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= psy16766
(621 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 112 bits (281), Expect = 5e-25, Method: Compositional matrix adjust.
Identities = 61/142 (42%), Positives = 83/142 (58%), Gaps = 5/142 (3%)
Query: 476 LQNSWHELQYNVDLLMDAK---LNINKTTGAHQIDGLKQMLDGKTGMIRQNMMGKRVNFA 532
+++ W LQY+V D + L +K + L Q L GK G R N+ GKRV+F+
Sbjct: 262 IEDLWDLLQYHVATYFDNEIPGLPPSKHRSGRPLRTLAQRLKGKEGRFRGNLSGKRVDFS 321
Query: 533 GRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNE 592
R+VI+PDP ++ID +GVP AKTLT P +TPWN+ LR+ VINGP+ +PGAN +
Sbjct: 322 SRTVISPDPNISIDEVGVPEIIAKTLTVPERITPWNIEKLRQFVINGPDKWPGANYVIRP 381
Query: 593 DGSVVRISSSQAVQRESLAKRL 614
DG RI R+ LA L
Sbjct: 382 DGR--RIDLRYVKDRKELASTL 401
Score = 81.6 bits (200), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 41/84 (48%), Positives = 53/84 (63%), Gaps = 2/84 (2%)
Query: 14 FPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQ 73
F R+VI+PDP ++ID +GVP AKTLT P +TPWN+ LR+ VINGP+ +PGAN +
Sbjct: 320 FSSRTVISPDPNISIDEVGVPEIIAKTLTVPERITPWNIEKLRQFVINGPDKWPGANYVI 379
Query: 74 NEDGSVVRISSSQAVQRESLAKRL 97
DG RI R+ LA L
Sbjct: 380 RPDGR--RIDLRYVKDRKELASTL 401
Score = 71.2 bits (173), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 34/99 (34%), Positives = 52/99 (52%), Gaps = 1/99 (1%)
Query: 124 LKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTK 183
+K + E++++SV + +P ++ G I G + D +G I E G C TCGN
Sbjct: 9 IKFGILSPDEIRKMSVTAIITPDVYDEDGTPIEGSVMDPRLGVI-EPGQKCPTCGNTLGN 67
Query: 184 CKGHIGHIELPVPVINTLFFRDVQLLLKLSCFLCHKINI 222
C GH GHIEL PVI+ + + LK +C C ++ I
Sbjct: 68 CPGHFGHIELVRPVIHVGLVKHIYEFLKATCRRCGRVKI 106
>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 = 111 bits (278), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 60/142 (42%), Positives = 83/142 (58%), Gaps = 5/142 (3%)
Query: 476 LQNSWHELQYNVDLLMDAK---LNINKTTGAHQIDGLKQMLDGKTGMIRQNMMGKRVNFA 532
+++ W LQY+V D + L +K + L Q L GK G R N+ GKRV+F+
Sbjct: 262 IEDLWDLLQYHVATYFDNEIPGLPPSKHRSGRPLRTLAQRLKGKEGRFRGNLSGKRVDFS 321
Query: 533 GRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNE 592
R+VI+PDP ++ID +GVP A+TLT P +TPWN+ LR+ VINGP+ +PGAN +
Sbjct: 322 SRTVISPDPNISIDEVGVPEIIARTLTVPERITPWNIEKLRQFVINGPDKWPGANYVIRP 381
Query: 593 DGSVVRISSSQAVQRESLAKRL 614
DG RI R+ LA L
Sbjct: 382 DGR--RIDLRYVKDRKELASTL 401
Score = 80.9 bits (198), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 40/84 (47%), Positives = 53/84 (63%), Gaps = 2/84 (2%)
Query: 14 FPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQ 73
F R+VI+PDP ++ID +GVP A+TLT P +TPWN+ LR+ VINGP+ +PGAN +
Sbjct: 320 FSSRTVISPDPNISIDEVGVPEIIARTLTVPERITPWNIEKLRQFVINGPDKWPGANYVI 379
Query: 74 NEDGSVVRISSSQAVQRESLAKRL 97
DG RI R+ LA L
Sbjct: 380 RPDGR--RIDLRYVKDRKELASTL 401
Score = 74.3 bits (181), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 36/99 (36%), Positives = 53/99 (53%), Gaps = 1/99 (1%)
Query: 124 LKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTK 183
+K + E++++SV + +P ++ G I G + D +G I E G C TCGN
Sbjct: 9 IKFGILSPDEIRKMSVTAIITPDVYDEDGTPIEGSVMDPRLGVI-EPGQKCPTCGNTLGN 67
Query: 184 CKGHIGHIELPVPVINTLFFRDVQLLLKLSCFLCHKINI 222
C GH GHIEL PVI+ F + V LK +C C ++ I
Sbjct: 68 CPGHFGHIELVRPVIHVGFVKHVYEFLKATCRRCGRVKI 106
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 1455
Score = 99.8 bits (247), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 53/129 (41%), Positives = 75/129 (58%), Gaps = 13/129 (10%)
Query: 483 LQYNVDLLMDAKLNINKTTGAHQ--------IDGLKQMLDGKTGMIRQNMMGKRVNFAGR 534
LQ++V MD N G Q + ++ L GK G IR N+MGKRV+F+ R
Sbjct: 296 LQFHVATYMD-----NDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSAR 350
Query: 535 SVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDG 594
+VI+ DP L +D +GVP AKTLTYP VTP+N+ L ++V NGPN +PGA + + G
Sbjct: 351 TVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSG 410
Query: 595 SVVRISSSQ 603
+ + S+
Sbjct: 411 DRIDLRYSK 419
Score = 72.0 bits (175), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 33/73 (45%), Positives = 47/73 (64%)
Query: 14 FPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQ 73
F R+VI+ DP L +D +GVP AKTLTYP VTP+N+ L ++V NGPN +PGA +
Sbjct: 347 FSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVI 406
Query: 74 NEDGSVVRISSSQ 86
+ G + + S+
Sbjct: 407 RDSGDRIDLRYSK 419
Score = 57.8 bits (138), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 31/107 (28%), Positives = 54/107 (50%), Gaps = 2/107 (1%)
Query: 124 LKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIP-GGLYDLAMGPISERGDPCTTCGNNYT 182
++ ++ +EV+ +SV K+ P T + GGL D +G I +R C TC
Sbjct: 17 VQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSI-DRNLKCQTCQEGMN 75
Query: 183 KCKGHIGHIELPVPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLL 229
+C GH GHI+L PV + F ++ + + C C K+ + ++L+
Sbjct: 76 ECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELM 122
>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 = 99.4 bits (246), Expect = 5e-21, Method: Compositional matrix adjust.
Identities = 53/129 (41%), Positives = 75/129 (58%), Gaps = 13/129 (10%)
Query: 483 LQYNVDLLMDAKLNINKTTGAHQ--------IDGLKQMLDGKTGMIRQNMMGKRVNFAGR 534
LQ++V MD N G Q + ++ L GK G IR N+MGKRV+F+ R
Sbjct: 296 LQFHVATYMD-----NDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSAR 350
Query: 535 SVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDG 594
+VI+ DP L +D +GVP AKTLTYP VTP+N+ L ++V NGPN +PGA + + G
Sbjct: 351 TVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSG 410
Query: 595 SVVRISSSQ 603
+ + S+
Sbjct: 411 DRIDLRYSK 419
Score = 71.6 bits (174), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 33/73 (45%), Positives = 47/73 (64%)
Query: 14 FPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQ 73
F R+VI+ DP L +D +GVP AKTLTYP VTP+N+ L ++V NGPN +PGA +
Sbjct: 347 FSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVI 406
Query: 74 NEDGSVVRISSSQ 86
+ G + + S+
Sbjct: 407 RDSGDRIDLRYSK 419
Score = 57.8 bits (138), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 31/107 (28%), Positives = 54/107 (50%), Gaps = 2/107 (1%)
Query: 124 LKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIP-GGLYDLAMGPISERGDPCTTCGNNYT 182
++ ++ +EV+ +SV K+ P T + GGL D +G I +R C TC
Sbjct: 17 VQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSI-DRNLKCQTCQEGMN 75
Query: 183 KCKGHIGHIELPVPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLL 229
+C GH GHI+L PV + F ++ + + C C K+ + ++L+
Sbjct: 76 ECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELM 122
>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 = 99.4 bits (246), Expect = 5e-21, Method: Compositional matrix adjust.
Identities = 53/129 (41%), Positives = 75/129 (58%), Gaps = 13/129 (10%)
Query: 483 LQYNVDLLMDAKLNINKTTGAHQ--------IDGLKQMLDGKTGMIRQNMMGKRVNFAGR 534
LQ++V MD N G Q + ++ L GK G IR N+MGKRV+F+ R
Sbjct: 296 LQFHVATYMD-----NDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSAR 350
Query: 535 SVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDG 594
+VI+ DP L +D +GVP AKTLTYP VTP+N+ L ++V NGPN +PGA + + G
Sbjct: 351 TVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSG 410
Query: 595 SVVRISSSQ 603
+ + S+
Sbjct: 411 DRIDLRYSK 419
Score = 71.6 bits (174), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 33/73 (45%), Positives = 47/73 (64%)
Query: 14 FPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQ 73
F R+VI+ DP L +D +GVP AKTLTYP VTP+N+ L ++V NGPN +PGA +
Sbjct: 347 FSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVI 406
Query: 74 NEDGSVVRISSSQ 86
+ G + + S+
Sbjct: 407 RDSGDRIDLRYSK 419
Score = 57.8 bits (138), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 31/107 (28%), Positives = 54/107 (50%), Gaps = 2/107 (1%)
Query: 124 LKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIP-GGLYDLAMGPISERGDPCTTCGNNYT 182
++ ++ +EV+ +SV K+ P T + GGL D +G I +R C TC
Sbjct: 17 VQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSI-DRNLKCQTCQEGMN 75
Query: 183 KCKGHIGHIELPVPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLL 229
+C GH GHI+L PV + F ++ + + C C K+ + ++L+
Sbjct: 76 ECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELM 122
>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 = 98.2 bits (243), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 52/123 (42%), Positives = 75/123 (60%), Gaps = 13/123 (10%)
Query: 483 LQYNVDLLMDAKLNINKTTGAHQ--------IDGLKQMLDGKTGMIRQNMMGKRVNFAGR 534
LQ++V MD N+ G Q + ++ L GK G +R N+MGKRV+F+ R
Sbjct: 302 LQFHVATYMD-----NEIAGQPQALQKSGRPLKSIRARLKGKEGRLRGNLMGKRVDFSAR 356
Query: 535 SVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDG 594
+VIT DP L++D +GVP AKTLTYP VTP+N+ L+++V NGP+ +PGA I + G
Sbjct: 357 TVITGDPNLSLDELGVPRSIAKTLTYPETVTPYNIYQLQELVRNGPDEHPGAKYIIRDTG 416
Query: 595 SVV 597
+
Sbjct: 417 ERI 419
Score = 71.6 bits (174), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 33/67 (49%), Positives = 46/67 (68%)
Query: 14 FPHRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQ 73
F R+VIT DP L++D +GVP AKTLTYP VTP+N+ L+++V NGP+ +PGA I
Sbjct: 353 FSARTVITGDPNLSLDELGVPRSIAKTLTYPETVTPYNIYQLQELVRNGPDEHPGAKYII 412
Query: 74 NEDGSVV 80
+ G +
Sbjct: 413 RDTGERI 419
Score = 67.4 bits (163), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 35/106 (33%), Positives = 56/106 (52%), Gaps = 2/106 (1%)
Query: 122 EILKLKYYTDQEVKQLSVVKVFSPITFNSLGHTIP-GGLYDLAMGPISERGDPCTTCGNN 180
E ++ + +E++ +SV K+ P T + G GGL D +G I +R C TCG
Sbjct: 17 EEVQFGILSPEEIRSMSVAKIEFPETMDESGQRPRVGGLLDPRLGTI-DRQFKCQTCGET 75
Query: 181 YTKCKGHIGHIELPVPVINTLFFRDVQLLLKLSCFLCHKINIPATS 226
C GH GHIEL PV + F ++ +L+ C+ C K+ I +++
Sbjct: 76 MADCPGHFGHIELAKPVFHIGFLSKIKKILECVCWNCGKLKIDSSN 121
>pdb|3QQC|A Chain A, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP
CLAMP DOMAIN
Length = 436
Score = 76.3 bits (186), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 38/105 (36%), Positives = 60/105 (57%), Gaps = 1/105 (0%)
Query: 132 QEVKQLSVVKVFSPITFNSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIGHI 191
QE++++S V+V P T++ G+ I GG+ D MG I G C TCG +C GH GHI
Sbjct: 80 QEIRKMSAVEVTVPDTYDDDGYPIEGGVMDKRMGVIDP-GLRCETCGGRAGECPGHFGHI 138
Query: 192 ELPVPVINTLFFRDVQLLLKLSCFLCHKINIPATSQLLFINQIKL 236
EL PVI+ F + + +L+ +C C +I + ++ +I+L
Sbjct: 139 ELARPVIHVGFAKTIYRILESTCRECGRIKLTDEEIEEYMKKIEL 183
>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 1413
Score = 65.9 bits (159), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 51/167 (30%), Positives = 79/167 (47%), Gaps = 32/167 (19%)
Query: 403 MFIRSLVVPPNNLRPLSMEQMPPVEHSR------NKLYQSILYSCGSLKSVIMAMKNKEQ 456
M + L V P +LRPL P++ R N LY+ ++ LK ++ +
Sbjct: 237 MILTVLPVLPPDLRPLV-----PLDGGRFATSDLNDLYRRVINRNNRLKRLL----DLAA 287
Query: 457 SDLLSEALKGIRGDTLNNKLQNSWHELQYNVDLLMDAKLNINKTTGAHQ--IDGLKQMLD 514
D++ ++N LQ VD L+D TG+++ + L M+
Sbjct: 288 PDII---------------VRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIK 332
Query: 515 GKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYP 561
GK G RQN++GKRV+++GRSVIT PYL + G+P + A L P
Sbjct: 333 GKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKP 379
>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 = 65.9 bits (159), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 51/167 (30%), Positives = 79/167 (47%), Gaps = 32/167 (19%)
Query: 403 MFIRSLVVPPNNLRPLSMEQMPPVEHSR------NKLYQSILYSCGSLKSVIMAMKNKEQ 456
M + L V P +LRPL P++ R N LY+ ++ LK ++ +
Sbjct: 237 MILTVLPVLPPDLRPLV-----PLDGGRFATSDLNDLYRRVINRNNRLKRLL----DLAA 287
Query: 457 SDLLSEALKGIRGDTLNNKLQNSWHELQYNVDLLMDAKLNINKTTGAHQ--IDGLKQMLD 514
D++ ++N LQ VD L+D TG+++ + L M+
Sbjct: 288 PDII---------------VRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIK 332
Query: 515 GKTGMIRQNMMGKRVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYP 561
GK G RQN++GKRV+++GRSVIT PYL + G+P + A L P
Sbjct: 333 GKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKP 379
>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 = 59.3 bits (142), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 43/127 (33%), Positives = 59/127 (46%), Gaps = 23/127 (18%)
Query: 476 LQNSWHELQYNVDLLMDAKLNINKTTGA--------HQIDGLKQMLDGKTGMIRQNMMGK 527
++N LQ VD L+D N GA + L +L GK G RQN++GK
Sbjct: 567 IRNEKRMLQEAVDALLD-----NGRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGK 621
Query: 528 RVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVING--PNVYPG 585
RV+++GRSVI P L + G+P A L P LL+KM G PNV
Sbjct: 622 RVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPF--------LLKKMEEKGIAPNVKAA 673
Query: 586 ANMIQNE 592
M++ +
Sbjct: 674 RRMLERQ 680
Score = 33.1 bits (74), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 38/85 (44%), Gaps = 10/85 (11%)
Query: 160 YDLAMGPISER---GDPCTTCGNNYTKC---KGHIGHIELPVPVINTLFFRDVQLLLKLS 213
Y+ A G + G C CG TK + +GHIEL P + F +DV K+
Sbjct: 56 YECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHIWFVKDVP--SKIG 113
Query: 214 CFLCHKINIPATSQLLFINQIKLLD 238
L ++ Q+L+ ++ +LD
Sbjct: 114 TLL--DLSATELEQVLYFSKYIVLD 136
>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 = 59.3 bits (142), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 43/127 (33%), Positives = 59/127 (46%), Gaps = 23/127 (18%)
Query: 476 LQNSWHELQYNVDLLMDAKLNINKTTGA--------HQIDGLKQMLDGKTGMIRQNMMGK 527
++N LQ VD L+D N GA + L +L GK G RQN++GK
Sbjct: 567 IRNEKRMLQEAVDALLD-----NGRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGK 621
Query: 528 RVNFAGRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVING--PNVYPG 585
RV+++GRSVI P L + G+P A L P LL+KM G PNV
Sbjct: 622 RVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPF--------LLKKMEEKGIAPNVKAA 673
Query: 586 ANMIQNE 592
M++ +
Sbjct: 674 RRMLERQ 680
Score = 33.1 bits (74), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 38/85 (44%), Gaps = 10/85 (11%)
Query: 160 YDLAMGPISER---GDPCTTCGNNYTKC---KGHIGHIELPVPVINTLFFRDVQLLLKLS 213
Y+ A G + G C CG TK + +GHIEL P + F +DV K+
Sbjct: 56 YECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHIWFVKDVP--SKIG 113
Query: 214 CFLCHKINIPATSQLLFINQIKLLD 238
L ++ Q+L+ ++ +LD
Sbjct: 114 TLL--DLSATELEQVLYFSKYIVLD 136
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1264
Score = 56.6 bits (135), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 40/122 (32%), Positives = 60/122 (49%), Gaps = 13/122 (10%)
Query: 476 LQNSWHELQYNVDLLMDAKLNINKTT--GAHQ-IDGLKQMLDGKTGMIRQNMMGKRVNFA 532
++N LQ VD ++D + T G+ + + L +L GK G RQN++GKRV+++
Sbjct: 307 IRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGKRVDYS 366
Query: 533 GRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVIN--GPNVYPGANMIQ 590
GRSVI P L + G+P A L P LL+KM PNV M++
Sbjct: 367 GRSVIVVGPQLKLHQCGLPKRMALELFKPF--------LLKKMEEKAFAPNVKAARRMLE 418
Query: 591 NE 592
+
Sbjct: 419 RQ 420
>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 = 56.2 bits (134), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 40/122 (32%), Positives = 60/122 (49%), Gaps = 13/122 (10%)
Query: 476 LQNSWHELQYNVDLLMDAKLNINKTT--GAHQ-IDGLKQMLDGKTGMIRQNMMGKRVNFA 532
++N LQ VD ++D + T G+ + + L +L GK G RQN++GKRV+++
Sbjct: 567 IRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGKRVDYS 626
Query: 533 GRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVIN--GPNVYPGANMIQ 590
GRSVI P L + G+P A L P LL+KM PNV M++
Sbjct: 627 GRSVIVVGPQLKLHQCGLPKRMALELFKPF--------LLKKMEEKAFAPNVKAARRMLE 678
Query: 591 NE 592
+
Sbjct: 679 RQ 680
Score = 33.9 bits (76), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 38/85 (44%), Gaps = 10/85 (11%)
Query: 160 YDLAMGPISER---GDPCTTCGNNYTKC---KGHIGHIELPVPVINTLFFRDVQLLLKLS 213
Y+ A G + G C CG T+ + +GHIEL P + F +DV K+
Sbjct: 56 YECACGKYKRQRFEGKVCERCGVEVTRSIVRRYRMGHIELATPAAHIWFVKDVP--SKIG 113
Query: 214 CFLCHKINIPATSQLLFINQIKLLD 238
L ++ Q+L+ N+ +LD
Sbjct: 114 TLL--DLSATELEQVLYFNKYIVLD 136
>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 = 56.2 bits (134), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 40/122 (32%), Positives = 60/122 (49%), Gaps = 13/122 (10%)
Query: 476 LQNSWHELQYNVDLLMDAKLNINKTT--GAHQ-IDGLKQMLDGKTGMIRQNMMGKRVNFA 532
++N LQ VD ++D + T G+ + + L +L GK G RQN++GKRV+++
Sbjct: 307 IRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGKRVDYS 366
Query: 533 GRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVIN--GPNVYPGANMIQ 590
GRSVI P L + G+P A L P LL+KM PNV M++
Sbjct: 367 GRSVIVVGPQLKLHQCGLPKRMALELFKPF--------LLKKMEEKAFAPNVKAARRMLE 418
Query: 591 NE 592
+
Sbjct: 419 RQ 420
Score = 32.7 bits (73), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 40/87 (45%), Gaps = 14/87 (16%)
Query: 160 YDLAMGPISER---GDPCTTCGNNYTKC---KGHIGHIELPVPVINTLFFRDVQLLLKLS 213
Y+ A G + G C CG T+ + +GHIEL P + F +DV K+
Sbjct: 56 YECACGKYKRQRFEGKVCERCGVEVTRSIVRRYRMGHIELATPAAHIWFVKDVP--SKIG 113
Query: 214 CFLCHKINIPAT--SQLLFINQIKLLD 238
L ++ AT Q+L+ N+ +LD
Sbjct: 114 TLL----DLFATELEQVLYFNKYIVLD 136
>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For
Structural Studies
Length = 1233
Score = 56.2 bits (134), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 40/122 (32%), Positives = 60/122 (49%), Gaps = 13/122 (10%)
Query: 476 LQNSWHELQYNVDLLMDAKLNINKTT--GAHQ-IDGLKQMLDGKTGMIRQNMMGKRVNFA 532
++N LQ VD ++D + T G+ + + L +L GK G RQN++GKRV+++
Sbjct: 276 IRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGKRVDYS 335
Query: 533 GRSVITPDPYLNIDSIGVPLEFAKTLTYPVPVTPWNVTLLRKMVIN--GPNVYPGANMIQ 590
GRSVI P L + G+P A L P LL+KM PNV M++
Sbjct: 336 GRSVIVVGPQLKLHQCGLPKRMALELFKPF--------LLKKMEEKAFAPNVKAARRMLE 387
Query: 591 NE 592
+
Sbjct: 388 RQ 389
Score = 33.9 bits (76), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 38/85 (44%), Gaps = 10/85 (11%)
Query: 160 YDLAMGPISER---GDPCTTCGNNYTKC---KGHIGHIELPVPVINTLFFRDVQLLLKLS 213
Y+ A G + G C CG T+ + +GHIEL P + F +DV K+
Sbjct: 56 YECACGKYKRQRFEGKVCERCGVEVTRSIVRRYRMGHIELATPAAHIWFVKDVP--SKIG 113
Query: 214 CFLCHKINIPATSQLLFINQIKLLD 238
L ++ Q+L+ N+ +LD
Sbjct: 114 TLL--DLSATELEQVLYFNKYIVLD 136
>pdb|1Z3X|A Chain A, Structure Of Gun4 From Thermosynechococcus Elongatus
Length = 238
Score = 33.1 bits (74), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 32/161 (19%), Positives = 68/161 (42%), Gaps = 23/161 (14%)
Query: 36 EFAK-TLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQAVQRESLA 94
EF K + T+ P PW +++ + P A + Q+ V+ + S + V + LA
Sbjct: 46 EFLKDSATFSPPPAPWIRGQAYRLLFHSPEASVQAFLQQHYPQGVIPLRSDRGVDYQELA 105
Query: 95 KRLITPEDQQHRAIMKEKIITRQEVVPEILKLKYYTDQEVKQL------SVVKVFSPITF 148
K L+ + + + +K+ + + + Y+T EV+QL ++ +++ +
Sbjct: 106 KLLVAEKFEAADRLTTQKLCELAGPLAQKRRWLYFT--EVEQLPIPDLQTIDQLWLAFSL 163
Query: 149 NSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIG 189
G+++ L+ +G CG N+ + IG
Sbjct: 164 GRFGYSVQRQLW---LG-----------CGQNWDRLWEKIG 190
>pdb|1Z3Y|A Chain A, Structure Of Gun4-1 From Thermosynechococcus Elongatus
Length = 238
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 31/161 (19%), Positives = 67/161 (41%), Gaps = 23/161 (14%)
Query: 36 EFAK-TLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQAVQRESLA 94
EF K + T+ P PW +++ + P A + Q+ V+ + S + V + LA
Sbjct: 46 EFLKDSATFSPPPAPWIRGQAYRLLFHSPEASVQAFLQQHYPQGVIPLRSDRGVDYQELA 105
Query: 95 KRLITPEDQQHRAIMKEKIITRQEVVPEILKLKYYTDQEVKQL------SVVKVFSPITF 148
K + + + + +K+ + + + Y+T EV+QL ++ +++ +
Sbjct: 106 KLFVAEKFEAADRLTTQKLCELAGPLAQKRRWLYFT--EVEQLPIPDLQTIDQLWLAFSL 163
Query: 149 NSLGHTIPGGLYDLAMGPISERGDPCTTCGNNYTKCKGHIG 189
G+++ L+ +G CG N+ + IG
Sbjct: 164 GRFGYSVQRQLW---LG-----------CGQNWDRLWEKIG 190
>pdb|3CMJ|A Chain A, Crystal Structure Of Engineered Beta-Glucosidase From Soil
Metagenome
Length = 465
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 43/145 (29%), Positives = 60/145 (41%), Gaps = 36/145 (24%)
Query: 31 IGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNED--GSVVRISSSQA- 87
+G+ L F YPV P +V R+M + QNE ++R +QA
Sbjct: 238 MGITLNF--NTIYPVSAEPADVEAARRM-----------HSFQNELFLEPLIRGQYNQAT 284
Query: 88 VQRESLAKRLITPEDQQHRAIMKEKIITRQEVVPEILKLKYYTDQEVKQ------LSVVK 141
+ I PED Q + I + L + YY VK + VV+
Sbjct: 285 LMAYPNLPEFIAPEDMQ---TISAPI--------DFLGVNYYNPMRVKSSPQPPGIEVVQ 333
Query: 142 VFSPITFNSLGHTI-PGGLYDLAMG 165
V SP+T ++G I P GLYDL MG
Sbjct: 334 VESPVT--AMGWEIAPEGLYDLLMG 356
>pdb|2ZJ2|A Chain A, Archaeal Dna Helicase Hjm Apo State In Form 1
pdb|2ZJ5|A Chain A, Archaeal Dna Helicase Hjm Complexed With Adp In Form 1
pdb|2ZJ8|A Chain A, Archaeal Dna Helicase Hjm Apo State In Form 2
pdb|2ZJA|A Chain A, Archaeal Dna Helicase Hjm Complexed With Amppcp In Form 2
Length = 720
Score = 31.2 bits (69), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 7/67 (10%)
Query: 30 SIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQAVQ 89
+IG P E A+ L + V+ W LR+ V Y G + EDGS+ R SS + +
Sbjct: 178 TIGNPEELAEWLNAELIVSDWRPVKLRRGVF-----YQG--FVTWEDGSIDRFSSWEELV 230
Query: 90 RESLAKR 96
+++ K+
Sbjct: 231 YDAIRKK 237
Score = 31.2 bits (69), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 7/67 (10%)
Query: 547 SIGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNEDGSVVRISSSQAVQ 606
+IG P E A+ L + V+ W LR+ V Y G + EDGS+ R SS + +
Sbjct: 178 TIGNPEELAEWLNAELIVSDWRPVKLRRGVF-----YQG--FVTWEDGSIDRFSSWEELV 230
Query: 607 RESLAKR 613
+++ K+
Sbjct: 231 YDAIRKK 237
>pdb|4HZ6|A Chain A, Crystal Structure Of Bglb
pdb|4HZ7|A Chain A, Crystal Structure Of Bglb With Glucose
pdb|4HZ8|A Chain A, Crystal Structure Of Bglb With Natural Substrate
Length = 444
Score = 31.2 bits (69), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 43/145 (29%), Positives = 60/145 (41%), Gaps = 36/145 (24%)
Query: 31 IGVPLEFAKTLTYPVPVTPWNVTLLRKMVINGPNVYPGANMIQNED--GSVVRISSSQA- 87
+G+ L F YPV P +V R+M + QNE ++R +QA
Sbjct: 217 MGITLNF--NTIYPVSAEPADVEAARRM-----------HSFQNELFLEPLIRGQYNQAT 263
Query: 88 VQRESLAKRLITPEDQQHRAIMKEKIITRQEVVPEILKLKYYTDQEVKQ------LSVVK 141
+ I PED Q + I + L + YY VK + VV+
Sbjct: 264 LMAYPNLPEFIAPEDMQ---TISAPI--------DFLGVNYYNPMRVKSSPQPPGIEVVQ 312
Query: 142 VFSPITFNSLGHTI-PGGLYDLAMG 165
V SP+T ++G I P GLYDL MG
Sbjct: 313 VESPVT--AMGWEIAPEGLYDLLMG 335
>pdb|2LIG|A Chain A, Three-Dimensional Structures Of The Ligand-Binding Domain
Of The Bacterial Aspartate Receptor With And Without A
Ligand
pdb|2LIG|B Chain B, Three-Dimensional Structures Of The Ligand-Binding Domain
Of The Bacterial Aspartate Receptor With And Without A
Ligand
pdb|1LIH|A Chain A, Three-Dimensional Structures Of The Ligand-Binding Domain
Of The Bacterial Aspartate Receptor With And Without A
Ligand
Length = 164
Score = 30.8 bits (68), Expect = 2.5, Method: Composition-based stats.
Identities = 18/92 (19%), Positives = 43/92 (46%), Gaps = 3/92 (3%)
Query: 468 RGDTLNNKLQNSWHELQYNVDLLMDAKLNINKTTGAHQIDGLKQMLDGKTGMI---RQNM 524
+G ++N+L+ EL DL++ ++N++++ +D Q KT ++ + +
Sbjct: 14 QGFVISNELRQQQSELTSTWDLMLQTRINLSRSAARMMMDASNQQSSAKTDLLQNAKTTL 73
Query: 525 MGKRVNFAGRSVITPDPYLNIDSIGVPLEFAK 556
++A +TP P + S V ++ +
Sbjct: 74 AQAAAHYANFKNMTPLPAMAEASANVDEKYQR 105
>pdb|1WAT|A Chain A, The Three-Dimensional Structure Of The Ligand-Binding
Domain Of A Wild-Type Bacterial Chemotaxis Receptor
pdb|1WAT|B Chain B, The Three-Dimensional Structure Of The Ligand-Binding
Domain Of A Wild-Type Bacterial Chemotaxis Receptor
pdb|1VLT|A Chain A, Ligand Binding Domain Of The Wild-Type Aspartate Receptor
With Aspartate
pdb|1VLT|B Chain B, Ligand Binding Domain Of The Wild-Type Aspartate Receptor
With Aspartate
pdb|1VLS|A Chain A, Ligand Binding Domain Of The Wild-Type Aspartate Receptor
pdb|1WAS|A Chain A, The Three-Dimensional Structure Of The Ligand-Binding
Domain Of A Wild-Type Bacterial Chemotaxis Receptor
Length = 146
Score = 30.0 bits (66), Expect = 3.6, Method: Composition-based stats.
Identities = 18/92 (19%), Positives = 43/92 (46%), Gaps = 3/92 (3%)
Query: 468 RGDTLNNKLQNSWHELQYNVDLLMDAKLNINKTTGAHQIDGLKQMLDGKTGMI---RQNM 524
+G ++N+L+ EL DL++ ++N++++ +D Q KT ++ + +
Sbjct: 4 QGFVISNELRQQQSELTSTWDLMLQTRINLSRSAARMMMDASNQQSSAKTDLLQNAKTTL 63
Query: 525 MGKRVNFAGRSVITPDPYLNIDSIGVPLEFAK 556
++A +TP P + S V ++ +
Sbjct: 64 AQAAAHYANFKNMTPLPAMAEASANVDEKYQR 95
>pdb|1JMW|A Chain A, Propagating Conformational Changes Over Long (And Short)
Distances
Length = 146
Score = 29.3 bits (64), Expect = 6.4, Method: Composition-based stats.
Identities = 18/92 (19%), Positives = 42/92 (45%), Gaps = 3/92 (3%)
Query: 468 RGDTLNNKLQNSWHELQYNVDLLMDAKLNINKTTGAHQIDGLKQMLDGKTGMI---RQNM 524
+G ++N+L+ EL DL++ ++N+ ++ +D Q KT ++ + +
Sbjct: 4 QGFVISNELRQQQSELTSTWDLMLQTRINLARSAARMMMDASNQQSSAKTDLLQNAKTTL 63
Query: 525 MGKRVNFAGRSVITPDPYLNIDSIGVPLEFAK 556
++A +TP P + S V ++ +
Sbjct: 64 AQAAAHYANFKNMTPLPAMAEASANVDEKYQR 95
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 0.135 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,734,842
Number of Sequences: 62578
Number of extensions: 714193
Number of successful extensions: 1659
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1607
Number of HSP's gapped (non-prelim): 55
length of query: 621
length of database: 14,973,337
effective HSP length: 105
effective length of query: 516
effective length of database: 8,402,647
effective search space: 4335765852
effective search space used: 4335765852
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: 54 (25.4 bits)