/88 (15%), Positives = 31/88 (35%), Gaps = 16/88 (18%)

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR-- 294
            K   ++             ++ V E +  +     L    I  +GDL+ +++ +++   
Sbjct: 173 EKIVREKQREWFCYQVRKKGIETVAEDDTELAIFRSL---GIYTIGDLLSKSDEELIEAF 229

Query: 295 ----------MANFGRKSLVEIKGVLGT 312
                     + +F +  L EIK  L  
Sbjct: 230 KEKYKPTADLLEHF-KNRLKEIKEKLKE 256


>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 = 42.7 bits (99), Expect = 0.077,   Method: Composition-based stats.
 Identities = 40/193 (20%), Positives = 76/193 (39%), Gaps = 34/193 (17%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR- 103
           NA+RR+++S +   AI  V I        +   + +++    L +  I  K   +S    
Sbjct: 28  NAIRRIMISEVPTYAIEDVYI------YENSSSMDDEILAHRLGLIPIKGKPLIESEVIT 81

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
            T+ K GP  V + D+++ N  EV   +  I  L     +++E     G G   AK    
Sbjct: 82  FTLEKEGPCTVYSSDLKSENG-EVAFKNIPIVKLGRGQKIKIECEAVPGIGKTHAKWQ-- 138

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
                     +A+Y  +                  D++   ++T G +  E+ +  A +I
Sbjct: 139 --------PCNAVYKQVA----------------EDEVEFFVETFGQMEAEEILEEAVKI 174

Query: 224 LQDQLGMFINFEE 236
           L+++   F+   E
Sbjct: 175 LKNKAESFLQQLE 187


>gi|39942270|ref|XP_360672.1| hypothetical protein MGG_03215 [Magnaporthe oryzae 70-15]
 gi|145015793|gb|EDK00283.1| hypothetical protein MGG_03215 [Magnaporthe oryzae 70-15]
          Length = 330

 Score = 42.7 bits (99), Expect = 0.078,   Method: Composition-based stats.
 Identities = 43/248 (17%), Positives = 86/248 (34%), Gaps = 44/248 (17%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTDIILNIKG 91
            +L N++RRV+++ +   AI   +I           + H +  +       ++++     
Sbjct: 36  LSLANSIRRVMLAEIPTVAIDNCEIKENTSVLADEFIAHRLGLVPLSARGASELVYARDC 95

Query: 92  INLKMSGDSHKRVTIFKRGPGV-------VTAGDIQTVN-----DI---EVLNPD---HV 133
              +   +    +TI  +           V A D+          +    + +PD    +
Sbjct: 96  DCEQYCENCSVIITIHAKCESEDPNYVMKVYARDMVVDGRRVNQSVGTPVITDPDGLGVI 155

Query: 134 ICNLDVDAVVRMELTVSKGHG-----YVPAKHHRTENDPIGLI-TIDALYSPIKKVSY-- 185
           +  L  +  V +     KG       + PA     E DP   +  +D  Y    K  +  
Sbjct: 156 LFKLRRNQEVHIRCVAKKGIAKEHAKWCPATAIGFEYDPHNKLRHLDLWYESNAKEEWPL 215

Query: 186 -----TVESAREGQVLDYD----KLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEE 236
                     +EG+  DYD    +    ++T G++  +  V    R+LQ++L   +   E
Sbjct: 216 SENAIREPPPQEGEPFDYDAVPNRFYFDVETCGALDPDVIVQEGLRVLQEKLANLVMLIE 275

Query: 237 PKKEVKED 244
              E K  
Sbjct: 276 KTDESKGM 283


>gi|110668834|ref|YP_658645.1| DNA-directed RNA polymerase subunit D [Haloquadratum walsbyi DSM
           16790]
 gi|109626581|emb|CAJ53045.1| DNA-directed RNA polymerase subunit D [Haloquadratum walsbyi DSM
           16790]
          Length = 262

 Score = 42.7 bits (99), Expect = 0.082,   Method: Composition-based stats.
 Identities = 36/254 (14%), Positives = 82/254 (32%), Gaps = 51/254 (20%)

Query: 15  IEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEIS 73
           IE+I     ++     +     RG    + N +RR +++ +   +I  V+  +       
Sbjct: 7   IEFIERD-TDDRSARFLV----RGVTPAVANGIRRAMVADIPTFSIEDVRFVENSSVMFD 61

Query: 74  SIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVND-IEVLNPDH 132
            + G+   L  +   +   ++         +++   GP    +GDI + +  +E  + + 
Sbjct: 62  EMIGLRLGLVPLTTPVDDFDI----GDTVTLSLDITGPQTAYSGDIVSSDRLVEPADENI 117

Query: 133 VICNLDVDAVVRME--LTVSKGH-----------GYVPAKHHRTENDPIGLITID----- 174
            I  L  +  + +E    +  G            GY   +      D       D     
Sbjct: 118 PIIELKENHRLELEADAVLDTGKSHAKQQGGVAVGYRHLQRIEVIGDADEFADEDPHILR 177

Query: 175 ------ALYSPIKKVSYTVESAREGQVLD----------------YDKLSMTIDTDGSIT 212
                 A    + + +   +     +  +                 + +   ++TDGS +
Sbjct: 178 GVIEEGAATHAVDETATNGDLIPTTEFDNDLTNRYPGKELTVSDVPNAVVFHVETDGSFS 237

Query: 213 GEDSVALASRILQD 226
             + V  A+R L D
Sbjct: 238 VPELVERAARSLGD 251


>gi|229126551|ref|ZP_04255565.1| hypothetical protein bcere0015_10080 [Bacillus cereus BDRD-Cer4]
 gi|228656940|gb|EEL12764.1| hypothetical protein bcere0015_10080 [Bacillus cereus BDRD-Cer4]
          Length = 95

 Score = 42.7 bits (99), Expect = 0.085,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  + +L + +E ++L++   G  SL +++ VL    L  
Sbjct: 42  LSAPARRALEHRGIQTVEELSKYSEKEILKLHGMGPASLPKLRKVLEESWLSF 94


>gi|150399384|ref|YP_001323151.1| RNA polymerase insert [Methanococcus vannielii SB]
 gi|150012087|gb|ABR54539.1| RNA polymerase insert [Methanococcus vannielii SB]
          Length = 195

 Score = 42.7 bits (99), Expect = 0.087,   Method: Composition-based stats.
 Identities = 39/160 (24%), Positives = 62/160 (38%), Gaps = 14/160 (8%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
           ALRR+++S +   AI  V      +  S    V      +I  +KG+ +  SGD     T
Sbjct: 29  ALRRLMISEVPTYAIENVYFY--ENTSSMYDEVLAHRLGLIP-VKGVPV--SGDEVVVFT 83

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
           + K GP  V + D+++    E+   +  I  L     +  E     G G   AK     N
Sbjct: 84  LSKEGPCTVYSSDLKSEAG-EIAFENIPIVKLAEGQKLEFEAEALVGTGKFHAKWQPC-N 141

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTI 205
                I+ D +        +T+ES       D  + S+ I
Sbjct: 142 VVYKQISNDEV-------EFTIESFGNMDAEDIIRSSLEI 174


>gi|253576488|ref|ZP_04853817.1| conserved hypothetical protein [Paenibacillus sp. oral taxon 786
           str. D14]
 gi|251844125|gb|EES72144.1| conserved hypothetical protein [Paenibacillus sp. oral taxon 786
           str. D14]
          Length = 64

 Score = 42.7 bits (99), Expect = 0.091,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 24/53 (45%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    +  +  L + +E ++LR    G  S+ ++K  L + GL  
Sbjct: 10  LSAPARRALEANGVTTLEKLAELSEQEVLRFHGMGPASIPKLKEALRSKGLTF 62


>gi|254167792|ref|ZP_04874642.1| RNA polymerase Rpb3/Rpb11 dimerisation domain [Aciduliprofundum
           boonei T469]
 gi|289597072|ref|YP_003483768.1| RNA polymerase insert [Aciduliprofundum boonei T469]
 gi|197623320|gb|EDY35885.1| RNA polymerase Rpb3/Rpb11 dimerisation domain [Aciduliprofundum
           boonei T469]
 gi|289534859|gb|ADD09206.1| RNA polymerase insert [Aciduliprofundum boonei T469]
          Length = 273

 Score = 42.7 bits (99), Expect = 0.094,   Method: Composition-based stats.
 Identities = 44/271 (16%), Positives = 86/271 (31%), Gaps = 62/271 (22%)

Query: 20  LGQEEENRTLMIAEPLPRGFAHT--LGNALRRVLMSSLRGAAITAVQI--------DGVL 69
           + + ++       +        T  + NALRR L++ +   AI  V          +G +
Sbjct: 5   ILELQDRYIKFEIK------GITPSVANALRRTLINDIPKLAIHKVIFHHGQIRDMEGNV 58

Query: 70  HEISS--IKGVHEDLTDIILNIKGINLKMSGDSHKRV-----------TIFKRGPGVVTA 116
           ++ S+     +      +I     +N+K   +                T+ K GP  V +
Sbjct: 59  YDSSTPLFDEIIAHRLGLIPLPTDLNMKFRDECDHPPDEGCPLCTVTYTLNKHGPATVYS 118

Query: 117 GDIQTVND--IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH------------- 161
           GD+  V D   + ++P   I  L     + +E     G     AK               
Sbjct: 119 GDLIPVGDEKFKPVDPLIPIVKLKEHQAILLEAEAIMGTAKEHAKWQVTSGVSYKYHREI 178

Query: 162 ------------RTENDPIGLITIDALY------SPIKKVSYTVESAREGQVLDYDKLSM 203
                         ++ P  +I  D  +       P K+++  +         D      
Sbjct: 179 KVNKKDSELWEKVKKSCPKNVIKEDDKFIIFTDDIPCKEIAEILSFENPEITEDDSWFIF 238

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINF 234
             +TDGS+   D++  A + L+ +       
Sbjct: 239 EFETDGSLKAIDTLEYAIKRLKTRFNTLREH 269


>gi|21228260|ref|NP_634182.1| DNA-directed RNA polymerase subunit D [Methanosarcina mazei Go1]
 gi|23822085|sp|Q8PV16|RPOD_METMA RecName: Full=DNA-directed RNA polymerase subunit D
 gi|20906717|gb|AAM31854.1| DNA-directed RNA polymerase subunit D [Methanosarcina mazei Go1]
          Length = 266

 Score = 42.7 bits (99), Expect = 0.094,   Method: Composition-based stats.
 Identities = 24/155 (15%), Positives = 53/155 (34%), Gaps = 15/155 (9%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSIK 76
           + + +  +     +        A    N +RR +++ +   AI  V + D          
Sbjct: 5   VDILELSDRSAKFVLS--RVSMA--FANGVRRAMIADVPTLAIEYVNLYDNTSVLYDEQL 60

Query: 77  GVHEDLTDIILNIKGINLKMSGD---------SHKRVTIFKRGPGVVTAGDIQT-VNDIE 126
            +   L  ++ +I+    +   +             +T+   GPG V + D+ +    I+
Sbjct: 61  ALRLSLIPLVTDIETYMPQAECEVCGGEGCPACEVSLTLSAEGPGTVYSRDLISSDPKIQ 120

Query: 127 VLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
             +P+  I  L     + +E     G+G    K  
Sbjct: 121 PADPNIPIVELKKGQKLVLEAIAHMGYGRDSVKWQ 155


>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 = 42.3 bits (98), Expect = 0.096,   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|124027415|ref|YP_001012735.1| DNA-directed RNA polymerase subunit D [Hyperthermus butylicus DSM
           5456]
 gi|123978109|gb|ABM80390.1| DNA-directed RNA polymerase subunit D [Hyperthermus butylicus DSM
           5456]
          Length = 281

 Score = 42.3 bits (98), Expect = 0.098,   Method: Composition-based stats.
 Identities = 40/264 (15%), Positives = 83/264 (31%), Gaps = 60/264 (22%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI---------DGV 68
           + +  ++     +  E    GF   L NA+RR   S +   A+  V++         + +
Sbjct: 4   LCILDKDRLTIRLYVE----GFGLPLVNAIRRAAYSDVPVMAVDVVEVFENNTVLYDEII 59

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR------GPGVVTAGDIQT- 121
            H +  I    ++        +       GD    V +            +V +GD++T 
Sbjct: 60  AHRLGLIPLTSKEALQKYKRPEECEKAELGDPSCYVVLRLEVETGPREERIVYSGDLETS 119

Query: 122 VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITI-----DAL 176
             D+  +  +  I  +  D  +R++     G+G   AK           + I     D +
Sbjct: 120 DPDVRPVYDNMPIVVMAPDQRLRLQAYARLGYGREHAKWMPVSVAAHRYLPILEFNLDEM 179

Query: 177 YSPIKKV--------SYTVESAREGQVL---------------------------DYDKL 201
                +         +  +   R G +                            D  + 
Sbjct: 180 SDECIRCIESGYPELAAKIREMRSGSIAVVEDVNTSGLYWCVQRRCGGKGVKLVYDDKRF 239

Query: 202 SMTIDTDGSITGEDSVALASRILQ 225
            + I++ G++  ED V  A+R + 
Sbjct: 240 ILKIESTGALPPEDIVREAARAIV 263


>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 = 42.3 bits (98), Expect = 0.098,   Method: Composition-based stats.
 Identities = 41/181 (22%), Positives = 73/181 (40%), Gaps = 32/181 (17%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
           ALRR+++S +   AI  V      +  S    V      +I  IKG+ +  SGD    +T
Sbjct: 14  ALRRIMISEVPTYAIENVYFY--ENTSSMYDEVLAHRLGLIP-IKGVPV--SGDEVIVLT 68

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
           I K GP +V + D+++ +       +  I  L     + +E     G G + AK      
Sbjct: 69  ISKEGPCMVYSSDLKSESGEPAF-ENIPIVKLAEGQKLELEAEALVGTGKIHAKWQ---- 123

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
                   +A+Y                + +  D++   I++ G++  ED V  +  IL+
Sbjct: 124 ------PCNAVY----------------KQISNDEVEFKIESFGNMDAEDIVRSSLEILK 161

Query: 226 D 226
           +
Sbjct: 162 N 162


>gi|21224924|ref|NP_630703.1| protein kinase [Streptomyces coelicolor A3(2)]
 gi|3451455|emb|CAA20514.1| putative protein kinase [Streptomyces coelicolor A3(2)]
          Length = 1557

 Score = 42.3 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 12/78 (15%), Positives = 26/78 (33%)

Query: 240 EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFG 299
               +     L         +    L+  + + L G  I  +G+L+  +   ++     G
Sbjct: 852 PETAEQQRDRLAAEVTRDTPLTVSGLTPAAQSFLYGLGITTVGELLDYSRRKLVNAPGLG 911

Query: 300 RKSLVEIKGVLGTMGLFL 317
            K+  E++      G  L
Sbjct: 912 AKTRNEVQQRQREWGERL 929


>gi|289809444|ref|ZP_06540073.1| DNA-directed RNA polymerase subunit alpha [Salmonella enterica
           subsp. enterica serovar Typhi str. AG3]
          Length = 45

 Score = 42.3 bits (98), Expect = 0.10,   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|330466646|ref|YP_004404389.1| hypothetical protein VAB18032_13385 [Verrucosispora maris
           AB-18-032]
 gi|328809617|gb|AEB43789.1| hypothetical protein VAB18032_13385 [Verrucosispora maris
           AB-18-032]
          Length = 65

 Score = 42.3 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 25/55 (45%)

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
           ++S  +T  L       + DL+  + A++  +   G K+L  I+  L    L LG
Sbjct: 10  KISAPATRALHNAGYATLRDLVGVSRAELAELHGMGPKALGIIQSALEEHNLTLG 64


>gi|68069197|ref|XP_676509.1| DNA-directed RNA polymerase I [Plasmodium berghei strain ANKA]
 gi|56496241|emb|CAH97452.1| DNA-directed RNA polymerase I, putative [Plasmodium berghei]
          Length = 334

 Score = 42.3 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 38/268 (14%), Positives = 84/268 (31%), Gaps = 48/268 (17%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQI---DGV--LHEISSIKGVH-----------EDLTD 84
            ++ NALRR+++S +   AI  V I    GV     +    G+            +D  +
Sbjct: 69  VSIANALRRIMISEVPTIAIEKVNIFQNTGVIADEILCHRLGLIPFKFDADLINFKDTHE 128

Query: 85  IILNIKGINLKMSGDSH--KRVTIFKRGPGVVTAGDIQ--------------TVNDIEVL 128
              N+     K+    +      I       + + D++                  +  +
Sbjct: 129 KYNNLNCFCFKLHVKCNSINNNKIGNENYQCIYSKDLKWCPLNEEQKIKFESNPPKV--V 186

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVE 188
           + + +I  L     + +   + KG G   AK                + + + K+  T +
Sbjct: 187 DDNILITKLGNGQEIELICFLEKGIGKTHAKWS-------------PVCTAVYKMFPTFD 233

Query: 189 SAREGQVLDYDKL-SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
                +  +Y+K   ++I        E+S  L ++   D        E+  +++      
Sbjct: 234 FDVHEKFTNYEKKDILSICPKNVFDIEESGNLVAKNPLDCSSCRACIEKYPQKISFQKKK 293

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRG 275
               F            +  ++ N L+ 
Sbjct: 294 NHFIFTVESTGCFSSANIFKKALNILKE 321


>gi|167044977|gb|ABZ09642.1| putative RNA polymerase Rpb3/RpoA insert domain protein [uncultured
           marine crenarchaeote HF4000_APKG8G2]
          Length = 214

 Score = 42.3 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 27/183 (14%), Positives = 59/183 (32%), Gaps = 40/183 (21%)

Query: 44  GNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIILNIKGINL 94
            NALRR+ ++ +   AI  V +         +G+ H +  I  +  +L     +   + L
Sbjct: 41  ANALRRICLNGVPIFAIDTVDVIENSSVIPDEGIAHTLGMIP-LKTELNGFDESNSRVIL 99

Query: 95  KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHG 154
            +  ++ +   I         A        ++ ++    I +L     +++E     G G
Sbjct: 100 VLDSEAAENTKIVTS------AELESKDQVVKPISKQIPIVHLAPGQRIKLEAYARLGRG 153

Query: 155 YVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
              AK +      +                              D+  +T++T GS+   
Sbjct: 154 TEHAKWNSANISVLT------------------------NTDKEDERILTVETTGSLEPR 189

Query: 215 DSV 217
             +
Sbjct: 190 QII 192


>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 = 42.3 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 17/107 (15%), Positives = 38/107 (35%), Gaps = 16/107 (14%)

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
             + +K          N       +E  +S +            + DL  +   ++  + 
Sbjct: 323 KNESIKAMDECLYEMQNNLEQMMNQEGAISSQ-----------QIHDLKAKVREEL--IK 369

Query: 297 NFGRKSL---VEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
           NF +KS+    E+K     +         D+  ++ E L ++++D C
Sbjct: 370 NFKKKSIASEEELKEFYEQLDRQFAEKFRDFKKKNKERLQERFQDMC 416


>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 = 42.3 bits (98), Expect = 0.12,   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|327402170|ref|YP_004343008.1| hypothetical protein Fluta_0161 [Fluviicola taffensis DSM 16823]
 gi|327317678|gb|AEA42170.1| hypothetical protein Fluta_0161 [Fluviicola taffensis DSM 16823]
          Length = 95

 Score = 42.3 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 11/53 (20%), Positives = 27/53 (50%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   ++  +I  + +L + +E ++++    G+ S+  +K +L   GL  
Sbjct: 41  LSAPARRAIQNNHISSLEELSKYSEKEIMKFHGIGKTSIPTLKKLLTDKGLSF 93


>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 = 42.3 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 35/223 (15%), Positives = 64/223 (28%), Gaps = 57/223 (25%)

Query: 1   MIQKNWQELIKPNNIEYIVLG--QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGA 58
           ++  N    + P  ++ + +   + +             G    + NA RR+L++ +   
Sbjct: 17  LLYSNVAPYLPPWKLKGLKIEFHKNDPLEASFSL----IGVDAAIANAFRRILLAEIPAL 72

Query: 59  AITAVQIDG---------VLHEISSIK-------------------------GVHEDLTD 84
           AI  V I           + H +  I                            HED   
Sbjct: 73  AIEYVYIQNNTSVIQDEVLAHRLGLIPLKGSLEGLNWLRWFKIPKEGDPDSGSTHEDSNT 132

Query: 85  IILNIKGINLKMSG---DSHKRVTIFKRGPGVVTAGDIQTVND------------IEVLN 129
           I+L +     K      D      ++      + A D+                 I+  N
Sbjct: 133 IVLRLVKECTKNRNSAPDEEDPTVLYNNAH--IYAKDLVFEPQGRQEKYFHGDGVIQPCN 190

Query: 130 PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT 172
           PD ++  L     + +E+   KG G   AK          L+ 
Sbjct: 191 PDTLLAKLRPGQKIDIEMHCIKGIGADHAKFSPVATASYRLLP 233


>gi|14702171|ref|NP_116558.1| DNA-directed RNA polymerase II subunit RPB3 [Homo sapiens]
 gi|109128647|ref|XP_001098417.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3 isoform 3
           [Macaca mulatta]
 gi|114662810|ref|XP_001148305.1| PREDICTED: DNA directed RNA polymerase II polypeptide C isoform 1
           [Pan troglodytes]
 gi|296231192|ref|XP_002761051.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-like
           [Callithrix jacchus]
 gi|297698834|ref|XP_002826511.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-like [Pongo
           abelii]
 gi|3915850|sp|P19387|RPB3_HUMAN RecName: Full=DNA-directed RNA polymerase II subunit RPB3;
           Short=RNA polymerase II subunit 3; Short=RNA polymerase
           II subunit B3; AltName: Full=DNA-directed RNA polymerase
           II 33 kDa polypeptide; Short=RPB33; AltName:
           Full=DNA-directed RNA polymerase II subunit C; AltName:
           Full=RPB31
 gi|2266931|gb|AAC14355.1| RNA polymerase II subunit hRPB33 [Homo sapiens]
 gi|3252823|gb|AAC24309.1| RNA polymerase II subunit hRPB33 [Homo sapiens]
 gi|12653281|gb|AAH00409.1| Polymerase (RNA) II (DNA directed) polypeptide C, 33kDa [Homo
           sapiens]
 gi|13111973|gb|AAH03159.1| Polymerase (RNA) II (DNA directed) polypeptide C, 33kDa [Homo
           sapiens]
 gi|20380436|gb|AAH28157.1| Polymerase (RNA) II (DNA directed) polypeptide C, 33kDa [Homo
           sapiens]
 gi|49457035|emb|CAG46838.1| POLR2C [Homo sapiens]
 gi|60823189|gb|AAX36635.1| polymerase II polypeptide C [synthetic construct]
 gi|90079489|dbj|BAE89424.1| unnamed protein product [Macaca fascicularis]
 gi|119603332|gb|EAW82926.1| hCG2025883, isoform CRA_b [Homo sapiens]
 gi|119603333|gb|EAW82927.1| hCG2025883, isoform CRA_b [Homo sapiens]
 gi|119603335|gb|EAW82929.1| hCG2025883, isoform CRA_b [Homo sapiens]
 gi|119603336|gb|EAW82930.1| hCG2025883, isoform CRA_b [Homo sapiens]
 gi|123981016|gb|ABM82337.1| polymerase (RNA) II (DNA directed) polypeptide C, 33kDa [synthetic
           construct]
 gi|123995821|gb|ABM85512.1| polymerase (RNA) II (DNA directed) polypeptide C, 33kDa [synthetic
           construct]
 gi|157928942|gb|ABW03756.1| polymerase (RNA) II (DNA directed) polypeptide C, 33kDa [synthetic
           construct]
 gi|158259685|dbj|BAF85801.1| unnamed protein product [Homo sapiens]
 gi|208967078|dbj|BAG73553.1| polymerase (RNA) II (DNA directed) polypeptide C [synthetic
           construct]
          Length = 275

 Score = 42.3 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 47/256 (18%), Positives = 90/256 (35%), Gaps = 51/256 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHT---LGNALRRVLMSSLRGAAITAVQIDG------- 67
           + + +  +     I E       +T   + N++RRV ++ +   AI  VQID        
Sbjct: 9   VRITELTDENVKFIIE-------NTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHD 61

Query: 68  --VLHEISSIKGVHEDLTDIILNIKG---------------INLKMSGDSHKRVT---IF 107
             + H +  I  + +D+ D +   +                ++++ + D  + VT   + 
Sbjct: 62  EFIAHRLGLIPLISDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDLI 121

Query: 108 KRGPGV--VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
              P V  VT+ +     +  V   D +I  L     +R+     KG G   AK + T  
Sbjct: 122 SNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181

Query: 166 DPIGLITIDALYSPIK-------KVSYT-----VESAREGQVLDYDKLSMTIDTDGSITG 213
                   +AL   +        K  Y+        A        ++    +++ GS+  
Sbjct: 182 VAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLRP 241

Query: 214 EDSVALASRILQDQLG 229
           E  V  A   L+ +L 
Sbjct: 242 ETIVLSALSGLKKKLS 257


>gi|46109130|ref|XP_381623.1| hypothetical protein FG01447.1 [Gibberella zeae PH-1]
          Length = 337

 Score = 42.3 bits (98), Expect = 0.12,   Method: Composition-based stats.
 Identities = 39/228 (17%), Positives = 79/228 (34%), Gaps = 42/228 (18%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTDIILNIKG 91
            +  NA+RRV+ + +   AI  V+I+          + H +  I    + + ++  +   
Sbjct: 36  LSFANAVRRVIQAEVPTIAIDLVEIETNSSVLADEFIAHRLGLIPLDSKGVAELNYSRDC 95

Query: 92  INLKMSGDSHKRVTIFKRGP----GVVTAGDIQTVNDI-------EVLNPDHV---ICNL 137
              +        +T+  +        V A D+              +++P+     I  L
Sbjct: 96  DCEQYCEQCSVTLTLHAKCTSDEIMKVYARDLVVDGRHGNSVGSPMIMDPEGYGCLIAKL 155

Query: 138 DVDAVVRMELTVSKGHGYVPAKHHR------TENDPIGLITID---------ALYSPIKK 182
                +++     KG     AK           +    L  ID         A+  P  K
Sbjct: 156 RKHQELKISCIAKKGIAKEHAKWMPTSAVGFEYDPHNKLNHIDWWFENDTDPAVEWPKSK 215

Query: 183 VSYTVESAREGQVLDYD----KLSMTIDTDGSITGEDSVALASRILQD 226
            +   ++ +EG+  DYD    +    +++ GS+  +  V    R+LQ 
Sbjct: 216 YAQWEDAPQEGEPFDYDAVPNRFYFEVESSGSMEPDQIVREGIRVLQQ 263


>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 = 41.9 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 1/77 (1%)

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLKKVEE-LELSVRSTNCLRGENIVYMGDLIQRTE 289
           +    + ++E ++++  +      A    +E+  EL       L    I  +  L   T 
Sbjct: 337 WKIDIKSEEEKRQEVEQQMSAMQGAPQTPIEQVTELGESVLEKLIAAGITTVESLADMTA 396

Query: 290 ADMLRMANFGRKSLVEI 306
            ++  +   G KS+ +I
Sbjct: 397 EELEEVPGIGEKSVEKI 413


>gi|225707818|gb|ACO09755.1| DNA-directed RNA polymerase II 33 kDa polypeptide [Osmerus mordax]
          Length = 275

 Score = 41.9 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 47/259 (18%), Positives = 91/259 (35%), Gaps = 57/259 (22%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHT---LGNALRRVLMSSLRGAAITAVQIDG------- 67
           + + +  +     + E       +T   + N++RRV MS +   AI  +QID        
Sbjct: 9   VKITELSDENVKFVIE-------NTDLAVANSIRRVFMSEVATIAIDWIQIDANSSVLHD 61

Query: 68  --VLHEISSIKGVHEDLTDIILNIKG---------------INLKMSGDSHKRVT---IF 107
             + H +  I    +D+ D +   +                ++++ + D  + VT   + 
Sbjct: 62  EFIAHRVGLIPLTSDDIVDKMQYSRDCTCDDFCPECSVELTLDVRCTEDQTRHVTSRDLL 121

Query: 108 KRGPGV--VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
              P V  VT+       +  V   D ++  L     +R+     KG G   AK + T  
Sbjct: 122 SNNPRVIPVTSRSRDNDPNDYVEQDDIILVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181

Query: 166 DPIGLITIDAL---------------YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
                   +AL               YS I++          G+    ++    +++ GS
Sbjct: 182 VSFEYDPDNALRHTVFPRPEEWPKSEYSEIEEDEVEAPYDPNGKP---ERFYYNVESCGS 238

Query: 211 ITGEDSVALASRILQDQLG 229
           +  E  V  A  +L+ +L 
Sbjct: 239 LRPETIVMSALAVLKKKLS 257


>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 = 41.9 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 45/274 (16%), Positives = 90/274 (32%), Gaps = 59/274 (21%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHT---LGNALRRVLMSSLRGAAITAVQID---GVLH- 70
           I L +  ++    I E        T   + N++RR +++ +   AI  V+I     VLH 
Sbjct: 9   IQLTELTDDNVKFIIE-------DTDLSVANSIRRTILAEVPTIAIDWVEIQANSSVLHD 61

Query: 71  EI-SSIKGVH-----EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGV----VTAGDI- 119
           E  S   G+      E +  +  N      +   D    +++  +        VT+ D+ 
Sbjct: 62  EFISHRVGLIPLTSDEVVDKLNFNRDCGCEEFCSDCSVELSLDVKCTDDQTRHVTSRDLL 121

Query: 120 -------------QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
                        Q  +D   ++ D +I  L     +R+     KG G   AK   T   
Sbjct: 122 SSNQKVVPVPSRNQESSDYGEVD-DILIVKLRKGQELRLRAYAKKGFGKDHAKWVPTAAI 180

Query: 167 PIGLITIDALYSPIKKVSY-------TVESAREGQVLDY---------DKLSMTIDTDGS 210
                      + ++   Y         E     +             +K    +++ G+
Sbjct: 181 AFEYDPD----NIMRHTVYPKPEEWPKSEFTEVDEDTAQGKFDGDAVPNKFFFNVESIGA 236

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKED 244
           +T E+ V     +L+ +L         + + + +
Sbjct: 237 LTPENIVFSGLSVLKKKLSDLQTQHSHEAQAQAE 270


>gi|325115249|emb|CBZ50804.1| rna polymerase II, related [Neospora caninum Liverpool]
          Length = 346

 Score = 41.9 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 43/246 (17%), Positives = 72/246 (29%), Gaps = 64/246 (26%)

Query: 45  NALRRVLMSSLRGAAITAVQI---DGVL------HEISSIKGVHEDLT-------DIILN 88
           NALRR+L+S +   AI  VQI    GV+      H +  I  V +              +
Sbjct: 84  NALRRILISEVPTIAIETVQIWQNTGVVQDEVLAHRLGLIPFVVDPTALNYRQPNQEFTD 143

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI------------EVLNPDHVICN 136
              + + +     ++     +    V A DI+                   ++PD +I  
Sbjct: 144 ENALRVSLHVKCTEQSLGPHQTSLPVYARDIKWEPMSPSQKEAFAANPPRAVHPDILITK 203

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHH---------RTENDPIGLIT---IDALYSPIKKVS 184
           L     + ++  + KG G   AK             E      I       L S      
Sbjct: 204 LRPGQEIELKAYLEKGVGKTHAKWSPVCTAVYRLEPEIVFKEPIQGEEASDLCSLCPMGV 263

Query: 185 YTVESA------------------------REGQVLDYDKLSMTIDTDGSITGEDSVALA 220
           + VE                                  D    +I++ GS+       +A
Sbjct: 264 FDVEDTTGEAYARYPRNCTTCRACIERFPNGIELRKIKDHFIFSIESTGSVPAPLLFKMA 323

Query: 221 SRILQD 226
             IL++
Sbjct: 324 IEILKE 329


>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 = 41.9 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 42/181 (23%), Positives = 73/181 (40%), Gaps = 32/181 (17%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
           ALRR+++S +   AI  V      +  S    V      +I  IKG+ +  SGD    +T
Sbjct: 14  ALRRIMISEVPTYAIENVYFY--ENTSSMYDEVLAHRLGLIP-IKGVPV--SGDEVIVLT 68

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
           I K GP +V + DI++ +       +  I  L     + +E     G G + AK      
Sbjct: 69  ISKEGPCMVYSSDIKSESGEPAF-ENIPIVKLAEGQKLELETEALVGTGKIHAKWQ---- 123

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
                   +A+Y                + +  D++   I++ G++  ED V  +  IL+
Sbjct: 124 ------PCNAVY----------------KQISNDEVEFKIESFGNMDAEDIVRSSLEILK 161

Query: 226 D 226
           +
Sbjct: 162 N 162


>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 = 41.9 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 40/181 (22%), Positives = 73/181 (40%), Gaps = 32/181 (17%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
           ALRR+++S +   AI  V      +  S    V      ++  IKG+ +  SGD    +T
Sbjct: 14  ALRRIMISEVPTYAIENVYFY--ENTSSMYDEVLAHRLGLVP-IKGVPV--SGDEVIVLT 68

Query: 106 IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
           I K GP +V + DI++ +       +  I  L     + +E     G G + AK      
Sbjct: 69  ISKEGPCMVYSSDIKSESGEPAF-ENIPIVKLAEGQKLELEAEALVGTGKIHAKWQ---- 123

Query: 166 DPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225
                   +A+Y                + +  D++   I++ G++  ED +  +  IL+
Sbjct: 124 ------PCNAVY----------------KQISNDEVEFKIESFGNMDAEDIIRSSLEILK 161

Query: 226 D 226
           +
Sbjct: 162 N 162


>gi|77735375|ref|NP_001029384.1| DNA-directed RNA polymerase II subunit RPB3 [Bos taurus]
 gi|73949776|ref|XP_535283.2| PREDICTED: similar to polymerase (RNA) II (DNA directed)
           polypeptide C (predicted) isoform 1 [Canis familiaris]
 gi|149699174|ref|XP_001494261.1| PREDICTED: similar to Polymerase (RNA) II (DNA directed)
           polypeptide C, 33kDa isoform 1 [Equus caballus]
 gi|301752940|ref|XP_002912312.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-like
           [Ailuropoda melanoleuca]
 gi|122146160|sp|Q3T0Q3|RPB3_BOVIN RecName: Full=DNA-directed RNA polymerase II subunit RPB3;
           Short=RNA polymerase II subunit 3; Short=RNA polymerase
           II subunit B3; AltName: Full=DNA-directed RNA polymerase
           II subunit C
 gi|74268238|gb|AAI02302.1| Polymerase (RNA) II (DNA directed) polypeptide C, 33kDa [Bos
           taurus]
 gi|152941118|gb|ABS44996.1| DNA directed RNA polymerase II polypeptide C [Bos taurus]
 gi|281346645|gb|EFB22229.1| hypothetical protein PANDA_000038 [Ailuropoda melanoleuca]
 gi|296477912|gb|DAA20027.1| DNA-directed RNA polymerase II subunit RPB3 [Bos taurus]
          Length = 275

 Score = 41.9 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 47/256 (18%), Positives = 89/256 (34%), Gaps = 51/256 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHT---LGNALRRVLMSSLRGAAITAVQIDG------- 67
           + + +  +     I E       +T   + N++RRV ++ +   AI  VQID        
Sbjct: 9   VRITELTDENVKFIIE-------NTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHD 61

Query: 68  --VLHEISSIKGVHEDLTDIILNIKG---------------INLKMSGDSHKRVT---IF 107
             + H +  I    +D+ D +   +                ++++ + D  + VT   + 
Sbjct: 62  EFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDLI 121

Query: 108 KRGPGV--VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
              P V  VT+ +     +  V   D +I  L     +R+     KG G   AK + T  
Sbjct: 122 SNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181

Query: 166 DPIGLITIDALYSPIK-------KVSYT-----VESAREGQVLDYDKLSMTIDTDGSITG 213
                   +AL   +        K  Y+        A        ++    +++ GS+  
Sbjct: 182 VAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLRP 241

Query: 214 EDSVALASRILQDQLG 229
           E  V  A   L+ +L 
Sbjct: 242 ETIVLSALSGLKKKLS 257


>gi|116205067|ref|XP_001228344.1| hypothetical protein CHGG_10417 [Chaetomium globosum CBS 148.51]
 gi|88176545|gb|EAQ84013.1| hypothetical protein CHGG_10417 [Chaetomium globosum CBS 148.51]
          Length = 338

 Score = 41.9 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 43/254 (16%), Positives = 84/254 (33%), Gaps = 45/254 (17%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG--------- 67
            + + Q +  R           FA    N+LRRV++  +   AI  V+I+          
Sbjct: 17  VVKISQADPIRVKFELSNADIAFA----NSLRRVMLGEIPTIAIDLVEIEENSSVLADEF 72

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGV----VTAGDIQTVN 123
           + H +  I    + +  ++                R+T+  +  G     V A D+    
Sbjct: 73  IAHRLGLIPLNADGVEGLLFARDCDCDGCCEHCSVRLTLHAKCTGDENMHVFARDLVPTG 132

Query: 124 -------DIEVLNPDH----VICNLDVDAVVRMELTVSKGHGYVPAKHHR------TEND 166
                     V++       +I  L     +++E    KG     AK           + 
Sbjct: 133 ERINQVLGTPVVSDSEGLGALILKLRPGQEIKLECIAKKGIAKEHAKWAPSAAIGFEYDP 192

Query: 167 PIGLITIDALYSPIKKVSY-------TVESAREGQVLDYD----KLSMTIDTDGSITGED 215
              L   D  Y    K  +         E  +EG+  DYD    +    +++ G++  + 
Sbjct: 193 HNKLRHTDFWYETDAKTEWPPSEYAAWEEPPQEGEPFDYDAVPNRFYFNVESAGNLPPDT 252

Query: 216 SVALASRILQDQLG 229
            V+   +++Q +L 
Sbjct: 253 IVSEGIKVIQQKLA 266


>gi|183222334|ref|YP_001840330.1| hypothetical protein LEPBI_I2987 [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
 gi|189912382|ref|YP_001963937.1| hypothetical protein LBF_2884 [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167777058|gb|ABZ95359.1| Conserved hypothetical protein [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167780756|gb|ABZ99054.1| Conserved hypothetical protein [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
          Length = 67

 Score = 41.9 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 13/41 (31%), Positives = 24/41 (58%)

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            I  + DL + ++ D+LR+  FG  SL +++  L  +G+ L
Sbjct: 25  GITKLEDLSRYSKQDLLRLHGFGPSSLPKLESELRKLGIQL 65


>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 = 41.9 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 19/113 (16%), Positives = 43/113 (38%), Gaps = 8/113 (7%)

Query: 216 SVALASRILQDQLGMFINFEEPKKEVKEDINVK-SLPFNPALLKKVEELELSVRSTNCLR 274
             A A+ +L+    +F+   +  +       V            ++  LELS ++ + L 
Sbjct: 740 RFATAADMLRAWRQVFLQASKESRHPTVHGEVPTCPVEEAQQDTQIGLLELSPQALDALS 799

Query: 275 GENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
             N+  + DL+++  + +      G K+  E+  ++  +          WP E
Sbjct: 800 RRNLNTVADLLKQNRSKVRAWPGVGIKTRNEVSELIRKLQ-------EKWPNE 845


>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 = 41.9 bits (97), Expect = 0.16,   Method: Composition-based stats.
 Identities = 40/197 (20%), Positives = 80/197 (40%), Gaps = 34/197 (17%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKR- 103
           NA+RR+++S +   AI  V I        +   + +++    L +  I  K   ++    
Sbjct: 28  NAIRRIMISEVPTFAIEDVYI------YENSSSMDDEILAHRLGLIPIKGKPLLENEVIT 81

Query: 104 VTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
            T+ K GP  V + D+++ N  EV   +  I  L     +++E     G G V AK    
Sbjct: 82  FTLEKEGPCTVYSSDLKSENG-EVAFKNIPIVKLGKGQRIQIECEAIPGIGKVHAKWQ-- 138

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
                     +A+Y                + +  D++   ++T G +  E+ +  A +I
Sbjct: 139 --------PCNAVY----------------KQIADDEVEFFVETFGQMEAEEILEEAVKI 174

Query: 224 LQDQLGMFINFEEPKKE 240
           L+++   F+   E  ++
Sbjct: 175 LKNKAESFLQQLEMIEQ 191


>gi|29336059|ref|NP_033116.2| DNA-directed RNA polymerase II subunit RPB3 [Mus musculus]
 gi|60223073|ref|NP_001012491.1| DNA-directed RNA polymerase II subunit RPB3 [Rattus norvegicus]
 gi|12805131|gb|AAH02023.1| Polymerase (RNA) II (DNA directed) polypeptide C [Mus musculus]
 gi|59808391|gb|AAH89905.1| Polymerase (RNA) II (DNA directed) polypeptide C, 33kDa [Rattus
           norvegicus]
 gi|68534485|gb|AAH99548.1| Polymerase (RNA) II (DNA directed) polypeptide C [Mus musculus]
 gi|74145092|dbj|BAE27415.1| unnamed protein product [Mus musculus]
 gi|74191349|dbj|BAE30257.1| unnamed protein product [Mus musculus]
 gi|74213568|dbj|BAE35592.1| unnamed protein product [Mus musculus]
 gi|149032426|gb|EDL87317.1| polymerase (RNA) II (DNA directed) polypeptide C, isoform CRA_b
           [Rattus norvegicus]
          Length = 275

 Score = 41.5 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 48/256 (18%), Positives = 89/256 (34%), Gaps = 51/256 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHT---LGNALRRVLMSSLRGAAITAVQIDG------- 67
           + + +  E     I E       +T   + N++RRV ++ +   AI  VQID        
Sbjct: 9   VRITELTEENVKFIIE-------NTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHD 61

Query: 68  --VLHEISSIKGVHEDLTDIILNIKG---------------INLKMSGDSHKRVT---IF 107
             + H +  I    +D+ D +   +                ++++ + D  + VT   + 
Sbjct: 62  EFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDLI 121

Query: 108 KRGPGV--VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
              P V  VT+ +     +  V   D +I  L     +R+     KG G   AK + T  
Sbjct: 122 SNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181

Query: 166 DPIGLITIDALYSPIK-------KVSYT-----VESAREGQVLDYDKLSMTIDTDGSITG 213
                   +AL   +        K  Y+        A        ++    +++ GS+  
Sbjct: 182 VAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLRP 241

Query: 214 EDSVALASRILQDQLG 229
           E  V  A   L+ +L 
Sbjct: 242 ETIVLSALSGLKKKLS 257


>gi|23098698|ref|NP_692164.1| hypothetical protein OB1243 [Oceanobacillus iheyensis HTE831]
 gi|22776925|dbj|BAC13199.1| hypothetical protein [Oceanobacillus iheyensis HTE831]
          Length = 96

 Score = 41.5 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 16/55 (29%), Positives = 26/55 (47%)

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            +LS  + N L  E I  +  L + TE ++L++   G  SL  ++  L   GL  
Sbjct: 40  SKLSSPARNALVHEGIDTLQALSKYTEKEILKIHGIGPVSLPIMRASLEEEGLSF 94


>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 = 41.5 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 31/191 (16%), Positives = 66/191 (34%), Gaps = 42/191 (21%)

Query: 47  LRRVLMSSLRGAAITAVQID-----------GVLHEISSIKGVHEDLTDIILNIKGINLK 95
           +RR L+  L    IT V               V+H    ++ + + L +I    K +  K
Sbjct: 39  IRRYLLLDLESWNITNVMFFVTNNLKNTSTFHVVHNFLGLEELKQSLLEITKKFKLLRFK 98

Query: 96  MSGDSHK----RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN-LDVDAVVRMELTVS 150
           +   S++       +         +GDI     +++LN   ++   +  +  +++ L + 
Sbjct: 99  LCSKSYQGNKFFAVLNAFEVKDFLSGDIIFPPHLKLLNSRELLFTKISFNITLKILLKIE 158

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALY-SPIKKVSYTVESAREGQVLDYDKLSMTIDTDG 209
                                   A +  PIK+++  +E            +   + TDG
Sbjct: 159 AKK---------------------ASFQKPIKRLNLIIEKDEFFDN----YMIFDLTTDG 193

Query: 210 SITGEDSVALA 220
           S+T  ++   A
Sbjct: 194 SVTPFNAFIKA 204


>gi|12837765|dbj|BAB23943.1| unnamed protein product [Mus musculus]
          Length = 275

 Score = 41.5 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 48/256 (18%), Positives = 89/256 (34%), Gaps = 51/256 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHT---LGNALRRVLMSSLRGAAITAVQIDG------- 67
           + + +  E     I E       +T   + N++RRV ++ +   AI  VQID        
Sbjct: 9   VRITELTEENVKFIIE-------NTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHD 61

Query: 68  --VLHEISSIKGVHEDLTDIILNIKG---------------INLKMSGDSHKRVT---IF 107
             + H +  I    +D+ D +   +                ++++ + D  + VT   + 
Sbjct: 62  EFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDLI 121

Query: 108 KRGPGV--VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
              P V  VT+ +     +  V   D +I  L     +R+     KG G   AK + T  
Sbjct: 122 SNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181

Query: 166 DPIGLITIDALYSPIK-------KVSYT-----VESAREGQVLDYDKLSMTIDTDGSITG 213
                   +AL   +        K  Y+        A        ++    +++ GS+  
Sbjct: 182 VAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPKGKPERFYYNVESCGSLRP 241

Query: 214 EDSVALASRILQDQLG 229
           E  V  A   L+ +L 
Sbjct: 242 ETIVLSALSGLKKKLS 257


>gi|227537029|ref|ZP_03967078.1| conserved domain protein [Sphingobacterium spiritivorum ATCC 33300]
 gi|227243121|gb|EEI93136.1| conserved domain protein [Sphingobacterium spiritivorum ATCC 33300]
          Length = 103

 Score = 41.5 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 23/53 (43%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  + N L    I  +  L   T  ++L +   G+ S+  ++ +L   GL  
Sbjct: 42  LSNPARNSLLHHGINTLEALSAYTRKEILNLHGIGKASIPTLEKLLAGQGLSF 94


>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 = 41.1 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 19/103 (18%), Positives = 32/103 (31%), Gaps = 10/103 (9%)

Query: 206 DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELEL 265
           +T   +  E     A+             E    E      V +          VE L L
Sbjct: 754 ETAEQMRTEWIACFAA----------APSEAGADEADGAPPVAADLSIFTEATPVEALPL 803

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
             R  N L    IV + +L+   +  +  +   GR++   I+ 
Sbjct: 804 GAREKNALDRSGIVTVRELLALPQNQLSAIRGVGRETARAIQD 846


>gi|45187753|ref|NP_983976.1| ADL120Cp [Ashbya gossypii ATCC 10895]
 gi|44982514|gb|AAS51800.1| ADL120Cp [Ashbya gossypii ATCC 10895]
          Length = 311

 Score = 41.1 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 27/136 (19%), Positives = 52/136 (38%), Gaps = 24/136 (17%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTDIILNIKG 91
            +L N+LRR++++ +   AI +V+I+          + H +  +    +D+  ++     
Sbjct: 27  LSLANSLRRIMIAEIPTLAIDSVEIESNTSVLADEFISHRLGLVPLQSKDIDQLVYCRDC 86

Query: 92  INLKMSGDSHKRVTIFKRGPGV----VTAGDIQTVNDIEVLNPDHV-----------ICN 136
                       +T+   G       V A D+Q V+D+   N  H            IC 
Sbjct: 87  FCEDHCDRCSVLLTLHAVGESESTTNVYAKDLQIVSDLGGKNIGHPIIQDKEANGVLICK 146

Query: 137 LDVDAVVRMELTVSKG 152
           L     +R++    KG
Sbjct: 147 LRKGQELRLKCVAKKG 162


>gi|115752775|ref|XP_781436.2| PREDICTED: hypothetical protein isoform 1, partial
           [Strongylocentrotus purpuratus]
          Length = 246

 Score = 41.1 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 40/246 (16%), Positives = 82/246 (33%), Gaps = 49/246 (19%)

Query: 43  LGNALRRVLMSSLRGAAITAVQID---GVLH-EI-SSIKGVH-----EDLTDIILNIKGI 92
           + N++RR +++ +   AI  V+I     VLH E  S   G+      E +  +  N    
Sbjct: 1   VANSIRRTILAEVPTIAIDWVEIQANSSVLHDEFISHRVGLIPLTSDEVVDKLNFNRDCG 60

Query: 93  NLKMSGDSHKRVTIFKRGPGV----VTAGDI--------------QTVNDIEVLNPDHVI 134
             +   D    +++  +        VT+ D+              Q  +D   ++ D +I
Sbjct: 61  CEEFCSDCSVELSLDVKCTDDQTRHVTSRDLLSSNQKVVPVPSRNQESSDYGEVD-DILI 119

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSY-------TV 187
             L     +R+     KG G   AK   T              + ++   Y         
Sbjct: 120 VKLRKGQELRLRAYAKKGFGKDHAKWVPTAAIAFEYDPD----NIMRHTVYPKPEEWPKS 175

Query: 188 ESAREGQVLDY---------DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
           E     +             +K    +++ G++T E+ V     +L+ +L         +
Sbjct: 176 EFTEVDEDTAQGKFDGDAVPNKFFFNVESIGALTPENIVFSGLSVLKKKLSDLQTQHSHE 235

Query: 239 KEVKED 244
            + + +
Sbjct: 236 AQAQAE 241


>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 = 41.1 bits (95), Expect = 0.23,   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|320101538|ref|YP_004177130.1| DNA-directed RNA polymerase subunit D [Desulfurococcus mucosus DSM
           2162]
 gi|319753890|gb|ADV65648.1| DNA-directed RNA polymerase, subunit D [Desulfurococcus mucosus DSM
           2162]
          Length = 280

 Score = 41.1 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 22/153 (14%), Positives = 45/153 (29%), Gaps = 29/153 (18%)

Query: 45  NALRRVLMSSLR-----GAAITA------------------VQIDGVLHEISSIKGVHED 81
           N+LRR ++S +        AIT                   ++ D  LH+    +   E 
Sbjct: 26  NSLRRTIISEVPTMAVDYVAITENSSVFYDEYIAHRLGLIPLKSDEALHKYKPPEECAEA 85

Query: 82  LTDIILNIKG-INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
               + +      L++     +   +      +       +  D+  +     +  L  +
Sbjct: 86  GEKGVFSQDCFATLRLEAKGPEDGVLTIYSEML-----ESSDPDVTPVYGKVPVVRLTRN 140

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITI 173
             +R+E     G G   AK           I +
Sbjct: 141 QSIRLEAYARLGRGKEHAKWSPVSVATHKYIPV 173


>gi|317127960|ref|YP_004094242.1| hypothetical protein Bcell_1246 [Bacillus cellulosilyticus DSM
           2522]
 gi|315472908|gb|ADU29511.1| hypothetical protein Bcell_1246 [Bacillus cellulosilyticus DSM
           2522]
          Length = 96

 Score = 41.1 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 16/55 (29%), Positives = 26/55 (47%)

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            +LS  + N L  E I  +  L + TE ++L++   G  SL  ++  L   GL  
Sbjct: 40  SKLSSPARNALIHEKIDTLPKLSKYTEKEILKIHGIGPASLPNLRASLKEAGLSF 94


>gi|327287828|ref|XP_003228630.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-like [Anolis
           carolinensis]
          Length = 275

 Score = 40.7 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 47/256 (18%), Positives = 88/256 (34%), Gaps = 51/256 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHT---LGNALRRVLMSSLRGAAITAVQIDG------- 67
           + + +  +     I E       +T   + N++RRV ++ +   AI  VQID        
Sbjct: 9   VRITELSDENVKFIVE-------NTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHD 61

Query: 68  --VLHEISSIKGVHEDLTDIILNIKG---------------INLKMSGDSHKRVT---IF 107
             + H +  I    +D+ D +   +                ++++ + D  + VT   + 
Sbjct: 62  EFIAHRLGLIPLTSDDVVDKLQYSRDCTCDEFCPECSVEFTLDVRCNEDQTRHVTSRDLI 121

Query: 108 KRGPGV--VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
              P V  VT+       +  V   D +I  L     +R+     KG G   AK + T  
Sbjct: 122 SNNPRVIPVTSRSRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181

Query: 166 DPIGLITIDALYSPIK-------KVSYT-----VESAREGQVLDYDKLSMTIDTDGSITG 213
                   +AL   +        K  Y+        A        ++    +++ GS+  
Sbjct: 182 VAFEYDPDNALRHTVYPKPEEWPKSEYSEIDEDEAQAPYDPNGKPERFYYNVESCGSLRP 241

Query: 214 EDSVALASRILQDQLG 229
           E  V  A   L+ +L 
Sbjct: 242 ETIVLSALSGLKKKLS 257


>gi|224063830|ref|XP_002197873.1| PREDICTED: putative DNA directed RNA polymerase II polypeptide C
           [Taeniopygia guttata]
 gi|197127827|gb|ACH44325.1| putative DNA directed RNA polymerase II polypeptide C [Taeniopygia
           guttata]
          Length = 275

 Score = 40.7 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 47/256 (18%), Positives = 89/256 (34%), Gaps = 51/256 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHT---LGNALRRVLMSSLRGAAITAVQIDG------- 67
           + + +  +     I E       +T   + N++RRV ++ +   AI  VQID        
Sbjct: 9   VRITELTDENVKFIIE-------NTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHD 61

Query: 68  --VLHEISSIKGVHEDLTDIILNIKG---------------INLKMSGDSHKRVT---IF 107
             + H +  I    +D+ D +   +                ++++ + D  + VT   + 
Sbjct: 62  EFIAHRLGLIPLTSDDIVDKMQYSRDCTCDEFCPECSVEFTLDVRCNEDQTRHVTSRDLI 121

Query: 108 KRGPGV--VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
              P V  VT+       +  V   D +I  L     +R+     KG G   AK + T  
Sbjct: 122 SNNPRVIPVTSRSRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181

Query: 166 DPIGLITIDALYSPIK-------KVSYTVESAREGQ-----VLDYDKLSMTIDTDGSITG 213
                   +AL   +        K  Y+     + Q         ++    +++ GS+  
Sbjct: 182 VAFEYDPDNALRHTVYPKPEEWPKSEYSEIDDEDAQAPYDPNGKPERFYYNVESCGSLRP 241

Query: 214 EDSVALASRILQDQLG 229
           E  V  A   L+ +L 
Sbjct: 242 ETIVLSALSGLKKKLS 257


>gi|170581298|ref|XP_001895623.1| DNA-directed RNA polymerase II 33 kDa polypeptide [Brugia malayi]
 gi|158597360|gb|EDP35528.1| DNA-directed RNA polymerase II 33 kDa polypeptide, putative [Brugia
           malayi]
          Length = 275

 Score = 40.7 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 43/230 (18%), Positives = 80/230 (34%), Gaps = 41/230 (17%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQID---GVLH-EISSIK--------GVHEDLTDIILN 88
            ++ N+LRR+ M+ +   AI  VQI+    VLH E  + +            D      +
Sbjct: 28  LSVANSLRRIFMAEVPTMAIDWVQIESNSSVLHDEFIAHRLGLIPLTSDSVVDQMQFSRD 87

Query: 89  IKGINLKMSGDSHKRVTIFK--RGPGVVTAGDIQTVN-------DIEVLN--------PD 131
            +            R+ +     G   VT  D++T N        + + N         D
Sbjct: 88  CQCTEFCQFCAVEMRLRVRCDDEGIRAVTTADLETSNPDVAPACGVHIRNRNAEENASDD 147

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK-------KVS 184
            +I  L     + ++    KG G   AK + T          +AL   +        K  
Sbjct: 148 ILIVKLRKGQDIDIKCIAKKGFGKEHAKWNPTCCVAFEYDPDNALRHTMLAKPEEWPKSE 207

Query: 185 YT-----VESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           Y+        A    +   +K   T+++ G++  E+ +     +L+ +L 
Sbjct: 208 YSQLEDDEYEAPFDPMAKPNKFWFTVESTGALKAENIILSGISVLKKKLA 257


>gi|313126017|ref|YP_004036287.1| DNA-directed RNA polymerase, subunit d [Halogeometricum borinquense
           DSM 11551]
 gi|312292382|gb|ADQ66842.1| DNA-directed RNA polymerase, subunit D [Halogeometricum borinquense
           DSM 11551]
          Length = 260

 Score = 40.7 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 24/148 (16%), Positives = 54/148 (36%), Gaps = 14/148 (9%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI-DGVLHEISSIK 76
           +   + ++ +   +     RG    + N +RR +++ +   +I  V+  +        + 
Sbjct: 7   VEFIERDDRKARFLV----RGMTPAVANGIRRAMIADVPTFSIDTVRFVENSSVMFDEMI 62

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP---DHV 133
           G+   L  +   +              + +   GP    +GDI+T ++  ++ P   +  
Sbjct: 63  GLRLGLVPLTTPLDD----FEQGDTVTLALDVEGPATAYSGDIETSDE--LVKPAEDNVP 116

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           I  L     + +E     G G   AKH 
Sbjct: 117 IIELKQGQRLELEADAVLGDGKSHAKHQ 144


>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 = 40.7 bits (94), Expect = 0.33,   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|312213137|emb|CBX93219.1| hypothetical protein [Leptosphaeria maculans]
          Length = 336

 Score = 40.7 bits (94), Expect = 0.34,   Method: Composition-based stats.
 Identities = 44/256 (17%), Positives = 81/256 (31%), Gaps = 57/256 (22%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI--------TAVQIDG-VLHEI 72
           Q +  R   I +           N+LRRV++S +   AI        T+V  D  V H +
Sbjct: 16  QADNQRAHFIVQNFN----LETANSLRRVMLSEIPTLAIDVVEVLDNTSVLADEFVCHRL 71

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG----VVTAGDIQTVN----- 123
             I    + + D++ +          +    +T+  +  G     V A D+   +     
Sbjct: 72  GLIPLCSKGVDDLLYSRDCDCEGYCSNCSVVLTLNAKCTGNEIMKVYARDLVVESMTPND 131

Query: 124 DI---EVLNPD---HVICNLDVDAVVRMELTVSKGHGYVPAKHHRT-------------- 163
           ++    + + D     I  L     + M     KG     AK   +              
Sbjct: 132 EVGRPVITDADGTGSCIVKLRRGQAIHMRCIAKKGIAKEHAKWAPSAAIGFEYDPANKLH 191

Query: 164 ------ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD----KLSMTIDTDGSITG 213
                 E DP      D       +++     A   +  DY+    +    ++T G +  
Sbjct: 192 HLDYWHEEDPDKEWPKDE-----DRINLDGGPANPDEPFDYNAAPTRFFYDVETVGGLDP 246

Query: 214 EDSVALASRILQDQLG 229
           +  V     +LQ +L 
Sbjct: 247 DQIVGKGITVLQHKLA 262


>gi|156089735|ref|XP_001612274.1| DNA-directed RNA polymerase, alpha subunit, N terminal domain
           containing protein [Babesia bovis]
 gi|154799528|gb|EDO08706.1| DNA-directed RNA polymerase, alpha subunit, N terminal domain
           containing protein [Babesia bovis]
          Length = 319

 Score = 40.7 bits (94), Expect = 0.34,   Method: Composition-based stats.
 Identities = 34/210 (16%), Positives = 69/210 (32%), Gaps = 45/210 (21%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID---GV----- 68
            I   +      +   E L       + NA+RR+L++ +   AI +V I    GV     
Sbjct: 35  KIKFLKNTRYHAIAEIEGLN----VAIANAIRRILLAEVPTLAIESVHIYQNTGVIQDEV 90

Query: 69  -LHEISSIK-GVHEDLTDIILN-----IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
             H +  +    + DL     N        +   +  +  K  ++  R    V AGD++ 
Sbjct: 91  LAHRLGLVPFDCNPDLIPYRDNEDLSDKNSVCFHLKVECKKE-SLAGRTNLPVYAGDMKW 149

Query: 122 VN------DIEVLNPDHVIC------NLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIG 169
           V       ++   NP   I        L     + ++  + KG G   AK          
Sbjct: 150 VPLSDEQAELFKDNPPKPIHKDILLTKLSPGQEIDLKAYLEKGIGKTHAKWS-------- 201

Query: 170 LITIDALYSPIKKVSYTVESAREGQVLDYD 199
                 + + + +    +  + +  + + +
Sbjct: 202 -----PVCTAVYRFKPDITFSEDEPLTNDE 226


>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 = 40.7 bits (94), Expect = 0.34,   Method: Composition-based stats.
 Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 4/60 (6%)

Query: 262 ELELSVRSTNCLRGENI----VYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           E +  V++ N  R   I      + DL + TE ++L +   G K++  ++  L   GL  
Sbjct: 11  ESDFPVKAGNPARRALIVAGYHRLADLTRATEKELLALHGVGPKAIGVLRAALAEKGLAF 70


>gi|50753469|ref|XP_414001.1| PREDICTED: hypothetical protein [Gallus gallus]
          Length = 275

 Score = 40.7 bits (94), Expect = 0.34,   Method: Composition-based stats.
 Identities = 46/256 (17%), Positives = 89/256 (34%), Gaps = 51/256 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHT---LGNALRRVLMSSLRGAAITAVQIDG------- 67
           + + +  +     I E       +T   + N++RRV ++ +   AI  VQID        
Sbjct: 9   VRITELTDENVKFIIE-------NTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHD 61

Query: 68  --VLHEISSIKGVHEDLTDIILNIKG---------------INLKMSGDSHKRVT---IF 107
             + H +  I    +D+ D +   +                ++++ + D  + VT   + 
Sbjct: 62  EFIAHRLGLIPLTSDDIVDKMQYSRDCTCDEFCPECSVEFTLDVRCNEDQTRHVTSRDLI 121

Query: 108 KRGPGV--VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
              P V  VT+       +  V   D +I  L     +++     KG G   AK + T  
Sbjct: 122 SNNPRVIPVTSRSRDNDPNDYVEQDDILIVKLRKGQELKLRAYAKKGFGKEHAKWNPTAG 181

Query: 166 DPIGLITIDALYSPIK-------KVSYTVESAREGQ-----VLDYDKLSMTIDTDGSITG 213
                   +AL   +        K  Y+     + Q         ++    +++ GS+  
Sbjct: 182 VAFEYDPDNALRHTVYPKPEEWPKSEYSEIDEEDAQAPYDPNGKPERFYYNVESCGSLRP 241

Query: 214 EDSVALASRILQDQLG 229
           E  V  A   L+ +L 
Sbjct: 242 ETIVLSALSGLKKKLS 257


>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 = 40.7 bits (94), Expect = 0.36,   Method: Composition-based stats.
 Identities = 45/254 (17%), Positives = 91/254 (35%), Gaps = 45/254 (17%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG--------- 67
            + + Q +  R     +     FA    N+LRRV+++ +   AI  V+I+          
Sbjct: 17  VVKISQADSVRVKFELQNADISFA----NSLRRVMLAEIPTIAIDLVEIESNSSVLADEF 72

Query: 68  VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG----VVTAGDIQTVN 123
           + H +  I    E +  ++ +      +   +   ++T+  +  G     V+A D+  V 
Sbjct: 73  IAHRLGLIPLNAEGVEHLLYSRDCDCEEYCENCSVKLTLHAKCTGYENMSVSARDLVPVG 132

Query: 124 -------DIEVLN----PDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR------TEND 166
                     V+N       +I  L  +  +++E    KG     AK           + 
Sbjct: 133 ERINQSLGTPVINDKDGTGPLILKLRPEQEIKLECIAKKGIAKEHAKWAPSAAIGFEYDP 192

Query: 167 PIGLITIDALYSPIKKVSY-------TVESAREGQVLDYDKL----SMTIDTDGSITGED 215
              L  +D  Y    K  +         E   EG+  D+D +       ++T G++  + 
Sbjct: 193 HNKLRHLDLWYEKDPKSEWPPSEYAKWEEPPVEGEPFDFDAVPNHFYYNVETAGNLPPDG 252

Query: 216 SVALASRILQDQLG 229
            V    +++Q +L 
Sbjct: 253 IVTEGIKVIQQKLA 266


>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 = 40.3 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 37/163 (22%), Positives = 62/163 (38%), Gaps = 20/163 (12%)

Query: 46  ALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT 105
           ALRR+++S     A     I+ V     +   ++++L    L +  I  K   +    + 
Sbjct: 29  ALRRIMISETPTYA-----IENVYF-YENTSSMYDELIAHRLGLIPIKGKPVSNDEVIIF 82

Query: 106 -IFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTE 164
            + K GP VV +GD+++    EV+     I  L     + +E     G G   AK     
Sbjct: 83  ALIKEGPCVVYSGDLESETG-EVVFKHIPIVKLKEGQKLELECEALVGTGKTHAKWQ--- 138

Query: 165 NDPIGLITIDALYSPIKK--VSYTVESAREGQVLDYDKLSMTI 205
                    +A+Y  +    V + VES       D    S+ I
Sbjct: 139 -------PCNAVYKLLNNDEVEFLVESYGNMDSEDLLISSVEI 174


>gi|45360897|ref|NP_989124.1| polymerase (RNA) II (DNA directed) polypeptide C, 33kDa [Xenopus
           (Silurana) tropicalis]
 gi|38511942|gb|AAH61444.1| polymerase (RNA) II (DNA directed) polypeptide C [Xenopus
           (Silurana) tropicalis]
 gi|89266865|emb|CAJ83921.1| polymerase (RNA) II (DNA directed) polypeptide C, 33kDa [Xenopus
           (Silurana) tropicalis]
 gi|111598412|gb|AAH80362.1| polymerase (RNA) II (DNA directed) polypeptide C [Xenopus
           (Silurana) tropicalis]
          Length = 275

 Score = 40.3 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 48/257 (18%), Positives = 89/257 (34%), Gaps = 53/257 (20%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHT---LGNALRRVLMSSLRGAAITAVQIDG------- 67
           + + +  +     I E       +T   + N++RRV ++ +   AI  VQID        
Sbjct: 9   VRITELTDENVKFIVE-------NTDLAIANSIRRVFIAEVPTIAIDWVQIDANSSVLHD 61

Query: 68  --VLHEISSIKGVHEDLTDIILNIKG---------------INLKMSGDSHKRVT---IF 107
             + H +  I    +D+ D +   +                ++++ + D  + VT   + 
Sbjct: 62  EFIAHRVGLIPLTSDDIVDKLQYSRDCTCDEFCPECSVEFTLDVRCNEDQTRHVTSRDLV 121

Query: 108 KRGPGV--VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
                V  VT+       +  V   D +I  L     +R+     KG G   AK + T  
Sbjct: 122 SNNLRVIPVTSRSRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181

Query: 166 DPIGLITIDALYSPIK-------KVSYTVESAREGQVLDY------DKLSMTIDTDGSIT 212
                   +AL   +        K  Y+ E   E     Y      ++    +++ GS+ 
Sbjct: 182 VAFEYDPDNALRHTVYPKPEEWPKSEYS-EIDEEEAEAPYDPTGKPERFYYNVESCGSLR 240

Query: 213 GEDSVALASRILQDQLG 229
            E  V  A   L+ +L 
Sbjct: 241 PETIVLSALSGLKKKLS 257


>gi|296109380|ref|YP_003616329.1| RNA polymerase insert [Methanocaldococcus infernus ME]
 gi|295434194|gb|ADG13365.1| RNA polymerase insert [Methanocaldococcus infernus ME]
          Length = 195

 Score = 40.3 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 40/199 (20%), Positives = 82/199 (41%), Gaps = 34/199 (17%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRV 104
           NA+RR+++S +   AI  V I        +   + +++    L +  I  K + ++   +
Sbjct: 28  NAIRRIMISEVPTFAIEDVFI------YENSSSMDDEILAHRLGLIPIKGKPAFENETIL 81

Query: 105 -TIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
            T+ K GP VV + D+++ N  EV   +  I  L     +++E     G G V AK    
Sbjct: 82  FTLEKEGPCVVYSSDLKSDNG-EVAFKNIPIVKLGEKQRIKIECEAVPGIGKVHAKWQ-- 138

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
                     +A+Y                + L  D++   +++ G +   + +  A++I
Sbjct: 139 --------PCNAVY----------------KQLSEDEVEFLVESFGQMDSLEILEEATKI 174

Query: 224 LQDQLGMFINFEEPKKEVK 242
           L+++   F+   E  +   
Sbjct: 175 LKNKAQEFLKQLEELEGED 193


>gi|294155884|ref|YP_003560268.1| DNA ligase (NAD(+)) [Mycoplasma crocodyli MP145]
 gi|291600422|gb|ADE19918.1| DNA ligase (NAD(+)) [Mycoplasma crocodyli MP145]
          Length = 657

 Score = 40.3 bits (93), Expect = 0.43,   Method: Composition-based stats.
 Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 1/53 (1%)

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT-MGLFLGMNLPDW 324
           L    I  + DL+     ++  + + G KS+  IK  L       L   L ++
Sbjct: 521 LISTKINKLSDLLTYNIDELENIDDIGPKSIASIKEFLSEDKNKELITFLDNY 573


>gi|11499863|ref|NP_071107.1| DNA-directed RNA polymerase subunit D [Archaeoglobus fulgidus DSM
           4304]
 gi|3122769|sp|O28002|RPOD_ARCFU RecName: Full=DNA-directed RNA polymerase subunit D
 gi|2648239|gb|AAB88973.1| DNA-directed RNA polymerase, subunit D (rpoD) [Archaeoglobus
           fulgidus DSM 4304]
          Length = 264

 Score = 40.3 bits (93), Expect = 0.43,   Method: Composition-based stats.
 Identities = 28/167 (16%), Positives = 51/167 (30%), Gaps = 18/167 (10%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           I + +E++ +   I +         L N+ RR + + +   A+  V I   L+       
Sbjct: 5   IEILEEKDFKIKFILKNASPA----LANSFRRAMKAEVPAMAVDYVDIY--LNSSYFYDE 58

Query: 78  VHED-LTDIILNIKGINLKMSGDSHK----------RVTIFKRGPGVVTAGDIQ-TVNDI 125
           V    L  + +        M  +                +   GP VV +GD      D+
Sbjct: 59  VIAHRLAMLPIKTYLDRFNMQSECSCGGEGCPNCQISFRLNVEGPKVVYSGDFISDDPDV 118

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT 172
                +  +  L     + +E     G G   AK          +I 
Sbjct: 119 VFAIDNIPVLELFEGQQLMLEAVARLGTGREHAKFQPVSVCVYKIIP 165


>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 = 0.43,   Method: Composition-based stats.
 Identities = 30/201 (14%), Positives = 80/201 (39%), Gaps = 47/201 (23%)

Query: 43  LGNALRRVLMSSLRGA-AITAVQ---------------IDGVLHEISSIKGVHEDLTDII 86
            GN +RR L+ +++    IT ++               I   ++E   I+ + E+L++I 
Sbjct: 35  FGNEIRRSLLLNIKKTMTITNIKFFISKSKSKHPKKLKIFHPVNEFFDIEEIKENLSNIC 94

Query: 87  LNIKGINLKMSGDSHK----RVTIFKRGPGVVTAGDIQTV--NDIEVLNPDHVICN-LDV 139
           +N+K +  K +  ++K     + +        +A DI     ++++++N    + N +  
Sbjct: 95  INLKKLRFKFNPKNNKEKKTFIILNSFNKKSFSAKDIIIPSTSNLKIVNLKEHLFNKISQ 154

Query: 140 DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD 199
              +++ + +     Y                     Y+PIK++++ +E           
Sbjct: 155 KINLKVLIKIENNENY--------------------FYNPIKRINFILEK----NNNIGK 190

Query: 200 KLSMTIDTDGSITGEDSVALA 220
            + + +++D +I    +   +
Sbjct: 191 YIILDLNSDININPFKAFIES 211


>gi|294495898|ref|YP_003542391.1| DNA-directed RNA polymerase, subunit D [Methanohalophilus mahii DSM
           5219]
 gi|292666897|gb|ADE36746.1| DNA-directed RNA polymerase, subunit D [Methanohalophilus mahii DSM
           5219]
          Length = 266

 Score = 40.3 bits (93), Expect = 0.45,   Method: Composition-based stats.
 Identities = 24/157 (15%), Positives = 48/157 (30%), Gaps = 17/157 (10%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE-ISSIK 76
           I + +  +     I   +   FA    N LRR +++ +   AI  V I            
Sbjct: 3   IDILELSDRSARFILSDVDAAFA----NGLRRAMLADVPTLAIDEVNIYNNTSVLYDEQI 58

Query: 77  GVHEDLTDIILNIKGINLKMSGDSHK-------RVTIFKR----GPGVVTAGDIQ-TVND 124
            +   L  ++               +        +T+           V +GD+      
Sbjct: 59  ALRLALVPLVTIFNEFTPHEECSCEEGCPACTVSLTLSVEAPMDEDKTVYSGDLVSADPK 118

Query: 125 IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH 161
           I+  + +  +  L     + +E     G+G+  AK  
Sbjct: 119 IKAADSNIAVVKLKGGQQLVLEGIAKMGYGHDHAKWQ 155


>gi|66801649|ref|XP_629750.1| RNA polymerase II core subunit [Dictyostelium discoideum AX4]
 gi|74851108|sp|Q54DH7|RPB3_DICDI RecName: Full=DNA-directed RNA polymerase II subunit rpb3;
           Short=RNA polymerase II subunit 3; Short=RNA polymerase
           II subunit B3; AltName: Full=DNA-directed RNA polymerase
           II subunit C
 gi|60463138|gb|EAL61332.1| RNA polymerase II core subunit [Dictyostelium discoideum AX4]
          Length = 302

 Score = 40.3 bits (93), Expect = 0.45,   Method: Composition-based stats.
 Identities = 44/301 (14%), Positives = 93/301 (30%), Gaps = 47/301 (15%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           + +   +L +   +E + +  +     + I          ++ NALRRV+++ +    I 
Sbjct: 1   MSQTVSQLTRQPELEILEIKNDS---IIFILSNTD----ISVANALRRVMIAEVPTMCID 53

Query: 62  AVQIDG---------VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRG-- 110
            V+ +          + H +  I  V +++                     + +  +   
Sbjct: 54  LVEFESNNSVLCDEFIAHRLGLIPLVSDNIDKFCYTRDCSCSDRCDQCSVELRLNVKCTE 113

Query: 111 --PGVVTAGD--------IQTVNDIEVLNPDH--VICNLDVDAVVRMELTVSKGHGYVPA 158
             P  VT+ D        I   + +   N +    I  L     +++     KG G   A
Sbjct: 114 NRPRDVTSSDLLSQNSAVIPVSSQVTSSNSEQEIPIVKLRRGQEIKLRAIAKKGVGKEHA 173

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
           K   +         I             +   R  ++ D  K        GS   +   +
Sbjct: 174 KWSPSCVATYQFQPI-----------IVLNQNRIDELTDQQK---EEWV-GSCPTK-VYS 217

Query: 219 LASRILQDQLGMFIN-FEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGEN 277
            +      Q+ +          E K+       P    L +K ++   +V S+  L+ E+
Sbjct: 218 YSPHQSTQQVTIEDPLRCVYCLECKKKAESFGKPDLVHLEQKQDKFIFTVESSGALKPED 277

Query: 278 I 278
           I
Sbjct: 278 I 278


>gi|182435393|ref|YP_001823112.1| putative serine/threonine protein kinase [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|178463909|dbj|BAG18429.1| putative serine/threonine protein kinase [Streptomyces griseus
           subsp. griseus NBRC 13350]
          Length = 1558

 Score = 40.3 bits (93), Expect = 0.46,   Method: Composition-based stats.
 Identities = 24/172 (13%), Positives = 50/172 (29%), Gaps = 8/172 (4%)

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIK--------KVSYTVESAREGQVLDYDKLS 202
            G G V  +    +  P   +  DA    ++        K  +   S R  ++       
Sbjct: 742 WGDGSVLPRQTDHKEFPYPTVAADAFEPAVRDGLVAFFQKALHRDVSRRYPELKPMRDAW 801

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEE 262
             I  D S T   S +  +                 + +  +     L  +      +  
Sbjct: 802 RKIFLDASQTVPSSFSRPASTPVPVSEDGRPAIADAEPLSAEQQRDRLAKDVTRETHLST 861

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
             L+  + + L    I  +G L+  +   ++     G K+  E++      G
Sbjct: 862 AGLTEAAQSFLYNLGITTVGGLLDYSRRKLVNAPGLGAKTRGEVQRRQREWG 913


>gi|218884674|ref|YP_002429056.1| DNA-directed RNA polymerase subunit D [Desulfurococcus
           kamchatkensis 1221n]
 gi|218766290|gb|ACL11689.1| DNA-directed RNA polymerase subunit D [Desulfurococcus
           kamchatkensis 1221n]
          Length = 280

 Score = 40.3 bits (93), Expect = 0.46,   Method: Composition-based stats.
 Identities = 24/147 (16%), Positives = 42/147 (28%), Gaps = 19/147 (12%)

Query: 45  NALRRVLMSSLRGAAITAVQI-DGVLHEISSIKGVHEDLTDIILN-----------IKGI 92
           N+LRR ++S +   A+  V I +               L  +  N               
Sbjct: 26  NSLRRTILSEVPTMAVDYVAITENSSVFYDEYISHRLGLIPLKSNEALNKYKPPEECAEA 85

Query: 93  NLKMSGDSHKRVTIFKRGPG------VVTAGDIQ-TVNDIEVLNPDHVICNLDVDAVVRM 145
             +        VT+     G       V + D+  +  D+  +  +  I  L  D  +R+
Sbjct: 86  GDRGIFSQDCFVTLRLEASGPEKDVLTVYSRDLVSSDPDVVPVYGEIPILKLIKDQSIRL 145

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLIT 172
           E     G G    K           + 
Sbjct: 146 EAYARLGRGKEHIKWSPVSTAAHKYVP 172


>gi|312083749|ref|XP_003143992.1| DNA-directed RNA polymerase II polypeptide [Loa loa]
 gi|307760845|gb|EFO20079.1| DNA-directed RNA polymerase II polypeptide [Loa loa]
          Length = 275

 Score = 40.0 bits (92), Expect = 0.48,   Method: Composition-based stats.
 Identities = 43/233 (18%), Positives = 79/233 (33%), Gaps = 47/233 (20%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQID---GVLH-EISSIK--------GVHEDLTDIILN 88
            ++ N+LRR+ M+ +   AI  VQI+    VLH E  + +            D      +
Sbjct: 28  LSVANSLRRIFMAEVPTMAIDWVQIESNTSVLHDEFIAHRLGLIPLTSDSVVDQMQFSRD 87

Query: 89  IKGINLKMSGDSHKRVTIFK--RGPGVVTAGDIQTVN-------DIEVLN--------PD 131
            +            R+ +     G   VT  D++T N        + + N         D
Sbjct: 88  CQCTEFCQFCAVEMRLRVRCDDEGIRAVTTADLETSNPDVAPACGVHIRNRNAEESASDD 147

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL--------------- 176
            +I  L     V ++    KG G   AK + T          +AL               
Sbjct: 148 ILIVKLRKGQDVDIKCIAKKGFGKEHAKWNPTCCVSFEYDPDNALRHTVLAKPEEWPKSE 207

Query: 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           YS ++   Y        +   +     T+++ G++  E+ +     +L+ +L 
Sbjct: 208 YSQLEDDEYEASFDPMAKPNKF---WFTVESTGALKAENIILSGISVLKKKLA 257


>gi|46048954|ref|NP_989646.1| integrin beta-3 precursor [Gallus gallus]
 gi|474039|emb|CAA51069.1| Integrin beta3 [Gallus gallus]
          Length = 781

 Score = 40.0 bits (92), Expect = 0.50,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 31/72 (43%), Gaps = 8/72 (11%)

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD--------WPPES 328
           +I Y+ DL    + D+  + N G K   E++ +   + +  G  +           PPE+
Sbjct: 131 DIYYLMDLSNSMKDDLKNIQNLGTKLASEMRKLTSNLRIGFGAFVDKPISPYMYISPPEA 190

Query: 329 IEELAKKYEDKC 340
           I+    +  +KC
Sbjct: 191 IKNPCYEIGEKC 202


>gi|329923259|ref|ZP_08278744.1| hypothetical protein HMPREF9412_0344 [Paenibacillus sp. HGF5]
 gi|328941494|gb|EGG37785.1| hypothetical protein HMPREF9412_0344 [Paenibacillus sp. HGF5]
          Length = 72

 Score = 40.0 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 4/60 (6%)

Query: 262 ELELSVRSTNCLRGENI----VYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           E +  V++ N  R   I      + DL + TE ++L +   G K++  ++  L   GL  
Sbjct: 11  ESDFPVKAGNPARRALIVAGYHQLADLTRATEKELLALHGVGPKAIGVLRAALAEKGLAF 70


>gi|126296213|ref|XP_001365715.1| PREDICTED: similar to Polymerase (RNA) II (DNA directed)
           polypeptide C, 33kDa [Monodelphis domestica]
          Length = 275

 Score = 40.0 bits (92), Expect = 0.54,   Method: Composition-based stats.
 Identities = 47/256 (18%), Positives = 87/256 (33%), Gaps = 51/256 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHT---LGNALRRVLMSSLRGAAITAVQIDG------- 67
           + + +  +     I E       +T   + N++RRV ++ +   AI  VQID        
Sbjct: 9   VRITELTDENVKFIIE-------NTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHD 61

Query: 68  --VLHEISSIKGVHEDLTDIILNIKG---------------INLKMSGDSHKRVT---IF 107
             + H +  I    +D+ D +   +                ++++ + D  + VT   + 
Sbjct: 62  EFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDLI 121

Query: 108 KRGPGV--VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
              P V  VT+          V   D +I  L     +R+     KG G   AK + T  
Sbjct: 122 SNTPRVIPVTSRSRDNDPSDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181

Query: 166 DPIGLITIDALYSPIK-------KVSYT-----VESAREGQVLDYDKLSMTIDTDGSITG 213
                   +AL   +        K  Y+        A        ++    +++ GS+  
Sbjct: 182 VAFEYDPDNALRHTVYPKPEEWPKSEYSEIDEDEAQAPYDPNGKPERFYYNVESCGSLRP 241

Query: 214 EDSVALASRILQDQLG 229
           E  V  A   L+ +L 
Sbjct: 242 ETIVLSALSGLKKKLS 257


>gi|153953110|ref|YP_001393875.1| hypothetical protein CKL_0473 [Clostridium kluyveri DSM 555]
 gi|219853760|ref|YP_002470882.1| hypothetical protein CKR_0417 [Clostridium kluyveri NBRC 12016]
 gi|146345991|gb|EDK32527.1| Conserved hypothetical protein [Clostridium kluyveri DSM 555]
 gi|219567484|dbj|BAH05468.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 332

 Score = 40.0 bits (92), Expect = 0.54,   Method: Composition-based stats.
 Identities = 17/106 (16%), Positives = 37/106 (34%), Gaps = 3/106 (2%)

Query: 211 ITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE---LSV 267
           +  E+            + +   +EE +    E  N+K+        +  +  +      
Sbjct: 19  VELEELAKEYKMSDSAIISIIRKYEELEAYSNEMENLKANNKMNEETELYDLCKLLKFHT 78

Query: 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
            S N L  +NI  +  L+  ++ +   + N G+ S   IK  +   
Sbjct: 79  HSINALIHKNIRSVDKLLSLSQEEFYAIKNLGKVSQKYIKECISEY 124


>gi|304414228|ref|ZP_07395596.1| transcription termination/antitermination L factor [Candidatus
           Regiella insecticola LSR1]
 gi|304283442|gb|EFL91838.1| transcription termination/antitermination L factor [Candidatus
           Regiella insecticola LSR1]
          Length = 506

 Score = 40.0 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 21/116 (18%), Positives = 41/116 (35%), Gaps = 8/116 (6%)

Query: 227 QLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQ 286
            +     +E     + E           A+   +E LE+       L       + +L  
Sbjct: 338 LVSQLSGWELNVMTINELKEKCQAETRTAIDMFIEHLEIDEECATVLVEAEFSSLEELAY 397

Query: 287 RTEADMLRMANFGRKSLVEIKG----VLGTMGL----FLGMNLPDWPPESIEELAK 334
             E+++  + +F +K L E++     VL T+ L      G N P     ++  L +
Sbjct: 398 VPESELPEIDSFDKKRLQELRDRAQNVLTTLALKKEESFGDNKPADDLLNLASLDR 453


>gi|307721033|ref|YP_003892173.1| isocitrate dehydrogenase, NADP-dependent [Sulfurimonas autotrophica
           DSM 16294]
 gi|306979126|gb|ADN09161.1| isocitrate dehydrogenase, NADP-dependent [Sulfurimonas autotrophica
           DSM 16294]
          Length = 725

 Score = 40.0 bits (92), Expect = 0.56,   Method: Composition-based stats.
 Identities = 24/119 (20%), Positives = 51/119 (42%), Gaps = 17/119 (14%)

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGE 276
           +  A  +    L   +N    +  V+   +  SL         + E EL+          
Sbjct: 9   IDEAPALATYSLLPIVNAFTKEAGVEVVTSDISLAGRVLAAMGLAENELAK--------- 59

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP--PESIEELA 333
               +G+L+Q+ EA+++++ N    S+ ++K  +  +    G ++P++P  P + EE A
Sbjct: 60  ----LGELVQKPEANIIKLPNISA-SVGQLKDCIAELQ-SQGYDIPNYPENPTNAEEEA 112


>gi|238063644|ref|ZP_04608353.1| hypothetical protein MCAG_04610 [Micromonospora sp. ATCC 39149]
 gi|237885455|gb|EEP74283.1| hypothetical protein MCAG_04610 [Micromonospora sp. ATCC 39149]
          Length = 64

 Score = 40.0 bits (92), Expect = 0.56,   Method: Composition-based stats.
 Identities = 13/47 (27%), Positives = 20/47 (42%)

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318
            L       + DL+    AD+ ++   G K+L  I+  L    L LG
Sbjct: 18  ALNNAGYSTLRDLVGVPRADLAKLHGMGPKALGIIQSALEQHDLSLG 64


>gi|254373566|ref|ZP_04989053.1| hypothetical protein FTCG_01522 [Francisella tularensis subsp.
           novicida GA99-3549]
 gi|151571291|gb|EDN36945.1| hypothetical protein FTCG_01522 [Francisella novicida GA99-3549]
          Length = 344

 Score = 40.0 bits (92), Expect = 0.56,   Method: Composition-based stats.
 Identities = 22/133 (16%), Positives = 49/133 (36%), Gaps = 9/133 (6%)

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDG--SITGEDSVALASR---ILQDQLGMFINFE 235
             V Y + S       D  ++++  +T+    +  ++S++ A     +        I ++
Sbjct: 139 DMVQYAINSLSPVDAADILEVNVDEETNSMDIVVKQESLSKAIGKNGVNVRLASSLIGWK 198

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
                  E    +       + K VE L++       L  E I  + DL     A++L +
Sbjct: 199 INVLSDAEQEEKQMS----IVEKFVEALDIDHDFALVLIEEGIETLEDLAYLDRAELLEI 254

Query: 296 ANFGRKSLVEIKG 308
             F  + + E++ 
Sbjct: 255 EGFDEEIVDELQE 267


>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 = 40.0 bits (92), Expect = 0.57,   Method: Composition-based stats.
 Identities = 34/212 (16%), Positives = 60/212 (28%), Gaps = 57/212 (26%)

Query: 12  PNNIEYIVLG--QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG-- 67
           P  ++ + +   + +             G    + NA RR+L++ +   AI  V I    
Sbjct: 54  PWKLKGLKIEFHKNDPLEASFSL----IGVDAAIANAFRRILLAEIPALAIEYVYIQNNT 109

Query: 68  -------VLHEISSIK-------------------------GVHEDLTDIILNIKGINLK 95
                  + H +  I                            HED   I+L +     K
Sbjct: 110 SVIQDEVLAHRLGLIPLKGSLEGLNWLRWFKIPKEGDPDSGSTHEDSNTIVLRLVKECTK 169

Query: 96  MSG---DSHKRVTIFKRGPGVVTAGDIQTVND------------IEVLNPDHVICNLDVD 140
                 D      ++      + A D+                 I+  NPD ++  L   
Sbjct: 170 NRNAAPDEEDPTVLYNNAH--IYAKDLVFEPQGRQEKYFHGDGVIQPCNPDILLAKLRPG 227

Query: 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLIT 172
             + +E+   KG G   AK          L+ 
Sbjct: 228 QKIDIEMHCIKGIGADHAKFSPVATASYRLLP 259


>gi|255513546|gb|EET89812.1| RNA polymerase insert [Candidatus Micrarchaeum acidiphilum ARMAN-2]
          Length = 191

 Score = 40.0 bits (92), Expect = 0.57,   Method: Composition-based stats.
 Identities = 27/119 (22%), Positives = 48/119 (40%), Gaps = 9/119 (7%)

Query: 44  GNALRRVLMSSLRGAAITAVQI-DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
            NALRR+ ++ ++  AI  V + +               +   I  +  I    S D  +
Sbjct: 25  ANALRRIAINGIKAFAIDKVTVYENTSSMFDEY------IAHRIGLVPLITPHGSSDKDE 78

Query: 103 RV-TIFKRGPGVVTAGDIQ-TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
            + T+   GPG + +  ++ +   + V NP+  I  L  D  +R+E     G     AK
Sbjct: 79  ILFTLEAAGPGTIYSKSLESSDKSVVVANPNIPIIKLGRDQKIRIEGKAVMGSALKHAK 137


>gi|109128649|ref|XP_001098211.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3 isoform 1
           [Macaca mulatta]
          Length = 257

 Score = 40.0 bits (92), Expect = 0.59,   Method: Composition-based stats.
 Identities = 37/191 (19%), Positives = 70/191 (36%), Gaps = 39/191 (20%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHT---LGNALRRVLMSSLRGAAITAVQIDG------- 67
           + + +  +     I E       +T   + N++RRV ++ +   AI  VQID        
Sbjct: 9   VRITELTDENVKFIIE-------NTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHD 61

Query: 68  --VLHEISSIKGVHEDLTDIILNIKG---------------INLKMSGDSHKRVT---IF 107
             + H +  I  + +D+ D +   +                ++++ + D  + VT   + 
Sbjct: 62  EFIAHRLGLIPLISDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDLI 121

Query: 108 KRGPGV--VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
              P V  VT+ +     +  V   D +I  L     +R+     KG G   AK + T  
Sbjct: 122 SNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181

Query: 166 DPIGLITIDAL 176
                   +AL
Sbjct: 182 VAFEYDPDNAL 192


>gi|148234336|ref|NP_001084998.1| polymerase (RNA) II (DNA directed) polypeptide C, 33kDa [Xenopus
           laevis]
 gi|47682270|gb|AAH70601.1| MGC81245 protein [Xenopus laevis]
          Length = 275

 Score = 40.0 bits (92), Expect = 0.61,   Method: Composition-based stats.
 Identities = 44/228 (19%), Positives = 80/228 (35%), Gaps = 41/228 (17%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTDIILNIKG-- 91
           + N++RRV ++ +   AI  VQID          + H +  I    +D+ D +   +   
Sbjct: 30  IANSIRRVFIAEVPTIAIDWVQIDANSSVLHDEFIAHRVGLIPLTSDDIVDKLQYSRDCT 89

Query: 92  -------------INLKMSGDSHKRVT---IFKRGPGV--VTAGDIQTVNDIEVLNPDHV 133
                        ++++ + D  + VT   +      V  VT+       +  V   D +
Sbjct: 90  CDEFCPECSVEFTLDVRCTEDQTRHVTSRDLVSNNLRVIPVTSRSRDNDPNDYVEQDDIL 149

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK-------KVSYT 186
           I  L     +R+     KG G   AK + T          +AL   +        K  Y+
Sbjct: 150 IVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVAFEYDPDNALRHTVYPKPEEWPKSEYS 209

Query: 187 VESAREGQVL-----DYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
                E Q         ++    +++ GS+  E  V  A   L+ +L 
Sbjct: 210 EIDEEEAQAPYDPTGKPERFYYNVESCGSLKPETIVLSALSGLKKKLS 257


>gi|326927174|ref|XP_003209769.1| PREDICTED: ubiquinone biosynthesis protein COQ9, mitochondrial-like
           [Meleagris gallopavo]
          Length = 549

 Score = 40.0 bits (92), Expect = 0.61,   Method: Composition-based stats.
 Identities = 43/227 (18%), Positives = 80/227 (35%), Gaps = 41/227 (18%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTDIILNIKG--- 91
            N++RRV ++ +   AI  VQID          + H +  I    +D+ D +   +    
Sbjct: 305 ANSIRRVFIAEVPIIAIDWVQIDANSSVLHDEFIAHRLGLIPLTSDDIVDKMQYSRDCTC 364

Query: 92  ------------INLKMSGDSHKRVT---IFKRGPGV--VTAGDIQTVNDIEVLNPDHVI 134
                       ++++ + D  + VT   +    P V  VT+       +  V   D +I
Sbjct: 365 DEFCPECSVEFTLDVRCNEDQTRHVTSRDLISNNPRVIPVTSRSRDNDPNDYVEQDDILI 424

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK-------KVSYTV 187
             L     +++     KG G   AK + T          +AL   +        K  Y+ 
Sbjct: 425 VKLRKGQELKLRAYAKKGFGKEHAKWNPTAGVAFEYDPDNALRHTVYPKPEEWPKSEYSE 484

Query: 188 ESAREGQ-----VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
               + Q         ++    +++ GS+  E  V  A   L+ +L 
Sbjct: 485 IDEEDAQAPYDPNGKPERFYYNVESCGSLRPETIVLSALSGLKKKLS 531


>gi|293511535|ref|ZP_06670229.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           M809]
 gi|291465493|gb|EFF08025.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           M809]
          Length = 170

 Score = 39.6 bits (91), Expect = 0.63,   Method: Composition-based stats.
 Identities = 11/55 (20%), Positives = 23/55 (41%)

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
            L  + I  + D+ Q T++ ++ M   G K++  ++  L    L     +    P
Sbjct: 13  ALNSQGIYTLEDVSQYTKSSLMEMHGVGPKAISILEQALFQHQLHFKTEVHSSLP 67


>gi|197294735|ref|YP_001799276.1| ATP-dependent Lon protease [Candidatus Phytoplasma australiense]
 gi|171854062|emb|CAM12035.1| ATP-dependent Lon protease [Candidatus Phytoplasma australiense]
          Length = 787

 Score = 39.6 bits (91), Expect = 0.63,   Method: Composition-based stats.
 Identities = 26/121 (21%), Positives = 51/121 (42%), Gaps = 14/121 (11%)

Query: 224 LQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGD 283
             +     I FE+  +++ + I       N    K ++E +L+ R  N LR  +I+ MG 
Sbjct: 162 SNNNFLEMIQFEQEVEKITDIIIFYLRIDNSEKYKYLKEADLNKRLFNILRDIDILTMGM 221

Query: 284 LIQRTEADMLRMANFGRKSLVE------IKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337
            +++   +  ++     KS+ E      ++  +  +   LG  +     E I EL KK  
Sbjct: 222 HLEQKINE--KVK----KSIDENQKEFYLREKMKAIQNELGDKVKKE--EEIAELRKKIN 273

Query: 338 D 338
           +
Sbjct: 274 N 274


>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 = 39.6 bits (91), Expect = 0.64,   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 VRLAAKLLQWKIDIKSEEEKRQEVEQQMQAMSGGPTTPIEQV----TELGEQILEKLIAA 383

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            I  +  +   T  ++ ++   G K++ +I
Sbjct: 384 GITTVEAVADMTAEELEQIPGIGEKTIEKI 413


>gi|85822798|gb|ABC84857.1| RNA polymerase gamma subunit [Peanut witches'-broom phytoplasma]
          Length = 1379

 Score = 39.6 bits (91), Expect = 0.66,   Method: Composition-based stats.
 Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 2/61 (3%)

Query: 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314
            L  K+E+  L+ R+   L+   I  +GD+      ++  + +   +S  E   +L   G
Sbjct: 1   MLNMKIEDFALTKRTLKNLKSIGINSLGDINNYHLNEL--ITSLNEESFEEFVIILKKYG 58

Query: 315 L 315
           L
Sbjct: 59  L 59


>gi|116670209|ref|YP_831142.1| hypothetical protein Arth_1648 [Arthrobacter sp. FB24]
 gi|116610318|gb|ABK03042.1| hypothetical protein Arth_1648 [Arthrobacter sp. FB24]
          Length = 72

 Score = 39.6 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 6/42 (14%), Positives = 21/42 (50%)

Query: 276 ENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
             +  +  ++Q  + ++L++   G K++ +++  +   GL  
Sbjct: 28  AGLETLEQVVQFGQRELLKLHGMGVKTMAQLEDAMDEHGLEF 69


>gi|254369910|ref|ZP_04985919.1| hypothetical protein FTAG_01671 [Francisella tularensis subsp.
           holarctica FSC022]
 gi|157122880|gb|EDO66997.1| hypothetical protein FTAG_01671 [Francisella tularensis subsp.
           holarctica FSC022]
          Length = 447

 Score = 39.6 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 13/64 (20%), Positives = 25/64 (39%)

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +       + K VE L++       L  E I  + DL     A++L +  F  + + 
Sbjct: 307 DAEQEEKQMSIVEKFVEALDIDHNFALVLIEEGIETLEDLAYLDRAELLEIEGFDEEIVD 366

Query: 305 EIKG 308
           E++ 
Sbjct: 367 ELQE 370


>gi|167045221|gb|ABZ09881.1| putative RNA polymerase Rpb3/RpoA insert domain protein [uncultured
           marine crenarchaeote HF4000_APKG8O8]
          Length = 201

 Score = 39.6 bits (91), Expect = 0.70,   Method: Composition-based stats.
 Identities = 32/190 (16%), Positives = 67/190 (35%), Gaps = 43/190 (22%)

Query: 40  AHTL--GNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIILN 88
             TL   NALRR+ ++ +   AI  V +         +G+ H +  I  +  DL+    +
Sbjct: 20  GVTLQYANALRRICLNGVAIYAIDTVDMIENSSVLADEGITHRLGLIP-LKTDLSRSDES 78

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH-VICNLDVDAVVRMEL 147
              I L +                +VT+ ++ + + +   + D   I +L     ++ E 
Sbjct: 79  DSRIMLTLDSGDD------TETGRMVTSAELLSDDKVVKPSSDQIPIIHLTPGQKLKFEA 132

Query: 148 TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDT 207
               G G   AK + +       + +D                        D+  +T++T
Sbjct: 133 YARLGRGTEHAKWNSSNIA----VLLDT--------------------KKEDEHILTVET 168

Query: 208 DGSITGEDSV 217
            G++   + +
Sbjct: 169 TGALKPGEII 178


>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 = 0.72,   Method: Composition-based stats.
 Identities = 35/193 (18%), Positives = 56/193 (29%), Gaps = 56/193 (29%)

Query: 34  PLPRGFAHT-----LGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIK--- 76
           PL   F+       + NA RR+L++ +   AI  V I           + H +  I    
Sbjct: 61  PLEASFSLIGVDAAIANAFRRILLAEIPALAIEYVYIQNNTSVIQDEVLAHRLGLIPLKG 120

Query: 77  ----------------------GVHEDLTDIILNIKGINLKMSG---DSHKRVTIFKRGP 111
                                   HED   I+L +     K      D      ++    
Sbjct: 121 SLEGLNWLRWFKIPKEGDPDSGSTHEDSNTIVLRLVKECTKNRNAAPDEEDPTVLYNNAH 180

Query: 112 GVVTAGDIQTVND------------IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             + A D+                 I+  NPD ++  L     + +E+   KG G   AK
Sbjct: 181 --IYAKDLVFEPQGRQEKYFHGDGVIQPCNPDILLAKLRPGQKIDIEMHCIKGIGADHAK 238

Query: 160 HHRTENDPIGLIT 172
                     L+ 
Sbjct: 239 FSPVATASYRLLP 251


>gi|295429277|ref|ZP_06821899.1| hypothetical protein SIAG_01485 [Staphylococcus aureus subsp.
           aureus EMRSA16]
 gi|295127036|gb|EFG56680.1| hypothetical protein SIAG_01485 [Staphylococcus aureus subsp.
           aureus EMRSA16]
          Length = 211

 Score = 39.6 bits (91), Expect = 0.74,   Method: Composition-based stats.
 Identities = 10/50 (20%), Positives = 22/50 (44%)

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
            L  + I  + D+ Q T++ ++ M   G K++  ++  L    L     +
Sbjct: 33  ALNSQGIYTLEDVSQYTKSSLMEMHGVGPKAISILEQALFQHQLHFKTEV 82


>gi|319653736|ref|ZP_08007833.1| hypothetical protein HMPREF1013_04451 [Bacillus sp. 2_A_57_CT2]
 gi|317394579|gb|EFV75320.1| hypothetical protein HMPREF1013_04451 [Bacillus sp. 2_A_57_CT2]
          Length = 96

 Score = 39.6 bits (91), Expect = 0.77,   Method: Composition-based stats.
 Identities = 16/55 (29%), Positives = 26/55 (47%)

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            +LS  + N L  E I  +  L + TE ++L++   G  SL  ++  L   GL  
Sbjct: 40  SKLSAPARNALVHEGIDTLKKLSKFTEKEILKIHGIGPSSLPIMRTSLKEEGLSF 94


>gi|32266695|ref|NP_860727.1| isocitrate dehydrogenase [Helicobacter hepaticus ATCC 51449]
 gi|32262746|gb|AAP77793.1| isocitrate dehydrogenase [Helicobacter hepaticus ATCC 51449]
          Length = 734

 Score = 39.6 bits (91), Expect = 0.77,   Method: Composition-based stats.
 Identities = 14/59 (23%), Positives = 33/59 (55%), Gaps = 2/59 (3%)

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           +GDL++  EA++++  N    S+ ++K  +  +    G ++P++P E   +  K  ++K
Sbjct: 66  LGDLVKTKEANLIKTPNISA-SIPQLKAAIKELQGK-GYDVPNFPDEPQNDTEKAIKEK 122


>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 = 0.79,   Method: Composition-based stats.
 Identities = 35/193 (18%), Positives = 56/193 (29%), Gaps = 56/193 (29%)

Query: 34  PLPRGFAHT-----LGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIK--- 76
           PL   F+       + NA RR+L++ +   AI  V I           + H +  I    
Sbjct: 61  PLEASFSLIGVDAAIANAFRRILLAEIPALAIEYVYIQNNTSVIQDEVLAHRLGLIPLKG 120

Query: 77  ----------------------GVHEDLTDIILNIKGINLKMSG---DSHKRVTIFKRGP 111
                                   HED   I+L +     K      D      ++    
Sbjct: 121 SLEGLNWLRWFKIPKEGDPDSGSTHEDSNTIVLRLVKECTKNRNAAPDEEDPTVLYNNAH 180

Query: 112 GVVTAGDIQTVND------------IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159
             + A D+                 I+  NPD ++  L     + +E+   KG G   AK
Sbjct: 181 --IYAKDLVFEPQGRQEKYFHGDGVIQPCNPDILLAKLRPGQKIDIEMHCIKGIGADHAK 238

Query: 160 HHRTENDPIGLIT 172
                     L+ 
Sbjct: 239 FSPVATASYRLLP 251


>gi|258423255|ref|ZP_05686147.1| conserved hypothetical protein [Staphylococcus aureus A9635]
 gi|257846584|gb|EEV70606.1| conserved hypothetical protein [Staphylococcus aureus A9635]
          Length = 191

 Score = 39.6 bits (91), Expect = 0.79,   Method: Composition-based stats.
 Identities = 11/55 (20%), Positives = 23/55 (41%)

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
            L  + I  + D+ Q T++ ++ M   G K++  ++  L    L     +    P
Sbjct: 13  ALNSQGIYTLEDVSQYTKSSLMEMHGVGPKAISILEQALFQHQLHFKTEVHSSLP 67


>gi|49484890|ref|YP_042114.1| hypothetical protein SAR2777 [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|221142451|ref|ZP_03566944.1| hypothetical protein SauraJ_12582 [Staphylococcus aureus subsp.
           aureus str. JKD6009]
 gi|257424176|ref|ZP_05600605.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257426854|ref|ZP_05603256.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257429490|ref|ZP_05605877.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257432137|ref|ZP_05608500.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257435098|ref|ZP_05611149.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           M876]
 gi|282907028|ref|ZP_06314876.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           Btn1260]
 gi|282910005|ref|ZP_06317813.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282912253|ref|ZP_06320049.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282912893|ref|ZP_06320685.1| putative DNA-binding protein [Staphylococcus aureus subsp. aureus
           M899]
 gi|282922521|ref|ZP_06330211.1| hypothetical protein SARG_00173 [Staphylococcus aureus subsp.
           aureus C101]
 gi|283959466|ref|ZP_06376907.1| putative DNA-binding protein [Staphylococcus aureus subsp. aureus
           A017934/97]
 gi|293497946|ref|ZP_06665800.1| hypothetical protein SCAG_00519 [Staphylococcus aureus subsp.
           aureus 58-424]
 gi|293550145|ref|ZP_06672817.1| putative DNA-binding protein [Staphylococcus aureus subsp. aureus
           M1015]
 gi|297589224|ref|ZP_06947865.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           MN8]
 gi|304379926|ref|ZP_07362655.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           ATCC BAA-39]
 gi|49243019|emb|CAG41752.1| putative DNA-binding protein [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|257273194|gb|EEV05296.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257276485|gb|EEV07936.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257279971|gb|EEV10558.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257283016|gb|EEV13148.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257285694|gb|EEV15810.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           M876]
 gi|269942280|emb|CBI50695.1| putative DNA-binding protein [Staphylococcus aureus subsp. aureus
           TW20]
 gi|282314742|gb|EFB45128.1| hypothetical protein SARG_00173 [Staphylococcus aureus subsp.
           aureus C101]
 gi|282322993|gb|EFB53312.1| putative DNA-binding protein [Staphylococcus aureus subsp. aureus
           M899]
 gi|282323949|gb|EFB54265.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282326071|gb|EFB56376.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282329927|gb|EFB59448.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           Btn1260]
 gi|283789058|gb|EFC27885.1| putative DNA-binding protein [Staphylococcus aureus subsp. aureus
           A017934/97]
 gi|290919192|gb|EFD96268.1| putative DNA-binding protein [Staphylococcus aureus subsp. aureus
           M1015]
 gi|291096877|gb|EFE27135.1| hypothetical protein SCAG_00519 [Staphylococcus aureus subsp.
           aureus 58-424]
 gi|297577735|gb|EFH96448.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           MN8]
 gi|302752570|gb|ADL66747.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           str. JKD6008]
 gi|304341506|gb|EFM07416.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           ATCC BAA-39]
 gi|312436881|gb|ADQ75952.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           TCH60]
 gi|315195204|gb|EFU25592.1| putative DNA-binding protein [Staphylococcus aureus subsp. aureus
           CGS00]
 gi|329315413|gb|AEB89826.1| Putative DNA-binding protein [Staphylococcus aureus subsp. aureus
           T0131]
          Length = 191

 Score = 39.6 bits (91), Expect = 0.79,   Method: Composition-based stats.
 Identities = 11/55 (20%), Positives = 23/55 (41%)

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
            L  + I  + D+ Q T++ ++ M   G K++  ++  L    L     +    P
Sbjct: 13  ALNSQGIYTLEDVSQYTKSSLMEMHGVGPKAISILEQALFQHQLHFKTEVHSSLP 67


>gi|237755727|ref|ZP_04584334.1| isocitrate dehydrogenase, NADP-dependent [Sulfurihydrogenibium
           yellowstonense SS-5]
 gi|237692119|gb|EEP61120.1| isocitrate dehydrogenase, NADP-dependent [Sulfurihydrogenibium
           yellowstonense SS-5]
          Length = 746

 Score = 39.2 bits (90), Expect = 0.81,   Method: Composition-based stats.
 Identities = 17/59 (28%), Positives = 33/59 (55%), Gaps = 2/59 (3%)

Query: 280 YMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           Y+G+L+ R EA+++++ N    S+ ++  V+  +    G NLPD+P +   E  K   +
Sbjct: 68  YLGELVLRPEANIMKLPNISA-SIPQLIEVIKELQ-SQGYNLPDFPEDPKTEEEKAIRE 124


>gi|241518314|ref|YP_002978942.1| hypothetical protein Rleg_5576 [Rhizobium leguminosarum bv.
           trifolii WSM1325]
 gi|240862727|gb|ACS60391.1| hypothetical protein Rleg_5576 [Rhizobium leguminosarum bv.
           trifolii WSM1325]
          Length = 87

 Score = 39.2 bits (90), Expect = 0.81,   Method: Composition-based stats.
 Identities = 10/63 (15%), Positives = 24/63 (38%)

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              K+     A    +   ++ V     L    I  +  L   T+ ++L +   G++++ 
Sbjct: 5   PARKTSKPRAASSDMLVRSKIPVWIVKALLSSGIKRVSKLSSMTDDELLALPGIGKRAIE 64

Query: 305 EIK 307
            I+
Sbjct: 65  LIR 67


>gi|89257073|ref|YP_514435.1| transcription elongation factor NusA [Francisella tularensis subsp.
           holarctica LVS]
 gi|115315429|ref|YP_764152.1| transcription elongation factor NusA [Francisella tularensis subsp.
           holarctica OSU18]
 gi|156503283|ref|YP_001429348.1| transcription elongation factor NusA [Francisella tularensis subsp.
           holarctica FTNF002-00]
 gi|167009460|ref|ZP_02274391.1| transcription termination factor NusA [Francisella tularensis
           subsp. holarctica FSC200]
 gi|290954351|ref|ZP_06558972.1| transcription elongation factor NusA [Francisella tularensis subsp.
           holarctica URFT1]
 gi|295312215|ref|ZP_06803015.1| transcription elongation factor NusA [Francisella tularensis subsp.
           holarctica URFT1]
 gi|89144904|emb|CAJ80249.1| N utilization substance protein A [Francisella tularensis subsp.
           holarctica LVS]
 gi|115130328|gb|ABI83515.1| N utilization substance protein A [Francisella tularensis subsp.
           holarctica OSU18]
 gi|156253886|gb|ABU62392.1| transcription termination factor NusA [Francisella tularensis
           subsp. holarctica FTNF002-00]
          Length = 489

 Score = 39.2 bits (90), Expect = 0.82,   Method: Composition-based stats.
 Identities = 13/64 (20%), Positives = 25/64 (39%)

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +       + K VE L++       L  E I  + DL     A++L +  F  + + 
Sbjct: 349 DAEQEEKQMSIVEKFVEALDIDHNFALVLIEEGIETLEDLAYLDRAELLEIEGFDEEIVD 408

Query: 305 EIKG 308
           E++ 
Sbjct: 409 ELQE 412


>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 = 39.2 bits (90), Expect = 0.83,   Method: Composition-based stats.
 Identities = 15/80 (18%), Positives = 31/80 (38%)

Query: 234 FEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
            E+ + E       ++      L + +  L LS  +  CL       + DL++    D++
Sbjct: 112 HEKQQLEFDFGPGFRNWISPIFLDEPIHILGLSQHAEKCLEKNGKCLIQDLLKADTQDLI 171

Query: 294 RMANFGRKSLVEIKGVLGTM 313
            +   G+  + EI+  L   
Sbjct: 172 FLKGMGQGHIDEIQQTLKKY 191


>gi|282918053|ref|ZP_06325803.1| hypothetical protein SATG_00955 [Staphylococcus aureus subsp.
           aureus D139]
 gi|283767772|ref|ZP_06340687.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           H19]
 gi|282318338|gb|EFB48698.1| hypothetical protein SATG_00955 [Staphylococcus aureus subsp.
           aureus D139]
 gi|283461651|gb|EFC08735.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           H19]
          Length = 191

 Score = 39.2 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 11/55 (20%), Positives = 23/55 (41%)

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326
            L  + I  + D+ Q T++ ++ M   G K++  ++  L    L     +    P
Sbjct: 13  ALNSQGIYTLEDVSQYTKSSLMEMHGVGPKAISILEQALFQHQLHFKTEVHSSLP 67


>gi|56707228|ref|YP_169124.1| transcription elongation factor NusA [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110669698|ref|YP_666255.1| transcription elongation factor NusA [Francisella tularensis subsp.
           tularensis FSC198]
 gi|134301263|ref|YP_001121231.1| transcription elongation factor NusA [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|224456289|ref|ZP_03664762.1| transcription elongation factor NusA [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|254369913|ref|ZP_04985921.1| hypothetical protein [Francisella tularensis subsp. tularensis
           FSC033]
 gi|254874067|ref|ZP_05246777.1| transcription factor nusA [Francisella tularensis subsp. tularensis
           MA00-2987]
 gi|56603720|emb|CAG44682.1| N utilization substance protein A [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110320031|emb|CAL08065.1| N utilization substance protein A [Francisella tularensis subsp.
           tularensis FSC198]
 gi|134049040|gb|ABO46111.1| transcription factor NusA [Francisella tularensis subsp. tularensis
           WY96-3418]
 gi|151568159|gb|EDN33813.1| hypothetical protein FTBG_01505 [Francisella tularensis subsp.
           tularensis FSC033]
 gi|254840066|gb|EET18502.1| transcription factor nusA [Francisella tularensis subsp. tularensis
           MA00-2987]
 gi|282158336|gb|ADA77727.1| transcription elongation factor NusA [Francisella tularensis subsp.
           tularensis NE061598]
          Length = 489

 Score = 39.2 bits (90), Expect = 0.86,   Method: Composition-based stats.
 Identities = 24/134 (17%), Positives = 50/134 (37%), Gaps = 11/134 (8%)

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITG---EDSVALASR---ILQDQLGMFINF 234
             V Y + S       D  ++++  +T+ SI     ++S++ A     +        I +
Sbjct: 284 DMVQYAINSLSPVDAADILEVNVDEETN-SIDIVVKQESLSKAIGKNGVNVRLASSLIGW 342

Query: 235 EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           +       E    +       + K VE L++       L  E I  + DL     A++L 
Sbjct: 343 KINVLSDAEQEEKQMS----IVEKFVEALDIDHDFALVLIEEGIETLEDLAYLDRAELLE 398

Query: 295 MANFGRKSLVEIKG 308
           +  F  + + E++ 
Sbjct: 399 IEGFDEEIVDELQE 412


>gi|289615067|emb|CBI58137.1| unnamed protein product [Sordaria macrospora]
          Length = 311

 Score = 39.2 bits (90), Expect = 0.88,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 4/50 (8%)

Query: 17 YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
           + + Q +  R           FA    N+LRRV+++ +   AI  V+I+
Sbjct: 17 VVKISQADSTRVKFELSNTELCFA----NSLRRVMLAEIPTIAIDLVEIE 62


>gi|260950839|ref|XP_002619716.1| hypothetical protein CLUG_00875 [Clavispora lusitaniae ATCC 42720]
 gi|238847288|gb|EEQ36752.1| hypothetical protein CLUG_00875 [Clavispora lusitaniae ATCC 42720]
          Length = 307

 Score = 39.2 bits (90), Expect = 0.88,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 84/248 (33%), Gaps = 45/248 (18%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHE------ 71
           + + Q E +    I     RG   ++ N+LRR ++S +   AI  V+ID V         
Sbjct: 12  VTIRQTERDHVDFIL----RGVDLSVANSLRRTMLSEVPTLAIDLVEID-VNTSVLADEL 66

Query: 72  ISSIKGVHEDLTDIILNIK--------------GINLKMSGDSHKRVTIFKRGPGVVTAG 117
           +S   G+    ++ I N+                + L+++       T+      +    
Sbjct: 67  LSHRLGLIPLNSEGIENLSYSRDCTCDQYCPNCSVKLELTAKCDSDSTMNVYSSDLAKFH 126

Query: 118 DIQTVNDIEVLNPDHV---ICNLDVDAVVRMELTVSKGHGYVPAKHHR-----TENDPIG 169
           +   + D  + +P H    IC L     +R+     KG     AK         E DP  
Sbjct: 127 NGSKLGDPVIRDPAHRGPLICKLRKHQELRLTCIAKKGIAKEHAKWSPCAAIGFEYDPWN 186

Query: 170 -------LITIDALYSPIKKVSYTVESARE-GQVLDYD----KLSMTIDTDGSITGEDSV 217
                      DA     K  +   E A +     DY+       + ++T GS+   + V
Sbjct: 187 KLKHTDFWYEDDAEAEWPKSANCEWEEAPDPEAPFDYNAKPANFYVDVETVGSLAPNEVV 246

Query: 218 ALASRILQ 225
                 LQ
Sbjct: 247 VRGIETLQ 254


>gi|46105474|ref|XP_380541.1| hypothetical protein FG00365.1 [Gibberella zeae PH-1]
          Length = 381

 Score = 39.2 bits (90), Expect = 0.88,   Method: Composition-based stats.
 Identities = 34/177 (19%), Positives = 56/177 (31%), Gaps = 47/177 (26%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIK--GVHEDLTDIIL---- 87
           L NA RR+L+S +   A+  V I+          + H +  I   G  E L + +     
Sbjct: 82  LANAFRRILLSEIPTLAVENVYIENNTSVIQDEVLAHRLGLIPFKGGREGLHNFLKWHKK 141

Query: 88  --------------NIKGINLKMSGDSHKRVT------IFKRGPGVVTAGDIQTVND--- 124
                         N   + L ++   ++  +      +       V A DI  V     
Sbjct: 142 PEAGDDPYAGCFDWNTVRLELNVTCTVNEDASPTENDPLKAYHNAHVYARDIVFVPTGRQ 201

Query: 125 ---------IEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT 172
                    I   NPD +I  L     + + + + KG G   AK          L+ 
Sbjct: 202 AEYFSGENAIAPTNPDILIAKLRPRQTINLAMHMHKGIGSDHAKFSPVATASYRLLP 258


>gi|15226523|ref|NP_179145.1| NRPB3; DNA binding / DNA-directed RNA polymerase/ protein
           dimerization [Arabidopsis thaliana]
 gi|11134646|sp|Q39211|RPB3A_ARATH RecName: Full=DNA-directed RNA polymerase II subunit RPB3-A;
           Short=RNA polymerase II subunit 3-A; Short=RNA
           polymerase II subunit B3-A; AltName: Full=DNA-directed
           RNA polymerase II 36 kDa polypeptide A
 gi|514318|gb|AAB03741.1| RNA polymerase II third largest subunit [Arabidopsis thaliana]
 gi|4544370|gb|AAD22281.1| DNA-directed RNA polymerase II, third largest subunit [Arabidopsis
           thaliana]
 gi|17381018|gb|AAL36321.1| putative DNA-directed RNA polymerase II third largest subunit
           [Arabidopsis thaliana]
 gi|20465883|gb|AAM20046.1| putative DNA-directed RNA polymerase II [Arabidopsis thaliana]
 gi|330251306|gb|AEC06400.1| DNA-directed RNA polymerase II subunit RPB3-A [Arabidopsis
           thaliana]
          Length = 319

 Score = 39.2 bits (90), Expect = 0.88,   Method: Composition-based stats.
 Identities = 28/174 (16%), Positives = 55/174 (31%), Gaps = 34/174 (19%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG--------- 67
            I + + +++          R    ++ NALRRV++S +   AI  V+I+          
Sbjct: 11  KIKIRELKDDYAKFEL----RETDVSMANALRRVMISEVPTVAIDLVEIEVNSSVLNDEF 66

Query: 68  VLHEISSIKGVHEDLTDI-------------ILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           + H +  I    E    +                   +  ++S       T+      + 
Sbjct: 67  IAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFRLSSKCVTDQTLDVTSRDLY 126

Query: 115 TAGDIQTVNDIEV--------LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
           +A    T  D  +         +   +I  L     +++     KG G   AK 
Sbjct: 127 SADPTVTPVDFTIDSSVSDSSEHKGIIIVKLRRGQELKLRAIARKGIGKDHAKW 180


>gi|161527936|ref|YP_001581762.1| RNA polymerase insert [Nitrosopumilus maritimus SCM1]
 gi|160339237|gb|ABX12324.1| RNA polymerase insert [Nitrosopumilus maritimus SCM1]
          Length = 221

 Score = 39.2 bits (90), Expect = 0.92,   Method: Composition-based stats.
 Identities = 30/146 (20%), Positives = 52/146 (35%), Gaps = 16/146 (10%)

Query: 44  GNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIILNIKGINL 94
            NALRRV ++ +   A+  V I         +G+ H +  I  +  DL+      K    
Sbjct: 35  ANALRRVCLNGVPVFAVDTVDIIENSSVLPDEGLAHRLGLIP-LKTDLSRFNEPSKCECQ 93

Query: 95  KMSGDSHKRVTIFK-RGPGVVTAGDIQT-----VNDIEVLNPDHVICNLDVDAVVRMELT 148
             +G S+ +V +    G   VT   +        + I  ++    I  L     +++E  
Sbjct: 94  SETGCSNCKVMLVLDSGDSDVTRTVLSNELSSEDDSITPISDKIPIVELAPGQRIKVECY 153

Query: 149 VSKGHGYVPAKHHRTENDPIGLITID 174
              G G   AK +      +     D
Sbjct: 154 ARLGRGTEHAKWNSANVSMLTETDKD 179


>gi|167038401|ref|YP_001665979.1| DNA-directed DNA polymerase [Thermoanaerobacter pseudethanolicus
           ATCC 33223]
 gi|167038865|ref|YP_001661850.1| DNA-directed DNA polymerase [Thermoanaerobacter sp. X514]
 gi|256751141|ref|ZP_05492023.1| DNA-directed DNA polymerase [Thermoanaerobacter ethanolicus CCSD1]
 gi|300913550|ref|ZP_07130867.1| DNA-directed DNA polymerase [Thermoanaerobacter sp. X561]
 gi|307723435|ref|YP_003903186.1| DNA-directed DNA polymerase [Thermoanaerobacter sp. X513]
 gi|320116805|ref|YP_004186964.1| DNA-directed DNA polymerase [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|166853105|gb|ABY91514.1| DNA-directed DNA polymerase [Thermoanaerobacter sp. X514]
 gi|166857235|gb|ABY95643.1| DNA-directed DNA polymerase [Thermoanaerobacter pseudethanolicus
           ATCC 33223]
 gi|256750047|gb|EEU63069.1| DNA-directed DNA polymerase [Thermoanaerobacter ethanolicus CCSD1]
 gi|300890235|gb|EFK85380.1| DNA-directed DNA polymerase [Thermoanaerobacter sp. X561]
 gi|307580496|gb|ADN53895.1| DNA-directed DNA polymerase [Thermoanaerobacter sp. X513]
 gi|319929896|gb|ADV80581.1| DNA-directed DNA polymerase [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
          Length = 389

 Score = 39.2 bits (90), Expect = 0.92,   Method: Composition-based stats.
 Identities = 18/163 (11%), Positives = 60/163 (36%), Gaps = 13/163 (7%)

Query: 188 ESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247
           E+  +   +D +   + ++    +     + +++ +  ++    +  +  K +    I  
Sbjct: 104 EAYLDVTDIDKNPEIIALEIKKKVKETTGLTISAGVSYNKFLAKLASDWNKPDGFMVITE 163

Query: 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADM------------LRM 295
             +P     L   +   +  +S   L+   I  +GDL++ ++ ++            LR+
Sbjct: 164 DMIPDILKPLPVSKVYGIGQKSEERLKSMGINTIGDLLKLSQENLVEIFGKVGVEIYLRI 223

Query: 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
                + +  ++ +  ++G    +       + +   AK + D
Sbjct: 224 RGIDERPVETMREI-KSIGKEKTLEKDTKDKKLLLRYAKLFSD 265


>gi|294500353|ref|YP_003564053.1| hypothetical protein BMQ_3606 [Bacillus megaterium QM B1551]
 gi|294350290|gb|ADE70619.1| conserved hypothetical protein [Bacillus megaterium QM B1551]
          Length = 56

 Score = 39.2 bits (90), Expect = 0.98,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 23/53 (43%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  +   L    I  +  L + +E ++L+    G  SL +++  L   GL  
Sbjct: 2   LSAPARRALENNGITSLQQLSKFSEKEILQFHGMGPASLPKLRTALQANGLAF 54


>gi|294634514|ref|ZP_06713049.1| L factor [Edwardsiella tarda ATCC 23685]
 gi|291092028|gb|EFE24589.1| L factor [Edwardsiella tarda ATCC 23685]
          Length = 495

 Score = 39.2 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 17/97 (17%), Positives = 34/97 (35%), Gaps = 8/97 (8%)

Query: 234 FEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           +E      ++         + A+    + L++       L  E    + +L    E ++L
Sbjct: 334 WELNVMTAEDLQAKHQAEAHAAIDTFTKHLDIDEEFATLLVEEGFSTLEELAYVPERELL 393

Query: 294 RMANFGRKSLVEI----KGVLGTMGL----FLGMNLP 322
            +     +S+  +    K  L T+ L     LG N P
Sbjct: 394 AIDGLDEESVEALRTRAKNALTTLALAQEESLGDNKP 430


>gi|21593370|gb|AAM65319.1| DNA-directed RNA polymerase II, third largest subunit [Arabidopsis
           thaliana]
          Length = 319

 Score = 39.2 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 29/174 (16%), Positives = 62/174 (35%), Gaps = 34/174 (19%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID---GVLH-EI 72
            I + + +++          R    ++ NALRRV++S +   AI  V+I+    VL+ E 
Sbjct: 11  KIKIRELKDDYAKFEL----RETDVSMANALRRVMISEVPTVAIDLVEIEVNSSVLNDEF 66

Query: 73  -SSIKGVHEDLTDIILNIK-----------------GINLKMSGDSHKRVTIFKRGPGVV 114
            +   G+    ++  ++++                  +  ++S       T+      + 
Sbjct: 67  IAHRLGLISLTSERAMSMRFSRDCDACDGDGQCEFCSVEFRLSSKCVTDQTLDVTSRDLY 126

Query: 115 TAGDIQTVNDIEV--------LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
           +A    T  D  +         +   +I  L     +++     KG G   AK 
Sbjct: 127 SADPTVTPVDFTIDSSVSDSSEHKGIIIVKLRRGQELKLRAIARKGIGKDHAKW 180


>gi|150009774|ref|YP_001304517.1| hypothetical protein BDI_3189 [Parabacteroides distasonis ATCC
           8503]
 gi|149938198|gb|ABR44895.1| conserved hypothetical protein [Parabacteroides distasonis ATCC
           8503]
          Length = 301

 Score = 39.2 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 4/60 (6%)

Query: 258 KKVEELELSVRSTNCLRGENIVYMGDLIQRTE----ADMLRMANFGRKSLVEIKGVLGTM 313
           + +  L LS     CL    I  + DL++  +      +L M  FG   L ++K  L   
Sbjct: 221 QPITNLTLSPYIRKCLAKLEIETIEDLLRYAKKKGLDSLLDMPGFGTLGLDQLKFQLEKH 280


>gi|172213|gb|AAA34889.1| RNA polymerase II (EC 2.7.7.6) [Saccharomyces cerevisiae]
          Length = 318

 Score = 39.2 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 43/271 (15%), Positives = 84/271 (30%), Gaps = 53/271 (19%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTDIILNIKGIN 93
           + N+LRRV+++ +   AI +V+++          + H +  I    + +    L      
Sbjct: 29  MANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIP--LQSMDIEQLEYSRDC 86

Query: 94  LKMSGDSHKRVTIFKRGPGV------VTAGDIQTVNDIEVLNPDHV-----------ICN 136
                     V +  +  G       V + D+  V+++   N  H            IC 
Sbjct: 87  FCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICK 146

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES------- 189
           L     +++     KG     AK                 ++ +K   Y  E        
Sbjct: 147 LRKGQELKLTCVAKKGIAKEHAKWGPAAGIEFEYDP----WNKLKHTDYWYEQDSAKEWP 202

Query: 190 ----------AREGQVLDY----DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
                       EG   DY    D   M +++ GSI  +  V      LQ ++   +   
Sbjct: 203 QSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLAL 262

Query: 236 EPKKEVKEDINVKSLPFNPALLKKVEELELS 266
               + K +           +L   E++ ++
Sbjct: 263 TQMDQDKVNFASGDNNTASNMLGSNEDVMMT 293


>gi|299536426|ref|ZP_07049738.1| hypothetical protein BFZC1_10407 [Lysinibacillus fusiformis ZC1]
 gi|298727910|gb|EFI68473.1| hypothetical protein BFZC1_10407 [Lysinibacillus fusiformis ZC1]
          Length = 94

 Score = 39.2 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 15/55 (27%), Positives = 24/55 (43%)

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            +LS  + N      +  +  L   TE D+L+M   G  SL  ++  L  +GL  
Sbjct: 39  SKLSSPARNAFVHAGVDTLEKLSMYTEKDILKMHGIGPASLPFMRSSLKEVGLSF 93


>gi|300707120|ref|XP_002995782.1| hypothetical protein NCER_101243 [Nosema ceranae BRL01]
 gi|239604995|gb|EEQ82111.1| hypothetical protein NCER_101243 [Nosema ceranae BRL01]
          Length = 233

 Score = 39.2 bits (90), Expect = 1.0,   Method: Composition-based stats.
 Identities = 30/157 (19%), Positives = 62/157 (39%), Gaps = 20/157 (12%)

Query: 17  YIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIK 76
            I++ +  +N            +A    NALRR+L+S +    I  V+I+  ++  S   
Sbjct: 2   KILIEESTDNIIKFTLRDTYVSYA----NALRRILISEVPTVTIDLVEIE--INNTSLPD 55

Query: 77  GVHEDLTDI--ILNIKGINLK-------MSGDSHKRVTIFKR----GPGVVTAGDIQTVN 123
            +      +  +   K +  +       +       +T+        P VVT  D+++ +
Sbjct: 56  EMISHRLGLVPLYTKKDLVFRDDCACDDICDKCSVSLTLNVSNNTDMPMVVTCKDLKSQD 115

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
           D+ + +   VIC L     +++     KG G + +K 
Sbjct: 116 DVVIRSSP-VICKLGTRQNLKVICKAFKGVGKIHSKW 151


>gi|283471912|emb|CAQ51123.1| putative DNA-binding protein [Staphylococcus aureus subsp. aureus
           ST398]
          Length = 191

 Score = 38.8 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 10/50 (20%), Positives = 22/50 (44%)

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
            L  + I  + D+ Q T++ ++ M   G K++  ++  L    L     +
Sbjct: 13  ALNSQGIYTLEDVSQYTKSSLMEMHGVGPKAISILENALFQHQLHFKTEV 62


>gi|329766306|ref|ZP_08257853.1| RNA polymerase insert [Candidatus Nitrosoarchaeum limnia SFB1]
 gi|329137208|gb|EGG41497.1| RNA polymerase insert [Candidatus Nitrosoarchaeum limnia SFB1]
          Length = 212

 Score = 38.8 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 28/138 (20%), Positives = 49/138 (35%), Gaps = 16/138 (11%)

Query: 44  GNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIILNIKGINL 94
            NALRR+ ++ +   AI  V I         +G+ H +  I  +  DL+      K    
Sbjct: 26  ANALRRICLNGIPVFAIDTVDIIENSSVLPDEGLAHRLGLIP-LQTDLSRFNEPSKCDCK 84

Query: 95  KMSGDSHKRVTIFK-RGPGVVTA-----GDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
             +G S+ +V +    G   VT              ++  +    I  L     +++E  
Sbjct: 85  SETGCSNCKVMLVLDSGDSDVTRTILSNELTSEDESVKPTSDKIPIVQLAAGQRIKVECY 144

Query: 149 VSKGHGYVPAKHHRTEND 166
              G G   AK + +   
Sbjct: 145 ARLGRGTEHAKWNSSNIS 162


>gi|268324993|emb|CBH38581.1| putative DNA-directed RNA polymerase, subunit D [uncultured
           archaeon]
          Length = 213

 Score = 38.8 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 31/205 (15%), Positives = 71/205 (34%), Gaps = 49/205 (23%)

Query: 43  LGNALRRVLMSSLRGAAITAVQI-DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSH 101
             NALRRV+++ +   AI  + I +           +   L  +  ++K           
Sbjct: 24  FANALRRVMIAEVPKLAIDELNIRENTSLLYDEQLALRLALVPLKTDLKD------YKEE 77

Query: 102 KRVTIFKRGPGVVTAGDI------------------QTVNDIEVLNPDHVICNLDVDA-- 141
            ++T+  +      AG                    + +  +++++ +  I  +   A  
Sbjct: 78  DQITLTLKATSPEKAGHTMVYSKELISSYPKVEAASENIPIVKLISTEREIGAIKTVARQ 137

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            + ++     G G   AK                   P+    Y     +     D + L
Sbjct: 138 KIDLDAIARWGRGEEHAKWQ-----------------PVTICGY-----KNISDEDVNNL 175

Query: 202 SMTIDTDGSITGEDSVALASRILQD 226
             T+++DG++  ++ +  A+RI+Q+
Sbjct: 176 LFTVESDGALPVDEIILEAARIMQE 200


>gi|299139239|ref|ZP_07032415.1| transcription termination factor NusA [Acidobacterium sp. MP5ACTX8]
 gi|298598919|gb|EFI55081.1| transcription termination factor NusA [Acidobacterium sp. MP5ACTX8]
          Length = 544

 Score = 38.8 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 17/90 (18%), Positives = 36/90 (40%), Gaps = 4/90 (4%)

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGE 276
           V LA+++LQ ++ +    E+ ++  ++   +   P  P         EL       L   
Sbjct: 328 VRLAAKLLQWKIDIKSEEEKRQEVEQQMQAMTGGPSTPIEQV----TELGESVMEKLIAA 383

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            I  +  L   T  ++  +   G K++ +I
Sbjct: 384 GITTVESLADMTAEELGEVPGIGDKTVEKI 413


>gi|156371210|ref|XP_001628658.1| predicted protein [Nematostella vectensis]
 gi|156215640|gb|EDO36595.1| predicted protein [Nematostella vectensis]
          Length = 274

 Score = 38.8 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 47/274 (17%), Positives = 93/274 (33%), Gaps = 52/274 (18%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG----- 67
           N     +L   +EN    I     +    ++ N LRR+ ++     AI  VQI+      
Sbjct: 5   NQPSVKILELTDENV-KFII---EKT-GMSMANGLRRIFIAETPTIAIDWVQIENNTSVL 59

Query: 68  ----VLHEISSIKGVHEDLTDIILNIKG---------------INLKMSGDSHKRVT--- 105
               + H +  +    +++ D +   +                +++K + DS + VT   
Sbjct: 60  HDEFIAHRLGLVPLTSDEVVDRMTFSRDCTCDEFCDDCSIEFTLDVKCTDDSTRHVTTQD 119

Query: 106 -IFKRGPGV-VTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
            I      V VT+ + +  +   +   D +I  L     +++     KG     AK + T
Sbjct: 120 LISTNPRCVPVTSRNREDDSREYMEQDDILIVKLRKGQELKLRAFAKKGFAKEHAKWNPT 179

Query: 164 ENDPIGLITIDAL---------------YSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208
                     +AL               Y+ +++  Y    A        DK  + +++ 
Sbjct: 180 AGVAFEYDPDNALRHTTYPRPEEWPKSEYTELEEDQY---QAPFDPNAKADKFYINVESC 236

Query: 209 GSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
           GS+  E+ V     IL+ +L         +    
Sbjct: 237 GSLKPENIVLSGLAILKKKLSDLQTQHSHEVAAD 270


>gi|332184778|gb|AEE27032.1| Transcription termination protein NusA [Francisella cf. novicida
           3523]
          Length = 489

 Score = 38.8 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 13/64 (20%), Positives = 25/64 (39%)

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +       + K VE L++       L  E I  + DL     A++L +  F  + + 
Sbjct: 349 DAEQEEKQMSIVEKFVEALDIDHDFALVLIEEGIETLEDLAYLDRAELLEIEGFDEEIVD 408

Query: 305 EIKG 308
           E++ 
Sbjct: 409 ELQE 412


>gi|331211573|ref|XP_003307056.1| RNA polymerase II subunit 3 [Puccinia graminis f. sp. tritici CRL
           75-36-700-3]
 gi|309297459|gb|EFP74050.1| RNA polymerase II subunit 3 [Puccinia graminis f. sp. tritici CRL
           75-36-700-3]
          Length = 312

 Score = 38.8 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 34/147 (23%), Positives = 51/147 (34%), Gaps = 17/147 (11%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + + + ++     I E +  G    L N+LRR +++ L   AI +V       E      
Sbjct: 21  VKVTELDDQHAAFILEGIELG----LANSLRRTMIADLTTIAIHSV-------EFEENTS 69

Query: 78  VHED--LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVT-AGDIQTVNDIEVLNPDHV- 133
           V  D  +   +  I  I L         V        V+T   D     D+    P  V 
Sbjct: 70  VLPDEMIAHRLGLIPLIILSTKCTLVGDVLAVNSHDLVITPREDGAHRGDVG--KPYRVL 127

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKH 160
           I  L     VR++    KG G   AK 
Sbjct: 128 ITKLRKGQEVRLKCRAIKGIGQEHAKW 154


>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 = 38.8 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 16/70 (22%), Positives = 31/70 (44%), Gaps = 1/70 (1%)

Query: 244 DINVKSLPFNPALLKKVEELE-LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 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|91772121|ref|YP_564813.1| DNA-directed RNA polymerase subunit D [Methanococcoides burtonii
           DSM 6242]
 gi|91711136|gb|ABE51063.1| DNA-directed RNA polymerase subunit D [Methanococcoides burtonii
           DSM 6242]
          Length = 267

 Score = 38.8 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 29/173 (16%), Positives = 57/173 (32%), Gaps = 24/173 (13%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHT---LGNALRRVLMSSLRGAAITAVQIDGVLHE-IS 73
           I + +  +     I         +T     N +RR +++ +   AI  V I         
Sbjct: 3   IDILELSDRSAKFILS-------NTTAAFANGVRRAMLADVPTLAIDDVNIYNNTSVLYD 55

Query: 74  SIKGVHEDLTDIILNIKGINL--KMSGD------SHKRVTIFKR----GPGVVTAGDIQ- 120
               +   L  +  +        K + D          +T+       G  +V +GDI  
Sbjct: 56  EQLALRLGLIPLTTSFDDFVPQDKCTCDGAGCPACTVSLTLSVETDESGQTIVHSGDIVS 115

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITI 173
           +  +++  + +  I +L V   V +E     G+G   AK          ++ I
Sbjct: 116 SDPNVQPADKNIPIIDLRVGQKVVLEAIAHMGYGNKHAKWQAGVACGYKIMPI 168


>gi|118498223|ref|YP_899273.1| transcription elongation factor NusA [Francisella tularensis subsp.
           novicida U112]
 gi|194324407|ref|ZP_03058180.1| transcription termination factor NusA [Francisella tularensis
           subsp. novicida FTE]
 gi|208780250|ref|ZP_03247592.1| transcription termination factor NusA [Francisella novicida FTG]
 gi|118424129|gb|ABK90519.1| transcription elongation factor [Francisella novicida U112]
 gi|194321472|gb|EDX18957.1| transcription termination factor NusA [Francisella tularensis
           subsp. novicida FTE]
 gi|208743899|gb|EDZ90201.1| transcription termination factor NusA [Francisella novicida FTG]
          Length = 489

 Score = 38.8 bits (89), Expect = 1.4,   Method: Composition-based stats.
 Identities = 13/64 (20%), Positives = 25/64 (39%)

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +       + K VE L++       L  E I  + DL     A++L +  F  + + 
Sbjct: 349 DAEQEEKQMSIVEKFVEALDIDHDFALVLIEEGIETLEDLAYLDRAELLEIEGFDEEIVD 408

Query: 305 EIKG 308
           E++ 
Sbjct: 409 ELQE 412


>gi|187931005|ref|YP_001890989.1| transcription elongation factor NusA [Francisella tularensis subsp.
           mediasiatica FSC147]
 gi|187711914|gb|ACD30211.1| transcription termination factor NusA [Francisella tularensis
           subsp. mediasiatica FSC147]
          Length = 489

 Score = 38.8 bits (89), Expect = 1.4,   Method: Composition-based stats.
 Identities = 13/64 (20%), Positives = 25/64 (39%)

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +       + K VE L++       L  E I  + DL     A++L +  F  + + 
Sbjct: 349 DAEQEEKQMSIVEKFVEALDIDHDFALVLIEEGIETLEDLAYLDRAELLEIEGFDEEIVD 408

Query: 305 EIKG 308
           E++ 
Sbjct: 409 ELQE 412


>gi|254375031|ref|ZP_04990511.1| transcription elongation factor [Francisella novicida GA99-3548]
 gi|151572749|gb|EDN38403.1| transcription elongation factor [Francisella novicida GA99-3548]
          Length = 489

 Score = 38.8 bits (89), Expect = 1.4,   Method: Composition-based stats.
 Identities = 13/64 (20%), Positives = 25/64 (39%)

Query: 245 INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
              +       + K VE L++       L  E I  + DL     A++L +  F  + + 
Sbjct: 349 DAEQEEKQMSIVEKFVEALDIDHDFALVLIEEGIETLEDLAYLDRAELLEIEGFDEEIVD 408

Query: 305 EIKG 308
           E++ 
Sbjct: 409 ELQE 412


>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 = 1.4,   Method: Composition-based stats.
 Identities = 23/134 (17%), Positives = 53/134 (39%), Gaps = 16/134 (11%)

Query: 44  GNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIILNIKGINL 94
            NALRR+ ++ +   A+  V I         +G+ H +  I  +  D ++   N+  I+ 
Sbjct: 26  ANALRRICLNGVPVFAVDTVDIVENTSVLADEGLAHRLGLIP-LRTDSSEF-KNLAEIDP 83

Query: 95  KMSGDSHKRVTIF----KRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVS 150
               +    +T+          V+++  +   + ++ ++    I  L     +++E    
Sbjct: 84  DDPINR-VMLTLDSGEAAETRTVLSSELVSEDSSVKPISDTIPIVELAPGQRIKVEAYAR 142

Query: 151 KGHGYVPAKHHRTE 164
            G G   AK + + 
Sbjct: 143 LGRGTEHAKWNSSN 156


>gi|91094813|ref|XP_970635.1| PREDICTED: similar to DNA-directed RNA polymerase II subunit
           [Tribolium castaneum]
 gi|270006567|gb|EFA03015.1| hypothetical protein TcasGA2_TC010438 [Tribolium castaneum]
          Length = 274

 Score = 38.4 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 43/259 (16%), Positives = 91/259 (35%), Gaps = 57/259 (22%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHT---LGNALRRVLMSSLRGAAITAVQIDG------- 67
           + +    ++      E        T   + N++RRVL++     AI  V+++        
Sbjct: 9   VHITDLTDDNVKFYIE-------DTDLSVANSIRRVLIAETPTLAIDWVKLEANSTVLSD 61

Query: 68  --VLHEISSIKGVHEDLTDIILNIKG---------------INLKMSGDSHKRVT---IF 107
             + H I  I  + +D+   +   +                +++K + D  + VT   + 
Sbjct: 62  EFLAHRIGLIPLISDDVVQRLQYPRDCICTDFCHECSVEFTLDVKCTDDHTRHVTTADLK 121

Query: 108 KRGPGVVTA-GDIQTVNDIEVLNPDHV-ICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
              P V+ A    +     E  + D + I  L     ++++    KG G   AK + T  
Sbjct: 122 SSDPRVIPATSKHRDDESSEYGDTDEILIIKLRKGQELKVKAYAKKGFGKEHAKWNPTAG 181

Query: 166 DPIGLITIDAL---------------YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS 210
                   +A+               YS + +  Y  +       L  +K    ++  G+
Sbjct: 182 VAFEYDPDNAMRHTLFPKPDEWPKSEYSELDEDQYEADFNW---ELKPNKFYFNVEAAGA 238

Query: 211 ITGEDSVALASRILQDQLG 229
           +  E+ V +   +L+D+L 
Sbjct: 239 LKPENIVIMGVAMLKDKLS 257


>gi|224141187|ref|XP_002323956.1| predicted protein [Populus trichocarpa]
 gi|222866958|gb|EEF04089.1| predicted protein [Populus trichocarpa]
          Length = 73

 Score = 38.4 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 13/62 (20%), Positives = 25/62 (40%), Gaps = 3/62 (4%)

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVL 196
           L     + + L + + HGY        +N   G  +IDA++  ++  ++ V S   G   
Sbjct: 9   LKEPIDLHIGLEIERNHGYC---MKPPKNFQDGSYSIDAIFMHVRNANHNVHSYGNGNEK 65

Query: 197 DY 198
             
Sbjct: 66  SQ 67


>gi|301310999|ref|ZP_07216928.1| conserved hypothetical protein [Bacteroides sp. 20_3]
 gi|300831062|gb|EFK61703.1| conserved hypothetical protein [Bacteroides sp. 20_3]
          Length = 301

 Score = 38.4 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 4/53 (7%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTE----ADMLRMANFGRKSLVEIKGVLGTM 313
           LS     CL+   +  M DL++         +L++  FG   L ++K  L   
Sbjct: 228 LSPYIRKCLQKLELETMEDLLRYARKKGLDSLLKIPGFGPLGLDQLKFQLEKH 280


>gi|302833623|ref|XP_002948375.1| hypothetical protein VOLCADRAFT_88650 [Volvox carteri f.
           nagariensis]
 gi|300266595|gb|EFJ50782.1| hypothetical protein VOLCADRAFT_88650 [Volvox carteri f.
           nagariensis]
          Length = 272

 Score = 38.4 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 43/266 (16%), Positives = 86/266 (32%), Gaps = 49/266 (18%)

Query: 44  GNALRRVLMSSLRGAAITAVQIDG----VLHEI-SSIKGVHEDLTDIILNIKGINLKMSG 98
            NALRRV+++ +   AI  V+++     +  E  +   G+   ++   +  K      + 
Sbjct: 13  ANALRRVMIAEVPTIAIDLVEMENNTTVLNDEFLAHRLGLLPLVSTEAVAWKRPFEWSND 72

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDH---------------VICNLDVDAVV 143
                          V      T ND+  LNP+H               VIC +     +
Sbjct: 73  ADMIETAFSLDVTCTVDGVMDVTSNDLVPLNPEHGVFPVNYQNPDEKPIVICKMRRGQQL 132

Query: 144 RMELTVSKGHGYVPAKHHRTENDPIGLITI-DALYSPIKKVSYTVESAREGQVLDYDKLS 202
           ++     KG G           D    I +  A++    K    +  +   ++ D +K  
Sbjct: 133 KLVARARKGIG----------KDHAKFIPVATAVFQ--YKPRIVLSHSAMAEMTDEEKQI 180

Query: 203 MTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKK--V 260
             + +D S T +                     E + E     + + L     L +   V
Sbjct: 181 F-VHSDPSKTFK-------------FNPITRMIEVENEEAYMYDEECLVKARELGRPDLV 226

Query: 261 EELELSVRSTNCLRGENIVYMGDLIQ 286
              +L       + G  ++ + D+++
Sbjct: 227 TITQLQDHFIFRVEGTGVLRVADIVR 252


>gi|152992166|ref|YP_001357887.1| isocitrate dehydrogenase, NADP-dependent [Sulfurovum sp. NBC37-1]
 gi|151424027|dbj|BAF71530.1| isocitrate dehydrogenase, NADP-dependent [Sulfurovum sp. NBC37-1]
          Length = 727

 Score = 38.4 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 25/119 (21%), Positives = 49/119 (41%), Gaps = 17/119 (14%)

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGE 276
           +  A  +    L   ++       V    +  SL         + E ELS          
Sbjct: 11  IDEAPALATYSLLPIVSKFTNAAGVDVKTSDISLAGRVLAAMGLAEDELSK--------- 61

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP--PESIEELA 333
               +G+L+ + EA+++++ N    S+ ++K  +  +    G ++PD+P  PE+ EE A
Sbjct: 62  ----LGELVHKPEANIIKLPNISA-SIGQLKECIAELQ-SQGFDIPDFPENPETEEEKA 114


>gi|268592826|ref|ZP_06127047.1| L factor [Providencia rettgeri DSM 1131]
 gi|291311611|gb|EFE52064.1| L factor [Providencia rettgeri DSM 1131]
          Length = 502

 Score = 38.4 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 19/126 (15%), Positives = 46/126 (36%), Gaps = 9/126 (7%)

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGE 276
           V LA+++L+        +E      +E         + ++    + L++       L  E
Sbjct: 325 VRLAAQLLKKH-RGDDKWELNVMTAEELNAKHQAEAHASIDTFTKHLDIDEEFATALVEE 383

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEIKG----VLGTMGL----FLGMNLPDWPPES 328
               + +L      ++L +     +++  ++      L T+ L     LG N P     +
Sbjct: 384 GFSTLEELAYVPINELLEIDGLDEETVEVLRERAKAALTTIELAQKESLGDNQPAEDLLN 443

Query: 329 IEELAK 334
           +E + +
Sbjct: 444 LEGMDR 449


>gi|150009203|ref|YP_001303946.1| hypothetical protein BDI_2605 [Parabacteroides distasonis ATCC
           8503]
 gi|149937627|gb|ABR44324.1| conserved hypothetical protein [Parabacteroides distasonis ATCC
           8503]
          Length = 301

 Score = 38.4 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 4/53 (7%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTE----ADMLRMANFGRKSLVEIKGVLGTM 313
           LS     CL+   +  M DL++         +L++  FG   L ++K  L   
Sbjct: 228 LSPYIRKCLQKLELETMEDLLRYARKKGLDSLLKIPGFGPLGLDQLKFQLEKH 280


>gi|298377009|ref|ZP_06986963.1| conserved hypothetical protein [Bacteroides sp. 3_1_19]
 gi|298265993|gb|EFI07652.1| conserved hypothetical protein [Bacteroides sp. 3_1_19]
          Length = 303

 Score = 38.4 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 4/53 (7%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTE----ADMLRMANFGRKSLVEIKGVLGTM 313
           LS     CL+   +  M DL++         +L++  FG   L ++K  L   
Sbjct: 230 LSPYIRKCLQKLELETMEDLLRYARKKGLDSLLKIPGFGPLGLDQLKFQLEKH 282


>gi|255015810|ref|ZP_05287936.1| hypothetical protein B2_18033 [Bacteroides sp. 2_1_7]
 gi|256841759|ref|ZP_05547265.1| conserved hypothetical protein [Parabacteroides sp. D13]
 gi|256736653|gb|EEU49981.1| conserved hypothetical protein [Parabacteroides sp. D13]
          Length = 303

 Score = 38.4 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 4/53 (7%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTE----ADMLRMANFGRKSLVEIKGVLGTM 313
           LS     CL+   +  M DL++         +L++  FG   L ++K  L   
Sbjct: 230 LSPYIRKCLQKLELETMEDLLRYARKKGLDSLLKIPGFGPLGLDQLKFQLEKH 282


>gi|262384091|ref|ZP_06077227.1| conserved hypothetical protein [Bacteroides sp. 2_1_33B]
 gi|262294989|gb|EEY82921.1| conserved hypothetical protein [Bacteroides sp. 2_1_33B]
          Length = 301

 Score = 38.4 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 4/53 (7%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTE----ADMLRMANFGRKSLVEIKGVLGTM 313
           LS     CL+   +  M DL++         +L++  FG   L ++K  L   
Sbjct: 228 LSPYIRKCLQKLELETMEDLLRYARKKGLDSLLKIPGFGPLGLDQLKFQLEKH 280


>gi|119872211|ref|YP_930218.1| RNA polymerase, insert [Pyrobaculum islandicum DSM 4184]
 gi|166229321|sp|A1RSE3|RPOD_PYRIL RecName: Full=DNA-directed RNA polymerase subunit D
 gi|119673619|gb|ABL87875.1| DNA-directed RNA polymerase, subunit D [Pyrobaculum islandicum DSM
           4184]
          Length = 262

 Score = 38.4 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 36/218 (16%), Positives = 66/218 (30%), Gaps = 33/218 (15%)

Query: 45  NALRRVLMSSLRGAAITAVQI-DGVLHEISSIKGVHEDLTDIILNIK--------GINLK 95
           N++RRV++S L   AI  V I          +      L  +   ++           L 
Sbjct: 27  NSIRRVIISELPVMAIDYVVIVSNTSVMYDEMLAHRLGLVPLTTPLQALPPIEDCETGLV 86

Query: 96  MSGDSHK--RVTIFKRGPGVVTAGDIQTV-NDIEVLNPDHVICNLDVDAVVRMELTVSKG 152
              +      + I      +V +GD+ +   D+  +  D  I  L     + +E     G
Sbjct: 87  DPSECTVRLMLQINAESDKIVYSGDLVSERPDVVPVYKDIPIVKLVKGQSIILEAYAKLG 146

Query: 153 HGYVPAKHHRTENDPIGLITI------------DALYSPIKKVSYTVESAREGQVLDYDK 200
                AK             I            D           T   A   + +  D+
Sbjct: 147 RAKEHAKWQAALASYYYYPRIKVLDEKCKEECKDICKELTNPFECTFNKAWTCRDICGDR 206

Query: 201 LSMT---------IDTDGSITGEDSVALASRILQDQLG 229
           L +          +++ G+   E ++  A RIL+ +  
Sbjct: 207 LIVEWDRYKYVFWVESFGNYDVETALREAFRILKKKFS 244


>gi|160886398|ref|ZP_02067401.1| hypothetical protein BACOVA_04409 [Bacteroides ovatus ATCC 8483]
 gi|156108283|gb|EDO10028.1| hypothetical protein BACOVA_04409 [Bacteroides ovatus ATCC 8483]
          Length = 288

 Score = 38.4 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 19/91 (20%), Positives = 34/91 (37%), Gaps = 9/91 (9%)

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
            +  E  +   +  I          L   + EL+  +RS   +   +I  + +L+Q T  
Sbjct: 184 MLMREAEETNPEIFIPEDIKAAKALLDTPITELKFDIRSQRIISEADIKTLRELLQITSQ 243

Query: 291 -------DMLRMANFGRKSLVEIKGVLGTMG 314
                  DML   NFG  S  +++  L  + 
Sbjct: 244 YGFRKLRDML--RNFGLVSQKKVEKRLKELN 272


>gi|326933967|ref|XP_003213069.1| PREDICTED: integrin beta-3-like [Meleagris gallopavo]
          Length = 781

 Score = 38.0 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 8/72 (11%)

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD--------WPPES 328
           +I Y+ DL    + D+  + N G K   E++ +   + +  G  +           PPE+
Sbjct: 131 DIYYLMDLSNSMKDDLRNIQNLGTKLASEMRKLTSNLRIGFGAFVDKPISPYMYISPPEA 190

Query: 329 IEELAKKYEDKC 340
           I     +  +KC
Sbjct: 191 IRNPCYEIGEKC 202


>gi|321475674|gb|EFX86636.1| hypothetical protein DAPPUDRAFT_313021 [Daphnia pulex]
          Length = 274

 Score = 38.0 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 40/231 (17%), Positives = 76/231 (32%), Gaps = 44/231 (19%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQIDGVLH----EI-SSIKGVH-----EDLTDIILNIK 90
            ++ N+LRRV ++     AI  VQ +        E  +   G+      E +  +  +  
Sbjct: 28  LSVANSLRRVFIAETPTLAIDWVQFEANSTVLFDEFLAHRVGLIPLTSDESVEKMQYSRD 87

Query: 91  GINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNP-------------------D 131
                   D     T+  +    VT     T  D++  +P                   +
Sbjct: 88  CTCPDFCVDCSVEFTLDVKCSEDVTRN--VTTADLKSTDPRVVPATSKRDEEPPDDNDNE 145

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI-------KKVS 184
            +I  L     ++M     KG G   AK + T          ++L   +        +  
Sbjct: 146 ILIVKLRKGQELKMRAYAKKGFGKEHAKWNPTAGVAFEYDPDNSLRHTLFPKPEEWPRSE 205

Query: 185 YTVESAREGQVLDYD------KLSMTIDTDGSITGEDSVALASRILQDQLG 229
           Y+     +     YD      K  + +++ GS+  E+ V +   IL+ +L 
Sbjct: 206 YSELGESDQHQAPYDPDGKPNKFFVNVESCGSLRPENIVLMGIAILKKKLS 256


>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 = 38.0 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 15/96 (15%), Positives = 30/96 (31%), Gaps = 4/96 (4%)

Query: 212 TGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTN 271
              +    A    +D L  +    +           + +         + EL+ SV + N
Sbjct: 763 DFRERFDNA----EDMLRDWRKIFDQADTQTAADPFEVIALRATRETAIGELDYSVEAQN 818

Query: 272 CLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            L    I  + +L+         + + G K   EI+
Sbjct: 819 VLDRMGIHSVRELLAVDRVRFRYLKSVGDKVRKEIR 854


>gi|281358582|ref|ZP_06245061.1| DNA ligase (NAD(+)) [Victivallis vadensis ATCC BAA-548]
 gi|281314930|gb|EFA98964.1| DNA ligase (NAD(+)) [Victivallis vadensis ATCC BAA-548]
          Length = 626

 Score = 38.0 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 15/64 (23%), Positives = 29/64 (45%), Gaps = 6/64 (9%)

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS----LVEIKG--VLGTMGLFLGM 319
                  +    + ++GDL + T  D+LR+  F  KS    + EI+   ++    L   +
Sbjct: 405 EPTLRKLMENSGVRHLGDLFELTAMDLLRLDGFAAKSAANLIEEIQKARIVNDYQLLAAL 464

Query: 320 NLPD 323
           N+P+
Sbjct: 465 NIPN 468


>gi|66517558|ref|XP_624836.1| PREDICTED: DNA-directed RNA polymerase II subunit RPB3-like [Apis
           mellifera]
          Length = 276

 Score = 38.0 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 40/256 (15%), Positives = 86/256 (33%), Gaps = 51/256 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------V 68
           + +    E       E        ++ N++RRV ++     AI  +Q++          +
Sbjct: 9   VHISDLTEENVKFQVEDTE----LSVANSMRRVFIAETPTMAIDWIQLEANSTVLSDEFL 64

Query: 69  LHEISSIKGVHEDLTDIILNIKG---------------INLKMSGDSHKRV-TIFKRGPG 112
            H I  I  + +D+ D I   +                +++K + D  + V T   +   
Sbjct: 65  AHRIGMIPLISDDVVDRIQYTRDCQCMDFCPECSVEFTLDVKCTEDQTRHVTTADFKSSD 124

Query: 113 ----VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
                VT+   +          + +I  L     +++     KG G   AK + T     
Sbjct: 125 PRVLPVTSRHREDDASEYGETDEILIVKLRKGQELKLRAYAKKGFGKEHAKWNPTAGVSF 184

Query: 169 GLITIDAL---------------YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
                +A+               YS +++  Y      E +   Y      +++ G++  
Sbjct: 185 EYDPDNAMRHTLFPKPDEWPKSEYSELEEDQYEAPFNWEAKPNKY---YFNVESSGALKP 241

Query: 214 EDSVALASRILQDQLG 229
           E+ V +    L+++L 
Sbjct: 242 ENIVMMGIAALKNKLS 257


>gi|319956111|ref|YP_004167374.1| isocitrate dehydrogenase, nADP-dependent [Nitratifractor salsuginis
           DSM 16511]
 gi|319418515|gb|ADV45625.1| isocitrate dehydrogenase, NADP-dependent [Nitratifractor salsuginis
           DSM 16511]
          Length = 728

 Score = 38.0 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 15/59 (25%), Positives = 32/59 (54%), Gaps = 2/59 (3%)

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
           +G+L+ + EA+++++ N    SL ++K  +  +    G ++PD+P     E  K+   K
Sbjct: 63  LGELVHKPEANIIKLPNISA-SLTQLKECIAELQEH-GHDIPDYPENPQTEEEKQIAAK 119


>gi|257471948|pdb|3I4M|C Chain C, 8-Oxoguanine Containing Rna Polymerase Ii Elongation
           Complex D
 gi|257471963|pdb|3I4N|C Chain C, 8-Oxoguanine Containing Rna Polymerase Ii Elongation
           Complex E
          Length = 324

 Score = 38.0 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 46/268 (17%), Positives = 88/268 (32%), Gaps = 47/268 (17%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTDIILNIKGIN 93
           + N+LRRV+++ +   AI +V+++          + H +  I    + +    L      
Sbjct: 35  MANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIP--LQSMDIEQLEYSRDC 92

Query: 94  LKMSGDSHKRVTIFKRGPGV------VTAGDIQTVNDIEVLNPDHV-----------ICN 136
                     V +  +  G       V + D+  V+++   N  H            IC 
Sbjct: 93  FCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICK 152

Query: 137 LDVDAVVRMELTVSKGHG-----YVPAKHHRTENDP-------IGLITIDAL--YSPIKK 182
           L     +++     KG       + PA     E DP             D+   +   K 
Sbjct: 153 LRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKN 212

Query: 183 VSYTVESAREGQVLDY----DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
             Y  +   EG   DY    D   M +++ GSI  +  V      LQ ++   +      
Sbjct: 213 CEYE-DPPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQM 271

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELS 266
            + K +           +L   E++ ++
Sbjct: 272 DQDKVNFASGDNNTASNMLGSNEDVMMT 299


>gi|6322168|ref|NP_012243.1| Rpb3p [Saccharomyces cerevisiae S288c]
 gi|730603|sp|P16370|RPB3_YEAST RecName: Full=DNA-directed RNA polymerase II subunit RPB3;
           Short=RNA polymerase II subunit 3; Short=RNA polymerase
           II subunit B3; AltName: Full=B44.5; AltName:
           Full=DNA-directed RNA polymerase II 45 kDa polypeptide
 gi|14278326|pdb|1I3Q|C Chain C, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
 gi|14278337|pdb|1I50|C Chain C, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
 gi|14278367|pdb|1I6H|C Chain C, Rna Polymerase Ii Elongation Complex
 gi|20150715|pdb|1K83|C Chain C, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
           With The Inhibitor Alpha Amanitin
 gi|30749618|pdb|1NIK|C Chain C, Wild Type Rna Polymerase Ii
 gi|30749739|pdb|1NT9|C Chain C, Complete 12-Subunit Rna Polymerase Ii
 gi|34810555|pdb|1PQV|C Chain C, Rna Polymerase Ii-Tfiis Complex
 gi|46015417|pdb|1R5U|C Chain C, Rna Polymerase Ii Tfiib Complex
 gi|46015782|pdb|1SFO|C Chain C, Rna Polymerase Ii Strand Separated Elongation Complex
 gi|56965913|pdb|1R9S|C Chain C, Rna Polymerase Ii Strand Separated Elongation Complex,
           Matched Nucleotide
 gi|56965925|pdb|1R9T|C Chain C, Rna Polymerase Ii Strand Separated Elongation Complex,
           Mismatched Nucleotide
 gi|56966109|pdb|1TWA|C Chain C, Rna Polymerase Ii Complexed With Atp
 gi|56966123|pdb|1TWC|C Chain C, Rna Polymerase Ii Complexed With Gtp
 gi|56966133|pdb|1TWF|C Chain C, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
 gi|56966143|pdb|1TWG|C Chain C, Rna Polymerase Ii Complexed With Ctp
 gi|56966153|pdb|1TWH|C Chain C, Rna Polymerase Ii Complexed With 2'datp
 gi|58177166|pdb|1WCM|C Chain C, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
 gi|61679446|pdb|1Y1W|C Chain C, Complete Rna Polymerase Ii Elongation Complex
 gi|61679463|pdb|1Y77|C Chain C, Complete Rna Polymerase Ii Elongation Complex With
           Substrate Analogue Gmpcpp
 gi|61679504|pdb|1Y1V|C Chain C, Refined Rna Polymerase Ii-Tfiis Complex
 gi|61679517|pdb|1Y1Y|C Chain C, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
 gi|83754245|pdb|2B63|C Chain C, Complete Rna Polymerase Ii-Rna Inhibitor Complex
 gi|110590856|pdb|2B8K|C Chain C, 12-Subunit Rna Polymerase Ii
 gi|122920063|pdb|2E2H|C Chain C, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
 gi|122920078|pdb|2E2I|C Chain C, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
           Dgtp
 gi|122920093|pdb|2E2J|C Chain C, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
           Gmpcpp
 gi|122921032|pdb|2NVQ|C Chain C, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
           2'dutp
 gi|122921068|pdb|2NVT|C Chain C, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
           Gmpcpp
 gi|122921084|pdb|2NVX|C Chain C, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
           Dutp
 gi|122921099|pdb|2NVY|C Chain C, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
 gi|122921111|pdb|2NVZ|C Chain C, Rna Polymerase Ii Elongation Complex With Utp, Updated
           112006
 gi|134104676|pdb|2JA5|C Chain C, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           A
 gi|134104691|pdb|2JA6|C Chain C, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           B
 gi|134104712|pdb|2JA7|C Chain C, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           C
 gi|134104724|pdb|2JA7|O Chain O, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           C
 gi|134104736|pdb|2JA8|C Chain C, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           D
 gi|146387186|pdb|2YU9|C Chain C, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
           Utp
 gi|160877775|pdb|2R7Z|C Chain C, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
           Complex
 gi|161172229|pdb|2R92|C Chain C, Elongation Complex Of Rna Polymerase Ii With Artificial
           Rdrp Scaffold
 gi|161172242|pdb|2R93|C Chain C, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
           Delta Virus-Derived Rna Stem Loop
 gi|190613464|pdb|2VUM|C Chain C, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
           Elongation Complex
 gi|194368736|pdb|3CQZ|C Chain C, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
           Complex With The Inhibitor Alpha-Amanitin
 gi|224983592|pdb|3FKI|C Chain C, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
 gi|239781918|pdb|3GTG|C Chain C, Backtracked Rna Polymerase Ii Complex With 12mer Rna
 gi|239781931|pdb|3GTJ|C Chain C, Backtracked Rna Polymerase Ii Complex With 13mer Rna
 gi|239781944|pdb|3GTK|C Chain C, Backtracked Rna Polymerase Ii Complex With 18mer Rna
 gi|239781957|pdb|3GTL|C Chain C, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
           Mismatch
 gi|239781970|pdb|3GTM|C Chain C, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
 gi|239781984|pdb|3GTO|C Chain C, Backtracked Rna Polymerase Ii Complex With 15mer Rna
 gi|239781997|pdb|3GTP|C Chain C, Backtracked Rna Polymerase Ii Complex With 24mer Rna
 gi|239782010|pdb|3GTQ|C Chain C, Backtracked Rna Polymerase Ii Complex Induced By Damage
 gi|240104513|pdb|3H3V|D Chain D, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
           Active Site
 gi|254839443|pdb|3HOU|C Chain C, Complete Rna Polymerase Ii Elongation Complex I With A T-U
           Mismatch
 gi|254839458|pdb|3HOU|O Chain O, Complete Rna Polymerase Ii Elongation Complex I With A T-U
           Mismatch
 gi|254839473|pdb|3HOV|C Chain C, Complete Rna Polymerase Ii Elongation Complex Ii
 gi|266618767|pdb|3K1F|C Chain C, Crystal Structure Of Rna Polymerase Ii In Complex With
           Tfiib
 gi|269914554|pdb|3K7A|C Chain C, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
 gi|295982477|pdb|3M3Y|C Chain C, Rna Polymerase Ii Elongation Complex C
 gi|295982490|pdb|3M4O|C Chain C, Rna Polymerase Ii Elongation Complex B
 gi|325053965|pdb|3PO2|C Chain C, Arrested Rna Polymerase Ii Elongation Complex
 gi|325053980|pdb|3PO3|C Chain C, Arrested Rna Polymerase Ii Reactivation Intermediate
 gi|326634540|pdb|3QT1|C Chain C, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
           Subunit
 gi|599978|emb|CAA86971.1| RNA polymerase II [Saccharomyces cerevisiae]
 gi|151943136|gb|EDN61471.1| RNA polymerase B [Saccharomyces cerevisiae YJM789]
 gi|190406243|gb|EDV09510.1| RNA polymerase II 45 kDa subunit [Saccharomyces cerevisiae RM11-1a]
 gi|207344276|gb|EDZ71474.1| YIL021Wp-like protein [Saccharomyces cerevisiae AWRI1631]
 gi|256272154|gb|EEU07153.1| Rpb3p [Saccharomyces cerevisiae JAY291]
 gi|259147237|emb|CAY80490.1| Rpb3p [Saccharomyces cerevisiae EC1118]
 gi|285812625|tpg|DAA08524.1| TPA: Rpb3p [Saccharomyces cerevisiae S288c]
 gi|323333059|gb|EGA74460.1| Rpb3p [Saccharomyces cerevisiae AWRI796]
 gi|323354620|gb|EGA86456.1| Rpb3p [Saccharomyces cerevisiae VL3]
          Length = 318

 Score = 38.0 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 46/268 (17%), Positives = 88/268 (32%), Gaps = 47/268 (17%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTDIILNIKGIN 93
           + N+LRRV+++ +   AI +V+++          + H +  I    + +    L      
Sbjct: 29  MANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIP--LQSMDIEQLEYSRDC 86

Query: 94  LKMSGDSHKRVTIFKRGPGV------VTAGDIQTVNDIEVLNPDHV-----------ICN 136
                     V +  +  G       V + D+  V+++   N  H            IC 
Sbjct: 87  FCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICK 146

Query: 137 LDVDAVVRMELTVSKGHG-----YVPAKHHRTENDP-------IGLITIDAL--YSPIKK 182
           L     +++     KG       + PA     E DP             D+   +   K 
Sbjct: 147 LRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKN 206

Query: 183 VSYTVESAREGQVLDY----DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
             Y  +   EG   DY    D   M +++ GSI  +  V      LQ ++   +      
Sbjct: 207 CEYE-DPPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQM 265

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELS 266
            + K +           +L   E++ ++
Sbjct: 266 DQDKVNFASGDNNTASNMLGSNEDVMMT 293


>gi|189199142|ref|XP_001935908.1| DNA-directed RNA polymerase subunit D [Pyrenophora tritici-repentis
           Pt-1C-BFP]
 gi|187983007|gb|EDU48495.1| DNA-directed RNA polymerase subunit D [Pyrenophora tritici-repentis
           Pt-1C-BFP]
          Length = 334

 Score = 38.0 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 41/260 (15%), Positives = 79/260 (30%), Gaps = 57/260 (21%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI--------TAVQIDG-VLHEI 72
           +    R   I +           N+LRRV++S +   AI        T+V  D  V H +
Sbjct: 16  EANSQRASFIVQNFN----LETANSLRRVMLSEIPTLAIDVVEVLDNTSVLADEFVCHRL 71

Query: 73  SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG----VVTAGDIQTVN----- 123
             +    + + D+I +          +    +++  +  G     V A D+   +     
Sbjct: 72  GLVPLSSKGVDDLIYSRDCDCEGYCDNCAVVLSLNAKCTGSEIMKVYARDLVIESRTPND 131

Query: 124 DI---EVLNPD---HVICNLDVDAVVRMELTVSKGHGYVPAKHHRT-------------- 163
           ++    + + +     I  L     + M     KG     AK   +              
Sbjct: 132 EVGKPVITDSEGTGSCIVKLRRGQAINMRCIAKKGIAKEHAKWAPSAAIGFEYDPANKLH 191

Query: 164 ------ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD----KLSMTIDTDGSITG 213
                 E DP      D       +++         +  D+D    +    ++T G I  
Sbjct: 192 HLDYWHEEDPEKEWPKDEA-----RINLDGGPENPDERFDFDAVPTRFFYDVETVGGIDP 246

Query: 214 EDSVALASRILQDQLGMFIN 233
           +  V      LQ +L   + 
Sbjct: 247 DQIVTKGIHRLQLKLAEIVQ 266


>gi|228982978|ref|ZP_04143237.1| RNA polymerase alpha subunit [Bacillus thuringiensis Bt407]
 gi|228777161|gb|EEM25469.1| RNA polymerase alpha subunit [Bacillus thuringiensis Bt407]
          Length = 85

 Score = 38.0 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 14/37 (37%), Positives = 23/37 (62%)

Query: 259 KVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRM 295
            +EEL+L   +   L+  NI  + DL+Q+TE D ++M
Sbjct: 12  PIEELKLQACTNRLLKQNNIHSLYDLLQKTEDDFMKM 48


>gi|328785531|ref|XP_625072.3| PREDICTED: DNA-directed RNA polymerases I and III subunit
          RPAC1-like [Apis mellifera]
          Length = 510

 Score = 38.0 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 22/61 (36%), Gaps = 5/61 (8%)

Query: 5  NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
          N     K   I+ +    E+             G+     NA RRVL+S +   AI  V 
Sbjct: 32 NLSNFKKEFKIQVMR-ESEDTRELEFDL----IGYPVGFANAFRRVLLSEVPTMAIEKVY 86

Query: 65 I 65
          I
Sbjct: 87 I 87


>gi|225851246|ref|YP_002731480.1| isocitrate dehydrogenase, NADP-dependent [Persephonella marina
           EX-H1]
 gi|225646248|gb|ACO04434.1| isocitrate dehydrogenase, NADP-dependent [Persephonella marina
           EX-H1]
          Length = 747

 Score = 38.0 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 17/59 (28%), Positives = 33/59 (55%), Gaps = 2/59 (3%)

Query: 280 YMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           YMG+L+ + EA+++++ N    S+ ++K  +  +    G  LPD+P     E  KK ++
Sbjct: 68  YMGELVWKPEANIMKLPNISA-SVPQLKEAIKELQEQ-GYPLPDYPENPQTEEEKKIKE 124


>gi|326389369|ref|ZP_08210937.1| DNA-directed DNA polymerase [Thermoanaerobacter ethanolicus JW 200]
 gi|325994732|gb|EGD53156.1| DNA-directed DNA polymerase [Thermoanaerobacter ethanolicus JW 200]
          Length = 389

 Score = 38.0 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 13/109 (11%), Positives = 43/109 (39%), Gaps = 2/109 (1%)

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           +D +   + ++    +     + +++ +  ++    +  +  K +    I    +P    
Sbjct: 112 IDKNPEIIALEIKKKVKETTGLTISAGVSYNKFLAKLASDWNKPDGFMVITEDMIPDILK 171

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
            L   +   +  +S   L+   I  + DL++ ++  ++ +  FG+  L 
Sbjct: 172 PLPVSKVYGIGEKSEQKLKAMGINTIDDLLKLSQESLIEI--FGKLGLE 218


>gi|260173471|ref|ZP_05759883.1| hypothetical protein BacD2_16485 [Bacteroides sp. D2]
 gi|299146878|ref|ZP_07039946.1| hypothetical protein HMPREF9010_02358 [Bacteroides sp. 3_1_23]
 gi|315921741|ref|ZP_07917981.1| conserved hypothetical protein [Bacteroides sp. D2]
 gi|298517369|gb|EFI41250.1| hypothetical protein HMPREF9010_02358 [Bacteroides sp. 3_1_23]
 gi|313695616|gb|EFS32451.1| conserved hypothetical protein [Bacteroides sp. D2]
          Length = 288

 Score = 38.0 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 19/91 (20%), Positives = 33/91 (36%), Gaps = 9/91 (9%)

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
               E  +   +  I          L   + EL+  +RS   +   +I  + +L+Q T  
Sbjct: 184 MFMREAEETNPEIFIPEDIKAAKALLDTPITELKFDIRSQRIISEADIKTLRELLQITSQ 243

Query: 291 -------DMLRMANFGRKSLVEIKGVLGTMG 314
                  DML   NFG  S  +++  L  + 
Sbjct: 244 YGFRKLRDML--RNFGLVSQKKVEKRLKELN 272


>gi|221113635|ref|XP_002157486.1| PREDICTED: similar to predicted protein [Hydra magnipapillata]
          Length = 289

 Score = 38.0 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 34/189 (17%), Positives = 65/189 (34%), Gaps = 36/189 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---VLH-EI- 72
           + + +  ++    I E        ++ N+LRR+ ++ +   AI  VQI+    VLH E  
Sbjct: 9   VKILEWTDDNLKFILENTD----LSVANSLRRIFIAEVPTIAIDWVQIENNTSVLHDEFI 64

Query: 73  SSIKGVH-----EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
           +   G+      E +  +  +      +   +   + T+  +  G  T     T  D+  
Sbjct: 65  AHRIGLIPLTSDEKVDKMCYSRDCTCSEFCDECSVKFTLDVKCTGETTR--HVTSRDLIS 122

Query: 128 LNP--------------------DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
            +P                    + VI  L     +++     KG G   AK + T    
Sbjct: 123 EDPKVIPVTSRIKDDDTGYGETDEIVIVKLRKGQELKLHAFAKKGFGKEHAKWNPTAGVS 182

Query: 168 IGLITIDAL 176
                 +AL
Sbjct: 183 FEYDPDNAL 191


>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 = 38.0 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 19/100 (19%), Positives = 36/100 (36%)

Query: 204 TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
            I  D S    + V   S      +  +      K      +N         L  K++ L
Sbjct: 173 DIWDDESYIANEHVLDTSNRHIIGIARYTLIAGEKPSASGILNNLHACPPWFLNDKLQNL 232

Query: 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303
             +VR  N  +G N+  +  +  +    +L++ N G+ S+
Sbjct: 233 NTTVRMANVFKGHNLSTVAHIAAKGYNGLLKLPNLGQGSV 272


>gi|325295318|ref|YP_004281832.1| isocitrate dehydrogenase, NADP-dependent [Desulfurobacterium
           thermolithotrophum DSM 11699]
 gi|325065766|gb|ADY73773.1| isocitrate dehydrogenase, NADP-dependent [Desulfurobacterium
           thermolithotrophum DSM 11699]
          Length = 735

 Score = 38.0 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 17/64 (26%), Positives = 34/64 (53%), Gaps = 5/64 (7%)

Query: 280 YMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE-- 337
           Y+G+L+ + EA+++++ N    S+ ++   +  +    G +LPD+P     E  K+    
Sbjct: 62  YLGELVWKPEANIMKLPNISA-SIPQLIDAVKELQ-SQGYDLPDFPENPQTEEEKEIRAK 119

Query: 338 -DKC 340
            DKC
Sbjct: 120 YDKC 123


>gi|298482936|ref|ZP_07001118.1| hypothetical protein HMPREF0106_03403 [Bacteroides sp. D22]
 gi|298270908|gb|EFI12487.1| hypothetical protein HMPREF0106_03403 [Bacteroides sp. D22]
          Length = 288

 Score = 38.0 bits (87), Expect = 2.3,   Method: Composition-based stats.
 Identities = 19/91 (20%), Positives = 33/91 (36%), Gaps = 9/91 (9%)

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
               E  +   +  I          L   + EL+  +RS   +   +I  + +L+Q T  
Sbjct: 184 MFMREAEETNPEIFIPEDIKAAKALLDTPITELKFDIRSQRIISEADIKTLRELLQITSQ 243

Query: 291 -------DMLRMANFGRKSLVEIKGVLGTMG 314
                  DML   NFG  S  +++  L  + 
Sbjct: 244 YGFRKLRDML--RNFGLVSQKKVEKRLKELN 272


>gi|307267048|ref|ZP_07548562.1| DNA-directed DNA polymerase [Thermoanaerobacter wiegelii Rt8.B1]
 gi|306917928|gb|EFN48188.1| DNA-directed DNA polymerase [Thermoanaerobacter wiegelii Rt8.B1]
          Length = 389

 Score = 38.0 bits (87), Expect = 2.3,   Method: Composition-based stats.
 Identities = 13/109 (11%), Positives = 43/109 (39%), Gaps = 2/109 (1%)

Query: 196 LDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
           +D +   + ++    +     + +++ +  ++    +  +  K +    I    +P    
Sbjct: 112 IDKNPEIIALEIKKKVKETTGLTISAGVSYNKFLAKLASDWNKPDGFMVITEDMIPDILK 171

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304
            L   +   +  +S   L+   I  + DL++ ++  ++ +  FG+  L 
Sbjct: 172 PLPVSKVYGIGEKSEQKLKAMGINTIDDLLKLSQESLIEI--FGKLGLE 218


>gi|293372761|ref|ZP_06619142.1| hypothetical protein CUY_2408 [Bacteroides ovatus SD CMC 3f]
 gi|292632270|gb|EFF50867.1| hypothetical protein CUY_2408 [Bacteroides ovatus SD CMC 3f]
          Length = 288

 Score = 37.7 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 19/91 (20%), Positives = 33/91 (36%), Gaps = 9/91 (9%)

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
               E  +   +  I          L   + EL+  +RS   +   +I  + +L+Q T  
Sbjct: 184 MFMREAEETNPEIFIPEDIKAAKALLDTPITELKFDIRSQRIISEADIKTLRELLQITSQ 243

Query: 291 -------DMLRMANFGRKSLVEIKGVLGTMG 314
                  DML   NFG  S  +++  L  + 
Sbjct: 244 YGFRKLRDML--RNFGLVSQKKVEKRLKELN 272


>gi|324521335|gb|ADY47834.1| DNA-directed RNA polymerase II subunit RPB3 [Ascaris suum]
          Length = 275

 Score = 37.7 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 46/292 (15%), Positives = 85/292 (29%), Gaps = 88/292 (30%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTDIILNIKG 91
            ++ N+LRR+ ++ +   AI  VQI+          + H +  I     ++ D     + 
Sbjct: 28  LSVANSLRRIFIAEVPTMAIDWVQIEANTSVLHDEFIAHRMGLIPLTSNNVVDKFQYSRD 87

Query: 92  INLKMSG-DSHKRVTIFKRGPGV----VTAGDIQTVNDIEV---------------LNPD 131
                   +    + +  R        VT  D+++ N   V                + D
Sbjct: 88  CQCNDFCPECAVEMRLSVRWDDEGTRSVTTADLESSNAAVVPACGRHLQGRNAEDGTSED 147

Query: 132 HVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191
            +I  L     +RM+    KG G   AK + T          +AL               
Sbjct: 148 ILIVKLRRGQEIRMKCYAKKGFGKEHAKWNPTCGVAFEYDPDNAL--------------- 192

Query: 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
                                                 +    E PK E  +    +   
Sbjct: 193 ----------------------------------RHTVLAKPEEWPKSEYSQLEEDEYEA 218

Query: 252 FNPALLKKVEELELSVRSTNCLRGENI---------VYMGDLIQRTEADMLR 294
               + K  +    +V S+  L+ ENI           +GDL  + + ++L+
Sbjct: 219 PYDPMAKPNKFW-FTVESSGALKAENIVLSGINVLKKKLGDLQNQLQRELLQ 269


>gi|330947784|ref|XP_003306966.1| hypothetical protein PTT_20284 [Pyrenophora teres f. teres 0-1]
 gi|311315237|gb|EFQ84939.1| hypothetical protein PTT_20284 [Pyrenophora teres f. teres 0-1]
          Length = 334

 Score = 37.7 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 43/264 (16%), Positives = 80/264 (30%), Gaps = 65/264 (24%)

Query: 22  QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI--------TAVQIDG-VLHEI 72
           +    R   I +           N+LRRV++S +   AI        T+V  D  V H +
Sbjct: 16  EASSQRASFIVQNFN----LETANSLRRVMLSEIPTLAIDVVEVLDNTSVLADEFVCHRL 71

Query: 73  SSIK----GVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG----VVTAGDIQTVN- 123
             I     GV + +     + +G       +    +++  +  G     V A D+   + 
Sbjct: 72  GLIPLSSKGVDDLVYSRDCDCEGYC----DNCAVVLSLNAKCTGSEIMKVYARDLVIESR 127

Query: 124 ----DI---EVLNPD---HVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---------- 163
               ++    + + +     I  L     + M     KG     AK   +          
Sbjct: 128 TPNDEVGKPVITDSEGTGSCIVKLRRGQAINMRCIAKKGIAKEHAKWAPSAAIGFEYDPA 187

Query: 164 ----------ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYD----KLSMTIDTDG 209
                     E DP      D       +++         +  D+D    +    ++T G
Sbjct: 188 NKLHHLDYWHEEDPEKEWPKDEA-----RINLDGGPENPDERFDFDAVPTRFFYDVETVG 242

Query: 210 SITGEDSVALASRILQDQLGMFIN 233
            I  +  V      LQ +L   + 
Sbjct: 243 GIDPDQIVTKGIHRLQLKLAEIVQ 266


>gi|254839488|pdb|3HOW|C Chain C, Complete Rna Polymerase Ii Elongation Complex Iii With A
           T-U Mismatch And A Frayed Rna 3'-Uridine
 gi|254839503|pdb|3HOX|C Chain C, Complete Rna Polymerase Ii Elongation Complex V
 gi|254839518|pdb|3HOY|C Chain C, Complete Rna Polymerase Ii Elongation Complex Vi
 gi|254839533|pdb|3HOZ|C Chain C, Complete Rna Polymerase Ii Elongation Complex Iv With A
           T-U Mismatch And A Frayed Rna 3'-Guanine
          Length = 347

 Score = 37.7 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 46/268 (17%), Positives = 88/268 (32%), Gaps = 47/268 (17%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTDIILNIKGIN 93
           + N+LRRV+++ +   AI +V+++          + H +  I    + +    L      
Sbjct: 58  MANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIP--LQSMDIEQLEYSRDC 115

Query: 94  LKMSGDSHKRVTIFKRGPGV------VTAGDIQTVNDIEVLNPDHV-----------ICN 136
                     V +  +  G       V + D+  V+++   N  H            IC 
Sbjct: 116 FCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICK 175

Query: 137 LDVDAVVRMELTVSKGHG-----YVPAKHHRTENDP-------IGLITIDAL--YSPIKK 182
           L     +++     KG       + PA     E DP             D+   +   K 
Sbjct: 176 LRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKN 235

Query: 183 VSYTVESAREGQVLDY----DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
             Y  +   EG   DY    D   M +++ GSI  +  V      LQ ++   +      
Sbjct: 236 CEYE-DPPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQM 294

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELS 266
            + K +           +L   E++ ++
Sbjct: 295 DQDKVNFASGDNNTASNMLGSNEDVMMT 322


>gi|237723263|ref|ZP_04553744.1| conserved hypothetical protein [Bacteroides sp. 2_2_4]
 gi|229447785|gb|EEO53576.1| conserved hypothetical protein [Bacteroides sp. 2_2_4]
          Length = 288

 Score = 37.7 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 19/91 (20%), Positives = 33/91 (36%), Gaps = 9/91 (9%)

Query: 231 FINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
               E  +   +  I          L   + EL+  +RS   +   +I  + +L+Q T  
Sbjct: 184 MFMREAEETNPEIFIPEDIKAAKALLDTPITELKFDIRSQRIISEADIKTLRELLQITSQ 243

Query: 291 -------DMLRMANFGRKSLVEIKGVLGTMG 314
                  DML   NFG  S  +++  L  + 
Sbjct: 244 YGFRKLRDML--RNFGLVSQKKVEKRLKELN 272


>gi|67611563|ref|XP_667165.1| DNA-directed RNA polymerase I [Cryptosporidium hominis TU502]
 gi|54658273|gb|EAL36936.1| DNA-directed RNA polymerase I [Cryptosporidium hominis]
          Length = 344

 Score = 37.7 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 33/176 (18%), Positives = 58/176 (32%), Gaps = 40/176 (22%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI---DGV------ 68
           I + + + +           G   ++ NALRR+L+  +   AI  VQI   +GV      
Sbjct: 57  IKVNELKSDYINFDIS----GIDASIANALRRILLVEIPTVAIETVQIYQNNGVIQDEVL 112

Query: 69  LHEISSIKGVHEDLTDIILNIKG-------INLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            H +  I  + +  T    N          +  K++    K           +T+  I +
Sbjct: 113 AHRLGLIPMLIDPNTIEFRNEDEDLNEKNSVCFKLNVKCTKD---DINHEKGITSKAIYS 169

Query: 122 VNDI-----------------EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
            + +                 +V+  D +I  L     +   L   K  G V AK 
Sbjct: 170 KDLVWIPLSDNQRKKFGKSPPKVVTDDILITKLRPGQSIEAILYCEKNIGRVHAKW 225


>gi|66356630|ref|XP_625493.1| RNA polymerase III C5 subunit [Cryptosporidium parvum Iowa II]
 gi|46226487|gb|EAK87481.1| RNA polymerase III C5 subunit [Cryptosporidium parvum Iowa II]
 gi|323509937|dbj|BAJ77861.1| cgd8_300 [Cryptosporidium parvum]
          Length = 344

 Score = 37.7 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 33/176 (18%), Positives = 58/176 (32%), Gaps = 40/176 (22%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI---DGV------ 68
           I + + + +           G   ++ NALRR+L+  +   AI  VQI   +GV      
Sbjct: 57  IKVNELKSDYINFDIS----GIDASIANALRRILLVEIPTVAIETVQIYQNNGVIQDEVL 112

Query: 69  LHEISSIKGVHEDLTDIILNIKG-------INLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            H +  I  + +  T    N          +  K++    K           +T+  I +
Sbjct: 113 AHRLGLIPMLIDPNTIEFRNEDEDLNEKNSVCFKLNVKCTKD---DINHEKGITSKAIYS 169

Query: 122 VNDI-----------------EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
            + +                 +V+  D +I  L     +   L   K  G V AK 
Sbjct: 170 KDLVWIPLSDNQRKKFGKTPPKVVTDDILITKLRPGQSIEAILYCEKNIGRVHAKW 225


>gi|85119573|ref|XP_965664.1| DNA-directed RNA polymerases I and III 40 kDa polypeptide
           [Neurospora crassa OR74A]
 gi|28927476|gb|EAA36428.1| DNA-directed RNA polymerases I and III 40 kDa polypeptide
           [Neurospora crassa OR74A]
          Length = 378

 Score = 37.7 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 36/208 (17%), Positives = 70/208 (33%), Gaps = 45/208 (21%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI---- 60
           +W ++ K      +V  Q +             G   ++ NA RR++++ +   AI    
Sbjct: 53  SW-DIEKFRESVRVVFHQNDPYEAQFSL----IGVDASIANAFRRIMIADIPTLAIEDIF 107

Query: 61  ----TAVQIDGVL-HEISSIK--GVHEDLTDIIL-----------NIKGINLKMSGDSHK 102
               T+V  D VL H +  I   G  E L + +            N   + LK+  ++++
Sbjct: 108 MWNNTSVIQDEVLGHRLGLIPFTGGKEGLHNFLKWYKKGETPCDYNTVELELKVKCENNE 167

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVL------------------NPDHVICNLDVDAVVR 144
                 + P  +         DI+ +                  NPD ++  +     + 
Sbjct: 168 SAPADSKDPKELYHNAHVYAKDIKFVPKGRQAKYFSGENAIRPTNPDILVAKMRPGQEID 227

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLIT 172
           + + + KG G   AK          L+ 
Sbjct: 228 LTMHMHKGVGSDHAKFSPVATASYRLMP 255


>gi|319641964|ref|ZP_07996631.1| hypothetical protein HMPREF9011_02230 [Bacteroides sp. 3_1_40A]
 gi|317386389|gb|EFV67301.1| hypothetical protein HMPREF9011_02230 [Bacteroides sp. 3_1_40A]
          Length = 219

 Score = 37.7 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 15/101 (14%), Positives = 33/101 (32%), Gaps = 6/101 (5%)

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENI 278
            A+ +                 +              L+  +  L+++ R    LR  NI
Sbjct: 106 YAALLT--HSQECGGQNFKNVVIVVREQDIPSECVDLLVTPLGNLDINFRVLRALRKYNI 163

Query: 279 VYMGDLIQRTE----ADMLRMANFGRKSLVEIKGVLGTMGL 315
             + DL++  +      + R+   G KS+ ++   L    +
Sbjct: 164 YQLEDLLRFIKYNGFDALCRIPGMGMKSVEQLYHTLKERNI 204


>gi|323308700|gb|EGA61941.1| Rpb3p [Saccharomyces cerevisiae FostersO]
          Length = 318

 Score = 37.7 bits (86), Expect = 2.9,   Method: Composition-based stats.
 Identities = 46/268 (17%), Positives = 87/268 (32%), Gaps = 47/268 (17%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTDIILNIKGIN 93
           + N+LRRV++  +   AI +V+++          + H +  I    + +    L      
Sbjct: 29  MANSLRRVMIXEIPTLAIDSVEVETNTTVLADEFIAHRLGLIP--LQSMDIEQLEYSRDC 86

Query: 94  LKMSGDSHKRVTIFKRGPGV------VTAGDIQTVNDIEVLNPDHV-----------ICN 136
                     V +  +  G       V + D+  V+++   N  H            IC 
Sbjct: 87  FCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICK 146

Query: 137 LDVDAVVRMELTVSKGHG-----YVPAKHHRTENDP-------IGLITIDAL--YSPIKK 182
           L     +++     KG       + PA     E DP             D+   +   K 
Sbjct: 147 LRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKN 206

Query: 183 VSYTVESAREGQVLDY----DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPK 238
             Y  +   EG   DY    D   M +++ GSI  +  V      LQ ++   +      
Sbjct: 207 CEYE-DPPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQM 265

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELS 266
            + K +           +L   E++ ++
Sbjct: 266 DQDKVNFASGDNNTASNMLGSNEDVMMT 293


>gi|254882695|ref|ZP_05255405.1| conserved hypothetical protein [Bacteroides sp. 4_3_47FAA]
 gi|254835488|gb|EET15797.1| conserved hypothetical protein [Bacteroides sp. 4_3_47FAA]
          Length = 226

 Score = 37.7 bits (86), Expect = 2.9,   Method: Composition-based stats.
 Identities = 15/101 (14%), Positives = 33/101 (32%), Gaps = 6/101 (5%)

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENI 278
            A+ +                 +              L+  +  L+++ R    LR  NI
Sbjct: 113 YAALLT--HSQECGGQNFKNVVIVVREQDIPSECVDLLVTPLGNLDINFRVLRALRKYNI 170

Query: 279 VYMGDLIQRTE----ADMLRMANFGRKSLVEIKGVLGTMGL 315
             + DL++  +      + R+   G KS+ ++   L    +
Sbjct: 171 YQLEDLLRFIKYNGFDALCRIPGMGMKSVEQLYHTLKERNI 211


>gi|94971244|ref|YP_593292.1| NusA antitermination factor [Candidatus Koribacter versatilis
           Ellin345]
 gi|94553294|gb|ABF43218.1| NusA antitermination factor [Candidatus Koribacter versatilis
           Ellin345]
          Length = 534

 Score = 37.7 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 19/90 (21%), Positives = 39/90 (43%), Gaps = 4/90 (4%)

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGE 276
           V LA+++L  ++ +  + EE ++EV++ ++    P    L K     +L       L   
Sbjct: 328 VRLAAKLLGWKIDI-KSEEEKRQEVEQQMSALVNPSITPLDKVP---DLGEAIIEKLSAA 383

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            I  +  L   T   +  +   G K++ +I
Sbjct: 384 GINSVEALADMTPEQLEEVPGIGPKTVDKI 413


>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 = 37.7 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 35/196 (17%), Positives = 60/196 (30%), Gaps = 57/196 (29%)

Query: 34  PLPRGFAHT-----LGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIK--G 77
           PL   F+ T     + NA RR+L+S +   AI  V I         + + H +  I   G
Sbjct: 59  PLDAQFSLTGIDTSVANAFRRILLSEIPTLAIEDVYIYQNTSIIQDEVLAHRLGLIPLCG 118

Query: 78  VHEDLTDIILNIKGINLK-----MSGDSHKRVTIFKRGP--------------------- 111
               L  +    K  +        + ++   +T+  +                       
Sbjct: 119 DRATLRRMKWYAKPTDEDEGSGGPTSENTVALTLKTKCTWQPGGVARAVAGETDPDRLYV 178

Query: 112 -GVVTAGDIQTVND--------------IEVLNPDHVICNLDVDAVVRMELTVSKGHGYV 156
              V A D++   +              I   NPD +IC +     + + +   KG G  
Sbjct: 179 GHNVYAKDMRFEPNGNQAENLSEAEGKHIRSTNPDILICKMRPGQELEIRMHAIKGIGQD 238

Query: 157 PAKHHRTENDPIGLIT 172
            AK          L+ 
Sbjct: 239 HAKFSPVATASYRLMP 254


>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 = 37.7 bits (86), Expect = 3.0,   Method: Composition-based stats.
 Identities = 11/57 (19%), Positives = 25/57 (43%), Gaps = 7/57 (12%)

Query: 264 ELSVRSTNCLRG-----ENIVYMGDLIQRTEADMLRM--ANFGRKSLVEIKGVLGTM 313
           ++S + +NC          +  +  L++    D+ ++   N  +KS+ EI   L  +
Sbjct: 87  DVSSKISNCRERIHNVRNALHTVKSLLELRRDDLKKLWHENAQQKSVCEIMAKLEEL 143


>gi|312792292|ref|YP_004025215.1| secretion protein hlyd family protein [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312179432|gb|ADQ39602.1| secretion protein HlyD family protein [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 542

 Score = 37.3 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 31/173 (17%), Positives = 64/173 (36%), Gaps = 21/173 (12%)

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           +L+  +   S+  +S R GQ L        I+T+GS+  + SV   +   Q    + I  
Sbjct: 170 SLFLTVAFPSWLFKSIRVGQKLKVVLTEYDIETEGSVDAKSSVFYINDNGQSVFDVKIVV 229

Query: 235 EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           +   K +        +  +    ++V  +            E I+ M +++ ++E +  R
Sbjct: 230 DNEGKSLPSGAKAFCVMTSGNFYQEVRSV-----------NEGILKMDEIVIKSEVE-GR 277

Query: 295 MANFGRKSLVEIK--GVLGTM-------GLFLGMNLPDWPPESIEELAKKYED 338
           +     K    IK   +L           + +  +      E+IE L K+  +
Sbjct: 278 IKKIFVKQYDRIKKGDILIEFFDQDIREQIDVKKDQIYETKEAIENLKKEINN 330


>gi|84996255|ref|XP_952849.1| meiotic recombination (DMC1-like) protein [Theileria annulata
           strain Ankara]
 gi|65303847|emb|CAI76224.1| meiotic recombination (DMC1-like) protein, putative [Theileria
           annulata]
          Length = 409

 Score = 37.3 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 13/72 (18%), Positives = 31/72 (43%)

Query: 237 PKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMA 296
             K V    +  ++      ++++EE+ ++V   N L+   I  +  +IQ T+ D+  + 
Sbjct: 8   KSKGVTIQSSTDTITKPFLPIERLEEMGINVSDINKLKSAGICTILGVIQTTKKDLCNIK 67

Query: 297 NFGRKSLVEIKG 308
                 + +I  
Sbjct: 68  GLTEMKVEKISD 79


>gi|196010261|ref|XP_002114995.1| hypothetical protein TRIADDRAFT_59063 [Trichoplax adhaerens]
 gi|190582378|gb|EDV22451.1| hypothetical protein TRIADDRAFT_59063 [Trichoplax adhaerens]
          Length = 349

 Score = 37.3 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 37/192 (19%), Positives = 62/192 (32%), Gaps = 46/192 (23%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64
           +     K   IE I +  EE             G   ++ NA RR+++S +   AI  V 
Sbjct: 39  SLNSFRKNFKIEIIKVDNEEMEFD-------MIGIDASIANAYRRIMLSEVPAMAIEKVV 91

Query: 65  IDG---------VLHEISSIK----------------GVHEDLTDIILNIKGINLKM-SG 98
           I           + H +  I                   +++     L IK I  +    
Sbjct: 92  IHNNTSIIQDEVLAHRLGLIPIAADPKLFDNFNPGDTPTNKNSITFTLQIKCIRNRSAHS 151

Query: 99  DSHKRVTIFKRGPGVVTAGDIQT-----------VNDIEVLNPDHVICNLDVDAVVRMEL 147
           D+     ++      VT  D++              DI  ++ D +I  L     + +E+
Sbjct: 152 DATDPEELYINS--KVTTKDLKLKYNEDQDNAIPNKDIRPVHEDILIAKLRPGQEIDLEM 209

Query: 148 TVSKGHGYVPAK 159
              KG G   AK
Sbjct: 210 ICVKGTGADHAK 221


>gi|322793846|gb|EFZ17186.1| hypothetical protein SINV_07940 [Solenopsis invicta]
          Length = 325

 Score = 37.3 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 50/304 (16%), Positives = 95/304 (31%), Gaps = 54/304 (17%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------V 68
           + +    E       E        ++ N++RRV ++     AI  +Q++          +
Sbjct: 9   VHISDLTEENVKFQVEDTE----LSVANSMRRVFIAETPTMAIDWIQLEANSTVLSDEFL 64

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSG-DSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
            H I  I  + +D+ D I   +         +     T+  +     T     T  D + 
Sbjct: 65  AHRIGMIPLISDDVVDRIQYTRDCQCMDFCPECSVEFTLDVKCTEDQTR--HVTTADFKS 122

Query: 128 LNP---------------------DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
            +P                     + +I  L     +++     KG G   AK + T   
Sbjct: 123 SDPRVLPVTSRHREDEASEYGETDEILIVKLRKGQELKLRAYAKKGFGKEHAKWNPTAGV 182

Query: 167 PIGLITIDALYSPIK-------KVSYT-VESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
                  +++   +        K  YT +E  +    L Y++  +       +T E    
Sbjct: 183 SFEYDPDNSMRHTLYPKPDEWPKSEYTELEEDQCEYNLFYERNIVM------MTSEIKFC 236

Query: 219 LASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENI 278
               I   Q     +  E    +   ++  S         K  +   +V S+  L+ ENI
Sbjct: 237 YGILIWLKQFTSIFSIGE---NLIFYMHHLSYEAPFNWEAKPNKYYFNVESSGALKPENI 293

Query: 279 VYMG 282
           V MG
Sbjct: 294 VMMG 297


>gi|321248338|ref|XP_003191096.1| small nucleolar ribonucleoprotein protein [Cryptococcus gattii
           WM276]
 gi|317457563|gb|ADV19309.1| small nucleolar ribonucleoprotein protein, putative [Cryptococcus
           gattii WM276]
          Length = 773

 Score = 37.3 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 22/139 (15%), Positives = 45/139 (32%), Gaps = 22/139 (15%)

Query: 205 IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELE 264
           + TDG    E   A      Q  +    + ++     +ED        +      +EE  
Sbjct: 110 LTTDGF-DPEQVWAQLELRAQGVVNAVKSIDDSNGNAEEDFEGNPGSDDSDEDMTLEEF- 167

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN-----FGRKSLVEIKGVLGTMGLFLGM 319
                   L+        D+   +E +++ M N         SL E + +L   G     
Sbjct: 168 -----REMLKEAGYD---DVDSMSEEELIEMRNEMEGGEDAMSLEEFREMLKESG----- 214

Query: 320 NLPDWPPESIEELAKKYED 338
              +    + E+L ++ ++
Sbjct: 215 --ENVDDMTEEKLMERMDE 231


>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 = 37.3 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 12/76 (15%), Positives = 29/76 (38%), Gaps = 2/76 (2%)

Query: 243 EDINVKSLPFNPALLKKVEELELSVRSTNCL-RGENIVYMGDLIQRTEA-DMLRMANFGR 300
           E+           +   ++   +  ++   L     I  + DL +  E  ++L++  FG 
Sbjct: 77  EEFEKLKQQVPDTIFTLLDIPGVGPKTVKLLYEELGIRSIEDLKRAIERGELLKLPGFGP 136

Query: 301 KSLVEIKGVLGTMGLF 316
           K + +IK  +  +   
Sbjct: 137 KRVEKIKKGIELLEKS 152


>gi|146320291|ref|YP_001200002.1| superfamily II helicase [Streptococcus suis 98HAH33]
 gi|145691097|gb|ABP91602.1| Superfamily II helicase [Streptococcus suis 98HAH33]
          Length = 117

 Score = 37.3 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 7/35 (20%), Positives = 15/35 (42%)

Query: 275 GENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              I  + D    TE ++L +   G  ++ ++K  
Sbjct: 77  EAGIQSVADFANHTEKELLALKGIGPATIKQLKEK 111


>gi|290559364|gb|EFD92697.1| RNA polymerase insert [Candidatus Parvarchaeum acidophilus ARMAN-5]
          Length = 247

 Score = 37.3 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 27/113 (23%), Positives = 48/113 (42%), Gaps = 5/113 (4%)

Query: 43  LGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK 102
           + NA+RR +++ +   AI  V I    +  S    V      +I     I +K  G    
Sbjct: 23  MANAIRRAIINGVYTLAIDDVTIY--KNTSSMFDEVLAARLGLIPIKTPIEVKGKGKF-- 78

Query: 103 RVTIFKRGPGVVTAGDIQ-TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHG 154
            + + + GP  V A D+  +  D+    P+ +I NL     + +E   + G+G
Sbjct: 79  LLKLKEMGPKAVHASDLVSSDKDVVPAIPEMLIINLKDGESLELEAETTWGNG 131


>gi|209524184|ref|ZP_03272734.1| DEAD/DEAH box helicase domain protein [Arthrospira maxima CS-328]
 gi|209495275|gb|EDZ95580.1| DEAD/DEAH box helicase domain protein [Arthrospira maxima CS-328]
          Length = 670

 Score = 37.3 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 25/156 (16%), Positives = 49/156 (31%), Gaps = 10/156 (6%)

Query: 142 VVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKL 201
            ++  L+V    G+   +           I+ID L   I   ++ +     G    Y +L
Sbjct: 10  RLQKALSVEAERGFNNIQGKEYRFHEFLQISIDKLIEIIPLEAHDLGRKLVGDFAIYSQL 69

Query: 202 SMT------IDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPA 255
                     +T   +   + +  A    Q +L      E         I  +  P    
Sbjct: 70  ITEDRQHLIAETRNFLLQAERLLEA----QKKLAPNQPPEPSPPPRSRSITQEVTPPKSP 125

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
            L +  +  +  R+++ L    I  + DL+     D
Sbjct: 126 QLDQGLKELVGPRNSDLLARLGIYTIYDLLYYYPRD 161


>gi|330832305|ref|YP_004401130.1| hypothetical protein SSUST3_0479 [Streptococcus suis ST3]
 gi|329306528|gb|AEB80944.1| hypothetical protein SSUST3_0479 [Streptococcus suis ST3]
          Length = 128

 Score = 37.3 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 7/35 (20%), Positives = 15/35 (42%)

Query: 275 GENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              I  + D    TE ++L +   G  ++ ++K  
Sbjct: 88  EAGIQSVADFANHTEKELLALKGIGPATIKQLKEK 122


>gi|300312899|ref|YP_003776991.1| transcription elongation factor protein [Herbaspirillum seropedicae
           SmR1]
 gi|300075684|gb|ADJ65083.1| transcription elongation factor protein [Herbaspirillum seropedicae
           SmR1]
          Length = 519

 Score = 37.3 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 13/92 (14%), Positives = 37/92 (40%), Gaps = 8/92 (8%)

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGE 276
           V LA+ + + Q+ +           +E  +  +          +E+L++     + L  E
Sbjct: 327 VRLAAELTRWQINIM--------TAEESADKSAAETALIRTLFMEKLDVDQEVADILVEE 378

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308
               + ++      +ML + +F  +++ E++ 
Sbjct: 379 GFSTLEEIAYVPINEMLEIESFDEETVNELRN 410


>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 = 37.3 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 11/57 (19%), Positives = 25/57 (43%), Gaps = 7/57 (12%)

Query: 264 ELSVRSTNCLRG-----ENIVYMGDLIQRTEADMLRM--ANFGRKSLVEIKGVLGTM 313
           ++S + +NC          +  +  L++    D+ ++   N  +KS+ EI   L  +
Sbjct: 87  DVSSKISNCRERIHNVRNALHTVKSLLELRRDDLKKLWHENAQQKSVCEIMAKLEEL 143


>gi|325679666|ref|ZP_08159241.1| acetolactate synthase, large subunit, biosynthetic type
           [Ruminococcus albus 8]
 gi|324108696|gb|EGC02937.1| acetolactate synthase, large subunit, biosynthetic type
           [Ruminococcus albus 8]
          Length = 565

 Score = 37.3 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 31/167 (18%), Positives = 58/167 (34%), Gaps = 11/167 (6%)

Query: 60  ITAVQIDGVL--HEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAG 117
           I  ++ID       IS    V  D+   I  +  +   M         +  +    V   
Sbjct: 296 IIHIEIDPAEIGKNISVYHHVTGDVKHAIARLNELLPDMQHPEWYNEVMGWKRDYEVHMQ 355

Query: 118 DIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALY 177
            I+  +++    PD VI  LD     +  ++   G   + A  +     P       A  
Sbjct: 356 PIEREDEVL---PDQVIAELDRLTDGKAIISTEVGQHQMWAAQYYNFKCPRSF----ASS 408

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGS--ITGEDSVALASR 222
             +  + Y + +A   +V + D+  + I  DGS  +   +  +LA  
Sbjct: 409 GGLGTMGYGLGAAMGCKVGNPDRTVVNIAGDGSFFMNCNELSSLAKH 455


>gi|300773134|ref|ZP_07083003.1| conserved domain protein [Sphingobacterium spiritivorum ATCC 33861]
 gi|300759305|gb|EFK56132.1| conserved domain protein [Sphingobacterium spiritivorum ATCC 33861]
          Length = 103

 Score = 37.3 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 22/53 (41%)

Query: 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
           LS  + N L    I  +  L   T   +L +   G+ S+  ++ +L   GL  
Sbjct: 42  LSNPAKNSLLYHGIDTLEALSAYTRKQILNLHGIGKASIPTLEKLLAGQGLSF 94


>gi|308499659|ref|XP_003112015.1| CRE-RPB-3 protein [Caenorhabditis remanei]
 gi|308268496|gb|EFP12449.1| CRE-RPB-3 protein [Caenorhabditis remanei]
          Length = 297

 Score = 37.3 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 26/141 (18%), Positives = 43/141 (30%), Gaps = 18/141 (12%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQID---GVLH-EI-SSIKGVH---EDLTDIILNIKGI 92
            ++ N+LRRV M+ +   AI  VQI+    VLH E  +   G+     D     +     
Sbjct: 28  LSVANSLRRVFMAEVPTIAIDWVQIETNTSVLHDEFIAHRMGLIPFLSDYHVEKMQYTRE 87

Query: 93  NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVV--------- 143
                      +    +      A    T  D+  +N D VI        +         
Sbjct: 88  CECAEFCDECSIPFILQMKCKDEATLAVTTADLRCMNNDTVIVCSKKVVTILACFQTVRP 147

Query: 144 -RMELTVSKGHGYVPAKHHRT 163
              +    +G G     +   
Sbjct: 148 ACGKALRERGTGREDFHNREE 168


>gi|24213642|ref|NP_711123.1| transcription elongation factor NusA [Leptospira interrogans
           serovar Lai str. 56601]
 gi|45658541|ref|YP_002627.1| transcription elongation factor NusA [Leptospira interrogans
           serovar Copenhageni str. Fiocruz L1-130]
 gi|24194444|gb|AAN48141.1| transcription elongation factor NusA [Leptospira interrogans
           serovar Lai str. 56601]
 gi|45601784|gb|AAS71264.1| NusA [Leptospira interrogans serovar Copenhageni str. Fiocruz
           L1-130]
          Length = 460

 Score = 37.3 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 15/74 (20%), Positives = 28/74 (37%)

Query: 239 KEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
             V+E            L    +   LS R    L+ E I  +  LI+ ++ D+ ++   
Sbjct: 379 SPVEETKVSMEQEEEEELTPLEDLPGLSARIVGILKSEGIKDLETLIEYSQDDLAKLQGI 438

Query: 299 GRKSLVEIKGVLGT 312
           G  +  +I  +L  
Sbjct: 439 GHTTAGQILKLLRE 452


>gi|223932586|ref|ZP_03624586.1| conserved hypothetical protein [Streptococcus suis 89/1591]
 gi|223898696|gb|EEF65057.1| conserved hypothetical protein [Streptococcus suis 89/1591]
          Length = 128

 Score = 37.3 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 7/35 (20%), Positives = 15/35 (42%)

Query: 275 GENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              I  + D    TE ++L +   G  ++ ++K  
Sbjct: 88  EAGIQSVADFANHTEKELLALKGIGPATIKQLKEK 122


>gi|256089309|ref|XP_002580754.1| DNA-directed rna polymerase II subunit [Schistosoma mansoni]
 gi|238666362|emb|CAZ36993.1| DNA-directed rna polymerase II subunit, putative [Schistosoma
           mansoni]
          Length = 266

 Score = 37.3 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 38/231 (16%), Positives = 79/231 (34%), Gaps = 45/231 (19%)

Query: 41  HTLGNALRRVLMSSLRGAAITAVQIDG----VLHEI-----SSIKGVHEDLTDIILNIKG 91
            ++ NA+RRV ++ +   AI  VQI+     +  E        I    +++ D +   + 
Sbjct: 28  LSVANAIRRVCIAEVPTLAIDWVQIEDNNTMLNDEFIAQRVGLIPLTCDNVVDKMTYFRE 87

Query: 92  INLKMSGD-SHKRVTIFK----RGPGVVTAGDIQTVN-DIEVL-----NPDHV------- 133
              +   +     +T+        P  VT  D+ + N D++ +     +           
Sbjct: 88  CPCREFCEQCSVELTLDVCCTTDAPRHVTGADLISSNRDVQPVPSRDADESSYVGQESIL 147

Query: 134 ICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL---------------YS 178
           I  +     +++     KG G   AK + T          +AL               YS
Sbjct: 148 IVKMRKGQRLKLRAIAKKGFGKEHAKWNPTAGVGFEYDPDNALRHTFLHKPEEWPRSEYS 207

Query: 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + +  +       G+    ++    I+T GS+     +     +L+ +L 
Sbjct: 208 TLPENEHQAPYDPTGKP---NRFYFNIETCGSLQPRAIIFSGLTVLKRKLQ 255


>gi|124507008|ref|XP_001352101.1| DNA-directed RNA polymerase II, putative [Plasmodium falciparum
           3D7]
 gi|23505130|emb|CAD51912.1| DNA-directed RNA polymerase II, putative [Plasmodium falciparum
           3D7]
          Length = 335

 Score = 37.3 bits (85), Expect = 3.8,   Method: Composition-based stats.
 Identities = 28/144 (19%), Positives = 50/144 (34%), Gaps = 26/144 (18%)

Query: 43  LGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIK----GVHEDLTDIILNI 89
           + NALRR+++S +   AI  V +         + + H +  I      V+          
Sbjct: 34  IANALRRIMLSEIPTLAIDVVNVYENTSAFHDEFIAHRLGLIPIDSRNVNNYEFREKCKC 93

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT---VNDIEVLNPD----------HVICN 136
           K    K +      V         V+  DI++     ++ +  P             I  
Sbjct: 94  KETCSKCTIQYIIEVKCNHSNKIDVSHYDIESLEHEPNVPMPIPHGNKNSVSENAIPIVT 153

Query: 137 LDVDAVVRMELTVSKGHGYVPAKH 160
           L  +  + M+L  +KG G + AK 
Sbjct: 154 LSKNQTLHMKLIATKGIGKMHAKW 177


>gi|291276638|ref|YP_003516410.1| isocitrate dehydrogenase [Helicobacter mustelae 12198]
 gi|290963832|emb|CBG39668.1| isocitrate dehydrogenase [Helicobacter mustelae 12198]
          Length = 742

 Score = 37.3 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 17/68 (25%), Positives = 36/68 (52%), Gaps = 9/68 (13%)

Query: 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
           S R  N L       +G+L++  +A++++  N    S+ ++K  +  +    G N+P++P
Sbjct: 56  SQRIPNALEA-----LGELVKHKDANLIKTPNISA-SIPQLKNAIAELQAK-GYNVPNYP 108

Query: 326 --PESIEE 331
             P++ EE
Sbjct: 109 DNPKNQEE 116


>gi|229199623|ref|ZP_04326277.1| DNA-damage repair protein [Bacillus cereus m1293]
 gi|228583849|gb|EEK42013.1| DNA-damage repair protein [Bacillus cereus m1293]
          Length = 421

 Score = 37.3 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 30/218 (13%), Positives = 64/218 (29%), Gaps = 31/218 (14%)

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           +DI ++NP              M+ +     G         +       +ID  +  +  
Sbjct: 76  SDIIIVNPIMHT---------YMKCST-YITGLALKYVAPED---FHQYSIDEFFMDMTA 122

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
             +   S      L + +                +     I  + L   +  +   K+ K
Sbjct: 123 SIHLFASNPREFALKFKREIYE---------RTRIESTIGIGPNLLLSKVAMDVEAKKNK 173

Query: 243 EDINVKSLPFNPALL----KKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + I   +    P  L       +   +S ++   L  + I  +GDL Q     + +  +F
Sbjct: 174 DGIAHWTYDDIPEKLWRIRPLSKFWGISYKTEIKLNRKGIHTIGDLAQYPLKYLKQ--SF 231

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKY 336
           G     E+   L + G+        + P +      + 
Sbjct: 232 GVIG-EELH--LHSNGIDFSRIAEKYVPATTSIAKSQI 266


>gi|297543787|ref|YP_003676089.1| DNA-directed DNA polymerase [Thermoanaerobacter mathranii subsp.
           mathranii str. A3]
 gi|296841562|gb|ADH60078.1| DNA-directed DNA polymerase [Thermoanaerobacter mathranii subsp.
           mathranii str. A3]
          Length = 389

 Score = 37.3 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 12/89 (13%), Positives = 38/89 (42%), Gaps = 2/89 (2%)

Query: 216 SVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRG 275
            + +++ +  ++    +  +  K +    I    +P     L   +   +  +S   L+ 
Sbjct: 132 GLTISAGVSYNKFLAKLASDWNKPDGFTVITEDMIPDILKPLPVSKVYGIGEKSEERLKS 191

Query: 276 ENIVYMGDLIQRTEADMLRMANFGRKSLV 304
             I  +GDL++ ++ +++ +  FG+  + 
Sbjct: 192 MGINTIGDLLKLSQENLVEI--FGKVGVE 218


>gi|253751300|ref|YP_003024441.1| hypothetical protein SSUSC84_0394 [Streptococcus suis SC84]
 gi|253753201|ref|YP_003026341.1| hypothetical protein SSU0409 [Streptococcus suis P1/7]
 gi|253755024|ref|YP_003028164.1| hypothetical protein SSUBM407_0397 [Streptococcus suis BM407]
 gi|251815589|emb|CAZ51172.1| conserved hypothetical protein [Streptococcus suis SC84]
 gi|251817488|emb|CAZ55229.1| conserved hypothetical protein [Streptococcus suis BM407]
 gi|251819446|emb|CAR44940.1| conserved hypothetical protein [Streptococcus suis P1/7]
 gi|292557870|gb|ADE30871.1| Superfamily II helicase [Streptococcus suis GZ1]
 gi|319757582|gb|ADV69524.1| hypothetical protein SSUJS14_0423 [Streptococcus suis JS14]
          Length = 128

 Score = 37.3 bits (85), Expect = 3.9,   Method: Composition-based stats.
 Identities = 7/35 (20%), Positives = 15/35 (42%)

Query: 275 GENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
              I  + D    TE ++L +   G  ++ ++K  
Sbjct: 88  EAGIQSVADFANHTEKELLALKGIGPATIKQLKEK 122


>gi|289577475|ref|YP_003476102.1| DNA-directed DNA polymerase [Thermoanaerobacter italicus Ab9]
 gi|289527188|gb|ADD01540.1| DNA-directed DNA polymerase [Thermoanaerobacter italicus Ab9]
          Length = 389

 Score = 36.9 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 12/89 (13%), Positives = 38/89 (42%), Gaps = 2/89 (2%)

Query: 216 SVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRG 275
            + +++ +  ++    +  +  K +    I    +P     L   +   +  +S   L+ 
Sbjct: 132 GLTISAGVSYNKFLAKLASDWNKPDGFTVITEDMIPDILKPLPVSKVYGIGEKSEERLKS 191

Query: 276 ENIVYMGDLIQRTEADMLRMANFGRKSLV 304
             I  +GDL++ ++ +++ +  FG+  + 
Sbjct: 192 MGINTIGDLLKLSQENLVEI--FGKVGVE 218


>gi|288556417|ref|YP_003428352.1| hypothetical protein BpOF4_17085 [Bacillus pseudofirmus OF4]
 gi|288547577|gb|ADC51460.1| hypothetical protein BpOF4_17085 [Bacillus pseudofirmus OF4]
          Length = 66

 Score = 36.9 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 15/55 (27%), Positives = 25/55 (45%)

Query: 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL 317
            +LS  + + L  E I  +  L   TE ++L++   G  SL  ++  L   GL  
Sbjct: 9   SKLSSPARSALVHEGIDTLEKLSTYTEKEILKLHGVGPASLPTMRASLVEAGLSF 63


>gi|288554984|ref|YP_003426919.1| NAD-dependent DNA ligase LigA [Bacillus pseudofirmus OF4]
 gi|288546144|gb|ADC50027.1| NAD-dependent DNA ligase LigA [Bacillus pseudofirmus OF4]
          Length = 668

 Score = 36.9 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 11/51 (21%), Positives = 22/51 (43%), Gaps = 8/51 (15%)

Query: 278 IVYMGDLIQRTEADMLRMANFGRKSLVEI--------KGVLGTMGLFLGMN 320
           I  + DL Q   +++L++   G KS+  +        +  L  +   LG+ 
Sbjct: 463 IHTVADLYQLDRSELLKLERMGEKSVDNLMKAIEASKENSLEKLLFGLGIR 513


>gi|307175611|gb|EFN65520.1| DNA-directed RNA polymerase II subunit RPB3 [Camponotus floridanus]
          Length = 276

 Score = 36.9 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 38/258 (14%), Positives = 82/258 (31%), Gaps = 55/258 (21%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------V 68
           + +    E       E        ++ N++RRV ++     AI  +Q++          +
Sbjct: 9   VHISDLTEENVKFQVEDTE----LSVANSMRRVFIAETPTMAIDWIQLEANSTVLSDEFL 64

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSG-DSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
            H I  I  + +D+ D I   +         +     T+  +     T     T  D + 
Sbjct: 65  AHRIGMIPLISDDVVDRIQFTRDCQCMDFCPECSVEFTLDVKCIEDQTR--HVTTADFKS 122

Query: 128 LNP---------------------DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166
            +P                     + +I  L     +++     KG G   AK + T   
Sbjct: 123 SDPRVLPVTSRHREDDASEYGETDEILIVKLRKGQELKLRAYAKKGFGKEHAKWNPTAGV 182

Query: 167 PIGLITIDAL---------------YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSI 211
                  +A+               Y+ +++  Y      E +   Y      +++ G++
Sbjct: 183 SFEYDPDNAMRHTLYPKPDEWPKSEYTELEEDQYEAPFNWEAKPNKY---YFNVESSGAL 239

Query: 212 TGEDSVALASRILQDQLG 229
             E+ V +    L+++L 
Sbjct: 240 KPENIVMMGIAALKNKLS 257


>gi|147901420|ref|NP_001085237.1| polymerase (RNA) I polypeptide C, 30kDa [Xenopus laevis]
 gi|47937458|gb|AAH72033.1| MGC78824 protein [Xenopus laevis]
          Length = 347

 Score = 36.9 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 39/211 (18%), Positives = 66/211 (31%), Gaps = 46/211 (21%)

Query: 9   LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI-------- 60
             K   I+ + +  +       I E    G   ++ NA RR+L+S +   A+        
Sbjct: 45  FEKNFRIDIVKMEDD-------ILEFDMVGIDASIANAFRRILLSEVPTVAVEKVYVYNN 97

Query: 61  TA---------------VQIDGVLHEI---SSIKGVHEDLTDIILNIKGI-NLKMSGDSH 101
           T+               ++ D  L E       +G   D     LN+K   N + S D  
Sbjct: 98  TSIIQDEILAHRLGLIPIRADPRLFEYRSADDAEGTEIDTLQFELNVKCTRNPRASKDCS 157

Query: 102 KRVTIFKRGPGVVTAGDIQTVNDIEV-----------LNPDHVICNLDVDAVVRMELTVS 150
               ++     V T          +V           ++ D +I  L     + + +   
Sbjct: 158 DPNELYLN-HKVYTGHMKWLPQGNQVDLFPETDPPRPVHKDILIAQLRPGQEINVIMHCV 216

Query: 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           KG G   AK          L+    L S I+
Sbjct: 217 KGIGKDHAKFSPVATASYRLLPEVTLLSSIE 247


>gi|308490301|ref|XP_003107343.1| hypothetical protein CRE_14524 [Caenorhabditis remanei]
 gi|308252449|gb|EFO96401.1| hypothetical protein CRE_14524 [Caenorhabditis remanei]
          Length = 1766

 Score = 36.9 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 17/125 (13%), Positives = 37/125 (29%), Gaps = 16/125 (12%)

Query: 210  SITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRS 269
            S+  ++ +  A+  ++    +    E  K   KE      L     +      L+   + 
Sbjct: 1436 SMDIQEILR-AASTIKKHAKILEKIENEKAADKEKEIEIHLAPKWGIDPTKSTLDEMEQL 1494

Query: 270  TNCLRGENIVYMGDLIQRTEAD---------------MLRMANFGRKSLVEIKGVLGTMG 314
               L+ E   +  DL    E +               + ++ N   K   E+      + 
Sbjct: 1495 IAQLKEEGAEFQKDLESAKEEERIAHQKFVCHLDKSKIKKIENLTVKRAEELNKEADELE 1554

Query: 315  LFLGM 319
              + M
Sbjct: 1555 KEVNM 1559


>gi|227357076|ref|ZP_03841446.1| transcription elongation protein (N utilization substance protein
           A) [Proteus mirabilis ATCC 29906]
 gi|227162768|gb|EEI47731.1| transcription elongation protein (N utilization substance protein
           A) [Proteus mirabilis ATCC 29906]
          Length = 502

 Score = 36.9 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 21/128 (16%), Positives = 46/128 (35%), Gaps = 9/128 (7%)

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGE 276
           V LA+++L+        +E       E         N A+    + L++       L  E
Sbjct: 325 VRLAAQLLKKH-RGDDKWELNVMTADELNAKHQAEANAAIEIFTKHLDIDEDFATVLVEE 383

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEIKG----VLGTMGL----FLGMNLPDWPPES 328
               + +L+     ++L +     +++  ++      L T+ L     LG N P     +
Sbjct: 384 GFSTLEELVYVPIDELLAIDGLDEETVEALRERAKAALTTIELAQKESLGDNQPAEDLLA 443

Query: 329 IEELAKKY 336
           +E + +  
Sbjct: 444 LEGMERSL 451


>gi|212224494|ref|YP_002307730.1| ski2-like helicase [Thermococcus onnurineus NA1]
 gi|212009451|gb|ACJ16833.1| DNA helicase [Thermococcus onnurineus NA1]
          Length = 726

 Score = 36.9 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 20/123 (16%), Positives = 46/123 (37%), Gaps = 10/123 (8%)

Query: 216 SVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTN---C 272
            + LA  ++   + ++  FE  K  +    ++     +    + +E + L          
Sbjct: 601 ILELADWLMYSLIELYKLFEPKKDVLDYLRDLHLRLKHGVREELLELVRLPNIGRKRARA 660

Query: 273 LRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEEL 332
           L         D+++   +++L +   G K       V+  + +  G+ LP    +S EE 
Sbjct: 661 LYNAGFRTTEDIMRAKVSELLAVEGIGLK-------VVEGLFMHFGVELPKASKKSTEEN 713

Query: 333 AKK 335
            K+
Sbjct: 714 RKR 716


>gi|66362260|ref|XP_628094.1| RNA polymerase II B3 subunit [Cryptosporidium parvum Iowa II]
 gi|46227424|gb|EAK88359.1| RNA polymerase II B3 subunit [Cryptosporidium parvum Iowa II]
          Length = 355

 Score = 36.9 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 36/171 (21%), Positives = 57/171 (33%), Gaps = 35/171 (20%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ-IDG--VLH-EISS 74
            + +   N               ++ N LRR++++ +   AI  V  ID   VLH E   
Sbjct: 13  EITELTPNSIRFTLSNTD----LSMANTLRRIILAEIPTLAIDLVTMIDNTSVLHDEF-- 66

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVT-------IFKRGPG----VVTAGDIQT-- 121
           I      +     NI+  N K   +  +R         +     G     VT  DIQ   
Sbjct: 67  IVHRMGLIPLDSTNIRDFNFKDRCECQERCNKCSVEYLLDVTCEGGATRNVTHYDIQPVA 126

Query: 122 ------------VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
                        + ++ +N   +I  L     + M +T  KG G   AK 
Sbjct: 127 TSTLVPMPVPKKDDSVDGMNNGILIAKLGPGQRIAMRMTACKGIGKFHAKW 177


>gi|289615804|emb|CBI57545.1| unnamed protein product [Sordaria macrospora]
          Length = 378

 Score = 36.9 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 36/208 (17%), Positives = 70/208 (33%), Gaps = 45/208 (21%)

Query: 5   NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI---- 60
           +W ++ K      +V  Q +             G   ++ NA RR++++ +   AI    
Sbjct: 53  SW-DIEKFRENVRVVFHQNDPYEAQFSL----IGVDASIANAFRRIMIADIPTLAIEDIF 107

Query: 61  ----TAVQIDGVL-HEISSIK--GVHEDLTDIIL-----------NIKGINLKMSGDSHK 102
               T+V  D VL H +  I   G  E L + +            N   + LK+  ++++
Sbjct: 108 MWNNTSVIQDEVLGHRLGLIPFTGGKEGLHNFLKWYKKGETPCDYNTVELELKVKCENNQ 167

Query: 103 RVTIFKRGPGVVTAGDIQTVNDIEVL------------------NPDHVICNLDVDAVVR 144
                 + P  +         DI+ +                  NPD ++  +     + 
Sbjct: 168 NAPTDSKDPKELYHNAHVYAKDIKFVPKGRQAKYFSGENVIRPTNPDILVAKMRPGQEID 227

Query: 145 MELTVSKGHGYVPAKHHRTENDPIGLIT 172
           + + + KG G   AK          L+ 
Sbjct: 228 LTMHMHKGVGSDHAKFSPVATASYRLMP 255


>gi|307202125|gb|EFN81625.1| DNA-directed RNA polymerase II subunit RPB3 [Harpegnathos saltator]
          Length = 276

 Score = 36.9 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 39/256 (15%), Positives = 86/256 (33%), Gaps = 51/256 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------V 68
           + +    E       E        ++ N++RRV ++     AI  +Q++          +
Sbjct: 9   VHISDLTEENVKFQVEYTE----LSVANSMRRVFIAETPTMAIDWIQLEANSTVLSDEFL 64

Query: 69  LHEISSIKGVHEDLTDIILNIKG---------------INLKMSGDSHKRV-TIFKRGPG 112
            H I  I  + +D+ D I   +                +++K + D  + V T   +   
Sbjct: 65  AHRIGMIPLISDDVVDRIQYTRDCQCMDFCPECSVEFTLDVKCTEDQTRHVTTADFKSSD 124

Query: 113 ----VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168
                VT+   +          + +I  L     +++     KG G   AK + T     
Sbjct: 125 PRVLPVTSRHREDDASEYGETDEILIVKLRKGQELKLRAYAKKGFGKEHAKWNPTAGVSF 184

Query: 169 GLITIDAL---------------YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITG 213
                +++               YS +++  Y      E +   Y      +++ G++  
Sbjct: 185 EYDPDNSMRHTLFPKPDEWPKSEYSELEEDQYEAPFNWEAKPNKY---YFNVESSGALKP 241

Query: 214 EDSVALASRILQDQLG 229
           E+ V +    L+++L 
Sbjct: 242 ENIVMMGIAALKNKLS 257


>gi|328772591|gb|EGF82629.1| hypothetical protein BATDEDRAFT_34351 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 354

 Score = 36.9 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 23/150 (15%), Positives = 55/150 (36%), Gaps = 17/150 (11%)

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           A  +    V YT     + Q   Y+++     T+  +  +        I+ DQL      
Sbjct: 164 AASASCLMVDYTSYFDVKIQNAIYERIVRN-TTNTPLLFD--------IMTDQLVA---- 210

Query: 235 EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
            +    + E+ +      +   + +++++ ++      L+ + I  +  +   T  ++L+
Sbjct: 211 -DQDVMLDENDSTGEGQLDFMEIDRLQDVGINQADIAKLKTQGITTIRGIQMATSRNLLK 269

Query: 295 MANFGRKSLVEIKG---VLGTMGLFLGMNL 321
           +  F    + +IK     L   G   G  L
Sbjct: 270 VKGFSEIKVEKIKDAASKLIANGFITGTEL 299


>gi|228912455|ref|ZP_04076136.1| DNA-damage repair protein [Bacillus thuringiensis IBL 200]
 gi|228847192|gb|EEM92165.1| DNA-damage repair protein [Bacillus thuringiensis IBL 200]
          Length = 421

 Score = 36.9 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 27/168 (16%), Positives = 52/168 (30%), Gaps = 18/168 (10%)

Query: 164 ENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRI 223
             +     +ID  +  I    +   +      L + +          I  +  +     I
Sbjct: 104 PIEDFHQYSIDEFFMDITDSIHLFANNPYEFALTFKRE---------IYAKTRIECTIGI 154

Query: 224 LQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKV----EELELSVRSTNCLRGENIV 279
             + L   I  +   K+ K  I        P  L  +    +   +S ++   L  + I 
Sbjct: 155 GPNPLMSKIALDIEAKKNKNGIAYWKYEDVPTKLWSIRPLNKFWGISYKTEEKLNRKGIH 214

Query: 280 YMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPE 327
            +GDL       + +  NFG K   E+   L + G+        + P 
Sbjct: 215 SIGDLANYPLKYLKQ--NFG-KIGEELH--LHSHGIDFSRISEKYVPA 257


>gi|67624207|ref|XP_668386.1| conjugation stage-specific protein [Cryptosporidium hominis TU502]
 gi|54659581|gb|EAL38151.1| conjugation stage-specific protein [Cryptosporidium hominis]
          Length = 355

 Score = 36.9 bits (84), Expect = 4.9,   Method: Composition-based stats.
 Identities = 36/171 (21%), Positives = 57/171 (33%), Gaps = 35/171 (20%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ-IDG--VLH-EISS 74
            + +   N               ++ N LRR++++ +   AI  V  ID   VLH E   
Sbjct: 13  EITELTPNSIRFTLSNTD----LSMANTLRRIILAEIPTLAIDLVTMIDNTSVLHDEF-- 66

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVT-------IFKRGPG----VVTAGDIQT-- 121
           I      +     NI+  N K   +  +R         +     G     VT  DIQ   
Sbjct: 67  IVHRMGLIPLDSTNIRDFNFKDRCECQERCNKCSVEYLLDVTCEGGATRNVTHYDIQPVA 126

Query: 122 ------------VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
                        + ++ +N   +I  L     + M +T  KG G   AK 
Sbjct: 127 TSTLVPMPVPKKDDSVDGMNNGILIAKLGPGQRIAMRMTACKGIGKFHAKW 177


>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 = 36.9 bits (84), Expect = 5.0,   Method: Composition-based stats.
 Identities = 38/260 (14%), Positives = 85/260 (32%), Gaps = 58/260 (22%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------V 68
           + + +  ++    + E        ++ N+LRRV ++     AI  VQ++          +
Sbjct: 9   VQITELTDDNVKFVLEDTE----LSVANSLRRVFIAETPTLAIDWVQLEANSTVLSDEFL 64

Query: 69  LHEISSIKGVHEDLTDIILNIKG-INLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEV 127
            H I  I  + +D+ + +   +  I L    +     T+  +     T     T  D++ 
Sbjct: 65  AHRIGLIPLISDDVVERLQYTRDCICLDFCPECSVEFTLDVKCSEEQTR--HVTTADLKT 122

Query: 128 LNP----------------------DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEN 165
            NP                      + +I  L     +++     KG G   AK + T  
Sbjct: 123 SNPKVLPVTSRNQGEEDNEYGESSDEILIIKLRKGQELKLRAYAKKGFGKEHAKWNPTAG 182

Query: 166 DPIGLITIDALYSPIKKVSY-------TVESAREGQ---------VLDYDKLSMTIDTDG 209
                       + ++   Y         E                   +K    +++ G
Sbjct: 183 VCFEYDPD----NCMRHTLYPKPDEWPKSEHTELEDDQFEAPYNWEAKPNKFFFNVESSG 238

Query: 210 SITGEDSVALASRILQDQLG 229
           ++  E+ V +  ++L+++L 
Sbjct: 239 ALKPENIVIMGVQVLKNKLS 258


>gi|270013672|gb|EFA10120.1| hypothetical protein TcasGA2_TC012300 [Tribolium castaneum]
          Length = 448

 Score = 36.9 bits (84), Expect = 5.0,   Method: Composition-based stats.
 Identities = 15/62 (24%), Positives = 30/62 (48%), Gaps = 10/62 (16%)

Query: 280 YMGDLIQ--RTEADMLRMAN-FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKY 336
            +G+ +    T  ++ ++ N F  +S  EIK  LG + L      P    E I +L +++
Sbjct: 130 TLGEAVTDTYTPDELKKIKNEF--RSYDEIKKTLGDLKLT-----PKMDAEIIADLLQRH 182

Query: 337 ED 338
           ++
Sbjct: 183 QE 184


>gi|195472723|ref|XP_002088649.1| GE18688 [Drosophila yakuba]
 gi|194174750|gb|EDW88361.1| GE18688 [Drosophila yakuba]
          Length = 275

 Score = 36.9 bits (84), Expect = 5.0,   Method: Composition-based stats.
 Identities = 38/258 (14%), Positives = 87/258 (33%), Gaps = 54/258 (20%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------V 68
           + + +  ++    + E        ++ N+LRRV ++     AI  VQ++          +
Sbjct: 9   VQITELTDDNVKFVLEDTE----LSVANSLRRVFIAETPTLAIDWVQLEANSTVLSDEFL 64

Query: 69  LHEISSIKGVHEDLTDIILNIKG-INLKMSGDSHKRVTIFKRGPGV----VTAGDI---- 119
            H I  I  + +D+ + +   +  I L    +     T+  +        VT  D+    
Sbjct: 65  AHRIGLIPLISDDVVERLQYTRDCICLDFCPECSVEFTLDVKCSEEQTRHVTTADLKSSN 124

Query: 120 ------------QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167
                       +  N+    N + +I  L     +++     KG G   AK + T    
Sbjct: 125 AKVLPVTSRNQGEEDNEYGESNDEILIIKLRKGQELKLRAYAKKGFGKEHAKWNPTAGVC 184

Query: 168 IGLITIDALYSPIKKVSY-------TVESAREGQ---------VLDYDKLSMTIDTDGSI 211
                 ++    ++   Y         E                   +K    +++ G++
Sbjct: 185 FEYDPDNS----MRHTLYPKPDEWPKSEHTELEDDQYEAPYNWEAKPNKFFFNVESSGAL 240

Query: 212 TGEDSVALASRILQDQLG 229
             E+ V +  ++L+++L 
Sbjct: 241 KPENIVVMGVQVLKNKLS 258


>gi|323508505|dbj|BAJ77146.1| cgd1_2710 [Cryptosporidium parvum]
          Length = 252

 Score = 36.9 bits (84), Expect = 5.1,   Method: Composition-based stats.
 Identities = 36/171 (21%), Positives = 57/171 (33%), Gaps = 35/171 (20%)

Query: 19  VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ-IDG--VLH-EISS 74
            + +   N               ++ N LRR++++ +   AI  V  ID   VLH E   
Sbjct: 13  EITELTPNSIRFTLSNTD----LSMANTLRRIILAEIPTLAIDLVTMIDNTSVLHDEF-- 66

Query: 75  IKGVHEDLTDIILNIKGINLKMSGDSHKRVT-------IFKRGPG----VVTAGDIQT-- 121
           I      +     NI+  N K   +  +R         +     G     VT  DIQ   
Sbjct: 67  IVHRMGLIPLDSTNIRDFNFKDRCECQERCNKCSVEYLLDVTCEGGATRNVTHYDIQPVA 126

Query: 122 ------------VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
                        + ++ +N   +I  L     + M +T  KG G   AK 
Sbjct: 127 TSTLVPMPVPKKDDSVDGMNNGILIAKLGPGQRIAMRMTACKGIGKFHAKW 177


>gi|221107404|ref|XP_002157633.1| PREDICTED: similar to predicted protein, partial [Hydra
           magnipapillata]
          Length = 349

 Score = 36.9 bits (84), Expect = 5.1,   Method: Composition-based stats.
 Identities = 10/45 (22%), Positives = 19/45 (42%)

Query: 279 VYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD 323
            Y+ D+ +  E D  ++ + G+K   EI  +     L  G  +  
Sbjct: 46  YYLMDMSKSMEDDQEKLKSLGKKIAEEINKITKNYQLAFGSFVDK 90


>gi|327399680|ref|YP_004340549.1| isocitrate dehydrogenase, NADP-dependent [Hippea maritima DSM
           10411]
 gi|327182309|gb|AEA34490.1| isocitrate dehydrogenase, NADP-dependent [Hippea maritima DSM
           10411]
          Length = 745

 Score = 36.9 bits (84), Expect = 5.2,   Method: Composition-based stats.
 Identities = 14/51 (27%), Positives = 33/51 (64%), Gaps = 2/51 (3%)

Query: 275 GENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP 325
            +++ Y+G+L+ + EA+++++ N    S+V++K  +  +    G N+PD+P
Sbjct: 65  NDDLAYLGELVNKPEANIIKLPNISA-SVVQLKEAIKELQEK-GYNVPDYP 113


>gi|319401348|gb|EFV89559.1| impB/mucB/samB family protein [Staphylococcus epidermidis FRI909]
          Length = 420

 Score = 36.5 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 24/181 (13%), Positives = 50/181 (27%), Gaps = 28/181 (15%)

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           NDI ++NP              M   ++               + +   +ID  +  +  
Sbjct: 76  NDIYIINP-------------SMRKYLNVSVAISKIALRYVPPEDLHQYSIDEFFMDVTD 122

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
             +   S        +    +          E  +     I  + L   +  +   K  +
Sbjct: 123 SYHRFNSTVFAFCKRFQNEILE---------ETGIHCTIGIGSNMLLSKVAMDIEAKHTE 173

Query: 243 EDINVKSLPFNPALLKKV----EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
             I        P  L  +    +   ++ R+   L    I  +GDL +     +    +F
Sbjct: 174 NGIAEWRYQDVPEKLWPIQPLRDFWGINKRTEKKLNKRGIFTIGDLAKYPYHYLK--RDF 231

Query: 299 G 299
           G
Sbjct: 232 G 232


>gi|254496140|ref|ZP_05109038.1| transcription elongation factor NusA [Legionella drancourtii
           LLAP12]
 gi|254354627|gb|EET13264.1| transcription elongation factor NusA [Legionella drancourtii
           LLAP12]
          Length = 502

 Score = 36.5 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 30/134 (22%), Positives = 50/134 (37%), Gaps = 19/134 (14%)

Query: 217 VALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGE 276
           V LAS++    L +    E   K  +E   +  L  +         LE+       L   
Sbjct: 337 VRLASQLTGWTLNVMTTDEFENKNQEESSKIVKLFTSA--------LEIDEEIATLLVAH 388

Query: 277 NIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV----LGTMGLFLGMNLPDWPPESI--- 329
               + ++    + ++L +  F  + + E++      L TM L  G  L   P ES+   
Sbjct: 389 GFSSLEEVAYVPKEELLAIEEFDDEIVEELRNRANDNLLTMALTSGKGLAGAPDESLLAM 448

Query: 330 ----EELAKKYEDK 339
               EELA K  +K
Sbjct: 449 DGMTEELANKLAEK 462


>gi|242242643|ref|ZP_04797088.1| possible DNA-directed DNA polymerase [Staphylococcus epidermidis
           W23144]
 gi|242233779|gb|EES36091.1| possible DNA-directed DNA polymerase [Staphylococcus epidermidis
           W23144]
          Length = 420

 Score = 36.5 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 24/181 (13%), Positives = 50/181 (27%), Gaps = 28/181 (15%)

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           NDI ++NP              M   ++               + +   +ID  +  +  
Sbjct: 76  NDIYIINP-------------SMRKYLNVSVAISKIALRYVPPEDLHQYSIDEFFMDVTD 122

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
             +   S        +    +          E  +     I  + L   +  +   K  +
Sbjct: 123 SYHRFNSTVFAFCKRFQNEILE---------ETGIHCTIGIGSNMLLSKVAMDIEAKHTE 173

Query: 243 EDINVKSLPFNPALLKKV----EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
             I        P  L  +    +   ++ R+   L    I  +GDL +     +    +F
Sbjct: 174 NGIAEWRYQDVPEKLWPIQPLRDFWGINKRTEKKLNKRGIFTIGDLAKYPYHYLK--RDF 231

Query: 299 G 299
           G
Sbjct: 232 G 232


>gi|242005128|ref|XP_002423425.1| conserved hypothetical protein [Pediculus humanus corporis]
 gi|212506494|gb|EEB10687.1| conserved hypothetical protein [Pediculus humanus corporis]
          Length = 1014

 Score = 36.5 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 24/121 (19%), Positives = 54/121 (44%), Gaps = 13/121 (10%)

Query: 228 LGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQR 287
           + +    EE +K++KE     S   NP  +   EE  ++ +     +        DL++ 
Sbjct: 825 IKLQQKMEEARKKLKELDVRLSAESNPDNISGSEEGSINSKDNQRSKRSQ----EDLVRI 880

Query: 288 TEA------DMLRMANFGRKSLVEIKGVLGTMGLFL---GMNLPDWPPESIEELAKKYED 338
           ++       D+ +  + GRK+L  +K +     L L   G ++ +   + +E+L ++ +D
Sbjct: 881 SKVTSNAPIDVGKTGSLGRKTLESLKEIEKNRQLHLAKQGSHVIEEERKRVEQLKRRAQD 940

Query: 339 K 339
           +
Sbjct: 941 E 941


>gi|145328718|ref|NP_001077894.1| NRPE3B; DNA binding / DNA-directed RNA polymerase/ protein
          dimerization [Arabidopsis thaliana]
 gi|330251304|gb|AEC06398.1| DNA-directed RNA polymerase II subunit RPB3-B [Arabidopsis
          thaliana]
          Length = 235

 Score = 36.5 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 4/49 (8%)

Query: 18 IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
          + + + +++          R    ++ NALRRV++S +   AI  V+I+
Sbjct: 12 VKIRELKDDYAKFEL----RETDVSMANALRRVMISEVPTMAIHLVKIE 56


>gi|514320|gb|AAB03740.1| RNA polymerase II third largest subunit [Arabidopsis thaliana]
          Length = 319

 Score = 36.5 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 4/49 (8%)

Query: 18 IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
          + + + +++          R    ++ NALRRV++S +   AI  V+I+
Sbjct: 12 VKIRELKDDYAKFEL----RETDVSMANALRRVMISEVPTMAIHLVKIE 56


>gi|15226509|ref|NP_179142.1| NRPE3B; DNA binding / DNA-directed RNA polymerase/ protein
          dimerization [Arabidopsis thaliana]
 gi|12643753|sp|Q39212|RPB3B_ARATH RecName: Full=DNA-directed RNA polymerase II subunit RPB3-B;
          Short=RNA polymerase II subunit 3-B; Short=RNA
          polymerase II subunit B3-B; AltName: Full=DNA-directed
          RNA polymerase II 36 kDa polypeptide B
 gi|4544373|gb|AAD22284.1| DNA-directed RNA polymerase II, third largest subunit
          [Arabidopsis thaliana]
 gi|28973621|gb|AAO64135.1| putative DNA-directed RNA polymerase II, third largest subunit
          [Arabidopsis thaliana]
 gi|29824193|gb|AAP04057.1| putative DNA-directed RNA polymerase II, third largest subunit
          [Arabidopsis thaliana]
 gi|110736768|dbj|BAF00345.1| DNA-directed RNA polymerase II, third largest subunit
          [Arabidopsis thaliana]
 gi|330251303|gb|AEC06397.1| DNA-directed RNA polymerase II subunit RPB3-B [Arabidopsis
          thaliana]
          Length = 319

 Score = 36.5 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 4/49 (8%)

Query: 18 IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID 66
          + + + +++          R    ++ NALRRV++S +   AI  V+I+
Sbjct: 12 VKIRELKDDYAKFEL----RETDVSMANALRRVMISEVPTMAIHLVKIE 56


>gi|297527612|ref|YP_003669636.1| RNA polymerase insert [Staphylothermus hellenicus DSM 12710]
 gi|297256528|gb|ADI32737.1| RNA polymerase insert [Staphylothermus hellenicus DSM 12710]
          Length = 280

 Score = 36.5 bits (83), Expect = 5.8,   Method: Composition-based stats.
 Identities = 30/147 (20%), Positives = 53/147 (36%), Gaps = 19/147 (12%)

Query: 45  NALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHE---DLTDIILNIKGI 92
           N++RRV+++ +   AI +V           + + H +  I    E   D        K  
Sbjct: 26  NSIRRVVIAEVPTMAIDSVVFTMNSSVFYDEYIAHRLGLIPLTSEAALDKYKSPEECKEA 85

Query: 93  NLKMSGDSHKRVTIFKRGPGV----VT--AGDIQT-VNDIEVLNPDHVICNLDVDAVVRM 145
           + +        V +   G G     VT  +GD++T   D++ +  +  I  L  +  +R+
Sbjct: 86  SDRGLFTEDCFVKLDLEGKGEEGKLVTLHSGDLKTSDPDVKPVYDNIPIIVLGKNQEIRL 145

Query: 146 ELTVSKGHGYVPAKHHRTENDPIGLIT 172
           E     G G   AK           I 
Sbjct: 146 EAYARLGRGKEHAKWSPVSIAAHKYIA 172


>gi|148643488|ref|YP_001274001.1| DNA-directed RNA polymerase subunit D [Methanobrevibacter smithii
           ATCC 35061]
 gi|261350417|ref|ZP_05975834.1| RNA polymerase Rpb3/Rpb11 dimerization domain protein
           [Methanobrevibacter smithii DSM 2374]
 gi|166229318|sp|A5UN55|RPOD_METS3 RecName: Full=DNA-directed RNA polymerase subunit D
 gi|148552505|gb|ABQ87633.1| DNA-directed RNA polymerase, subunit D, RpoD [Methanobrevibacter
           smithii ATCC 35061]
 gi|288861200|gb|EFC93498.1| RNA polymerase Rpb3/Rpb11 dimerization domain protein
           [Methanobrevibacter smithii DSM 2374]
          Length = 274

 Score = 36.5 bits (83), Expect = 5.8,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 81/247 (32%), Gaps = 57/247 (23%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED---LTDIILNIK---GINLKMSG 98
           NA+RR  M ++   AI  V I  + ++ +    V      LT ++ N+    G+ L    
Sbjct: 26  NAIRRCAMVNVPKIAIEDVNI--MRNDSAMFNEVLAHRLGLTPLVSNMDAIEGLPLPGDD 83

Query: 99  DSHK----RVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           D  +      ++ + GP VV + D+ +  + I+ +     +  L     + +E     G+
Sbjct: 84  DYEENNSVMFSLKEEGPKVVYSKDLISSDSKIKPVYDTIPLVKLKEGEKLNIEAVAKVGY 143

Query: 154 GYVPAKHHRTENDPIGLIT--------------IDALYSPIKKVSYTVESAREGQVLD-- 197
           G   AK   T                        DA    + K     +  +   + D  
Sbjct: 144 GKEHAKWMPTTVCVYKQYPEITFNEDVGIDYECADACPRGVLKSDKRSKEIKILDIEDCA 203

Query: 198 ----------------------------YDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
                                        +     I+TDGS+  ++ +  A   L ++  
Sbjct: 204 MCKSCVRASIRNAQSEGKDESYINVGYHENDFIFRIETDGSMPPKEVLLQACDELGEKAD 263

Query: 230 MFINFEE 236
            FI F E
Sbjct: 264 KFIRFSE 270


>gi|156537038|ref|XP_001601281.1| PREDICTED: similar to ENSANGP00000013316 [Nasonia vitripennis]
          Length = 461

 Score = 36.5 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 29/144 (20%), Positives = 51/144 (35%), Gaps = 3/144 (2%)

Query: 194 QVLDYDKLSMTIDTDGSIT-GEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPF 252
           Q LDY K+    +T GS+  G++ + +++ I Q     F       K   ++        
Sbjct: 19  QKLDYTKVYRVSET-GSLALGKEEIKMSAIIGQPFWTTFKVIPPEGKRDNKNYRKGPPST 77

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
                K     +L     +     +I   G   + ++ D+L + + G KS  EI   L  
Sbjct: 78  LVVAEKSDTLEDLKKAVASGCDNRSINDDGKSQKLSKDDILGLRDAG-KSGREIVSSLIE 136

Query: 313 MGLFLGMNLPDWPPESIEELAKKY 336
                         + I +  KKY
Sbjct: 137 NNASFSEKTEYSQEKYIRKKEKKY 160


>gi|189240695|ref|XP_973127.2| PREDICTED: similar to sil1 [Tribolium castaneum]
          Length = 391

 Score = 36.5 bits (83), Expect = 6.1,   Method: Composition-based stats.
 Identities = 15/62 (24%), Positives = 30/62 (48%), Gaps = 10/62 (16%)

Query: 280 YMGDLIQ--RTEADMLRMAN-FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKY 336
            +G+ +    T  ++ ++ N F  +S  EIK  LG + L      P    E I +L +++
Sbjct: 73  TLGEAVTDTYTPDELKKIKNEF--RSYDEIKKTLGDLKLT-----PKMDAEIIADLLQRH 125

Query: 337 ED 338
           ++
Sbjct: 126 QE 127


>gi|229012374|ref|ZP_04169551.1| DNA-damage repair protein [Bacillus mycoides DSM 2048]
 gi|228749010|gb|EEL98858.1| DNA-damage repair protein [Bacillus mycoides DSM 2048]
          Length = 421

 Score = 36.5 bits (83), Expect = 6.1,   Method: Composition-based stats.
 Identities = 30/218 (13%), Positives = 64/218 (29%), Gaps = 31/218 (14%)

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
            DI ++NP              M+ +     G         +       +ID  +  +  
Sbjct: 76  PDIIIVNPIMHT---------YMKCST-YITGLALQYVAPED---FHQYSIDEFFMDMTA 122

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
             +   S      L + +                +     I  + L   +  +   K+ K
Sbjct: 123 SIHLFASNPCEFALKFKREIYE---------RTRIESTIGIGPNLLLSKVAMDVEAKKNK 173

Query: 243 EDINVKSLPFNPALLKKV----EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
           + I   +    P  L  +    +   +S ++   L  + I  +GDL Q     + +  +F
Sbjct: 174 DGIAYWTYDDIPEKLWSIRPLSKFWGISYKTEMKLNRKGIHTIGDLAQYPLKYLKQ--SF 231

Query: 299 GRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKY 336
           G     E+   L + G+        + P +      + 
Sbjct: 232 GVIG-EELH--LHSNGIDFSRIAEKYVPATTSIAKSQI 266


>gi|332179033|gb|AEE14722.1| isocitrate dehydrogenase, NADP-dependent [Thermodesulfobium
           narugense DSM 14796]
          Length = 745

 Score = 36.5 bits (83), Expect = 6.4,   Method: Composition-based stats.
 Identities = 13/58 (22%), Positives = 30/58 (51%), Gaps = 2/58 (3%)

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           +G+L+ + +  ++++ N    SL ++K  +  +    G N+PD+P E      +K  +
Sbjct: 70  LGELVNKPDTILIKLPNISA-SLPQLKDAIKELQAK-GFNIPDYPDELKSAQDEKIRE 125


>gi|70945964|ref|XP_742745.1| DNA-directed RNA polymerase II [Plasmodium chabaudi chabaudi]
 gi|56521898|emb|CAH80621.1| DNA-directed RNA polymerase II, putative [Plasmodium chabaudi
           chabaudi]
          Length = 331

 Score = 36.5 bits (83), Expect = 6.6,   Method: Composition-based stats.
 Identities = 31/177 (17%), Positives = 56/177 (31%), Gaps = 33/177 (18%)

Query: 13  NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEI 72
           +    I +    +N    I           L NALRR+++S +   A+  V +       
Sbjct: 6   SKKHEIEIKSISKNEMSFILY----NSNTALANALRRIMLSEVPTLAVDIVNVYENTSPF 61

Query: 73  --SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVT-------IFKRG---------PGVV 114
               I      +     NIK    +      +  +       I  +             +
Sbjct: 62  HDEFIAHRIGLIPIDSRNIKSYEFRERCKCKETCSRCTVQYIIEVKCNNANKIDVSHYDI 121

Query: 115 TAGDIQTV-----------NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH 160
            A D +             N+I+ ++    I  L  +  + M+LT +KG G + AK 
Sbjct: 122 EALDHEPNIPMPIPNDNKHNNIDKMDTAIPIVTLSKNQTLHMKLTATKGIGKMHAKW 178


>gi|154493649|ref|ZP_02032969.1| hypothetical protein PARMER_02989 [Parabacteroides merdae ATCC
           43184]
 gi|154086859|gb|EDN85904.1| hypothetical protein PARMER_02989 [Parabacteroides merdae ATCC
           43184]
          Length = 310

 Score = 36.5 bits (83), Expect = 6.7,   Method: Composition-based stats.
 Identities = 26/160 (16%), Positives = 56/160 (35%), Gaps = 6/160 (3%)

Query: 137 LDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           L  +  +++EL   K  G+ P      H  E         D  Y  +      VE     
Sbjct: 57  LLSNTPLQVELDFMKIKGHTPKNTPIEHMKEFYKDFDEMQDDFYDGMIITGAPVEQMPFE 116

Query: 194 QVLDYDKLSMTI--DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           +V  +++++  I       +T    +  A++           ++ P K      +    P
Sbjct: 117 EVNYWEEVT-EIFDWARTHVTSTLYICWAAQAGLYHFYGVPKYDLPAKMFGVFRHTLREP 175

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           + P      +E  +       +R E+++ + DL   +E++
Sbjct: 176 YVPIFRGFDDEFYVPHSRHTEIRREDVMKVPDLTLLSESE 215


>gi|115975016|ref|XP_001187974.1| PREDICTED: similar to p107 [Strongylocentrotus purpuratus]
          Length = 985

 Score = 36.5 bits (83), Expect = 6.7,   Method: Composition-based stats.
 Identities = 20/114 (17%), Positives = 38/114 (33%), Gaps = 3/114 (2%)

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           +    LK + ++ +   I   GP +V      T  +I  ++P   I +   D       T
Sbjct: 297 LSHECLKSNRNAPRNCNI---GPLIVNKRPSPTTPEIITIDPGMPIASEGDDIEFDCSTT 353

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           +  G+            +   +I+ D  +  IK V           +   +KL 
Sbjct: 354 LEDGNAVWFPIGGEPPPEDHIIISDDGSHMAIKNVRTNDTDVMACGIFCQEKLV 407


>gi|77410377|ref|ZP_00786773.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
          agalactiae COH1]
 gi|77171014|gb|EAO74487.1| DNA-directed RNA polymerase, alpha subunit [Streptococcus
          agalactiae COH1]
          Length = 30

 Score = 36.5 bits (83), Expect = 6.8,   Method: Composition-based stats.
 Identities = 10/32 (31%), Positives = 14/32 (43%), Gaps = 4/32 (12%)

Query: 8  ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGF 39
          E  KP     I    E ++    + EPL RG+
Sbjct: 3  EFEKP----IITKIDENKDYGRFVIEPLERGY 30


>gi|237654460|ref|YP_002890774.1| hypothetical protein Tmz1t_3808 [Thauera sp. MZ1T]
 gi|237625707|gb|ACR02397.1| protein of unknown function DUF820 [Thauera sp. MZ1T]
          Length = 187

 Score = 36.1 bits (82), Expect = 6.8,   Method: Composition-based stats.
 Identities = 18/122 (14%), Positives = 48/122 (39%), Gaps = 7/122 (5%)

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESA 190
           DHV+  L++   +       +             +  + ++  DA++ P   VS   E  
Sbjct: 42  DHVVVALNIATSL-------RQKLRGTPCRAYISDMQLEVMQADAVFYPDVMVSCHPEDL 94

Query: 191 REGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250
              +VL + ++ + + +D +   +     A+  + D L  ++  +  ++ V+    + S 
Sbjct: 95  AAERVLHHPRVIIEVLSDSTAAYDRGAKFAAYRMLDSLQEYVLVDPERRSVEIFRRLPSN 154

Query: 251 PF 252
            +
Sbjct: 155 DW 156


>gi|225871009|ref|YP_002746956.1| DNA-binding protein [Streptococcus equi subsp. equi 4047]
 gi|225700413|emb|CAW94788.1| putative DNA-binding protein [Streptococcus equi subsp. equi 4047]
          Length = 322

 Score = 36.1 bits (82), Expect = 6.8,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 23/52 (44%)

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            L  +EEL+L +   N      I  + D    T  ++L +   G++ +  +K
Sbjct: 262 ELTFLEELDLPLSKVNLFNQYGIHTLEDFSAWTTQELLDIPGVGKQMIARLK 313


>gi|218262695|ref|ZP_03477053.1| hypothetical protein PRABACTJOHN_02732 [Parabacteroides johnsonii
           DSM 18315]
 gi|218223246|gb|EEC95896.1| hypothetical protein PRABACTJOHN_02732 [Parabacteroides johnsonii
           DSM 18315]
          Length = 310

 Score = 36.1 bits (82), Expect = 6.8,   Method: Composition-based stats.
 Identities = 26/160 (16%), Positives = 56/160 (35%), Gaps = 6/160 (3%)

Query: 137 LDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           L  +  +++EL   K  G+ P      H  E         D  Y  +      VE     
Sbjct: 57  LLSNTPLQVELDFMKIKGHTPKNTPIEHMQEFYKDFDEMQDDFYDGMIITGAPVEQMPFE 116

Query: 194 QVLDYDKLSMTI--DTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           +V  +++++  I       +T    +  A++           ++ P K      +    P
Sbjct: 117 EVNYWEEVT-EIFDWARTHVTSTLYICWAAQAGLYHFYGVPKYDLPAKMFGVFRHTLREP 175

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           + P      +E  +       +R E+++ + DL   +E++
Sbjct: 176 YVPIFRGFDDEFYVPHSRHTEIRREDVMKVPDLTLLSESE 215


>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 = 6.8,   Method: Composition-based stats.
 Identities = 43/263 (16%), Positives = 81/263 (30%), Gaps = 63/263 (23%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHT---LGNALRRVLMSSLRGAAITAVQIDG------- 67
           + + +  E+    + E        T     N++RRV ++ +   AI  +QI+        
Sbjct: 9   VSITELTEDNVKFVVE-------DTDLSTANSVRRVFIAEVPTLAIDWIQIEENSSVLND 61

Query: 68  --VLHEISSIKGVHEDLTDIILNIKGINLKMSG-DSHKRVTIFKRGPGVVTAGDIQTVND 124
             + H I  I    +D+ D I   +         D      +  +  G  T     T  D
Sbjct: 62  EFLSHRIGLIPLTSDDVVDKIQYSRDCMCDDFCQDCSVEFYLDVKCTGEGTRQ--VTTRD 119

Query: 125 IEVLNP---------------------DHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
           +  +NP                     D +I  L     ++ +    KG G   AK    
Sbjct: 120 LISMNPKVVPITSRSRGDSSKSFGEQDDILIAKLRKGQSLKFKAFAKKGFGKEHAKWQCV 179

Query: 164 ENDPIGLITIDAL---------------YS--PIKKVSYTVESAREGQVLDYDKLSMTID 206
                     +AL               YS     +  Y  +    G+   +      ++
Sbjct: 180 SAVAFEYDPDNALRHTTYPKPEEWPKSEYSELADDEDKYQADFDPHGKPNKF---FFNVE 236

Query: 207 TDGSITGEDSVALASRILQDQLG 229
           + G++  E+ V     +L+ +L 
Sbjct: 237 STGALRPENIVLNGLAVLKKKLS 259


>gi|115707234|ref|XP_792215.2| PREDICTED: similar to p107 [Strongylocentrotus purpuratus]
          Length = 930

 Score = 36.1 bits (82), Expect = 6.8,   Method: Composition-based stats.
 Identities = 20/114 (17%), Positives = 38/114 (33%), Gaps = 3/114 (2%)

Query: 89  IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELT 148
           +    LK + ++ +   I   GP +V      T  +I  ++P   I +   D       T
Sbjct: 297 LSHECLKSNRNAPRNCNI---GPLIVNKRPSPTTPEIITIDPGMPIASEGDDIEFDCSTT 353

Query: 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLS 202
           +  G+            +   +I+ D  +  IK V           +   +KL 
Sbjct: 354 LEDGNAVWFPIGGEPPPEDHIIISDDGSHMAIKNVRTNDTDVMACGIFCQEKLV 407


>gi|57242655|ref|ZP_00370592.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter upsaliensis
           RM3195]
 gi|57016584|gb|EAL53368.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter upsaliensis
           RM3195]
          Length = 734

 Score = 36.1 bits (82), Expect = 6.8,   Method: Composition-based stats.
 Identities = 17/80 (21%), Positives = 40/80 (50%), Gaps = 9/80 (11%)

Query: 254 PALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313
             + +  E L+   +  N L       +G+L+++ +A++++  N    S+ ++K  +  +
Sbjct: 44  RIIAEFSESLKEEQKCENALEN-----LGELVKKADANLIKTPNISA-SIPQLKAAIEEL 97

Query: 314 GLFLGMNLPDWP--PESIEE 331
               G  LP++P  P++ EE
Sbjct: 98  QKK-GYMLPNYPDEPKNDEE 116


>gi|332017912|gb|EGI58566.1| DNA-directed RNA polymerase II subunit RPB3 [Acromyrmex echinatior]
          Length = 256

 Score = 36.1 bits (82), Expect = 6.9,   Method: Composition-based stats.
 Identities = 34/236 (14%), Positives = 79/236 (33%), Gaps = 31/236 (13%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKG 77
           + +    E       E        ++ N++RRV ++     AI  +Q++     +  I+ 
Sbjct: 9   VHISDLTEENVKFQVEDTE----LSVANSMRRVFIAETPTMAIDWIQLEANSTVVDRIQY 64

Query: 78  VHE----DLTDIILNIKGINLKMSGDSHKRV-TIFKRGPG----VVTAGDIQTVNDIEVL 128
             +    D          +++K + +  + V T   +        VT+   +        
Sbjct: 65  TRDCQCMDFCPECSVEFTLDVKCTEEQTRHVTTADFKSSDPRVLPVTSRHREDDASEYGE 124

Query: 129 NPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITID-------------- 174
             + +I  L     +++     KG G   AK + T          +              
Sbjct: 125 TDEILIVKLRKGQELKLRAYAKKGFGKEHAKWNPTAGVSFEYDPDNTMRHTLFPKADEWP 184

Query: 175 -ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
            + YS +++  Y      E +   Y      +++ G++  E+ V +    L+++L 
Sbjct: 185 KSEYSELEEDQYEASFNWEAKPNKY---YFNVESSGALKPENIVMMGIAALKNKLS 237


>gi|167044506|gb|ABZ09181.1| putative RNA polymerase Rpb3/RpoA insert domain protein [uncultured
           marine crenarchaeote HF4000_APKG6J21]
          Length = 200

 Score = 36.1 bits (82), Expect = 7.0,   Method: Composition-based stats.
 Identities = 29/183 (15%), Positives = 59/183 (32%), Gaps = 40/183 (21%)

Query: 44  GNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIILNIKGINL 94
            NALRR+ ++ +   AI  V I         +G+   +  I  +  +L     +   + L
Sbjct: 26  ANALRRICLNGVPIFAIDTVDIIENSSVIPDEGLALTLGMIP-LKTELNGFDESNSRVIL 84

Query: 95  KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHG 154
            +  ++ +   I         A        ++ ++    I +L     +++E     G G
Sbjct: 85  VLDSEAAETTKIVTS------AELESKDQVVKPISKQIPIVHLAPGQRIKLEAYARLGRG 138

Query: 155 YVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
              AK +             A  S +       E              +T++T GS+   
Sbjct: 139 TEHAKWNS------------ANISVLTNADKEGEH------------ILTVETTGSLEPR 174

Query: 215 DSV 217
             +
Sbjct: 175 QII 177


>gi|86149178|ref|ZP_01067410.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           subsp. jejuni CF93-6]
 gi|88596941|ref|ZP_01100177.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           subsp. jejuni 84-25]
 gi|218562183|ref|YP_002343962.1| isocitrate dehydrogenase [Campylobacter jejuni subsp. jejuni NCTC
           11168]
 gi|85840536|gb|EAQ57793.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           subsp. jejuni CF93-6]
 gi|88190630|gb|EAQ94603.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           subsp. jejuni 84-25]
 gi|112359889|emb|CAL34677.1| isocitrate dehydrogenase [Campylobacter jejuni subsp. jejuni NCTC
           11168]
          Length = 734

 Score = 36.1 bits (82), Expect = 7.0,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 34/54 (62%), Gaps = 4/54 (7%)

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP--PESIEEL 332
           +G+L++R++A++++  N    S+ ++K  +  +    G  LP++P  P++ EEL
Sbjct: 66  LGELVKRSDANLIKTPNISA-SIPQLKAAIKELQDK-GYMLPNYPDEPKNDEEL 117


>gi|195978634|ref|YP_002123878.1| hypothetical protein Sez_1532 [Streptococcus equi subsp.
           zooepidemicus MGCS10565]
 gi|195975339|gb|ACG62865.1| hypothetical protein Sez_1532 [Streptococcus equi subsp.
           zooepidemicus MGCS10565]
          Length = 322

 Score = 36.1 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 23/52 (44%)

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            L  +EEL+L +   N      I  + D    T  ++L +   G++ +  +K
Sbjct: 262 ELTFLEELDLPLSKVNLFNQYGIHTLEDFSAWTTQELLDIPGVGKQMIARLK 313


>gi|57238269|ref|YP_178650.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           RM1221]
 gi|57167073|gb|AAW35852.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           RM1221]
 gi|315057949|gb|ADT72278.1| Isocitrate dehydrogenase (NADP) ; Monomeric isocitrate
           dehydrogenase (NADP) [Campylobacter jejuni subsp. jejuni
           S3]
          Length = 734

 Score = 36.1 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 34/54 (62%), Gaps = 4/54 (7%)

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP--PESIEEL 332
           +G+L++R++A++++  N    S+ ++K  +  +    G  LP++P  P++ EEL
Sbjct: 66  LGELVKRSDANLIKTPNISA-SIPQLKAAIKELQDK-GYMLPNYPDEPKNDEEL 117


>gi|225868039|ref|YP_002743987.1| DNA-binding protein [Streptococcus equi subsp. zooepidemicus]
 gi|225701315|emb|CAW98334.1| putative DNA-binding protein [Streptococcus equi subsp.
           zooepidemicus]
          Length = 322

 Score = 36.1 bits (82), Expect = 7.2,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 23/52 (44%)

Query: 256 LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307
            L  +EEL+L +   N      I  + D    T  ++L +   G++ +  +K
Sbjct: 262 ELTFLEELDLPLSKVNLFNQYGIHTLEDFSAWTTQELLDIPGVGKQMIARLK 313


>gi|189212048|ref|XP_001942351.1| fatty acid synthase subunit alpha reductase [Pyrenophora
            tritici-repentis Pt-1C-BFP]
 gi|187979550|gb|EDU46176.1| fatty acid synthase subunit alpha reductase [Pyrenophora
            tritici-repentis Pt-1C-BFP]
          Length = 1618

 Score = 36.1 bits (82), Expect = 7.2,   Method: Composition-based stats.
 Identities = 27/140 (19%), Positives = 54/140 (38%), Gaps = 28/140 (20%)

Query: 204  TIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEEL 263
             +++DGS++ E  + +A           +   + +     D +      + A  K V++ 
Sbjct: 916  EMESDGSLSLEGCIEMA---------WIMGLIKHQTANPMDDDGVVGWVDAATQKPVKDS 966

Query: 264  ELS-VRSTNCLRGENIVYMG-DLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNL 321
            E+     +  L    I  +  ++            +F ++SL E         L L  +L
Sbjct: 967  EIPAQYLSRILEHSGIRTIEPEICDNGYD-----PDF-KESLQE---------LVLKRDL 1011

Query: 322  PDWP--PESIEELAKKYEDK 339
            P +    ES E+L +K+ DK
Sbjct: 1012 PPFETSAESAEDLRRKHGDK 1031


>gi|27467964|ref|NP_764601.1| DNA-damage repair protein [Staphylococcus epidermidis ATCC 12228]
 gi|57866878|ref|YP_188513.1| ImpB/MucB/SamB family protein [Staphylococcus epidermidis RP62A]
 gi|251810796|ref|ZP_04825269.1| possible DNA-directed DNA polymerase [Staphylococcus epidermidis
           BCM-HMP0060]
 gi|282876200|ref|ZP_06285067.1| ImpB/MucB/SamB family protein [Staphylococcus epidermidis SK135]
 gi|293366670|ref|ZP_06613347.1| ImpB/MucB/SamB family protein [Staphylococcus epidermidis
           M23864:W2(grey)]
 gi|27315509|gb|AAO04643.1|AE016747_140 DNA-damage repair protein [Staphylococcus epidermidis ATCC 12228]
 gi|57637536|gb|AAW54324.1| ImpB/MucB/SamB family protein [Staphylococcus epidermidis RP62A]
 gi|251805631|gb|EES58288.1| possible DNA-directed DNA polymerase [Staphylococcus epidermidis
           BCM-HMP0060]
 gi|281295225|gb|EFA87752.1| ImpB/MucB/SamB family protein [Staphylococcus epidermidis SK135]
 gi|291319439|gb|EFE59808.1| ImpB/MucB/SamB family protein [Staphylococcus epidermidis
           M23864:W2(grey)]
 gi|329729814|gb|EGG66210.1| ImpB/MucB/SamB family protein [Staphylococcus epidermidis VCU144]
 gi|329735718|gb|EGG72000.1| ImpB/MucB/SamB family protein [Staphylococcus epidermidis VCU045]
          Length = 420

 Score = 36.1 bits (82), Expect = 7.2,   Method: Composition-based stats.
 Identities = 24/181 (13%), Positives = 50/181 (27%), Gaps = 28/181 (15%)

Query: 123 NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKK 182
           NDI ++NP              M   ++               + +   +ID  +  +  
Sbjct: 76  NDIYIINP-------------SMRKYLNVSVAISKIALRYVPPEDLHQYSIDEFFMDVTD 122

Query: 183 VSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK 242
             +   S        +    +          E  +     I  + L   +  +   K  +
Sbjct: 123 SYHRFNSTVFAFCKRFQNEILE---------ETGIHCTIGIGSNMLLSKVAMDIEAKHSE 173

Query: 243 EDINVKSLPFNPALLKKV----EELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANF 298
             I        P  L  +    +   ++ R+   L    I  +GDL +     +    +F
Sbjct: 174 NGIAEWRYQDVPEKLWPIQPLRDFWGINKRTEKKLNKRGIFTIGDLAKYPYHYLK--RDF 231

Query: 299 G 299
           G
Sbjct: 232 G 232


>gi|303256975|ref|ZP_07342989.1| transcription termination factor NusA [Burkholderiales bacterium
           1_1_47]
 gi|330999163|ref|ZP_08322882.1| transcription termination factor NusA [Parasutterella
           excrementihominis YIT 11859]
 gi|302860466|gb|EFL83543.1| transcription termination factor NusA [Burkholderiales bacterium
           1_1_47]
 gi|329575363|gb|EGG56907.1| transcription termination factor NusA [Parasutterella
           excrementihominis YIT 11859]
          Length = 499

 Score = 36.1 bits (82), Expect = 7.3,   Method: Composition-based stats.
 Identities = 9/74 (12%), Positives = 27/74 (36%)

Query: 234 FEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
           +E    +  +    +     P   +  + L++       L    I  + ++    E ++L
Sbjct: 345 WEIEVMDDDQAAKKREDEIAPRRQELCDRLDIDEEVAQVLIENGIETLEEVAYLPEEELL 404

Query: 294 RMANFGRKSLVEIK 307
            +  F   ++ E++
Sbjct: 405 SIEQFDEDTVKELR 418


>gi|205355387|ref|ZP_03222158.1| isocitrate dehydrogenase [Campylobacter jejuni subsp. jejuni
           CG8421]
 gi|205346621|gb|EDZ33253.1| isocitrate dehydrogenase [Campylobacter jejuni subsp. jejuni
           CG8421]
          Length = 734

 Score = 36.1 bits (82), Expect = 7.3,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 34/54 (62%), Gaps = 4/54 (7%)

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP--PESIEEL 332
           +G+L++R++A++++  N    S+ ++K  +  +    G  LP++P  P++ EEL
Sbjct: 66  LGELVKRSDANLIKTPNISA-SIPQLKAAIKELQDK-GYMLPNYPDEPKNDEEL 117


>gi|86153463|ref|ZP_01071667.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           subsp. jejuni HB93-13]
 gi|85843189|gb|EAQ60400.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           subsp. jejuni HB93-13]
          Length = 734

 Score = 36.1 bits (82), Expect = 7.3,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 34/54 (62%), Gaps = 4/54 (7%)

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP--PESIEEL 332
           +G+L++R++A++++  N    S+ ++K  +  +    G  LP++P  P++ EEL
Sbjct: 66  LGELVKRSDANLIKTPNISA-SIPQLKAAIKELQDK-GYMLPNYPDEPKNDEEL 117


>gi|157414812|ref|YP_001482068.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           subsp. jejuni 81116]
 gi|157385776|gb|ABV52091.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           subsp. jejuni 81116]
 gi|307747450|gb|ADN90720.1| Isocitrate dehydrogenase [NADP] [Campylobacter jejuni subsp. jejuni
           M1]
 gi|315931725|gb|EFV10680.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           subsp. jejuni 327]
          Length = 734

 Score = 36.1 bits (82), Expect = 7.3,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 34/54 (62%), Gaps = 4/54 (7%)

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP--PESIEEL 332
           +G+L++R++A++++  N    S+ ++K  +  +    G  LP++P  P++ EEL
Sbjct: 66  LGELVKRSDANLIKTPNISA-SIPQLKAAIKELQDK-GYMLPNYPDEPKNDEEL 117


>gi|86151846|ref|ZP_01070060.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           subsp. jejuni 260.94]
 gi|85841475|gb|EAQ58723.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           subsp. jejuni 260.94]
          Length = 734

 Score = 36.1 bits (82), Expect = 7.4,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 34/54 (62%), Gaps = 4/54 (7%)

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP--PESIEEL 332
           +G+L++R++A++++  N    S+ ++K  +  +    G  LP++P  P++ EEL
Sbjct: 66  LGELVKRSDANLIKTPNISA-SIPQLKAAIKELQDK-GYMLPNYPDEPKNDEEL 117


>gi|315927029|gb|EFV06384.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           subsp. jejuni DFVF1099]
 gi|315930923|gb|EFV09903.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           subsp. jejuni 305]
          Length = 767

 Score = 36.1 bits (82), Expect = 7.5,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 34/54 (62%), Gaps = 4/54 (7%)

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP--PESIEEL 332
           +G+L++R++A++++  N    S+ ++K  +  +    G  LP++P  P++ EEL
Sbjct: 99  LGELVKRSDANLIKTPNISA-SIPQLKAAIKELQDK-GYMLPNYPDEPKNDEEL 150


>gi|315124055|ref|YP_004066059.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           subsp. jejuni ICDCCJ07001]
 gi|315017777|gb|ADT65870.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           subsp. jejuni ICDCCJ07001]
          Length = 734

 Score = 36.1 bits (82), Expect = 7.5,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 34/54 (62%), Gaps = 4/54 (7%)

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP--PESIEEL 332
           +G+L++R++A++++  N    S+ ++K  +  +    G  LP++P  P++ EEL
Sbjct: 66  LGELVKRSDANLIKTPNISA-SIPQLKAAIKELQDK-GYMLPNYPDEPKNDEEL 117


>gi|47223252|emb|CAF98636.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 1830

 Score = 36.1 bits (82), Expect = 7.7,   Method: Composition-based stats.
 Identities = 44/265 (16%), Positives = 85/265 (32%), Gaps = 28/265 (10%)

Query: 66  DGVLHEI----SSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
           D V +E     S    V +++  +   ++    ++   S +RV         + A   + 
Sbjct: 320 DSVFNEYRLIMSERDQVIKEVDKLQTELESAEARLKNTSSERVVAS----EELEALRQEL 375

Query: 122 VNDIEVLNPDHVICNLDV-------DAVVRMELTVSKGHGYVPAKHHRTENDPIGLITID 174
            +   +++ D  IC  +        +   + E            +  R E D  G    +
Sbjct: 376 NSS--LVDRDRAICERNELLEKYCHEVKDKAEAQKELSQACKDIEMVREERDVAGKERTE 433

Query: 175 ALYSPIKKVSYTVESAREGQ-----VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLG 229
           A+   I++     E  +  Q      L++D          ++  E +      +L+ Q  
Sbjct: 434 AI---IQRDQLLREYYQARQVAATAGLNFDSTRSEKQDTATLDMERANKE-IEVLRKQYE 489

Query: 230 MFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQ--R 287
                 +   +  E    +         K V E E      + LR E    + DL    R
Sbjct: 490 AMSQELKEATQEAEVAKCRRDWAFQERDKIVAERESIRTLCDNLRRERDRAVSDLADALR 549

Query: 288 TEADMLRMANFGRKSLVEIKGVLGT 312
              DM +  N   + L EIK  + +
Sbjct: 550 NLDDMRKQKNDALRELKEIKEKMES 574


>gi|284925794|gb|ADC28146.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           subsp. jejuni IA3902]
          Length = 767

 Score = 36.1 bits (82), Expect = 7.9,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 34/54 (62%), Gaps = 4/54 (7%)

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP--PESIEEL 332
           +G+L++R++A++++  N    S+ ++K  +  +    G  LP++P  P++ EEL
Sbjct: 99  LGELVKRSDANLIKTPNISA-SIPQLKAAIKELQDK-GYMLPNYPDEPKNDEEL 150


>gi|330433115|gb|AEC18174.1| transcription elongation factor NusA [Gallibacterium anatis UMN179]
          Length = 495

 Score = 36.1 bits (82), Expect = 7.9,   Method: Composition-based stats.
 Identities = 25/170 (14%), Positives = 49/170 (28%), Gaps = 36/170 (21%)

Query: 202 SMTIDTDGSITGEDSVALASRILQ---------DQLGMFINFEEPKKEVKEDINVKSLPF 252
            ++I  D      D    A+ + Q         +       ++       E  N   L  
Sbjct: 293 VVSIVVDEDKKSMDIAVEAANLAQAIGRNGQNVNLASRLTGWKLNVMSSDELENKHQLEN 352

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG---- 308
              +   +E L+L     N L  E    + ++      ++L +  F      E++     
Sbjct: 353 QKTVNLFMESLDLDEEFANLLTEEGFRTLEEIAYVPTEELLEIDGFDEDLAEELRNRAKE 412

Query: 309 -----------------------VLGTMGLFLGMNLPDWPPESIEELAKK 335
                                   L  M   L + L +    ++EELA++
Sbjct: 413 VLTKIALAEEQALANIDVEEALLKLDGMNRHLAVKLAEKKITTLEELAEQ 462


>gi|150008125|ref|YP_001302868.1| homoserine O-succinyltransferase [Parabacteroides distasonis ATCC
           8503]
 gi|255015078|ref|ZP_05287204.1| homoserine O-succinyltransferase [Bacteroides sp. 2_1_7]
 gi|256840696|ref|ZP_05546204.1| homoserine O-succinyltransferase [Parabacteroides sp. D13]
 gi|262381300|ref|ZP_06074438.1| homoserine O-succinyltransferase [Bacteroides sp. 2_1_33B]
 gi|298376450|ref|ZP_06986405.1| homoserine O-succinyltransferase [Bacteroides sp. 3_1_19]
 gi|301309770|ref|ZP_07215709.1| homoserine O-succinyltransferase [Bacteroides sp. 20_3]
 gi|166233685|sp|A6LC32|META_PARD8 RecName: Full=Homoserine O-succinyltransferase; AltName:
           Full=Homoserine O-transsuccinylase; Short=HTS
 gi|149936549|gb|ABR43246.1| homoserine O-succinyltransferase [Parabacteroides distasonis ATCC
           8503]
 gi|256737968|gb|EEU51294.1| homoserine O-succinyltransferase [Parabacteroides sp. D13]
 gi|262296477|gb|EEY84407.1| homoserine O-succinyltransferase [Bacteroides sp. 2_1_33B]
 gi|298266328|gb|EFI07986.1| homoserine O-succinyltransferase [Bacteroides sp. 3_1_19]
 gi|300831344|gb|EFK61975.1| homoserine O-succinyltransferase [Bacteroides sp. 20_3]
          Length = 310

 Score = 36.1 bits (82), Expect = 7.9,   Method: Composition-based stats.
 Identities = 26/160 (16%), Positives = 54/160 (33%), Gaps = 6/160 (3%)

Query: 137 LDVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALYSPIKKVSYTVESAREG 193
           L  +  +++EL   K  G+ P      H  E         D  Y  +      VE     
Sbjct: 57  LLSNTPLQVELDFMKIKGHTPKNTPIEHMQEFYKDFDEMADDFYDGMIVTGAPVEQMPFE 116

Query: 194 QVLDYDKL--SMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           +V  ++++           +T    +  A++           ++ P K      +    P
Sbjct: 117 EVSYWEEITQIFD-WARTHVTSTLYICWAAQAGLYHFYGVPKYDLPAKMFGVFRHSLREP 175

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           F P      +E  +       +R E+I+ + +L   +E++
Sbjct: 176 FVPIFRGFDDEFFVPHSRHTEIRREDIMKVPELTLLSESE 215


>gi|283955953|ref|ZP_06373443.1| isocitrate dehydrogenase [Campylobacter jejuni subsp. jejuni 1336]
 gi|283792613|gb|EFC31392.1| isocitrate dehydrogenase [Campylobacter jejuni subsp. jejuni 1336]
          Length = 767

 Score = 36.1 bits (82), Expect = 8.0,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 34/54 (62%), Gaps = 4/54 (7%)

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP--PESIEEL 332
           +G+L++R++A++++  N    S+ ++K  +  +    G  LP++P  P++ EEL
Sbjct: 99  LGELVKRSDANLIKTPNISA-SIPQLKAAIKELQDK-GYMLPNYPDEPKNDEEL 150


>gi|121612541|ref|YP_001000231.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|167005187|ref|ZP_02270945.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|121504172|gb|EAQ73167.2| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           subsp. jejuni 81-176]
          Length = 767

 Score = 36.1 bits (82), Expect = 8.1,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 34/54 (62%), Gaps = 4/54 (7%)

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP--PESIEEL 332
           +G+L++R++A++++  N    S+ ++K  +  +    G  LP++P  P++ EEL
Sbjct: 99  LGELVKRSDANLIKTPNISA-SIPQLKAAIKELQDK-GYMLPNYPDEPKNDEEL 150


>gi|153951562|ref|YP_001398441.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           subsp. doylei 269.97]
 gi|152939008|gb|ABS43749.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           subsp. doylei 269.97]
          Length = 767

 Score = 36.1 bits (82), Expect = 8.1,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 34/54 (62%), Gaps = 4/54 (7%)

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP--PESIEEL 332
           +G+L++R++A++++  N    S+ ++K  +  +    G  LP++P  P++ EEL
Sbjct: 99  LGELVKRSDANLIKTPNISA-SIPQLKAAIKELQDK-GYMLPNYPDEPKNDEEL 150


>gi|12545427|ref|NP_074977.1| hypothetical protein AsloCp17 [Euglena longa]
 gi|12329891|emb|CAC24588.1| hypothetical protein [Euglena longa]
          Length = 170

 Score = 36.1 bits (82), Expect = 8.1,   Method: Composition-based stats.
 Identities = 23/158 (14%), Positives = 63/158 (39%), Gaps = 27/158 (17%)

Query: 69  LHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK----RVTIFKRGPGVVTAGDIQTV-- 122
           ++E   I+ + E+L++I +N+K +  K +  ++K     + +        +A DI     
Sbjct: 27  VNEFFDIEEIKENLSNICINLKKLRFKFNPKNNKEKKTFIILNSFNKKSFSAKDIIIPST 86

Query: 123 NDIEVLNPDHVICN-LDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           ++++++N    + N +     +++ + +     Y                     Y+PIK
Sbjct: 87  SNLKIVNLKEHLFNKISQKINLKVLIKIENNENY--------------------FYNPIK 126

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVAL 219
           ++++ +E            L+  I+ +      +S+  
Sbjct: 127 RINFILEKNNNIGKYIILDLNSDININPFKAFIESLKY 164


>gi|170064093|ref|XP_001867382.1| myosin I [Culex quinquefasciatus]
 gi|167881523|gb|EDS44906.1| myosin I [Culex quinquefasciatus]
          Length = 488

 Score = 36.1 bits (82), Expect = 8.2,   Method: Composition-based stats.
 Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 6/67 (8%)

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMG-DLIQRTEADMLRMANFGR 300
           ++D  V     + A +K +EE   + R+    +       G DL + +E D+  +  FG+
Sbjct: 105 EDDAQVGEDEVDLAKMKSLEEKSKNSRARVHYKK---FTRGKDLSRASEKDLANI--FGK 159

Query: 301 KSLVEIK 307
           KSL E+K
Sbjct: 160 KSLEEVK 166


>gi|222445013|ref|ZP_03607528.1| hypothetical protein METSMIALI_00629 [Methanobrevibacter smithii
           DSM 2375]
 gi|222434578|gb|EEE41743.1| hypothetical protein METSMIALI_00629 [Methanobrevibacter smithii
           DSM 2375]
          Length = 274

 Score = 36.1 bits (82), Expect = 8.3,   Method: Composition-based stats.
 Identities = 45/247 (18%), Positives = 82/247 (33%), Gaps = 57/247 (23%)

Query: 45  NALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED---LTDIILNIK---GINLKMSG 98
           NA+RR  M ++   AI  V I  + ++ +    V      LT ++ N+    G+ L    
Sbjct: 26  NAIRRCAMVNVPKIAIEDVNI--MRNDSAMFNEVLAHRLGLTPLVSNMDAIEGLPLPGDD 83

Query: 99  DSHK----RVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVSKGH 153
           D  +      ++ + GP VV + D+ +  + I+ +     +  L     + +E     G+
Sbjct: 84  DYEENNSVMFSLKEEGPKVVYSKDLISSDSKIKPVYDTIPLVKLKEGEKLNIEAVAKVGY 143

Query: 154 GYVPAKHHRTENDPIGLIT--------------IDALYSPIKKVSYTVESARE------- 192
           G   AK   T                        DA    + K     +  +        
Sbjct: 144 GKEHAKWMPTTVCVYKQYPEITFNEDVGIDYECADACPRGVLKSDKRSKEIKILDIENCA 203

Query: 193 ----------------GQVLDY-------DKLSMTIDTDGSITGEDSVALASRILQDQLG 229
                           G+   Y       +     I+TDGS+  ++ +  A   L ++  
Sbjct: 204 MCKSCVRASIRNAQSEGKDESYINVGYHENDFIFRIETDGSMPPKEVLLQACDELGEKAD 263

Query: 230 MFINFEE 236
            FI F E
Sbjct: 264 KFIRFSE 270


>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 = 36.1 bits (82), Expect = 8.3,   Method: Composition-based stats.
 Identities = 30/176 (17%), Positives = 62/176 (35%), Gaps = 34/176 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------V 68
           + + +  ++    + E        ++ N+LRRV ++     AI  VQ++          +
Sbjct: 9   VQITELTDDNVKFVLEDTE----LSVANSLRRVFIAETPTLAIDWVQLEANSTVLSDEFL 64

Query: 69  LHEISSIKGVHEDLTDIILNIKG-INLKMSGDSHKRVTIFKRGPGV----VTAGDI---- 119
            H I  I  + +D+ + +   +  I L    +     T+  +        VT  D+    
Sbjct: 65  AHRIGLIPLISDDVVERLQYTRDCICLDFCPECSVEFTLDVKCSEEQTRHVTTADLKSSN 124

Query: 120 ------------QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
                       +  N+    N + +I  L     +++     KG G   AK + T
Sbjct: 125 AKVLPVTSRNQGEEDNEYGESNDEILIIKLRKGQELKLRAYAKKGFGKEHAKWNPT 180


>gi|283954181|ref|ZP_06371706.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           subsp. jejuni 414]
 gi|283794460|gb|EFC33204.1| isocitrate dehydrogenase, NADP-dependent [Campylobacter jejuni
           subsp. jejuni 414]
          Length = 734

 Score = 36.1 bits (82), Expect = 8.4,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 34/54 (62%), Gaps = 4/54 (7%)

Query: 281 MGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWP--PESIEEL 332
           +G+L++R++A++++  N    S+ ++K  +  +    G  LP++P  P++ EEL
Sbjct: 66  LGELVKRSDANLIKTPNISA-SIPQLKAAIKELQDK-GYMLPNYPDEPKNDEEL 117


>gi|160880928|ref|YP_001559896.1| hypothetical protein Cphy_2797 [Clostridium phytofermentans ISDg]
 gi|189039771|sp|A9KNY7|Y2797_CLOPH RecName: Full=UPF0210 protein Cphy_2797
 gi|160429594|gb|ABX43157.1| protein of unknown function DUF711 [Clostridium phytofermentans
           ISDg]
          Length = 454

 Score = 36.1 bits (82), Expect = 8.5,   Method: Composition-based stats.
 Identities = 34/265 (12%), Positives = 80/265 (30%), Gaps = 23/265 (8%)

Query: 73  SSIKGVHEDLTDIILNIKGINL-------KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDI 125
           S+++ +++++ D I  +    +       +  G       I      ++ A   +T +D 
Sbjct: 36  SNLEELNQNIYDKITTVAKDLVTTGKKIERQFGIPVVNKRISVTPIAMIGASACKTPSDF 95

Query: 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK---- 181
             +          V        +     G   ++    E+ P  L   + + S +     
Sbjct: 96  VTIAKTLDRAANTVGVNFIGGYSALVSKGMTSSERLLIESIPEALAVTERVCSSVNVGST 155

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEV 241
           K    +++ +    +  D    T + D S+     V   +    +           + + 
Sbjct: 156 KTGINMDAVKLLGQIMLDTAEYTKEKD-SLGCAKLVIFCNAPDDNPFMAGAFHGVTEADA 214

Query: 242 KEDINVKSLPFNPALLKKVEELELSVRSTNCLRGE-NIVYMGDLIQRTEADMLRMANFGR 300
             ++ V         L+ V   +         +    I  +G L+    + ML +  FG 
Sbjct: 215 IINVGVSGPGVVKTALESVRGEDFGTLCETIKKTAFKITRVGQLVAMEASKMLNIP-FGI 273

Query: 301 KSL---------VEIKGVLGTMGLF 316
             L           +  +L  +GL 
Sbjct: 274 VDLSLAPTPAVGDSVAEILQEIGLE 298


>gi|222529563|ref|YP_002573445.1| hypothetical protein Athe_1576 [Caldicellulosiruptor bescii DSM
           6725]
 gi|222456410|gb|ACM60672.1| conserved hypothetical protein [Caldicellulosiruptor bescii DSM
           6725]
          Length = 538

 Score = 36.1 bits (82), Expect = 8.7,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 60/166 (36%), Gaps = 21/166 (12%)

Query: 175 ALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           +L+  +   S+   S R GQ L        I+T+G +  + S+   +   Q    + I  
Sbjct: 166 SLFLTVAFPSWLFNSIRVGQRLKVVLTEYDIETEGFVDAKSSLFYVNDNGQSVFDVKICV 225

Query: 235 EEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLR 294
           +   + +        +  +    +++  +            E I+ M +++ ++E +  R
Sbjct: 226 DNEGRSLPSGAKAFCVITSKNPYQEIRSV-----------NEGILKMDEIVIKSEVE-GR 273

Query: 295 MANFGRKSLVEIK--GVLGTMGLFLGMNLPDWPPESIEELAKKYED 338
           +     K    IK   +L         ++     E I+ L  + ++
Sbjct: 274 IKKIFVKQYDRIKKGDILIEF---FDQDI----KEQIDGLKDQIDE 312


>gi|195338303|ref|XP_002035764.1| GM15286 [Drosophila sechellia]
 gi|194129644|gb|EDW51687.1| GM15286 [Drosophila sechellia]
          Length = 275

 Score = 35.7 bits (81), Expect = 8.9,   Method: Composition-based stats.
 Identities = 30/176 (17%), Positives = 62/176 (35%), Gaps = 34/176 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------V 68
           + + +  ++    + E        ++ N+LRRV ++     AI  VQ++          +
Sbjct: 9   VQITELTDDNVKFVLEDTE----LSVANSLRRVFIAETPTLAIDWVQLEANSTVLSDEFL 64

Query: 69  LHEISSIKGVHEDLTDIILNIKG-INLKMSGDSHKRVTIFKRGPGV----VTAGDI---- 119
            H I  I  + +D+ + +   +  I L    +     T+  +        VT  D+    
Sbjct: 65  AHRIGLIPLISDDVVERLQYTRDCICLDFCPECSVEFTLDVKCSEEQTRHVTTADLKSSN 124

Query: 120 ------------QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
                       +  N+    N + +I  L     +++     KG G   AK + T
Sbjct: 125 AKVLPVTSRHQGEEDNEYGESNDEILIIKLRKGQELKLRAYAKKGFGKEHAKWNPT 180


>gi|195579088|ref|XP_002079394.1| GD23930 [Drosophila simulans]
 gi|194191403|gb|EDX04979.1| GD23930 [Drosophila simulans]
          Length = 275

 Score = 35.7 bits (81), Expect = 9.0,   Method: Composition-based stats.
 Identities = 30/176 (17%), Positives = 62/176 (35%), Gaps = 34/176 (19%)

Query: 18  IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------V 68
           + + +  ++    + E        ++ N+LRRV ++     AI  VQ++          +
Sbjct: 9   VQITELTDDNVKFVLEDTE----LSVANSLRRVFIAETPTLAIDWVQLEANSTVLSDEFL 64

Query: 69  LHEISSIKGVHEDLTDIILNIKG-INLKMSGDSHKRVTIFKRGPGV----VTAGDI---- 119
            H I  I  + +D+ + +   +  I L    +     T+  +        VT  D+    
Sbjct: 65  AHRIGLIPLISDDVVERLQYTRDCICLDFCPECSVEFTLDVKCSEEQTRHVTTADLKSSN 124

Query: 120 ------------QTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT 163
                       +  N+    N + +I  L     +++     KG G   AK + T
Sbjct: 125 AKVLPVTSRNQGEEDNEYGESNDEILIIKLRKGQELKLRAYAKKGFGKEHAKWNPT 180


>gi|156097458|ref|XP_001614762.1| DNA-directed RNA polymerase II [Plasmodium vivax SaI-1]
 gi|148803636|gb|EDL45035.1| DNA-directed RNA polymerase II, putative [Plasmodium vivax]
          Length = 333

 Score = 35.7 bits (81), Expect = 9.0,   Method: Composition-based stats.
 Identities = 28/146 (19%), Positives = 50/146 (34%), Gaps = 28/146 (19%)

Query: 43  LGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIK----GVHEDLTDIILNI 89
           + NALRR+++S +   AI  V +         + + H +  I      V           
Sbjct: 35  MANALRRIMLSEIPTLAIDVVNVYENTSPFHDEFLAHRLGLIPIDSTNVKNFEFREKCKC 94

Query: 90  KGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT---VNDIEVLNP------------DHVI 134
           K    K +     +V         +T  DI++     ++ +  P               I
Sbjct: 95  KETCSKCTIQYLIQVKCNNVSKIEITHHDIESVEHEPNVPMPVPLEDRNNQMAESNAIPI 154

Query: 135 CNLDVDAVVRMELTVSKGHGYVPAKH 160
             L  +  + M+L  +KG G + AK 
Sbjct: 155 VTLSKNQTLHMKLIATKGIGKMHAKW 180


>gi|167044152|gb|ABZ08834.1| putative RNA polymerase Rpb3/RpoA insert domain protein [uncultured
           marine crenarchaeote HF4000_APKG5E24]
          Length = 200

 Score = 35.7 bits (81), Expect = 9.7,   Method: Composition-based stats.
 Identities = 29/183 (15%), Positives = 60/183 (32%), Gaps = 40/183 (21%)

Query: 44  GNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIILNIKGINL 94
            NALRR+ ++ +   AI  V I         +G+   +  I  +  +L     +   + L
Sbjct: 26  ANALRRICLNGVPIFAIDTVDIIENSSVIPDEGLALTLGMIP-LKTELNGFDESNSRVIL 84

Query: 95  KMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHG 154
            +  ++ +   I         A        ++ ++    I +L     +++E     G G
Sbjct: 85  VLDSEAAETTKIVTS------AELESKDQVVKPISKQIPIVHLAPGQRIKLEAYARLGRG 138

Query: 155 YVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGE 214
              AK +             A  S +       E              +T++T GS+  +
Sbjct: 139 TEHAKWNS------------ANISVLTNADKEGEH------------ILTVETTGSLEPK 174

Query: 215 DSV 217
             +
Sbjct: 175 QII 177


  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
   0.312    0.142    0.404 

Lambda     K      H
   0.267   0.0436    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,247,929,520
Number of Sequences: 13984884
Number of extensions: 159309041
Number of successful extensions: 441833
Number of sequences better than 10.0: 3788
Number of HSP's better than 10.0 without gapping: 3339
Number of HSP's successfully gapped in prelim test: 449
Number of HSP's that attempted gapping in prelim test: 432508
Number of HSP's gapped (non-prelim): 4086
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 (21.3 bits)
S2: 82 (36.1 bits)