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= psy3023
(392 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 362 bits (930), Expect = e-100, Method: Compositional matrix adjust.
Identities = 192/398 (48%), Positives = 256/398 (64%), Gaps = 27/398 (6%)
Query: 6 SKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETME--GGRPKLGGLMDPRQGVIDRS 63
S PLR V++VQFGILSP+EIR MSV + I+FPETM+ G RP++GGL+DPR G IDR
Sbjct: 9 SSVPLRRVEEVQFGILSPEEIRSMSVAK--IEFPETMDESGQRPRVGGLLDPRLGTIDRQ 66
Query: 64 SRCQTCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRD 123
+CQTC M +CPGHFGHI+LAKPVFH+GF++K KIL CVC+ C KL + S+PK D
Sbjct: 67 FKCQTCGETMADCPGHFGHIELAKPVFHIGFLSKIKKILECVCWNCGKLKIDSSNPKFND 126
Query: 124 VVLKTKGQSRRRQAFIYDLCKGKNICE-----GGDEMDINKDGAEDPNSLQNKKQGHGGC 178
+ + R ++++CK K +C+ G D D++ A GHGGC
Sbjct: 127 T--QRYRDPKNRLNAVWNVCKTKMVCDTGLSAGSDNFDLSNPSA---------NMGHGGC 175
Query: 179 GRYQPNIRRSGLDLTAEWKHVNEDSQ--EKKI--PLTGKGVLLN-KKQGHGGCGRYQPNI 233
G QP IR+ GL L WK ++S EK++ PL + + + G +
Sbjct: 176 GAAQPTIRKDGLRLWGSWKRGKDESDLPEKRLLSPLEVHTIFTHISSEDLAHLGLNEQYA 235
Query: 234 RRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATH 293
R + +T + T +G DDLTHKL+DIIK N + R E GA H
Sbjct: 236 RPDWMIITVLPVPPPSVRPSISVDGTSRGE--DDLTHKLSDIIKANANVRRCEQEGAPAH 293
Query: 294 VIAENIKMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDF 353
+++E ++LQFHVAT DN++ G P+A+QKSG+PLK+I+ARLKGKEGR+RGNLMGKRVDF
Sbjct: 294 IVSEYEQLLQFHVATYMDNEIAGQPQALQKSGRPLKSIRARLKGKEGRLRGNLMGKRVDF 353
Query: 354 SARTVITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNM 391
SARTVIT DPNL +D++GVPRSIA+ +T+PE VTP+N+
Sbjct: 354 SARTVITGDPNLSLDELGVPRSIAKTLTYPETVTPYNI 391
>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 = 348 bits (892), Expect = 4e-96, Method: Compositional matrix adjust.
Identities = 194/396 (48%), Positives = 250/396 (63%), Gaps = 25/396 (6%)
Query: 6 SKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETME--GGRPKLGGLMDPRQGVIDRS 63
S APLR VK+VQFG+ SP+E+R +SV + I+FPETM+ R K+GGL DPR G IDR+
Sbjct: 7 SSAPLRTVKEVQFGLFSPEEVRAISVAK--IRFPETMDETQTRAKIGGLNDPRLGSIDRN 64
Query: 64 SRCQTCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRD 123
+CQTC M ECPGHFGHIDLAKPVFHVGF+ K K+ CVC +C KLL+ H ++
Sbjct: 65 LKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLD-EHNELMR 123
Query: 124 VVLKTKGQSRRRQAFIYDLCKGKNICEGGDEMDINKDGAEDPNSLQNKKQGHGGCGRYQP 183
L K S++R A I+ LCK K +C E D+ + +DP L ++ GGCG QP
Sbjct: 124 QALAIK-DSKKRFAAIWTLCKTKMVC----ETDVPSE--DDPTQLVSR----GGCGNTQP 172
Query: 184 NIRRSGLDLTAEWK--HVNEDSQEKKIPLTGKGVLLN-----KKQGHGGCGRYQPNIRRS 236
IR+ GL L WK D+ E ++ + +LN + G + R
Sbjct: 173 TIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPE 232
Query: 237 GLDLTAEWKHVNEDSQEKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIA 296
+ LT + +G DDLT KLADI+K N L E +GA H I
Sbjct: 233 WMILTCLPVPPPPVRPSISFNESQRGE--DDLTFKLADILKANISLETLEHNGAPHHAIE 290
Query: 297 ENIKMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSAR 356
E +LQFHVAT DND+ G P+A+QKSG+P+K+I+ARLKGKEGRIRGNLMGKRVDFSAR
Sbjct: 291 EAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSAR 350
Query: 357 TVITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNMD 392
TVI+ DPNL +DQVGVP+SIA+ +T+PE+VTP+N+D
Sbjct: 351 TVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNID 386
>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 = 348 bits (892), Expect = 4e-96, Method: Compositional matrix adjust.
Identities = 194/396 (48%), Positives = 250/396 (63%), Gaps = 25/396 (6%)
Query: 6 SKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETME--GGRPKLGGLMDPRQGVIDRS 63
S APLR VK+VQFG+ SP+E+R +SV + I+FPETM+ R K+GGL DPR G IDR+
Sbjct: 7 SSAPLRTVKEVQFGLFSPEEVRAISVAK--IRFPETMDETQTRAKIGGLNDPRLGSIDRN 64
Query: 64 SRCQTCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRD 123
+CQTC M ECPGHFGHIDLAKPVFHVGF+ K K+ CVC +C KLL+ H ++
Sbjct: 65 LKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLD-EHNELMR 123
Query: 124 VVLKTKGQSRRRQAFIYDLCKGKNICEGGDEMDINKDGAEDPNSLQNKKQGHGGCGRYQP 183
L K S++R A I+ LCK K +C E D+ + +DP L ++ GGCG QP
Sbjct: 124 QALAIK-DSKKRFAAIWTLCKTKMVC----ETDVPSE--DDPTQLVSR----GGCGNTQP 172
Query: 184 NIRRSGLDLTAEWK--HVNEDSQEKKIPLTGKGVLLN-----KKQGHGGCGRYQPNIRRS 236
IR+ GL L WK D+ E ++ + +LN + G + R
Sbjct: 173 TIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPE 232
Query: 237 GLDLTAEWKHVNEDSQEKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIA 296
+ LT + +G DDLT KLADI+K N L E +GA H I
Sbjct: 233 WMILTCLPVPPPPVRPSISFNESQRGE--DDLTFKLADILKANISLETLEHNGAPHHAIE 290
Query: 297 ENIKMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSAR 356
E +LQFHVAT DND+ G P+A+QKSG+P+K+I+ARLKGKEGRIRGNLMGKRVDFSAR
Sbjct: 291 EAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSAR 350
Query: 357 TVITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNMD 392
TVI+ DPNL +DQVGVP+SIA+ +T+PE+VTP+N+D
Sbjct: 351 TVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNID 386
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 1455
Score = 348 bits (892), Expect = 4e-96, Method: Compositional matrix adjust.
Identities = 194/396 (48%), Positives = 250/396 (63%), Gaps = 25/396 (6%)
Query: 6 SKAPLRCVKKVQFGILSPDEIRRMSVTEGGIKFPETME--GGRPKLGGLMDPRQGVIDRS 63
S APLR VK+VQFG+ SP+E+R +SV + I+FPETM+ R K+GGL DPR G IDR+
Sbjct: 7 SSAPLRTVKEVQFGLFSPEEVRAISVAK--IRFPETMDETQTRAKIGGLNDPRLGSIDRN 64
Query: 64 SRCQTCAGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRD 123
+CQTC M ECPGHFGHIDLAKPVFHVGF+ K K+ CVC +C KLL+ H ++
Sbjct: 65 LKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLD-EHNELMR 123
Query: 124 VVLKTKGQSRRRQAFIYDLCKGKNICEGGDEMDINKDGAEDPNSLQNKKQGHGGCGRYQP 183
L K S++R A I+ LCK K +C E D+ + +DP L ++ GGCG QP
Sbjct: 124 QALAIK-DSKKRFAAIWTLCKTKMVC----ETDVPSE--DDPTQLVSR----GGCGNTQP 172
Query: 184 NIRRSGLDLTAEWK--HVNEDSQEKKIPLTGKGVLLN-----KKQGHGGCGRYQPNIRRS 236
IR+ GL L WK D+ E ++ + +LN + G + R
Sbjct: 173 TIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPE 232
Query: 237 GLDLTAEWKHVNEDSQEKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIA 296
+ LT + +G DDLT KLADI+K N L E +GA H I
Sbjct: 233 WMILTCLPVPPPPVRPSISFNESQRGE--DDLTFKLADILKANISLETLEHNGAPHHAIE 290
Query: 297 ENIKMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSAR 356
E +LQFHVAT DND+ G P+A+QKSG+P+K+I+ARLKGKEGRIRGNLMGKRVDFSAR
Sbjct: 291 EAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSAR 350
Query: 357 TVITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNMD 392
TVI+ DPNL +DQVGVP+SIA+ +T+PE+VTP+N+D
Sbjct: 351 TVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNID 386
>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 = 238 bits (606), Expect = 5e-63, Method: Compositional matrix adjust.
Identities = 143/394 (36%), Positives = 209/394 (53%), Gaps = 54/394 (13%)
Query: 13 VKKVQFGILSPDEIRRMSVTEGGIKFPETM-EGGRPKLGGLMDPRQGVIDRSSRCQTCAG 71
+K ++FGILSPDEIR+MSVT I P+ E G P G +MDPR GVI+ +C TC
Sbjct: 6 IKGIKFGILSPDEIRKMSVT--AIITPDVYDEDGTPIEGSVMDPRLGVIEPGQKCPTCGN 63
Query: 72 NMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPS----HPKVRDVVLK 127
+ CPGHFGHI+L +PV HVGFV + L+ C C ++ +S + ++ + + K
Sbjct: 64 TLGNCPGHFGHIELVRPVIHVGFVKHVYEFLKATCRRCGRVKISEDEIEKYSRIYNAIKK 123
Query: 128 -TKGQSRRRQAFIYDLCKGKNICEGGDEMDINKDGAEDPNSLQNKKQGHGGCGRYQPNIR 186
+RR ++ +C E + N + +K+G + P+
Sbjct: 124 RWPSAARRLTEYVKKTAMKAQVCPHCGEKQFKIKLEKPYNFYEERKEG---VAKLTPSDI 180
Query: 187 RSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLNKKQGHGGCGRYQPNIRRSGLDLTAEWKH 246
R L+ K+P + +L Y P R EW
Sbjct: 181 RERLE---------------KVPESDVEIL-----------GYDPTTSR------PEWMI 208
Query: 247 VNEDSQEKKIPLTGKGVLL--------DDLTHKLADIIKCNNELIRNESSGAATHVIAEN 298
+ + P+T + ++ DDLTHKL DI++ N L + +GA +I +
Sbjct: 209 L---TVLPVPPITIRPSIMIESGIRAEDDLTHKLVDIVRINERLKESIDAGAPQLIIEDL 265
Query: 299 IKMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTV 358
+LQ+HVAT DN++PGLP + +SG+PL+ + RLKGKEGR RGNL GKRVDFS+RTV
Sbjct: 266 WDLLQYHVATYFDNEIPGLPPSKHRSGRPLRTLAQRLKGKEGRFRGNLSGKRVDFSSRTV 325
Query: 359 ITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNMD 392
I+PDPN+ ID+VGVP IA+ +T PE +TP+N++
Sbjct: 326 ISPDPNISIDEVGVPEIIARTLTVPERITPWNIE 359
>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 = 236 bits (602), Expect = 2e-62, Method: Compositional matrix adjust.
Identities = 143/394 (36%), Positives = 209/394 (53%), Gaps = 54/394 (13%)
Query: 13 VKKVQFGILSPDEIRRMSVTEGGIKFPETM-EGGRPKLGGLMDPRQGVIDRSSRCQTCAG 71
+K ++FGILSPDEIR+MSVT I P+ E G P G +MDPR GVI+ +C TC
Sbjct: 6 IKGIKFGILSPDEIRKMSVT--AIITPDVYDEDGTPIEGSVMDPRLGVIEPGQKCPTCGN 63
Query: 72 NMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPS----HPKVRDVVLK 127
+ CPGHFGHI+L +PV HVG V + L+ C C ++ +S + ++ + + K
Sbjct: 64 TLGNCPGHFGHIELVRPVIHVGLVKHIYEFLKATCRRCGRVKISEDEIEKYSRIYNAIKK 123
Query: 128 -TKGQSRRRQAFIYDLCKGKNICEGGDEMDINKDGAEDPNSLQNKKQGHGGCGRYQPNIR 186
+RR ++ +C +E + N + +K+G + P+
Sbjct: 124 RWPSAARRLTEYVKKTAMKAQVCPHCNEKQYKIKLEKPYNFYEERKEG---VAKLTPSDI 180
Query: 187 RSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLNKKQGHGGCGRYQPNIRRSGLDLTAEWKH 246
R L+ KIP + +L Y P R EW
Sbjct: 181 RERLE---------------KIPDSDVEIL-----------GYDPTTSR------PEWMI 208
Query: 247 VNEDSQEKKIPLTGKGVLL--------DDLTHKLADIIKCNNELIRNESSGAATHVIAEN 298
+ + P+T + ++ DDLTHKL DI++ N L + +GA +I +
Sbjct: 209 L---TVLPVPPITIRPSIMIESGIRAEDDLTHKLVDIVRINERLKESIDAGAPQLIIEDL 265
Query: 299 IKMLQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTV 358
+LQ+HVAT DN++PGLP + +SG+PL+ + RLKGKEGR RGNL GKRVDFS+RTV
Sbjct: 266 WDLLQYHVATYFDNEIPGLPPSKHRSGRPLRTLAQRLKGKEGRFRGNLSGKRVDFSSRTV 325
Query: 359 ITPDPNLRIDQVGVPRSIAQNMTFPEIVTPFNMD 392
I+PDPN+ ID+VGVP IA+ +T PE +TP+N++
Sbjct: 326 ISPDPNISIDEVGVPEIIAKTLTVPERITPWNIE 359
>pdb|3QQC|A Chain A, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP
CLAMP DOMAIN
Length = 436
Score = 181 bits (459), Expect = 7e-46, Method: Compositional matrix adjust.
Identities = 123/345 (35%), Positives = 173/345 (50%), Gaps = 40/345 (11%)
Query: 11 RCVKKVQFGILSPDEIRRMSVTEGGIKFPETMEG-GRPKLGGLMDPRQGVIDRSSRCQTC 69
+ + ++FGILSP EIR+MS E + P+T + G P GG+MD R GVID RC+TC
Sbjct: 67 KVIGSIEFGILSPQEIRKMSAVE--VTVPDTYDDDGYPIEGGVMDKRMGVIDPGLRCETC 124
Query: 70 AGNMTECPGHFGHIDLAKPVFHVGFVTKTIKILRCVCFYCSKLLVSPSHPKVRDVVLKTK 129
G ECPGHFGHI+LA+PV HVGF +IL C C ++ ++ ++ + + K +
Sbjct: 125 GGRAGECPGHFGHIELARPVIHVGFAKTIYRILESTCRECGRIKLTDE--EIEEYMKKIE 182
Query: 130 GQSRRRQAF------IYDLCKGKNICE--GGDEMDINKDGAEDPNSLQNKKQGHGGCGRY 181
RR F I+ K + +C G + I + ++ +QG+ R
Sbjct: 183 LARNRRSEFNEIIKEIHKKAKERMVCPHCGAPQYPIKFEKPTIYWEIRKDEQGNEYRHRL 242
Query: 182 QPNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLNKKQGHGGCGRYQPNIRRSGLDLT 241
P R L E +K +PL G L+ ++ R + LT
Sbjct: 243 MPTEVRDWL----------EKIPDKDLPLLG----LDPEKS-----------RPEWMVLT 277
Query: 242 AEWKHVNEDSQEKKIPLTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKM 301
V + I L DDLTHKL DII+ NN L +N +GA +I + +
Sbjct: 278 V--LPVPPVTARPSITLETGIRAEDDLTHKLVDIIRINNRLKQNIEAGAPQLIIEDLWDL 335
Query: 302 LQFHVATLTDNDMPGLPRAMQKSGKPLKAIKARLKGKEGRIRGNL 346
LQ+HV T +N+ PG+P A KSG+PLK + RLKGKEGR RGNL
Sbjct: 336 LQYHVTTYINNEAPGVPPAKHKSGRPLKTLAQRLKGKEGRFRGNL 380
>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 1413
Score = 91.3 bits (225), Expect = 9e-19, Method: Compositional matrix adjust.
Identities = 110/404 (27%), Positives = 164/404 (40%), Gaps = 76/404 (18%)
Query: 16 VQFGILSPDEIRRMSVTEGGIKFPETM--EGGRPKLGGLMDPR---------------QG 58
++ + SPD IR S G +K PET+ +P+ GL R +
Sbjct: 20 IKIALASPDMIRSWSF--GEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKR 77
Query: 59 VIDRSSRCQTCAGNMTECP---GHFGHIDLAKPVFHVGFV----TKTIKILRCVCFYCSK 111
+ R C+ C +T+ GHI+LA P H+ F+ ++ +L +
Sbjct: 78 LKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIER 137
Query: 112 LLVSPSHPKVRDVVLKTKGQSRRRQAFIYDLCKGKNICEGGDEMDINKDGAEDPNSLQNK 171
+L S+ VV++ + RQ + + + E GDE D K GAE +L
Sbjct: 138 VLYFESY-----VVIEGGMTNLERQQILTEEQYLDALEEFGDEFD-AKMGAEAIQALLKS 191
Query: 172 KQGHGGCGRYQPNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLNKKQGHGGCGRYQ- 230
C + L E N +++ KK LT + LL G +
Sbjct: 192 MDLEQECEQ-----------LREELNETNSETKRKK--LTKRIKLLEAFVQSGNKPEWMI 238
Query: 231 --------PNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLDDLTHKLADIIKCNNEL 282
P++R +PL G DL +I NN L
Sbjct: 239 LTVLPVLPPDLR-------------------PLVPLDGGRFATSDLNDLYRRVINRNNRL 279
Query: 283 IRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKSGK-PLKAIKARLKGKEGR 341
R A ++ +MLQ V L DN G RA+ S K PLK++ +KGK+GR
Sbjct: 280 KRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRG--RAITGSNKRPLKSLADMIKGKQGR 337
Query: 342 IRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEI 385
R NL+GKRVD+S R+VIT P LR+ Q G+P+ +A + P I
Sbjct: 338 FRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFI 381
>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 = 91.3 bits (225), Expect = 9e-19, Method: Compositional matrix adjust.
Identities = 110/404 (27%), Positives = 164/404 (40%), Gaps = 76/404 (18%)
Query: 16 VQFGILSPDEIRRMSVTEGGIKFPETM--EGGRPKLGGLMDPR---------------QG 58
++ + SPD IR S G +K PET+ +P+ GL R +
Sbjct: 20 IKIALASPDMIRSWSF--GEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKR 77
Query: 59 VIDRSSRCQTCAGNMTECP---GHFGHIDLAKPVFHVGFV----TKTIKILRCVCFYCSK 111
+ R C+ C +T+ GHI+LA P H+ F+ ++ +L +
Sbjct: 78 LKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIER 137
Query: 112 LLVSPSHPKVRDVVLKTKGQSRRRQAFIYDLCKGKNICEGGDEMDINKDGAEDPNSLQNK 171
+L S+ VV++ + RQ + + + E GDE D K GAE +L
Sbjct: 138 VLYFESY-----VVIEGGMTNLERQQILTEEQYLDALEEFGDEFD-AKMGAEAIQALLKS 191
Query: 172 KQGHGGCGRYQPNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLNKKQGHGGCGRYQ- 230
C + L E N +++ KK LT + LL G +
Sbjct: 192 MDLEQECEQ-----------LREELNETNSETKRKK--LTKRIKLLEAFVQSGNKPEWMI 238
Query: 231 --------PNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLDDLTHKLADIIKCNNEL 282
P++R +PL G DL +I NN L
Sbjct: 239 LTVLPVLPPDLR-------------------PLVPLDGGRFATSDLNDLYRRVINRNNRL 279
Query: 283 IRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKSGK-PLKAIKARLKGKEGR 341
R A ++ +MLQ V L DN G RA+ S K PLK++ +KGK+GR
Sbjct: 280 KRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRG--RAITGSNKRPLKSLADMIKGKQGR 337
Query: 342 IRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFPEI 385
R NL+GKRVD+S R+VIT P LR+ Q G+P+ +A + P I
Sbjct: 338 FRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFI 381
>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 = 82.0 bits (201), Expect = 6e-16, Method: Composition-based stats.
Identities = 47/119 (39%), Positives = 67/119 (56%), Gaps = 3/119 (2%)
Query: 265 LDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKS 324
L+DL +L I NN L + + GA +I +MLQ V L DN G P S
Sbjct: 540 LNDLYRRL---INRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGS 596
Query: 325 GKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFP 383
+PL+++ L GK+GR R NL+GKRVD+S R+VI P L++ Q G+P+ +A + P
Sbjct: 597 DRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKP 655
Score = 34.7 bits (78), Expect = 0.088, Method: Composition-based stats.
Identities = 30/103 (29%), Positives = 47/103 (45%), Gaps = 22/103 (21%)
Query: 13 VKKVQFGILSPDEIRRMSVTEGGIKFPETM--EGGRPKLGGLMDPR--------QGVIDR 62
V+KV+ + SP++IR S G ++ PET+ +P+ GL D R + +
Sbjct: 5 VRKVRIALASPEKIRSWSY--GEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGK 62
Query: 63 SSR-------CQTCAGNMTEC---PGHFGHIDLAKPVFHVGFV 95
R C+ C +T+ GHI+LA P H+ FV
Sbjct: 63 YKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHIWFV 105
>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 = 82.0 bits (201), Expect = 6e-16, Method: Composition-based stats.
Identities = 47/119 (39%), Positives = 67/119 (56%), Gaps = 3/119 (2%)
Query: 265 LDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKS 324
L+DL +L I NN L + + GA +I +MLQ V L DN G P S
Sbjct: 540 LNDLYRRL---INRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGS 596
Query: 325 GKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFP 383
+PL+++ L GK+GR R NL+GKRVD+S R+VI P L++ Q G+P+ +A + P
Sbjct: 597 DRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKP 655
Score = 34.7 bits (78), Expect = 0.088, Method: Composition-based stats.
Identities = 30/103 (29%), Positives = 47/103 (45%), Gaps = 22/103 (21%)
Query: 13 VKKVQFGILSPDEIRRMSVTEGGIKFPETM--EGGRPKLGGLMDPR--------QGVIDR 62
V+KV+ + SP++IR S G ++ PET+ +P+ GL D R + +
Sbjct: 5 VRKVRIALASPEKIRSWSY--GEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGK 62
Query: 63 SSR-------CQTCAGNMTEC---PGHFGHIDLAKPVFHVGFV 95
R C+ C +T+ GHI+LA P H+ FV
Sbjct: 63 YKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHIWFV 105
>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 = 80.1 bits (196), Expect = 2e-15, Method: Composition-based stats.
Identities = 46/119 (38%), Positives = 67/119 (56%), Gaps = 3/119 (2%)
Query: 265 LDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKS 324
L+DL +L I NN L + + GA +I +MLQ V + DN G P S
Sbjct: 540 LNDLYRRL---INRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGS 596
Query: 325 GKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFP 383
+PL+++ L GK+GR R NL+GKRVD+S R+VI P L++ Q G+P+ +A + P
Sbjct: 597 ERPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKP 655
Score = 34.7 bits (78), Expect = 0.097, Method: Composition-based stats.
Identities = 32/103 (31%), Positives = 46/103 (44%), Gaps = 22/103 (21%)
Query: 13 VKKVQFGILSPDEIRRMSVTEGGIKFPETM--EGGRPKLGGLMDPR--QGVIDRSSRC-- 66
V+KV+ + SP++IR S G ++ PET+ +P+ GL D R + D C
Sbjct: 5 VRKVRIALASPEKIRSWSY--GEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGK 62
Query: 67 ---QTCAGNMTECPG-----------HFGHIDLAKPVFHVGFV 95
Q G + E G GHI+LA P H+ FV
Sbjct: 63 YKRQRFEGKVCERCGVEVTRSIVRRYRMGHIELATPAAHIWFV 105
>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For
Structural Studies
Length = 1233
Score = 77.8 bits (190), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 46/119 (38%), Positives = 67/119 (56%), Gaps = 3/119 (2%)
Query: 265 LDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKS 324
L+DL +L I NN L + + GA +I +MLQ V + DN G P S
Sbjct: 249 LNDLYRRL---INRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGS 305
Query: 325 GKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFP 383
+PL+++ L GK+GR R NL+GKRVD+S R+VI P L++ Q G+P+ +A + P
Sbjct: 306 ERPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKP 364
Score = 35.4 bits (80), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 31/103 (30%), Positives = 46/103 (44%), Gaps = 22/103 (21%)
Query: 13 VKKVQFGILSPDEIRRMSVTEGGIKFPETM--EGGRPKLGGLMDPRQ-----------GV 59
V+KV+ + SP++IR S + G ++ PET+ +P+ GL D R G
Sbjct: 5 VRKVRIALASPEKIR--SWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGK 62
Query: 60 IDRS----SRCQTCAGNMTEC---PGHFGHIDLAKPVFHVGFV 95
R C+ C +T GHI+LA P H+ FV
Sbjct: 63 YKRQRFEGKVCERCGVEVTRSIVRRYRMGHIELATPAAHIWFV 105
>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 = 77.4 bits (189), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 46/119 (38%), Positives = 67/119 (56%), Gaps = 3/119 (2%)
Query: 265 LDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKS 324
L+DL +L I NN L + + GA +I +MLQ V + DN G P S
Sbjct: 280 LNDLYRRL---INRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGS 336
Query: 325 GKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFP 383
+PL+++ L GK+GR R NL+GKRVD+S R+VI P L++ Q G+P+ +A + P
Sbjct: 337 ERPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKP 395
Score = 35.4 bits (80), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 31/103 (30%), Positives = 45/103 (43%), Gaps = 22/103 (21%)
Query: 13 VKKVQFGILSPDEIRRMSVTEGGIKFPETM--EGGRPKLGGLMDPRQ-----------GV 59
V+KV+ + SP++IR S G ++ PET+ +P+ GL D R G
Sbjct: 5 VRKVRIALASPEKIRSWSY--GEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGK 62
Query: 60 IDRS----SRCQTCAGNMTEC---PGHFGHIDLAKPVFHVGFV 95
R C+ C +T GHI+LA P H+ FV
Sbjct: 63 YKRQRFEGKVCERCGVEVTRSIVRRYRMGHIELATPAAHIWFV 105
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1264
Score = 77.4 bits (189), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 46/119 (38%), Positives = 67/119 (56%), Gaps = 3/119 (2%)
Query: 265 LDDLTHKLADIIKCNNELIRNESSGAATHVIAENIKMLQFHVATLTDNDMPGLPRAMQKS 324
L+DL +L I NN L + + GA +I +MLQ V + DN G P S
Sbjct: 280 LNDLYRRL---INRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGS 336
Query: 325 GKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTVITPDPNLRIDQVGVPRSIAQNMTFP 383
+PL+++ L GK+GR R NL+GKRVD+S R+VI P L++ Q G+P+ +A + P
Sbjct: 337 ERPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKP 395
Score = 36.2 bits (82), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 31/103 (30%), Positives = 47/103 (45%), Gaps = 22/103 (21%)
Query: 13 VKKVQFGILSPDEIRRMSVTEGGIKFPETM--EGGRPKLGGLMDPRQ-----------GV 59
V+KV+ + SP++IR S + G ++ PET+ +P+ GL D R G
Sbjct: 5 VRKVRIALASPEKIR--SWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGK 62
Query: 60 IDR----SSRCQTCAGNMTEC---PGHFGHIDLAKPVFHVGFV 95
R + C+ CA +T HI+LA P H+ FV
Sbjct: 63 YKRQRFEAKVCERCAVEVTRSIVRRYRMAHIELATPAAHIWFV 105
>pdb|2GWC|A Chain A, Crystal Structure Of Plant Glutamate Cysteine Ligase In
Complex With A Transition State Analogue
pdb|2GWC|B Chain B, Crystal Structure Of Plant Glutamate Cysteine Ligase In
Complex With A Transition State Analogue
pdb|2GWC|C Chain C, Crystal Structure Of Plant Glutamate Cysteine Ligase In
Complex With A Transition State Analogue
pdb|2GWC|D Chain D, Crystal Structure Of Plant Glutamate Cysteine Ligase In
Complex With A Transition State Analogue
pdb|2GWC|E Chain E, Crystal Structure Of Plant Glutamate Cysteine Ligase In
Complex With A Transition State Analogue
pdb|2GWC|F Chain F, Crystal Structure Of Plant Glutamate Cysteine Ligase In
Complex With A Transition State Analogue
pdb|2GWC|G Chain G, Crystal Structure Of Plant Glutamate Cysteine Ligase In
Complex With A Transition State Analogue
pdb|2GWC|H Chain H, Crystal Structure Of Plant Glutamate Cysteine Ligase In
Complex With A Transition State Analogue
Length = 449
Score = 32.7 bits (73), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 229 YQPNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLDD--LTHKLADIIK 277
Y ++ +S LDLTA+W + K+P+TG D L H D++K
Sbjct: 344 YDEDVLQSVLDLTADWTPAEREXLRNKVPVTGLKTPFRDGLLKHVAEDVLK 394
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 181 YQPNIRRSGLDLTAEWKHVNEDSQEKKIPLTG 212
Y ++ +S LDLTA+W + K+P+TG
Sbjct: 344 YDEDVLQSVLDLTADWTPAEREXLRNKVPVTG 375
>pdb|2GWD|A Chain A, Crystal Structure Of Plant Glutamate Cysteine Ligase In
Complex With Mg2+ And L-glutamate
Length = 449
Score = 32.7 bits (73), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 229 YQPNIRRSGLDLTAEWKHVNEDSQEKKIPLTGKGVLLDD--LTHKLADIIK 277
Y ++ +S LDLTA+W + K+P+TG D L H D++K
Sbjct: 344 YDEDVLQSVLDLTADWTPAEREMLRNKVPVTGLKTPFRDGLLKHVAEDVLK 394
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 181 YQPNIRRSGLDLTAEWKHVNEDSQEKKIPLTG 212
Y ++ +S LDLTA+W + K+P+TG
Sbjct: 344 YDEDVLQSVLDLTADWTPAEREMLRNKVPVTG 375
>pdb|3BRJ|A Chain A, Crystal Structure Of Mannitol Operon Repressor (Mtlr) From
Vibrio Parahaemolyticus Rimd 2210633
pdb|3BRJ|B Chain B, Crystal Structure Of Mannitol Operon Repressor (Mtlr) From
Vibrio Parahaemolyticus Rimd 2210633
pdb|3BRJ|C Chain C, Crystal Structure Of Mannitol Operon Repressor (Mtlr) From
Vibrio Parahaemolyticus Rimd 2210633
pdb|3BRJ|D Chain D, Crystal Structure Of Mannitol Operon Repressor (Mtlr) From
Vibrio Parahaemolyticus Rimd 2210633
Length = 175
Score = 29.6 bits (65), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 258 LTGKGVLLDDLTHKLADIIKCNNELIRNESSGAATH-VIAENIKMLQF 304
L G GVL DD+ H + DIIK N L + S T I E IK L
Sbjct: 77 LFGLGVLPDDIYHDIEDIIKLKNHLNSDASDYEFTDPNILEPIKKLHL 124
>pdb|4FYD|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
Dna/rna And Dgtp
pdb|4FYD|B Chain B, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
Dna/rna And Dgtp
Length = 910
Score = 29.3 bits (64), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 129 KGQSRRRQAFIYDLCKGKNICEGGDEM 155
+G S FI D+C G+ IC+ +EM
Sbjct: 329 RGNSNMNHFFISDICSGRLICDIANEM 355
>pdb|4FVM|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha
pdb|4FXD|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
Dna/rna
pdb|4FXD|B Chain B, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
Dna/rna
Length = 910
Score = 29.3 bits (64), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 129 KGQSRRRQAFIYDLCKGKNICEGGDEM 155
+G S FI D+C G+ IC+ +EM
Sbjct: 329 RGNSNMNHFFISDICSGRLICDIANEM 355
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
0.319 0.137 0.415
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,584,024
Number of Sequences: 62578
Number of extensions: 559531
Number of successful extensions: 1190
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1112
Number of HSP's gapped (non-prelim): 70
length of query: 392
length of database: 14,973,337
effective HSP length: 101
effective length of query: 291
effective length of database: 8,652,959
effective search space: 2518011069
effective search space used: 2518011069
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)