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= 000525
(1443 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|Q Chain Q, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|A Chain A, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|I Chain I, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 880
Score = 191 bits (486), Expect = 2e-48, Method: Compositional matrix adjust.
Identities = 234/923 (25%), Positives = 380/923 (41%), Gaps = 151/923 (16%)
Query: 17 LTGISLGISTDTEKEKLSVMEI---------GAVSE--VTNPRLGLPNPTNECSSCGAKD 65
+ GI GI + E K+SV I G E V +PRLG+ P +C +CG
Sbjct: 6 IKGIKFGILSPDEIRKMSVTAIITPDVYDEDGTPIEGSVMDPRLGVIEPGQKCPTCG-NT 64
Query: 66 RKACEGHFGFIKFPFTILHPYFLSDIAKLLNSICPKCKTIR----------------KER 109
C GHFG I+ ++H + I + L + C +C ++ K+R
Sbjct: 65 LGNCPGHFGHIELVRPVIHVGLVKHIYEFLKATCRRCGRVKISEDEIEKYSRIYNAIKKR 124
Query: 110 QKGAGSSRKE-------QPRVCKYCVRNPAQWYPRMR--FKLSSKDLSGKTAII-VEIDE 159
A E + +VC +C N Q+ ++ + + G + +I E
Sbjct: 125 WPSAARRLTEYVKKTAMKAQVCPHC--NEKQYKIKLEKPYNFYEERKEGVAKLTPSDIRE 182
Query: 160 KLSKKNKKLPDDYWGFIPFDAQQEENSVKPNRKVLSCKQVSYLLKDVDPSIR-EEFILSK 218
+L +K+PD + +D + +P +L+ V + + PSI E I ++
Sbjct: 183 RL----EKIPDSDVEILGYDP----TTSRPEWMILTVLPVPPIT--IRPSIMIESGIRAE 232
Query: 219 DAPFLKCFPVTPNNHRVTEVPHAFSHEKKLFFDNWTRHLKKMVDYRGRDIELSHLVQDCL 278
D K + N R+ E A + + + D W + Y +I L
Sbjct: 233 DDLTHKLVDIVRINERLKESIDAGA-PQLIIEDLWDLLQYHVATYFDNEIP-------GL 284
Query: 279 KISKLHLDKSSRKDSAEVRQKKNIDISNSSGLRWIKDVVLGKRNDDCFRMVVTGDPNIKL 338
SK + R + ++ K+ N SG KR D R V++ DPNI +
Sbjct: 285 PPSKHRSGRPLRTLAQRLKGKEGRFRGNLSG----------KRVDFSSRTVISPDPNISI 334
Query: 339 KEIGIPCQVAERLQISERLNSWNWERL-SVCISFRLLEKGELYVCRKGGLVRIRRID--- 394
E+G+P +A+ L + ER+ WN E+L I+ G YV R G RRID
Sbjct: 335 DEVGVPEIIAKTLTVPERITPWNIEKLRQFVINGPDKWPGANYVIRPDG----RRIDLRY 390
Query: 395 ---------ALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKVLPISSVVTINPLC 445
L G II R L DGDIVL NR PS+H S++A V+VL +N L
Sbjct: 391 VKDRKELASTLAPGYIIERHLIDGDIVLFNRQPSLHRISMMAHRVRVLK-GLTFRLNLLV 449
Query: 446 CSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRNLLSLGQDSLTAAHLL 505
C P++ DFDGD ++ ++PQ+ A E E++ + K +I + G ++ QD ++ A+LL
Sbjct: 450 CPPYNADFDGDEMNLHVPQSEEAIAEAKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLL 509
Query: 506 MEDSVXXXXXXXXXXXXFCPHRFLSPDIFKISKDSVWSGKQLFSMLLPPDFEYTFPSK-- 563
+ + + ++ ++GKQ+ S LP DF + +
Sbjct: 510 TVKTTLLTKEEAQQILGVADVKIDLGEPAILAPREYYTGKQVISAFLPKDFNFHGQANVS 569
Query: 564 -------------DVYISGGKLISAEGSSWLRDYEGN-----LFQYLIKRYRDK----VL 601
D Y+ I EG + + GN + +LIK Y D+ ++
Sbjct: 570 SGPRLCKNEDCPHDSYVVIKNGILLEG-VFDKKAIGNQQPESILHWLIKEYSDEYGKWLM 628
Query: 602 DFLYAAQEVLCEWLSVRGMTVSLSDLYLASHSCSRKILMDEIFYGLREAQDTCNFQQLMV 661
D L+ V ++ ++G T+ L D+ L D++ +E + + ++ V
Sbjct: 629 DNLF---RVFIRFVELQGFTMRLEDVSLG----------DDV---KKEIYNEIDRAKVEV 672
Query: 662 DSHMNFLMSAKDSESTRSLQGEHLSYEKQRSAALSQASVDAFKHVFWDIQNLAYKYGSKD 721
D N + K+ E + G L +L +D + ++A KY
Sbjct: 673 D---NLIQKYKNGE-LEPIPGRTL------EESLENYILDTLDKLRSTAGDIASKYLDPF 722
Query: 722 NSLLAMFKAGSKGNLLKLVQHSLCLGLQHSLAPLSFRFPHELSCAAWNRLRAGDNTECAK 781
N M + G++G++L + Q + LG Q R + D + A+
Sbjct: 723 NFAYVMARTGARGSVLNITQMAAMLGQQSVRGE---RIKRGYMTRTLPHFKPYDISPEAR 779
Query: 782 SYIPSAVVENSFLTGLNPLECFIHSVTSRDSSFSDNA---DLPGTLTRRLMFFMRDLCTA 838
+I S SF TGL P E F H+ R+ D A G + RRL+ + DL
Sbjct: 780 GFIYS-----SFRTGLKPTELFFHAAGGRE-GLVDTAVRTSQSGYMQRRLINALSDLRAE 833
Query: 839 YDGTVRNAYGNQIVQFSYNIEGT 861
YDGTVR+ YG ++VQ +Y +G
Sbjct: 834 YDGTVRSLYG-EVVQVAYGDDGV 855
>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 = 189 bits (481), Expect = 6e-48, Method: Compositional matrix adjust.
Identities = 230/928 (24%), Positives = 380/928 (40%), Gaps = 161/928 (17%)
Query: 17 LTGISLGISTDTEKEKLSVMEI---------GAVSE--VTNPRLGLPNPTNECSSCGAKD 65
+ GI GI + E K+SV I G E V +PRLG+ P +C +CG
Sbjct: 6 IKGIKFGILSPDEIRKMSVTAIITPDVYDEDGTPIEGSVMDPRLGVIEPGQKCPTCG-NT 64
Query: 66 RKACEGHFGFIKFPFTILHPYFLSDIAKLLNSICPKCKTIR----------------KER 109
C GHFG I+ ++H F+ + + L + C +C ++ K+R
Sbjct: 65 LGNCPGHFGHIELVRPVIHVGFVKHVYEFLKATCRRCGRVKISEDEIEKYSRIYNAIKKR 124
Query: 110 QKGAGSSRKE-------QPRVCKYC--------VRNPAQWYPRMRFKLSSKDLSGKTAII 154
A E + +VC +C + P +Y + ++ S
Sbjct: 125 WPSAARRLTEYVKKTAMKAQVCPHCGEKQFKIKLEKPYNFYEERKEGVAKLTPS------ 178
Query: 155 VEIDEKLSKKNKKLPDDYWGFIPFDAQQEENSVKPNRKVLSCKQVSYLLKDVDPSIR-EE 213
+I E+L +K+P+ + +D + +P +L+ V + + PSI E
Sbjct: 179 -DIRERL----EKVPESDVEILGYDP----TTSRPEWMILTVLPVPPIT--IRPSIMIES 227
Query: 214 FILSKDAPFLKCFPVTPNNHRVTEVPHAFSHEKKLFFDNWTRHLKKMVDYRGRDIELSHL 273
I ++D K + N R+ E A + + + D W + Y +I
Sbjct: 228 GIRAEDDLTHKLVDIVRINERLKESIDAGA-PQLIIEDLWDLLQYHVATYFDNEIP---- 282
Query: 274 VQDCLKISKLHLDKSSRKDSAEVRQKKNIDISNSSGLRWIKDVVLGKRNDDCFRMVVTGD 333
L SK + R + ++ K+ N SG KR D R V++ D
Sbjct: 283 ---GLPPSKHRSGRPLRTLAQRLKGKEGRFRGNLSG----------KRVDFSSRTVISPD 329
Query: 334 PNIKLKEIGIPCQVAERLQISERLNSWNWERL-SVCISFRLLEKGELYVCRKGGLVRIRR 392
PNI + E+G+P +A L + ER+ WN E+L I+ G YV R G RR
Sbjct: 330 PNISIDEVGVPEIIARTLTVPERITPWNIEKLRQFVINGPDKWPGANYVIRPDG----RR 385
Query: 393 ID------------ALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTVKVLPISSVVT 440
ID L G ++ R LTDGD+VL NR PS+H S++A V+VL
Sbjct: 386 IDLRYVKDRKELASTLAPGYVVERHLTDGDVVLFNRQPSLHRISMMAHRVRVLK-GLTFR 444
Query: 441 INPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRNLLSLGQDSLT 500
+N L C P++ DFDGD ++ ++PQ+ A E E++ + K +I + G ++ QD ++
Sbjct: 445 LNLLVCPPYNADFDGDEMNLHVPQSEEAIAEAKEIMLVHKNIITPRYGGPIIGAAQDYIS 504
Query: 501 AAHLLMEDSVXXXXXXXXXXXXFCPHRFLSPDIFKISKDSVWSGKQLFSMLLPPDFEYTF 560
A+LL + + + ++ ++GKQ+ S LP DF +
Sbjct: 505 GAYLLTVKTTLLTKEEAQQILGVADVKIDLGEPAILAPREYYTGKQVVSAFLPKDFNFHG 564
Query: 561 PSK---------------DVYISGGKLISAEGSSWLRDYEGN-----LFQYLIKRYRDK- 599
+ D Y+ I EG + + GN + +LIK Y D+
Sbjct: 565 QANVSSGPRLCKNEDCPHDSYVVIKNGILLEG-VFDKKAIGNQQPESILHWLIKEYSDEY 623
Query: 600 ---VLDFLYAAQEVLCEWLSVRGMTVSLSDLYLASHSCSRKILMDEIFYGLREAQDTCNF 656
++D L+ V ++ ++G T+ L D+ L D++ +E + +
Sbjct: 624 GKWLMDNLF---RVFIRFVELQGFTMRLEDVSLG----------DDV---KKEIYNEIDR 667
Query: 657 QQLMVDSHMNFLMSAKDSESTRSLQGEHLSYEKQRSAALSQASVDAFKHVFWDIQNLAYK 716
++ VD N + K+ E + G L +L +D + ++A K
Sbjct: 668 AKVEVD---NLIQKYKNGE-LEPIPGRTL------EESLENYILDTLDKLRSTAGDIASK 717
Query: 717 YGSKDNSLLAMFKAGSKGNLLKLVQHSLCLGLQHSLAPLSFRFPHELSCAAWNRLRAGDN 776
Y N M + G++G++L + Q + LG Q R + D
Sbjct: 718 YLDPFNFAYVMARTGARGSVLNITQMAAMLGQQSVRGE---RIKRGYMTRTLPHFKPYDI 774
Query: 777 TECAKSYIPSAVVENSFLTGLNPLECFIHSVTSRDSSFSDNA---DLPGTLTRRLMFFMR 833
+ A+ +I S SF TGL P E F H+ R+ D A G + RRL+ +
Sbjct: 775 SPEARGFIYS-----SFRTGLKPTELFFHAAGGRE-GLVDTAVRTSQSGYMQRRLINALS 828
Query: 834 DLCTAYDGTVRNAYGNQIVQFSYNIEGT 861
DL YDGTVR+ YG +++Q +Y +G
Sbjct: 829 DLRAEYDGTVRSLYG-EVIQVAYGDDGV 855
>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 = 178 bits (451), Expect = 3e-44, Method: Compositional matrix adjust.
Identities = 154/578 (26%), Positives = 263/578 (45%), Gaps = 79/578 (13%)
Query: 317 VLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWERLSVCISFRLLEK 376
++GKR D R V+TGDPN+ L E+G+P +A+ L E + +N +L + E
Sbjct: 346 LMGKRVDFSARTVITGDPNLSLDELGVPRSIAKTLTYPETVTPYNIYQLQELVRNGPDEH 405
Query: 377 -GELYVCRKGGLVRIRRID----------ALELGDIIYRPLTDGDIVLINRPPSIHPHSL 425
G Y+ R G RID L G + R + DGD+V+ NR PS+H S+
Sbjct: 406 PGAKYIIRDTG----ERIDLRYHKRAGDIPLRYGWRVERHIRDGDVVIFNRQPSLHKMSM 461
Query: 426 IALTVKVLPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQ 485
+ ++V+P S+ +N SP++ DFDGD ++ ++PQ+ R E+ E+ + KQ+++
Sbjct: 462 MGHRIRVMPYSTF-RLNLSVTSPYNADFDGDEMNMHVPQSEETRAEIQEITMVPKQIVSP 520
Query: 486 QSGRNLLSLGQDSLTAAHLLMEDSVXXXXXXXXXXXXFCP--HRFLSPDIFKISKDSVWS 543
QS + ++ + QD+L + P L P + + +W+
Sbjct: 521 QSNKPVMGIVQDTLAGVRKFSLRDNFLTRNAVMNIMLWVPDWDGILPPPVI-LKPKVLWT 579
Query: 544 GKQLFSMLLPPDFE---------YTFPSKD-VYISGGKLI-SAEGSSWLRDYEGNLFQYL 592
GKQ+ S+++P + P+ + I G++I + +G L +
Sbjct: 580 GKQILSLIIPKGINLIRDDDKQSLSNPTDSGMLIENGEIIYGVVDKKTVGASQGGLVHTI 639
Query: 593 IKRYRDKVLD-FLYAAQEVLCEWLSVRGMTVSLSDLYLASHSCSRKILMDEIFYGLREAQ 651
K ++ F Q V+ WL G ++ + D + + M E+ ++EA+
Sbjct: 640 WKEKGPEICKGFFNGIQRVVNYWLLHNGFSIGIGDTIADADT------MKEVTRTVKEAR 693
Query: 652 DTCNFQQLMVDSHMNFLMSAKDSESTRSLQGEHLSYEKQRSAALSQASVDAFKHVFWDIQ 711
+ + D+ N L E +L+ S+E + S L+QA +A +
Sbjct: 694 R--QVAECIQDAQHNRL----KPEPGMTLRE---SFEAKVSRILNQARDNAGR------- 737
Query: 712 NLAYKYGSKD-NSLLAMFKAGSKGNLLKLVQHSLCLGLQ---HSLAPLSFRF---PHELS 764
+ ++ KD N++ M AGSKG+ + + Q S C+G Q P F++ PH
Sbjct: 738 --SAEHSLKDSNNVKQMVAAGSKGSFINISQMSACVGQQIVEGKRIPFGFKYRTLPH--- 792
Query: 765 CAAWNRLRAGDNTECAKSYIPSAVVENSFLTGLNPLECFIHSVTSRDSSFSDNADLP--G 822
D++ ++ +I ENS+L GL P E F H++ R+ G
Sbjct: 793 ------FPKDDDSPESRGFI-----ENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETG 841
Query: 823 TLTRRLMFFMRDLCTAYDGTVRNAYGNQIVQFSYNIEG 860
+ RRL+ M D+ YDGTVRNA G+ I+QF+Y +G
Sbjct: 842 YIQRRLVKAMEDVMVRYDGTVRNAMGD-IIQFAYGEDG 878
Score = 47.8 bits (112), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 41 VSEVTNPRLGLPNPTNECSSCGAKDRKACEGHFGFIKFPFTILHPYFLSDIAKLLNSICP 100
V + +PRLG + +C +CG + C GHFG I+ + H FLS I K+L +C
Sbjct: 52 VGGLLDPRLGTIDRQFKCQTCG-ETMADCPGHFGHIELAKPVFHIGFLSKIKKILECVCW 110
Query: 101 KCKTIR 106
C ++
Sbjct: 111 NCGKLK 116
Score = 39.3 bits (90), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 27/128 (21%), Positives = 58/128 (45%), Gaps = 6/128 (4%)
Query: 1132 IDWTRSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLSATGEF 1191
+D TR++ ++ GI+A L L + I G + HL ++ + +++ G
Sbjct: 1328 VDATRTYSNSFVEILQILGIEATRSALLKELRNVIEFDGSYVNYRHLALLCDVMTSRGHL 1387
Query: 1192 VGLNAKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWGKVPSV 1251
+ + G+ + + + ++ F + AA +G D+ +G + + G++ +
Sbjct: 1388 MAITRHGI-----NRAETGALMRCSFEETVEILMDAAASGEKDDCKGISENIMLGQLAPM 1442
Query: 1252 GTGGHFDI 1259
GTG FDI
Sbjct: 1443 GTGA-FDI 1449
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 1455
Score = 169 bits (429), Expect = 8e-42, Method: Compositional matrix adjust.
Identities = 171/633 (27%), Positives = 281/633 (44%), Gaps = 82/633 (12%)
Query: 313 IKDVVLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWERLSVCISFR 372
I+ ++GKR D R V++GDPN++L ++G+P +A+ L E + +N +RL+ +
Sbjct: 336 IRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNG 395
Query: 373 LLEK-GELYVCRKGGLVRIRRID----------ALELGDIIYRPLTDGDIVLINRPPSIH 421
E G YV R G RID L+ G + R + D D VL NR PS+H
Sbjct: 396 PNEHPGAKYVIRDSG----DRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLH 451
Query: 422 PHSLIALTVKVLPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQ 481
S++A VKV+P S+ +N SP++ DFDGD ++ ++PQ+ R EL++L A+ Q
Sbjct: 452 KMSMMAHRVKVIPYSTF-RLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQ 510
Query: 482 LINQQSGRNLLSLGQDSLTAAH-LLMEDSVXXXXXXXXXXXXFCPHRFLSPDIFKISKDS 540
+++ QS + + + QD+L L + D+ + P I
Sbjct: 511 IVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKP 570
Query: 541 VWSGKQLFSMLLPPDFEYT--------FPSKD---VYISGGKLISAEGSSWLRDYEGNLF 589
+WSGKQ+ S+ +P KD + I G + + G L
Sbjct: 571 LWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLI 630
Query: 590 QYLIKRYRDKVLDFLYA-AQEVLCEWLSVRGMTVSLSDLYLASHSCSRKILMDEIFYGLR 648
+ + +V L+ Q+V+ WL G + + D + + M EI +
Sbjct: 631 HVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGD------TIADGPTMREITETIA 684
Query: 649 EAQDTCNFQQLMVDSHMNFLMSAKDSESTRSLQGEHLSYEKQRSAALSQASVDAFKHVFW 708
EA+ + ++ N L++AK + R S+E L++A A +
Sbjct: 685 EAKK--KVLDVTKEAQAN-LLTAKHGMTLRE------SFEDNVVRFLNEARDKAGRLAEV 735
Query: 709 DIQNLAYKYGSKDNSLLAMFKAGSKGNLLKLVQHSLCLGLQHSLAP-LSFRF-----PHE 762
++++L N++ M AGSKG+ + + Q S C+G Q ++F F PH
Sbjct: 736 NLKDL--------NNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPH- 786
Query: 763 LSCAAWNRLRAGDNTECAKSYIPSAVVENSFLTGLNPLECFIHSVTSRDSSFSDNADLP- 821
D + +K + VENS+L GL P E F H++ R+
Sbjct: 787 --------FSKDDYSPESKGF-----VENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAE 833
Query: 822 -GTLTRRLMFFMRDLCTAYDGTVRNAYGNQIVQFSYNIEGTSTPTGEIGDQPVGSLSACA 880
G + RRL+ + D+ YD T RN+ GN ++QF Y +G I Q SL
Sbjct: 834 TGYIQRRLVKALEDIMVHYDNTTRNSLGN-VIQFIYGEDGMD--AAHIEKQ---SLDTIG 887
Query: 881 ISEAAYSALDQPISLLETSPLLNLKNVLECGSK 913
S+AA+ + + LL T L+ ++LE GS+
Sbjct: 888 GSDAAFEKRYR-VDLLNTDHTLD-PSLLESGSE 918
Score = 40.8 bits (94), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 4/76 (5%)
Query: 27 DTEKEKLSVMEIGAVSEVTNPRLGLPNPTNECSSCGAKDRKACEGHFGFIKFPFTILHPY 86
+T E + +IG ++ +PRLG + +C +C + C GHFG I + H
Sbjct: 39 ETMDETQTRAKIGGLN---DPRLGSIDRNLKCQTC-QEGMNECPGHFGHIDLAKPVFHVG 94
Query: 87 FLSDIAKLLNSICPKC 102
F++ I K+ +C C
Sbjct: 95 FIAKIKKVCECVCMHC 110
>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 = 169 bits (429), Expect = 8e-42, Method: Compositional matrix adjust.
Identities = 172/633 (27%), Positives = 282/633 (44%), Gaps = 82/633 (12%)
Query: 313 IKDVVLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWERLSVCISFR 372
I+ ++GKR D R V++GDPN++L ++G+P +A+ L E + +N +RL+ +
Sbjct: 336 IRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNG 395
Query: 373 LLEK-GELYVCRKGGLVRIRRID---ALELGDI-------IYRPLTDGDIVLINRPPSIH 421
E G YV R G RID + GDI + R + D D VL NR PS+H
Sbjct: 396 PNEHPGAKYVIRDSG----DRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLH 451
Query: 422 PHSLIALTVKVLPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQ 481
S++A VKV+P S+ +N SP++ DFDGD ++ ++PQ+ R EL++L A+ Q
Sbjct: 452 KMSMMAHRVKVIPYSTF-RLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQ 510
Query: 482 LINQQSGRNLLSLGQDSLTAAH-LLMEDSVXXXXXXXXXXXXFCPHRFLSPDIFKISKDS 540
+++ QS + + + QD+L L + D+ + P I
Sbjct: 511 IVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKP 570
Query: 541 VWSGKQLFSMLLPPDFEYT--------FPSKD---VYISGGKLISAEGSSWLRDYEGNLF 589
+WSGKQ+ S+ +P KD + I G + + G L
Sbjct: 571 LWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLI 630
Query: 590 QYLIKRYRDKVLDFLYA-AQEVLCEWLSVRGMTVSLSDLYLASHSCSRKILMDEIFYGLR 648
+ + +V L+ Q+V+ WL G + + D + + M EI +
Sbjct: 631 HVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGD------TIADGPTMREITETIA 684
Query: 649 EAQDTCNFQQLMVDSHMNFLMSAKDSESTRSLQGEHLSYEKQRSAALSQASVDAFKHVFW 708
EA+ + ++ N L++AK + R S+E L++A A +
Sbjct: 685 EAKKKV--LDVTKEAQAN-LLTAKHGMTLRE------SFEDNVVRFLNEARDKAGRLAEV 735
Query: 709 DIQNLAYKYGSKDNSLLAMFKAGSKGNLLKLVQHSLCLGLQHSLAP-LSFRF-----PHE 762
++++L N++ M AGSKG+ + + Q S C+G Q ++F F PH
Sbjct: 736 NLKDL--------NNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPH- 786
Query: 763 LSCAAWNRLRAGDNTECAKSYIPSAVVENSFLTGLNPLECFIHSVTSRDSSFSDNADLP- 821
D + +K + VENS+L GL P E F H++ R+
Sbjct: 787 --------FSKDDYSPESKGF-----VENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAE 833
Query: 822 -GTLTRRLMFFMRDLCTAYDGTVRNAYGNQIVQFSYNIEGTSTPTGEIGDQPVGSLSACA 880
G + RRL+ + D+ YD T RN+ GN ++QF Y +G I Q SL
Sbjct: 834 TGYIQRRLVKALEDIMVHYDNTTRNSLGN-VIQFIYGEDGMD--AAHIEKQ---SLDTIG 887
Query: 881 ISEAAYSALDQPISLLETSPLLNLKNVLECGSK 913
S+AA+ + + LL T L+ ++LE GS+
Sbjct: 888 GSDAAFEKRYR-VDLLNTDHTLD-PSLLESGSE 918
Score = 40.0 bits (92), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 4/76 (5%)
Query: 27 DTEKEKLSVMEIGAVSEVTNPRLGLPNPTNECSSCGAKDRKACEGHFGFIKFPFTILHPY 86
+T E + +IG +++ PRLG + +C +C + C GHFG I + H
Sbjct: 39 ETMDETQTRAKIGGLND---PRLGSIDRNLKCQTC-QEGMNECPGHFGHIDLAKPVFHVG 94
Query: 87 FLSDIAKLLNSICPKC 102
F++ I K+ +C C
Sbjct: 95 FIAKIKKVCECVCMHC 110
>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 = 169 bits (429), Expect = 9e-42, Method: Compositional matrix adjust.
Identities = 171/633 (27%), Positives = 281/633 (44%), Gaps = 82/633 (12%)
Query: 313 IKDVVLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWERLSVCISFR 372
I+ ++GKR D R V++GDPN++L ++G+P +A+ L E + +N +RL+ +
Sbjct: 336 IRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNG 395
Query: 373 LLEK-GELYVCRKGGLVRIRRID----------ALELGDIIYRPLTDGDIVLINRPPSIH 421
E G YV R G RID L+ G + R + D D VL NR PS+H
Sbjct: 396 PNEHPGAKYVIRDSG----DRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLH 451
Query: 422 PHSLIALTVKVLPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQ 481
S++A VKV+P S+ +N SP++ DFDGD ++ ++PQ+ R EL++L A+ Q
Sbjct: 452 KMSMMAHRVKVIPYSTF-RLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQ 510
Query: 482 LINQQSGRNLLSLGQDSLTAAH-LLMEDSVXXXXXXXXXXXXFCPHRFLSPDIFKISKDS 540
+++ QS + + + QD+L L + D+ + P I
Sbjct: 511 IVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKP 570
Query: 541 VWSGKQLFSMLLPPDFEYT--------FPSKD---VYISGGKLISAEGSSWLRDYEGNLF 589
+WSGKQ+ S+ +P KD + I G + + G L
Sbjct: 571 LWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLI 630
Query: 590 QYLIKRYRDKVLDFLYA-AQEVLCEWLSVRGMTVSLSDLYLASHSCSRKILMDEIFYGLR 648
+ + +V L+ Q+V+ WL G + + D + + M EI +
Sbjct: 631 HVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGD------TIADGPTMREITETIA 684
Query: 649 EAQDTCNFQQLMVDSHMNFLMSAKDSESTRSLQGEHLSYEKQRSAALSQASVDAFKHVFW 708
EA+ + ++ N L++AK + R S+E L++A A +
Sbjct: 685 EAKKKV--LDVTKEAQAN-LLTAKHGMTLRE------SFEDNVVRFLNEARDKAGRLAEV 735
Query: 709 DIQNLAYKYGSKDNSLLAMFKAGSKGNLLKLVQHSLCLGLQHSLAP-LSFRF-----PHE 762
++++L N++ M AGSKG+ + + Q S C+G Q ++F F PH
Sbjct: 736 NLKDL--------NNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPH- 786
Query: 763 LSCAAWNRLRAGDNTECAKSYIPSAVVENSFLTGLNPLECFIHSVTSRDSSFSDNADLP- 821
D + +K + VENS+L GL P E F H++ R+
Sbjct: 787 --------FSKDDYSPESKGF-----VENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAE 833
Query: 822 -GTLTRRLMFFMRDLCTAYDGTVRNAYGNQIVQFSYNIEGTSTPTGEIGDQPVGSLSACA 880
G + RRL+ + D+ YD T RN+ GN ++QF Y +G I Q SL
Sbjct: 834 TGYIQRRLVKALEDIMVHYDNTTRNSLGN-VIQFIYGEDGMD--AAHIEKQ---SLDTIG 887
Query: 881 ISEAAYSALDQPISLLETSPLLNLKNVLECGSK 913
S+AA+ + + LL T L+ ++LE GS+
Sbjct: 888 GSDAAFEKRYR-VDLLNTDHTLD-PSLLESGSE 918
Score = 40.0 bits (92), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 4/76 (5%)
Query: 27 DTEKEKLSVMEIGAVSEVTNPRLGLPNPTNECSSCGAKDRKACEGHFGFIKFPFTILHPY 86
+T E + +IG +++ PRLG + +C +C + C GHFG I + H
Sbjct: 39 ETMDETQTRAKIGGLND---PRLGSIDRNLKCQTC-QEGMNECPGHFGHIDLAKPVFHVG 94
Query: 87 FLSDIAKLLNSICPKC 102
F++ I K+ +C C
Sbjct: 95 FIAKIKKVCECVCMHC 110
>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 1413
Score = 61.2 bits (147), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 77/320 (24%), Positives = 136/320 (42%), Gaps = 47/320 (14%)
Query: 212 EEFILSKDAP---FLKCFPVTPNNHRVTEVP-----HAFSHEKKLF--FDNWTRHLKKMV 261
E F+ S + P L PV P + R VP A S L+ N LK+++
Sbjct: 225 EAFVQSGNKPEWMILTVLPVLPPDLRPL-VPLDGGRFATSDLNDLYRRVINRNNRLKRLL 283
Query: 262 DYRGRDIELSHLVQDCLKISKLHLDKSSRKDSAEVRQKKNIDISNSSGLRWIKDVV---- 317
D DI + + + + LD R+ + I SN L+ + D++
Sbjct: 284 DLAAPDIIVRNEKRMLQEAVDALLDNG--------RRGRAITGSNKRPLKSLADMIKGKQ 335
Query: 318 -------LGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWERLSVCIS 370
LGKR D R V+T P ++L + G+P ++A E I
Sbjct: 336 GRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMA-------------LELFKPFIY 382
Query: 371 FRLLEKGELYVCRKGGLVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTV 430
+L +G L K + R +A+ + DI+ + + VL+NR P++H + A
Sbjct: 383 GKLELRG-LATTIKAAKKMVEREEAV-VWDILDEVIREHP-VLLNRAPTLHRLGIQAFE- 438
Query: 431 KVLPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRN 490
VL + ++PL C+ ++ DFDGD + ++P + A++E L+ +++ +G
Sbjct: 439 PVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEP 498
Query: 491 LLSLGQDSLTAAHLLMEDSV 510
++ QD + + + D V
Sbjct: 499 IIVPSQDVVLGLYYMTRDCV 518
>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 = 61.2 bits (147), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 77/320 (24%), Positives = 136/320 (42%), Gaps = 47/320 (14%)
Query: 212 EEFILSKDAP---FLKCFPVTPNNHRVTEVP-----HAFSHEKKLF--FDNWTRHLKKMV 261
E F+ S + P L PV P + R VP A S L+ N LK+++
Sbjct: 225 EAFVQSGNKPEWMILTVLPVLPPDLRPL-VPLDGGRFATSDLNDLYRRVINRNNRLKRLL 283
Query: 262 DYRGRDIELSHLVQDCLKISKLHLDKSSRKDSAEVRQKKNIDISNSSGLRWIKDVV---- 317
D DI + + + + LD R+ + I SN L+ + D++
Sbjct: 284 DLAAPDIIVRNEKRMLQEAVDALLDNG--------RRGRAITGSNKRPLKSLADMIKGKQ 335
Query: 318 -------LGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWERLSVCIS 370
LGKR D R V+T P ++L + G+P ++A E I
Sbjct: 336 GRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMA-------------LELFKPFIY 382
Query: 371 FRLLEKGELYVCRKGGLVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALTV 430
+L +G L K + R +A+ + DI+ + + VL+NR P++H + A
Sbjct: 383 GKLELRG-LATTIKAAKKMVEREEAV-VWDILDEVIREHP-VLLNRAPTLHRLGIQAFE- 438
Query: 431 KVLPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGRN 490
VL + ++PL C+ ++ DFDGD + ++P + A++E L+ +++ +G
Sbjct: 439 PVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEP 498
Query: 491 LLSLGQDSLTAAHLLMEDSV 510
++ QD + + + D V
Sbjct: 499 IIVPSQDVVLGLYYMTRDCV 518
>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 = 57.0 bits (136), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 54/203 (26%), Positives = 94/203 (46%), Gaps = 38/203 (18%)
Query: 317 VLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERL-------QISERLNSWNWERLSVCI 369
+LGKR D R V+ P +KL + G+P ++A L ++ E+ + N V
Sbjct: 358 LLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPN-----VKA 412
Query: 370 SFRLLE-----KGELYVCRKGGLVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHS 424
+ R+LE K E++ DALE ++I+ G +VL+NR P++H
Sbjct: 413 ARRMLERQRDIKDEVW-------------DALE--EVIH-----GKVVLLNRAPTLHRLG 452
Query: 425 LIALTVKVLPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLIN 484
+ A VL + ++PL C F+ DFDGD + ++P + A+ E + L++
Sbjct: 453 IQAFQ-PVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLS 511
Query: 485 QQSGRNLLSLGQDSLTAAHLLME 507
SG L +D + + + +
Sbjct: 512 PASGEPLAKPSRDIILGLYYITQ 534
>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For
Structural Studies
Length = 1233
Score = 56.6 bits (135), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 54/203 (26%), Positives = 94/203 (46%), Gaps = 38/203 (18%)
Query: 317 VLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERL-------QISERLNSWNWERLSVCI 369
+LGKR D R V+ P +KL + G+P ++A L ++ E+ + N V
Sbjct: 327 LLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPN-----VKA 381
Query: 370 SFRLLE-----KGELYVCRKGGLVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHS 424
+ R+LE K E++ DALE ++I+ G +VL+NR P++H
Sbjct: 382 ARRMLERQRDIKDEVW-------------DALE--EVIH-----GKVVLLNRAPTLHRLG 421
Query: 425 LIALTVKVLPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLIN 484
+ A VL + ++PL C F+ DFDGD + ++P + A+ E + L++
Sbjct: 422 IQAFQ-PVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLS 480
Query: 485 QQSGRNLLSLGQDSLTAAHLLME 507
SG L +D + + + +
Sbjct: 481 PASGEPLAKPSRDIILGLYYITQ 503
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1264
Score = 56.6 bits (135), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 54/203 (26%), Positives = 94/203 (46%), Gaps = 38/203 (18%)
Query: 317 VLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERL-------QISERLNSWNWERLSVCI 369
+LGKR D R V+ P +KL + G+P ++A L ++ E+ + N V
Sbjct: 358 LLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPN-----VKA 412
Query: 370 SFRLLE-----KGELYVCRKGGLVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHS 424
+ R+LE K E++ DALE ++I+ G +VL+NR P++H
Sbjct: 413 ARRMLERQRDIKDEVW-------------DALE--EVIH-----GKVVLLNRAPTLHRLG 452
Query: 425 LIALTVKVLPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLIN 484
+ A VL + ++PL C F+ DFDGD + ++P + A+ E + L++
Sbjct: 453 IQAFQ-PVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLS 511
Query: 485 QQSGRNLLSLGQDSLTAAHLLME 507
SG L +D + + + +
Sbjct: 512 PASGEPLAKPSRDIILGLYYITQ 534
>pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|M Chain M, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9Z|D Chain D, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
pdb|1YNJ|D Chain D, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNJ|J Chain J, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNN|D Chain D, Taq Rna Polymerase-rifampicin Complex
pdb|1YNN|J Chain J, Taq Rna Polymerase-rifampicin Complex
Length = 1524
Score = 56.6 bits (135), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 54/203 (26%), Positives = 94/203 (46%), Gaps = 38/203 (18%)
Query: 317 VLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERL-------QISERLNSWNWERLSVCI 369
+LGKR D R V+ P +KL + G+P ++A L ++ E+ + N V
Sbjct: 618 LLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAPN-----VKA 672
Query: 370 SFRLLE-----KGELYVCRKGGLVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHS 424
+ R+LE K E++ DALE ++I+ G +VL+NR P++H
Sbjct: 673 ARRMLERQRDIKDEVW-------------DALE--EVIH-----GKVVLLNRAPTLHRLG 712
Query: 425 LIALTVKVLPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLIN 484
+ A VL + ++PL C F+ DFDGD + ++P + A+ E + L++
Sbjct: 713 IQAFQ-PVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLS 771
Query: 485 QQSGRNLLSLGQDSLTAAHLLME 507
SG L +D + + + +
Sbjct: 772 PASGEPLAKPSRDIILGLYYITQ 794
>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 = 56.2 bits (134), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 53/198 (26%), Positives = 92/198 (46%), Gaps = 28/198 (14%)
Query: 317 VLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWERLS--VCISFRLL 374
+LGKR D R V+ P +KL + G+P ++A L L + ++ V + R+L
Sbjct: 618 LLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRML 677
Query: 375 E-----KGELYVCRKGGLVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALT 429
E K E++ DALE ++I+ G +VL+NR P++H + A
Sbjct: 678 ERQRDIKDEVW-------------DALE--EVIH-----GKVVLLNRAPTLHRLGIQAFQ 717
Query: 430 VKVLPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGR 489
VL + ++PL C F+ DFDGD + ++P + A+ E + L++ SG
Sbjct: 718 -PVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGE 776
Query: 490 NLLSLGQDSLTAAHLLME 507
L +D + + + +
Sbjct: 777 PLAKPSRDIILGLYYITQ 794
>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 = 56.2 bits (134), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 53/198 (26%), Positives = 92/198 (46%), Gaps = 28/198 (14%)
Query: 317 VLGKRNDDCFRMVVTGDPNIKLKEIGIPCQVAERLQISERLNSWNWERLS--VCISFRLL 374
+LGKR D R V+ P +KL + G+P ++A L L + ++ V + R+L
Sbjct: 618 LLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRML 677
Query: 375 E-----KGELYVCRKGGLVRIRRIDALELGDIIYRPLTDGDIVLINRPPSIHPHSLIALT 429
E K E++ DALE ++I+ G +VL+NR P++H + A
Sbjct: 678 ERQRDIKDEVW-------------DALE--EVIH-----GKVVLLNRAPTLHRLGIQAFQ 717
Query: 430 VKVLPISSVVTINPLCCSPFHGDFDGDCLHGYIPQAIGARVELTELVALDKQLINQQSGR 489
VL + ++PL C F+ DFDGD + ++P + A+ E + L++ SG
Sbjct: 718 -PVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGE 776
Query: 490 NLLSLGQDSLTAAHLLME 507
L +D + + + +
Sbjct: 777 PLAKPSRDIILGLYYITQ 794
>pdb|3QQC|A Chain A, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP
CLAMP DOMAIN
Length = 436
Score = 50.8 bits (120), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 48/102 (47%), Gaps = 12/102 (11%)
Query: 16 ILTGISLGISTDTEKEKLSVMEIGAVSE-----------VTNPRLGLPNPTNECSSCGAK 64
++ I GI + E K+S +E+ V + R+G+ +P C +CG +
Sbjct: 68 VIGSIEFGILSPQEIRKMSAVEVTVPDTYDDDGYPIEGGVMDKRMGVIDPGLRCETCGGR 127
Query: 65 DRKACEGHFGFIKFPFTILHPYFLSDIAKLLNSICPKCKTIR 106
+ C GHFG I+ ++H F I ++L S C +C I+
Sbjct: 128 AGE-CPGHFGHIELARPVIHVGFAKTIYRILESTCRECGRIK 168
>pdb|2K0M|A Chain A, Solution Nmr Structure Of The Uncharacterized Protein From
Rhodospirillum Rubrum Gene Locus Rru_a0810. Northeast
Structural Genomics Target Rrr43
Length = 104
Score = 48.1 bits (113), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 41/76 (53%), Gaps = 2/76 (2%)
Query: 1344 LKKILHKYSIGQRLSEKDKTTVIRALYFHPRRNEKLGIEPPDIEVTYHPEHQNSRCFSLV 1403
+K +L++Y G +S D ++ AL HP K+G + EV ++CF ++
Sbjct: 24 MKVMLNRYRPGDIVSTVDGAFLVEALKRHPDATSKIGPGVRNFEV--RSADYGTQCFWIL 81
Query: 1404 REDGSIEDFSYHKCVI 1419
R DGS E FSY KCV+
Sbjct: 82 RTDGSEERFSYKKCVL 97
>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 = 44.7 bits (104), Expect = 3e-04, Method: Composition-based stats.
Identities = 73/359 (20%), Positives = 145/359 (40%), Gaps = 72/359 (20%)
Query: 897 ETSPLLNLKNVLE-CGSKKSNADQTMSLFLSNKLGKRRHGFEYGALEVKNHLECLMLSDI 955
E + L L ++E +KK + M+++L+++ + R ALEV LE + ++
Sbjct: 97 ELNVTLGLPRLIEIVDAKKVPSTPMMTIYLTDEYKRDRDK----ALEVARKLEYTKIENV 152
Query: 956 VSTSMIIYSPQTGSMKHFSPWICHFHVRKEIMKRTGLKEHSIIDSLYRQCKAARTELKIS 1015
VS++ I SM + E++K G+ +D + K A LK+
Sbjct: 153 VSSTSI----DIASMSII------LQLDNEMLKDKGVT----VDDV----KKAIGRLKLG 194
Query: 1016 VPDMLISNKDCSSINMQKECNDAFCVTVMIVENFKRTSIDLETIQMWVMPFLLKTVVKGF 1075
D +I + S++N+ NF +ID + +L T +KG
Sbjct: 195 --DFMIEESEDSTLNI----------------NF--ANIDSIAALFKLRDKILNTKIKGI 234
Query: 1076 REIKKVDILWKDKQKASKSHDDSFGELYLRVSMSGQCHITSLWSALMNDCHQIMDMIDWT 1135
+ IK+ + + D + L ++SG + +D
Sbjct: 235 KGIKRAIV---------QKKGDEYIILTDGSNLSGVLSVKG---------------VDVA 270
Query: 1136 RSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLSATGEFVGLN 1195
+ +NIR +GI+A + + + +++ G ++ H+L++A+ ++ TG +
Sbjct: 271 KVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDIRHILLIADVMTRTGIVRQIG 330
Query: 1196 AKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWGKVPSVGTG 1254
G+ ++ +S +A F + AA G V+ +G V+ + G +GTG
Sbjct: 331 RHGVTGEK-----NSVLARAAFEVTVKHLLDAAARGDVEEFKGVVENIIIGHPIKLGTG 384
>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 = 44.7 bits (104), Expect = 3e-04, Method: Composition-based stats.
Identities = 73/359 (20%), Positives = 145/359 (40%), Gaps = 72/359 (20%)
Query: 897 ETSPLLNLKNVLE-CGSKKSNADQTMSLFLSNKLGKRRHGFEYGALEVKNHLECLMLSDI 955
E + L L ++E +KK + M+++L+++ + R ALEV LE + ++
Sbjct: 94 ELNVTLGLPRLIEIVDAKKVPSTPMMTIYLTDEYKRDRDK----ALEVARKLEYTKIENV 149
Query: 956 VSTSMIIYSPQTGSMKHFSPWICHFHVRKEIMKRTGLKEHSIIDSLYRQCKAARTELKIS 1015
VS++ I SM + E++K G+ +D + K A LK+
Sbjct: 150 VSSTSI----DIASMSII------LQLDNEMLKDKGVT----VDDV----KKAIGRLKLG 191
Query: 1016 VPDMLISNKDCSSINMQKECNDAFCVTVMIVENFKRTSIDLETIQMWVMPFLLKTVVKGF 1075
D +I + S++N+ NF +ID + +L T +KG
Sbjct: 192 --DFMIEESEDSTLNI----------------NF--ANIDSIAALFKLRDKILNTKIKGI 231
Query: 1076 REIKKVDILWKDKQKASKSHDDSFGELYLRVSMSGQCHITSLWSALMNDCHQIMDMIDWT 1135
+ IK+ + + D + L ++SG + +D
Sbjct: 232 KGIKRAIV---------QKKGDEYIILTDGSNLSGVLSVKG---------------VDVA 267
Query: 1136 RSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLSATGEFVGLN 1195
+ +NIR +GI+A + + + +++ G ++ H+L++A+ ++ TG +
Sbjct: 268 KVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDIRHILLIADVMTRTGIVRQIG 327
Query: 1196 AKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWGKVPSVGTG 1254
G+ ++ +S +A F + AA G V+ +G V+ + G +GTG
Sbjct: 328 RHGVTGEK-----NSVLARAAFEVTVKHLLDAAARGDVEEFKGVVENIIIGHPIKLGTG 381
>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 = 44.3 bits (103), Expect = 5e-04, Method: Composition-based stats.
Identities = 28/123 (22%), Positives = 58/123 (47%), Gaps = 5/123 (4%)
Query: 1132 IDWTRSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLSATGEF 1191
+D + +NIR +GI+A + + + +++ G ++ H+L+VA+ ++ TG
Sbjct: 267 VDIAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDMRHILLVADVMTRTGVV 326
Query: 1192 VGLNAKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWGKVPSV 1251
+ G+ ++ +S +A F + AA G V+ +G V+ + G +
Sbjct: 327 RQIGRHGVTGEK-----NSVLARAAFEVTVKHLLDAAARGDVEEFKGVVENIIIGHPIKL 381
Query: 1252 GTG 1254
GTG
Sbjct: 382 GTG 384
>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 = 44.3 bits (103), Expect = 5e-04, Method: Composition-based stats.
Identities = 28/123 (22%), Positives = 58/123 (47%), Gaps = 5/123 (4%)
Query: 1132 IDWTRSHPDNIRSFCLAYGIDAGLQFFLTNLESAISDTGKNILPEHLLIVANTLSATGEF 1191
+D + +NIR +GI+A + + + +++ G ++ H+L+VA+ ++ TG
Sbjct: 267 VDIAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLDVDMRHILLVADVMTRTGVV 326
Query: 1192 VGLNAKGLALQRKHSSVSSPFVQAFFSNPGASFIKAAKAGAVDNLQGSVDALGWGKVPSV 1251
+ G+ ++ +S +A F + AA G V+ +G V+ + G +
Sbjct: 327 RQIGRHGVTGEK-----NSVLARAAFEVTVKHLLDAAARGDVEEFKGVVENIIIGHPIKL 381
Query: 1252 GTG 1254
GTG
Sbjct: 382 GTG 384
>pdb|3RB9|A Chain A, Crystal Structure Of The M. Tuberculosis Beta Clamp
pdb|3RB9|B Chain B, Crystal Structure Of The M. Tuberculosis Beta Clamp
Length = 395
Score = 32.3 bits (72), Expect = 1.9, Method: Composition-based stats.
Identities = 32/104 (30%), Positives = 44/104 (42%), Gaps = 6/104 (5%)
Query: 1163 ESAISDTGKNILPEHLLIVANTLSATGEFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGA 1222
+ AI+ + LP I L T + LA++ S SSP ++A P
Sbjct: 143 QVAIAAGRDDTLPMLTGIRVEILGETVVLAATDRFRLAVRELKWSASSPDIEAAVLVPAK 202
Query: 1223 SFIKAAKAGAVDNLQGSVDALGWGKVPSVGTGGHFDIIYSGEGR 1266
+ +AAKAG + GS L G P VG G I SG G+
Sbjct: 203 TLAEAAKAG----IGGSDVRLSLGTGPGVGKDGLLGI--SGNGK 240
>pdb|3P16|A Chain A, Crystal Structure Of Dna Polymerase Iii Sliding Clamp
pdb|3P16|B Chain B, Crystal Structure Of Dna Polymerase Iii Sliding Clamp
pdb|3P16|C Chain C, Crystal Structure Of Dna Polymerase Iii Sliding Clamp
pdb|3P16|D Chain D, Crystal Structure Of Dna Polymerase Iii Sliding Clamp
pdb|3P16|E Chain E, Crystal Structure Of Dna Polymerase Iii Sliding Clamp
pdb|3P16|F Chain F, Crystal Structure Of Dna Polymerase Iii Sliding Clamp
Length = 408
Score = 32.3 bits (72), Expect = 1.9, Method: Composition-based stats.
Identities = 32/104 (30%), Positives = 44/104 (42%), Gaps = 6/104 (5%)
Query: 1163 ESAISDTGKNILPEHLLIVANTLSATGEFVGLNAKGLALQRKHSSVSSPFVQAFFSNPGA 1222
+ AI+ + LP I L T + LA++ S SSP ++A P
Sbjct: 156 QVAIAAGRDDTLPMLTGIRVEILGETVVLAATDRFRLAVRELKWSASSPDIEAAVLVPAK 215
Query: 1223 SFIKAAKAGAVDNLQGSVDALGWGKVPSVGTGGHFDIIYSGEGR 1266
+ +AAKAG + GS L G P VG G I SG G+
Sbjct: 216 TLAEAAKAG----IGGSDVRLSLGTGPGVGKDGLLGI--SGNGK 253
>pdb|1QQK|A Chain A, The Crystal Structure Of Fibroblast Growth Factor 7
(Keratinocyte Growth Factor)
pdb|1QQK|B Chain B, The Crystal Structure Of Fibroblast Growth Factor 7
(Keratinocyte Growth Factor)
Length = 140
Score = 31.6 bits (70), Expect = 3.2, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 21/33 (63%)
Query: 644 FYGLREAQDTCNFQQLMVDSHMNFLMSAKDSES 676
Y +E + CNF++L++++H N SAK + S
Sbjct: 73 LYAKKECNEDCNFKELILENHYNTYASAKWTHS 105
>pdb|3IP1|A Chain A, Structure Of Putative Alcohol Dehydrogenase (Tm_042) From
Thermotoga Maritima
pdb|3IP1|B Chain B, Structure Of Putative Alcohol Dehydrogenase (Tm_042) From
Thermotoga Maritima
pdb|3IP1|C Chain C, Structure Of Putative Alcohol Dehydrogenase (Tm_042) From
Thermotoga Maritima
pdb|3IP1|D Chain D, Structure Of Putative Alcohol Dehydrogenase (Tm_042) From
Thermotoga Maritima
Length = 404
Score = 31.6 bits (70), Expect = 3.4, Method: Composition-based stats.
Identities = 32/104 (30%), Positives = 42/104 (40%), Gaps = 17/104 (16%)
Query: 128 VRNPAQWYPRMRFKLSSKDLSGKTAIIVEIDEKLSKKNKKLPDDYWGFIPFDAQQEENSV 187
VR A+W PR FKL KD+ GK L K + P+ +P E
Sbjct: 6 VRLHAKWDPRPEFKLGPKDIEGKLTW-------LGSKVWRYPEVRVEEVP-----EPRIE 53
Query: 188 KPNRKVLSCKQVSYLLKDVDPSIREE--FILSKDAPFLKCFPVT 229
KP ++ K DV + +E +IL P L FPVT
Sbjct: 54 KPTEIIIKVKACGICGSDVHXAQTDEEGYILY---PGLTGFPVT 94
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
0.320 0.136 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 42,785,456
Number of Sequences: 62578
Number of extensions: 1789687
Number of successful extensions: 4305
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 22
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 4209
Number of HSP's gapped (non-prelim): 48
length of query: 1443
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1332
effective length of database: 8,027,179
effective search space: 10692202428
effective search space used: 10692202428
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.9 bits)