RPS-BLAST 2.2.22 [Sep-27-2009]

Database: pdb70 
           24,244 sequences; 5,693,230 total letters

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

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



>3lu0_A DNA-directed RNA polymerase subunit alpha; E. coli RNA polymerase,
           nucleotidyltransferase, transcription, transferase;
           11.20A {Escherichia coli} PDB: 3iyd_A
          Length = 329

 Score =  376 bits (966), Expect = e-105
 Identities = 146/334 (43%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++     Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIE---QVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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-DVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA       +   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 RQPEVKE---EKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

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


>3iyd_A DNA-directed RNA polymerase subunit alpha; transcription,
           initiation, class I, activator, RNA polymerase,
           holoenzyme, sigma70, open complex, CAP, CRP,
           CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli
           k-12}
          Length = 329

 Score =  346 bits (890), Expect = 3e-96
 Identities = 146/334 (43%), 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   MQGSVTEFLKPRLVDIE---QVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 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 VNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L   +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 RQPEVKEE---KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

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


>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme,
           streptolydigin, antibiotic, transcription regulation;
           HET: STD; 2.40A {Thermus thermophilus} SCOP: d.74.3.1
           d.181.1.1 PDB: 1smy_A* 1zyr_A* 1iw7_A* 2a69_A* 2a6e_A
           2a68_A* 2be5_A* 2cw0_A 2o5i_A 2o5j_A* 2ppb_A* 3dxj_A*
           3eql_A* 1i6v_A* 1ynj_A* 1l9z_A 1l9u_A* 1ynn_A* 2gho_A
           1hqm_A ...
          Length = 315

 Score =  297 bits (762), Expect = 2e-81
 Identities = 115/316 (36%), Positives = 167/316 (52%), Gaps = 8/316 (2%)

Query: 6   WQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65
               +K         G         + EPL RGF  TLGN LRR+L+SS+ G A+T+V I
Sbjct: 2   LDSKLKAPVFTVRTQG---REYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYI 58

Query: 66  DGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKR--GPGVVTAGDIQTVN 123
           + VLHE S+I GV ED+ +IILN+K + ++    S + VT+  +  GP  V A D   V 
Sbjct: 59  EDVLHEFSTIPGVKEDVVEIILNLKELVVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVA 118

Query: 124 DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKV 183
           D+E++NPD  I  L+    + ME+ V +G GYVPA+ H    D I  I +DA++SP+++V
Sbjct: 119 DVEIMNPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGI-KDRINAIPVDAVFSPVRRV 177

Query: 184 SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE 243
           ++ VE  R GQ  D DKL++ I TDGS+T  +++  A  IL++ L  F N +       E
Sbjct: 178 AFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQAAAVAAPE 237

Query: 244 DINVKS--LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRK 301
           +             L   +EEL LS R  + L+ E I  +  L+     D+  +   G +
Sbjct: 238 EAKEPEAPPEQEEELDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGER 297

Query: 302 SLVEIKGVLGTMGLFL 317
           SL EIK  L   G  L
Sbjct: 298 SLEEIKEALEKKGFTL 313


>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble;
           2.50A {Escherichia coli} SCOP: d.74.3.1 d.181.1.1
          Length = 235

 Score =  241 bits (617), Expect = 1e-64
 Identities = 99/237 (41%), Positives = 151/237 (63%), Gaps = 7/237 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++     Q       +  EPL RGF HTLGNALR +L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIE---QVSSTHAKVTLEPLERGFGHTLGNALRAILLSSMPGCAVT 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 VNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPA---KHHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L   +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++ 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDL 234


>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding
           motif, platform for RNA polymerase assembly,
           transferase; 1.76A {Sulfolobus solfataricus P2} PDB:
           2pmz_D 3hkz_D 2waq_D 2wb1_D
          Length = 265

 Score =  132 bits (334), Expect = 8e-32
 Identities = 34/246 (13%), Positives = 77/246 (31%), Gaps = 44/246 (17%)

Query: 32  AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDL 82
            + +  G+     NA+RR  M  +   A+  V           + + H ++ I  + E+ 
Sbjct: 13  IDLVFEGYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAHRLALIPFMSEEA 72

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKR-----GPGVVTAGDIQTVND-IEVLNPDHVICN 136
            D     +               I+        P ++ + DI++ +  +  ++ D  I  
Sbjct: 73  LDTYRWPEECIECTENCEKCYTKIYIEAEAPNEPRMIYSKDIKSEDPSVVPISGDIPIVL 132

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHRT---------------------ENDPIGLITI-- 173
           L  +  + +E  +  G+G   AK                            P G+  +  
Sbjct: 133 LGTNQKISLEARLRLGYGKEHAKFIPVSLSVVRYYPKVEILANCEKAVNVCPEGVFELKD 192

Query: 174 ------DALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQ 227
                 + L   + +      +         DK  + I++ GS+  E  +  A + +  +
Sbjct: 193 GKLSVKNELSCTLCEECLRYCNGSIRISFVEDKYILEIESVGSLKPERILLEAGKSIIRK 252

Query: 228 LGMFIN 233
           +     
Sbjct: 253 IEELEK 258


>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide;
           transcription, mRNA, multiprotein complex; HET: UTP;
           2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.1
           d.181.1.1 PDB: 1i3q_C 1i6h_C 1k83_C* 1nik_C 1nt9_C
           1pqv_C 1r5u_C 1r9s_C* 1r9t_C* 1sfo_C* 1twa_C* 1twc_C*
           1i50_C* 1twg_C* 1twh_C* 1wcm_C 1y1v_C 1y1w_C 1y1y_C
           1y77_C* ...
          Length = 318

 Score =  131 bits (331), Expect = 2e-31
 Identities = 40/260 (15%), Positives = 81/260 (31%), Gaps = 43/260 (16%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIIL 87
                 + N+LRRV+++ +   AI +V++         + + H +  I     D+  +  
Sbjct: 23  SNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEY 82

Query: 88  NIKGINLKMSGDSHK----RVTIFKRGPGVVTAGDIQTVND-----------IEVLNPDH 132
           +                  +          V + D+  V++            +      
Sbjct: 83  SRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGV 142

Query: 133 VICNLDVDAVVRMELTVSKGHGYVPAK-------------HHRTENDPIGLITIDALYSP 179
           +IC L     +++     KG     AK              ++ ++         A   P
Sbjct: 143 LICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWP 202

Query: 180 IKKVSYTVESAREGQVLDY----DKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
             K     +   EG   DY    D   M +++ GSI  +  V      LQ ++   +   
Sbjct: 203 QSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASIL--L 260

Query: 236 EPKKEVKEDINVKSLPFNPA 255
              +  ++ +N  S   N A
Sbjct: 261 ALTQMDQDKVNFASGDNNTA 280


>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription,
           multi-protein complex, DNA- binding, magnesium; 3.65A
           {Schizosaccharomyces pombe}
          Length = 297

 Score =  126 bits (316), Expect = 9e-30
 Identities = 40/253 (15%), Positives = 84/253 (33%), Gaps = 45/253 (17%)

Query: 37  RGFAHTLGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIIL 87
              +  + N+LRRV+++ +   AI  V+I         + + H +  I     ++ +   
Sbjct: 22  TNTSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFLAHRLGMIPLDSSNIDEPPP 81

Query: 88  NIKGINLKMSGDS---------HKRVTIFKRGPGVVTAGDIQTVNDIEVLNP-------- 130
                      D                   G   + A D+   ++  + +P        
Sbjct: 82  VGLEYTRNCDCDQYCPKCSVELFLNAKCTGEGTMEIYARDLVVSSNSSLGHPILADPKSR 141

Query: 131 DHVICNLDVDAVVRMELTVSKGHGYVPAKHH-------------RTENDPIGLITIDALY 177
             +IC L  +  + +     KG     AK               + ++            
Sbjct: 142 GPLICKLRKEQEISLRCIAKKGIAKEHAKWSPTSAVAFEYDPWNKLQHTDYWFENDADAE 201

Query: 178 SPIKKVSYTVESAREGQVLDY----DKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
            P  K +   E  REG+  ++     +  M +++ GSI   + +    RILQ++L + + 
Sbjct: 202 WPKSKNADWEEPPREGEPFNFQEEPRRFYMDVESVGSIPPNEIMVQGLRILQEKLAVLVR 261

Query: 234 F--EEPKKEVKED 244
              EE   ++  +
Sbjct: 262 DLDEEQPTQLSAN 274


>1lb2_B DNA-directed RNA polymerase alpha chain; protein-DNA complex,
           gene-regulatory, gene regulation/DNA complex; HET: CMP;
           3.10A {Escherichia coli} SCOP: a.60.3.1 PDB: 1xs9_D
          Length = 84

 Score =  120 bits (304), Expect = 3e-28
 Identities = 46/80 (57%), Positives = 61/80 (76%)

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
           F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL 
Sbjct: 4   FDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLA 63

Query: 312 TMGLFLGMNLPDWPPESIEE 331
           + GL LGM L +WPP SI +
Sbjct: 64  SRGLSLGMRLENWPPASIAD 83


>1coo_A RNA polymerase alpha subunit; transcription regulation, nucleotidyl
           transferase; NMR {Escherichia coli K12} SCOP: a.60.3.1
           PDB: 2jzb_A
          Length = 98

 Score =  118 bits (298), Expect = 2e-27
 Identities = 50/101 (49%), Positives = 71/101 (70%), Gaps = 5/101 (4%)

Query: 232 INFEEPKK-EVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEA 290
           ++  + ++ EVKE+       F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE 
Sbjct: 1   MDLRDVREPEVKEE----KPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEV 56

Query: 291 DMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           ++L+  N G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 57  ELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 97


>3k4g_A DNA-directed RNA polymerase subunit alpha; bacterial transcription
           regulation, DNA-directed RNA polymer
           nucleotidyltransferase; HET: MLY; 2.05A {Escherichia
           coli k-12} PDB: 1lb2_B* 1xs9_D
          Length = 86

 Score =  117 bits (296), Expect = 3e-27
 Identities = 44/80 (55%), Positives = 56/80 (70%)

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
           F+P LL+ V++LEL+VRS NCL  E I Y+GDL+QRTE ++L   N G  SL EI  VL 
Sbjct: 6   FDPILLRPVDDLELTVRSANCLXAEAIHYIGDLVQRTEVELLXTPNLGXXSLTEIXDVLA 65

Query: 312 TMGLFLGMNLPDWPPESIEE 331
           + GL LGM L +WPP SI +
Sbjct: 66  SRGLSLGMRLENWPPASIAD 85


>3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex,
           cytoplasm, redox-active center, stress response,
           transcription; 2.30A {Bacillus subtilis}
          Length = 79

 Score = 95.1 bits (237), Expect = 2e-20
 Identities = 30/70 (42%), Positives = 42/70 (60%)

Query: 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310
                L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L
Sbjct: 9   QKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKL 68

Query: 311 GTMGLFLGMN 320
             +GL L  +
Sbjct: 69  EELGLGLRKD 78


>1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription
           regulation, disulfide stress; 1.50A {Bacillus subtilis}
           SCOP: a.60.3.1
          Length = 73

 Score = 94.3 bits (235), Expect = 3e-20
 Identities = 30/68 (44%), Positives = 42/68 (61%)

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
              L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L  
Sbjct: 4   EKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEE 63

Query: 313 MGLFLGMN 320
           +GL L  +
Sbjct: 64  LGLGLRKD 71


>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
           acyl-carrier-protein, beta-ketoacyl reductase,
           beta-ketoacyl synthase, dehydratase; 4.00A
           {Saccharomyces cerevisiae}
          Length = 2006

 Score = 34.9 bits (80), Expect = 0.023
 Identities = 19/103 (18%), Positives = 33/103 (32%), Gaps = 35/103 (33%)

Query: 202 SMTIDTDGSITGEDSVALASRI------LQDQLGMFIN-FEEPKKEVKEDINVKS----- 249
            +T+ + GS+  E  + + +        LQ+Q   F     EP +    D    +     
Sbjct: 8   PLTL-SHGSL--EHVLLVPTASFFIASQLQEQ---FNKILPEPTEGFAADDEPTTPAELV 61

Query: 250 ---LPFNPALLKKVEE---------LELSVRS--TNCLRGENI 278
              L +   +   VE          L L +       L G +I
Sbjct: 62  GKFLGY---VSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDI 101



 Score = 31.8 bits (72), Expect = 0.20
 Identities = 53/383 (13%), Positives = 102/383 (26%), Gaps = 159/383 (41%)

Query: 30  MIAEPLPRGFAHTLGNALRRVLMSSLRGAA-ITAV---Q--IDGVLHEISSIKGVHEDL- 82
           M   P  +       +AL R   +   G A + A+   Q   D    E+  +   +  L 
Sbjct: 132 MAKRPFDK--KSN--SALFR---AVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLV 184

Query: 83  TDIILNIKGINLKMSGDSHKRVTIFKRG-------------PGV---VTA-------GDI 119
            D+I        ++   +     +F +G             P     ++        G I
Sbjct: 185 GDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVI 244

Query: 120 QTVNDIEVLNPDH--VIC-NLDVD-AVVRMELTVSKGH--GYVPAKHHRTENDPIGLITI 173
           Q           H  V    L      +R  L  + GH  G V A            + I
Sbjct: 245 QLA---------HYVVTAKLLGFTPGELRSYLKGATGHSQGLVTA------------VAI 283

Query: 174 ------DALYSPIKKV-------------SY--------TVESAR---EGQ------V-- 195
                 ++ +  ++K              +Y         +E +    EG       +  
Sbjct: 284 AETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISN 343

Query: 196 LDYDKLSMTIDTDGSITGED---SVALA-SRILQDQL----------GMFINFEEPKKEV 241
           L  +++   ++   S         ++L         L          G+ +   + K   
Sbjct: 344 LTQEQVQDYVNKTNSHLPAGKQVEISLVNGA---KNLVVSGPPQSLYGLNLTLRKAKAPS 400

Query: 242 KEDIN--------VK--------SLPFNPALLKKVEE-----------------LELSVR 268
             D +        +K        + PF+  LL    +                 +++ V 
Sbjct: 401 GLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVY 460

Query: 269 STNC---LR--GENIVYMGDLIQ 286
            T     LR    +I     ++ 
Sbjct: 461 DTFDGSDLRVLSGSIS--ERIVD 481



 Score = 31.1 bits (70), Expect = 0.42
 Identities = 21/145 (14%), Positives = 37/145 (25%), Gaps = 70/145 (48%)

Query: 25  ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTD 84
            NR L +A P    F H+            L  A+               I    +DL  
Sbjct: 417 SNRFLPVASP----F-HS----------HLLVPAS-------------DLIN---KDLVK 445

Query: 85  IILNIKGINLKMSGDSHKRVTIFKRGPGVV----TAGDIQTVNDIEVLNPDHV--ICNLD 138
             ++    ++++              P  V       D++ ++    ++   V  I  L 
Sbjct: 446 NNVSFNAKDIQI--------------P--VYDTFDGSDLRVLS--GSISERIVDCIIRLP 487

Query: 139 VD---AVVRMELTVSKGHGYVPAKH 160
           V                     A H
Sbjct: 488 VKWETTTQ------------FKATH 500



 Score = 26.4 bits (58), Expect = 9.2
 Identities = 8/29 (27%), Positives = 10/29 (34%), Gaps = 9/29 (31%)

Query: 316 FLGMNLP--------DWPPESIEELAKKY 336
           F    LP        D  P +  EL  K+
Sbjct: 37  FN-KILPEPTEGFAADDEPTTPAELVGKF 64


>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion
           ATPase, ATP-binding, FIMB nucleotide-binding, transport;
           HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB:
           3jvu_A*
          Length = 356

 Score = 33.0 bits (75), Expect = 0.100
 Identities = 18/86 (20%), Positives = 30/86 (34%), Gaps = 16/86 (18%)

Query: 65  IDGVLHEISSIKGVHEDLTDIILNIKG--------------INLKMSGDSHKRVTIFK-- 108
           +DG +  I+     H+ +  +I +I                 + ++ G +  RV  F   
Sbjct: 30  VDGDVRRINLPPLEHKQVHALIYDIMNDKQRKDFEEFLETDFSFEVPGVARFRVNAFNQN 89

Query: 109 RGPGVVTAGDIQTVNDIEVLNPDHVI 134
           RG G V       V  +E L    V 
Sbjct: 90  RGAGAVFRTIPSKVLTMEELGMGEVF 115


>1qfg_A FHUA, protein (ferric hydroxamate uptake receptor); TONB-dependent
           receptor, integral outer membrane protein,
           ferrichrome-iron receptor; HET: PA1 GCN KDO GMH GLC GLA
           FTT DAO MYR DDQ; 2.50A {Escherichia coli} SCOP: f.4.3.3
           PDB: 1qff_A* 1qjq_A* 1qkc_A* 2grx_A* 1fi1_A* 2fcp_A*
           1by5_A* 1by3_A* 1fcp_A*
          Length = 725

 Score = 32.1 bits (71), Expect = 0.21
 Identities = 10/72 (13%), Positives = 27/72 (37%), Gaps = 2/72 (2%)

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
            + + +    G+++   G S+    +  RG           +N +++    +    +D  
Sbjct: 65  SVKEALSYTPGVSVGTRGASNTYDHLIIRGFAAEGQSQNNYLNGLKLQGNFYNDAVIDPY 124

Query: 141 AVVRMELTVSKG 152
            + R E  + +G
Sbjct: 125 MLERAE--IMRG 134


>3cz1_A Pheromone-binding protein Asp1; honey BEE, signal transduction,
           queen mandibular pheromone; HET: NBB; 1.50A {Apis
           mellifera} PDB: 2h8v_A* 3bfa_A* 3bfb_A* 3bfh_A* 3cab_A
           3cdn_A 3cyz_A* 3cz0_A* 3bjh_A* 3cz2_A 3d78_A* 3d75_A*
           3d76_A* 3d77_A* 3d73_A* 3d74_A*
          Length = 119

 Score = 29.5 bits (66), Expect = 1.0
 Identities = 6/19 (31%), Positives = 11/19 (57%)

Query: 322 PDWPPESIEELAKKYEDKC 340
           PDW P  + +L  + + +C
Sbjct: 2   PDWVPPEVFDLVAEDKARC 20


>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
           photosynthetic reaction center, peripheral antenna; HET:
           CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
          Length = 154

 Score = 29.2 bits (64), Expect = 1.2
 Identities = 12/32 (37%), Positives = 14/32 (43%), Gaps = 11/32 (34%)

Query: 192 EGQVLDYDKL--SMTIDTDGSITGEDSV-ALA 220
           E Q L   KL  S+ +  D      DS  ALA
Sbjct: 18  EKQALK--KLQASLKLYAD------DSAPALA 41


>3k9v_A 1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial;
           mitochondrial cytochrome P450, monotopic membrane
           protein, monooxygenase; HET: HEM CPS; 2.50A {Rattus
           norvegicus} PDB: 3k9y_A*
          Length = 482

 Score = 27.7 bits (60), Expect = 3.8
 Identities = 7/41 (17%), Positives = 18/41 (43%), Gaps = 5/41 (12%)

Query: 301 KSLVEIKG-----VLGTMGLFLGMNLPDWPPESIEELAKKY 336
           +++ ++ G     +LG++             +++ E  KKY
Sbjct: 21  RNVTDLPGPTNWPLLGSLLEIFWKGGLKKQHDTLAEYHKKY 61


>3ogn_A Odorant-binding protein; helix bundle, transport protein; HET: 3OG;
           1.30A {Culex quinquefasciatus} PDB: 2erb_A* 3k1e_A*
          Length = 124

 Score = 27.7 bits (61), Expect = 4.0
 Identities = 6/19 (31%), Positives = 9/19 (47%)

Query: 322 PDWPPESIEELAKKYEDKC 340
            ++PP  + E  K   D C
Sbjct: 7   AEYPPPELLEALKPLHDIC 25


>1twf_K B13.6, DNA-directed RNA polymerase II 13.6 kDa polypeptide;
          transcription, mRNA, multiprotein complex; HET: UTP;
          2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.2 PDB:
          1i3q_K 1i6h_K 1k83_K* 1nik_K 1nt9_K 1pqv_K 1r5u_K
          1r9s_K* 1r9t_K* 1sfo_K* 1twa_K* 1twc_K* 1i50_K* 1twg_K*
          1twh_K* 1wcm_K 1y1v_K 1y1w_K 1y1y_K 1y77_K* ...
          Length = 120

 Score = 27.1 bits (60), Expect = 6.4
 Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 7/49 (14%)

Query: 11 KPNNIEYIVLGQEEENRTLMIAEPLPRGF-------AHTLGNALRRVLM 52
           P+  E  +LG+ E    +      P           HTLGN +R  L+
Sbjct: 3  APDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELL 51


>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty
            acid synthase, acyl-carrier-protein, beta-ketoacyl
            reductase, beta-ketoacyl synthase, dehydratase; 4.00A
            {Saccharomyces cerevisiae}
          Length = 1688

 Score = 26.7 bits (58), Expect = 6.8
 Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 7/57 (12%)

Query: 287  RTEADMLRMANFGRKSLVEIKG----VLGTMGLFLGMNLPDWPPESIEELAKKYEDK 339
            RT A+M R A   R   +E +G    ++    L L M +P +    I  +A    DK
Sbjct: 1161 RTPAEMSRPATTTRNGFMEAQGAGIQIIMQADLALKMGVPIY---GIVAMAATATDK 1214


>2vcc_A Alpha-N-acetylglucosaminidase; GH89, naGlu, sanfilippo disease,
           hydrolase, mucopolysaccharidosis, family 89 glycoside
           hydrolase; 2.0A {Clostridium perfringens} PDB: 2vc9_A*
           2vcb_A* 2vca_A
          Length = 891

 Score = 26.8 bits (59), Expect = 7.6
 Identities = 12/57 (21%), Positives = 25/57 (43%), Gaps = 7/57 (12%)

Query: 172 TIDALYSPIKKV-------SYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALAS 221
           T++ + + + +V        +  E   +    D  ++S + D    I G + V+LAS
Sbjct: 170 TLNEIKNLVGRVIGREFKDKFIFEIRDQLNGNDVFEVSDSGDGKVLIKGNNGVSLAS 226


  Database: pdb70
    Posted date:  Jan 26, 2011 11:21 AM
  Number of letters in database: 5,693,230
  Number of sequences in database:  24,244
  
Lambda     K      H
   0.317    0.136    0.386 

Gapped
Lambda     K      H
   0.267   0.0541    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,897,589
Number of extensions: 135416
Number of successful extensions: 394
Number of sequences better than 10.0: 1
Number of HSP's gapped: 375
Number of HSP's successfully gapped: 37
Length of query: 340
Length of database: 5,693,230
Length adjustment: 93
Effective length of query: 247
Effective length of database: 3,438,538
Effective search space: 849318886
Effective search space used: 849318886
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (26.2 bits)