RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 003180
(842 letters)
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1210
Score = 1329 bits (3440), Expect = 0.0
Identities = 556/863 (64%), Positives = 675/863 (78%), Gaps = 34/863 (3%)
Query: 1 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRM 60
+LPH+ T + ET+KA++ GY+IHR+LLCAL RR DDRDH+G KRLDLAGPLL LFRM
Sbjct: 346 LLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRM 405
Query: 61 LFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWG-QANAAGTRAGV 119
LFRK+TRDV Y+QKCV+ ++ NL A+K+ IT+GL+YSLATGNWG Q + R GV
Sbjct: 406 LFRKMTRDVYKYMQKCVETNREFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGV 465
Query: 120 SQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNL 179
SQVLNR T+ASTLSHLRR N+PIGR+GKLAKPRQLHN+ WGM+CPAETPEGQACGLVKNL
Sbjct: 466 SQVLNRYTFASTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNL 525
Query: 180 ALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKT 239
+LM Y++VGS + PI+EFLEEWG E E+ +P+ P ATK+FVNG W+G+HRDP L +T
Sbjct: 526 SLMSYVSVGSPSAPIIEFLEEWGLETLEDYNPSASPNATKVFVNGVWLGVHRDPAHLTET 585
Query: 240 LRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVE-------KQRLLIKKRDI 292
LR LRRR+D++ EV +VRDIR KELR++TD GR RPLFIV+ + L I+K I
Sbjct: 586 LRSLRRRLDISAEVSIVRDIREKELRLFTDAGRICRPLFIVDNNPNSERRGELCIRKEHI 645
Query: 293 IALQQRESPEDG------GWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLH----- 341
L + + D GW LV+ G IEY+D EEEET MI+M+ DL +R
Sbjct: 646 QQLIEDKDRYDIDPEQRFGWTALVSSGLIEYLDAEEEETVMIAMSPEDLEASRQMQAGYE 705
Query: 342 -------------PEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQ 388
+ +THCEIHP++ILG+ ASIIPFPDHNQSPRNTYQSAMGKQ
Sbjct: 706 VKEELDPAQRVKPAPNPHVHAWTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQ 765
Query: 389 AMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQE 448
AMG+Y+TNYQ RMDT+A +LYYPQKPL TTR+ME+L FR+LPAG NAIVAI CYSGYNQE
Sbjct: 766 AMGVYLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQE 825
Query: 449 DSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDD 508
DS+IMNQ+SIDRG FRS+F+R+Y D+EKK+G V E+F RP RS T+ M+HG+YDKL+DD
Sbjct: 826 DSIIMNQASIDRGLFRSIFYRTYTDQEKKIGMTVMEEFERPVRSTTLRMKHGTYDKLEDD 885
Query: 509 GLAPPGTRVSGEDVIIGKTTPISQDEAQ--GQASRYTRRDHSISLRHSETGMVDQVLLTT 566
GL PGTRVSGED+IIGKT PI D + + + +RD S LR +E+G+VDQV++TT
Sbjct: 886 GLIAPGTRVSGEDIIIGKTAPIPLDHEELGQRTQLHAKRDVSTPLRSTESGIVDQVMVTT 945
Query: 567 NADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHA 626
N +GL+FVKVR+RS RIPQIGDKF+SRHGQKGT+GMTY EDMP++ +GI PDII+NPHA
Sbjct: 946 NQEGLKFVKVRMRSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHA 1005
Query: 627 IPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGH 686
IPSRMT+ L+EC + KV+A G EGDATPFTDVTV+ +SK L G+Q RGFE MY+GH
Sbjct: 1006 IPSRMTVAHLVECQLSKVSALSGFEGDATPFTDVTVEAVSKLLRSHGFQSRGFEVMYHGH 1065
Query: 687 TGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERD 746
TGR+L A +FLGPTYYQRLKH+VDDKIH+R RGPVQILTRQP EGRSRDGGLRFGEMERD
Sbjct: 1066 TGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERD 1125
Query: 747 CMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIP 806
C I+HG S L+ERLFD SDAYRV VC+ CGLIAIA+ KK+S+ECR C+N+T QV++P
Sbjct: 1126 CQISHGCSSVLRERLFDCSDAYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQVYLP 1185
Query: 807 YACKLLFQELMAMAIAPRMLTKE 829
YA KLLFQELM+M IAPR+ TK
Sbjct: 1186 YAAKLLFQELMSMNIAPRLFTKN 1208
>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B
1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B*
1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B*
1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ...
Length = 1224
Score = 1312 bits (3396), Expect = 0.0
Identities = 556/861 (64%), Positives = 670/861 (77%), Gaps = 32/861 (3%)
Query: 1 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRM 60
LPH+ + E++KA++ GY+I+RLLLCAL R+ +DDRDH+G KRLDLAGPLL LF+
Sbjct: 360 FLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKT 419
Query: 61 LFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWG-QANAAGTRAGV 119
LF+KLT+D+ Y+Q+ V+ D N++ AI AKTITSGLKY+LATGNWG Q A +RAGV
Sbjct: 420 LFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGV 479
Query: 120 SQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNL 179
SQVLNR TY+STLSHLRR N+PIGR+GKLAKPRQLHN+ WG++CPAETPEGQACGLVKNL
Sbjct: 480 SQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNL 539
Query: 180 ALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKT 239
+LM I+VG+ PI+ FL EWG E E+ P P AT++FVNG W G+HR+P L++T
Sbjct: 540 SLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMET 599
Query: 240 LRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVE------KQRLLIKKRDII 293
LR LRR+ D+N EV ++RDIR KEL+I+TD GR RPLFIVE + L ++K I
Sbjct: 600 LRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIA 659
Query: 294 ALQQR---------ESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEE 344
L E E+ W L+ +G +EYID EEEE+ +I+M DL A + E
Sbjct: 660 KLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEEN 719
Query: 345 -------------AYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 391
+A T+THCEIHPS+ILGV ASIIPFPDHNQSPRNTYQSAMGKQAMG
Sbjct: 720 DLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMG 779
Query: 392 IYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSV 451
+++TNY RMDT+A +LYYPQKPL TTRAME+L FR+LPAG NAIVAIACYSGYNQEDS+
Sbjct: 780 VFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSM 839
Query: 452 IMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLA 511
IMNQSSIDRG FRSLFFRSY D+EKK G + E F +P R+NT+ M+HG+YDKLDDDGL
Sbjct: 840 IMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLI 899
Query: 512 PPGTRVSGEDVIIGKTTPISQDEAQ--GQASRYTRRDHSISLRHSETGMVDQVLLTTNAD 569
PG RVSGEDVIIGKTTPIS DE + + + +++RD S LR +E G+VDQVL+TTN D
Sbjct: 900 APGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQD 959
Query: 570 GLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPS 629
GL+FVKVRVR+ +IPQIGDKF+SRHGQKGT+G+TY +EDMP+T EGI PD+I+NPHAIPS
Sbjct: 960 GLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPS 1019
Query: 630 RMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGR 689
RMT+ LIEC++ KVAA G EGDA+PFTD+TV+ ISK L + GYQ RGFE MYNGHTG+
Sbjct: 1020 RMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGK 1079
Query: 690 RLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMI 749
+L A IF GPTYYQRL+HMVDDKIH+R RGP+Q+LTRQP EGRSRDGGLRFGEMERDCMI
Sbjct: 1080 KLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMI 1139
Query: 750 AHGASHFLKERLFDQSDAYRVHVCEHCGLIA-IANLKKNSFECRGCKNKTDIVQVHIPYA 808
AHGA+ FLKERL + SDA+RVH+C CGL+ IA L N FEC+GC NK DI Q+HIPYA
Sbjct: 1140 AHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYA 1199
Query: 809 CKLLFQELMAMAIAPRMLTKE 829
KLLFQELMAM I PR+ T
Sbjct: 1200 AKLLFQELMAMNITPRLYTDR 1220
>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B
2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B
Length = 1131
Score = 1235 bits (3196), Expect = 0.0
Identities = 380/847 (44%), Positives = 517/847 (61%), Gaps = 32/847 (3%)
Query: 1 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRM 60
LPH+GT KKAYY Y I +++ LGRR DD+DHY NKRL LAG L LFR+
Sbjct: 300 FLPHLGTSADDRRKKAYYLAYAISKVIELYLGRREPDDKDHYANKRLRLAGDLFASLFRV 359
Query: 61 LFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVS 120
F+ +D+ ++K G+ + L+ ++ +T ++++LATGNW R GVS
Sbjct: 360 AFKAFVKDLTYQLEKSKVRGRKLALKALVRPDIVTERIRHALATGNWVG-----GRTGVS 414
Query: 121 QVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLA 180
Q+L+R + S LSHLRR+ S + R + R LH +QWG MCP ETPEG GLVKNLA
Sbjct: 415 QLLDRTNWLSMLSHLRRVISSLARGQPNFEARDLHGTQWGRMCPFETPEGPNSGLVKNLA 474
Query: 181 LMVYITVGSAAYPILEFLEEWGTENFEEISPAVI---------PQATKIFVNGCWVGIHR 231
LM I VG + + L E G EE+ V + +K+ +NG VG +R
Sbjct: 475 LMAQIAVGINEKIVEKTLYEMGVVPVEEVIRRVTEGGEDQNEYLKWSKVILNGRLVGYYR 534
Query: 232 DPEMLVKTLRRLRRRVDVNTEVGVVRDIR--LKELRIYTDYGRCSRPLFIVEKQRLLIKK 289
D E L K +R RR+ +++ EV V + + E+ + D GR RPL IV L+ +
Sbjct: 535 DGEELAKKIRERRRKGEISDEVNVGHIVTDFINEVHVNCDSGRVRRPLIIVSNGNPLVTR 594
Query: 290 RDIIALQQRESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADT 349
DI L + DLV +G IEY+D EEEE +++ +DL
Sbjct: 595 EDIEKLDSGSI----TFDDLVRQGKIEYLDAEEEENAYVALEPSDL-----------TPE 639
Query: 350 YTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLY 409
+TH EI ILG+ ASIIP+P+HNQSPRNTYQSAM KQA+G+Y NYQ R DT A++L+
Sbjct: 640 HTHLEIWSPAILGITASIIPYPEHNQSPRNTYQSAMAKQALGLYAANYQLRTDTRAHLLH 699
Query: 410 YPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFR 469
YPQ+PLV TRA++ + + PAG NAI+A+ ++GYN EDS+IMN+SS++RG +RS FFR
Sbjct: 700 YPQRPLVQTRALDIIGYTNRPAGNNAILAVISFTGYNMEDSIIMNRSSVERGMYRSTFFR 759
Query: 470 SYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP 529
Y EE K ++ P+ Y L+D+G+ P V G DV+IGK +P
Sbjct: 760 LYSTEEVKYPGGQEDKIVMPEPGVRGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSP 819
Query: 530 I-SQDEAQGQASRYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGD 588
E + + +RD SI RH E G+VD VL+T A+G + VKVRVR +RIP IGD
Sbjct: 820 PRFLQEFKELSPEQAKRDTSIVTRHGEMGIVDLVLITETAEGNKLVKVRVRDLRIPSIGD 879
Query: 589 KFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHM 648
KF+SRHGQKG +GM Q DMP+TV+G+ PD+I+NPHA+PSRMT+GQ++E I GK AA
Sbjct: 880 KFASRHGQKGVIGMLIPQVDMPYTVKGVVPDVILNPHALPSRMTLGQIMEGIAGKYAALS 939
Query: 649 GKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHM 708
G DATPF ++ + + K GY E Y+G TG+++ + I+ G YYQ+L HM
Sbjct: 940 GNIVDATPFYKTPIEQLQNEILKYGYLPDATEVTYDGRTGQKIKSRIYFGVVYYQKLHHM 999
Query: 709 VDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAY 768
V DKIH+R RGPVQILTRQP EGR+R+GGLRFGEMERDC+I G + LK+RL D SD
Sbjct: 1000 VADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGFGTAMLLKDRLLDNSDRT 1059
Query: 769 RVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTK 828
++VC+ CG I + KN + C +K+++ V + YA KLL QELM+M I+PR++ +
Sbjct: 1060 TIYVCDQCGYIGWYDKNKNKYVCPIHGDKSNLFPVTVSYAFKLLIQELMSMIISPRLILE 1119
Query: 829 EDTKQSK 835
+ S
Sbjct: 1120 DRVGLSG 1126
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1
PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C*
2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C*
3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ...
Length = 1119
Score = 174 bits (442), Expect = 9e-45
Identities = 115/404 (28%), Positives = 182/404 (45%), Gaps = 83/404 (20%)
Query: 432 GINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSY----RDEEKKMGTLVKEDFG 487
G N +VAI + GYN ED++++++ + R F+ S+ Y RD K+G E
Sbjct: 669 GQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDT--KLG---PERIT 723
Query: 488 R--PDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ--------- 536
R P S +R LD++G+ G V D+++G+T+ + E++
Sbjct: 724 RDIPHLSEAA-LRD-----LDEEGVVRIGAEVKPGDILVGRTSF--KGESEPTPEERLLR 775
Query: 537 ---GQASRYTRRDHSISLRHSETGMV-DQVLLTTNADG-------LRFVKVRVRSVRIPQ 585
G+ +R +D S+ + E G+V V L G V+V V R Q
Sbjct: 776 SIFGEKAR-DVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQ 834
Query: 586 IGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVA 645
+GDK ++RHG KG V EDMP +G D+I+NP +PSRM +GQ++E +G
Sbjct: 835 VGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAG 894
Query: 646 AHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFE------------------------- 680
+G+ + F I + L + G
Sbjct: 895 YFLGQRYISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVT 954
Query: 681 ------------------TMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQ 722
+Y+G TG + I +G + +L HMV+DK+H+R GP
Sbjct: 955 PGKTPEEQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYS 1014
Query: 723 ILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSD 766
++T+QP G+++ GG RFGEME + A+GA+H L+E L +SD
Sbjct: 1015 LITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSD 1058
Score = 51.1 bits (123), Expect = 2e-06
Identities = 43/156 (27%), Positives = 69/156 (44%), Gaps = 34/156 (21%)
Query: 37 DDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITS 96
DD DH GN+R+ G L+ FR+ +L R VR + + + + + ++ + +
Sbjct: 323 DDIDHLGNRRIRTVGELMTDQFRVGLARLARGVRE--RMLMGSEDSLTPAKLVNSRPLEA 380
Query: 97 GLK-----YSLATGNWGQANAAGTRAGVSQVL---NRLTYASTLSHLRRLNS--PIG--R 144
++ L SQ N L S+L H RR+++ P G R
Sbjct: 381 AIREFFSRSQL-----------------SQFKDETNPL---SSLRHKRRISALGPGGLTR 420
Query: 145 EGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLA 180
E R +H + +G +CP ETPEG GL+ +LA
Sbjct: 421 ERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLA 456
Score = 29.6 bits (67), Expect = 5.3
Identities = 26/121 (21%), Positives = 42/121 (34%), Gaps = 30/121 (24%)
Query: 315 IEYIDTEEEETTMISM---------TINDLVQARLHPE--EAYADTYTHCEIHPSLILGV 363
+ Y+ EE+ I+ + V AR E + ++ P + V
Sbjct: 483 VVYMTATEEDRYTIAQANTPLEGNRIAAERVVARRKGEPVIVSPEEVEFMDVSPKQVFSV 542
Query: 364 CASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYV-LYYPQKPLVTTRAME 422
++IPF +H+ + R S M QA V L Q P+V T +E
Sbjct: 543 NTNLIPFLEHDDANRALMGSNMQTQA-----------------VPLIRAQAPVVMT-GLE 584
Query: 423 H 423
Sbjct: 585 E 585
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase,
nucleotidyltransferase, transcription, transferase;
11.20A {Escherichia coli} PDB: 3iyd_C*
Length = 1342
Score = 109 bits (275), Expect = 1e-24
Identities = 74/245 (30%), Positives = 111/245 (45%), Gaps = 54/245 (22%)
Query: 571 LRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSR 630
L+ VKV + R Q GDK + RHG KG + EDMP+ G DI++NP +PSR
Sbjct: 1047 LKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSR 1106
Query: 631 MTIGQLIECIMG--------KVAAHMGKEGD----------------------------- 653
M IGQ++E +G K+ A + ++ +
Sbjct: 1107 MNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSD 1166
Query: 654 ----------------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIF 696
ATP F I + L G +Y+G TG + +
Sbjct: 1167 EEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVT 1226
Query: 697 LGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHF 756
+G Y +L H+VDDK+H+R G ++T+QP G+++ GG RFGEME + A+GA++
Sbjct: 1227 VGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1286
Query: 757 LKERL 761
L+E L
Sbjct: 1287 LQEML 1291
Score = 76.7 bits (189), Expect = 2e-14
Identities = 43/163 (26%), Positives = 79/163 (48%), Gaps = 18/163 (11%)
Query: 22 IIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGK 81
++ +L+ G+ DD DH GN+R+ G + FR+ ++ R V+ + + +
Sbjct: 428 VMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLS--LGDLD 485
Query: 82 DVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS- 140
+ Q I AK I++ +K + +SQ + + S ++H RR+++
Sbjct: 486 TLMPQDMINAKPISAAVKEFFGSSQ------------LSQFMVQNNPLSEITHKRRISAL 533
Query: 141 -PIG--REGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLA 180
P G RE + R +H + +G +CP ETPEG GL+ +L+
Sbjct: 534 GPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLS 576
Score = 47.4 bits (113), Expect = 2e-05
Identities = 32/142 (22%), Positives = 62/142 (43%), Gaps = 24/142 (16%)
Query: 432 GINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDE--EKKMGTLVKEDFGR- 488
G N VA ++GYN EDS+++++ + F ++ + + K+G E+
Sbjct: 797 GQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLG---PEEITAD 853
Query: 489 -PDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ----------G 537
P+ KLD+ G+ G V+G D+++GK TP + + G
Sbjct: 854 IPNVGEAA------LSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFG 907
Query: 538 QASRYTRRDHSISLRHSETGMV 559
+ + +D S+ + + +G V
Sbjct: 908 EKASDV-KDSSLRVPNGVSGTV 928
Score = 44.7 bits (106), Expect = 1e-04
Identities = 29/121 (23%), Positives = 45/121 (37%), Gaps = 29/121 (23%)
Query: 315 IEYIDTEEEETTMISMT----------INDLVQARLHPE--EAYADTYTHCEIHPSLILG 362
I Y+ EE +I+ + DLV R E D + ++ ++
Sbjct: 603 IHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVS 662
Query: 363 VCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAME 422
V AS+IPF +H+ + R + M +QA+ KPLV T ME
Sbjct: 663 VGASLIPFLEHDDANRALMGANMQRQAVP----------------TLRADKPLVGT-GME 705
Query: 423 H 423
Sbjct: 706 R 706
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 76.4 bits (187), Expect = 2e-14
Identities = 92/688 (13%), Positives = 181/688 (26%), Gaps = 271/688 (39%)
Query: 59 RMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAG 118
LF L VQK V+ +N +F + S +K +
Sbjct: 65 LRLFWTLLSKQEEMVQKFVEEVLRINYKF------LMSPIKT--------EQRQPS---- 106
Query: 119 VSQVLNRLTYASTLSHLRRLNSP-----IGREGKLAKPR----QLHNSQW----GMMCPA 165
+ Y L N + R K R +L ++ G++
Sbjct: 107 ----MMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVL--- 159
Query: 166 ETPEGQACGLVKN-LALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNG 224
G G K +AL V +Y + + +F KIF
Sbjct: 160 ----G--SG--KTWVALDVC-----LSYKVQCKM------DF------------KIF--- 185
Query: 225 CW--VGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDI-----------RLKELRIYTDYG 271
W + PE +++ L++L ++D N L+ L Y
Sbjct: 186 -WLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYE 244
Query: 272 RCSRPLFIV----EKQ---------RLLIKKRD------IIALQQRESPEDGGWHDLVAK 312
C L ++ + ++L+ R + A D +
Sbjct: 245 NC---LLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDH-----HSM 296
Query: 313 GFIEYIDTEEEETTM----ISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASII 368
T +E ++ + DL P E +P + + SI
Sbjct: 297 TL-----TPDEVKSLLLKYLDCRPQDL------PREV-------LTTNPRRLSIIAESIR 338
Query: 369 PFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAM--EHL-- 424
N++ + L T L
Sbjct: 339 DGLATWD--------------------NWK----------HVNCDKLTTIIESSLNVLEP 368
Query: 425 -----HFRQL---PAGIN---AIVAIACYSGYNQEDSVIMNQ----SSIDRGFFRSLF-- 467
F +L P + ++++ + + V++N+ S +++ S
Sbjct: 369 AEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISI 428
Query: 468 ---FRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRH----GSY---DKLDDDGLAPPGTRV 517
+ + + + L H Y D D L PP
Sbjct: 429 PSIYLELKVKLENEYAL-----------------HRSIVDHYNIPKTFDSDDLIPP---- 467
Query: 518 SGED----VIIGKTTPISQDEAQGQASRYTRRDHSISLRHSE-TGMVDQVLLTTNADGLR 572
D IG + H ++ H E + V L D R
Sbjct: 468 -YLDQYFYSHIG----------------H----HLKNIEHPERMTLFRMVFL----D-FR 501
Query: 573 FVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMT 632
F++ ++R + + T + + + I + R+
Sbjct: 502 FLEQKIRHDSTA-----------WNASGSILNTLQQLKFYKPYICDN-----DPKYERL- 544
Query: 633 IGQLIECIMGKVAAHMGKEGDATPFTDV 660
+ +++ + K+ ++ + +TD+
Sbjct: 545 VNAILDFLP-KIEENLIC----SKYTDL 567
Score = 48.3 bits (114), Expect = 1e-05
Identities = 72/571 (12%), Positives = 149/571 (26%), Gaps = 177/571 (30%)
Query: 317 YIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSL--ILG--VCASIIPFPD 372
++D E T D++ E+A+ D + ++ IL II D
Sbjct: 6 HMDFE---TGEHQYQYKDILS---VFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKD 59
Query: 373 HNQ-----------SPRNTYQSAMGKQAMGIYVTNYQFRMDTLA---------YVLYYPQ 412
Q + + NY+F M + +Y Q
Sbjct: 60 AVSGTLRLFWTLLSKQEEMVQKFVE----EVLRINYKFLMSPIKTEQRQPSMMTRMYIEQ 115
Query: 413 K-----------PLVTTRAMEHLHFR----QLPAGINAIVAIACY----SGYNQEDSVIM 453
+ +R +L R +L N ++ SG + +
Sbjct: 116 RDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLI----DGVLGSG----KTWVA 167
Query: 454 NQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNT-MGMRHGSYDKLDDDGLAP 512
+ + F+ + L + + T + M ++D + +
Sbjct: 168 LDVCLSYKVQCKMDFKIF--------WL---NLKNCNSPETVLEMLQKLLYQIDPNWTSR 216
Query: 513 PGTRVSGEDVIIGKTTPISQDEAQGQASRY-TRRDHSISL------RHSETGMVD----- 560
+ Q + R + + L ++++ +
Sbjct: 217 SD---------HSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKA--WNAFNLS 265
Query: 561 -QVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPD 619
++LLTT R Q+ D S T T + +TPD
Sbjct: 266 CKILLTT---------------RFKQVTDFLS---------AATTTHISLDHHSMTLTPD 301
Query: 620 ---------IIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDAT--PFTDVTVDNISKA 668
+ P +P + + +A + ++G AT + V D ++
Sbjct: 302 EVKSLLLKYLDCRPQDLPREVLTTNPRRLSI--IAESI-RDGLATWDNWKHVNCDKLTTI 358
Query: 669 LHKCGYQMRGFETMYNGHTGRRLTAMIFLGPT----YYQRLKHMVDD-KIHSRGRGPVQI 723
+ N L P + RL I P +
Sbjct: 359 IESS----------LN-----------VLEPAEYRKMFDRLSVFPPSAHI------PTIL 391
Query: 724 LTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCE----HCGLI 779
L+ + D + ++ + ++ + +V + H ++
Sbjct: 392 LSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTI-SIPSIYLELKVKLENEYALHRSIV 450
Query: 780 AIANLKKNSFECRGC-KNKTD--IVQVHIPY 807
N+ K F+ D HI +
Sbjct: 451 DHYNIPKT-FDSDDLIPPYLDQYFYS-HIGH 479
Score = 42.5 bits (99), Expect = 6e-04
Identities = 48/385 (12%), Positives = 96/385 (24%), Gaps = 152/385 (39%)
Query: 2 LPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGN-KRLDLAGPLLGGLFRM 60
LP E + L + D + N K ++ L +
Sbjct: 318 LPR-------EVLT-------TNPRRLSIIAESIRDGLATWDNWKHVNCDK--LTTIIES 361
Query: 61 LFRKLT-RDVRAYVQKCVDNGKDVNLQFAIKAKT---------------ITSGL-KYSLA 103
L + R + + I + + L KYSL
Sbjct: 362 SLNVLEPAEYRKMFDRLSVFPPSAH----IPTILLSLIWFDVIKSDVMVVVNKLHKYSLV 417
Query: 104 TGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNS------ 157
T ++ + KL LH S
Sbjct: 418 EKQP----------------KESTI--SIPSIYLELKV-----KLENEYALHRSIVDHYN 454
Query: 158 ------QWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPI---LEFLEEWGTENFEE 208
++ P + Y ++ I L+ +E E
Sbjct: 455 IPKTFDSDDLIPPYL--DQ-------------YF----YSH-IGHHLKNIEH--PERMTL 492
Query: 209 ISPAVIPQATKIFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIRLKELRIYT 268
+F++ ++ +++R G + + L++L+ Y
Sbjct: 493 FR--------MVFLDFRFLE------------QKIRHDSTAWNASGSILNT-LQQLKFYK 531
Query: 269 DYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDTEEEETTMI 328
Y + P + +RL+ I+ F+ I E +I
Sbjct: 532 PYICDNDPKY----ERLV---NAILD-------------------FLPKI-----EENLI 560
Query: 329 SMTINDLVQ-ARLHPEEA-YADTYT 351
DL++ A + +EA + + +
Sbjct: 561 CSKYTDLLRIALMAEDEAIFEEAHK 585
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 70.8 bits (173), Expect = 2e-12
Identities = 96/549 (17%), Positives = 160/549 (29%), Gaps = 183/549 (33%)
Query: 274 SRPLFI----VEKQRLLIKKRD-IIALQQRES-------PEDGGWHD--------LVAKG 313
+RPL + +E LL+ IA Q +E P +G D LV K
Sbjct: 6 TRPLTLSHGSLE-HVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGK- 63
Query: 314 FIEYIDTEEEETTMISMTINDLVQARL-HPEEAYADTYTHCEIHPSLILGVCASIIPFPD 372
F+ Y+ + E + + ++ L E Y +IH +L A ++ D
Sbjct: 64 FLGYVSSLVEPSKVGQFD--QVLNLCLTEFENCYL---EGNDIH-ALA----AKLLQEND 113
Query: 373 HNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAG 432
+ NY +A ++P + FR + G
Sbjct: 114 TTLVKTKE------------LIKNY-ITARIMA------KRPF--DKKSNSALFRAVGEG 152
Query: 433 INAIVAIACYSGYNQEDSVIMNQSSIDRGF--FRSLFFRSYRDEEKKMGTLVK------E 484
+VAI + G Q + D F R L +++Y +G L+K
Sbjct: 153 NAQLVAI--FGG----------QGNTDDYFEELRDL-YQTYHVL---VGDLIKFSAETLS 196
Query: 485 DFGRPDRSNTMGMRHGSYDK---LDDDGLAPPG-----TRVSGEDVIIGKTTPISQDEAQ 536
+ R G + L++ P +S +IG
Sbjct: 197 ELIRTTLDAEKVFTQG-LNILEWLENPSNTPDKDYLLSIPISC--PLIGVI--------- 244
Query: 537 GQASRYTRRDHSISLRHSETGMVDQVL-LTTNADGL-------------RFVKVRVRSVR 582
Q + Y + E + + T ++ GL F +++
Sbjct: 245 -QLAHYVVTAKLLGFTPGE--LRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAIT 301
Query: 583 IP-QIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRM------TIGQ 635
+ IG R + Y +P I D + N +PS M T Q
Sbjct: 302 VLFFIG----VR-CYE-----AYPNTSLP---PSILEDSLENNEGVPSPMLSISNLTQEQ 348
Query: 636 LIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMI 695
+ + + K +H+ + +L NG ++
Sbjct: 349 V-QDYVNKTNSHLPAGKQ-----------VEISL-------------VNGA-----KNLV 378
Query: 696 FLGPTYYQRLKHMVDD--KIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIA--- 750
GP Q L + K + G Q +R P R RF +A
Sbjct: 379 VSGPP--QSLYGLNLTLRKAKAP-SGLDQ--SRIPFSERKLKFSNRFLP------VASPF 427
Query: 751 HGASHFLKE 759
H SH L
Sbjct: 428 H--SHLLVP 434
Score = 53.5 bits (128), Expect = 3e-07
Identities = 75/471 (15%), Positives = 137/471 (29%), Gaps = 197/471 (41%)
Query: 261 LKELR-IYTDYGRCSRPLFIVEKQRL--LIKKR-----------DIIA-LQQRES-PEDG 304
+ELR +Y Y L + L LI+ +I+ L+ + P+
Sbjct: 170 FEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDK- 228
Query: 305 GWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADT-----YTHCEIHPSL 359
+Y+ + IS + ++Q H Y T +T E+ L
Sbjct: 229 -----------DYLLSIP-----ISCPLIGVIQL-AH----YVVTAKLLGFTPGELRSYL 267
Query: 360 --ILGVCASIIP--FPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYV-----LYY 410
G ++ S + + S ++A+ + L ++ Y
Sbjct: 268 KGATGHSQGLVTAVAIAETDSWESFFVSV--RKAITV-----------LFFIGVRCYEAY 314
Query: 411 PQK---PLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLF 467
P P + ++E+ +P+ +++I S QE Q +++
Sbjct: 315 PNTSLPPSILEDSLENNE--GVPS---PMLSI---SNLTQEQV----QDYVNK------- 355
Query: 468 FRSYRDEEKKMG-TLVKEDFGRPDRSNTMGMRH----GSYDKLDDDGL--------APPG 514
S+ K++ +LV N G ++ G L GL AP G
Sbjct: 356 TNSHLPAGKQVEISLV----------N--GAKNLVVSGPPQSLY--GLNLTLRKAKAPSG 401
Query: 515 ---TRVSGEDVIIGKTTPISQDEAQGQASRYTRRDHSISLR--------HSE--TGMVDQ 561
+R+ P S+ R S R HS D
Sbjct: 402 LDQSRI-----------PFSE------------RKLKFSNRFLPVASPFHSHLLVPASDL 438
Query: 562 VLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDII 621
+ + + F + ++IP V T+ D+ I+ I+
Sbjct: 439 INKDLVKNNVSF---NAKDIQIP---------------VYDTFDGSDLRVLSGSISERIV 480
Query: 622 -------VN---------PHAI---PSRMT-IGQLIECIMGKVAAHMGKEG 652
V H + P + +G L H K+G
Sbjct: 481 DCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLT---------HRNKDG 522
Score = 45.8 bits (108), Expect = 7e-05
Identities = 59/338 (17%), Positives = 96/338 (28%), Gaps = 135/338 (39%)
Query: 386 GKQA--MGIYVTNYQFRMDTLAYVLY--YPQKPLVTTRAMEHLHFRQLPAGINAIV---- 437
G Q MG MD LY V RA H I IV
Sbjct: 1625 GSQEQGMG---------MD-----LYKTSKAAQDVWNRADNHF-KDTYGFSILDIVINNP 1669
Query: 438 -AIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKE--------DFGR 488
+ + G + + N + ++ F + D + K + KE F
Sbjct: 1670 VNLTIHFGGEKGKRIREN--------YSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRS 1721
Query: 489 PDR-----SNT----MGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQGQA 539
T M +++ L GL P +G
Sbjct: 1722 EKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAG-------------------- 1761
Query: 540 SRYTRRDHSISLRHSETGMVDQVL-----LTTNADGLRF---VK-VRVR----SVRIPQI 586
HS L L + AD + V+ V R V +P+
Sbjct: 1762 -------------HS--------LGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPR- 1799
Query: 587 GDKFSSRHG----QKGTVGMTYTQEDMPWTVEGI---TPDI--IVNPHAIPSRMTIGQLI 637
+ S +G G V +++QE + + VE + T + IVN + + + Q +
Sbjct: 1800 DELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVN-YNVEN----QQYV 1854
Query: 638 ECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQ 675
G + A +D ++ L+ Q
Sbjct: 1855 --AAGDLRA---------------LDTVTNVLNFIKLQ 1875
Score = 45.0 bits (106), Expect = 1e-04
Identities = 71/462 (15%), Positives = 135/462 (29%), Gaps = 159/462 (34%)
Query: 6 GTGD--FCETKKAY--YFGYI---IHRL--LLCALGRRAEDDRDHYGNKRLDL------- 49
G D F E + Y Y + I L L R D + + L++
Sbjct: 164 GNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFT-QGLNILEWLENP 222
Query: 50 --------------AGPLLG----GLFRMLFRKL---TRDVRAYVQKCVDNGKDVNLQFA 88
+ PL+G + + + L ++R+Y++ + + +
Sbjct: 223 SNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGL----- 277
Query: 89 IKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKL 148
+ A I T +W + +A + L + IG
Sbjct: 278 VTAVAIA-------ETDSWESFFVSVRKA-----ITVLFF-------------IGVRCYE 312
Query: 149 AKPRQ-LHNSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFE 207
A P L S + E EG M+ I+ + +++ + N
Sbjct: 313 AYPNTSLPPSI--LEDSLENNEGVPS-------PMLSIS-NLTQEQVQDYVNK---TN-- 357
Query: 208 EISPAVIPQATKIF---VNGCWVGIHRDPEMLV-----KTLRRLR---RRVDVNTEVGVV 256
+ +P ++ VNG + LV ++L L R+ + +
Sbjct: 358 ----SHLPAGKQVEISLVNG--------AKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQS 405
Query: 257 RDIRLKE--LRIYTDYGRCSRPLF-----------IVE---KQRLLIKKRDI-IALQQRE 299
R I E L+ + + P F I + K + +DI I +
Sbjct: 406 R-IPFSERKLKFSNRFLPVASP-FHSHLLVPASDLINKDLVKNNVSFNAKDIQIPV---Y 460
Query: 300 SPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHC-EIHPS 358
DG DL ++ ++ +++ + E TH + P
Sbjct: 461 DTFDG--SDL-----------RVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPG 507
Query: 359 LILGV-----------CASIIPFPDHNQSPRNTYQSAMG-KQ 388
G+ +I + +P + Y G KQ
Sbjct: 508 GASGLGVLTHRNKDGTGVRVIVAGTLDINPDDDY----GFKQ 545
Score = 29.2 bits (65), Expect = 8.1
Identities = 26/151 (17%), Positives = 44/151 (29%), Gaps = 57/151 (37%)
Query: 67 RDV--RA-------Y---VQKCV-DNGKDVNLQF-AIKAKTITSG-LKYSLATGNWGQAN 111
+DV RA Y + V +N ++ + F K K I T G+
Sbjct: 1643 QDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLK 1702
Query: 112 AAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQ 171
+++ T+ S +G L+ + +Q P
Sbjct: 1703 TEKIFKEINEHSTSYTF----------RSE---KGLLSATQ---FTQ---------P--- 1734
Query: 172 ACGLVKNLALMVYITVGSAAYPILEFLEEWG 202
AL + AA+ E L+ G
Sbjct: 1735 --------ALT---LMEKAAF---EDLKSKG 1751
>3qqc_A DNA-directed RNA polymerase subunit B, DNA-direct polymerase
subunit A', DNA-directed...; transcription, fusion
protein, chimera protein, multiprotein; 3.30A
{Pyrococcus furiosus}
Length = 436
Score = 36.2 bits (84), Expect = 0.047
Identities = 25/64 (39%), Positives = 35/64 (54%)
Query: 770 VHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKE 829
V VCE+CG IA+ + ++ C C + I +V + YA KLL EL AM I P++ E
Sbjct: 5 VWVCENCGHIALEDKRRRRVYCPVCGEEERISKVEMSYAFKLLLDELKAMVIRPKLNLSE 64
Query: 830 DTKQ 833
K
Sbjct: 65 GGKV 68
>3tbi_B DNA-directed RNA polymerase subunit beta; transcription accessory
protein, transcription; 3.00A {Escherichia coli}
Length = 228
Score = 32.3 bits (74), Expect = 0.47
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 504 KLDDDGLAPPGTRVSGEDVIIGKTTP 529
KLD+ G+ G V+G D+++GK TP
Sbjct: 35 KLDESGIVYIGAEVTGGDILVGKVTP 60
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 30.5 bits (68), Expect = 1.6
Identities = 11/70 (15%), Positives = 22/70 (31%), Gaps = 15/70 (21%)
Query: 281 EKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIE--YIDTEEEETTMISMTINDLVQA 338
E+QR +++ D + + W + AK +E E+
Sbjct: 92 EEQRKRLQELDAASKVMEQE-----WRE-KAKKDLEEWNQRQSEQVEKNKI-------NN 138
Query: 339 RLHPEEAYAD 348
R+ + Y
Sbjct: 139 RIADKAFYQQ 148
>3b98_A Prostaglandin I2 synthase; prostacyclin synthase, cytochrome P450
8A1, CYP8A1, isomerase; HET: HEM; 2.08A {Danio rerio}
PDB: 3b99_A*
Length = 475
Score = 30.7 bits (70), Expect = 2.1
Identities = 3/22 (13%), Positives = 10/22 (45%), Gaps = 1/22 (4%)
Query: 213 VIPQATKIFVNGCWVGIHRDPE 234
+ + ++ V ++ DP+
Sbjct: 347 HLRRGDRLCVF-PFISPQMDPQ 367
>3mpx_A FYVE, rhogef and PH domain-containing protein 5; structural
genomics consortium, DH domain, SGC, L binding protein;
2.80A {Homo sapiens}
Length = 434
Score = 30.3 bits (68), Expect = 3.2
Identities = 14/49 (28%), Positives = 19/49 (38%), Gaps = 7/49 (14%)
Query: 768 YRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQEL 816
R H C CG I N +N + + K++ V C F EL
Sbjct: 389 LRRHHCHACGKIVCRNCSRNKYPLKYLKDRMAKV-------CDGCFGEL 430
>3nvz_C Xanthine dehydrogenase/oxidase; hydroxylase, homodimer, xanthine
oxidase, indole-3-aldehyde, oxidoreductase; HET: FAD MTE
I3A; 1.60A {Bos taurus} PDB: 3ns1_C* 3etr_C* 3nvv_C*
3nvw_C* 3nrz_C* 3nvy_C* 3eub_C* 3b9j_C* 1fiq_C* 3rca_C*
3sr6_C*
Length = 755
Score = 30.3 bits (69), Expect = 3.4
Identities = 14/58 (24%), Positives = 16/58 (27%), Gaps = 17/58 (29%)
Query: 637 IECIMGKVAAHMG------------KEGDATPFTDVTVDN-----ISKALHKCGYQMR 677
E M +VA G KEGD T F + L Y R
Sbjct: 353 AENWMSEVAVTCGLPAEEVRWKNMYKEGDLTHFNQRLEGFSVPRCWDECLKSSQYYAR 410
>3nxu_A Cytochrome P450 3A4; alpha beta protein, cytochrome P450 fold,
hemoprotein, monoo cytochrome P450 reductase,
endoplasmic reticulum; HET: HEM RIT; 2.00A {Homo
sapiens} PDB: 1w0e_A* 1w0g_A* 2j0d_A* 2v0m_A* 1w0f_A*
1tqn_A* 3ua1_A* 3tjs_A*
Length = 485
Score = 29.8 bits (68), Expect = 4.4
Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 3/43 (6%)
Query: 192 YPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPE 234
+PI LE ++ E I+ IP+ + + +HRDP+
Sbjct: 345 FPIAMRLERVCKKDVE-INGMFIPKGVVVMIPSY--ALHRDPK 384
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.322 0.137 0.414
Gapped
Lambda K H
0.267 0.0620 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 13,238,129
Number of extensions: 842773
Number of successful extensions: 1560
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1531
Number of HSP's successfully gapped: 35
Length of query: 842
Length of database: 6,701,793
Length adjustment: 102
Effective length of query: 740
Effective length of database: 3,853,851
Effective search space: 2851849740
Effective search space used: 2851849740
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 61 (27.5 bits)