BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 000829
(1265 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 1455
Score = 557 bits (1436), Expect = e-158, Method: Compositional matrix adjust.
Identities = 365/998 (36%), Positives = 541/998 (54%), Gaps = 96/998 (9%)
Query: 85 ILNPVNVLFLFKRMTDTDCEVLYLSE---RPEKLIITNIAVPPIAIRPSVIMDGSQSNEN 141
+L+ +L +FK ++ D L +E RPE +I+T + VPP +RPS+ + SQ E+
Sbjct: 201 VLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGED 260
Query: 142 DITERLKRIIQTNASLQQELVEANSA-FKSLAGWETL-QVEVAQYINSDVRGVPFSMQVA 199
D+T +L I++ N SL E +E N A ++ E+L Q VA Y+++D+ G P ++Q +
Sbjct: 261 DLTFKLADILKANISL--ETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKS 318
Query: 200 -RPLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYPE 258
RP+ RLKGK+GR RGNL GKRV+++ RTVIS DPNL++ +V +P +A+ LTYPE
Sbjct: 319 GRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPE 378
Query: 259 RVSDHNIEKLRQCIQNGPDKYPGARMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLE 318
V+ +NI++L Q ++NGP+++PGA+ + D R+ + ++L+ G V+RH+
Sbjct: 379 VVTPYNIDRLTQLVRNGPNEHPGAKYV-IRDSGDRIDLRYSKRAGDIQLQYGWKVERHIM 437
Query: 319 DGDVVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEA 378
D D VLFNRQPSLH+MS+M HR +++P+ T R N SV +PYNADFDGDEMN+HVPQ+EE
Sbjct: 438 DNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 497
Query: 379 RTEALLLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRAAFSLMCCYMGDGM 438
R E L V + +P++ + + QD L +T +DTF + M ++ D
Sbjct: 498 RAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPD-W 556
Query: 439 DRVDLPTPAILKPVELWTGKQLFSVLIRPHANMRVYVNLTVKEKTYSNKLIRTEGDEEIR 498
D V +PTPAI+KP LW+GKQ+ SV I +++ + DE
Sbjct: 557 DGV-IPTPAIIKPKPLWSGKQILSVAIPNGIHLQRF-------------------DEGTT 596
Query: 499 IETMCPNDGFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLS 558
+ + P D + + ++I G + K T+G+ N GL V+ R+ G + + K+
Sbjct: 597 L--LSPKDNGMLIIDGQIIFGVVEKKTVGSSNG-GLIHVVTREKGPQVCAKLFGNIQKVV 653
Query: 559 ARWIGNHGFSIGIDDVQPKKELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQT 618
W+ ++GFS GI D + + I+E + KE L K G ++
Sbjct: 654 NFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRES 713
Query: 619 LEAVITDILNRIREDAGKACMGSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQSVGGR 678
E + LN R+ AG+ +L N+ M GSKGS INI+QM ACVGQQSV G+
Sbjct: 714 FEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGK 773
Query: 679 RAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGREGLVDTAVKTAD 738
R GF+DR+LPHF + P +KGFV NS+ GL+ EFFFH MGGREGL+DTAVKTA+
Sbjct: 774 RIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAE 833
Query: 739 TGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEGKS-----GEPLNF 793
TGY+ RRL+KALED+ + YDN+ RN+ G ++QF+YG+DGMD A++E +S G F
Sbjct: 834 TGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAF 893
Query: 794 DRL----LMKVKATCPP----AGQRYLSPQQVSEIVEKQLAAYGKES--CSEAFLN---- 839
++ L+ T P +G L ++ +++++ K+ E F++
Sbjct: 894 EKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEAN 953
Query: 840 -----SLRKFFEGQQ-----DKLDKKIKFVEDI--GWDDKSQILEEVTHKTSGITEKQLE 887
++R+ + Q D ++DI G D + L + K I Q +
Sbjct: 954 WPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRD 1013
Query: 888 VFIQTC------------FSRYRVKRVEAGTAIGAIGAQ------------------SIG 917
C YR+ + + I AQ SIG
Sbjct: 1014 AVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIG 1073
Query: 918 EPGTQMTLKTFHFAGVASMNITQGVPRIKEIINGAKRISTPIITAELECND--NENAARV 975
EP TQMTL TFHFAGVAS +T GVPR+KEI+N AK + TP +T LE ++ A++
Sbjct: 1074 EPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKL 1133
Query: 976 VKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQ 1013
++ IE T L V + +I S VI D E IQ
Sbjct: 1134 IRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQ 1171
Score = 97.4 bits (241), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 49/140 (35%), Positives = 75/140 (53%)
Query: 1106 YRLLVEGTGLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSI 1165
+ L +G L VM GID + +N ++ + LGIEA R + E+ + + G +
Sbjct: 1304 WVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYV 1363
Query: 1166 DKRHMMLLADLMTFRGEVLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEG 1225
+ RHM LL D+MT +G + +TR G + + LM SFE+T + LF A + D G
Sbjct: 1364 NYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRG 1423
Query: 1226 VSECIIMGIPMPLGTGILKI 1245
VSE +I+G P+GTG +
Sbjct: 1424 VSENVILGQMAPIGTGAFDV 1443
>pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|A Chain A, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|A Chain A, Rna Polymerase Ii Elongation Complex Containing A Cpd Lesion
Length = 1732
Score = 555 bits (1431), Expect = e-158, Method: Compositional matrix adjust.
Identities = 365/998 (36%), Positives = 541/998 (54%), Gaps = 96/998 (9%)
Query: 85 ILNPVNVLFLFKRMTDTDCEVLYLSE---RPEKLIITNIAVPPIAIRPSVIMDGSQSNEN 141
+L+ +L +FK ++ D L +E RPE +I+T + VPP +RPS+ + SQ E+
Sbjct: 201 VLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGED 260
Query: 142 DITERLKRIIQTNASLQQELVEANSA-FKSLAGWETL-QVEVAQYINSDVRGVPFSMQVA 199
D+T +L I++ N SL E +E N A ++ E+L Q VA Y+++D+ G P ++Q +
Sbjct: 261 DLTFKLADILKANISL--ETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKS 318
Query: 200 -RPLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYPE 258
RP+ RLKGK+GR RGNL GKRV+++ RTVIS DPNL++ +V +P +A+ LTYPE
Sbjct: 319 GRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPE 378
Query: 259 RVSDHNIEKLRQCIQNGPDKYPGARMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLE 318
V+ +NI++L Q ++NGP+++PGA+ + D R+ + ++L+ G V+RH+
Sbjct: 379 VVTPYNIDRLTQLVRNGPNEHPGAKYV-IRDSGDRIDLRYSKRAGDIQLQYGWKVERHIM 437
Query: 319 DGDVVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEA 378
D D VLFNRQPSLH+MS+M HR +++P+ T R N SV +PYNADFDGDEMN+HVPQ+EE
Sbjct: 438 DNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 497
Query: 379 RTEALLLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRAAFSLMCCYMGDGM 438
R E L V + +P++ + + QD L +T +DTF + M ++ D
Sbjct: 498 RAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPD-W 556
Query: 439 DRVDLPTPAILKPVELWTGKQLFSVLIRPHANMRVYVNLTVKEKTYSNKLIRTEGDEEIR 498
D V +PTPAI+KP LW+GKQ+ SV I +++ + DE
Sbjct: 557 DGV-IPTPAIIKPKPLWSGKQILSVAIPNGIHLQRF-------------------DEGTT 596
Query: 499 IETMCPNDGFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLS 558
+ + P D + + ++I G + K T+G+ N GL V+ R+ G + + K+
Sbjct: 597 L--LSPKDNGMLIIDGQIIFGVVEKKTVGSSNG-GLIHVVTREKGPQVCAKLFGNIQKVV 653
Query: 559 ARWIGNHGFSIGIDDVQPKKELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQT 618
W+ ++GFS GI D + + I+E + KE L K G ++
Sbjct: 654 NFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRES 713
Query: 619 LEAVITDILNRIREDAGKACMGSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQSVGGR 678
E + LN R+ AG+ +L N+ M GSKGS INI+QM ACVGQQSV G+
Sbjct: 714 FEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGK 773
Query: 679 RAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGREGLVDTAVKTAD 738
R GF+DR+LPHF + P +KGFV NS+ GL+ EFFFH MGGREGL+DTAVKTA+
Sbjct: 774 RIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAE 833
Query: 739 TGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEGKS-----GEPLNF 793
TGY+ RRL+KALED+ + YDN+ RN+ G ++QF+YG+DGMD A++E +S G F
Sbjct: 834 TGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAF 893
Query: 794 DRL----LMKVKATCPP----AGQRYLSPQQVSEIVEKQLAAYGKES--CSEAFLN---- 839
++ L+ T P +G L ++ +++++ K+ E F++
Sbjct: 894 EKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEAN 953
Query: 840 -----SLRKFFEGQQ-----DKLDKKIKFVEDI--GWDDKSQILEEVTHKTSGITEKQLE 887
++R+ + Q D ++DI G D + L + K I Q +
Sbjct: 954 WPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRD 1013
Query: 888 VFIQTC------------FSRYRVKRVEAGTAIGAIGAQ------------------SIG 917
C YR+ + + I AQ SIG
Sbjct: 1014 AVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIG 1073
Query: 918 EPGTQMTLKTFHFAGVASMNITQGVPRIKEIINGAKRISTPIITAELECND--NENAARV 975
EP TQMTL TFHFAGVAS +T GVPR+KEI+N AK + TP +T LE ++ A++
Sbjct: 1074 EPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKL 1133
Query: 976 VKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQ 1013
++ IE T L V + +I S VI D E IQ
Sbjct: 1134 IRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQ 1171
Score = 98.2 bits (243), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 49/140 (35%), Positives = 75/140 (53%)
Query: 1106 YRLLVEGTGLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSI 1165
+ L +G L VM GID + +N ++ + LGIEA R + E+ + + G +
Sbjct: 1304 WVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYV 1363
Query: 1166 DKRHMMLLADLMTFRGEVLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEG 1225
+ RHM LL D+MT +G + +TR G + + LM SFE+T + LF A + D G
Sbjct: 1364 NYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRG 1423
Query: 1226 VSECIIMGIPMPLGTGILKI 1245
VSE +I+G P+GTG +
Sbjct: 1424 VSENVILGQMAPIGTGAFDV 1443
>pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|A Chain A, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|A Chain A, Rna Polymerase Ii Elongation Complex
pdb|1K83|A Chain A, Crystal Structure Of Yeast Rna Polymerase Ii Complexed With
The Inhibitor Alpha Amanitin
pdb|1NIK|A Chain A, Wild Type Rna Polymerase Ii
pdb|1NT9|A Chain A, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|A Chain A, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|A Chain A, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|A Chain A, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|A Chain A, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|A Chain A, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|A Chain A, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|A Chain A, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|A Chain A, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|A Chain A, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|A Chain A, Complete Rna Polymerase Ii Elongation Complex With Substrate
Analogue Gmpcpp
pdb|1Y1V|A Chain A, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|A Chain A, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|A Chain A, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|A Chain A, 12-Subunit Rna Polymerase Ii
pdb|2E2H|A Chain A, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|A Chain A, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|A Chain A, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex A
pdb|2JA6|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex B
pdb|2JA7|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex C
pdb|2JA7|M Chain M, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex C
pdb|2JA8|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex D
pdb|2YU9|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With Utp
pdb|2R7Z|A Chain A, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|A Chain A, Elongation Complex Of Rna Polymerase Ii With Artificial Rdrp
Scaffold
pdb|2R93|A Chain A, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|A Chain A, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|A Chain A, Crystal Structure Of 10 Subunit Rna Polymerase Ii In Complex
With The Inhibitor Alpha-Amanitin
pdb|3FKI|A Chain A, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|A Chain A, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|A Chain A, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|A Chain A, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|A Chain A, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|A Chain A, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|A Chain A, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|B Chain B, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|A Chain A, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|M Chain M, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|A Chain A, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iii With A T-U
Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|A Chain A, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|A Chain A, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iv With A T-U
Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation Complex
D
pdb|3I4N|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation Complex
E
pdb|3K1F|A Chain A, Crystal Structure Of Rna Polymerase Ii In Complex With Tfiib
pdb|3K7A|A Chain A, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|A Chain A, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|A Chain A, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|A Chain A, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|A Chain A, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|A Chain A, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|A Chain A, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|A Chain A, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|A Chain A, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|A Chain A, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|4BBR|A Chain A, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|A Chain A, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 1733
Score = 555 bits (1431), Expect = e-158, Method: Compositional matrix adjust.
Identities = 365/998 (36%), Positives = 541/998 (54%), Gaps = 96/998 (9%)
Query: 85 ILNPVNVLFLFKRMTDTDCEVLYLSE---RPEKLIITNIAVPPIAIRPSVIMDGSQSNEN 141
+L+ +L +FK ++ D L +E RPE +I+T + VPP +RPS+ + SQ E+
Sbjct: 201 VLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGED 260
Query: 142 DITERLKRIIQTNASLQQELVEANSA-FKSLAGWETL-QVEVAQYINSDVRGVPFSMQVA 199
D+T +L I++ N SL E +E N A ++ E+L Q VA Y+++D+ G P ++Q +
Sbjct: 261 DLTFKLADILKANISL--ETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKS 318
Query: 200 -RPLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYPE 258
RP+ RLKGK+GR RGNL GKRV+++ RTVIS DPNL++ +V +P +A+ LTYPE
Sbjct: 319 GRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPE 378
Query: 259 RVSDHNIEKLRQCIQNGPDKYPGARMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLE 318
V+ +NI++L Q ++NGP+++PGA+ + D R+ + ++L+ G V+RH+
Sbjct: 379 VVTPYNIDRLTQLVRNGPNEHPGAKYV-IRDSGDRIDLRYSKRAGDIQLQYGWKVERHIM 437
Query: 319 DGDVVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEA 378
D D VLFNRQPSLH+MS+M HR +++P+ T R N SV +PYNADFDGDEMN+HVPQ+EE
Sbjct: 438 DNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEET 497
Query: 379 RTEALLLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRAAFSLMCCYMGDGM 438
R E L V + +P++ + + QD L +T +DTF + M ++ D
Sbjct: 498 RAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPD-W 556
Query: 439 DRVDLPTPAILKPVELWTGKQLFSVLIRPHANMRVYVNLTVKEKTYSNKLIRTEGDEEIR 498
D V +PTPAI+KP LW+GKQ+ SV I +++ + DE
Sbjct: 557 DGV-IPTPAIIKPKPLWSGKQILSVAIPNGIHLQRF-------------------DEGTT 596
Query: 499 IETMCPNDGFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLS 558
+ + P D + + ++I G + K T+G+ N GL V+ R+ G + + K+
Sbjct: 597 L--LSPKDNGMLIIDGQIIFGVVEKKTVGSSNG-GLIHVVTREKGPQVCAKLFGNIQKVV 653
Query: 559 ARWIGNHGFSIGIDDVQPKKELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQT 618
W+ ++GFS GI D + + I+E + KE L K G ++
Sbjct: 654 NFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRES 713
Query: 619 LEAVITDILNRIREDAGKACMGSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQSVGGR 678
E + LN R+ AG+ +L N+ M GSKGS INI+QM ACVGQQSV G+
Sbjct: 714 FEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGK 773
Query: 679 RAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGREGLVDTAVKTAD 738
R GF+DR+LPHF + P +KGFV NS+ GL+ EFFFH MGGREGL+DTAVKTA+
Sbjct: 774 RIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAE 833
Query: 739 TGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEGKS-----GEPLNF 793
TGY+ RRL+KALED+ + YDN+ RN+ G ++QF+YG+DGMD A++E +S G F
Sbjct: 834 TGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAF 893
Query: 794 DRL----LMKVKATCPP----AGQRYLSPQQVSEIVEKQLAAYGKES--CSEAFLN---- 839
++ L+ T P +G L ++ +++++ K+ E F++
Sbjct: 894 EKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEAN 953
Query: 840 -----SLRKFFEGQQ-----DKLDKKIKFVEDI--GWDDKSQILEEVTHKTSGITEKQLE 887
++R+ + Q D ++DI G D + L + K I Q +
Sbjct: 954 WPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRD 1013
Query: 888 VFIQTC------------FSRYRVKRVEAGTAIGAIGAQ------------------SIG 917
C YR+ + + I AQ SIG
Sbjct: 1014 AVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIG 1073
Query: 918 EPGTQMTLKTFHFAGVASMNITQGVPRIKEIINGAKRISTPIITAELECND--NENAARV 975
EP TQMTL TFHFAGVAS +T GVPR+KEI+N AK + TP +T LE ++ A++
Sbjct: 1074 EPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKL 1133
Query: 976 VKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETIQ 1013
++ IE T L V + +I S VI D E IQ
Sbjct: 1134 IRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQ 1171
Score = 98.2 bits (243), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 49/140 (35%), Positives = 75/140 (53%)
Query: 1106 YRLLVEGTGLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSI 1165
+ L +G L VM GID + +N ++ + LGIEA R + E+ + + G +
Sbjct: 1304 WVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYV 1363
Query: 1166 DKRHMMLLADLMTFRGEVLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEG 1225
+ RHM LL D+MT +G + +TR G + + LM SFE+T + LF A + D G
Sbjct: 1364 NYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRG 1423
Query: 1226 VSECIIMGIPMPLGTGILKI 1245
VSE +I+G P+GTG +
Sbjct: 1424 VSENVILGQMAPIGTGAFDV 1443
>pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|W Chain W, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|A Chain A, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|W Chain W, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|A Chain A, Rnap At 3.2ang
pdb|4B1O|A Chain A, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|W Chain W, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 880
Score = 533 bits (1373), Expect = e-151, Method: Compositional matrix adjust.
Identities = 294/724 (40%), Positives = 430/724 (59%), Gaps = 32/724 (4%)
Query: 86 LNPVNVLFLFKRMTDTDCEVLYL---SERPEKLIITNIAVPPIAIRPSVIMDGSQSNEND 142
L P ++ +++ ++D E+L + RPE +I+T + VPPI IRPS++++ E+D
Sbjct: 175 LTPSDIRERLEKVPESDVEILGYDPTTSRPEWMILTVLPVPPITIRPSIMIESGIRAEDD 234
Query: 143 ITERLKRIIQTNASLQQELVEANSAFKSLAGWETLQVEVAQYINSDVRGVPFS-MQVARP 201
+T +L I++ N L++ + W+ LQ VA Y ++++ G+P S + RP
Sbjct: 235 LTHKLVDIVRINERLKESIDAGAPQLIIEDLWDLLQYHVATYFDNEIPGLPPSKHRSGRP 294
Query: 202 LSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYPERVS 261
L QRLKGK+GRFRGNLSGKRV+++ RTVISPDPN+ I EV +P +AR LT PER++
Sbjct: 295 LRTLAQRLKGKEGRFRGNLSGKRVDFSSRTVISPDPNISIDEVGVPEIIARTLTVPERIT 354
Query: 262 DHNIEKLRQCIQNGPDKYPGARMIRYPDGTARVL-YGKFRNQLAVELKSGCIVDRHLEDG 320
NIEKLRQ + NGPDK+PGA + PDG L Y K R +LA L G +V+RHL DG
Sbjct: 355 PWNIEKLRQFVINGPDKWPGANYVIRPDGRRIDLRYVKDRKELASTLAPGYVVERHLTDG 414
Query: 321 DVVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEART 380
DVVLFNRQPSLHR+S+M HR R++ T R N VC PYNADFDGDEMN+HVPQ+EEA
Sbjct: 415 DVVLFNRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPYNADFDGDEMNLHVPQSEEAIA 474
Query: 381 EALLLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRAAFSLMCCYMGDGMDR 440
EA +M V N+ TP+ G ++ + QD+++ ++L+T K T + + +G +
Sbjct: 475 EAKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLTKEEAQQI---LGVADVK 531
Query: 441 VDLPTPAILKPVELWTGKQLFSVLIRPHANMRVYVNLTVKEKTYSNKLIRTEGDEEIRIE 500
+DL PAIL P E +TGKQ+ S + N N++ + N+
Sbjct: 532 IDLGEPAILAPREYYTGKQVVSAFLPKDFNFHGQANVSSGPRLCKNE------------- 578
Query: 501 TMCPNDGFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSAR 560
CP+D +V +N L+ G K +GN + + L+++Y M+ L ++ R
Sbjct: 579 -DCPHDSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDEYGKWLMDNLFRVFIR 637
Query: 561 WIGNHGFSIGIDDVQPKKELSDKKGKLISENYEVCNVK----IKEYNEGKLQLKPGCDAA 616
++ GF++ ++DV L D K I + V+ I++Y G+L+ PG
Sbjct: 638 FVELQGFTMRLEDVS----LGDDVKKEIYNEIDRAKVEVDNLIQKYKNGELEPIPGRTLE 693
Query: 617 QTLEAVITDILNRIREDAGKACMGSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQSVG 676
++LE I D L+++R AG L N +M++ G++GS +NI+QM A +GQQSV
Sbjct: 694 ESLENYILDTLDKLRSTAGDIASKYLDPFNFAYVMARTGARGSVLNITQMAAMLGQQSVR 753
Query: 677 GRRAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGREGLVDTAVKT 736
G R G++ R+LPHF P A+GF+ +SF +GL TE FFH GGREGLVDTAV+T
Sbjct: 754 GERIKRGYMTRTLPHFKPYDISPEARGFIYSSFRTGLKPTELFFHAAGGREGLVDTAVRT 813
Query: 737 ADTGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEGKSGEPLNFDRL 796
+ +GYM RRLI AL DL +YD +VR+ G ++Q YGDDG+ P M G+ ++ +R+
Sbjct: 814 SQSGYMQRRLINALSDLRAEYDGTVRSLYGEVIQVAYGDDGVFP--MYSAHGKTVDVNRI 871
Query: 797 LMKV 800
+V
Sbjct: 872 FERV 875
>pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|Q Chain Q, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|A Chain A, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|I Chain I, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 880
Score = 533 bits (1373), Expect = e-151, Method: Compositional matrix adjust.
Identities = 294/724 (40%), Positives = 430/724 (59%), Gaps = 32/724 (4%)
Query: 86 LNPVNVLFLFKRMTDTDCEVLYL---SERPEKLIITNIAVPPIAIRPSVIMDGSQSNEND 142
L P ++ +++ D+D E+L + RPE +I+T + VPPI IRPS++++ E+D
Sbjct: 175 LTPSDIRERLEKIPDSDVEILGYDPTTSRPEWMILTVLPVPPITIRPSIMIESGIRAEDD 234
Query: 143 ITERLKRIIQTNASLQQELVEANSAFKSLAGWETLQVEVAQYINSDVRGVPFS-MQVARP 201
+T +L I++ N L++ + W+ LQ VA Y ++++ G+P S + RP
Sbjct: 235 LTHKLVDIVRINERLKESIDAGAPQLIIEDLWDLLQYHVATYFDNEIPGLPPSKHRSGRP 294
Query: 202 LSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYPERVS 261
L QRLKGK+GRFRGNLSGKRV+++ RTVISPDPN+ I EV +P +A+ LT PER++
Sbjct: 295 LRTLAQRLKGKEGRFRGNLSGKRVDFSSRTVISPDPNISIDEVGVPEIIAKTLTVPERIT 354
Query: 262 DHNIEKLRQCIQNGPDKYPGARMIRYPDGTARVL-YGKFRNQLAVELKSGCIVDRHLEDG 320
NIEKLRQ + NGPDK+PGA + PDG L Y K R +LA L G I++RHL DG
Sbjct: 355 PWNIEKLRQFVINGPDKWPGANYVIRPDGRRIDLRYVKDRKELASTLAPGYIIERHLIDG 414
Query: 321 DVVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEART 380
D+VLFNRQPSLHR+S+M HR R++ T R N VC PYNADFDGDEMN+HVPQ+EEA
Sbjct: 415 DIVLFNRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPYNADFDGDEMNLHVPQSEEAIA 474
Query: 381 EALLLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRAAFSLMCCYMGDGMDR 440
EA +M V N+ TP+ G ++ + QD+++ ++L+T K T + + +G +
Sbjct: 475 EAKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLTKEEAQQI---LGVADVK 531
Query: 441 VDLPTPAILKPVELWTGKQLFSVLIRPHANMRVYVNLTVKEKTYSNKLIRTEGDEEIRIE 500
+DL PAIL P E +TGKQ+ S + N N++ + N+
Sbjct: 532 IDLGEPAILAPREYYTGKQVISAFLPKDFNFHGQANVSSGPRLCKNE------------- 578
Query: 501 TMCPNDGFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSAR 560
CP+D +V +N L+ G K +GN + + L+++Y M+ L ++ R
Sbjct: 579 -DCPHDSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDEYGKWLMDNLFRVFIR 637
Query: 561 WIGNHGFSIGIDDVQPKKELSDKKGKLISENYEVCNVK----IKEYNEGKLQLKPGCDAA 616
++ GF++ ++DV L D K I + V+ I++Y G+L+ PG
Sbjct: 638 FVELQGFTMRLEDVS----LGDDVKKEIYNEIDRAKVEVDNLIQKYKNGELEPIPGRTLE 693
Query: 617 QTLEAVITDILNRIREDAGKACMGSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQSVG 676
++LE I D L+++R AG L N +M++ G++GS +NI+QM A +GQQSV
Sbjct: 694 ESLENYILDTLDKLRSTAGDIASKYLDPFNFAYVMARTGARGSVLNITQMAAMLGQQSVR 753
Query: 677 GRRAPNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGREGLVDTAVKT 736
G R G++ R+LPHF P A+GF+ +SF +GL TE FFH GGREGLVDTAV+T
Sbjct: 754 GERIKRGYMTRTLPHFKPYDISPEARGFIYSSFRTGLKPTELFFHAAGGREGLVDTAVRT 813
Query: 737 ADTGYMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEGKSGEPLNFDRL 796
+ +GYM RRLI AL DL +YD +VR+ G +VQ YGDDG+ P M G+ ++ +R+
Sbjct: 814 SQSGYMQRRLINALSDLRAEYDGTVRSLYGEVVQVAYGDDGVFP--MYSAHGKTVDVNRI 871
Query: 797 LMKV 800
+V
Sbjct: 872 FERV 875
>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|M Chain M, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 1752
Score = 517 bits (1331), Expect = e-146, Method: Compositional matrix adjust.
Identities = 292/721 (40%), Positives = 434/721 (60%), Gaps = 34/721 (4%)
Query: 85 ILNPVNVLFLFKRMTDTDCEVLYLSE---RPEKLIITNIAVPPIAIRPSVIMDGSQSNEN 141
+L+P+ V +F ++ D L L+E RP+ +IIT + VPP ++RPS+ +DG+ E+
Sbjct: 207 LLSPLEVHTIFTHISSEDLAHLGLNEQYARPDWMIITVLPVPPPSVRPSISVDGTSRGED 266
Query: 142 DITERLKRIIQTNASLQQELVEANSAFKSLAGWETLQVEVAQYINSDVRGVPFSMQVA-R 200
D+T +L II+ NA++++ E A + LQ VA Y+++++ G P ++Q + R
Sbjct: 267 DLTHKLSDIIKANANVRRCEQEGAPAHIVSEYEQLLQFHVATYMDNEIAGQPQALQKSGR 326
Query: 201 PLSGFVQRLKGKQGRFRGNLSGKRVEYTGRTVISPDPNLKITEVAIPIRMARILTYPERV 260
PL RLKGK+GR RGNL GKRV+++ RTVI+ DPNL + E+ +P +A+ LTYPE V
Sbjct: 327 PLKSIRARLKGKEGRLRGNLMGKRVDFSARTVITGDPNLSLDELGVPRSIAKTLTYPETV 386
Query: 261 SDHNIEKLRQCIQNGPDKYPGARMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDG 320
+ +NI +L++ ++NGPD++PGA+ I D R+ + + L+ G V+RH+ DG
Sbjct: 387 TPYNIYQLQELVRNGPDEHPGAKYI-IRDTGERIDLRYHKRAGDIPLRYGWRVERHIRDG 445
Query: 321 DVVLFNRQPSLHRMSIMCHRARIMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEART 380
DVV+FNRQPSLH+MS+M HR R+MP+ T R N SV +PYNADFDGDEMNMHVPQ+EE R
Sbjct: 446 DVVIFNRQPSLHKMSMMGHRIRVMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSEETRA 505
Query: 381 EALLLMGVQNNLCTPKNGEILVASTQDFLTSSFLITRKDTFYDRAAFSLMCCYMGDGMDR 440
E + V + +P++ + ++ QD L + +D F R A + ++ D D
Sbjct: 506 EIQEITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTRNAVMNIMLWVPD-WDG 564
Query: 441 VDLPTPAILKPVELWTGKQLFSVLIRPHANMRVYVNLTVKEKTYSNKLIRTEGDEEIRIE 500
+ LP P ILKP LWTGKQ+ S++I N LIR + + +
Sbjct: 565 I-LPPPVILKPKVLWTGKQILSLIIPKGIN-----------------LIRDDDKQSLS-- 604
Query: 501 TMCPNDGFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSAR 560
P D + N E+I G + K T+G ++ GL + ++ G G N + ++
Sbjct: 605 --NPTDSGMLIENGEIIYGVVDKKTVG-ASQGGLVHTIWKEKGPEICKGFFNGIQRVVNY 661
Query: 561 WIGNHGFSIGIDDVQPKKELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQTLE 620
W+ ++GFSIGI D + + + + E I++ +L+ +PG ++ E
Sbjct: 662 WLLHNGFSIGIGDTIADADTMKEVTRTVKEARRQVAECIQDAQHNRLKPEPGMTLRESFE 721
Query: 621 AVITDILNRIREDAGKACMGSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQSVGGRRA 680
A ++ ILN+ R++AG++ SL N+ M GSKGS INISQM ACVGQQ V G+R
Sbjct: 722 AKVSRILNQARDNAGRSAEHSLKDSNNVKQMVAAGSKGSFINISQMSACVGQQIVEGKRI 781
Query: 681 PNGFIDRSLPHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGREGLVDTAVKTADTG 740
P GF R+LPHFP+ P ++GF+ NS+ GL+ EFFFH M GREGL+DTAVKTA+TG
Sbjct: 782 PFGFKYRTLPHFPKDDDSPESRGFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETG 841
Query: 741 YMSRRLIKALEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEGKSGEPLNFDRLLMKV 800
Y+ RRL+KA+ED+ ++YD +VRNA G I+QF YG+DG+D +E + FD L +
Sbjct: 842 YIQRRLVKAMEDVMVRYDGTVRNAMGDIIQFAYGEDGLDATLVEYQV-----FDSLRLST 896
Query: 801 K 801
K
Sbjct: 897 K 897
Score = 174 bits (442), Expect = 2e-43, Method: Compositional matrix adjust.
Identities = 127/398 (31%), Positives = 192/398 (48%), Gaps = 49/398 (12%)
Query: 895 SRYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQGVPRIKEIINGAKR 954
+R++ V G +G + AQSIGEP TQMTL TFH+AGV+S N+T GVPR+KEI+N AK
Sbjct: 1054 ARFQQAVVSPGEMVGTLAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEILNVAKN 1113
Query: 955 ISTPIITAEL--ECNDNENAARVVKGRIEKTLLGQVAKSIKIVMTSRLASIVIALDMETI 1012
I TP +T L N + A+ V+ +IE T L V + +I VI D + +
Sbjct: 1114 IKTPSLTIYLMPWIAANMDLAKNVQTQIEHTTLSTVTSATEIHYDPDPQDTVIEEDKDFV 1173
Query: 1013 QDAHLCINADIVKESIV-QTPK-IKLKQQHIKVLDFRKLEIFPPVDKSKIHFE-----LY 1065
+ A I + V+E++ Q+P ++L+ K+LD +KL + K FE ++
Sbjct: 1174 E-AFFAIPDEEVEENLYKQSPWLLRLELDRAKMLD-KKLSMSDVAGKIAESFERDLFTIW 1231
Query: 1066 SLKNVLPMVI------------------------VKGIKTXXXXXXXXXXXXXXXXXXXX 1101
S N ++I +K I+
Sbjct: 1232 SEDNADKLIIRCRIIRDDDRKAEDDDNMIEEDVFLKTIEGHMLESISLRGVPNITRVYMM 1291
Query: 1102 XXXXYRLLVEGT--------------GLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAAR 1147
R + +GT L M EG+D +T SN E+ Q LGIEA R
Sbjct: 1292 EHKIVRQIEDGTFERADEWVLETDGINLTEAMTVEGVDATRTYSNSFVEILQILGIEATR 1351
Query: 1148 ICIIDEINETMKAHGMSIDKRHMMLLADLMTFRGEVLGITRFGIQKMDKSVLMLASFEKT 1207
++ E+ ++ G ++ RH+ LL D+MT RG ++ ITR GI + + LM SFE+T
Sbjct: 1352 SALLKELRNVIEFDGSYVNYRHLALLCDVMTSRGHLMAITRHGINRAETGALMRCSFEET 1411
Query: 1208 ADHLFNASVNGRDDRIEGVSECIIMGIPMPLGTGILKI 1245
+ L +A+ +G D +G+SE I++G P+GTG I
Sbjct: 1412 VEILMDAAASGEKDDCKGISENIMLGQLAPMGTGAFDI 1449
>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 1413
Score = 227 bits (579), Expect = 3e-59, Method: Compositional matrix adjust.
Identities = 227/847 (26%), Positives = 356/847 (42%), Gaps = 165/847 (19%)
Query: 111 RPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKS 170
+PE +I+T + V P +RP V +DG + +D+ + +R+I N L++ L A
Sbjct: 233 KPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIV 292
Query: 171 LAGWETLQVEVAQYINSDVRGVPFSMQVARPLSGFVQRLKGKQGRFRGNLSGKRVEYTGR 230
LQ V +++ RG + RPL +KGKQGRFR NL GKRV+Y+GR
Sbjct: 293 RNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGR 352
Query: 231 TVISPDPNLKITEVAIPIRMARILTYPERVSDHNIEKLRQCIQNGPDKYPGARMIRYPDG 290
+VI+ P L++ + +P +MA L P + L I+ +M+
Sbjct: 353 SVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIK------AAKKMVE---- 402
Query: 291 TARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRARIMPWRTLR 350
R + V ++ H VL NR P+LHR+ I ++ + ++
Sbjct: 403 ---------REEAVVWDILDEVIREH-----PVLLNRAPTLHRLGIQAFEPVLIEGKAIQ 448
Query: 351 FNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVASTQDFLT 410
+ VC YNADFDGD+M +HVP T EA+ EA LM NN+ +P NGE ++ +QD +
Sbjct: 449 LHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVL 508
Query: 411 SSFLITRKDTFYDRAAFSLMCCYM-GDGMDRVDLPTPAILKPVELWTGKQLF-SVLIRPH 468
+ +TR C G+GM + P E ++L+ S L H
Sbjct: 509 GLYYMTRD------------CVNAKGEGM--------VLTGPKE---AERLYRSGLASLH 545
Query: 469 ANMRVYVNLTVKEKTYSNKLIRTEGDEEIR----IETMCPNDGFVYFRNSELISGQLGKA 524
A RV V +T EK + +L+ ++ I M G Y +++ LGK
Sbjct: 546 A--RVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPY----SIVNQALGKK 599
Query: 525 TLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHGFSIGIDDVQPKKELSDKK 584
+ + + R G T +++ + G S+GIDD+ + +KK
Sbjct: 600 AISK-----MLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMV----IPEKK 650
Query: 585 GKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQTLEAVITDILNRIREDAGKACMGSLPW 644
++ISE ++ E E Q + G A + DI + KA M +L
Sbjct: 651 HEIISE----AEAEVAEIQE---QFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQT 703
Query: 645 R---------------NSPLIMSQCGSKGSPINISQMVACVGQQSVGGRRAPNGFIDRSL 689
NS +M+ G++GS I Q+ G + P+G S+
Sbjct: 704 ETVINRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMA-----KPDG----SI 754
Query: 690 PHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGREGLVDTAVKTADTGYMSRRLIKA 749
P + +F GL+ ++F T G R+GL DTA+KTA++GY++RRL+
Sbjct: 755 IETP-----------ITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDV 803
Query: 750 LEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEGKSGEPLNFDRLLMKVKA--TCPPA 807
+DL + D+ + G + + G G EPL DR+L +V A P
Sbjct: 804 AQDLVVTEDDCGTHEGIMMTPVIEG----------GDVKEPLR-DRVLGRVTAEDVLKPG 852
Query: 808 GQRYLSPQQVSEIVEKQLAAYGKESCSEAFLNSLRKFFEGQQDKLDKKIKFVEDIGWDDK 867
L P+ ++ +Q +E+ +A K+ + D G
Sbjct: 853 TADILVPRNT--LLHEQWCDLLEENSVDAV-------------KVRSVVSCDTDFG---- 893
Query: 868 SQILEEVTHKTSGITEKQLEVFIQTCFSR--YRVKRVEAGTAIGAIGAQSIGEPGTQMTL 925
C+ R R + G AIG I AQSIGEPGTQ+T+
Sbjct: 894 ---------------------VCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTM 932
Query: 926 KTFHFAG 932
+TFH G
Sbjct: 933 RTFHIGG 939
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 1178 TFRGEVLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMP 1237
T+ ++LGIT+ + +S + ASF++T L A+V G+ D + G+ E +I+G +P
Sbjct: 1301 TYSRDLLGITKASLAT--ESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIP 1358
Query: 1238 LGTG 1241
GTG
Sbjct: 1359 AGTG 1362
>pdb|3LU0|D Chain D, Molecular Model Of Escherichia Coli Core Rna Polymerase
pdb|4IGC|D Chain D, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|I Chain I, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 1407
Score = 227 bits (579), Expect = 3e-59, Method: Compositional matrix adjust.
Identities = 227/847 (26%), Positives = 356/847 (42%), Gaps = 165/847 (19%)
Query: 111 RPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKS 170
+PE +I+T + V P +RP V +DG + +D+ + +R+I N L++ L A
Sbjct: 233 KPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIV 292
Query: 171 LAGWETLQVEVAQYINSDVRGVPFSMQVARPLSGFVQRLKGKQGRFRGNLSGKRVEYTGR 230
LQ V +++ RG + RPL +KGKQGRFR NL GKRV+Y+GR
Sbjct: 293 RNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGR 352
Query: 231 TVISPDPNLKITEVAIPIRMARILTYPERVSDHNIEKLRQCIQNGPDKYPGARMIRYPDG 290
+VI+ P L++ + +P +MA L P + L I+ +M+
Sbjct: 353 SVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIK------AAKKMVE---- 402
Query: 291 TARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRARIMPWRTLR 350
R + V ++ H VL NR P+LHR+ I ++ + ++
Sbjct: 403 ---------REEAVVWDILDEVIREH-----PVLLNRAPTLHRLGIQAFEPVLIEGKAIQ 448
Query: 351 FNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILVASTQDFLT 410
+ VC YNADFDGD+M +HVP T EA+ EA LM NN+ +P NGE ++ +QD +
Sbjct: 449 LHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVL 508
Query: 411 SSFLITRKDTFYDRAAFSLMCCYM-GDGMDRVDLPTPAILKPVELWTGKQLF-SVLIRPH 468
+ +TR C G+GM + P E ++L+ S L H
Sbjct: 509 GLYYMTRD------------CVNAKGEGM--------VLTGPKE---AERLYRSGLASLH 545
Query: 469 ANMRVYVNLTVKEKTYSNKLIRTEGDEEIR----IETMCPNDGFVYFRNSELISGQLGKA 524
A RV V +T EK + +L+ ++ I M G Y +++ LGK
Sbjct: 546 A--RVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPY----SIVNQALGKK 599
Query: 525 TLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHGFSIGIDDVQPKKELSDKK 584
+ + + R G T +++ + G S+GIDD+ + +KK
Sbjct: 600 AISK-----MLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMV----IPEKK 650
Query: 585 GKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQTLEAVITDILNRIREDAGKACMGSLPW 644
++ISE ++ E E Q + G A + DI + KA M +L
Sbjct: 651 HEIISE----AEAEVAEIQE---QFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQT 703
Query: 645 R---------------NSPLIMSQCGSKGSPINISQMVACVGQQSVGGRRAPNGFIDRSL 689
NS +M+ G++GS I Q+ G + P+G S+
Sbjct: 704 ETVINRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMA-----KPDG----SI 754
Query: 690 PHFPRKAKEPAAKGFVANSFYSGLSATEFFFHTMGGREGLVDTAVKTADTGYMSRRLIKA 749
P + +F GL+ ++F T G R+GL DTA+KTA++GY++RRL+
Sbjct: 755 IETP-----------ITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDV 803
Query: 750 LEDLSIQYDNSVRNAGGCIVQFLYGDDGMDPANMEGKSGEPLNFDRLLMKVKA--TCPPA 807
+DL + D+ + G + + G G EPL DR+L +V A P
Sbjct: 804 AQDLVVTEDDCGTHEGIMMTPVIEG----------GDVKEPLR-DRVLGRVTAEDVLKPG 852
Query: 808 GQRYLSPQQVSEIVEKQLAAYGKESCSEAFLNSLRKFFEGQQDKLDKKIKFVEDIGWDDK 867
L P+ ++ +Q +E+ +A K+ + D G
Sbjct: 853 TADILVPRNT--LLHEQWCDLLEENSVDAV-------------KVRSVVSCDTDFG---- 893
Query: 868 SQILEEVTHKTSGITEKQLEVFIQTCFSR--YRVKRVEAGTAIGAIGAQSIGEPGTQMTL 925
C+ R R + G AIG I AQSIGEPGTQ+T+
Sbjct: 894 ---------------------VCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTM 932
Query: 926 KTFHFAG 932
+TFH G
Sbjct: 933 RTFHIGG 939
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 1178 TFRGEVLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMP 1237
T+ ++LGIT+ + +S + ASF++T L A+V G+ D + G+ E +I+G +P
Sbjct: 1301 TYSRDLLGITKASLAT--ESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIP 1358
Query: 1238 LGTG 1241
GTG
Sbjct: 1359 AGTG 1362
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1264
Score = 203 bits (516), Expect = 5e-52, Method: Compositional matrix adjust.
Identities = 187/682 (27%), Positives = 303/682 (44%), Gaps = 117/682 (17%)
Query: 111 RPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKS 170
RPE +I+ + V P +RP V +DG + +D+ + +R+I N L++ L +
Sbjct: 248 RPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIII 307
Query: 171 LAGWETLQVEVAQYINSDVRGVPFSMQVA-RPLSGFVQRLKGKQGRFRGNLSGKRVEYTG 229
LQ V I++ RG P + + RPL L GKQGRFR NL GKRV+Y+G
Sbjct: 308 RNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGKRVDYSG 367
Query: 230 RTVISPDPNLKITEVAIPIRMARILTYP-------ERVSDHNIEKLRQCIQNGPDKYPGA 282
R+VI P LK+ + +P RMA L P E+ N++ R+ ++ D
Sbjct: 368 RSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAARRMLERQRDIKDEV 427
Query: 283 RMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRAR 342
D V++GK VVL NR P+LHR+ I +
Sbjct: 428 W-----DALEEVIHGK-----------------------VVLLNRAPTLHRLGIQAFQPV 459
Query: 343 IMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILV 402
++ ++++ + VC +NADFDGD+M +HVP + A+ EA + M +NL +P +GE L
Sbjct: 460 LVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLA 519
Query: 403 ASTQDFLTSSFLIT--RKDTFYDRAAF-----SLMCCYMGDGMDRVDLPTPAILKPVELW 455
++D + + IT RK+ AF +L G+ V L P ++ E
Sbjct: 520 KPSRDIILGLYYITQVRKEKKGAGMAFATPEEALAAYERGE----VALNAPIVVAGRETS 575
Query: 456 TGKQLFSVLIRPHANMRVYVNLTVKEKTYSNKLIRTEGDEEIRIETMCPNDGFVYFRN-- 513
G+ F A + V L + T + + + R+ET + G + F
Sbjct: 576 VGRLKFVFANPDEALLAVAHGLLDLQDTVTTRYLGR------RLET---SPGRILFARIV 626
Query: 514 ----------SELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIG 563
ELI Q+ N KD +Y LR G T+ ++ L
Sbjct: 627 GEAVGDEKVAQELI--QMDVPQEKNSLKDLVYQAFLR-LGMEKTARLLDALKYYGFTLST 683
Query: 564 NHGFSIGIDD-VQPKK-----ELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQ 617
G +IGIDD V P++ E +D+K + I + YE+ + +E + +QL +
Sbjct: 684 TSGITIGIDDAVIPEEKQRYLEEADRKLRQIEQAYEMGFLTDRERYDQVIQL-----WTE 738
Query: 618 TLEAVITDILNRIREDAGKACMGSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQSVGG 677
T E V + N E+ P+ N +M+Q G++G+P I Q+ G
Sbjct: 739 TTEKVTQAVFNNFEEN--------YPF-NPLYVMAQSGARGNPQQIRQLCGMRGLM---- 785
Query: 678 RRAPNGFIDRSLPHFPRKAKEPAAKGF---VANSFYSGLSATEFFFHTMGGREGLVDTAV 734
++P+ + F V +SF GL+ E+F + G R+G DTA+
Sbjct: 786 -------------------QKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTAL 826
Query: 735 KTADTGYMSRRLIKALEDLSIQ 756
+TAD+GY++R+L+ ++ ++
Sbjct: 827 RTADSGYLTRKLVDVAHEIVVR 848
Score = 64.7 bits (156), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 35/87 (40%), Positives = 52/87 (59%), Gaps = 14/87 (16%)
Query: 892 TCFSRYRV------------KRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVA-SMNI 938
TC +RY V + V G A+G + A+SIGEPGTQ+T++TFH GVA +I
Sbjct: 933 TCQTRYGVCQKCYGYDLSMARPVSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDI 992
Query: 939 TQGVPRIKEIINGAKRISTPIITAELE 965
TQG+PR+ E+ A+R + +E++
Sbjct: 993 TQGLPRVIELFE-ARRPKAKAVISEID 1018
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 57/140 (40%), Gaps = 42/140 (30%)
Query: 1142 GIEAARICIIDEINETMKAHGMSIDKRHMMLL-------------ADLMTFRGEVL---- 1184
G EA ++DEI + +A G+ + +H+ ++ D G+VL
Sbjct: 1080 GPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSRLLEGQVLEKWD 1139
Query: 1185 -----------------------GITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDD 1221
G+T+ + KS L ASF+ T L A++ G+ D
Sbjct: 1140 VEALNERLIAEGKVPVAWKPLLMGVTKSALST--KSWLSAASFQNTTHVLTEAAIAGKKD 1197
Query: 1222 RIEGVSECIIMGIPMPLGTG 1241
+ G+ E +I+G +P GTG
Sbjct: 1198 ELIGLKENVILGRLIPAGTG 1217
>pdb|1HQM|D Chain D, 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 = 1265
Score = 201 bits (510), Expect = 3e-51, Method: Compositional matrix adjust.
Identities = 188/683 (27%), Positives = 303/683 (44%), Gaps = 118/683 (17%)
Query: 111 RPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKS 170
RPE +I+ + V P +RP V +DG + +D+ + +R+I N L++ L +
Sbjct: 248 RPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIII 307
Query: 171 LAGWETLQVEVAQYINSDVRGVPFSMQVA-RPLSGFVQRLKGKQGRFRGNLSGKRVEYTG 229
LQ V I++ RG P + + RPL L GKQGRFR NL GKRV+Y+G
Sbjct: 308 RNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGKRVDYSG 367
Query: 230 RTVISPDPNLKITEVAIPIRMARILTYP-------ERVSDHNIEKLRQCIQNGPDKYPGA 282
R+VI P LK+ + +P RMA L P E+ N++ R+ ++ D
Sbjct: 368 RSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAARRMLERQRDIKDEV 427
Query: 283 RMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRAR 342
D V++GK VVL NR P+LHR+ I +
Sbjct: 428 W-----DALEEVIHGK-----------------------VVLLNRAPTLHRLGIQAFQPV 459
Query: 343 IMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILV 402
++ ++++ + VC +NADFDGD+M +HVP + A+ EA + M +NL +P +GE L
Sbjct: 460 LVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLA 519
Query: 403 ASTQDFLTSSFLIT--RKDTFYDRAAF-----SLMCCYMGDGMDRVDLPTPAILKPVELW 455
++D + + IT RK+ AF +L G+ V L P ++ E
Sbjct: 520 KPSRDIILGLYYITQVRKEKKGAGMAFATPEEALAAYERGE----VALNAPIVVAGRETS 575
Query: 456 TGKQLFSVLIRPHANMRVYVNLTVKEKTYSNKLIRTEGDEEIRIETMCPNDGFVYFRN-- 513
G+ F A + V L + T + + + R+ET N G + F
Sbjct: 576 VGRLKFVFANPDEALLAVAHGLLDLQDTVTTRYLGR------RLET---NPGRILFARIV 626
Query: 514 ----------SELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIG 563
ELI Q+ N KD +Y LR G T+ ++ L
Sbjct: 627 GEAVGDEKVAQELI--QMDVPQEKNSLKDLVYQAFLR-LGMEKTARLLDALKYYGFTLST 683
Query: 564 NHG-FSIGIDD-VQPKK-----ELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAA 616
G +IGIDD V P++ E +D+K + I + YE+ + +E + +QL
Sbjct: 684 TSGIITIGIDDAVIPEEKQRYLEEADRKLRQIEQAYEMGFLTDRERYDQVIQL-----WT 738
Query: 617 QTLEAVITDILNRIREDAGKACMGSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQSVG 676
+T E V + N E+ P+ N +M+Q G++G+P I Q+ G
Sbjct: 739 ETTEKVTQAVFNNFEEN--------YPF-NPLYVMAQSGARGNPQQIRQLCGMRGLM--- 786
Query: 677 GRRAPNGFIDRSLPHFPRKAKEPAAKGF---VANSFYSGLSATEFFFHTMGGREGLVDTA 733
++P+ + F V +SF GL+ E+F + G R+G DTA
Sbjct: 787 --------------------QKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTA 826
Query: 734 VKTADTGYMSRRLIKALEDLSIQ 756
++TAD+GY++R+L+ ++ ++
Sbjct: 827 LRTADSGYLTRKLVDVAHEIVVR 849
Score = 64.7 bits (156), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 35/87 (40%), Positives = 52/87 (59%), Gaps = 14/87 (16%)
Query: 892 TCFSRYRV------------KRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVA-SMNI 938
TC +RY V + V G A+G + A+SIGEPGTQ+T++TFH GVA +I
Sbjct: 934 TCQTRYGVCQKCYGYDLSMARPVSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDI 993
Query: 939 TQGVPRIKEIINGAKRISTPIITAELE 965
TQG+PR+ E+ A+R + +E++
Sbjct: 994 TQGLPRVIELFE-ARRPKAKAVISEID 1019
Score = 41.6 bits (96), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 57/140 (40%), Gaps = 42/140 (30%)
Query: 1142 GIEAARICIIDEINETMKAHGMSIDKRHMMLLADLMT-------------FRGEVL---- 1184
G EA ++DEI + +A G+ + +H+ ++ M G+VL
Sbjct: 1081 GPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSPLLEGQVLEKWD 1140
Query: 1185 -----------------------GITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDD 1221
G+T+ + KS L ASF+ T L A++ G+ D
Sbjct: 1141 VEALNERLIAEGKVPVAWKPLLMGVTKSALST--KSWLSAASFQNTTHVLTEAAIAGKKD 1198
Query: 1222 RIEGVSECIIMGIPMPLGTG 1241
+ G+ E +I+G +P GTG
Sbjct: 1199 ELIGLKENVILGRLIPAGTG 1218
>pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|M Chain M, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9Z|D Chain D, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
pdb|1YNJ|D Chain D, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNJ|J Chain J, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNN|D Chain D, Taq Rna Polymerase-rifampicin Complex
pdb|1YNN|J Chain J, Taq Rna Polymerase-rifampicin Complex
Length = 1524
Score = 200 bits (508), Expect = 4e-51, Method: Compositional matrix adjust.
Identities = 187/679 (27%), Positives = 304/679 (44%), Gaps = 111/679 (16%)
Query: 111 RPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKS 170
RPE +I+ + V P +RP V +DG + +D+ + +R+I N L++ L +
Sbjct: 508 RPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIII 567
Query: 171 LAGWETLQVEVAQYINSDVRGVPFSMQVA-RPLSGFVQRLKGKQGRFRGNLSGKRVEYTG 229
LQ V I++ RG P + + RPL L GKQGRFR NL GKRV+Y+G
Sbjct: 568 RNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGKRVDYSG 627
Query: 230 RTVISPDPNLKITEVAIPIRMARILTYP-------ERVSDHNIEKLRQCIQNGPDKYPGA 282
R+VI P LK+ + +P RMA L P E+ N++ R+ ++ D
Sbjct: 628 RSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAARRMLERQRDIKDEV 687
Query: 283 RMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRAR 342
D V++GK VVL NR P+LHR+ I +
Sbjct: 688 W-----DALEEVIHGK-----------------------VVLLNRAPTLHRLGIQAFQPV 719
Query: 343 IMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILV 402
++ ++++ + VC +NADFDGD+M +HVP + A+ EA + M +NL +P +GE L
Sbjct: 720 LVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLA 779
Query: 403 ASTQDFLTSSFLIT--RKDTFYDRAAF-----SLMCCYMGDGMDRVDLPTPAILKPVELW 455
++D + + IT RK+ AF +L G+ V L P ++ E
Sbjct: 780 KPSRDIILGLYYITQVRKEKKGAGMAFATPEEALAAYERGE----VALNAPIVVAGRETS 835
Query: 456 TGKQLF-------SVLIRPHANMRVYVNLTVKEKTYSNKLIRTEGDEEI--RIETMCPND 506
G+ F ++L H + + +TV+ Y + + T + RI D
Sbjct: 836 VGRLKFVFANPDEALLAVAHGLLDLQDVVTVR---YLGRRLETSPGRILFARIVGEAVGD 892
Query: 507 GFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHG 566
V ELI Q+ N KD +Y LR G T+ ++ L G
Sbjct: 893 EKV---AQELI--QMDVPQEKNSLKDLVYQAFLR-LGMEKTARLLDALKYYGFTLSTTSG 946
Query: 567 FSIGIDD-VQPKK-----ELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQTLE 620
+IGIDD V P++ E +D+K + I + YE+ + +E + +QL +T E
Sbjct: 947 ITIGIDDAVIPEEKQRYLEEADRKLRQIEQAYEMGFLTDRERYDQVIQL-----WTETTE 1001
Query: 621 AVITDILNRIREDAGKACMGSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQSVGGRRA 680
V + E+ P+ N +M+Q G++G+P I Q+ G
Sbjct: 1002 KVTQAVFKNFEEN--------YPF-NPLYVMAQSGARGNPQQIRQLCGMRGLM------- 1045
Query: 681 PNGFIDRSLPHFPRKAKEPAAKGF---VANSFYSGLSATEFFFHTMGGREGLVDTAVKTA 737
++P+ + F V +SF GL+ E+F + G R+G DTA++TA
Sbjct: 1046 ----------------QKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTA 1089
Query: 738 DTGYMSRRLIKALEDLSIQ 756
D+GY++R+L+ ++ ++
Sbjct: 1090 DSGYLTRKLVDVAHEIVVR 1108
Score = 64.7 bits (156), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 35/87 (40%), Positives = 52/87 (59%), Gaps = 14/87 (16%)
Query: 892 TCFSRYRV------------KRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVA-SMNI 938
TC +RY V + V G A+G + A+SIGEPGTQ+T++TFH GVA +I
Sbjct: 1193 TCQTRYGVCQKCYGYDLSMARPVSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDI 1252
Query: 939 TQGVPRIKEIINGAKRISTPIITAELE 965
TQG+PR+ E+ A+R + +E++
Sbjct: 1253 TQGLPRVIELFE-ARRPKAKAVISEID 1278
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 57/140 (40%), Gaps = 42/140 (30%)
Query: 1142 GIEAARICIIDEINETMKAHGMSIDKRHMMLL-------------ADLMTFRGEVL---- 1184
G EA ++DEI + +A G+ + +H+ ++ D G+VL
Sbjct: 1340 GPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSRLLEGQVLEKWD 1399
Query: 1185 -----------------------GITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDD 1221
G+T+ + KS L ASF+ T L A++ G+ D
Sbjct: 1400 VEALNERLIAEGKVPVAWKPLLMGVTKSALST--KSWLSAASFQNTTHVLTEAAIAGKKD 1457
Query: 1222 RIEGVSECIIMGIPMPLGTG 1241
+ G+ E +I+G +P GTG
Sbjct: 1458 ELIGLKENVILGRLIPAGTG 1477
>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For
Structural Studies
Length = 1233
Score = 200 bits (508), Expect = 4e-51, Method: Compositional matrix adjust.
Identities = 187/679 (27%), Positives = 304/679 (44%), Gaps = 111/679 (16%)
Query: 111 RPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKS 170
RPE +I+ + V P +RP V +DG + +D+ + +R+I N L++ L +
Sbjct: 217 RPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIII 276
Query: 171 LAGWETLQVEVAQYINSDVRGVPFSMQVA-RPLSGFVQRLKGKQGRFRGNLSGKRVEYTG 229
LQ V I++ RG P + + RPL L GKQGRFR NL GKRV+Y+G
Sbjct: 277 RNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGKRVDYSG 336
Query: 230 RTVISPDPNLKITEVAIPIRMARILTYP-------ERVSDHNIEKLRQCIQNGPDKYPGA 282
R+VI P LK+ + +P RMA L P E+ N++ R+ ++ D
Sbjct: 337 RSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPNVKAARRMLERQRDIKDEV 396
Query: 283 RMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRAR 342
D V++GK VVL NR P+LHR+ I +
Sbjct: 397 W-----DALEEVIHGK-----------------------VVLLNRAPTLHRLGIQAFQPV 428
Query: 343 IMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILV 402
++ ++++ + VC +NADFDGD+M +HVP + A+ EA + M +NL +P +GE L
Sbjct: 429 LVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLA 488
Query: 403 ASTQDFLTSSFLIT--RKDTFYDRAAF-----SLMCCYMGDGMDRVDLPTPAILKPVELW 455
++D + + IT RK+ AF +L G+ V L P ++ E
Sbjct: 489 KPSRDIILGLYYITQVRKEKKGAGMAFATPEEALAAYERGE----VALNAPIVVAGRETS 544
Query: 456 TGKQLF-------SVLIRPHANMRVYVNLTVKEKTYSNKLIRTEGDEEI--RIETMCPND 506
G+ F ++L H + + +TV+ Y + + T + RI D
Sbjct: 545 VGRLKFVFANPDEALLAVAHGLLDLQDVVTVR---YLGRRLETSPGRILFARIVGEAVGD 601
Query: 507 GFVYFRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHG 566
V ELI Q+ N KD +Y LR G T+ ++ L G
Sbjct: 602 EKV---AQELI--QMDVPQEKNSLKDLVYQAFLR-LGMEKTARLLDALKYYGFTLSTTSG 655
Query: 567 FSIGIDD-VQPKK-----ELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQTLE 620
+IGIDD V P++ E +D+K + I + YE+ + +E + +QL +T E
Sbjct: 656 ITIGIDDAVIPEEKQRYLEEADRKLRQIEQAYEMGFLTDRERYDQVIQL-----WTETTE 710
Query: 621 AVITDILNRIREDAGKACMGSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQSVGGRRA 680
V + E+ P+ N +M+Q G++G+P I Q+ G
Sbjct: 711 KVTQAVFKNFEEN--------YPF-NPLYVMAQSGARGNPQQIRQLCGMRGLM------- 754
Query: 681 PNGFIDRSLPHFPRKAKEPAAKGF---VANSFYSGLSATEFFFHTMGGREGLVDTAVKTA 737
++P+ + F V +SF GL+ E+F + G R+G DTA++TA
Sbjct: 755 ----------------QKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTA 798
Query: 738 DTGYMSRRLIKALEDLSIQ 756
D+GY++R+L+ ++ ++
Sbjct: 799 DSGYLTRKLVDVAHEIVVR 817
Score = 64.7 bits (156), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 35/87 (40%), Positives = 52/87 (59%), Gaps = 14/87 (16%)
Query: 892 TCFSRYRV------------KRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVA-SMNI 938
TC +RY V + V G A+G + A+SIGEPGTQ+T++TFH GVA +I
Sbjct: 902 TCQTRYGVCQKCYGYDLSMARPVSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDI 961
Query: 939 TQGVPRIKEIINGAKRISTPIITAELE 965
TQG+PR+ E+ A+R + +E++
Sbjct: 962 TQGLPRVIELFE-ARRPKAKAVISEID 987
Score = 42.0 bits (97), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 57/140 (40%), Gaps = 42/140 (30%)
Query: 1142 GIEAARICIIDEINETMKAHGMSIDKRHMMLL-------------ADLMTFRGEVL---- 1184
G EA ++DEI + +A G+ + +H+ ++ D G+VL
Sbjct: 1049 GPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSRLLEGQVLEKWD 1108
Query: 1185 -----------------------GITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDD 1221
G+T+ + KS L ASF+ T L A++ G+ D
Sbjct: 1109 VEALNERLIAEGKVPVAWKPLLMGVTKSALST--KSWLSAASFQNTTHVLTEAAIAGKKD 1166
Query: 1222 RIEGVSECIIMGIPMPLGTG 1241
+ G+ E +I+G +P GTG
Sbjct: 1167 ELIGLKENVILGRLIPAGTG 1186
>pdb|4GZY|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
pdb|4GZZ|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
Length = 1534
Score = 196 bits (499), Expect = 5e-50, Method: Compositional matrix adjust.
Identities = 183/675 (27%), Positives = 297/675 (44%), Gaps = 103/675 (15%)
Query: 111 RPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKS 170
RPE +I+ + V P +RP V +DG + +D+ + +R+I N L++ L +
Sbjct: 508 RPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIII 567
Query: 171 LAGWETLQVEVAQYINSDVRGVPFSMQVA-RPLSGFVQRLKGKQGRFRGNLSGKRVEYTG 229
LQ V +++ RG P + + RPL L GKQGRFR NL GKRV+Y+G
Sbjct: 568 RNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSG 627
Query: 230 RTVISPDPNLKITEVAIPIRMARILTYP-------ERVSDHNIEKLRQCIQNGPDKYPGA 282
R+VI P LK+ + +P RMA L P E+ N++ R+ ++ D
Sbjct: 628 RSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRDIKDEV 687
Query: 283 RMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRAR 342
D V++GK VVL NR P+LHR+ I +
Sbjct: 688 W-----DALEEVIHGK-----------------------VVLLNRAPTLHRLGIQAFQPV 719
Query: 343 IMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILV 402
++ ++++ + VC +NADFDGD+M +HVP + A+ EA + M +NL +P +GE L
Sbjct: 720 LVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLA 779
Query: 403 ASTQDFLTSSFLITRKDTFYDRAAFSLMC---CYMGDGMDRVDLPTPAILKPVELWTGKQ 459
++D + + IT+ A V L P + E G+
Sbjct: 780 KPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRL 839
Query: 460 LF-------SVLIRPHANMRVYVNLTVKEKTYSNKLIRTEGDEEI--RIETMCPNDGFVY 510
+ ++L H + + +TV+ Y K + T + RI D V
Sbjct: 840 KYVFANPDEALLAVAHGIVDLQDVVTVR---YMGKRLETSPGRILFARIVAEAVEDEKVA 896
Query: 511 FRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHGFSIG 570
+ ELI QL N KD +Y LR G T+ ++ L + G +IG
Sbjct: 897 W---ELI--QLDVPQEKNSLKDLVYQAFLR-LGMEKTARLLDALKYYGFTFSTTSGITIG 950
Query: 571 IDD-VQPKK-----ELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQTLEAVIT 624
IDD V P++ E +D+K I + YE+ + +E + LQL +T E V
Sbjct: 951 IDDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQL-----WTETTEKVTQ 1005
Query: 625 DILNRIREDAGKACMGSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQSVGGRRAPNGF 684
+ E+ P+ N +M+Q G++G+P I Q+ G
Sbjct: 1006 AVFKNFEEN--------YPF-NPLYVMAQSGARGNPQQIRQLCGLRGLM----------- 1045
Query: 685 IDRSLPHFPRKAKEPAAKGF---VANSFYSGLSATEFFFHTMGGREGLVDTAVKTADTGY 741
++P+ + F V +SF GL+ E+F + G R+G DTA++TAD+GY
Sbjct: 1046 ------------QKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGY 1093
Query: 742 MSRRLIKALEDLSIQ 756
++R+L+ ++ ++
Sbjct: 1094 LTRKLVDVTHEIVVR 1108
Score = 66.2 bits (160), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 36/87 (41%), Positives = 53/87 (60%), Gaps = 14/87 (16%)
Query: 892 TCFSRYRV------------KRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVA-SMNI 938
TC +RY V + V G A+G + AQSIGEPGTQ+T++TFH GVA + +I
Sbjct: 1193 TCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADI 1252
Query: 939 TQGVPRIKEIINGAKRISTPIITAELE 965
TQG+PR+ E+ A+R + +E++
Sbjct: 1253 TQGLPRVIELFE-ARRPKAKAVISEID 1278
Score = 40.4 bits (93), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 33/140 (23%), Positives = 57/140 (40%), Gaps = 42/140 (30%)
Query: 1142 GIEAARICIIDEINETMKAHGMSIDKRHMMLL-------------ADLMTFRGEVL---- 1184
G EA +++EI + +A G+ + +H+ ++ D G+VL
Sbjct: 1340 GPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWD 1399
Query: 1185 -----------------------GITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDD 1221
G+T+ + KS L ASF+ T L A++ G+ D
Sbjct: 1400 VEALNERLIAEGKTPVAWKPLLMGVTKSALST--KSWLSAASFQNTTHVLTEAAIAGKKD 1457
Query: 1222 RIEGVSECIIMGIPMPLGTG 1241
+ G+ E +I+G +P GTG
Sbjct: 1458 ELIGLKENVILGRLIPAGTG 1477
>pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|N Chain N, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1SMY|D Chain D, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1SMY|N Chain N, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1ZYR|D Chain D, Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme
In Complex With The Antibiotic Streptolydigin
pdb|1ZYR|N Chain N, Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme
In Complex With The Antibiotic Streptolydigin
pdb|2A68|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A68|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A69|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A69|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A6E|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6E|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6H|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2A6H|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2CW0|D Chain D, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2CW0|N Chain N, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2BE5|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2BE5|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2O5I|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5I|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5J|D Chain D, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2O5J|N Chain N, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2PPB|D Chain D, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|2PPB|N Chain N, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|3DXJ|D Chain D, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3DXJ|N Chain N, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3EQL|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3EQL|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3AOH|D Chain D, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|I Chain I, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|N Chain N, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOI|D Chain D, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|I Chain I, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|N Chain N, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|4G7H|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7H|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7O|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7O|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7Z|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4G7Z|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
Length = 1524
Score = 196 bits (499), Expect = 5e-50, Method: Compositional matrix adjust.
Identities = 183/675 (27%), Positives = 297/675 (44%), Gaps = 103/675 (15%)
Query: 111 RPEKLIITNIAVPPIAIRPSVIMDGSQSNENDITERLKRIIQTNASLQQELVEANSAFKS 170
RPE +I+ + V P +RP V +DG + +D+ + +R+I N L++ L +
Sbjct: 508 RPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIII 567
Query: 171 LAGWETLQVEVAQYINSDVRGVPFSMQVA-RPLSGFVQRLKGKQGRFRGNLSGKRVEYTG 229
LQ V +++ RG P + + RPL L GKQGRFR NL GKRV+Y+G
Sbjct: 568 RNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSG 627
Query: 230 RTVISPDPNLKITEVAIPIRMARILTYP-------ERVSDHNIEKLRQCIQNGPDKYPGA 282
R+VI P LK+ + +P RMA L P E+ N++ R+ ++ D
Sbjct: 628 RSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRDIKDEV 687
Query: 283 RMIRYPDGTARVLYGKFRNQLAVELKSGCIVDRHLEDGDVVLFNRQPSLHRMSIMCHRAR 342
D V++GK VVL NR P+LHR+ I +
Sbjct: 688 W-----DALEEVIHGK-----------------------VVLLNRAPTLHRLGIQAFQPV 719
Query: 343 IMPWRTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILV 402
++ ++++ + VC +NADFDGD+M +HVP + A+ EA + M +NL +P +GE L
Sbjct: 720 LVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLA 779
Query: 403 ASTQDFLTSSFLITRKDTFYDRAAFSLMC---CYMGDGMDRVDLPTPAILKPVELWTGKQ 459
++D + + IT+ A V L P + E G+
Sbjct: 780 KPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRL 839
Query: 460 LF-------SVLIRPHANMRVYVNLTVKEKTYSNKLIRTEGDEEI--RIETMCPNDGFVY 510
+ ++L H + + +TV+ Y K + T + RI D V
Sbjct: 840 KYVFANPDEALLAVAHGIVDLQDVVTVR---YMGKRLETSPGRILFARIVAEAVEDEKVA 896
Query: 511 FRNSELISGQLGKATLGNGNKDGLYSVLLRDYGAHATSGCMNRLAKLSARWIGNHGFSIG 570
+ ELI QL N KD +Y LR G T+ ++ L + G +IG
Sbjct: 897 W---ELI--QLDVPQEKNSLKDLVYQAFLR-LGMEKTARLLDALKYYGFTFSTTSGITIG 950
Query: 571 IDD-VQPKK-----ELSDKKGKLISENYEVCNVKIKEYNEGKLQLKPGCDAAQTLEAVIT 624
IDD V P++ E +D+K I + YE+ + +E + LQL +T E V
Sbjct: 951 IDDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQL-----WTETTEKVTQ 1005
Query: 625 DILNRIREDAGKACMGSLPWRNSPLIMSQCGSKGSPINISQMVACVGQQSVGGRRAPNGF 684
+ E+ P+ N +M+Q G++G+P I Q+ G
Sbjct: 1006 AVFKNFEEN--------YPF-NPLYVMAQSGARGNPQQIRQLCGLRGLM----------- 1045
Query: 685 IDRSLPHFPRKAKEPAAKGF---VANSFYSGLSATEFFFHTMGGREGLVDTAVKTADTGY 741
++P+ + F V +SF GL+ E+F + G R+G DTA++TAD+GY
Sbjct: 1046 ------------QKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGY 1093
Query: 742 MSRRLIKALEDLSIQ 756
++R+L+ ++ ++
Sbjct: 1094 LTRKLVDVTHEIVVR 1108
Score = 66.2 bits (160), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 36/87 (41%), Positives = 53/87 (60%), Gaps = 14/87 (16%)
Query: 892 TCFSRYRV------------KRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVA-SMNI 938
TC +RY V + V G A+G + AQSIGEPGTQ+T++TFH GVA + +I
Sbjct: 1193 TCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADI 1252
Query: 939 TQGVPRIKEIINGAKRISTPIITAELE 965
TQG+PR+ E+ A+R + +E++
Sbjct: 1253 TQGLPRVIELFE-ARRPKAKAVISEID 1278
Score = 40.4 bits (93), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 33/140 (23%), Positives = 57/140 (40%), Gaps = 42/140 (30%)
Query: 1142 GIEAARICIIDEINETMKAHGMSIDKRHMMLL-------------ADLMTFRGEVL---- 1184
G EA +++EI + +A G+ + +H+ ++ D G+VL
Sbjct: 1340 GPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWD 1399
Query: 1185 -----------------------GITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDD 1221
G+T+ + KS L ASF+ T L A++ G+ D
Sbjct: 1400 VEALNERLIAEGKTPVAWKPLLMGVTKSALST--KSWLSAASFQNTTHVLTEAAIAGKKD 1457
Query: 1222 RIEGVSECIIMGIPMPLGTG 1241
+ G+ E +I+G +P GTG
Sbjct: 1458 ELIGLKENVILGRLIPAGTG 1477
>pdb|2Y0S|C Chain C, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|Y Chain Y, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|C Chain C, Rnap At 3.2ang
pdb|4B1O|C Chain C, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|Y Chain Y, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 395
Score = 192 bits (489), Expect = 8e-49, Method: Compositional matrix adjust.
Identities = 131/387 (33%), Positives = 210/387 (54%), Gaps = 31/387 (8%)
Query: 874 VTHKTSGITEKQLEVFIQTCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGV 933
+++K +T +++ Y + G AIG + AQS+GEPGTQMTL+TFHFAG+
Sbjct: 36 ISNKEVLVTRDEIDKIFDLAIKEYSEGLIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGI 95
Query: 934 ASMNITQGVPRIKEIINGAKRISTPIITAELE---CNDNENAARVVKGRIEKTLLGQVAK 990
+N+T G+PR+ EI++ K STP++T L +D E A V + ++E T + V
Sbjct: 96 RELNVTLGLPRLIEIVDAKKVPSTPMMTIYLTDEYKHDKEKALEVAR-KLEYTKIENVVS 154
Query: 991 SIKIVMTSRLASIVIALDMETIQDAHLCINADIVKESIVQTPKIKLKQQHIKVLDFRKLE 1050
S I + S SI++ LD E ++D + + D VK++I ++KL + I + L
Sbjct: 155 STSIDIAS--MSIILQLDNEMLKDKGVTV--DDVKKAI---NRLKLGEFVIDESEGNTLN 207
Query: 1051 I-FPPVDKSKIHFELYSLKNVLPMVIVKGIKTXXXXXXXXXXXXXXXXXXXXXXXXYRLL 1109
I F +D L+ L++ + +KGIK Y +L
Sbjct: 208 ISFANIDSIA---ALFKLRDKILNTKIKGIK------------GIKRAIVQKKGDEYIIL 252
Query: 1110 VEGTGLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRH 1169
+G+ L V+ +G+D K ++N+I E+++ GIEAAR II EI++ + G+ +D RH
Sbjct: 253 TDGSNLSGVLSVKGVDIAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDMRH 312
Query: 1170 MMLLADLMTFRGEVLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSEC 1229
++L+AD+MT G V I R G+ SVL A+FE T HL +A+ G + +GV E
Sbjct: 313 ILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVTVKHLLDAAARGDVEEFKGVVEN 372
Query: 1230 IIMGIPMPLGTGILKIRQRDAVPPMLK 1256
II+G P+ LGTG++++ R P+L+
Sbjct: 373 IIIGHPIKLGTGMVELTMR----PILR 395
>pdb|2WAQ|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|Y Chain Y, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
Length = 395
Score = 192 bits (488), Expect = 9e-49, Method: Compositional matrix adjust.
Identities = 131/387 (33%), Positives = 210/387 (54%), Gaps = 31/387 (8%)
Query: 874 VTHKTSGITEKQLEVFIQTCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGV 933
+++K +T +++ Y + G AIG + AQS+GEPGTQMTL+TFHFAG+
Sbjct: 36 ISNKEVLVTRDEIDKIFDLAIKEYSEGLIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGI 95
Query: 934 ASMNITQGVPRIKEIINGAKRISTPIITAELE---CNDNENAARVVKGRIEKTLLGQVAK 990
+N+T G+PR+ EI++ K STP++T L +D E A V + ++E T + V
Sbjct: 96 RELNVTLGLPRLIEIVDAKKVPSTPMMTIYLTDEYKHDKEKALEVAR-KLEYTKIENVVS 154
Query: 991 SIKIVMTSRLASIVIALDMETIQDAHLCINADIVKESIVQTPKIKLKQQHIKVLDFRKLE 1050
S I + S SI++ LD E ++D + + D VK++I ++KL + I + L
Sbjct: 155 STSIDIAS--MSIILQLDNEMLKDKGVTV--DDVKKAI---NRLKLGEFVIDESEGTTLN 207
Query: 1051 I-FPPVDKSKIHFELYSLKNVLPMVIVKGIKTXXXXXXXXXXXXXXXXXXXXXXXXYRLL 1109
I F +D L+ L++ + +KGIK Y +L
Sbjct: 208 ISFANIDSIA---ALFKLRDKILNTKIKGIK------------GIKRAIVQKKGDEYIIL 252
Query: 1110 VEGTGLQAVMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRH 1169
+G+ L V+ +G+D K ++N+I E+++ GIEAAR II EI++ + G+ +D RH
Sbjct: 253 TDGSNLSGVLSVKGVDIAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDMRH 312
Query: 1170 MMLLADLMTFRGEVLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSEC 1229
++L+AD+MT G V I R G+ SVL A+FE T HL +A+ G + +GV E
Sbjct: 313 ILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVTVKHLLDAAARGDVEEFKGVVEN 372
Query: 1230 IIMGIPMPLGTGILKIRQRDAVPPMLK 1256
II+G P+ LGTG++++ R P+L+
Sbjct: 373 IIIGHPIKLGTGMVELTMR----PILR 395
>pdb|2PMZ|C Chain C, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|G Chain G, Archaeal Rna Polymerase From Sulfolobus Solfataricus
Length = 392
Score = 190 bits (483), Expect = 4e-48, Method: Compositional matrix adjust.
Identities = 129/379 (34%), Positives = 205/379 (54%), Gaps = 29/379 (7%)
Query: 881 ITEKQLEVFIQTCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQ 940
+T +++ Y + G AIG + AQS+GEPGTQMTL+TFHFAG+ +N+T
Sbjct: 40 VTRDEIDKIFDLAIKEYSEGLIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTL 99
Query: 941 GVPRIKEIINGAKRISTPIITAEL--ECNDNENAARVVKGRIEKTLLGQVAKSIKIVMTS 998
G+PR+ EI++ K STP++T L E + + A V ++E T + V S I + S
Sbjct: 100 GLPRLIEIVDAKKVPSTPMMTIYLTDEYKRDRDKALEVARKLEYTKIENVVSSTSIDIAS 159
Query: 999 RLASIVIALDMETIQDAHLCINADIVKESIVQTPKIKLKQQHIKVLDFRKLEI-FPPVDK 1057
SI++ LD E ++D + + D VK++I ++KL I+ + L I F +D
Sbjct: 160 --MSIILQLDNEMLKDKGVTV--DDVKKAI---GRLKLGDFMIEESEDSTLNINFANIDS 212
Query: 1058 SKIHFELYSLKNVLPMVIVKGIKTXXXXXXXXXXXXXXXXXXXXXXXXYRLLVEGTGLQA 1117
L+ L++ + +KGIK Y +L +G+ L
Sbjct: 213 IA---ALFKLRDKILNTKIKGIK------------GIKRAIVQKKGDEYIILTDGSNLSG 257
Query: 1118 VMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLM 1177
V+ +G+D K ++N+I E+++ GIEAAR II EI++ + G+ +D RH++L+AD+M
Sbjct: 258 VLSVKGVDVAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDIRHILLIADVM 317
Query: 1178 TFRGEVLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMP 1237
T G V I R G+ SVL A+FE T HL +A+ G + +GV E II+G P+
Sbjct: 318 TRTGIVRQIGRHGVTGEKNSVLARAAFEVTVKHLLDAAARGDVEEFKGVVENIIIGHPIK 377
Query: 1238 LGTGILKIRQRDAVPPMLK 1256
LGTG++++ R P+L+
Sbjct: 378 LGTGMVELTMR----PILR 392
>pdb|3HKZ|C Chain C, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|M Chain M, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 395
Score = 190 bits (483), Expect = 4e-48, Method: Compositional matrix adjust.
Identities = 129/379 (34%), Positives = 205/379 (54%), Gaps = 29/379 (7%)
Query: 881 ITEKQLEVFIQTCFSRYRVKRVEAGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNITQ 940
+T +++ Y + G AIG + AQS+GEPGTQMTL+TFHFAG+ +N+T
Sbjct: 43 VTRDEIDKIFDLAIKEYSEGLIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTL 102
Query: 941 GVPRIKEIINGAKRISTPIITAEL--ECNDNENAARVVKGRIEKTLLGQVAKSIKIVMTS 998
G+PR+ EI++ K STP++T L E + + A V ++E T + V S I + S
Sbjct: 103 GLPRLIEIVDAKKVPSTPMMTIYLTDEYKRDRDKALEVARKLEYTKIENVVSSTSIDIAS 162
Query: 999 RLASIVIALDMETIQDAHLCINADIVKESIVQTPKIKLKQQHIKVLDFRKLEI-FPPVDK 1057
SI++ LD E ++D + + D VK++I ++KL I+ + L I F +D
Sbjct: 163 --MSIILQLDNEMLKDKGVTV--DDVKKAI---GRLKLGDFMIEESEDSTLNINFANIDS 215
Query: 1058 SKIHFELYSLKNVLPMVIVKGIKTXXXXXXXXXXXXXXXXXXXXXXXXYRLLVEGTGLQA 1117
L+ L++ + +KGIK Y +L +G+ L
Sbjct: 216 IA---ALFKLRDKILNTKIKGIK------------GIKRAIVQKKGDEYIILTDGSNLSG 260
Query: 1118 VMGAEGIDGCKTKSNHIFEVQQTLGIEAARICIIDEINETMKAHGMSIDKRHMMLLADLM 1177
V+ +G+D K ++N+I E+++ GIEAAR II EI++ + G+ +D RH++L+AD+M
Sbjct: 261 VLSVKGVDVAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDIRHILLIADVM 320
Query: 1178 TFRGEVLGITRFGIQKMDKSVLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMGIPMP 1237
T G V I R G+ SVL A+FE T HL +A+ G + +GV E II+G P+
Sbjct: 321 TRTGIVRQIGRHGVTGEKNSVLARAAFEVTVKHLLDAAARGDVEEFKGVVENIIIGHPIK 380
Query: 1238 LGTGILKIRQRDAVPPMLK 1256
LGTG++++ R P+L+
Sbjct: 381 LGTGMVELTMR----PILR 395
>pdb|3QQC|A Chain A, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP
CLAMP DOMAIN
Length = 436
Score = 94.4 bits (233), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 53/145 (36%), Positives = 78/145 (53%), Gaps = 4/145 (2%)
Query: 80 NVATYILNPVNVLFLFKRMTDTDCEVLYLS---ERPEKLIITNIAVPPIAIRPSVIMDGS 136
N + L P V +++ D D +L L RPE +++T + VPP+ RPS+ ++
Sbjct: 236 NEYRHRLMPTEVRDWLEKIPDKDLPLLGLDPEKSRPEWMVLTVLPVPPVTARPSITLETG 295
Query: 137 QSNENDITERLKRIIQTNASLQQELVEANSAFKSLAGWETLQVEVAQYINSDVRGVPFS- 195
E+D+T +L II+ N L+Q + W+ LQ V YIN++ GVP +
Sbjct: 296 IRAEDDLTHKLVDIIRINNRLKQNIEAGAPQLIIEDLWDLLQYHVTTYINNEAPGVPPAK 355
Query: 196 MQVARPLSGFVQRLKGKQGRFRGNL 220
+ RPL QRLKGK+GRFRGNL
Sbjct: 356 HKSGRPLKTLAQRLKGKEGRFRGNL 380
Score = 34.3 bits (77), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 22/36 (61%)
Query: 1198 VLMLASFEKTADHLFNASVNGRDDRIEGVSECIIMG 1233
VL A+FE T HLF A+ G D + GV E +++G
Sbjct: 393 VLARAAFEITVQHLFEAAEKGEVDNLNGVIENVLIG 428
>pdb|3IBV|A Chain A, Karyopherin Cytosolic State
pdb|3IBV|B Chain B, Karyopherin Cytosolic State
pdb|3ICQ|T Chain T, Karyopherin Nuclear State
pdb|3ICQ|U Chain U, Karyopherin Nuclear State
Length = 980
Score = 33.5 bits (75), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 31/118 (26%), Positives = 48/118 (40%), Gaps = 16/118 (13%)
Query: 806 PAGQRYLS------PQQVSEIVEKQLAAYGKESCSEAFLNSLRKFFEGQQDKLDKKIKFV 859
P RYLS V + L + KES S+ SL++F + + + KK+K+
Sbjct: 335 PYLIRYLSDDYDETSTAVFPFLSDLLVSLRKESSSKELSASLKEFLKSLLEAIIKKMKYD 394
Query: 860 EDIGWDDKSQILEEVTHKTSGITEKQLEVFIQT-------CFSRYRVKRVEAGTAIGA 910
E WDD EE + K+L++F T FS Y + + + A
Sbjct: 395 ESQEWDDDPDSEEEAEFQE---MRKKLKIFQDTINSIDSSLFSSYMYSAITSSLSTAA 449
>pdb|3TSB|A Chain A, Crystal Structure Of Inosine-5'-Monophosphate Dehydrogenase
From Bacillus Anthracis Str. Ames
pdb|3TSB|B Chain B, Crystal Structure Of Inosine-5'-Monophosphate Dehydrogenase
From Bacillus Anthracis Str. Ames
pdb|3TSD|A Chain A, Crystal Structure Of Inosine-5'-Monophosphate Dehydrogenase
From Bacillus Anthracis Str. Ames Complexed With Xmp
pdb|3TSD|B Chain B, Crystal Structure Of Inosine-5'-Monophosphate Dehydrogenase
From Bacillus Anthracis Str. Ames Complexed With Xmp
Length = 511
Score = 33.1 bits (74), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 36/72 (50%)
Query: 999 RLASIVIALDMETIQDAHLCINADIVKESIVQTPKIKLKQQHIKVLDFRKLEIFPPVDKS 1058
+L I+ DM IQD + I+ + KE ++ P + K+L K+E P VD +
Sbjct: 157 KLVGIITNRDMRFIQDYSIKISDVMTKEQLITAPVGTTLSEAEKILQKYKIEKLPLVDNN 216
Query: 1059 KIHFELYSLKNV 1070
+ L ++K++
Sbjct: 217 GVLQGLITIKDI 228
>pdb|3QFV|A Chain A, Mrck Beta In Complex With Tpca-1
pdb|3QFV|B Chain B, Mrck Beta In Complex With Tpca-1
Length = 415
Score = 30.0 bits (66), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 31/143 (21%), Positives = 61/143 (42%), Gaps = 24/143 (16%)
Query: 727 EGLVDTAVKTADTGYMSRRLIKALEDLSIQY--DNSVRNAGGCIVQFLYGDDGMDPANME 784
+G V ++V Y+S +++A+ED +Y + + G C+ + LYG+ ++
Sbjct: 228 DGTVQSSVAVGTPDYISPEILQAMEDGMGKYGPECDWWSLGVCMYEMLYGETPFYAESLV 287
Query: 785 GKSGEPLNFDRLLMKVKATCPPAGQRYLSPQQVSEIVEKQLAAYGKESCSEAFLNSLRKF 844
G+ +N + +R+ P V+++ E+ + CS R+
Sbjct: 288 ETYGKIMNHE--------------ERFQFPSHVTDVSEEAKDLIQRLICS-------RER 326
Query: 845 FEGQQDKLD-KKIKFVEDIGWDD 866
GQ D KK F E + W++
Sbjct: 327 RLGQNGIEDFKKHAFFEGLNWEN 349
>pdb|2O30|A Chain A, Nuclear Movement Protein From E. Cuniculi Gb-M1
pdb|2O30|B Chain B, Nuclear Movement Protein From E. Cuniculi Gb-M1
Length = 131
Score = 30.0 bits (66), Expect = 9.4, Method: Composition-based stats.
Identities = 13/44 (29%), Positives = 24/44 (54%)
Query: 359 YNADFDGDEMNMHVPQTEEARTEALLLMGVQNNLCTPKNGEILV 402
Y D + +E+N+ P T +A + A+ + V +C GEI++
Sbjct: 7 YTWDQELNEINIQFPVTGDADSSAIKIRXVGKKICVKNQGEIVI 50
>pdb|3TKU|A Chain A, Mrck Beta In Complex With Fasudil
pdb|3TKU|B Chain B, Mrck Beta In Complex With Fasudil
Length = 433
Score = 30.0 bits (66), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 31/143 (21%), Positives = 61/143 (42%), Gaps = 24/143 (16%)
Query: 727 EGLVDTAVKTADTGYMSRRLIKALEDLSIQY--DNSVRNAGGCIVQFLYGDDGMDPANME 784
+G V ++V Y+S +++A+ED +Y + + G C+ + LYG+ ++
Sbjct: 244 DGTVQSSVAVGTPDYISPEILQAMEDGMGKYGPECDWWSLGVCMYEMLYGETPFYAESLV 303
Query: 785 GKSGEPLNFDRLLMKVKATCPPAGQRYLSPQQVSEIVEKQLAAYGKESCSEAFLNSLRKF 844
G+ +N + +R+ P V+++ E+ + CS R+
Sbjct: 304 ETYGKIMNHE--------------ERFQFPSHVTDVSEEAKDLIQRLICS-------RER 342
Query: 845 FEGQQDKLD-KKIKFVEDIGWDD 866
GQ D KK F E + W++
Sbjct: 343 RLGQNGIEDFKKHAFFEGLNWEN 365
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.136 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 35,098,977
Number of Sequences: 62578
Number of extensions: 1442012
Number of successful extensions: 3029
Number of sequences better than 100.0: 27
Number of HSP's better than 100.0 without gapping: 24
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 2891
Number of HSP's gapped (non-prelim): 80
length of query: 1265
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1155
effective length of database: 8,089,757
effective search space: 9343669335
effective search space used: 9343669335
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (26.6 bits)