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= 000235
(1815 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 = 1687 bits (4368), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 856/1537 (55%), Positives = 1089/1537 (70%), Gaps = 87/1537 (5%)
Query: 7 YSPAEVA--KVRMVQFGILSPDEIRQMSVVQIEHGETTERG--KPKPGGLSDPRLGTIDR 62
+SP+ V +V VQFGILSP+EIR MSV +IE ET + +P+ GGL DPRLGTIDR
Sbjct: 6 FSPSSVPLRRVEEVQFGILSPEEIRSMSVAKIEFPETMDESGQRPRVGGLLDPRLGTIDR 65
Query: 63 KMKCETCTANMAECPGHFGHLELAKPMFHIGFMKTVLSIMRSVCFNCSKILADEDDHKFK 122
+ KC+TC MA+CPGHFGH+ELAKP+FHIGF+ + I+ VC+NC K+ D + KF
Sbjct: 66 QFKCQTCGETMADCPGHFGHIELAKPVFHIGFLSKIKKILECVCWNCGKLKIDSSNPKFN 125
Query: 123 QALKIRNPKNRLKKILDACKNKTKCEGGDEIDVPGQDGEEP-LKKNKGGCGAQQPKLTIE 181
+ R+PKNRL + + CK K C+ G D P GGCGA QP + +
Sbjct: 126 DTQRYRDPKNRLNAVWNVCKTKMVCDTGLSAGSDNFDLSNPSANMGHGGCGAAQPTIRKD 185
Query: 182 GMKMIAEYKAQRKKNDDQEQLPEPVERKQTLTAERVLGVLKRISDEDCQLLGLNPKYARP 241
G+++ +K + D+ LPE K+ L+ V + IS ED LGLN +YARP
Sbjct: 186 GLRLWGSWK----RGKDESDLPE----KRLLSPLEVHTIFTHISSEDLAHLGLNEQYARP 237
Query: 242 DWMILQVLXXXXX----------XXXXSDDLTHQLAMIIRHNENLRRQERNGAPAHIISE 291
DWMI+ VL DDLTH+L+ II+ N N+RR E+ GAPAHI+SE
Sbjct: 238 DWMIITVLPVPPPSVRPSISVDGTSRGEDDLTHKLSDIIKANANVRRCEQEGAPAHIVSE 297
Query: 292 FAQLLQFHIATYFDNELPGQPRATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSART 351
+ QLLQFH+ATY DNE+ GQP+A Q+SGRP+KSI +RLK KEGR+RGNLMGKRVDFSART
Sbjct: 298 YEQLLQFHVATYMDNEIAGQPQALQKSGRPLKSIRARLKGKEGRLRGNLMGKRVDFSART 357
Query: 352 VITPDPTINIDQLGVPWSIALNLTYPETVTPYNIERLKELVEYGPHPPPGKTGAKYIIRD 411
VIT DP +++D+LGVP SIA LTYPETVTPYNI +L+ELV GP PG AKYIIRD
Sbjct: 358 VITGDPNLSLDELGVPRSIAKTLTYPETVTPYNIYQLQELVRNGPDEHPG---AKYIIRD 414
Query: 412 DGQRLDLRYLKKSSDHHLELGYKVERHLNDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTF 471
G+R+DLRY K++ D L G++VERH+ DGD V+FNRQPSLHKMS+MGHRI++MPYSTF
Sbjct: 415 TGERIDLRYHKRAGDIPLRYGWRVERHIRDGDVVIFNRQPSLHKMSMMGHRIRVMPYSTF 474
Query: 472 RLNLSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGIVQDTL 531
RLNLSVTSPYNADFDGDEMNMHVPQS ETRAE+ E+ MVPK IVSPQSN+PVMGIVQDTL
Sbjct: 475 RLNLSVTSPYNADFDGDEMNMHVPQSEETRAEIQEITMVPKQIVSPQSNKPVMGIVQDTL 534
Query: 532 LGCRKITKRDTFIEKDVFMNILMWWEDFDGKVPQPTILKPRPLWTGKQVFNLIIPKQINL 591
G RK + RD F+ ++ MNI++W D+DG +P P ILKP+ LWTGKQ+ +LIIPK INL
Sbjct: 535 AGVRKFSLRDNFLTRNAVMNIMLWVPDWDGILPPPVILKPKVLWTGKQILSLIIPKGINL 594
Query: 592 FRTAAWHADNDKGILT-AGDTLVRIEKGELLSGTLCKKTLGTSTGSLIHVIWEEVGPDAA 650
R D+DK L+ D+ + IE GE++ G + KKT+G S G L+H IW+E GP+
Sbjct: 595 IR------DDDKQSLSNPTDSGMLIENGEIIYGVVDKKTVGASQGGLVHTIWKEKGPEIC 648
Query: 651 RKFLGHTQWLVNYWLLQNAFSIGIGDTIADAKTMETINDTISKAKNNVKNLIKQAQDKSL 710
+ F Q +VNYWLL N FSIGIGDTIADA TM+ + T+ +A+ V I+ AQ L
Sbjct: 649 KGFFNGIQRVVNYWLLHNGFSIGIGDTIADADTMKEVTRTVKEARRQVAECIQDAQHNRL 708
Query: 711 EPEPGRTMMESFENKVNQVLNTARDEAGSSAQKSLSESNNLKAMVTAGSKGSFINISQMT 770
+PEPG T+ ESFE KV+++LN ARD AG SA+ SL +SNN+K MV AGSKGSFINISQM+
Sbjct: 709 KPEPGMTLRESFEAKVSRILNQARDNAGRSAEHSLKDSNNVKQMVAAGSKGSFINISQMS 768
Query: 771 ACVGQQNVEGKRIPFGFVDRTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGRE 830
ACVGQQ VEGKRIPFGF RTLPHF KDD PESRGF+ENSYLRGLTPQEFFFHAM GRE
Sbjct: 769 ACVGQQIVEGKRIPFGFKYRTLPHFPKDDDSPESRGFIENSYLRGLTPQEFFFHAMAGRE 828
Query: 831 GLIDTAVKTSETGYIQRRLVKAMEDIMVKYDGTVRNSLGDVIQFLYGEDGMDSVWIESQT 890
GLIDTAVKT+ETGYIQRRLVKAMED+MV+YDGTVRN++GD+IQF YGEDG+D+ +E Q
Sbjct: 829 GLIDTAVKTAETGYIQRRLVKAMEDVMVRYDGTVRNAMGDIIQFAYGEDGLDATLVEYQV 888
Query: 891 LDSLKMKKSEFDKAFRFEMDEENWNPNYMLQEYIDDLKTIKELRDVFDAEVQKLEADRYQ 950
DSL++ +F+K +R ++ E+ YM +D ++D+ D E +L ADR
Sbjct: 889 FDSLRLSTKQFEKKYRIDLMEDRSLSLYMENSIEND----SSVQDLLDEEYTQLVADREL 944
Query: 951 LATEIATSGDSSWPLPVNLKRLIWNAQKTFKVDPRRPSDMHPMEVVEAVDKLQERLKVVP 1010
L I GD+ WPLPVN++R+I NA + F ++ ++P+D+ P +++ +++L +L +
Sbjct: 945 LCKFIFPKGDARWPLPVNVQRIIQNALQIFHLEAKKPTDLLPSDIINGLNELIAKLTIFR 1004
Query: 1011 GEDPLSVEAQKNATLFFNILLRSTFASKRVLKEHRLTREAFEWVIGEIESRFLQSLVAPG 1070
G D ++ + Q NATL F ILLRS FA KRV+ E+RL + AFEW++GE+E+RF Q++V+PG
Sbjct: 1005 GSDRITRDVQNNATLLFQILLRSKFAVKRVIMEYRLNKVAFEWIMGEVEARFQQAVVSPG 1064
Query: 1071 EMIGCVAAQSIGEPATQMTLNTFHYAGVSAKNVTLGVPRLREIINVAKKIKTPSLSVFLK 1130
EM+G +AAQSIGEPATQMTLNTFHYAGVS+KNVTLGVPRL+EI+NVAK IKTPSL+++L
Sbjct: 1065 EMVGTLAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEILNVAKNIKTPSLTIYLM 1124
Query: 1131 PGVNSTKERAKNVQCALEYTTLRSVTEATEVWYDPDPMGTIIEEDVEFVKSYYEMPDEDI 1190
P + + + AKNVQ +E+TTL +VT ATE+ YDPDP T+IEED +FV++++ +PDE++
Sbjct: 1125 PWIAANMDLAKNVQTQIEHTTLSTVTSATEIHYDPDPQDTVIEEDKDFVEAFFAIPDEEV 1184
Query: 1191 APE--KISPWLLRIELNREMMVDKKLSMAAVAEKINQEFDDDLTCIFNDDNADKLILRIR 1248
K SPWLLR+EL+R M+DKKLSM+ VA KI + F+ DL I+++DNADKLI+R R
Sbjct: 1185 EENLYKQSPWLLRLELDRAKMLDKKLSMSDVAGKIAESFERDLFTIWSEDNADKLIIRCR 1244
Query: 1249 IMNDEAPKGELNDESAEDDVFLKKIESNMLTEMALRGV---------------------- 1286
I+ D+ K E +D E+DVFLK IE +ML ++LRGV
Sbjct: 1245 IIRDDDRKAEDDDNMIEEDVFLKTIEGHMLESISLRGVPNITRVYMMEHKIVRQIEDGTF 1304
Query: 1287 -------------NLLAVMCHEDVDARRTTSNHLIEIIEVLGIEAVRRALLDELRVVISF 1333
NL M E VDA RT SN +EI+++LGIEA R ALL ELR VI F
Sbjct: 1305 ERADEWVLETDGINLTEAMTVEGVDATRTYSNSFVEILQILGIEATRSALLKELRNVIEF 1364
Query: 1334 DGSYVNYRHLAILCDTMTYRGHLMAITRHGINRNDTGPMMRCSFEETVDILLDAAVFAES 1393
DGSYVNYRHLA+LCD MT RGHLMAITRHGINR +TG +MRCSFEETV+IL+DAA E
Sbjct: 1365 DGSYVNYRHLALLCDVMTSRGHLMAITRHGINRAETGALMRCSFEETVEILMDAAASGEK 1424
Query: 1394 DYLRGVTENIMLGQLAPIGTGDCSLYLNDEMLKN-AIELQLPSYMEGLEFGMTPARSPV- 1451
D +G++ENIMLGQLAP+GTG +YL+ +ML N ++ +P+ GM ++ P
Sbjct: 1425 DDCKGISENIMLGQLAPMGTGAFDIYLDQDMLMNYSLGTAVPTLAGS---GMGTSQLPEG 1481
Query: 1452 SGTPYHDG-MMSPGYLFSPNLRLSPVTDAQFSPYVGG 1487
+GTPY M+ G++ SP+ A FSP V G
Sbjct: 1482 AGTPYERSPMVDSGFVGSPDA-------AAFSPLVQG 1511
>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 = 1533 bits (3968), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 789/1517 (52%), Positives = 1046/1517 (68%), Gaps = 82/1517 (5%)
Query: 7 YSPAEVAKVRMVQFGILSPDEIRQMSVVQIEHGETTE--RGKPKPGGLSDPRLGTIDRKM 64
YS A + V+ VQFG+ SP+E+R +SV +I ET + + + K GGL+DPRLG+IDR +
Sbjct: 6 YSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNL 65
Query: 65 KCETCTANMAECPGHFGHLELAKPMFHIGFMKTVLSIMRSVCFNCSKILADEDDHKFKQA 124
KC+TC M ECPGHFGH++LAKP+FH+GF+ + + VC +C K+L DE + +QA
Sbjct: 66 KCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQA 125
Query: 125 LKIRNPKNRLKKILDACKNKTKCEGGDEIDVPGQDGEEPLKKNKGGCGAQQPKLTIEGMK 184
L I++ K R I CK K CE DVP +D L ++GGCG QP + +G+K
Sbjct: 126 LAIKDSKKRFAAIWTLCKTKMVCE----TDVPSEDDPTQLV-SRGGCGNTQPTIRKDGLK 180
Query: 185 MIAEYKAQRKKNDDQEQLPEPVERKQTLTAERVLGVLKRISDEDCQLLGLNPKYARPDWM 244
++ +K R D E PE + L+ E +L + K IS +D LG N ++RP+WM
Sbjct: 181 LVGSWKKDRATGDADE--PE----LRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWM 234
Query: 245 ILQVLXXXXXXXXXS----------DDLTHQLAMIIRHNENLRRQERNGAPAHIISEFAQ 294
IL L S DDLT +LA I++ N +L E NGAP H I E
Sbjct: 235 ILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAES 294
Query: 295 LLQFHIATYFDNELPGQPRATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSARTVIT 354
LLQFH+ATY DN++ GQP+A Q+SGRP+KSI +RLK KEGRIRGNLMGKRVDFSARTVI+
Sbjct: 295 LLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVIS 354
Query: 355 PDPTINIDQLGVPWSIALNLTYPETVTPYNIERLKELVEYGPHPPPGKTGAKYIIRDDGQ 414
DP + +DQ+GVP SIA LTYPE VTPYNI+RL +LV GP+ PG AKY+IRD G
Sbjct: 355 GDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPG---AKYVIRDSGD 411
Query: 415 RLDLRYLKKSSDHHLELGYKVERHLNDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLN 474
R+DLRY K++ D L+ G+KVERH+ D D VLFNRQPSLHKMS+M HR+K++PYSTFRLN
Sbjct: 412 RIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLN 471
Query: 475 LSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGIVQDTLLGC 534
LSVTSPYNADFDGDEMN+HVPQS ETRAE+ +L VP IVSPQSN+P MGIVQDTL G
Sbjct: 472 LSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGI 531
Query: 535 RKITKRDTFIEKDVFMNILMWWEDFDGKVPQPTILKPRPLWTGKQVFNLIIPKQINLFRT 594
RK+T RDTFIE D +N+L W D+DG +P P I+KP+PLW+GKQ+ ++ IP I+L R
Sbjct: 532 RKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQR- 590
Query: 595 AAWHADNDKGILTAGDTLVRIEKGELLSGTLCKKTLGTSTGSLIHVIWEEVGPDAARKFL 654
D +L+ D + I G+++ G + KKT+G+S G LIHV+ E GP K
Sbjct: 591 ----FDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLF 646
Query: 655 GHTQWLVNYWLLQNAFSIGIGDTIADAKTMETINDTISKAKNNVKNLIKQAQDKSLEPEP 714
G+ Q +VN+WLL N FS GIGDTIAD TM I +TI++AK V ++ K+AQ L +
Sbjct: 647 GNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKH 706
Query: 715 GRTMMESFENKVNQVLNTARDEAGSSAQKSLSESNNLKAMVTAGSKGSFINISQMTACVG 774
G T+ ESFE+ V + LN ARD+AG A+ +L + NN+K MV AGSKGSFINI+QM+ACVG
Sbjct: 707 GMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVG 766
Query: 775 QQNVEGKRIPFGFVDRTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLID 834
QQ+VEGKRI FGFVDRTLPHF+KDDY PES+GFVENSYLRGLTPQEFFFHAMGGREGLID
Sbjct: 767 QQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLID 826
Query: 835 TAVKTSETGYIQRRLVKAMEDIMVKYDGTVRNSLGDVIQFLYGEDGMDSVWIESQTLDSL 894
TAVKT+ETGYIQRRLVKA+EDIMV YD T RNSLG+VIQF+YGEDGMD+ IE Q+LD++
Sbjct: 827 TAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTI 886
Query: 895 KMKKSEFDKAFRFEM--DEENWNPNYML--QEYIDDLKTIKELRDVFDAEVQKLEADRYQ 950
+ F+K +R ++ + +P+ + E + DLK L+ + D E ++L DR +
Sbjct: 887 GGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLK----LQVLLDEEYKQLVKDR-K 941
Query: 951 LATEIATSGDSSWPLPVNLKRLIWNAQKTFKVDPRRPSDMHPMEVVEAVDKLQERLKVVP 1010
E+ G+++WPLPVN++R+I NAQ+TF +D +PSD+ ++V V LQE L V+
Sbjct: 942 FLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLR 1001
Query: 1011 GEDPLSVEAQKNATLFFNILLRSTFASKRVLKEHRLTREAFEWVIGEIESRFLQSLVAPG 1070
G++ + AQ++A F LLRS A++RVL+E+RLT++AF+WV+ IE++FL+S+V PG
Sbjct: 1002 GKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPG 1061
Query: 1071 EMIGCVAAQSIGEPATQMTLNTFHYAGVSAKNVTLGVPRLREIINVAKKIKTPSLSVFLK 1130
EM+G +AAQSIGEPATQMTLNTFH+AGV++K VT GVPRL+EI+NVAK +KTPSL+V+L+
Sbjct: 1062 EMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLE 1121
Query: 1131 PGVNSTKERAKNVQCALEYTTLRSVTEATEVWYDPDPMGTIIEEDVEFVKSYYEMPDEDI 1190
PG + +E+AK ++ A+E+TTL+SVT A+E++YDPDP T+I ED E ++ ++ + DE+
Sbjct: 1122 PGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEA 1181
Query: 1191 --APEKISPWLLRIELNREMMVDKKLSMAAVAEKINQEFDDDLTCIFNDDNADKLILRIR 1248
+ ++ SPWLLR+EL+R M DK L+M V E+I Q F +DL I+++DN +KLI+R R
Sbjct: 1182 EQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCR 1241
Query: 1249 IMNDEAPKGELNDESAEDDVFLKKIESNMLTEMALR------------------------ 1284
++ PK + AE+D LKKIE+ ML + LR
Sbjct: 1242 VVR---PKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEY 1298
Query: 1285 -----------GVNLLAVMCHEDVDARRTTSNHLIEIIEVLGIEAVRRALLDELRVVISF 1333
GVNL VM +D R +N I+I+EVLGIEA R AL E+ VI+
Sbjct: 1299 VKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIAS 1358
Query: 1334 DGSYVNYRHLAILCDTMTYRGHLMAITRHGINRNDTGPMMRCSFEETVDILLDAAVFAES 1393
DGSYVNYRH+A+L D MT +G L ++TRHG NR++TG +MRCSFEETV+IL +A AE
Sbjct: 1359 DGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAEL 1418
Query: 1394 DYLRGVTENIMLGQLAPIGTGDCSLYLNDE-MLKNAIELQLPSYMEGLEFGMTPARSPVS 1452
D RGV+EN++LGQ+APIGTG + +++E ++K E ++ +G + G+TP S S
Sbjct: 1419 DDCRGVSENVILGQMAPIGTGAFDVMIDEESLVKYMPEQKITEIEDGQDGGVTP-YSNES 1477
Query: 1453 GTPYHDGMMSPGYLFSP 1469
G D + +FSP
Sbjct: 1478 GLVNADLDVKDELMFSP 1494
>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 = 1533 bits (3968), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 789/1517 (52%), Positives = 1046/1517 (68%), Gaps = 82/1517 (5%)
Query: 7 YSPAEVAKVRMVQFGILSPDEIRQMSVVQIEHGETTE--RGKPKPGGLSDPRLGTIDRKM 64
YS A + V+ VQFG+ SP+E+R +SV +I ET + + + K GGL+DPRLG+IDR +
Sbjct: 6 YSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNL 65
Query: 65 KCETCTANMAECPGHFGHLELAKPMFHIGFMKTVLSIMRSVCFNCSKILADEDDHKFKQA 124
KC+TC M ECPGHFGH++LAKP+FH+GF+ + + VC +C K+L DE + +QA
Sbjct: 66 KCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQA 125
Query: 125 LKIRNPKNRLKKILDACKNKTKCEGGDEIDVPGQDGEEPLKKNKGGCGAQQPKLTIEGMK 184
L I++ K R I CK K CE DVP +D L ++GGCG QP + +G+K
Sbjct: 126 LAIKDSKKRFAAIWTLCKTKMVCE----TDVPSEDDPTQLV-SRGGCGNTQPTIRKDGLK 180
Query: 185 MIAEYKAQRKKNDDQEQLPEPVERKQTLTAERVLGVLKRISDEDCQLLGLNPKYARPDWM 244
++ +K R D E PE + L+ E +L + K IS +D LG N ++RP+WM
Sbjct: 181 LVGSWKKDRATGDADE--PE----LRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWM 234
Query: 245 ILQVLXXXXXXXXXS----------DDLTHQLAMIIRHNENLRRQERNGAPAHIISEFAQ 294
IL L S DDLT +LA I++ N +L E NGAP H I E
Sbjct: 235 ILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAES 294
Query: 295 LLQFHIATYFDNELPGQPRATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSARTVIT 354
LLQFH+ATY DN++ GQP+A Q+SGRP+KSI +RLK KEGRIRGNLMGKRVDFSARTVI+
Sbjct: 295 LLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVIS 354
Query: 355 PDPTINIDQLGVPWSIALNLTYPETVTPYNIERLKELVEYGPHPPPGKTGAKYIIRDDGQ 414
DP + +DQ+GVP SIA LTYPE VTPYNI+RL +LV GP+ PG AKY+IRD G
Sbjct: 355 GDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPG---AKYVIRDSGD 411
Query: 415 RLDLRYLKKSSDHHLELGYKVERHLNDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLN 474
R+DLRY K++ D L+ G+KVERH+ D D VLFNRQPSLHKMS+M HR+K++PYSTFRLN
Sbjct: 412 RIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLN 471
Query: 475 LSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGIVQDTLLGC 534
LSVTSPYNADFDGDEMN+HVPQS ETRAE+ +L VP IVSPQSN+P MGIVQDTL G
Sbjct: 472 LSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGI 531
Query: 535 RKITKRDTFIEKDVFMNILMWWEDFDGKVPQPTILKPRPLWTGKQVFNLIIPKQINLFRT 594
RK+T RDTFIE D +N+L W D+DG +P P I+KP+PLW+GKQ+ ++ IP I+L R
Sbjct: 532 RKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQR- 590
Query: 595 AAWHADNDKGILTAGDTLVRIEKGELLSGTLCKKTLGTSTGSLIHVIWEEVGPDAARKFL 654
D +L+ D + I G+++ G + KKT+G+S G LIHV+ E GP K
Sbjct: 591 ----FDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLF 646
Query: 655 GHTQWLVNYWLLQNAFSIGIGDTIADAKTMETINDTISKAKNNVKNLIKQAQDKSLEPEP 714
G+ Q +VN+WLL N FS GIGDTIAD TM I +TI++AK V ++ K+AQ L +
Sbjct: 647 GNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKH 706
Query: 715 GRTMMESFENKVNQVLNTARDEAGSSAQKSLSESNNLKAMVTAGSKGSFINISQMTACVG 774
G T+ ESFE+ V + LN ARD+AG A+ +L + NN+K MV AGSKGSFINI+QM+ACVG
Sbjct: 707 GMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVG 766
Query: 775 QQNVEGKRIPFGFVDRTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLID 834
QQ+VEGKRI FGFVDRTLPHF+KDDY PES+GFVENSYLRGLTPQEFFFHAMGGREGLID
Sbjct: 767 QQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLID 826
Query: 835 TAVKTSETGYIQRRLVKAMEDIMVKYDGTVRNSLGDVIQFLYGEDGMDSVWIESQTLDSL 894
TAVKT+ETGYIQRRLVKA+EDIMV YD T RNSLG+VIQF+YGEDGMD+ IE Q+LD++
Sbjct: 827 TAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTI 886
Query: 895 KMKKSEFDKAFRFEM--DEENWNPNYML--QEYIDDLKTIKELRDVFDAEVQKLEADRYQ 950
+ F+K +R ++ + +P+ + E + DLK L+ + D E ++L DR +
Sbjct: 887 GGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLK----LQVLLDEEYKQLVKDR-K 941
Query: 951 LATEIATSGDSSWPLPVNLKRLIWNAQKTFKVDPRRPSDMHPMEVVEAVDKLQERLKVVP 1010
E+ G+++WPLPVN++R+I NAQ+TF +D +PSD+ ++V V LQE L V+
Sbjct: 942 FLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLR 1001
Query: 1011 GEDPLSVEAQKNATLFFNILLRSTFASKRVLKEHRLTREAFEWVIGEIESRFLQSLVAPG 1070
G++ + AQ++A F LLRS A++RVL+E+RLT++AF+WV+ IE++FL+S+V PG
Sbjct: 1002 GKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPG 1061
Query: 1071 EMIGCVAAQSIGEPATQMTLNTFHYAGVSAKNVTLGVPRLREIINVAKKIKTPSLSVFLK 1130
EM+G +AAQSIGEPATQMTLNTFH+AGV++K VT GVPRL+EI+NVAK +KTPSL+V+L+
Sbjct: 1062 EMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLE 1121
Query: 1131 PGVNSTKERAKNVQCALEYTTLRSVTEATEVWYDPDPMGTIIEEDVEFVKSYYEMPDEDI 1190
PG + +E+AK ++ A+E+TTL+SVT A+E++YDPDP T+I ED E ++ ++ + DE+
Sbjct: 1122 PGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEA 1181
Query: 1191 --APEKISPWLLRIELNREMMVDKKLSMAAVAEKINQEFDDDLTCIFNDDNADKLILRIR 1248
+ ++ SPWLLR+EL+R M DK L+M V E+I Q F +DL I+++DN +KLI+R R
Sbjct: 1182 EQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCR 1241
Query: 1249 IMNDEAPKGELNDESAEDDVFLKKIESNMLTEMALR------------------------ 1284
++ PK + AE+D LKKIE+ ML + LR
Sbjct: 1242 VVR---PKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEY 1298
Query: 1285 -----------GVNLLAVMCHEDVDARRTTSNHLIEIIEVLGIEAVRRALLDELRVVISF 1333
GVNL VM +D R +N I+I+EVLGIEA R AL E+ VI+
Sbjct: 1299 VKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIAS 1358
Query: 1334 DGSYVNYRHLAILCDTMTYRGHLMAITRHGINRNDTGPMMRCSFEETVDILLDAAVFAES 1393
DGSYVNYRH+A+L D MT +G L ++TRHG NR++TG +MRCSFEETV+IL +A AE
Sbjct: 1359 DGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAEL 1418
Query: 1394 DYLRGVTENIMLGQLAPIGTGDCSLYLNDE-MLKNAIELQLPSYMEGLEFGMTPARSPVS 1452
D RGV+EN++LGQ+APIGTG + +++E ++K E ++ +G + G+TP S S
Sbjct: 1419 DDCRGVSENVILGQMAPIGTGAFDVMIDEESLVKYMPEQKITEIEDGQDGGVTP-YSNES 1477
Query: 1453 GTPYHDGMMSPGYLFSP 1469
G D + +FSP
Sbjct: 1478 GLVNADLDVKDELMFSP 1494
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 1455
Score = 1528 bits (3955), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 777/1472 (52%), Positives = 1025/1472 (69%), Gaps = 80/1472 (5%)
Query: 7 YSPAEVAKVRMVQFGILSPDEIRQMSVVQIEHGETTE--RGKPKPGGLSDPRLGTIDRKM 64
YS A + V+ VQFG+ SP+E+R +SV +I ET + + + K GGL+DPRLG+IDR +
Sbjct: 6 YSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNL 65
Query: 65 KCETCTANMAECPGHFGHLELAKPMFHIGFMKTVLSIMRSVCFNCSKILADEDDHKFKQA 124
KC+TC M ECPGHFGH++LAKP+FH+GF+ + + VC +C K+L DE + +QA
Sbjct: 66 KCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQA 125
Query: 125 LKIRNPKNRLKKILDACKNKTKCEGGDEIDVPGQDGEEPLKKNKGGCGAQQPKLTIEGMK 184
L I++ K R I CK K CE DVP +D L ++GGCG QP + +G+K
Sbjct: 126 LAIKDSKKRFAAIWTLCKTKMVCE----TDVPSEDDPTQLV-SRGGCGNTQPTIRKDGLK 180
Query: 185 MIAEYKAQRKKNDDQEQLPEPVERKQTLTAERVLGVLKRISDEDCQLLGLNPKYARPDWM 244
++ +K R D E PE + L+ E +L + K IS +D LG N ++RP+WM
Sbjct: 181 LVGSWKKDRATGDADE--PE----LRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWM 234
Query: 245 ILQVLXXXXXXXXXS----------DDLTHQLAMIIRHNENLRRQERNGAPAHIISEFAQ 294
IL L S DDLT +LA I++ N +L E NGAP H I E
Sbjct: 235 ILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAES 294
Query: 295 LLQFHIATYFDNELPGQPRATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSARTVIT 354
LLQFH+ATY DN++ GQP+A Q+SGRP+KSI +RLK KEGRIRGNLMGKRVDFSARTVI+
Sbjct: 295 LLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVIS 354
Query: 355 PDPTINIDQLGVPWSIALNLTYPETVTPYNIERLKELVEYGPHPPPGKTGAKYIIRDDGQ 414
DP + +DQ+GVP SIA LTYPE VTPYNI+RL +LV GP+ PG AKY+IRD G
Sbjct: 355 GDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPG---AKYVIRDSGD 411
Query: 415 RLDLRYLKKSSDHHLELGYKVERHLNDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLN 474
R+DLRY K++ D L+ G+KVERH+ D D VLFNRQPSLHKMS+M HR+K++PYSTFRLN
Sbjct: 412 RIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLN 471
Query: 475 LSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGIVQDTLLGC 534
LSVTSPYNADFDGDEMN+HVPQS ETRAE+ +L VP IVSPQSN+P MGIVQDTL G
Sbjct: 472 LSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGI 531
Query: 535 RKITKRDTFIEKDVFMNILMWWEDFDGKVPQPTILKPRPLWTGKQVFNLIIPKQINLFRT 594
RK+T RDTFIE D +N+L W D+DG +P P I+KP+PLW+GKQ+ ++ IP I+L R
Sbjct: 532 RKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQR- 590
Query: 595 AAWHADNDKGILTAGDTLVRIEKGELLSGTLCKKTLGTSTGSLIHVIWEEVGPDAARKFL 654
D +L+ D + I G+++ G + KKT+G+S G LIHV+ E GP K
Sbjct: 591 ----FDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLF 646
Query: 655 GHTQWLVNYWLLQNAFSIGIGDTIADAKTMETINDTISKAKNNVKNLIKQAQDKSLEPEP 714
G+ Q +VN+WLL N FS GIGDTIAD TM I +TI++AK V ++ K+AQ L +
Sbjct: 647 GNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKH 706
Query: 715 GRTMMESFENKVNQVLNTARDEAGSSAQKSLSESNNLKAMVTAGSKGSFINISQMTACVG 774
G T+ ESFE+ V + LN ARD+AG A+ +L + NN+K MV AGSKGSFINI+QM+ACVG
Sbjct: 707 GMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVG 766
Query: 775 QQNVEGKRIPFGFVDRTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLID 834
QQ+VEGKRI FGFVDRTLPHF+KDDY PES+GFVENSYLRGLTPQEFFFHAMGGREGLID
Sbjct: 767 QQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLID 826
Query: 835 TAVKTSETGYIQRRLVKAMEDIMVKYDGTVRNSLGDVIQFLYGEDGMDSVWIESQTLDSL 894
TAVKT+ETGYIQRRLVKA+EDIMV YD T RNSLG+VIQF+YGEDGMD+ IE Q+LD++
Sbjct: 827 TAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTI 886
Query: 895 KMKKSEFDKAFRFEM--DEENWNPNYML--QEYIDDLKTIKELRDVFDAEVQKLEADRYQ 950
+ F+K +R ++ + +P+ + E + DLK L+ + D E ++L DR +
Sbjct: 887 GGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLK----LQVLLDEEYKQLVKDR-K 941
Query: 951 LATEIATSGDSSWPLPVNLKRLIWNAQKTFKVDPRRPSDMHPMEVVEAVDKLQERLKVVP 1010
E+ G+++WPLPVN++R+I NAQ+TF +D +PSD+ ++V V LQE L V+
Sbjct: 942 FLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLR 1001
Query: 1011 GEDPLSVEAQKNATLFFNILLRSTFASKRVLKEHRLTREAFEWVIGEIESRFLQSLVAPG 1070
G++ + AQ++A F LLRS A++RVL+E+RLT++AF+WV+ IE++FL+S+V PG
Sbjct: 1002 GKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPG 1061
Query: 1071 EMIGCVAAQSIGEPATQMTLNTFHYAGVSAKNVTLGVPRLREIINVAKKIKTPSLSVFLK 1130
EM+G +AAQSIGEPATQMTLNTFH+AGV++K VT GVPRL+EI+NVAK +KTPSL+V+L+
Sbjct: 1062 EMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLE 1121
Query: 1131 PGVNSTKERAKNVQCALEYTTLRSVTEATEVWYDPDPMGTIIEEDVEFVKSYYEMPDEDI 1190
PG + +E+AK ++ A+E+TTL+SVT A+E++YDPDP T+I ED E ++ ++ + DE+
Sbjct: 1122 PGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEA 1181
Query: 1191 --APEKISPWLLRIELNREMMVDKKLSMAAVAEKINQEFDDDLTCIFNDDNADKLILRIR 1248
+ ++ SPWLLR+EL+R M DK L+M V E+I Q F +DL I+++DN +KLI+R R
Sbjct: 1182 EQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCR 1241
Query: 1249 IMNDEAPKGELNDESAEDDVFLKKIESNMLTEMALR------------------------ 1284
++ PK + AE+D LKKIE+ ML + LR
Sbjct: 1242 VVR---PKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEY 1298
Query: 1285 -----------GVNLLAVMCHEDVDARRTTSNHLIEIIEVLGIEAVRRALLDELRVVISF 1333
GVNL VM +D R +N I+I+EVLGIEA R AL E+ VI+
Sbjct: 1299 VKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIAS 1358
Query: 1334 DGSYVNYRHLAILCDTMTYRGHLMAITRHGINRNDTGPMMRCSFEETVDILLDAAVFAES 1393
DGSYVNYRH+A+L D MT +G L ++TRHG NR++TG +MRCSFEETV+IL +A AE
Sbjct: 1359 DGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAEL 1418
Query: 1394 DYLRGVTENIMLGQLAPIGTGDCSLYLNDEML 1425
D RGV+EN++LGQ+APIGTG + +++E L
Sbjct: 1419 DDCRGVSENVILGQMAPIGTGAFDVMIDEESL 1450
>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 = 659 bits (1700), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 374/890 (42%), Positives = 520/890 (58%), Gaps = 63/890 (7%)
Query: 15 VRMVQFGILSPDEIRQMSVVQIEHGETT-ERGKPKPGGLSDPRLGTIDRKMKCETCTANM 73
++ ++FGILSPDEIR+MSV I + E G P G + DPRLG I+ KC TC +
Sbjct: 6 IKGIKFGILSPDEIRKMSVTAIITPDVYDEDGTPIEGSVMDPRLGVIEPGQKCPTCGNTL 65
Query: 74 AECPGHFGHLELAKPMFHIGFMKTVLSIMRSVCFNCSKILADEDD----HKFKQALKIRN 129
CPGHFGH+EL +P+ H+GF+K V +++ C C ++ ED+ + A+K R
Sbjct: 66 GNCPGHFGHIELVRPVIHVGFVKHVYEFLKATCRRCGRVKISEDEIEKYSRIYNAIKKRW 125
Query: 130 PK--NRLKKILDACKNKTK-CEGGDEIDVPGQDGEEPLKKNKGGCGAQQPKLTIEGMKMI 186
P RL + + K + C CG +Q K+ +E
Sbjct: 126 PSAARRLTEYVKKTAMKAQVCPH---------------------CGEKQFKIKLE----- 159
Query: 187 AEYKAQRKKNDDQEQLPEPVERKQTLTAERVLGVLKRISDEDCQLLGLNPKYARPDWMIL 246
K + E+ E V + LT + L+++ + D ++LG +P +RP+WMIL
Sbjct: 160 -------KPYNFYEERKEGVAK---LTPSDIRERLEKVPESDVEILGYDPTTSRPEWMIL 209
Query: 247 QVLXXXXXXXXXS----------DDLTHQLAMIIRHNENLRRQERNGAPAHIISEFAQLL 296
VL S DDLTH+L I+R NE L+ GAP II + LL
Sbjct: 210 TVLPVPPITIRPSIMIESGIRAEDDLTHKLVDIVRINERLKESIDAGAPQLIIEDLWDLL 269
Query: 297 QFHIATYFDNELPGQPRATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSARTVITPD 356
Q+H+ATYFDNE+PG P + RSGRP++++ RLK KEGR RGNL GKRVDFS+RTVI+PD
Sbjct: 270 QYHVATYFDNEIPGLPPSKHRSGRPLRTLAQRLKGKEGRFRGNLSGKRVDFSSRTVISPD 329
Query: 357 PTINIDQLGVPWSIALNLTYPETVTPYNIERLKELVEYGPHPPPGKTGAKYIIRDDGQRL 416
P I+ID++GVP IA LT PE +TP+NIE+L++ V GP PG A Y+IR DG+R+
Sbjct: 330 PNISIDEVGVPEIIARTLTVPERITPWNIEKLRQFVINGPDKWPG---ANYVIRPDGRRI 386
Query: 417 DLRYLK--KSSDHHLELGYKVERHLNDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLN 474
DLRY+K K L GY VERHL DGD VLFNRQPSLH++S+M HR++++ TFRLN
Sbjct: 387 DLRYVKDRKELASTLAPGYVVERHLTDGDVVLFNRQPSLHRISMMAHRVRVLKGLTFRLN 446
Query: 475 LSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGIVQDTLLGC 534
L V PYNADFDGDEMN+HVPQS E AE E+M+V K I++P+ P++G QD + G
Sbjct: 447 LLVCPPYNADFDGDEMNLHVPQSEEAIAEAKEIMLVHKNIITPRYGGPIIGAAQDYISGA 506
Query: 535 RKITKRDTFIEKDVFMNILMWWEDFDGKVPQPTILKPRPLWTGKQVFNLIIPKQINLFRT 594
+T + T + K+ IL D + +P IL PR +TGKQV + +PK N
Sbjct: 507 YLLTVKTTLLTKEEAQQIL-GVADVKIDLGEPAILAPREYYTGKQVVSAFLPKDFNFHGQ 565
Query: 595 AAWHADND--KGILTAGDTLVRIEKGELLSGTLCKKTLGTSTG-SLIHVIWEEVGPDAAR 651
A + K D+ V I+ G LL G KK +G S++H + +E + +
Sbjct: 566 ANVSSGPRLCKNEDCPHDSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDEYGK 625
Query: 652 KFLGHTQWLVNYWLLQNAFSIGIGDTIADAKTMETINDTISKAKNNVKNLIKQAQDKSLE 711
+ + + ++ F++ + D + I + I +AK V NLI++ ++ LE
Sbjct: 626 WLMDNLFRVFIRFVELQGFTMRLEDVSLGDDVKKEIYNEIDRAKVEVDNLIQKYKNGELE 685
Query: 712 PEPGRTMMESFENKVNQVLNTARDEAGSSAQKSLSESNNLKAMVTAGSKGSFINISQMTA 771
P PGRT+ ES EN + L+ R AG A K L N M G++GS +NI+QM A
Sbjct: 686 PIPGRTLEESLENYILDTLDKLRSTAGDIASKYLDPFNFAYVMARTGARGSVLNITQMAA 745
Query: 772 CVGQQNVEGKRIPFGFVDRTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREG 831
+GQQ+V G+RI G++ RTLPHF D PE+RGF+ +S+ GL P E FFHA GGREG
Sbjct: 746 MLGQQSVRGERIKRGYMTRTLPHFKPYDISPEARGFIYSSFRTGLKPTELFFHAAGGREG 805
Query: 832 LIDTAVKTSETGYIQRRLVKAMEDIMVKYDGTVRNSLGDVIQFLYGEDGM 881
L+DTAV+TS++GY+QRRL+ A+ D+ +YDGTVR+ G+VIQ YG+DG+
Sbjct: 806 LVDTAVRTSQSGYMQRRLINALSDLRAEYDGTVRSLYGEVIQVAYGDDGV 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 = 655 bits (1689), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 371/890 (41%), Positives = 518/890 (58%), Gaps = 63/890 (7%)
Query: 15 VRMVQFGILSPDEIRQMSVVQIEHGETT-ERGKPKPGGLSDPRLGTIDRKMKCETCTANM 73
++ ++FGILSPDEIR+MSV I + E G P G + DPRLG I+ KC TC +
Sbjct: 6 IKGIKFGILSPDEIRKMSVTAIITPDVYDEDGTPIEGSVMDPRLGVIEPGQKCPTCGNTL 65
Query: 74 AECPGHFGHLELAKPMFHIGFMKTVLSIMRSVCFNCSKILADEDD----HKFKQALKIRN 129
CPGHFGH+EL +P+ H+G +K + +++ C C ++ ED+ + A+K R
Sbjct: 66 GNCPGHFGHIELVRPVIHVGLVKHIYEFLKATCRRCGRVKISEDEIEKYSRIYNAIKKRW 125
Query: 130 PK--NRLKKILDACKNKTK-CEGGDEIDVPGQDGEEPLKKNKGGCGAQQPKLTIEGMKMI 186
P RL + + K + C C +Q K+ +E
Sbjct: 126 PSAARRLTEYVKKTAMKAQVCPH---------------------CNEKQYKIKLE----- 159
Query: 187 AEYKAQRKKNDDQEQLPEPVERKQTLTAERVLGVLKRISDEDCQLLGLNPKYARPDWMIL 246
K + E+ E V + LT + L++I D D ++LG +P +RP+WMIL
Sbjct: 160 -------KPYNFYEERKEGVAK---LTPSDIRERLEKIPDSDVEILGYDPTTSRPEWMIL 209
Query: 247 QVLXXXXXXXXXS----------DDLTHQLAMIIRHNENLRRQERNGAPAHIISEFAQLL 296
VL S DDLTH+L I+R NE L+ GAP II + LL
Sbjct: 210 TVLPVPPITIRPSIMIESGIRAEDDLTHKLVDIVRINERLKESIDAGAPQLIIEDLWDLL 269
Query: 297 QFHIATYFDNELPGQPRATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSARTVITPD 356
Q+H+ATYFDNE+PG P + RSGRP++++ RLK KEGR RGNL GKRVDFS+RTVI+PD
Sbjct: 270 QYHVATYFDNEIPGLPPSKHRSGRPLRTLAQRLKGKEGRFRGNLSGKRVDFSSRTVISPD 329
Query: 357 PTINIDQLGVPWSIALNLTYPETVTPYNIERLKELVEYGPHPPPGKTGAKYIIRDDGQRL 416
P I+ID++GVP IA LT PE +TP+NIE+L++ V GP PG A Y+IR DG+R+
Sbjct: 330 PNISIDEVGVPEIIAKTLTVPERITPWNIEKLRQFVINGPDKWPG---ANYVIRPDGRRI 386
Query: 417 DLRYLK--KSSDHHLELGYKVERHLNDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLN 474
DLRY+K K L GY +ERHL DGD VLFNRQPSLH++S+M HR++++ TFRLN
Sbjct: 387 DLRYVKDRKELASTLAPGYIIERHLIDGDIVLFNRQPSLHRISMMAHRVRVLKGLTFRLN 446
Query: 475 LSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGIVQDTLLGC 534
L V PYNADFDGDEMN+HVPQS E AE E+M+V K I++P+ P++G QD + G
Sbjct: 447 LLVCPPYNADFDGDEMNLHVPQSEEAIAEAKEIMLVHKNIITPRYGGPIIGAAQDYISGA 506
Query: 535 RKITKRDTFIEKDVFMNILMWWEDFDGKVPQPTILKPRPLWTGKQVFNLIIPKQINLFRT 594
+T + T + K+ IL D + +P IL PR +TGKQV + +PK N
Sbjct: 507 YLLTVKTTLLTKEEAQQIL-GVADVKIDLGEPAILAPREYYTGKQVISAFLPKDFNFHGQ 565
Query: 595 AAWHADND--KGILTAGDTLVRIEKGELLSGTLCKKTLGTSTG-SLIHVIWEEVGPDAAR 651
A + K D+ V I+ G LL G KK +G S++H + +E + +
Sbjct: 566 ANVSSGPRLCKNEDCPHDSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDEYGK 625
Query: 652 KFLGHTQWLVNYWLLQNAFSIGIGDTIADAKTMETINDTISKAKNNVKNLIKQAQDKSLE 711
+ + + ++ F++ + D + I + I +AK V NLI++ ++ LE
Sbjct: 626 WLMDNLFRVFIRFVELQGFTMRLEDVSLGDDVKKEIYNEIDRAKVEVDNLIQKYKNGELE 685
Query: 712 PEPGRTMMESFENKVNQVLNTARDEAGSSAQKSLSESNNLKAMVTAGSKGSFINISQMTA 771
P PGRT+ ES EN + L+ R AG A K L N M G++GS +NI+QM A
Sbjct: 686 PIPGRTLEESLENYILDTLDKLRSTAGDIASKYLDPFNFAYVMARTGARGSVLNITQMAA 745
Query: 772 CVGQQNVEGKRIPFGFVDRTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREG 831
+GQQ+V G+RI G++ RTLPHF D PE+RGF+ +S+ GL P E FFHA GGREG
Sbjct: 746 MLGQQSVRGERIKRGYMTRTLPHFKPYDISPEARGFIYSSFRTGLKPTELFFHAAGGREG 805
Query: 832 LIDTAVKTSETGYIQRRLVKAMEDIMVKYDGTVRNSLGDVIQFLYGEDGM 881
L+DTAV+TS++GY+QRRL+ A+ D+ +YDGTVR+ G+V+Q YG+DG+
Sbjct: 806 LVDTAVRTSQSGYMQRRLINALSDLRAEYDGTVRSLYGEVVQVAYGDDGV 855
>pdb|3QQC|A Chain A, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP
CLAMP DOMAIN
Length = 436
Score = 223 bits (568), Expect = 8e-58, Method: Compositional matrix adjust.
Identities = 128/336 (38%), Positives = 183/336 (54%), Gaps = 40/336 (11%)
Query: 18 VQFGILSPDEIRQMSVVQIEHGET-TERGKPKPGGLSDPRLGTIDRKMKCETCTANMAEC 76
++FGILSP EIR+MS V++ +T + G P GG+ D R+G ID ++CETC EC
Sbjct: 72 IEFGILSPQEIRKMSAVEVTVPDTYDDDGYPIEGGVMDKRMGVIDPGLRCETCGGRAGEC 131
Query: 77 PGHFGHLELAKPMFHIGFMKTVLSIMRSVCFNCSKI-LADEDDHKFKQALKI-RNPKNRL 134
PGHFGH+ELA+P+ H+GF KT+ I+ S C C +I L DE+ ++ + +++ RN ++
Sbjct: 132 PGHFGHIELARPVIHVGFAKTIYRILESTCRECGRIKLTDEEIEEYMKKIELARNRRSEF 191
Query: 135 KKILDACKNKTKCEGGDEIDVPGQDGEEPLKKNKGGCGAQQPKLTIEGMKMIAEYKAQRK 194
+I+ K K + + P CGA Q + E + E + +
Sbjct: 192 NEIIKEIHKKAK----ERMVCPH-------------CGAPQYPIKFEKPTIYWEIRKDEQ 234
Query: 195 KNDDQEQLPEPVERKQTLTAERVLGVLKRISDEDCQLLGLNPKYARPDWMILQVLXXXXX 254
N E + L V L++I D+D LLGL+P+ +RP+WM+L VL
Sbjct: 235 GN----------EYRHRLMPTEVRDWLEKIPDKDLPLLGLDPEKSRPEWMVLTVLPVPPV 284
Query: 255 XXXXS----------DDLTHQLAMIIRHNENLRRQERNGAPAHIISEFAQLLQFHIATYF 304
S DDLTH+L IIR N L++ GAP II + LLQ+H+ TY
Sbjct: 285 TARPSITLETGIRAEDDLTHKLVDIIRINNRLKQNIEAGAPQLIIEDLWDLLQYHVTTYI 344
Query: 305 DNELPGQPRATQRSGRPIKSICSRLKAKEGRIRGNL 340
+NE PG P A +SGRP+K++ RLK KEGR RGNL
Sbjct: 345 NNEAPGVPPAKHKSGRPLKTLAQRLKGKEGRFRGNL 380
Score = 35.8 bits (81), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 23/36 (63%)
Query: 1372 MMRCSFEETVDILLDAAVFAESDYLRGVTENIMLGQ 1407
+ R +FE TV L +AA E D L GV EN+++GQ
Sbjct: 394 LARAAFEITVQHLFEAAEKGEVDNLNGVIENVLIGQ 429
>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 = 183 bits (464), Expect = 8e-46, Method: Compositional matrix adjust.
Identities = 133/392 (33%), Positives = 206/392 (52%), Gaps = 35/392 (8%)
Query: 1031 LRSTFASKRVLKEHRLTREAFEWVIGEIESRFLQSLVAPGEMIGCVAAQSIGEPATQMTL 1090
L++ ++K VL + F+ I E + + L+APGE IG VAAQS+GEP TQMTL
Sbjct: 32 LKNLISNKEVLVTRDEIDKIFDLAIKE----YSEGLIAPGEAIGIVAAQSVGEPGTQMTL 87
Query: 1091 NTFHYAGVSAKNVTLGVPRLREIINVAKKIKTPSLSVFLKPGVNSTKERAKNVQCALEYT 1150
TFH+AG+ NVTLG+PRL EI++ K TP ++++L KE+A V LEYT
Sbjct: 88 RTFHFAGIRELNVTLGLPRLIEIVDAKKVPSTPMMTIYLTDEYKHDKEKALEVARKLEYT 147
Query: 1151 TLRSVTEATEVWYDPDPMGTIIEEDVEFVKSYYEMPDEDIAPEKISPWLLRIELNREMMV 1210
+ +V +T + D M I++ D E +K D+ + + + + R++L E ++
Sbjct: 148 KIENVVSSTSI--DIASMSIILQLDNEMLK------DKGVTVDDVKKAINRLKLG-EFVI 198
Query: 1211 DKKLSMAAVAEKINQEFD--DDLTCIFNDDNADKLILRIRIMNDEAPKGELNDESAEDDV 1268
D+ + +N F D + +F LR +I+N + KG + A V
Sbjct: 199 DE-----SEGNTLNISFANIDSIAALFK--------LRDKILNTKI-KGIKGIKRA--IV 242
Query: 1269 FLKKIESNMLTEMALRGVNLLAVMCHEDVDARRTTSNHLIEIIEVLGIEAVRRALLDELR 1328
K E +LT+ G NL V+ + VD + +N++ EI EV GIEA R ++ E+
Sbjct: 243 QKKGDEYIILTD----GSNLSGVLSVKGVDIAKVETNNIREIEEVFGIEAAREIIIREIS 298
Query: 1329 VVISFDGSYVNYRHLAILCDTMTYRGHLMAITRHGINRNDTGPMMRCSFEETVDILLDAA 1388
V++ G V+ RH+ ++ D MT G + I RHG+ + R +FE TV LLDAA
Sbjct: 299 KVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVTVKHLLDAA 358
Query: 1389 VFAESDYLRGVTENIMLGQLAPIGTGDCSLYL 1420
+ + +GV ENI++G +GTG L +
Sbjct: 359 ARGDVEEFKGVVENIIIGHPIKLGTGMVELTM 390
>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 = 183 bits (464), Expect = 8e-46, Method: Compositional matrix adjust.
Identities = 133/392 (33%), Positives = 206/392 (52%), Gaps = 35/392 (8%)
Query: 1031 LRSTFASKRVLKEHRLTREAFEWVIGEIESRFLQSLVAPGEMIGCVAAQSIGEPATQMTL 1090
L++ ++K VL + F+ I E + + L+APGE IG VAAQS+GEP TQMTL
Sbjct: 32 LKNLISNKEVLVTRDEIDKIFDLAIKE----YSEGLIAPGEAIGIVAAQSVGEPGTQMTL 87
Query: 1091 NTFHYAGVSAKNVTLGVPRLREIINVAKKIKTPSLSVFLKPGVNSTKERAKNVQCALEYT 1150
TFH+AG+ NVTLG+PRL EI++ K TP ++++L KE+A V LEYT
Sbjct: 88 RTFHFAGIRELNVTLGLPRLIEIVDAKKVPSTPMMTIYLTDEYKHDKEKALEVARKLEYT 147
Query: 1151 TLRSVTEATEVWYDPDPMGTIIEEDVEFVKSYYEMPDEDIAPEKISPWLLRIELNREMMV 1210
+ +V +T + D M I++ D E +K D+ + + + + R++L E ++
Sbjct: 148 KIENVVSSTSI--DIASMSIILQLDNEMLK------DKGVTVDDVKKAINRLKLG-EFVI 198
Query: 1211 DKKLSMAAVAEKINQEFD--DDLTCIFNDDNADKLILRIRIMNDEAPKGELNDESAEDDV 1268
D+ + +N F D + +F LR +I+N + KG + A V
Sbjct: 199 DE-----SEGTTLNISFANIDSIAALFK--------LRDKILNTKI-KGIKGIKRA--IV 242
Query: 1269 FLKKIESNMLTEMALRGVNLLAVMCHEDVDARRTTSNHLIEIIEVLGIEAVRRALLDELR 1328
K E +LT+ G NL V+ + VD + +N++ EI EV GIEA R ++ E+
Sbjct: 243 QKKGDEYIILTD----GSNLSGVLSVKGVDIAKVETNNIREIEEVFGIEAAREIIIREIS 298
Query: 1329 VVISFDGSYVNYRHLAILCDTMTYRGHLMAITRHGINRNDTGPMMRCSFEETVDILLDAA 1388
V++ G V+ RH+ ++ D MT G + I RHG+ + R +FE TV LLDAA
Sbjct: 299 KVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVTVKHLLDAA 358
Query: 1389 VFAESDYLRGVTENIMLGQLAPIGTGDCSLYL 1420
+ + +GV ENI++G +GTG L +
Sbjct: 359 ARGDVEEFKGVVENIIIGHPIKLGTGMVELTM 390
>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 = 181 bits (459), Expect = 3e-45, Method: Compositional matrix adjust.
Identities = 128/379 (33%), Positives = 199/379 (52%), Gaps = 27/379 (7%)
Query: 1042 KEHRLTREAFEWVIGEIESRFLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHYAGVSAK 1101
KE +TR+ + + + + L+APGE IG VAAQS+GEP TQMTL TFH+AG+
Sbjct: 39 KEIIVTRDEIDKIFDLAIKEYSEGLIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIREL 98
Query: 1102 NVTLGVPRLREIINVAKKIKTPSLSVFLKPGVNSTKERAKNVQCALEYTTLRSVTEATEV 1161
NVTLG+PRL EI++ K TP ++++L +++A V LEYT + +V +T +
Sbjct: 99 NVTLGLPRLIEIVDAKKVPSTPMMTIYLTDEYKRDRDKALEVARKLEYTKIENVVSSTSI 158
Query: 1162 WYDPDPMGTIIEEDVEFVKSYYEMPDEDIAPEKISPWLLRIELNREMMVDKKLSMAAVAE 1221
D M I++ D E +K D+ + + + + R++L M+ + + S
Sbjct: 159 --DIASMSIILQLDNEMLK------DKGVTVDDVKKAIGRLKLGDFMIEESEDSTL---- 206
Query: 1222 KINQEFDDDLTCIFNDDNADKLILRIRIMNDEAPKGELNDESAEDDVFLKKIESNMLTEM 1281
IN D + +F LR +I+N + KG + A V K E +LT+
Sbjct: 207 NINFANIDSIAALFK--------LRDKILNTKI-KGIKGIKRA--IVQKKGDEYIILTD- 254
Query: 1282 ALRGVNLLAVMCHEDVDARRTTSNHLIEIIEVLGIEAVRRALLDELRVVISFDGSYVNYR 1341
G NL V+ + VD + +N++ EI EV GIEA R ++ E+ V++ G V+ R
Sbjct: 255 ---GSNLSGVLSVKGVDVAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDIR 311
Query: 1342 HLAILCDTMTYRGHLMAITRHGINRNDTGPMMRCSFEETVDILLDAAVFAESDYLRGVTE 1401
H+ ++ D MT G + I RHG+ + R +FE TV LLDAA + + +GV E
Sbjct: 312 HILLIADVMTRTGIVRQIGRHGVTGEKNSVLARAAFEVTVKHLLDAAARGDVEEFKGVVE 371
Query: 1402 NIMLGQLAPIGTGDCSLYL 1420
NI++G +GTG L +
Sbjct: 372 NIIIGHPIKLGTGMVELTM 390
>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 = 181 bits (458), Expect = 4e-45, Method: Compositional matrix adjust.
Identities = 128/379 (33%), Positives = 199/379 (52%), Gaps = 27/379 (7%)
Query: 1042 KEHRLTREAFEWVIGEIESRFLQSLVAPGEMIGCVAAQSIGEPATQMTLNTFHYAGVSAK 1101
KE +TR+ + + + + L+APGE IG VAAQS+GEP TQMTL TFH+AG+
Sbjct: 36 KEIIVTRDEIDKIFDLAIKEYSEGLIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIREL 95
Query: 1102 NVTLGVPRLREIINVAKKIKTPSLSVFLKPGVNSTKERAKNVQCALEYTTLRSVTEATEV 1161
NVTLG+PRL EI++ K TP ++++L +++A V LEYT + +V +T +
Sbjct: 96 NVTLGLPRLIEIVDAKKVPSTPMMTIYLTDEYKRDRDKALEVARKLEYTKIENVVSSTSI 155
Query: 1162 WYDPDPMGTIIEEDVEFVKSYYEMPDEDIAPEKISPWLLRIELNREMMVDKKLSMAAVAE 1221
D M I++ D E +K D+ + + + + R++L M+ + + S
Sbjct: 156 --DIASMSIILQLDNEMLK------DKGVTVDDVKKAIGRLKLGDFMIEESEDSTL---- 203
Query: 1222 KINQEFDDDLTCIFNDDNADKLILRIRIMNDEAPKGELNDESAEDDVFLKKIESNMLTEM 1281
IN D + +F LR +I+N + KG + A V K E +LT+
Sbjct: 204 NINFANIDSIAALFK--------LRDKILNTKI-KGIKGIKRA--IVQKKGDEYIILTD- 251
Query: 1282 ALRGVNLLAVMCHEDVDARRTTSNHLIEIIEVLGIEAVRRALLDELRVVISFDGSYVNYR 1341
G NL V+ + VD + +N++ EI EV GIEA R ++ E+ V++ G V+ R
Sbjct: 252 ---GSNLSGVLSVKGVDVAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDIR 308
Query: 1342 HLAILCDTMTYRGHLMAITRHGINRNDTGPMMRCSFEETVDILLDAAVFAESDYLRGVTE 1401
H+ ++ D MT G + I RHG+ + R +FE TV LLDAA + + +GV E
Sbjct: 309 HILLIADVMTRTGIVRQIGRHGVTGEKNSVLARAAFEVTVKHLLDAAARGDVEEFKGVVE 368
Query: 1402 NIMLGQLAPIGTGDCSLYL 1420
NI++G +GTG L +
Sbjct: 369 NIIIGHPIKLGTGMVELTM 387
>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 1413
Score = 176 bits (447), Expect = 8e-44, Method: Compositional matrix adjust.
Identities = 223/926 (24%), Positives = 362/926 (39%), Gaps = 215/926 (23%)
Query: 18 VQFGILSPDEIRQMSVVQIEHGETT--ERGKPKPGGLSDPRL-GTID------------- 61
++ + SPD IR S +++ ET KP+ GL R+ G +
Sbjct: 20 IKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLK 79
Query: 62 -RKMKCETCTANMAECP---GHFGHLELAKPMFHIGFMKTVLS------------IMRSV 105
R + CE C + + GH+ELA P HI F+K++ S I R +
Sbjct: 80 HRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVL 139
Query: 106 CFNCSKILADEDDHKFKQALKIRNPKNRLKKILDACKNKTKCEGGDEIDVPGQDGEEPLK 165
F ++ + +Q + ++ LDA + E GDE D
Sbjct: 140 YFESYVVIEGGMTNLERQQILTE------EQYLDALE-----EFGDEFDAK--------- 179
Query: 166 KNKGGCGAQQPKLTIEGMKMIAEYKAQRKKNDDQEQLPEPVERKQTLTAERVLGVLKRIS 225
GA+ + ++ M + E EQL E + + T + L KRI
Sbjct: 180 -----MGAEAIQALLKSMDLEQEC----------EQLREELNETNSETKRKKL--TKRIK 222
Query: 226 DEDCQLLGLNPKYARPDWMILQVLXXX----------XXXXXXSDDLTHQLAMIIRHNEN 275
+ + N +P+WMIL VL + DL +I N
Sbjct: 223 LLEAFVQSGN----KPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNR 278
Query: 276 LRRQERNGAPAHIISEFAQLLQFHIATYFDNELPGQPRATQRSGRPIKSICSRLKAKEGR 335
L+R AP I+ ++LQ + DN G+ T + RP+KS+ +K K+GR
Sbjct: 279 LKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRA-ITGSNKRPLKSLADMIKGKQGR 337
Query: 336 IRGNLMGKRVDFSARTVITPDPTINIDQLGVPWSIALNLTYPETVTPYNIERLKELVEYG 395
R NL+GKRVD+S R+VIT P + + Q G+P +AL L P + L +
Sbjct: 338 FRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTI--- 394
Query: 396 PHPPPGKTGAKYIIRDDGQRLDLRYLKKSSDHHLELGYKVERHLNDGDFVLFNRQPSLHK 455
K K + R++ D+ L + H VL NR P+LH+
Sbjct: 395 ------KAAKKMVEREEAVVWDI------------LDEVIREHP-----VLLNRAPTLHR 431
Query: 456 MSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIV 515
+ I ++ +L+ V + YNADFDGD+M +HVP + E + E LMM I+
Sbjct: 432 LGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNIL 491
Query: 516 SPQSNRPVMGIVQDTLLGCRKITKRDTF-------------------------IEKDVFM 550
SP + P++ QD +LG +T RD + V +
Sbjct: 492 SPANGEPIIVPSQDVVLGLYYMT-RDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKV 550
Query: 551 NILMWWEDFDGKVPQPTILKPRPLWTGKQVFNLIIPKQINLFRTAAWHADNDKGILTAGD 610
I + +D +G++ T LK + G+ + +I+PK +
Sbjct: 551 RITEYEKDANGELVAKTSLKDTTV--GRAILWMIVPKGLPY------------------- 589
Query: 611 TLVRIEKGELLSGTLCKKTLGTSTGSLIHVIWEEVGPDAARKFLGHTQWLVNYWLLQNAF 670
+++ L KK + +++ + +G F + + ++
Sbjct: 590 --------SIVNQALGKKAI----SKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGA 637
Query: 671 SIGIGDTIADAKTMETINDTISKAKNNVKNLIKQAQDKSLEPEPGRTMMESFENKVNQVL 730
S+GI D + K E IS+A+ V + +Q Q + T E + NKV +
Sbjct: 638 SVGIDDMVIPEKKHE----IISEAEAEVAEIQEQFQSGLV------TAGERY-NKVIDIW 686
Query: 731 NTARDEAGSSAQKSLSES---------------NNLKAMVTAGSKGSFINISQMTACVGQ 775
A D + +L N++ M +G++GS I Q+ G
Sbjct: 687 AAANDRVSKAMMDNLQTETVINRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLA---GM 743
Query: 776 QNVEGKRIPFGFVDRTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDT 835
+ + K P G + T P + F E GL ++F G R+GL DT
Sbjct: 744 RGLMAK--PDGSIIET----------PITANFRE-----GLNVLQYFISTHGARKGLADT 786
Query: 836 AVKTSETGYIQRRLVKAMEDIMVKYD 861
A+KT+ +GY+ RRLV +D++V D
Sbjct: 787 ALKTANSGYLTRRLVDVAQDLVVTED 812
Score = 53.5 bits (127), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 40/160 (25%), Positives = 68/160 (42%), Gaps = 44/160 (27%)
Query: 1309 EIIEVLGIEAVRRALLDELRVVISFDGSYVNYRHLAILCDTM------------------ 1350
+I+ + G+ AV R +++E++ V G +N +H+ ++ M
Sbjct: 1219 DILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGE 1278
Query: 1351 ----------------------TYRGHLMAITRHGINRNDTGPMMRCSFEETVDILLDAA 1388
TY L+ IT+ + + SF+ET +L +AA
Sbjct: 1279 QVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESF--ISAASFQETTRVLTEAA 1336
Query: 1389 VFAESDYLRGVTENIMLGQLAPIGTGDCSLYLNDEMLKNA 1428
V + D LRG+ EN+++G+L P GTG Y D M + A
Sbjct: 1337 VAGKRDELRGLKENVIVGRLIPAGTGYA--YHQDRMRRRA 1374
Score = 47.8 bits (112), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 19/32 (59%), Positives = 24/32 (75%)
Query: 1066 LVAPGEMIGCVAAQSIGEPATQMTLNTFHYAG 1097
++ GE IG +AAQSIGEP TQ+T+ TFH G
Sbjct: 908 IINKGEAIGVIAAQSIGEPGTQLTMRTFHIGG 939
>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 = 176 bits (447), Expect = 8e-44, Method: Compositional matrix adjust.
Identities = 223/926 (24%), Positives = 362/926 (39%), Gaps = 215/926 (23%)
Query: 18 VQFGILSPDEIRQMSVVQIEHGETT--ERGKPKPGGLSDPRL-GTID------------- 61
++ + SPD IR S +++ ET KP+ GL R+ G +
Sbjct: 20 IKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLK 79
Query: 62 -RKMKCETCTANMAECP---GHFGHLELAKPMFHIGFMKTVLS------------IMRSV 105
R + CE C + + GH+ELA P HI F+K++ S I R +
Sbjct: 80 HRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVL 139
Query: 106 CFNCSKILADEDDHKFKQALKIRNPKNRLKKILDACKNKTKCEGGDEIDVPGQDGEEPLK 165
F ++ + +Q + ++ LDA + E GDE D
Sbjct: 140 YFESYVVIEGGMTNLERQQILTE------EQYLDALE-----EFGDEFDAK--------- 179
Query: 166 KNKGGCGAQQPKLTIEGMKMIAEYKAQRKKNDDQEQLPEPVERKQTLTAERVLGVLKRIS 225
GA+ + ++ M + E EQL E + + T + L KRI
Sbjct: 180 -----MGAEAIQALLKSMDLEQEC----------EQLREELNETNSETKRKKL--TKRIK 222
Query: 226 DEDCQLLGLNPKYARPDWMILQVLXXX----------XXXXXXSDDLTHQLAMIIRHNEN 275
+ + N +P+WMIL VL + DL +I N
Sbjct: 223 LLEAFVQSGN----KPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNR 278
Query: 276 LRRQERNGAPAHIISEFAQLLQFHIATYFDNELPGQPRATQRSGRPIKSICSRLKAKEGR 335
L+R AP I+ ++LQ + DN G+ T + RP+KS+ +K K+GR
Sbjct: 279 LKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRA-ITGSNKRPLKSLADMIKGKQGR 337
Query: 336 IRGNLMGKRVDFSARTVITPDPTINIDQLGVPWSIALNLTYPETVTPYNIERLKELVEYG 395
R NL+GKRVD+S R+VIT P + + Q G+P +AL L P + L +
Sbjct: 338 FRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTI--- 394
Query: 396 PHPPPGKTGAKYIIRDDGQRLDLRYLKKSSDHHLELGYKVERHLNDGDFVLFNRQPSLHK 455
K K + R++ D+ L + H VL NR P+LH+
Sbjct: 395 ------KAAKKMVEREEAVVWDI------------LDEVIREHP-----VLLNRAPTLHR 431
Query: 456 MSIMGHRIKIMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIV 515
+ I ++ +L+ V + YNADFDGD+M +HVP + E + E LMM I+
Sbjct: 432 LGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNIL 491
Query: 516 SPQSNRPVMGIVQDTLLGCRKITKRDTF-------------------------IEKDVFM 550
SP + P++ QD +LG +T RD + V +
Sbjct: 492 SPANGEPIIVPSQDVVLGLYYMT-RDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKV 550
Query: 551 NILMWWEDFDGKVPQPTILKPRPLWTGKQVFNLIIPKQINLFRTAAWHADNDKGILTAGD 610
I + +D +G++ T LK + G+ + +I+PK +
Sbjct: 551 RITEYEKDANGELVAKTSLKDTTV--GRAILWMIVPKGLPY------------------- 589
Query: 611 TLVRIEKGELLSGTLCKKTLGTSTGSLIHVIWEEVGPDAARKFLGHTQWLVNYWLLQNAF 670
+++ L KK + +++ + +G F + + ++
Sbjct: 590 --------SIVNQALGKKAI----SKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGA 637
Query: 671 SIGIGDTIADAKTMETINDTISKAKNNVKNLIKQAQDKSLEPEPGRTMMESFENKVNQVL 730
S+GI D + K E IS+A+ V + +Q Q + T E + NKV +
Sbjct: 638 SVGIDDMVIPEKKHE----IISEAEAEVAEIQEQFQSGLV------TAGERY-NKVIDIW 686
Query: 731 NTARDEAGSSAQKSLSES---------------NNLKAMVTAGSKGSFINISQMTACVGQ 775
A D + +L N++ M +G++GS I Q+ G
Sbjct: 687 AAANDRVSKAMMDNLQTETVINRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLA---GM 743
Query: 776 QNVEGKRIPFGFVDRTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDT 835
+ + K P G + T P + F E GL ++F G R+GL DT
Sbjct: 744 RGLMAK--PDGSIIET----------PITANFRE-----GLNVLQYFISTHGARKGLADT 786
Query: 836 AVKTSETGYIQRRLVKAMEDIMVKYD 861
A+KT+ +GY+ RRLV +D++V D
Sbjct: 787 ALKTANSGYLTRRLVDVAQDLVVTED 812
Score = 53.5 bits (127), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 40/160 (25%), Positives = 68/160 (42%), Gaps = 44/160 (27%)
Query: 1309 EIIEVLGIEAVRRALLDELRVVISFDGSYVNYRHLAILCDTM------------------ 1350
+I+ + G+ AV R +++E++ V G +N +H+ ++ M
Sbjct: 1219 DILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGE 1278
Query: 1351 ----------------------TYRGHLMAITRHGINRNDTGPMMRCSFEETVDILLDAA 1388
TY L+ IT+ + + SF+ET +L +AA
Sbjct: 1279 QVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESF--ISAASFQETTRVLTEAA 1336
Query: 1389 VFAESDYLRGVTENIMLGQLAPIGTGDCSLYLNDEMLKNA 1428
V + D LRG+ EN+++G+L P GTG Y D M + A
Sbjct: 1337 VAGKRDELRGLKENVIVGRLIPAGTGYA--YHQDRMRRRA 1374
Score = 47.8 bits (112), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 19/32 (59%), Positives = 24/32 (75%)
Query: 1066 LVAPGEMIGCVAAQSIGEPATQMTLNTFHYAG 1097
++ GE IG +AAQSIGEP TQ+T+ TFH G
Sbjct: 908 IINKGEAIGVIAAQSIGEPGTQLTMRTFHIGG 939
>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For
Structural Studies
Length = 1233
Score = 164 bits (414), Expect = 5e-40, Method: Compositional matrix adjust.
Identities = 157/658 (23%), Positives = 276/658 (41%), Gaps = 95/658 (14%)
Query: 240 RPDWMILQV----------LXXXXXXXXXSDDLTHQLAMIIRHNENLRRQERNGAPAHII 289
RP+WMIL+ + + DL +I N L++ GAP II
Sbjct: 217 RPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIII 276
Query: 290 SEFAQLLQFHIATYFDNELPGQPRATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSA 349
++LQ + DN G P S RP++S+ L K+GR R NL+GKRVD+S
Sbjct: 277 RNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGKRVDYSG 336
Query: 350 RTVITPDPTINIDQLGVPWSIALNLTYPETVTPYNIERLKELVEYGPHPPPGKTGAKYII 409
R+VI P + + Q G+P +AL L P+ +++++E + P+ +
Sbjct: 337 RSVIVVGPQLKLHQCGLPKRMALEL-----FKPFLLKKMEEKA-FAPNVKAAR------- 383
Query: 410 RDDGQRLDLRYLKKSSDHHLELGYKVERHLNDGDFVLFNRQPSLHKMSIMGHRIKIMPYS 469
R L++ D E+ +E ++ G VL NR P+LH++ I + ++
Sbjct: 384 ---------RMLERQRDIKDEVWDALEEVIH-GKVVLLNRAPTLHRLGIQAFQPVLVEGQ 433
Query: 470 TFRLNLSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGIVQD 529
+ +L+ V +NADFDGD+M +HVP S +AE M+ ++SP S P+ +D
Sbjct: 434 SIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRD 493
Query: 530 TLLGCRKIT-----KRDTFIEKDVFMNILMWWEDFDGKVPQPTILKPRPLWTGKQVFNLI 584
+LG IT K+ + L +E + + P ++ R G+ F
Sbjct: 494 IILGLYYITQVRKEKKGAGMAFATPEEALAAYERGEVALNAPIVVAGRETSVGRLKFVFA 553
Query: 585 IPKQINLFRTAAWHADND-KGILTAGDTLVRIEK--GELLSGTLCKKTLG---------- 631
P + L A H D + ++T R+E G +L + + +G
Sbjct: 554 NPDEALL---AVAHGLLDLQDVVTVRYLGRRLETSPGRILFARIVGEAVGDEKVAQELIQ 610
Query: 632 -------TSTGSLIHVIWEEVGPDAARKFLGHTQWLVNYWLLQNAFSIGIGDTIADAKTM 684
S L++ + +G + + L ++ + +IGI D + +
Sbjct: 611 MDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTLSTTSGITIGIDDAVIPEEKQ 670
Query: 685 ETINDTISKAKNNVKNLIKQAQDKSLEPEPGRTMMESFENKVNQVLNTARDEAGSSAQKS 744
+ + K + I+QA + + R ++V Q+ ++ + K+
Sbjct: 671 RYLEEADRKLRQ-----IEQAYEMGFLTDRERY------DQVIQLWTETTEKVTQAVFKN 719
Query: 745 LSES---NNLKAMVTAGSKGSFINISQMTACVGQQNVEGKRIPFGFVDRTLPHFTKDDYG 801
E+ N L M +G++G+ I Q+ G + G
Sbjct: 720 FEENYPFNPLYVMAQSGARGNPQQIRQLCGMRG--------------------LMQKPSG 759
Query: 802 PESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVK 859
V +S+ GLT E+F + G R+G DTA++T+++GY+ R+LV +I+V+
Sbjct: 760 ETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVAHEIVVR 817
Score = 55.5 bits (132), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 25/53 (47%), Positives = 37/53 (69%), Gaps = 1/53 (1%)
Query: 1067 VAPGEMIGCVAAQSIGEPATQMTLNTFHYAGVS-AKNVTLGVPRLREIINVAK 1118
V+ GE +G VAA+SIGEP TQ+T+ TFH GV+ ++T G+PR+ E+ +
Sbjct: 924 VSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELFEARR 976
Score = 47.8 bits (112), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 35/146 (23%), Positives = 62/146 (42%), Gaps = 42/146 (28%)
Query: 1309 EIIEVLGIEAVRRALLDELRVVISFDGSYVNYRHLAILCDTM------------------ 1350
+++E G EAV R L+DE++ V G ++ +H+ I+ M
Sbjct: 1043 QLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSRLLEGQ 1102
Query: 1351 ----------------------TYRGHLMAITRHGINRNDTGPMMRCSFEETVDILLDAA 1388
++ LM +T+ ++ + SF+ T +L +AA
Sbjct: 1103 VLEKWDVEALNERLIAEGKVPVAWKPLLMGVTKSALSTKSW--LSAASFQNTTHVLTEAA 1160
Query: 1389 VFAESDYLRGVTENIMLGQLAPIGTG 1414
+ + D L G+ EN++LG+L P GTG
Sbjct: 1161 IAGKKDELIGLKENVILGRLIPAGTG 1186
Score = 40.8 bits (94), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 34/107 (31%), Positives = 47/107 (43%), Gaps = 20/107 (18%)
Query: 14 KVRMVQFGILSPDEIRQMSVVQIEHGETTERG--KPKPGGLSDPRL-----------GTI 60
+VR V+ + SP++IR S ++E ET KP+ GL D R+ G
Sbjct: 4 EVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKY 63
Query: 61 DRKM----KCETCTANMAEC---PGHFGHLELAKPMFHIGFMKTVLS 100
R+ CE C + GH+ELA P HI F+K V S
Sbjct: 64 KRQRFEGKVCERCGVEVTRSIVRRYRMGHIELATPAAHIWFVKDVPS 110
>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 = 163 bits (413), Expect = 7e-40, Method: Compositional matrix adjust.
Identities = 157/658 (23%), Positives = 276/658 (41%), Gaps = 95/658 (14%)
Query: 240 RPDWMILQV----------LXXXXXXXXXSDDLTHQLAMIIRHNENLRRQERNGAPAHII 289
RP+WMIL+ + + DL +I N L++ GAP II
Sbjct: 508 RPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIII 567
Query: 290 SEFAQLLQFHIATYFDNELPGQPRATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSA 349
++LQ + DN G P S RP++S+ L K+GR R NL+GKRVD+S
Sbjct: 568 RNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGKRVDYSG 627
Query: 350 RTVITPDPTINIDQLGVPWSIALNLTYPETVTPYNIERLKELVEYGPHPPPGKTGAKYII 409
R+VI P + + Q G+P +AL L P+ +++++E + P+ +
Sbjct: 628 RSVIVVGPQLKLHQCGLPKRMALEL-----FKPFLLKKMEEKA-FAPNVKAAR------- 674
Query: 410 RDDGQRLDLRYLKKSSDHHLELGYKVERHLNDGDFVLFNRQPSLHKMSIMGHRIKIMPYS 469
R L++ D E+ +E ++ G VL NR P+LH++ I + ++
Sbjct: 675 ---------RMLERQRDIKDEVWDALEEVIH-GKVVLLNRAPTLHRLGIQAFQPVLVEGQ 724
Query: 470 TFRLNLSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGIVQD 529
+ +L+ V +NADFDGD+M +HVP S +AE M+ ++SP S P+ +D
Sbjct: 725 SIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRD 784
Query: 530 TLLGCRKIT-----KRDTFIEKDVFMNILMWWEDFDGKVPQPTILKPRPLWTGKQVFNLI 584
+LG IT K+ + L +E + + P ++ R G+ F
Sbjct: 785 IILGLYYITQVRKEKKGAGMAFATPEEALAAYERGEVALNAPIVVAGRETSVGRLKFVFA 844
Query: 585 IPKQINLFRTAAWHADND-KGILTAGDTLVRIEK--GELLSGTLCKKTLG---------- 631
P + L A H D + ++T R+E G +L + + +G
Sbjct: 845 NPDEALL---AVAHGLLDLQDVVTVRYLGRRLETSPGRILFARIVGEAVGDEKVAQELIQ 901
Query: 632 -------TSTGSLIHVIWEEVGPDAARKFLGHTQWLVNYWLLQNAFSIGIGDTIADAKTM 684
S L++ + +G + + L ++ + +IGI D + +
Sbjct: 902 MDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTLSTTSGITIGIDDAVIPEEKQ 961
Query: 685 ETINDTISKAKNNVKNLIKQAQDKSLEPEPGRTMMESFENKVNQVLNTARDEAGSSAQKS 744
+ + K + I+QA + + R ++V Q+ ++ + K+
Sbjct: 962 RYLEEADRKLRQ-----IEQAYEMGFLTDRERY------DQVIQLWTETTEKVTQAVFKN 1010
Query: 745 LSES---NNLKAMVTAGSKGSFINISQMTACVGQQNVEGKRIPFGFVDRTLPHFTKDDYG 801
E+ N L M +G++G+ I Q+ G + G
Sbjct: 1011 FEENYPFNPLYVMAQSGARGNPQQIRQLCGMRG--------------------LMQKPSG 1050
Query: 802 PESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDIMVK 859
V +S+ GLT E+F + G R+G DTA++T+++GY+ R+LV +I+V+
Sbjct: 1051 ETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVAHEIVVR 1108
Score = 55.5 bits (132), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 25/53 (47%), Positives = 37/53 (69%), Gaps = 1/53 (1%)
Query: 1067 VAPGEMIGCVAAQSIGEPATQMTLNTFHYAGVS-AKNVTLGVPRLREIINVAK 1118
V+ GE +G VAA+SIGEP TQ+T+ TFH GV+ ++T G+PR+ E+ +
Sbjct: 1215 VSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELFEARR 1267
Score = 47.8 bits (112), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 35/146 (23%), Positives = 62/146 (42%), Gaps = 42/146 (28%)
Query: 1309 EIIEVLGIEAVRRALLDELRVVISFDGSYVNYRHLAILCDTM------------------ 1350
+++E G EAV R L+DE++ V G ++ +H+ I+ M
Sbjct: 1334 QLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSRLLEGQ 1393
Query: 1351 ----------------------TYRGHLMAITRHGINRNDTGPMMRCSFEETVDILLDAA 1388
++ LM +T+ ++ + SF+ T +L +AA
Sbjct: 1394 VLEKWDVEALNERLIAEGKVPVAWKPLLMGVTKSALSTKSW--LSAASFQNTTHVLTEAA 1451
Query: 1389 VFAESDYLRGVTENIMLGQLAPIGTG 1414
+ + D L G+ EN++LG+L P GTG
Sbjct: 1452 IAGKKDELIGLKENVILGRLIPAGTG 1477
Score = 40.8 bits (94), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 34/107 (31%), Positives = 47/107 (43%), Gaps = 20/107 (18%)
Query: 14 KVRMVQFGILSPDEIRQMSVVQIEHGETTERG--KPKPGGLSDPRL-----------GTI 60
+VR V+ + SP++IR S ++E ET KP+ GL D R+ G
Sbjct: 4 EVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKY 63
Query: 61 DRKM----KCETCTANMAEC---PGHFGHLELAKPMFHIGFMKTVLS 100
R+ CE C + GH+ELA P HI F+K V S
Sbjct: 64 KRQRFEGKVCERCGVEVTRSIVRRYRMGHIELATPAAHIWFVKDVPS 110
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1264
Score = 163 bits (412), Expect = 9e-40, Method: Compositional matrix adjust.
Identities = 158/663 (23%), Positives = 276/663 (41%), Gaps = 105/663 (15%)
Query: 240 RPDWMILQV----------LXXXXXXXXXSDDLTHQLAMIIRHNENLRRQERNGAPAHII 289
RP+WMIL+ + + DL +I N L++ GAP II
Sbjct: 248 RPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIII 307
Query: 290 SEFAQLLQFHIATYFDNELPGQPRATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSA 349
++LQ + DN G P S RP++S+ L K+GR R NL+GKRVD+S
Sbjct: 308 RNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGKRVDYSG 367
Query: 350 RTVITPDPTINIDQLGVPWSIALNLTYPETVTPYNIERLKELVEYGPHPPPGKTGAKYII 409
R+VI P + + Q G+P +AL L P+ +++++E + P+ +
Sbjct: 368 RSVIVVGPQLKLHQCGLPKRMALEL-----FKPFLLKKMEEKA-FAPNVKAAR------- 414
Query: 410 RDDGQRLDLRYLKKSSDHHLELGYKVERHLNDGDFVLFNRQPSLHKMSIMGHRIKIMPYS 469
R L++ D E+ +E ++ G VL NR P+LH++ I + ++
Sbjct: 415 ---------RMLERQRDIKDEVWDALEEVIH-GKVVLLNRAPTLHRLGIQAFQPVLVEGQ 464
Query: 470 TFRLNLSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGIVQD 529
+ +L+ V +NADFDGD+M +HVP S +AE M+ ++SP S P+ +D
Sbjct: 465 SIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRD 524
Query: 530 TLLGCRKIT-----KRDTFIEKDVFMNILMWWEDFDGKVPQPTILKPRPLWTGKQVFNLI 584
+LG IT K+ + L +E + + P ++ R G+ F
Sbjct: 525 IILGLYYITQVRKEKKGAGMAFATPEEALAAYERGEVALNAPIVVAGRETSVGRLKFVFA 584
Query: 585 IPKQINLFRTAAWHADNDKGILTAGDTLV------RIEK--GELLSGTLCKKTLG----- 631
P + L A H G+L DT+ R+E G +L + + +G
Sbjct: 585 NPDEALL---AVAH-----GLLDLQDTVTTRYLGRRLETSPGRILFARIVGEAVGDEKVA 636
Query: 632 ------------TSTGSLIHVIWEEVGPDAARKFLGHTQWLVNYWLLQNAFSIGIGDTIA 679
S L++ + +G + + L ++ + +IGI D +
Sbjct: 637 QELIQMDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTLSTTSGITIGIDDAVI 696
Query: 680 DAKTMETINDTISKAKNNVKNLIKQAQDKSLEPEPGRTMMESFENKVNQVLNTARDEAGS 739
+ + + K + I+QA + + R ++V Q+ ++
Sbjct: 697 PEEKQRYLEEADRKLRQ-----IEQAYEMGFLTDRERY------DQVIQLWTETTEKVTQ 745
Query: 740 SAQKSLSES---NNLKAMVTAGSKGSFINISQMTACVGQQNVEGKRIPFGFVDRTLPHFT 796
+ + E+ N L M +G++G+ I Q+ G
Sbjct: 746 AVFNNFEENYPFNPLYVMAQSGARGNPQQIRQLCGMRG--------------------LM 785
Query: 797 KDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDI 856
+ G V +S+ GLT E+F + G R+G DTA++T+++GY+ R+LV +I
Sbjct: 786 QKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVAHEI 845
Query: 857 MVK 859
+V+
Sbjct: 846 VVR 848
Score = 55.5 bits (132), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 25/53 (47%), Positives = 37/53 (69%), Gaps = 1/53 (1%)
Query: 1067 VAPGEMIGCVAAQSIGEPATQMTLNTFHYAGVS-AKNVTLGVPRLREIINVAK 1118
V+ GE +G VAA+SIGEP TQ+T+ TFH GV+ ++T G+PR+ E+ +
Sbjct: 955 VSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELFEARR 1007
Score = 47.8 bits (112), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 35/146 (23%), Positives = 62/146 (42%), Gaps = 42/146 (28%)
Query: 1309 EIIEVLGIEAVRRALLDELRVVISFDGSYVNYRHLAILCDTM------------------ 1350
+++E G EAV R L+DE++ V G ++ +H+ I+ M
Sbjct: 1074 QLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSRLLEGQ 1133
Query: 1351 ----------------------TYRGHLMAITRHGINRNDTGPMMRCSFEETVDILLDAA 1388
++ LM +T+ ++ + SF+ T +L +AA
Sbjct: 1134 VLEKWDVEALNERLIAEGKVPVAWKPLLMGVTKSALSTKSW--LSAASFQNTTHVLTEAA 1191
Query: 1389 VFAESDYLRGVTENIMLGQLAPIGTG 1414
+ + D L G+ EN++LG+L P GTG
Sbjct: 1192 IAGKKDELIGLKENVILGRLIPAGTG 1217
Score = 39.3 bits (90), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 33/107 (30%), Positives = 46/107 (42%), Gaps = 20/107 (18%)
Query: 14 KVRMVQFGILSPDEIRQMSVVQIEHGETTERG--KPKPGGLSDPRL-----------GTI 60
+VR V+ + SP++IR S ++E ET KP+ GL D R+ G
Sbjct: 4 EVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKY 63
Query: 61 DRKM----KCETCTANMAEC---PGHFGHLELAKPMFHIGFMKTVLS 100
R+ CE C + H+ELA P HI F+K V S
Sbjct: 64 KRQRFEAKVCERCAVEVTRSIVRRYRMAHIELATPAAHIWFVKDVPS 110
>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 = 160 bits (406), Expect = 4e-39, Method: Compositional matrix adjust.
Identities = 162/663 (24%), Positives = 279/663 (42%), Gaps = 104/663 (15%)
Query: 240 RPDWMILQV----------LXXXXXXXXXSDDLTHQLAMIIRHNENLRRQERNGAPAHII 289
RP+WMIL+ + + DL +I N L++ GAP II
Sbjct: 248 RPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIII 307
Query: 290 SEFAQLLQFHIATYFDNELPGQPRATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSA 349
++LQ + DN G P S RP++S+ L K+GR R NL+GKRVD+S
Sbjct: 308 RNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQNLLGKRVDYSG 367
Query: 350 RTVITPDPTINIDQLGVPWSIALNLTYPETVTPYNIERLKELVEYGPHPPPGKTGAKYII 409
R+VI P + + Q G+P +AL L P+ +++++E + P+ +
Sbjct: 368 RSVIVVGPQLKLHQCGLPKRMALEL-----FKPFLLKKMEEKA-FAPNVKAAR------- 414
Query: 410 RDDGQRLDLRYLKKSSDHHLELGYKVERHLNDGDFVLFNRQPSLHKMSIMGHRIKIMPYS 469
R L++ D E+ +E ++ G VL NR P+LH++ I + ++
Sbjct: 415 ---------RMLERQRDIKDEVWDALEEVIH-GKVVLLNRAPTLHRLGIQAFQPVLVEGQ 464
Query: 470 TFRLNLSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGIVQD 529
+ +L+ V +NADFDGD+M +HVP S +AE M+ ++SP S P+ +D
Sbjct: 465 SIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRD 524
Query: 530 TLLGCRKIT-----KRDTFIEKDVFMNILMWWEDFDGKVPQPTILKPRPLWTGKQVFNLI 584
+LG IT K+ + L +E + + P ++ R G+ F
Sbjct: 525 IILGLYYITQVRKEKKGAGMAFATPEEALAAYERGEVALNAPIVVAGRETSVGRLKFVFA 584
Query: 585 IPKQINLFRTAAWHADNDKGILTAGDTLV------RIEK--GELLSGTLCKKTLG----- 631
P + L A H G+L DT+ R+E G +L + + +G
Sbjct: 585 NPDEALL---AVAH-----GLLDLQDTVTTRYLGRRLETNPGRILFARIVGEAVGDEKVA 636
Query: 632 ------------TSTGSLIHVIWEEVGPDAARKFLGHTQWLVNYWLLQNAFSIGIGDTIA 679
S L++ + +G + + L ++ + L + I IG I
Sbjct: 637 QELIQMDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYY-GFTLSTTSGIITIG--ID 693
Query: 680 DAKTMETINDTISKAKNNVKNLIKQAQDKSLEPEPGRTMMESFENKVNQVLNTARDEAGS 739
DA E + +A ++ I+QA + + R ++V Q+ ++
Sbjct: 694 DAVIPEEKQRYLEEADRKLRQ-IEQAYEMGFLTDRERY------DQVIQLWTETTEKVTQ 746
Query: 740 SAQKSLSES---NNLKAMVTAGSKGSFINISQMTACVGQQNVEGKRIPFGFVDRTLPHFT 796
+ + E+ N L M +G++G+ I Q+ G
Sbjct: 747 AVFNNFEENYPFNPLYVMAQSGARGNPQQIRQLCGMRG--------------------LM 786
Query: 797 KDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRLVKAMEDI 856
+ G V +S+ GLT E+F + G R+G DTA++T+++GY+ R+LV +I
Sbjct: 787 QKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVAHEI 846
Query: 857 MVK 859
+V+
Sbjct: 847 VVR 849
Score = 55.5 bits (132), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 25/53 (47%), Positives = 37/53 (69%), Gaps = 1/53 (1%)
Query: 1067 VAPGEMIGCVAAQSIGEPATQMTLNTFHYAGVS-AKNVTLGVPRLREIINVAK 1118
V+ GE +G VAA+SIGEP TQ+T+ TFH GV+ ++T G+PR+ E+ +
Sbjct: 956 VSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELFEARR 1008
Score = 47.8 bits (112), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 35/146 (23%), Positives = 62/146 (42%), Gaps = 42/146 (28%)
Query: 1309 EIIEVLGIEAVRRALLDELRVVISFDGSYVNYRHLAILCDTM------------------ 1350
+++E G EAV R L+DE++ V G ++ +H+ I+ M
Sbjct: 1075 QLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSPLLEGQ 1134
Query: 1351 ----------------------TYRGHLMAITRHGINRNDTGPMMRCSFEETVDILLDAA 1388
++ LM +T+ ++ + SF+ T +L +AA
Sbjct: 1135 VLEKWDVEALNERLIAEGKVPVAWKPLLMGVTKSALSTKSW--LSAASFQNTTHVLTEAA 1192
Query: 1389 VFAESDYLRGVTENIMLGQLAPIGTG 1414
+ + D L G+ EN++LG+L P GTG
Sbjct: 1193 IAGKKDELIGLKENVILGRLIPAGTG 1218
Score = 40.8 bits (94), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 34/107 (31%), Positives = 47/107 (43%), Gaps = 20/107 (18%)
Query: 14 KVRMVQFGILSPDEIRQMSVVQIEHGETTERG--KPKPGGLSDPRL-----------GTI 60
+VR V+ + SP++IR S ++E ET KP+ GL D R+ G
Sbjct: 4 EVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKY 63
Query: 61 DRKM----KCETCTANMAEC---PGHFGHLELAKPMFHIGFMKTVLS 100
R+ CE C + GH+ELA P HI F+K V S
Sbjct: 64 KRQRFEGKVCERCGVEVTRSIVRRYRMGHIELATPAAHIWFVKDVPS 110
>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 = 158 bits (399), Expect = 3e-38, Method: Compositional matrix adjust.
Identities = 166/670 (24%), Positives = 276/670 (41%), Gaps = 119/670 (17%)
Query: 240 RPDWMILQV----------LXXXXXXXXXSDDLTHQLAMIIRHNENLRRQERNGAPAHII 289
RP+WMIL+ + + DL +I N L++ GAP II
Sbjct: 508 RPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIII 567
Query: 290 SEFAQLLQFHIATYFDNELPGQPRATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSA 349
++LQ + DN G P S RP++S+ L K+GR R NL+GKRVD+S
Sbjct: 568 RNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSG 627
Query: 350 RTVITPDPTINIDQLGVPWSIALNLTYPETVTPYNIERLKELVEYGPHPPPGKTGAKYII 409
R+VI P + + Q G+P +AL L P LK++ E G P
Sbjct: 628 RSVIVVGPQLKLHQCGLPKRMALELFKPFL--------LKKMEEKGIAP----------- 668
Query: 410 RDDGQRLDLRYLKKSSDHHLELGYKVERHLNDGDFVLFNRQPSLHKMSIMGHRIKIMPYS 469
+ R L++ D E+ +E ++ G VL NR P+LH++ I + ++
Sbjct: 669 ---NVKAARRMLERQRDIKDEVWDALEEVIH-GKVVLLNRAPTLHRLGIQAFQPVLVEGQ 724
Query: 470 TFRLNLSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGIVQD 529
+ +L+ V +NADFDGD+M +HVP S +AE M+ ++SP S P+ +D
Sbjct: 725 SIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRD 784
Query: 530 TLLGCRKIT-----KRDTFIEKDVFMNILMWWEDFDGKVPQPTILKPRPLWTG--KQVFN 582
+LG IT K+ +E L E + + P + R G K VF
Sbjct: 785 IILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVF- 843
Query: 583 LIIPKQINLFRTAAWHADNDKGILTAGDTLVRIEKGELLSGTLCKKTLGTSTGSLI---- 638
A+ D+ +L +V ++ ++++ K L TS G ++
Sbjct: 844 ----------------ANPDEALLAVAHGIVDLQ--DVVTVRYMGKRLETSPGRILFARI 885
Query: 639 --------HVIWEEVGPDAAR-----KFLGHTQWL-------------VNYWLLQNAFSI 672
V WE + D + K L + +L + Y+ + +
Sbjct: 886 VAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTS 945
Query: 673 GIGDTIADAKTMETINDTISKAKNNVKNLIKQAQDKSLEPEPGRTMMESFENKVNQVLNT 732
GI I DA E + +A + I+QA + + R +++ Q+
Sbjct: 946 GITIGIDDAVIPEEKKQYLEEADRKLLQ-IEQAYEMGFLTDRERY------DQILQLWTE 998
Query: 733 ARDEAGSSAQKSLSES---NNLKAMVTAGSKGSFINISQMTACVGQQNVEGKRIPFGFVD 789
++ + K+ E+ N L M +G++G+ I Q+ G
Sbjct: 999 TTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRG--------------- 1043
Query: 790 RTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRL 849
+ G V +S+ GLT E+F + G R+G DTA++T+++GY+ R+L
Sbjct: 1044 -----LMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKL 1098
Query: 850 VKAMEDIMVK 859
V +I+V+
Sbjct: 1099 VDVTHEIVVR 1108
Score = 58.2 bits (139), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 27/53 (50%), Positives = 38/53 (71%), Gaps = 1/53 (1%)
Query: 1067 VAPGEMIGCVAAQSIGEPATQMTLNTFHYAGVS-AKNVTLGVPRLREIINVAK 1118
V+ GE +G VAAQSIGEP TQ+T+ TFH GV+ A ++T G+PR+ E+ +
Sbjct: 1215 VSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELFEARR 1267
Score = 47.0 bits (110), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 50/91 (54%), Gaps = 2/91 (2%)
Query: 1324 LDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMAITRHGINRNDTGPMMRCSFEETVDI 1383
L E +V+ +D +N R +A + ++ LM +T+ ++ + SF+ T +
Sbjct: 1389 LLEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSW--LSAASFQNTTHV 1446
Query: 1384 LLDAAVFAESDYLRGVTENIMLGQLAPIGTG 1414
L +AA+ + D L G+ EN++LG+L P GTG
Sbjct: 1447 LTEAAIAGKKDELIGLKENVILGRLIPAGTG 1477
Score = 41.2 bits (95), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 34/107 (31%), Positives = 48/107 (44%), Gaps = 20/107 (18%)
Query: 14 KVRMVQFGILSPDEIRQMSVVQIEHGETTERG--KPKPGGLSDPRL-----------GTI 60
+VR V+ + SP++IR S ++E ET KP+ GL D R+ G
Sbjct: 4 EVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKY 63
Query: 61 DRKM----KCETCTANMAEC---PGHFGHLELAKPMFHIGFMKTVLS 100
R+ CE C + + GH+ELA P HI F+K V S
Sbjct: 64 KRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHIWFVKDVPS 110
>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 = 158 bits (399), Expect = 3e-38, Method: Compositional matrix adjust.
Identities = 166/670 (24%), Positives = 276/670 (41%), Gaps = 119/670 (17%)
Query: 240 RPDWMILQV----------LXXXXXXXXXSDDLTHQLAMIIRHNENLRRQERNGAPAHII 289
RP+WMIL+ + + DL +I N L++ GAP II
Sbjct: 508 RPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIII 567
Query: 290 SEFAQLLQFHIATYFDNELPGQPRATQRSGRPIKSICSRLKAKEGRIRGNLMGKRVDFSA 349
++LQ + DN G P S RP++S+ L K+GR R NL+GKRVD+S
Sbjct: 568 RNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSG 627
Query: 350 RTVITPDPTINIDQLGVPWSIALNLTYPETVTPYNIERLKELVEYGPHPPPGKTGAKYII 409
R+VI P + + Q G+P +AL L P LK++ E G P
Sbjct: 628 RSVIVVGPQLKLHQCGLPKRMALELFKPFL--------LKKMEEKGIAP----------- 668
Query: 410 RDDGQRLDLRYLKKSSDHHLELGYKVERHLNDGDFVLFNRQPSLHKMSIMGHRIKIMPYS 469
+ R L++ D E+ +E ++ G VL NR P+LH++ I + ++
Sbjct: 669 ---NVKAARRMLERQRDIKDEVWDALEEVIH-GKVVLLNRAPTLHRLGIQAFQPVLVEGQ 724
Query: 470 TFRLNLSVTSPYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVMGIVQD 529
+ +L+ V +NADFDGD+M +HVP S +AE M+ ++SP S P+ +D
Sbjct: 725 SIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRD 784
Query: 530 TLLGCRKIT-----KRDTFIEKDVFMNILMWWEDFDGKVPQPTILKPRPLWTG--KQVFN 582
+LG IT K+ +E L E + + P + R G K VF
Sbjct: 785 IILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVF- 843
Query: 583 LIIPKQINLFRTAAWHADNDKGILTAGDTLVRIEKGELLSGTLCKKTLGTSTGSLI---- 638
A+ D+ +L +V ++ ++++ K L TS G ++
Sbjct: 844 ----------------ANPDEALLAVAHGIVDLQ--DVVTVRYMGKRLETSPGRILFARI 885
Query: 639 --------HVIWEEVGPDAAR-----KFLGHTQWL-------------VNYWLLQNAFSI 672
V WE + D + K L + +L + Y+ + +
Sbjct: 886 VAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTS 945
Query: 673 GIGDTIADAKTMETINDTISKAKNNVKNLIKQAQDKSLEPEPGRTMMESFENKVNQVLNT 732
GI I DA E + +A + I+QA + + R +++ Q+
Sbjct: 946 GITIGIDDAVIPEEKKQYLEEADRKLLQ-IEQAYEMGFLTDRERY------DQILQLWTE 998
Query: 733 ARDEAGSSAQKSLSES---NNLKAMVTAGSKGSFINISQMTACVGQQNVEGKRIPFGFVD 789
++ + K+ E+ N L M +G++G+ I Q+ G
Sbjct: 999 TTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRG--------------- 1043
Query: 790 RTLPHFTKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTSETGYIQRRL 849
+ G V +S+ GLT E+F + G R+G DTA++T+++GY+ R+L
Sbjct: 1044 -----LMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKL 1098
Query: 850 VKAMEDIMVK 859
V +I+V+
Sbjct: 1099 VDVTHEIVVR 1108
Score = 58.2 bits (139), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 27/53 (50%), Positives = 38/53 (71%), Gaps = 1/53 (1%)
Query: 1067 VAPGEMIGCVAAQSIGEPATQMTLNTFHYAGVS-AKNVTLGVPRLREIINVAK 1118
V+ GE +G VAAQSIGEP TQ+T+ TFH GV+ A ++T G+PR+ E+ +
Sbjct: 1215 VSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELFEARR 1267
Score = 47.0 bits (110), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 50/91 (54%), Gaps = 2/91 (2%)
Query: 1324 LDELRVVISFDGSYVNYRHLAILCDTMTYRGHLMAITRHGINRNDTGPMMRCSFEETVDI 1383
L E +V+ +D +N R +A + ++ LM +T+ ++ + SF+ T +
Sbjct: 1389 LLEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSW--LSAASFQNTTHV 1446
Query: 1384 LLDAAVFAESDYLRGVTENIMLGQLAPIGTG 1414
L +AA+ + D L G+ EN++LG+L P GTG
Sbjct: 1447 LTEAAIAGKKDELIGLKENVILGRLIPAGTG 1477
Score = 41.2 bits (95), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 34/107 (31%), Positives = 48/107 (44%), Gaps = 20/107 (18%)
Query: 14 KVRMVQFGILSPDEIRQMSVVQIEHGETTERG--KPKPGGLSDPRL-----------GTI 60
+VR V+ + SP++IR S ++E ET KP+ GL D R+ G
Sbjct: 4 EVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKY 63
Query: 61 DRKM----KCETCTANMAEC---PGHFGHLELAKPMFHIGFMKTVLS 100
R+ CE C + + GH+ELA P HI F+K V S
Sbjct: 64 KRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHIWFVKDVPS 110
>pdb|2NYF|A Chain A, Crystal Structure Of Phenylalanine Ammonia-Lyase From
Nostoc Punctiforme
Length = 567
Score = 35.0 bits (79), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 40/168 (23%), Positives = 71/168 (42%), Gaps = 16/168 (9%)
Query: 420 YLKKSSDHHLELGYKVERHLNDGDFVLFNRQPSLHKMSIMGHRIKIMPYSTFRLNLSVTS 479
+L +S LEL ++E LN G P +++ +G + + Y T L + +
Sbjct: 132 HLYGASGIRLELIQRIETFLNAG------VTPHVYEFGSIGXDLVPLSYITGAL-IGLDP 184
Query: 480 PYNADFDGDEMNMHVPQSFETRAEVLELMMVPKCIVSPQSNRPVM-GIVQDTLLGCRKIT 538
+ DFDG EM+ S R + +L + PK ++ + VM GI + + + +
Sbjct: 185 SFTVDFDGKEMDAVTALS---RLGLPKLQLQPKEGLAMMNGTSVMTGIAANCVYDAKVLL 241
Query: 539 KRDTFIEKDVFMNILMWWEDFDGKVPQPTILKPRP--LWTGKQVFNLI 584
+ + + F + Q KP P LWT Q+F+L+
Sbjct: 242 ALTMGVHALAIQGLYGTNQSFHPFIHQ---CKPHPGQLWTADQMFSLL 286
>pdb|3H0L|B Chain B, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0L|E Chain E, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0L|H Chain H, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0L|K Chain K, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0L|N Chain N, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0L|Q Chain Q, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0L|T Chain T, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0L|W Chain W, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0M|B Chain B, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0M|E Chain E, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0M|H Chain H, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0M|K Chain K, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0M|N Chain N, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0M|Q Chain Q, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0M|T Chain T, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0M|W Chain W, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0R|B Chain B, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0R|E Chain E, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0R|H Chain H, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0R|K Chain K, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0R|N Chain N, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0R|Q Chain Q, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0R|T Chain T, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
pdb|3H0R|W Chain W, Structure Of Trna-Dependent Amidotransferase Gatcab From
Aquifex Aeolicus
Length = 478
Score = 33.1 bits (74), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 44/137 (32%), Positives = 59/137 (43%), Gaps = 19/137 (13%)
Query: 1091 NTFHYAGVSAKNVTLGVPRLREIINVA---KKIKTPSLSVFLKPGVNSTKERAKNVQCAL 1147
N YAGVS ++ G +LR INV+ K K V +K VNS + VQ AL
Sbjct: 175 NIMRYAGVSKADMEKG--QLRCDINVSIRPKGSKEFGTRVEIK-NVNSFR----FVQKAL 227
Query: 1148 EYTTLRS---VTEATEV-----WYDPDPMGTIIEEDVEFVKSYYEMPDEDIAPEKISP-W 1198
EY R V E EV +DP T E + Y PD D+ P K+ W
Sbjct: 228 EYEIERQINVVEEGGEVVQETRTFDPQTGKTYPMRTKEEAEDYRYFPDPDLVPLKVKKEW 287
Query: 1199 LLRIELNREMMVDKKLS 1215
+ I+ N + D++
Sbjct: 288 IEEIKKNMPELPDQRFE 304
>pdb|2Q1F|A Chain A, Crystal Structure Of Chondroitin Sulfate Lyase Abc From
Bacteroides Thetaiotaomicron Wal2926
pdb|2Q1F|B Chain B, Crystal Structure Of Chondroitin Sulfate Lyase Abc From
Bacteroides Thetaiotaomicron Wal2926
Length = 1022
Score = 32.3 bits (72), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 34/71 (47%), Gaps = 10/71 (14%)
Query: 1416 CSLYLN-----DEMLKNAIELQLPSYMEGLEFGMTPARSPVSGTPYHDGMMSPGYLFSPN 1470
C +LN DE + E QLP+ + G++ ++ +SG Y DG S + F PN
Sbjct: 8 CPAFLNAQIVTDERXFSFEEPQLPACITGVQ-----SQLGISGAHYKDGKHSLEWTFEPN 62
Query: 1471 LRLSPVTDAQF 1481
RL D +F
Sbjct: 63 GRLELRKDLKF 73
>pdb|3DN7|A Chain A, Cyclic Nucleotide Binding Regulatory Protein From
Cytophaga Hutchinsonii.
pdb|3DN7|B Chain B, Cyclic Nucleotide Binding Regulatory Protein From
Cytophaga Hutchinsonii
Length = 194
Score = 32.3 bits (72), Expect = 2.8, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 34/81 (41%), Gaps = 2/81 (2%)
Query: 589 INLFRTAAWHADNDKGILTAGDTLVRIEKGELL--SGTLCKKTLGTSTGSLIHVIWEEVG 646
IN R + D D G L+A L ++ K E L +G +C+ G L +E G
Sbjct: 9 INHIRKFIFLTDEDAGTLSAFFQLKKVRKKETLLKTGEICRINYFVVKGCLRLFFIDEKG 68
Query: 647 PDAARKFLGHTQWLVNYWLLQ 667
+ +F WL +Y Q
Sbjct: 69 IEQTTQFAIENWWLSDYXAFQ 89
>pdb|1WP6|A Chain A, Crystal Structure Of Maltohexaose-producing Amylase From
Alkalophilic Bacillus Sp.707.
pdb|1WPC|A Chain A, Crystal Structure Of Maltohexaose-Producing Amylase
Complexed With Pseudo-Maltononaose
pdb|2D3L|A Chain A, Crystal Structure Of Maltohexaose-Producing Amylase From
Bacillus Sp.707 Complexed With Maltopentaose.
pdb|2D3N|A Chain A, Crystal Structure Of Maltohexaose-Producing Amylase From
Bacillus Sp.707 Complexed With Maltohexaose
Length = 485
Score = 32.0 bits (71), Expect = 3.4, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 876 YGEDGMDSVWIESQTLDSLKMKKSEFDKAFRFEMDEENWNPNYMLQEYI--DDLKTIKEL 933
Y DG+D W +S+ L++ K KA+ +E+D EN N +Y++ I D + + EL
Sbjct: 160 YHFDGVD--WDQSRRLNNRIYKFRGHGKAWDWEVDTENGNYDYLMYADIDMDHPEVVNEL 217
Query: 934 RD 935
R+
Sbjct: 218 RN 219
>pdb|2DIE|A Chain A, Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378
Length = 485
Score = 30.4 bits (67), Expect = 8.9, Method: Composition-based stats.
Identities = 28/92 (30%), Positives = 41/92 (44%), Gaps = 6/92 (6%)
Query: 876 YGEDGMDSVWIESQTLDSLKMKKSEFDKAFRFEMDEENWNPNYMLQEYI--DDLKTIKEL 933
Y DG D W +S+ L + K KA+ +E+D EN N +Y++ I D + I EL
Sbjct: 160 YHFDGTD--WDQSRQLQNKIYKFRGTGKAWDWEVDIENGNYDYLMYADIDMDHPEVINEL 217
Query: 934 RD--VFDAEVQKLEADRYQLATEIATSGDSSW 963
R+ V+ L+ R I S W
Sbjct: 218 RNWGVWYTNTLNLDGFRIDAVKHIKYSYTRDW 249
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
0.318 0.135 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 45,285,572
Number of Sequences: 62578
Number of extensions: 1918973
Number of successful extensions: 4503
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 4355
Number of HSP's gapped (non-prelim): 83
length of query: 1815
length of database: 14,973,337
effective HSP length: 113
effective length of query: 1702
effective length of database: 7,902,023
effective search space: 13449243146
effective search space used: 13449243146
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: 59 (27.3 bits)