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= psy16767
(1020 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 = 247 bits (630), Expect = 3e-65, Method: Compositional matrix adjust.
Identities = 159/439 (36%), Positives = 240/439 (54%), Gaps = 46/439 (10%)
Query: 9 SHFLKAEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSLRDTFLTRAEYMNLVYQA 68
S +AE + V Q + P+ P+ G++QD + K SLRD FLTR MN++
Sbjct: 500 SEETRAEIQEITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTRNAVMNIM--- 556
Query: 69 LCILNTEIRTLPPTIWKPMPLWTGKQVLSTVIINLTPKDKVIIRHGELLSGILDKKQFGS 128
L + + + PP I KP LWTGKQ+LS +I PK +IR D KQ S
Sbjct: 557 LWVPDWDGILPPPVILKPKVLWTGKQILSLII----PKGINLIRD--------DDKQSLS 604
Query: 129 TQYGLVHAVWDTHVTIRHGELLSGILDKKQFGSTQYGLVHAVWDTHGAEHAISLLSCLAK 188
D+ + I +GE++ G++DKK G++Q GLVH +W G E + + +
Sbjct: 605 NPT-------DSGMLIENGEIIYGVVDKKTVGASQGGLVHTIWKEKGPEICKGFFNGIQR 657
Query: 189 LFTVYLQRVGFTLGVRDILVRQERDRKRTKIINKARRLGTEAACNALGLPLDTDPEIISS 248
+ +L GF++G+ D + + ++ T+ + +ARR E +A L +P +
Sbjct: 658 VVNYWLLHNGFSIGIGDTIADADTMKEVTRTVKEARRQVAECIQDAQHNRLKPEPGMT-- 715
Query: 249 QLQEAYASIPQFRAQIDRQYKSLLDKVTNNINQVCLPEGLIEPFPANNLQFMVESGAKGS 308
L+E+ F A++ R +L++ +N + E ++ +NN++ MV +G+KGS
Sbjct: 716 -LRES------FEAKVSR----ILNQARDNAGRSA--EHSLKD--SNNVKQMVAAGSKGS 760
Query: 309 TVNTMQISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFF 368
+N Q+S +GQ +EGKR RTLP F + SP + GF++ ++ G+ PQEFF
Sbjct: 761 FINISQMSACVGQQIVEGKRIPFGFKYRTLPHFPKDDDSPESRGFIENSYLRGLTPQEFF 820
Query: 369 FHCMAGREGLIDTAVKTSRSGYLQRCLVKHLEGLTVHYDMTVRDSDLSLIQVLYGEDGLD 428
FH MAGREGLIDTAVKT+ +GY+QR LVK +E + V YD TVR++ +IQ YGEDGLD
Sbjct: 821 FHAMAGREGLIDTAVKTAETGYIQRRLVKAMEDVMVRYDGTVRNAMGDIIQFAYGEDGLD 880
Query: 429 VTKRQY-------LTDKQF 440
T +Y L+ KQF
Sbjct: 881 ATLVEYQVFDSLRLSTKQF 899
Score = 92.4 bits (228), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 49/98 (50%), Positives = 65/98 (66%), Gaps = 1/98 (1%)
Query: 570 SLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMMATKAIKTP 629
++ +PGE VG LAAQSIGEP+TQMTLNTFH+AG NVTLG+PRL+EIL +A K IKTP
Sbjct: 1059 AVVSPGEMVGTLAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEILNVA-KNIKTP 1117
Query: 630 SMEIPFLPDMPKLEKKANRLAKSMTRITMADVLEKVKI 667
S+ I +P + A + + T++ V +I
Sbjct: 1118 SLTIYLMPWIAANMDLAKNVQTQIEHTTLSTVTSATEI 1155
Score = 80.1 bits (196), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 47/146 (32%), Positives = 76/146 (52%), Gaps = 2/146 (1%)
Query: 862 EKESKHLLKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFA 921
E+ + +L+TDGIN+ + D + Y N + GIEA +++E++NV
Sbjct: 1305 ERADEWVLETDGINLTEAMTVEGV-DATRTYSNSFVEILQILGIEATRSALLKELRNVIE 1363
Query: 922 VYGIEVDPRHLSLVADYMTHSGTYVAMNRNGI-RLNPSFIQKMTFEMPLEKIRQASMQGR 980
G V+ RHL+L+ D MT G +A+ R+GI R + + +FE +E + A+ G
Sbjct: 1364 FDGSYVNYRHLALLCDVMTSRGHLMAITRHGINRAETGALMRCSFEETVEILMDAAASGE 1423
Query: 981 EDSLRAPSARVMLGQECRQGTGLFQL 1006
+D + S +MLGQ GTG F +
Sbjct: 1424 KDDCKGISENIMLGQLAPMGTGAFDI 1449
>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 = 221 bits (562), Expect = 2e-57, Method: Compositional matrix adjust.
Identities = 147/426 (34%), Positives = 218/426 (51%), Gaps = 49/426 (11%)
Query: 9 SHFLKAEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSLRDTFLTRAEYMNLVYQA 68
S +AE S L V Q + P+ P G++QD + KL+LRDTF+ + +N++Y
Sbjct: 494 SEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLY-- 551
Query: 69 LCILNTEIRTLPPTIWKPMPLWTGKQVLSTVIINLTPKDKVIIRHGELLSGI-LDKKQFG 127
+ + + P I KP PLW+GKQ+LS I N GI L + G
Sbjct: 552 -WVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPN----------------GIHLQRFDEG 594
Query: 128 STQYGLVHAVWDTHVTIRHGELLSGILDKKQFGSTQYGLVHAVWDTHGAEHAISLLSCLA 187
+T + + D + I G+++ G+++KK GS+ GL+H V G + L +
Sbjct: 595 TT----LLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQ 650
Query: 188 KLFTVYLQRVGFTLGVRDILVRQERDRKRTKIINKARR----LGTEAACNALGLPLDTDP 243
K+ +L GF+ G+ D + R+ T+ I +A++ + EA N L
Sbjct: 651 KVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLL-------- 702
Query: 244 EIISSQLQEAYASIPQFRAQIDRQYKSLLDKVTNNINQVCLPEGLIEPFPANNLQFMVES 303
+ F + R DK + +V L + NN++ MV +
Sbjct: 703 -----TAKHGMTLRESFEDNVVRFLNEARDKA-GRLAEVNLKD-------LNNVKQMVMA 749
Query: 304 GAKGSTVNTMQISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQ 363
G+KGS +N Q+S +GQ +EGKR A RTLP F + SP + GFV+ ++ G+
Sbjct: 750 GSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLT 809
Query: 364 PQEFFFHCMAGREGLIDTAVKTSRSGYLQRCLVKHLEGLTVHYDMTVRDSDLSLIQVLYG 423
PQEFFFH M GREGLIDTAVKT+ +GY+QR LVK LE + VHYD T R+S ++IQ +YG
Sbjct: 810 PQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYG 869
Query: 424 EDGLDV 429
EDG+D
Sbjct: 870 EDGMDA 875
Score = 92.0 bits (227), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 52/110 (47%), Positives = 70/110 (63%), Gaps = 5/110 (4%)
Query: 568 LLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMMATKAIK 627
L S+ +PGE VGVLAAQSIGEP+TQMTLNTFHFAG VT G+PRL+EIL +A K +K
Sbjct: 1054 LRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVA-KNMK 1112
Query: 628 TPSMEIPFLPDMPKLEKKANRLAKSMTRITMADVLEKVKIKEWLEISPEP 677
TPS+ + P +++A + ++ T L+ V I + P+P
Sbjct: 1113 TPSLTVYLEPGHAADQEQAKLIRSAIEHTT----LKSVTIASEIYYDPDP 1158
Score = 78.6 bits (192), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 60/193 (31%), Positives = 94/193 (48%), Gaps = 13/193 (6%)
Query: 816 KIEFRDSTNVFVKDVVNQHNIVHKYSYDKKNHMWCKLLFLPSNLFEE-KESKHLLKTDGI 874
KIE N+ ++ V N +V YD+K +PS E KE + +L+TDG+
Sbjct: 1262 KIENTMLENITLRGVENIERVVM-MKYDRK---------VPSPTGEYVKEPEWVLETDGV 1311
Query: 875 NVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSL 934
N++ + + D ++Y N + GIEA + +EV NV A G V+ RH++L
Sbjct: 1312 NLSEVMTVPGI-DPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMAL 1370
Query: 935 VADYMTHSGTYVAMNRNGI-RLNPSFIQKMTFEMPLEKIRQASMQGREDSLRAPSARVML 993
+ D MT G ++ R+G R N + + +FE +E + +A D R S V+L
Sbjct: 1371 LVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVIL 1430
Query: 994 GQECRQGTGLFQL 1006
GQ GTG F +
Sbjct: 1431 GQMAPIGTGAFDV 1443
>pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|A Chain A, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|A Chain A, Rna Polymerase Ii Elongation Complex
pdb|1K83|A Chain A, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1NIK|A Chain A, Wild Type Rna Polymerase Ii
pdb|1NT9|A Chain A, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|A Chain A, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|A Chain A, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|A Chain A, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|A Chain A, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|A Chain A, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|A Chain A, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|A Chain A, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|A Chain A, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|A Chain A, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|A Chain A, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|A Chain A, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|A Chain A, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|A Chain A, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|A Chain A, 12-Subunit Rna Polymerase Ii
pdb|2E2H|A Chain A, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|A Chain A, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|A Chain A, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|M Chain M, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2YU9|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Utp
pdb|2R7Z|A Chain A, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|A Chain A, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|A Chain A, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|A Chain A, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|A Chain A, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
Complex With The Inhibitor Alpha-Amanitin
pdb|3FKI|A Chain A, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|A Chain A, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|A Chain A, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|A Chain A, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|A Chain A, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|A Chain A, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|A Chain A, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|B Chain B, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|A Chain A, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|M Chain M, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|A Chain A, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|A Chain A, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|A Chain A, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|A Chain A, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3K7A|A Chain A, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|A Chain A, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|A Chain A, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|A Chain A, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|A Chain A, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|A Chain A, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|A Chain A, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|A Chain A, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|A Chain A, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|A Chain A, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|4BBR|A Chain A, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|A Chain A, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 1733
Score = 220 bits (561), Expect = 2e-57, Method: Compositional matrix adjust.
Identities = 147/426 (34%), Positives = 218/426 (51%), Gaps = 49/426 (11%)
Query: 9 SHFLKAEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSLRDTFLTRAEYMNLVYQA 68
S +AE S L V Q + P+ P G++QD + KL+LRDTF+ + +N++Y
Sbjct: 494 SEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLY-- 551
Query: 69 LCILNTEIRTLPPTIWKPMPLWTGKQVLSTVIINLTPKDKVIIRHGELLSGI-LDKKQFG 127
+ + + P I KP PLW+GKQ+LS I N GI L + G
Sbjct: 552 -WVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPN----------------GIHLQRFDEG 594
Query: 128 STQYGLVHAVWDTHVTIRHGELLSGILDKKQFGSTQYGLVHAVWDTHGAEHAISLLSCLA 187
+T + + D + I G+++ G+++KK GS+ GL+H V G + L +
Sbjct: 595 TT----LLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQ 650
Query: 188 KLFTVYLQRVGFTLGVRDILVRQERDRKRTKIINKARR----LGTEAACNALGLPLDTDP 243
K+ +L GF+ G+ D + R+ T+ I +A++ + EA N L
Sbjct: 651 KVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLL-------- 702
Query: 244 EIISSQLQEAYASIPQFRAQIDRQYKSLLDKVTNNINQVCLPEGLIEPFPANNLQFMVES 303
+ F + R DK + +V L + NN++ MV +
Sbjct: 703 -----TAKHGMTLRESFEDNVVRFLNEARDKA-GRLAEVNLKD-------LNNVKQMVMA 749
Query: 304 GAKGSTVNTMQISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQ 363
G+KGS +N Q+S +GQ +EGKR A RTLP F + SP + GFV+ ++ G+
Sbjct: 750 GSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLT 809
Query: 364 PQEFFFHCMAGREGLIDTAVKTSRSGYLQRCLVKHLEGLTVHYDMTVRDSDLSLIQVLYG 423
PQEFFFH M GREGLIDTAVKT+ +GY+QR LVK LE + VHYD T R+S ++IQ +YG
Sbjct: 810 PQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYG 869
Query: 424 EDGLDV 429
EDG+D
Sbjct: 870 EDGMDA 875
Score = 92.0 bits (227), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 52/110 (47%), Positives = 70/110 (63%), Gaps = 5/110 (4%)
Query: 568 LLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMMATKAIK 627
L S+ +PGE VGVLAAQSIGEP+TQMTLNTFHFAG VT G+PRL+EIL +A K +K
Sbjct: 1054 LRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVA-KNMK 1112
Query: 628 TPSMEIPFLPDMPKLEKKANRLAKSMTRITMADVLEKVKIKEWLEISPEP 677
TPS+ + P +++A + ++ T L+ V I + P+P
Sbjct: 1113 TPSLTVYLEPGHAADQEQAKLIRSAIEHTT----LKSVTIASEIYYDPDP 1158
Score = 78.6 bits (192), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 60/193 (31%), Positives = 94/193 (48%), Gaps = 13/193 (6%)
Query: 816 KIEFRDSTNVFVKDVVNQHNIVHKYSYDKKNHMWCKLLFLPSNLFEE-KESKHLLKTDGI 874
KIE N+ ++ V N +V YD+K +PS E KE + +L+TDG+
Sbjct: 1262 KIENTMLENITLRGVENIERVVM-MKYDRK---------VPSPTGEYVKEPEWVLETDGV 1311
Query: 875 NVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSL 934
N++ + + D ++Y N + GIEA + +EV NV A G V+ RH++L
Sbjct: 1312 NLSEVMTVPGI-DPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMAL 1370
Query: 935 VADYMTHSGTYVAMNRNGI-RLNPSFIQKMTFEMPLEKIRQASMQGREDSLRAPSARVML 993
+ D MT G ++ R+G R N + + +FE +E + +A D R S V+L
Sbjct: 1371 LVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVIL 1430
Query: 994 GQECRQGTGLFQL 1006
GQ GTG F +
Sbjct: 1431 GQMAPIGTGAFDV 1443
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 1455
Score = 220 bits (561), Expect = 3e-57, Method: Compositional matrix adjust.
Identities = 147/427 (34%), Positives = 218/427 (51%), Gaps = 49/427 (11%)
Query: 9 SHFLKAEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSLRDTFLTRAEYMNLVYQA 68
S +AE S L V Q + P+ P G++QD + KL+LRDTF+ + +N++Y
Sbjct: 494 SEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLY-- 551
Query: 69 LCILNTEIRTLPPTIWKPMPLWTGKQVLSTVIINLTPKDKVIIRHGELLSGI-LDKKQFG 127
+ + + P I KP PLW+GKQ+LS I N GI L + G
Sbjct: 552 -WVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPN----------------GIHLQRFDEG 594
Query: 128 STQYGLVHAVWDTHVTIRHGELLSGILDKKQFGSTQYGLVHAVWDTHGAEHAISLLSCLA 187
+T + + D + I G+++ G+++KK GS+ GL+H V G + L +
Sbjct: 595 TT----LLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQ 650
Query: 188 KLFTVYLQRVGFTLGVRDILVRQERDRKRTKIINKARR----LGTEAACNALGLPLDTDP 243
K+ +L GF+ G+ D + R+ T+ I +A++ + EA N L
Sbjct: 651 KVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLL-------- 702
Query: 244 EIISSQLQEAYASIPQFRAQIDRQYKSLLDKVTNNINQVCLPEGLIEPFPANNLQFMVES 303
+ F + R DK + +V L + NN++ MV +
Sbjct: 703 -----TAKHGMTLRESFEDNVVRFLNEARDK-AGRLAEVNLKD-------LNNVKQMVMA 749
Query: 304 GAKGSTVNTMQISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQ 363
G+KGS +N Q+S +GQ +EGKR A RTLP F + SP + GFV+ ++ G+
Sbjct: 750 GSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLT 809
Query: 364 PQEFFFHCMAGREGLIDTAVKTSRSGYLQRCLVKHLEGLTVHYDMTVRDSDLSLIQVLYG 423
PQEFFFH M GREGLIDTAVKT+ +GY+QR LVK LE + VHYD T R+S ++IQ +YG
Sbjct: 810 PQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYG 869
Query: 424 EDGLDVT 430
EDG+D
Sbjct: 870 EDGMDAA 876
Score = 92.4 bits (228), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 52/110 (47%), Positives = 70/110 (63%), Gaps = 5/110 (4%)
Query: 568 LLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMMATKAIK 627
L S+ +PGE VGVLAAQSIGEP+TQMTLNTFHFAG VT G+PRL+EIL +A K +K
Sbjct: 1054 LRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVA-KNMK 1112
Query: 628 TPSMEIPFLPDMPKLEKKANRLAKSMTRITMADVLEKVKIKEWLEISPEP 677
TPS+ + P +++A + ++ T L+ V I + P+P
Sbjct: 1113 TPSLTVYLEPGHAADQEQAKLIRSAIEHTT----LKSVTIASEIYYDPDP 1158
Score = 78.2 bits (191), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 60/193 (31%), Positives = 94/193 (48%), Gaps = 13/193 (6%)
Query: 816 KIEFRDSTNVFVKDVVNQHNIVHKYSYDKKNHMWCKLLFLPSNLFEE-KESKHLLKTDGI 874
KIE N+ ++ V N +V YD+K +PS E KE + +L+TDG+
Sbjct: 1262 KIENTMLENITLRGVENIERVVM-MKYDRK---------VPSPTGEYVKEPEWVLETDGV 1311
Query: 875 NVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSL 934
N++ + + D ++Y N + GIEA + +EV NV A G V+ RH++L
Sbjct: 1312 NLSEVMTVPGI-DPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMAL 1370
Query: 935 VADYMTHSGTYVAMNRNGI-RLNPSFIQKMTFEMPLEKIRQASMQGREDSLRAPSARVML 993
+ D MT G ++ R+G R N + + +FE +E + +A D R S V+L
Sbjct: 1371 LVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVIL 1430
Query: 994 GQECRQGTGLFQL 1006
GQ GTG F +
Sbjct: 1431 GQMAPIGTGAFDV 1443
>pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|W Chain W, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|A Chain A, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|W Chain W, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|A Chain A, Rnap At 3.2ang
pdb|4B1O|A Chain A, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|W Chain W, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 880
Score = 181 bits (458), Expect = 2e-45, Method: Compositional matrix adjust.
Identities = 135/417 (32%), Positives = 200/417 (47%), Gaps = 38/417 (9%)
Query: 14 AEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSLRDTFLTRAEYMNLVYQALCILN 73
AEA +M V + P+ G P+ G QD+ ISGA L T L E Q L + +
Sbjct: 474 AEAKEIMLVHKNIITPRYGGPIIGAAQDY-ISGAYLLTVKTTLLTKEEAQ---QILGVAD 529
Query: 74 TEIRTLPPTIWKPMPLWTGKQVLSTVIINLTPKDKVIIRHGELLSGILDKKQFGSTQYGL 133
+I P I P +TGKQV+S + PKD + SG K
Sbjct: 530 VKIDLGEPAILAPREYYTGKQVVSAFL----PKDFNFHGQANVSSGPRLCKNEDCPH--- 582
Query: 134 VHAVWDTHVTIRHGELLSGILDKKQFGSTQ-YGLVHAVWDTHGAEHAISLLSCLAKLFTV 192
D++V I++G LL G+ DKK G+ Q ++H + + E+ L+ L ++F
Sbjct: 583 -----DSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDEYGKWLMDNLFRVFIR 637
Query: 193 YLQRVGFTLGVRDILVRQERDRKRTKIINKARRLGTEAACNALGLPLDTDPEIISSQLQE 252
+++ GFT+ + D+ + D + +I N+ R E +I
Sbjct: 638 FVELQGFTMRLEDVSLG---DDVKKEIYNEIDRAKVEVD------------NLIQKYKNG 682
Query: 253 AYASIP--QFRAQIDRQYKSLLDKVTNNINQVCLPEGLIEPFPANNLQFMVESGAKGSTV 310
IP ++ LDK+ + + ++PF N M +GA+GS +
Sbjct: 683 ELEPIPGRTLEESLENYILDTLDKLRSTAGDIA--SKYLDPF--NFAYVMARTGARGSVL 738
Query: 311 NTMQISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFH 370
N Q++ +LGQ + G+R RTLP F PY++SP A GF+ F TG++P E FFH
Sbjct: 739 NITQMAAMLGQQSVRGERIKRGYMTRTLPHFKPYDISPEARGFIYSSFRTGLKPTELFFH 798
Query: 371 CMAGREGLIDTAVKTSRSGYLQRCLVKHLEGLTVHYDMTVRDSDLSLIQVLYGEDGL 427
GREGL+DTAV+TS+SGY+QR L+ L L YD TVR +IQV YG+DG+
Sbjct: 799 AAGGREGLVDTAVRTSQSGYMQRRLINALSDLRAEYDGTVRSLYGEVIQVAYGDDGV 855
>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 = 181 bits (458), Expect = 2e-45, Method: Compositional matrix adjust.
Identities = 134/417 (32%), Positives = 200/417 (47%), Gaps = 38/417 (9%)
Query: 14 AEASFLMNVSSQYLVPKDGSPLSGLIQDHVISGAKLSLRDTFLTRAEYMNLVYQALCILN 73
AEA +M V + P+ G P+ G QD+ ISGA L T L E Q L + +
Sbjct: 474 AEAKEIMLVHKNIITPRYGGPIIGAAQDY-ISGAYLLTVKTTLLTKEEAQ---QILGVAD 529
Query: 74 TEIRTLPPTIWKPMPLWTGKQVLSTVIINLTPKDKVIIRHGELLSGILDKKQFGSTQYGL 133
+I P I P +TGKQV+S + PKD + SG K
Sbjct: 530 VKIDLGEPAILAPREYYTGKQVISAFL----PKDFNFHGQANVSSGPRLCKNEDCPH--- 582
Query: 134 VHAVWDTHVTIRHGELLSGILDKKQFGSTQ-YGLVHAVWDTHGAEHAISLLSCLAKLFTV 192
D++V I++G LL G+ DKK G+ Q ++H + + E+ L+ L ++F
Sbjct: 583 -----DSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDEYGKWLMDNLFRVFIR 637
Query: 193 YLQRVGFTLGVRDILVRQERDRKRTKIINKARRLGTEAACNALGLPLDTDPEIISSQLQE 252
+++ GFT+ + D+ + D + +I N+ R E +I
Sbjct: 638 FVELQGFTMRLEDVSLG---DDVKKEIYNEIDRAKVEVD------------NLIQKYKNG 682
Query: 253 AYASIP--QFRAQIDRQYKSLLDKVTNNINQVCLPEGLIEPFPANNLQFMVESGAKGSTV 310
IP ++ LDK+ + + ++PF N M +GA+GS +
Sbjct: 683 ELEPIPGRTLEESLENYILDTLDKLRSTAGDIA--SKYLDPF--NFAYVMARTGARGSVL 738
Query: 311 NTMQISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFH 370
N Q++ +LGQ + G+R RTLP F PY++SP A GF+ F TG++P E FFH
Sbjct: 739 NITQMAAMLGQQSVRGERIKRGYMTRTLPHFKPYDISPEARGFIYSSFRTGLKPTELFFH 798
Query: 371 CMAGREGLIDTAVKTSRSGYLQRCLVKHLEGLTVHYDMTVRDSDLSLIQVLYGEDGL 427
GREGL+DTAV+TS+SGY+QR L+ L L YD TVR ++QV YG+DG+
Sbjct: 799 AAGGREGLVDTAVRTSQSGYMQRRLINALSDLRAEYDGTVRSLYGEVVQVAYGDDGV 855
>pdb|2WAQ|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|Y Chain Y, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
Length = 395
Score = 87.8 bits (216), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 51/114 (44%), Positives = 71/114 (62%), Gaps = 3/114 (2%)
Query: 555 HVDKFYDMIFYKNLLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPR 614
+DK +D+ + L PGE +G++AAQS+GEP TQMTL TFHFAG ++NVTLG+PR
Sbjct: 47 EIDKIFDLAIKEYSEGLIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPR 106
Query: 615 LREILMMATKAIKTPSMEIPFLPDMPKLEK-KANRLAKSMTRITMADVLEKVKI 667
L EI+ A K TP M I +L D K +K KA +A+ + + +V+ I
Sbjct: 107 LIEIV-DAKKVPSTPMMTI-YLTDEYKHDKEKALEVARKLEYTKIENVVSSTSI 158
Score = 87.0 bits (214), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 45/152 (29%), Positives = 87/152 (57%), Gaps = 2/152 (1%)
Query: 859 LFEEKESKHLLKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKN 918
+ ++K ++++ TDG N++ + + + D+ K+ N+I + +GIEAA +IIRE+
Sbjct: 241 IVQKKGDEYIILTDGSNLSGVLSVKGV-DIAKVETNNIREIEEVFGIEAAREIIIREISK 299
Query: 919 VFAVYGIEVDPRHLSLVADYMTHSGTYVAMNRNGIRLNP-SFIQKMTFEMPLEKIRQASM 977
V A G++VD RH+ LVAD MT +G + R+G+ S + + FE+ ++ + A+
Sbjct: 300 VLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVTVKHLLDAAA 359
Query: 978 QGREDSLRAPSARVMLGQECRQGTGLFQLRNR 1009
+G + + +++G + GTG+ +L R
Sbjct: 360 RGDVEEFKGVVENIIIGHPIKLGTGMVELTMR 391
>pdb|2Y0S|C Chain C, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|Y Chain Y, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|C Chain C, Rnap At 3.2ang
pdb|4B1O|C Chain C, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|Y Chain Y, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 395
Score = 87.8 bits (216), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 51/114 (44%), Positives = 71/114 (62%), Gaps = 3/114 (2%)
Query: 555 HVDKFYDMIFYKNLLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPR 614
+DK +D+ + L PGE +G++AAQS+GEP TQMTL TFHFAG ++NVTLG+PR
Sbjct: 47 EIDKIFDLAIKEYSEGLIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPR 106
Query: 615 LREILMMATKAIKTPSMEIPFLPDMPKLEK-KANRLAKSMTRITMADVLEKVKI 667
L EI+ A K TP M I +L D K +K KA +A+ + + +V+ I
Sbjct: 107 LIEIV-DAKKVPSTPMMTI-YLTDEYKHDKEKALEVARKLEYTKIENVVSSTSI 158
Score = 87.0 bits (214), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 45/152 (29%), Positives = 87/152 (57%), Gaps = 2/152 (1%)
Query: 859 LFEEKESKHLLKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKN 918
+ ++K ++++ TDG N++ + + + D+ K+ N+I + +GIEAA +IIRE+
Sbjct: 241 IVQKKGDEYIILTDGSNLSGVLSVKGV-DIAKVETNNIREIEEVFGIEAAREIIIREISK 299
Query: 919 VFAVYGIEVDPRHLSLVADYMTHSGTYVAMNRNGIRLNP-SFIQKMTFEMPLEKIRQASM 977
V A G++VD RH+ LVAD MT +G + R+G+ S + + FE+ ++ + A+
Sbjct: 300 VLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVTVKHLLDAAA 359
Query: 978 QGREDSLRAPSARVMLGQECRQGTGLFQLRNR 1009
+G + + +++G + GTG+ +L R
Sbjct: 360 RGDVEEFKGVVENIIIGHPIKLGTGMVELTMR 391
>pdb|3HKZ|C Chain C, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|M Chain M, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 395
Score = 87.4 bits (215), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 47/113 (41%), Positives = 67/113 (59%), Gaps = 1/113 (0%)
Query: 555 HVDKFYDMIFYKNLLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPR 614
+DK +D+ + L PGE +G++AAQS+GEP TQMTL TFHFAG ++NVTLG+PR
Sbjct: 47 EIDKIFDLAIKEYSEGLIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPR 106
Query: 615 LREILMMATKAIKTPSMEIPFLPDMPKLEKKANRLAKSMTRITMADVLEKVKI 667
L EI+ A K TP M I + + KA +A+ + + +V+ I
Sbjct: 107 LIEIV-DAKKVPSTPMMTIYLTDEYKRDRDKALEVARKLEYTKIENVVSSTSI 158
Score = 85.9 bits (211), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 44/152 (28%), Positives = 87/152 (57%), Gaps = 2/152 (1%)
Query: 859 LFEEKESKHLLKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKN 918
+ ++K ++++ TDG N++ + + + D+ K+ N+I + +GIEAA +IIRE+
Sbjct: 241 IVQKKGDEYIILTDGSNLSGVLSVKGV-DVAKVETNNIREIEEVFGIEAAREIIIREISK 299
Query: 919 VFAVYGIEVDPRHLSLVADYMTHSGTYVAMNRNGIRLNP-SFIQKMTFEMPLEKIRQASM 977
V A G++VD RH+ L+AD MT +G + R+G+ S + + FE+ ++ + A+
Sbjct: 300 VLAEQGLDVDIRHILLIADVMTRTGIVRQIGRHGVTGEKNSVLARAAFEVTVKHLLDAAA 359
Query: 978 QGREDSLRAPSARVMLGQECRQGTGLFQLRNR 1009
+G + + +++G + GTG+ +L R
Sbjct: 360 RGDVEEFKGVVENIIIGHPIKLGTGMVELTMR 391
>pdb|2PMZ|C Chain C, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|G Chain G, Archaeal Rna Polymerase From Sulfolobus Solfataricus
Length = 392
Score = 87.4 bits (215), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 47/113 (41%), Positives = 67/113 (59%), Gaps = 1/113 (0%)
Query: 555 HVDKFYDMIFYKNLLSLANPGENVGVLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPR 614
+DK +D+ + L PGE +G++AAQS+GEP TQMTL TFHFAG ++NVTLG+PR
Sbjct: 44 EIDKIFDLAIKEYSEGLIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPR 103
Query: 615 LREILMMATKAIKTPSMEIPFLPDMPKLEKKANRLAKSMTRITMADVLEKVKI 667
L EI+ A K TP M I + + KA +A+ + + +V+ I
Sbjct: 104 LIEIV-DAKKVPSTPMMTIYLTDEYKRDRDKALEVARKLEYTKIENVVSSTSI 155
Score = 85.9 bits (211), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 44/152 (28%), Positives = 87/152 (57%), Gaps = 2/152 (1%)
Query: 859 LFEEKESKHLLKTDGINVNFISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKN 918
+ ++K ++++ TDG N++ + + + D+ K+ N+I + +GIEAA +IIRE+
Sbjct: 238 IVQKKGDEYIILTDGSNLSGVLSVKGV-DVAKVETNNIREIEEVFGIEAAREIIIREISK 296
Query: 919 VFAVYGIEVDPRHLSLVADYMTHSGTYVAMNRNGIRLNP-SFIQKMTFEMPLEKIRQASM 977
V A G++VD RH+ L+AD MT +G + R+G+ S + + FE+ ++ + A+
Sbjct: 297 VLAEQGLDVDIRHILLIADVMTRTGIVRQIGRHGVTGEKNSVLARAAFEVTVKHLLDAAA 356
Query: 978 QGREDSLRAPSARVMLGQECRQGTGLFQLRNR 1009
+G + + +++G + GTG+ +L R
Sbjct: 357 RGDVEEFKGVVENIIIGHPIKLGTGMVELTMR 388
>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 = 58.9 bits (141), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 30/59 (50%), Positives = 40/59 (67%), Gaps = 4/59 (6%)
Query: 565 YKNLLSLANP---GENVGVLAAQSIGEPSTQMTLNTFHFAG-RGDMNVTLGIPRLREIL 619
Y LS+A P GE VG++AAQSIGEP TQ+T+ TFH G G ++T G+PR+ E+
Sbjct: 1205 YGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELF 1263
Score = 55.5 bits (132), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 67/261 (25%), Positives = 106/261 (40%), Gaps = 51/261 (19%)
Query: 154 LDKKQFGSTQYGLVHAVWDTHGAEHAISLLSCLAKLFTVYLQRVGFTLGVRDILVRQERD 213
LD Q ++ LV+ + G E LL L + G T+G+ D ++ +E
Sbjct: 902 LDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEE-- 959
Query: 214 RKRTKIINKARRLGTEAACNALGLPLDTDPEIISSQLQEAYASIPQFRAQIDRQYKSLLD 273
K+ + R+L +G D +E Y I Q L
Sbjct: 960 -KKQYLEEADRKLLQIEQAYEMGFLTD----------RERYDQILQ-----------LWT 997
Query: 274 KVTNNINQVCLPEGLIEPFPANNLQFMVESGAKGSTVNTMQISCLLGQIELEGKRPAMMV 333
+ T + Q + E +P N L M +SGA+G+ Q+ L G ++ +P
Sbjct: 998 ETTEKVTQAVF-KNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQ----KP---- 1048
Query: 334 SGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFHCMAGREGLIDTAVKTSRSGYLQR 393
SG T +EV R+ F G+ E+F R+G DTA++T+ SGYL R
Sbjct: 1049 SGET------FEVPVRSS------FREGLTVLEYFISSHGARKGGADTALRTADSGYLTR 1096
Query: 394 CLVKHLEGLTVHYDMTVRDSD 414
LV V +++ VR++D
Sbjct: 1097 KLV------DVTHEIVVREAD 1111
Score = 31.2 bits (69), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 24/45 (53%)
Query: 895 DIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYM 939
D H + G EA R ++ E++ V+ G+++ +H+ +V M
Sbjct: 1331 DPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQM 1375
>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 = 58.9 bits (141), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 30/59 (50%), Positives = 40/59 (67%), Gaps = 4/59 (6%)
Query: 565 YKNLLSLANP---GENVGVLAAQSIGEPSTQMTLNTFHFAG-RGDMNVTLGIPRLREIL 619
Y LS+A P GE VG++AAQSIGEP TQ+T+ TFH G G ++T G+PR+ E+
Sbjct: 1205 YGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELF 1263
Score = 55.5 bits (132), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 67/261 (25%), Positives = 106/261 (40%), Gaps = 51/261 (19%)
Query: 154 LDKKQFGSTQYGLVHAVWDTHGAEHAISLLSCLAKLFTVYLQRVGFTLGVRDILVRQERD 213
LD Q ++ LV+ + G E LL L + G T+G+ D ++ +E
Sbjct: 902 LDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEE-- 959
Query: 214 RKRTKIINKARRLGTEAACNALGLPLDTDPEIISSQLQEAYASIPQFRAQIDRQYKSLLD 273
K+ + R+L +G D +E Y I Q L
Sbjct: 960 -KKQYLEEADRKLLQIEQAYEMGFLTD----------RERYDQILQ-----------LWT 997
Query: 274 KVTNNINQVCLPEGLIEPFPANNLQFMVESGAKGSTVNTMQISCLLGQIELEGKRPAMMV 333
+ T + Q + E +P N L M +SGA+G+ Q+ L G ++ +P
Sbjct: 998 ETTEKVTQAVF-KNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQ----KP---- 1048
Query: 334 SGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFHCMAGREGLIDTAVKTSRSGYLQR 393
SG T +EV R+ F G+ E+F R+G DTA++T+ SGYL R
Sbjct: 1049 SGET------FEVPVRSS------FREGLTVLEYFISSHGARKGGADTALRTADSGYLTR 1096
Query: 394 CLVKHLEGLTVHYDMTVRDSD 414
LV V +++ VR++D
Sbjct: 1097 KLV------DVTHEIVVREAD 1111
Score = 31.2 bits (69), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 24/45 (53%)
Query: 895 DIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYM 939
D H + G EA R ++ E++ V+ G+++ +H+ +V M
Sbjct: 1331 DPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQM 1375
>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 = 55.8 bits (133), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 106/431 (24%), Positives = 162/431 (37%), Gaps = 96/431 (22%)
Query: 9 SHFLKAEASFLMNVSSQYLVPKDGSPLSGLIQDHVIS------------GAKLSLRDTFL 56
S F +AEA M + L P G PL+ +D ++ GA ++ F
Sbjct: 752 SSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGMA----FA 807
Query: 57 TRAEYMNLVYQALCILNTEIRTLPPTIWKPMPLWTGKQVLSTVIINLTPKDKVI-IRHGE 115
T E + + LN P + G+ L V N P + ++ + HG
Sbjct: 808 TPEEALAAYERGEVALNA------PIVVAGRETSVGR--LKFVFAN--PDEALLAVAHGL 857
Query: 116 L-LSGILDKKQFG---STQYGLV-------HAVWDTHVTIRHGELLSGILDKKQFGSTQY 164
L L ++ + G T G + AV D V EL+ +D Q ++
Sbjct: 858 LDLQDVVTVRYLGRRLETSPGRILFARIVGEAVGDEKVA---QELIQ--MDVPQEKNSLK 912
Query: 165 GLVHAVWDTHGAEHAISLLSCLAKLFTVYLQRVGFTLGVRDILVRQERDRKRTKIINKAR 224
LV+ + G E LL L G T+G+ D ++ +E+ R + K R
Sbjct: 913 DLVYQAFLRLGMEKTARLLDALKYYGFTLSTTSGITIGIDDAVIPEEKQRYLEEADRKLR 972
Query: 225 RLGTEAACNALGLPLDTDPEIISSQLQEAYA-SIPQFRAQIDRQYKSLLDKVTNNINQVC 283
Q+++AY R + D Q L + T + Q
Sbjct: 973 ------------------------QIEQAYEMGFLTDRERYD-QVIQLWTETTEKVTQAV 1007
Query: 284 LPEGLIEPFPANNLQFMVESGAKGSTVNTMQISCLLGQIELEGKRPAMMVSGRTLPSFLP 343
+ E +P N L M +SGA+G N QI L G L K PS
Sbjct: 1008 F-KNFEENYPFNPLYVMAQSGARG---NPQQIRQLCGMRGLMQK-----------PSGET 1052
Query: 344 YEVSPRAGGFVDGRFMTGIQPQEFFFHCMAGREGLIDTAVKTSRSGYLQRCLVKHLEGLT 403
+EV R+ F G+ E+F R+G DTA++T+ SGYL R LV
Sbjct: 1053 FEVPVRSS------FREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLV------D 1100
Query: 404 VHYDMTVRDSD 414
V +++ VR++D
Sbjct: 1101 VAHEIVVREAD 1111
Score = 55.5 bits (132), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/59 (49%), Positives = 39/59 (66%), Gaps = 4/59 (6%)
Query: 565 YKNLLSLANP---GENVGVLAAQSIGEPSTQMTLNTFHFAGRG-DMNVTLGIPRLREIL 619
Y LS+A P GE VGV+AA+SIGEP TQ+T+ TFH G ++T G+PR+ E+
Sbjct: 1205 YGYDLSMARPVSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELF 1263
Score = 30.4 bits (67), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 24/45 (53%)
Query: 895 DIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYM 939
D H + G EA R ++ E++ V+ G+++ +H+ +V M
Sbjct: 1331 DPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQM 1375
>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For
Structural Studies
Length = 1233
Score = 55.5 bits (132), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 106/431 (24%), Positives = 162/431 (37%), Gaps = 96/431 (22%)
Query: 9 SHFLKAEASFLMNVSSQYLVPKDGSPLSGLIQDHVIS------------GAKLSLRDTFL 56
S F +AEA M + L P G PL+ +D ++ GA ++ F
Sbjct: 461 SSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGMA----FA 516
Query: 57 TRAEYMNLVYQALCILNTEIRTLPPTIWKPMPLWTGKQVLSTVIINLTPKDKVI-IRHGE 115
T E + + LN P + G+ L V N P + ++ + HG
Sbjct: 517 TPEEALAAYERGEVALNA------PIVVAGRETSVGR--LKFVFAN--PDEALLAVAHGL 566
Query: 116 L-LSGILDKKQFG---STQYGLV-------HAVWDTHVTIRHGELLSGILDKKQFGSTQY 164
L L ++ + G T G + AV D V EL+ +D Q ++
Sbjct: 567 LDLQDVVTVRYLGRRLETSPGRILFARIVGEAVGDEKVA---QELIQ--MDVPQEKNSLK 621
Query: 165 GLVHAVWDTHGAEHAISLLSCLAKLFTVYLQRVGFTLGVRDILVRQERDRKRTKIINKAR 224
LV+ + G E LL L G T+G+ D ++ +E+ R + K R
Sbjct: 622 DLVYQAFLRLGMEKTARLLDALKYYGFTLSTTSGITIGIDDAVIPEEKQRYLEEADRKLR 681
Query: 225 RLGTEAACNALGLPLDTDPEIISSQLQEAYA-SIPQFRAQIDRQYKSLLDKVTNNINQVC 283
Q+++AY R + D Q L + T + Q
Sbjct: 682 ------------------------QIEQAYEMGFLTDRERYD-QVIQLWTETTEKVTQAV 716
Query: 284 LPEGLIEPFPANNLQFMVESGAKGSTVNTMQISCLLGQIELEGKRPAMMVSGRTLPSFLP 343
+ E +P N L M +SGA+G N QI L G L K PS
Sbjct: 717 F-KNFEENYPFNPLYVMAQSGARG---NPQQIRQLCGMRGLMQK-----------PSGET 761
Query: 344 YEVSPRAGGFVDGRFMTGIQPQEFFFHCMAGREGLIDTAVKTSRSGYLQRCLVKHLEGLT 403
+EV R+ F G+ E+F R+G DTA++T+ SGYL R LV
Sbjct: 762 FEVPVRSS------FREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLV------D 809
Query: 404 VHYDMTVRDSD 414
V +++ VR++D
Sbjct: 810 VAHEIVVREAD 820
Score = 55.5 bits (132), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/59 (49%), Positives = 39/59 (66%), Gaps = 4/59 (6%)
Query: 565 YKNLLSLANP---GENVGVLAAQSIGEPSTQMTLNTFHFAGRG-DMNVTLGIPRLREIL 619
Y LS+A P GE VGV+AA+SIGEP TQ+T+ TFH G ++T G+PR+ E+
Sbjct: 914 YGYDLSMARPVSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELF 972
Score = 30.8 bits (68), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 24/45 (53%)
Query: 895 DIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYM 939
D H + G EA R ++ E++ V+ G+++ +H+ +V M
Sbjct: 1040 DPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQM 1084
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1264
Score = 55.5 bits (132), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/55 (50%), Positives = 38/55 (69%), Gaps = 4/55 (7%)
Query: 569 LSLANP---GENVGVLAAQSIGEPSTQMTLNTFHFAGRG-DMNVTLGIPRLREIL 619
LS+A P GE VGV+AA+SIGEP TQ+T+ TFH G ++T G+PR+ E+
Sbjct: 949 LSMARPVSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELF 1003
Score = 54.7 bits (130), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 68/261 (26%), Positives = 103/261 (39%), Gaps = 51/261 (19%)
Query: 154 LDKKQFGSTQYGLVHAVWDTHGAEHAISLLSCLAKLFTVYLQRVGFTLGVRDILVRQERD 213
+D Q ++ LV+ + G E LL L G T+G+ D ++ +E+
Sbjct: 642 MDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTLSTTSGITIGIDDAVIPEEKQ 701
Query: 214 RKRTKIINKARRLGTEAACNALGLPLDTDPEIISSQLQEAYASIPQFRAQIDRQYKSLLD 273
R + K R++ A + TD +E Y + Q L
Sbjct: 702 RYLEEADRKLRQIE-----QAYEMGFLTD--------RERYDQVIQ-----------LWT 737
Query: 274 KVTNNINQVCLPEGLIEPFPANNLQFMVESGAKGSTVNTMQISCLLGQIELEGKRPAMMV 333
+ T + Q E +P N L M +SGA+G N QI L G L K
Sbjct: 738 ETTEKVTQAVF-NNFEENYPFNPLYVMAQSGARG---NPQQIRQLCGMRGLMQK------ 787
Query: 334 SGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFHCMAGREGLIDTAVKTSRSGYLQR 393
PS +EV R+ F G+ E+F R+G DTA++T+ SGYL R
Sbjct: 788 -----PSGETFEVPVRSS------FREGLTVLEYFISSHGARKGGADTALRTADSGYLTR 836
Query: 394 CLVKHLEGLTVHYDMTVRDSD 414
LV V +++ VR++D
Sbjct: 837 KLVD------VAHEIVVREAD 851
Score = 30.8 bits (68), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 24/45 (53%)
Query: 895 DIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYM 939
D H + G EA R ++ E++ V+ G+++ +H+ +V M
Sbjct: 1071 DPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQM 1115
>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 = 55.1 bits (131), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/59 (49%), Positives = 39/59 (66%), Gaps = 4/59 (6%)
Query: 565 YKNLLSLANP---GENVGVLAAQSIGEPSTQMTLNTFHFAGRG-DMNVTLGIPRLREIL 619
Y LS+A P GE VGV+AA+SIGEP TQ+T+ TFH G ++T G+PR+ E+
Sbjct: 946 YGYDLSMARPVSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELF 1004
Score = 52.8 bits (125), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 69/263 (26%), Positives = 104/263 (39%), Gaps = 54/263 (20%)
Query: 154 LDKKQFGSTQYGLVHAVWDTHGAEHAISLLSCLAKL-FTVYLQRVGFTLGVRDILVRQER 212
+D Q ++ LV+ + G E LL L FT+ T+G+ D ++ +E+
Sbjct: 642 MDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTLSTTSGIITIGIDDAVIPEEK 701
Query: 213 DRKRTKIINKARRLGTEAACNALGLPLDTDPEIISSQLQEAYA-SIPQFRAQIDRQYKSL 271
R + K R Q+++AY R + D Q L
Sbjct: 702 QRYLEEADRKLR------------------------QIEQAYEMGFLTDRERYD-QVIQL 736
Query: 272 LDKVTNNINQVCLPEGLIEPFPANNLQFMVESGAKGSTVNTMQISCLLGQIELEGKRPAM 331
+ T + Q E +P N L M +SGA+G N QI L G L K
Sbjct: 737 WTETTEKVTQAVF-NNFEENYPFNPLYVMAQSGARG---NPQQIRQLCGMRGLMQK---- 788
Query: 332 MVSGRTLPSFLPYEVSPRAGGFVDGRFMTGIQPQEFFFHCMAGREGLIDTAVKTSRSGYL 391
PS +EV R+ F G+ E+F R+G DTA++T+ SGYL
Sbjct: 789 -------PSGETFEVPVRSS------FREGLTVLEYFISSHGARKGGADTALRTADSGYL 835
Query: 392 QRCLVKHLEGLTVHYDMTVRDSD 414
R LV V +++ VR++D
Sbjct: 836 TRKLV------DVAHEIVVREAD 852
Score = 30.8 bits (68), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 24/45 (53%)
Query: 895 DIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYM 939
D H + G EA R ++ E++ V+ G+++ +H+ +V M
Sbjct: 1072 DPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQM 1116
>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 1413
Score = 49.7 bits (117), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 20/32 (62%), Positives = 25/32 (78%)
Query: 571 LANPGENVGVLAAQSIGEPSTQMTLNTFHFAG 602
+ N GE +GV+AAQSIGEP TQ+T+ TFH G
Sbjct: 908 IINKGEAIGVIAAQSIGEPGTQLTMRTFHIGG 939
Score = 48.5 bits (114), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 58/243 (23%), Positives = 98/243 (40%), Gaps = 53/243 (21%)
Query: 193 YLQRVGFTLGVRDILVRQERDRKRTKIINKARRLGTEAACNALGLPLDTDPEIISSQLQE 252
Y R G ++G+ D+++ + K+ +II++A E I Q Q
Sbjct: 631 YAARSGASVGIDDMVIPE----KKHEIISEAEAEVAE----------------IQEQFQS 670
Query: 253 AYAS--------IPQFRAQIDRQYKSLLDKVTNN--INQVCLPEGLIEPFPANNLQFMVE 302
+ I + A DR K+++D + IN+ E + N++ M +
Sbjct: 671 GLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVS---FNSIYMMAD 727
Query: 303 SGAKGSTVNTMQISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGI 362
SGA+GS Q++ + G L K ++ +P + F G+
Sbjct: 728 SGARGSAAQIRQLAGMRG---LMAKPDGSIIE------------TP-----ITANFREGL 767
Query: 363 QPQEFFFHCMAGREGLIDTAVKTSRSGYLQRCLVKHLEGLTVHYDMTVRDSDLSLIQVLY 422
++F R+GL DTA+KT+ SGYL R LV + L V D + + V+
Sbjct: 768 NVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVIE 827
Query: 423 GED 425
G D
Sbjct: 828 GGD 830
>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 = 49.7 bits (117), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 20/32 (62%), Positives = 25/32 (78%)
Query: 571 LANPGENVGVLAAQSIGEPSTQMTLNTFHFAG 602
+ N GE +GV+AAQSIGEP TQ+T+ TFH G
Sbjct: 908 IINKGEAIGVIAAQSIGEPGTQLTMRTFHIGG 939
Score = 48.5 bits (114), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 58/243 (23%), Positives = 98/243 (40%), Gaps = 53/243 (21%)
Query: 193 YLQRVGFTLGVRDILVRQERDRKRTKIINKARRLGTEAACNALGLPLDTDPEIISSQLQE 252
Y R G ++G+ D+++ + K+ +II++A E I Q Q
Sbjct: 631 YAARSGASVGIDDMVIPE----KKHEIISEAEAEVAE----------------IQEQFQS 670
Query: 253 AYAS--------IPQFRAQIDRQYKSLLDKVTNN--INQVCLPEGLIEPFPANNLQFMVE 302
+ I + A DR K+++D + IN+ E + N++ M +
Sbjct: 671 GLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVS---FNSIYMMAD 727
Query: 303 SGAKGSTVNTMQISCLLGQIELEGKRPAMMVSGRTLPSFLPYEVSPRAGGFVDGRFMTGI 362
SGA+GS Q++ + G L K ++ +P + F G+
Sbjct: 728 SGARGSAAQIRQLAGMRG---LMAKPDGSIIE------------TP-----ITANFREGL 767
Query: 363 QPQEFFFHCMAGREGLIDTAVKTSRSGYLQRCLVKHLEGLTVHYDMTVRDSDLSLIQVLY 422
++F R+GL DTA+KT+ SGYL R LV + L V D + + V+
Sbjct: 768 NVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVIE 827
Query: 423 GED 425
G D
Sbjct: 828 GGD 830
>pdb|2WZI|A Chain A, Btgh84 D243n In Complex With 5f-Oxazoline
pdb|2WZI|B Chain B, Btgh84 D243n In Complex With 5f-Oxazoline
Length = 737
Score = 30.0 bits (66), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 7/84 (8%)
Query: 520 QPLISTFQPDAHFGSISENLADSVVKYTKGRTDA------SHVDKFYDMIFYKNLLSLAN 573
+PLI P H ++ + + V+K +GR ++ +HV +FY + S N
Sbjct: 510 KPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQN 569
Query: 574 PGENVGVLAAQSIGEPSTQMTLNT 597
P + GV A + +P T T
Sbjct: 570 PYQ-PGVKTATRVIKPLIDRTFAT 592
>pdb|2WZH|A Chain A, Btgh84 D242n In Complex With Meumb-Derived Oxazoline
pdb|4AIU|A Chain A, A Complex Structure Of Btgh84
Length = 737
Score = 30.0 bits (66), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 7/84 (8%)
Query: 520 QPLISTFQPDAHFGSISENLADSVVKYTKGRTDA------SHVDKFYDMIFYKNLLSLAN 573
+PLI P H ++ + + V+K +GR ++ +HV +FY + S N
Sbjct: 510 KPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQN 569
Query: 574 PGENVGVLAAQSIGEPSTQMTLNT 597
P + GV A + +P T T
Sbjct: 570 PYQ-PGVKTATRVIKPLIDRTFAT 592
>pdb|2VVN|A Chain A, Btgh84 In Complex With Nh-Butylthiazoline
pdb|2VVN|B Chain B, Btgh84 In Complex With Nh-Butylthiazoline
pdb|2VVS|A Chain A, Btgh84 Structure In Complex With Pugnac
pdb|2X0H|A Chain A, Btgh84 Michaelis Complex
pdb|2X0H|B Chain B, Btgh84 Michaelis Complex
pdb|4AIS|A Chain A, A Complex Structure Of Btgh84
pdb|4AIS|B Chain B, A Complex Structure Of Btgh84
Length = 737
Score = 30.0 bits (66), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 7/84 (8%)
Query: 520 QPLISTFQPDAHFGSISENLADSVVKYTKGRTDA------SHVDKFYDMIFYKNLLSLAN 573
+PLI P H ++ + + V+K +GR ++ +HV +FY + S N
Sbjct: 510 KPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQN 569
Query: 574 PGENVGVLAAQSIGEPSTQMTLNT 597
P + GV A + +P T T
Sbjct: 570 PYQ-PGVKTATRVIKPLIDRTFAT 592
>pdb|2J47|A Chain A, Bacteroides Thetaiotaomicron Gh84 O-Glcnacase In Complex
With A Imidazole-Pugnac Hybrid Inhibitor
pdb|2W4X|A Chain A, Btgh84 In Complex With Stz
pdb|2W66|A Chain A, Btgh84 In Complex With Hq602
pdb|2W66|B Chain B, Btgh84 In Complex With Hq602
pdb|2W67|A Chain A, Btgh84 In Complex With Fma34
pdb|2W67|B Chain B, Btgh84 In Complex With Fma34
pdb|2WCA|A Chain A, Btgh84 In Complex With N-Butyl Pugnac
pdb|2XJ7|A Chain A, Btgh84 In Complex With 6-Acetamido-6-Deoxy-Castanospermine
pdb|2XJ7|B Chain B, Btgh84 In Complex With 6-Acetamido-6-Deoxy-Castanospermine
pdb|2XM1|A Chain A, Btgh84 In Complex With N-Acetyl Gluconolactam
pdb|2XM1|B Chain B, Btgh84 In Complex With N-Acetyl Gluconolactam
pdb|2XM2|A Chain A, Btgh84 In Complex With Lognac
pdb|2XM2|B Chain B, Btgh84 In Complex With Lognac
Length = 716
Score = 30.0 bits (66), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 7/84 (8%)
Query: 520 QPLISTFQPDAHFGSISENLADSVVKYTKGRTDA------SHVDKFYDMIFYKNLLSLAN 573
+PLI P H ++ + + V+K +GR ++ +HV +FY + S N
Sbjct: 489 KPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQN 548
Query: 574 PGENVGVLAAQSIGEPSTQMTLNT 597
P + GV A + +P T T
Sbjct: 549 PYQ-PGVKTATRVIKPLIDRTFAT 571
>pdb|2JIW|A Chain A, Bacteroides Thetaiotaomicron Gh84 O-glcnacase In Complex
With 2-acetylamino-2-deoxy-1-epivalienamine
pdb|2JIW|B Chain B, Bacteroides Thetaiotaomicron Gh84 O-glcnacase In Complex
With 2-acetylamino-2-deoxy-1-epivalienamine
Length = 716
Score = 30.0 bits (66), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 7/84 (8%)
Query: 520 QPLISTFQPDAHFGSISENLADSVVKYTKGRTDA------SHVDKFYDMIFYKNLLSLAN 573
+PLI P H ++ + + V+K +GR ++ +HV +FY + S N
Sbjct: 489 KPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQN 548
Query: 574 PGENVGVLAAQSIGEPSTQMTLNT 597
P + GV A + +P T T
Sbjct: 549 PYQ-PGVKTATRVIKPLIDRTFAT 571
>pdb|2J4G|A Chain A, Bacteroides Thetaiotaomicron Gh84 O-Glcnacase In Complex
With N-Butyl-Thiazoline Inhibitor
pdb|2J4G|B Chain B, Bacteroides Thetaiotaomicron Gh84 O-Glcnacase In Complex
With N-Butyl-Thiazoline Inhibitor
Length = 715
Score = 30.0 bits (66), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 7/84 (8%)
Query: 520 QPLISTFQPDAHFGSISENLADSVVKYTKGRTDA------SHVDKFYDMIFYKNLLSLAN 573
+PLI P H ++ + + V+K +GR ++ +HV +FY + S N
Sbjct: 488 KPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQN 547
Query: 574 PGENVGVLAAQSIGEPSTQMTLNT 597
P + GV A + +P T T
Sbjct: 548 PYQ-PGVKTATRVIKPLIDRTFAT 570
>pdb|2CHO|A Chain A, Bacteroides Thetaiotaomicron Hexosaminidase With O-
Glcnacase Activity
pdb|2CHO|B Chain B, Bacteroides Thetaiotaomicron Hexosaminidase With O-
Glcnacase Activity
Length = 716
Score = 30.0 bits (66), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 7/84 (8%)
Query: 520 QPLISTFQPDAHFGSISENLADSVVKYTKGRTDA------SHVDKFYDMIFYKNLLSLAN 573
+PLI P H ++ + + V+K +GR ++ +HV +FY + S N
Sbjct: 489 KPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQN 548
Query: 574 PGENVGVLAAQSIGEPSTQMTLNT 597
P + GV A + +P T T
Sbjct: 549 PYQ-PGVKTATRVIKPLIDRTFAT 571
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 0.136 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,374,642
Number of Sequences: 62578
Number of extensions: 1042353
Number of successful extensions: 2421
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 2298
Number of HSP's gapped (non-prelim): 84
length of query: 1020
length of database: 14,973,337
effective HSP length: 109
effective length of query: 911
effective length of database: 8,152,335
effective search space: 7426777185
effective search space used: 7426777185
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (26.2 bits)