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= 045123
(219 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 = 174 bits (442), Expect = 2e-44, Method: Compositional matrix adjust.
Identities = 92/210 (43%), Positives = 123/210 (58%), Gaps = 20/210 (9%)
Query: 7 FSPFKVA--KVRMVQFSILSPDEIRKMSVTEIDHGKTTERG--MPMAGGLSDLRLGTIDK 62
FSP V +V VQF ILSP+EIR MSV +I+ +T + P GGL D RLGTID+
Sbjct: 6 FSPSSVPLRRVEEVQFGILSPEEIRSMSVAKIEFPETMDESGQRPRVGGLLDPRLGTIDR 65
Query: 63 RFKCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFK 122
+FKC+TC M +CPGHFGH+ELAKP+FHIGF+ + I+ CVC+NC K+ D + KF
Sbjct: 66 QFKCQTCGETMADCPGHFGHIELAKPVFHIGFLSKIKKILECVCWNCGKLKIDSSNPKFN 125
Query: 123 LALKIRHPKSRLEQILCACKTKNKCE-----GGDEIDVLSLLGHDGEEPLRKRKSGCGAL 177
+ R PK+RL + CKTK C+ G D D+ + + G GCGA
Sbjct: 126 DTQRYRDPKNRLNAVWNVCKTKMVCDTGLSAGSDNFDLSNPSANMGH-------GGCGAA 178
Query: 178 QPTLTIDGMNMIAEYKAQRKKNDDQGQLPE 207
QPT+ DG+ + + K+ D+ LPE
Sbjct: 179 QPTIRKDGLRLWGSW----KRGKDESDLPE 204
>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 = 154 bits (390), Expect = 3e-38, Method: Compositional matrix adjust.
Identities = 81/196 (41%), Positives = 113/196 (57%), Gaps = 10/196 (5%)
Query: 7 FSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMA--GGLSDLRLGTIDKRF 64
+S + V+ VQF + SP+E+R +SV +I +T + A GGL+D RLG+ID+
Sbjct: 6 YSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNL 65
Query: 65 KCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLA 124
KC+TC M ECPGHFGH++LAKP+FH+GF+ + + CVC +C K+L DE ++ + A
Sbjct: 66 KCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQA 125
Query: 125 LKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLTID 184
L I+ K R I CKTK C E DV S D L R GCG QPT+ D
Sbjct: 126 LAIKDSKKRFAAIWTLCKTKMVC----ETDVPS---EDDPTQLVSR-GGCGNTQPTIRKD 177
Query: 185 GMNMIAEYKAQRKKND 200
G+ ++ +K R D
Sbjct: 178 GLKLVGSWKKDRATGD 193
>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 = 154 bits (390), Expect = 3e-38, Method: Compositional matrix adjust.
Identities = 81/196 (41%), Positives = 113/196 (57%), Gaps = 10/196 (5%)
Query: 7 FSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMA--GGLSDLRLGTIDKRF 64
+S + V+ VQF + SP+E+R +SV +I +T + A GGL+D RLG+ID+
Sbjct: 6 YSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNL 65
Query: 65 KCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLA 124
KC+TC M ECPGHFGH++LAKP+FH+GF+ + + CVC +C K+L DE ++ + A
Sbjct: 66 KCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQA 125
Query: 125 LKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLTID 184
L I+ K R I CKTK C E DV S D L R GCG QPT+ D
Sbjct: 126 LAIKDSKKRFAAIWTLCKTKMVC----ETDVPS---EDDPTQLVSR-GGCGNTQPTIRKD 177
Query: 185 GMNMIAEYKAQRKKND 200
G+ ++ +K R D
Sbjct: 178 GLKLVGSWKKDRATGD 193
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 1455
Score = 154 bits (390), Expect = 3e-38, Method: Compositional matrix adjust.
Identities = 81/196 (41%), Positives = 113/196 (57%), Gaps = 10/196 (5%)
Query: 7 FSPFKVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGMPMA--GGLSDLRLGTIDKRF 64
+S + V+ VQF + SP+E+R +SV +I +T + A GGL+D RLG+ID+
Sbjct: 6 YSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNL 65
Query: 65 KCETCSSNMGECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKILADEEDDKFKLA 124
KC+TC M ECPGHFGH++LAKP+FH+GF+ + + CVC +C K+L DE ++ + A
Sbjct: 66 KCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQA 125
Query: 125 LKIRHPKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLRKRKSGCGALQPTLTID 184
L I+ K R I CKTK C E DV S D L R GCG QPT+ D
Sbjct: 126 LAIKDSKKRFAAIWTLCKTKMVC----ETDVPS---EDDPTQLVSR-GGCGNTQPTIRKD 177
Query: 185 GMNMIAEYKAQRKKND 200
G+ ++ +K R D
Sbjct: 178 GLKLVGSWKKDRATGD 193
>pdb|3QQC|A Chain A, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP
CLAMP DOMAIN
Length = 436
Score = 115 bits (289), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 57/132 (43%), Positives = 82/132 (62%), Gaps = 3/132 (2%)
Query: 18 VQFSILSPDEIRKMSVTEIDHGKTTER-GMPMAGGLSDLRLGTIDKRFKCETCSSNMGEC 76
++F ILSP EIRKMS E+ T + G P+ GG+ D R+G ID +CETC GEC
Sbjct: 72 IEFGILSPQEIRKMSAVEVTVPDTYDDDGYPIEGGVMDKRMGVIDPGLRCETCGGRAGEC 131
Query: 77 PGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKI-LADEEDDKFKLALKI-RHPKSRL 134
PGHFGH+ELA+P+ H+GF KT+ I+ C C +I L DEE +++ +++ R+ +S
Sbjct: 132 PGHFGHIELARPVIHVGFAKTIYRILESTCRECGRIKLTDEEIEEYMKKIELARNRRSEF 191
Query: 135 EQILCACKTKNK 146
+I+ K K
Sbjct: 192 NEIIKEIHKKAK 203
>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 = 107 bits (268), Expect = 4e-24, Method: Composition-based stats.
Identities = 66/209 (31%), Positives = 103/209 (49%), Gaps = 25/209 (11%)
Query: 15 VRMVQFSILSPDEIRKMSVTEIDHGKT-TERGMPMAGGLSDLRLGTIDKRFKCETCSSNM 73
++ ++F ILSPDEIRKMSVT I E G P+ G + D RLG I+ KC TC + +
Sbjct: 6 IKGIKFGILSPDEIRKMSVTAIITPDVYDEDGTPIEGSVMDPRLGVIEPGQKCPTCGNTL 65
Query: 74 GECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKI-LADEEDDKFKL---ALKIRH 129
G CPGHFGH+EL +P+ H+GF+K + ++ C C ++ ++++E +K+ A+K R
Sbjct: 66 GNCPGHFGHIELVRPVIHVGFVKHVYEFLKATCRRCGRVKISEDEIEKYSRIYNAIKKRW 125
Query: 130 PKSRLEQILCACKTKNKCEGGDEIDVLSLLGHDGEEPLR-----------KRKSGCGALQ 178
P + KT K + + H GE+ + +RK G L
Sbjct: 126 PSAARRLTEYVKKTAMKAQ---------VCPHCGEKQFKIKLEKPYNFYEERKEGVAKLT 176
Query: 179 PTLTIDGMNMIAEYKAQRKKNDDQGQLPE 207
P+ + + + E + D PE
Sbjct: 177 PSDIRERLEKVPESDVEILGYDPTTSRPE 205
>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 = 105 bits (263), Expect = 1e-23, Method: Composition-based stats.
Identities = 50/123 (40%), Positives = 77/123 (62%), Gaps = 5/123 (4%)
Query: 15 VRMVQFSILSPDEIRKMSVTEIDHGKT-TERGMPMAGGLSDLRLGTIDKRFKCETCSSNM 73
++ ++F ILSPDEIRKMSVT I E G P+ G + D RLG I+ KC TC + +
Sbjct: 6 IKGIKFGILSPDEIRKMSVTAIITPDVYDEDGTPIEGSVMDPRLGVIEPGQKCPTCGNTL 65
Query: 74 GECPGHFGHLELAKPMFHIGFMKTLLTIMRCVCFNCSKI-LADEEDDKFKL---ALKIRH 129
G CPGHFGH+EL +P+ H+G +K + ++ C C ++ ++++E +K+ A+K R
Sbjct: 66 GNCPGHFGHIELVRPVIHVGLVKHIYEFLKATCRRCGRVKISEDEIEKYSRIYNAIKKRW 125
Query: 130 PKS 132
P +
Sbjct: 126 PSA 128
>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 = 36.6 bits (83), Expect = 0.012, Method: Composition-based stats.
Identities = 33/103 (32%), Positives = 50/103 (48%), Gaps = 20/103 (19%)
Query: 14 KVRMVQFSILSPDEIRKMSVTEIDHGKTTE-RGM-PMAGGLSDLRL-GTID--------- 61
+VR V+ ++ SP++IR S E++ +T R + P GL D R+ G I
Sbjct: 4 EVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKY 63
Query: 62 --KRFK---CETCSSNMGEC---PGHFGHLELAKPMFHIGFMK 96
+RF+ CE C + + GH+ELA P HI F+K
Sbjct: 64 KRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHIWFVK 106
>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 = 36.6 bits (83), Expect = 0.012, Method: Composition-based stats.
Identities = 33/103 (32%), Positives = 50/103 (48%), Gaps = 20/103 (19%)
Query: 14 KVRMVQFSILSPDEIRKMSVTEIDHGKTTE-RGM-PMAGGLSDLRL-GTID--------- 61
+VR V+ ++ SP++IR S E++ +T R + P GL D R+ G I
Sbjct: 4 EVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKY 63
Query: 62 --KRFK---CETCSSNMGEC---PGHFGHLELAKPMFHIGFMK 96
+RF+ CE C + + GH+ELA P HI F+K
Sbjct: 64 KRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHIWFVK 106
>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 = 36.2 bits (82), Expect = 0.015, Method: Composition-based stats.
Identities = 33/103 (32%), Positives = 49/103 (47%), Gaps = 20/103 (19%)
Query: 14 KVRMVQFSILSPDEIRKMSVTEIDHGKTTE-RGM-PMAGGLSDLRL-GTID--------- 61
+VR V+ ++ SP++IR S E++ +T R + P GL D R+ G I
Sbjct: 4 EVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKY 63
Query: 62 --KRFK---CETCSSNMGEC---PGHFGHLELAKPMFHIGFMK 96
+RF+ CE C + GH+ELA P HI F+K
Sbjct: 64 KRQRFEGKVCERCGVEVTRSIVRRYRMGHIELATPAAHIWFVK 106
>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 = 35.8 bits (81), Expect = 0.018, Method: Composition-based stats.
Identities = 33/103 (32%), Positives = 49/103 (47%), Gaps = 20/103 (19%)
Query: 14 KVRMVQFSILSPDEIRKMSVTEIDHGKTTE-RGM-PMAGGLSDLRL-GTID--------- 61
+VR V+ ++ SP++IR S E++ +T R + P GL D R+ G I
Sbjct: 4 EVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKY 63
Query: 62 --KRFK---CETCSSNMGEC---PGHFGHLELAKPMFHIGFMK 96
+RF+ CE C + GH+ELA P HI F+K
Sbjct: 64 KRQRFEGKVCERCGVEVTRSIVRRYRMGHIELATPAAHIWFVK 106
>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For
Structural Studies
Length = 1233
Score = 35.8 bits (81), Expect = 0.018, Method: Composition-based stats.
Identities = 33/103 (32%), Positives = 49/103 (47%), Gaps = 20/103 (19%)
Query: 14 KVRMVQFSILSPDEIRKMSVTEIDHGKTTE-RGM-PMAGGLSDLRL-GTID--------- 61
+VR V+ ++ SP++IR S E++ +T R + P GL D R+ G I
Sbjct: 4 EVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKY 63
Query: 62 --KRFK---CETCSSNMGEC---PGHFGHLELAKPMFHIGFMK 96
+RF+ CE C + GH+ELA P HI F+K
Sbjct: 64 KRQRFEGKVCERCGVEVTRSIVRRYRMGHIELATPAAHIWFVK 106
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1264
Score = 34.3 bits (77), Expect = 0.057, Method: Composition-based stats.
Identities = 32/103 (31%), Positives = 49/103 (47%), Gaps = 20/103 (19%)
Query: 14 KVRMVQFSILSPDEIRKMSVTEIDHGKTTE-RGM-PMAGGLSDLRL-GTID--------- 61
+VR V+ ++ SP++IR S E++ +T R + P GL D R+ G I
Sbjct: 4 EVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKY 63
Query: 62 --KRFK---CETCSSNMGEC---PGHFGHLELAKPMFHIGFMK 96
+RF+ CE C+ + H+ELA P HI F+K
Sbjct: 64 KRQRFEAKVCERCAVEVTRSIVRRYRMAHIELATPAAHIWFVK 106
>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 1413
Score = 33.9 bits (76), Expect = 0.076, Method: Composition-based stats.
Identities = 31/108 (28%), Positives = 45/108 (41%), Gaps = 20/108 (18%)
Query: 11 KVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGM--PMAGGLSDLRL-GTID------ 61
K + ++ ++ SPD IR S E+ +T P GL R+ G +
Sbjct: 13 KTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLC 72
Query: 62 ---KRFK-----CETCSSNMGECP---GHFGHLELAKPMFHIGFMKTL 98
KR K CE C + + GH+ELA P HI F+K+L
Sbjct: 73 GKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSL 120
>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 = 33.9 bits (76), Expect = 0.076, Method: Composition-based stats.
Identities = 31/108 (28%), Positives = 45/108 (41%), Gaps = 20/108 (18%)
Query: 11 KVAKVRMVQFSILSPDEIRKMSVTEIDHGKTTERGM--PMAGGLSDLRL-GTID------ 61
K + ++ ++ SPD IR S E+ +T P GL R+ G +
Sbjct: 13 KTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLC 72
Query: 62 ---KRFK-----CETCSSNMGECP---GHFGHLELAKPMFHIGFMKTL 98
KR K CE C + + GH+ELA P HI F+K+L
Sbjct: 73 GKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSL 120
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
0.321 0.137 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,387,179
Number of Sequences: 62578
Number of extensions: 250520
Number of successful extensions: 505
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 483
Number of HSP's gapped (non-prelim): 18
length of query: 219
length of database: 14,973,337
effective HSP length: 95
effective length of query: 124
effective length of database: 9,028,427
effective search space: 1119524948
effective search space used: 1119524948
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: 49 (23.5 bits)