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= 020983
(319 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1I3Q|C Chain C, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|C Chain C, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|C Chain C, Rna Polymerase Ii Elongation Complex
pdb|1K83|C Chain C, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1NIK|C Chain C, Wild Type Rna Polymerase Ii
pdb|1NT9|C Chain C, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|C Chain C, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|C Chain C, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|C Chain C, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|C Chain C, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|C Chain C, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|C Chain C, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|C Chain C, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|C Chain C, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|C Chain C, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|C Chain C, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|C Chain C, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|C Chain C, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|C Chain C, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|C Chain C, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|C Chain C, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|C Chain C, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|C Chain C, 12-Subunit Rna Polymerase Ii
pdb|2E2H|C Chain C, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|C Chain C, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|C Chain C, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|C Chain C, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|C Chain C, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|C Chain C, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|C Chain C, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|C Chain C, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|C Chain C, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|C Chain C, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|C Chain C, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|O Chain O, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|C Chain C, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2YU9|C Chain C, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Utp
pdb|2R7Z|C Chain C, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|C Chain C, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|C Chain C, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|C Chain C, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|C Chain C, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
Complex With The Inhibitor Alpha-Amanitin
pdb|3FKI|C Chain C, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|C Chain C, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|C Chain C, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|C Chain C, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|C Chain C, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|C Chain C, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|C Chain C, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|C Chain C, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|C Chain C, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|D Chain D, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|C Chain C, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|O Chain O, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|C Chain C, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3K1F|C Chain C, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3K7A|C Chain C, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|C Chain C, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|C Chain C, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|C Chain C, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|C Chain C, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|C Chain C, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|C Chain C, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|C Chain C, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|C Chain C, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|C Chain C, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|C Chain C, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|C Chain C, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|C Chain C, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|C Chain C, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|C Chain C, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|C Chain C, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|C Chain C, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|C Chain C, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|4A3C|C Chain C, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|C Chain C, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|C Chain C, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|C Chain C, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|C Chain C, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|C Chain C, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|C Chain C, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|C Chain C, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|C Chain C, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|C Chain C, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|C Chain C, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|C Chain C, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
pdb|4BBR|C Chain C, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|C Chain C, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 318
Score = 184 bits (466), Expect = 7e-47, Method: Compositional matrix adjust.
Identities = 115/299 (38%), Positives = 167/299 (55%), Gaps = 38/299 (12%)
Query: 10 PKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAH 69
P+VKIRE D F L + D +MAN+LRRVMIAE+PT+AID VE+E N++VL DEFIAH
Sbjct: 6 PQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAH 65
Query: 70 RLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSD 129
RLGLIPL S + +SRDC D C+ CSV L+A S+ T +V SKDL
Sbjct: 66 RLGLIPLQSMDIEQLEYSRDCFCED---HCDKCSVVLTLQAFGESESTTNVYSKDLVIVS 122
Query: 130 HSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFM 189
+ ++ + P D + G++I KLR+GQEL+L +A+KGI K+HAKW PAA + F
Sbjct: 123 N-LMGRNIGHPIIQDK--EGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFE 179
Query: 190 YEP--EIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKK 247
Y+P ++ + E S +E W +S + ++ PN G + A+A
Sbjct: 180 YDPWNKLKHTDYWYEQDSAKE---WPQSKNCE-YEDPPNEGDPFDYKAQA---------- 225
Query: 248 AEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSEDTVEAD 306
D+F VES G+I Q+V+ I+ L++K+ ++ L+ ++ D
Sbjct: 226 ----------------DTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQD 268
>pdb|3I4M|C Chain C, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|C Chain C, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
Length = 324
Score = 184 bits (466), Expect = 7e-47, Method: Compositional matrix adjust.
Identities = 115/299 (38%), Positives = 167/299 (55%), Gaps = 38/299 (12%)
Query: 10 PKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAH 69
P+VKIRE D F L + D +MAN+LRRVMIAE+PT+AID VE+E N++VL DEFIAH
Sbjct: 12 PQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAH 71
Query: 70 RLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSD 129
RLGLIPL S + +SRDC D C+ CSV L+A S+ T +V SKDL
Sbjct: 72 RLGLIPLQSMDIEQLEYSRDCFCED---HCDKCSVVLTLQAFGESESTTNVYSKDLVIVS 128
Query: 130 HSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFM 189
+ ++ + P D + G++I KLR+GQEL+L +A+KGI K+HAKW PAA + F
Sbjct: 129 N-LMGRNIGHPIIQDK--EGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFE 185
Query: 190 YEP--EIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKK 247
Y+P ++ + E S +E W +S + ++ PN G + A+A
Sbjct: 186 YDPWNKLKHTDYWYEQDSAKE---WPQSKNCE-YEDPPNEGDPFDYKAQA---------- 231
Query: 248 AEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSEDTVEAD 306
D+F VES G+I Q+V+ I+ L++K+ ++ L+ ++ D
Sbjct: 232 ----------------DTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQD 274
>pdb|3HOW|C Chain C, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|C Chain C, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|C Chain C, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|C Chain C, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
Length = 347
Score = 184 bits (466), Expect = 8e-47, Method: Compositional matrix adjust.
Identities = 115/299 (38%), Positives = 167/299 (55%), Gaps = 38/299 (12%)
Query: 10 PKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAH 69
P+VKIRE D F L + D +MAN+LRRVMIAE+PT+AID VE+E N++VL DEFIAH
Sbjct: 35 PQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAH 94
Query: 70 RLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSD 129
RLGLIPL S + +SRDC D C+ CSV L+A S+ T +V SKDL
Sbjct: 95 RLGLIPLQSMDIEQLEYSRDCFCED---HCDKCSVVLTLQAFGESESTTNVYSKDLVIVS 151
Query: 130 HSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFM 189
+ ++ + P D + G++I KLR+GQEL+L +A+KGI K+HAKW PAA + F
Sbjct: 152 N-LMGRNIGHPIIQDK--EGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFE 208
Query: 190 YEP--EIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKK 247
Y+P ++ + E S +E W +S + ++ PN G + A+A
Sbjct: 209 YDPWNKLKHTDYWYEQDSAKE---WPQSKNCE-YEDPPNEGDPFDYKAQA---------- 254
Query: 248 AEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSEDTVEAD 306
D+F VES G+I Q+V+ I+ L++K+ ++ L+ ++ D
Sbjct: 255 ----------------DTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQD 297
>pdb|3J0K|C Chain C, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 268
Score = 182 bits (462), Expect = 2e-46, Method: Compositional matrix adjust.
Identities = 116/299 (38%), Positives = 166/299 (55%), Gaps = 38/299 (12%)
Query: 10 PKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAH 69
P+VKIRE D F L + D +MAN+LRRVMIAE+PT+AID VE+E N++VL DEFIAH
Sbjct: 6 PQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAH 65
Query: 70 RLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSD 129
RLGLIPL S + +SRDC D C+ CSV L+A S+ T +V SKDL
Sbjct: 66 RLGLIPLQSMDIEQLEYSRDCFCED---HCDKCSVVLTLQAFGESESTTNVYSKDLVIVS 122
Query: 130 HSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFM 189
+ ++ + P D + G++I KLR+GQEL+L +A+KGI K+HAKW PAA + F
Sbjct: 123 N-LMGRNIGHPIIQDK--EGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFE 179
Query: 190 YEP--EIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKK 247
Y+P ++ + E S +E W +S + D PN G + A+A
Sbjct: 180 YDPWNKLKHTDYWYEQDSAKE---WPQSKNCEYED-PPNEGDPFDYKAQA---------- 225
Query: 248 AEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSEDTVEAD 306
D+F VES G+I Q+V+ I+ L++K+ ++ L+ ++ D
Sbjct: 226 ----------------DTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQD 268
>pdb|3H0G|C Chain C, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|O Chain O, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 297
Score = 171 bits (434), Expect = 4e-43, Method: Compositional matrix adjust.
Identities = 102/289 (35%), Positives = 156/289 (53%), Gaps = 46/289 (15%)
Query: 12 VKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRL 71
+ IR + + F L +T ++AN+LRRV++AE+PT+AIDLVEI VN+SV+ DEF+AHRL
Sbjct: 7 ITIRNISKNSVDFVLTNTSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFLAHRL 66
Query: 72 GLIPLTSER-----AMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLY 126
G+IPL S + + ++R+CD D C CSVE L AKC + T+++ ++DL
Sbjct: 67 GMIPLDSSNIDEPPPVGLEYTRNCDC---DQYCPKCSVELFLNAKCTGEGTMEIYARDLV 123
Query: 127 SSDHSVV--PVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAA 184
S +S + P+ DP + RG +I KLR+ QE+ LR IA+KGI K+HAKWSP +
Sbjct: 124 VSSNSSLGHPI-LADP-------KSRGPLICKLRKEQEISLRCIAKKGIAKEHAKWSPTS 175
Query: 185 TVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEV 244
V F Y+P L+ W E+ DAE +
Sbjct: 176 AVAFEYDP----------WNKLQHTDYWFEND----------------ADAEWPKSKNAD 209
Query: 245 IKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKL 293
++ G+P + F VES G+I +++++ + +L++KL
Sbjct: 210 WEEPPREGEP--FNFQEEPRRFYMDVESVGSIPPNEIMVQGLRILQEKL 256
>pdb|2WAQ|D Chain D, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|D Chain D, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|S Chain S, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|D Chain D, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|S Chain S, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|D Chain D, Rnap At 3.2ang
pdb|4B1O|D Chain D, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|S Chain S, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 265
Score = 110 bits (275), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 89/269 (33%), Positives = 138/269 (51%), Gaps = 40/269 (14%)
Query: 33 MANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAM-SMRFSRDCD 91
NA+RR + VP ++ID V N+S L DE +AHRL LIP TSE A+ + R+ +C
Sbjct: 24 FVNAIRRAAMLYVPVMSIDDVYFIENNSPLYDEILAHRLALIPFTSEEALDTYRWPEECI 83
Query: 92 ACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRG 151
C + CE C + ++ A+ ++ + + SKD+ S D S+VP+ S D
Sbjct: 84 DCTEN--CEKCYTKIYIEAEALNEPKM-LYSKDIKSEDPSIVPI---------SGD---- 127
Query: 152 IIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQS 211
I IV L Q++ L A R G GK+HAK+ P + Y P++ I L EK +
Sbjct: 128 IPIVLLGANQKISLEARLRLGYGKEHAKFIPVSLAIVRYYPKVEI-------LGNCEKGA 180
Query: 212 WVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVE 271
V P VF++ G++ V + A T +E ++ GL+ I + ED +I +E
Sbjct: 181 TV--CPEGVFEL--KDGKLSVKNELACTLCEECLRYCN-----GLIRISSVEDKYILELE 231
Query: 272 STGAIKASQLVLNA-------IEVLKQKL 293
S G++K +++L A IE L++KL
Sbjct: 232 SVGSLKPERILLEAGKSIIRKIEELEKKL 260
>pdb|2PA8|D Chain D, X-Ray Crystal Structure Of The DL SUBCOMPLEX OF THE
SULFOLOBUS Solfataricus Rna Polymerase
pdb|2PMZ|D Chain D, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|S Chain S, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|D Chain D, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|O Chain O, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 265
Score = 107 bits (266), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 85/269 (31%), Positives = 133/269 (49%), Gaps = 40/269 (14%)
Query: 33 MANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAM-SMRFSRDCD 91
NA+RR + VP +A+D V N+S L DE +AHRL LIP SE A+ + R+ +C
Sbjct: 24 FVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAHRLALIPFMSEEALDTYRWPEECI 83
Query: 92 ACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRG 151
C + CE C + ++ A+ ++ + + SKD+ S D SVVP+ S D
Sbjct: 84 ECTEN--CEKCYTKIYIEAEAPNEPRM-IYSKDIKSEDPSVVPI---------SGD---- 127
Query: 152 IIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQS 211
I IV L Q++ L A R G GK+HAK+ P + Y P++ I L +
Sbjct: 128 IPIVLLGTNQKISLEARLRLGYGKEHAKFIPVSLSVVRYYPKVEI---------LANCEK 178
Query: 212 WVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVE 271
V P VF++ G++ V + + T +E ++ G + I ED +I +E
Sbjct: 179 AVNVCPEGVFEL--KDGKLSVKNELSCTLCEECLRYCN-----GSIRISFVEDKYILEIE 231
Query: 272 STGAIKASQLVLNA-------IEVLKQKL 293
S G++K +++L A IE L++KL
Sbjct: 232 SVGSLKPERILLEAGKSIIRKIEELEKKL 260
>pdb|3IYD|A Chain A, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
pdb|3IYD|B Chain B, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
pdb|3LU0|A Chain A, Molecular Model Of Escherichia Coli Core Rna Polymerase
pdb|3LU0|B Chain B, Molecular Model Of Escherichia Coli Core Rna Polymerase
pdb|4IGC|A Chain A, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|B Chain B, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|F Chain F, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|G Chain G, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 329
Score = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 4/49 (8%)
Query: 12 VKIRELKDDYAKFEL----RDTDASMANALRRVMIAEVPTIAIDLVEIE 56
V I ++ +AK L R ++ NALRR++++ +P A+ VEI+
Sbjct: 14 VDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEID 62
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
0.317 0.134 0.379
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,184,772
Number of Sequences: 62578
Number of extensions: 370518
Number of successful extensions: 881
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 853
Number of HSP's gapped (non-prelim): 18
length of query: 319
length of database: 14,973,337
effective HSP length: 99
effective length of query: 220
effective length of database: 8,778,115
effective search space: 1931185300
effective search space used: 1931185300
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)