RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 001021
(1186 letters)
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1210
Score = 1794 bits (4647), Expect = 0.0
Identities = 749/1208 (62%), Positives = 926/1208 (76%), Gaps = 52/1208 (4%)
Query: 15 EEEDEEEEITQEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQ 74
E+ E +TQED W VIS++FEE L RQQL SFDEF+QNTMQEIVD+ + + + +Q
Sbjct: 4 EDYQYNETLTQEDCWTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQ 63
Query: 75 HNPGQQSD-------FAEIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRV 127
H Q F +IYLS+P MTE+DG T T+FP+ ARLRNLTYS+PLYVD+ K+V
Sbjct: 64 HTGAQGDVTRRYEINFGQIYLSRPTMTEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKV 123
Query: 128 IKKGHDGEEVTETQDF--------TKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYD 179
+ + E + +KVFIGK+PIMLRS++C L S+ +L +L ECPYD
Sbjct: 124 MVAADSNVPIGEEEWLVEEEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYD 183
Query: 180 QGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRM 239
QGGYFIINGSEKV+IAQE+ + N V VFKK P+ AYVAE+RS E +R S+M +++
Sbjct: 184 QGGYFIINGSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKL 243
Query: 240 LSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFQDTQMMELL 299
++R +SGQ IRATLPYIR++IPI+IVFRALG V D+DILEHICYD D QM+E++
Sbjct: 244 MAR---NTENSGQTIRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMM 300
Query: 300 RPSLEEAFVIQNQQVALDYIGKRGATVGVTRDKRIKYAKEILQKEMLPHVGTGDFCETKK 359
+P +EEAFVIQ++ +ALDYIGKRG+T GVTR+KR++YA +ILQKE+LPH+ T + ET+K
Sbjct: 301 KPCIEEAFVIQDKDIALDYIGKRGSTTGVTREKRLRYAHDILQKELLPHITTMEGFETRK 360
Query: 360 AYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQK 419
A++ GY+IHR+LLCAL RR DDRDH+G KRLDLAGPLL LFRMLFRK+TRDV Y+QK
Sbjct: 361 AFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQK 420
Query: 420 CVDNGKDVNLQFAIKAKTITSGLKYSLATGNWG-QANAAGTRAGVSQVLNRLTYASTLSH 478
CV+ ++ NL A+K+ IT+GL+YSLATGNWG Q + R GVSQVLNR T+ASTLSH
Sbjct: 421 CVETNREFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSH 480
Query: 479 LRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPI 538
LRR N+PIGR+GKLAKPRQLHN+ WGM+CPAETPEGQACGLVKNL+LM Y++VGS + PI
Sbjct: 481 LRRTNTPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPI 540
Query: 539 LEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVG 598
+EFLEEWG E E+ +P+ P ATK+FVNG W+G+HRDP L +TLR LRRR+D++ EV
Sbjct: 541 IEFLEEWGLETLEDYNPSASPNATKVFVNGVWLGVHRDPAHLTETLRSLRRRLDISAEVS 600
Query: 599 VVRDIRLKELRIYTDYGRCSRPLFIVE-------KQRLLIKKRDIIALQQRESPEDG--- 648
+VRDIR KELR++TD GR RPLFIV+ + L I+K I L + + D
Sbjct: 601 IVRDIREKELRLFTDAGRICRPLFIVDNNPNSERRGELCIRKEHIQQLIEDKDRYDIDPE 660
Query: 649 ---GWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLH------------------PE 687
GW LV+ G IEY+D EEEET MI+M+ DL +R
Sbjct: 661 QRFGWTALVSSGLIEYLDAEEEETVMIAMSPEDLEASRQMQAGYEVKEELDPAQRVKPAP 720
Query: 688 EAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDT 747
+ +THCEIHP++ILG+ ASIIPFPDHNQSPRNTYQSAMGKQAMG+Y+TNYQ RMDT
Sbjct: 721 NPHVHAWTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDT 780
Query: 748 LAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFF 807
+A +LYYPQKPL TTR+ME+L FR+LPAG NAIVAI CYSGYNQEDS+IMNQ+SIDRG F
Sbjct: 781 MANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLF 840
Query: 808 RSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVI 867
RS+F+R+Y D+EKK+G V E+F RP RS T+ M+HG+YDKL+DDGL PGTRVSGED+I
Sbjct: 841 RSIFYRTYTDQEKKIGMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDII 900
Query: 868 IGKTTPISQDEAQ--GQASRYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSV 925
IGKT PI D + + + +RD S LR +E+G+VDQV++TTN +GL+FVKVR+RS
Sbjct: 901 IGKTAPIPLDHEELGQRTQLHAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRST 960
Query: 926 RIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIM 985
RIPQIGDKF+SRHGQKGT+GMTY EDMP++ +GI PDII+NPHAIPSRMT+ L+EC +
Sbjct: 961 RIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQL 1020
Query: 986 GKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTY 1045
KV+A G EGDATPFTDVTV+ +SK L G+Q RGFE MY+GHTGR+L A +FLGPTY
Sbjct: 1021 SKVSALSGFEGDATPFTDVTVEAVSKLLRSHGFQSRGFEVMYHGHTGRKLVAQVFLGPTY 1080
Query: 1046 YQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERL 1105
YQRLKH+VDDKIH+R RGPVQILTRQP EGRSRDGGLRFGEMERDC I+HG S L+ERL
Sbjct: 1081 YQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERDCQISHGCSSVLRERL 1140
Query: 1106 FDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAI 1165
FD SDAYRV VC+ CGLIAIA+ KK+S+ECR C+N+T QV++PYA KLLFQELM+M I
Sbjct: 1141 FDCSDAYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQVYLPYAAKLLFQELMSMNI 1200
Query: 1166 APRMLTKE 1173
APR+ TK
Sbjct: 1201 APRLFTKN 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 = 1782 bits (4618), Expect = 0.0
Identities = 732/1221 (59%), Positives = 915/1221 (74%), Gaps = 53/1221 (4%)
Query: 2 MEDDYDYEEQHQQEEEDEEEEITQEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIV 61
+ + Y ++ EDE IT ED+WAVISA+F EKGLV QQLDSF++F+ T+Q+I+
Sbjct: 4 LANSEKYYDEDPYGFEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDII 63
Query: 62 DESADIEIRPESQHNPGQQSD-------FAEIYLSKPMMTESDGETATLFPKAARLRNLT 114
E + + + +QH + F +IY++KPM+ ESDG T L+P+ ARLRNLT
Sbjct: 64 CEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLT 123
Query: 115 YSAPLYVDVTKRVIKKG----------HDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQ 164
YS+ L+VDV KR + EE + + KVFIG++PIMLRS C L +
Sbjct: 124 YSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSE 183
Query: 165 NSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSM 224
+E DL +L ECP+D GGYFIINGSEKVLIAQE+ + N V VFKK P+ ++VAE+RS
Sbjct: 184 ATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSA 243
Query: 225 AESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILE 284
E +R ST+ V++ + GSS + I+ATLPYI+ +IPI+I+FRALG + D +ILE
Sbjct: 244 LEKGSRFISTLQVKLYG----REGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILE 299
Query: 285 HICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGATVGVTRDKRIKYAKEILQKE 344
HICYD D QM+E+L+P +E+ FVIQ+++ ALD+IG+RG +G+ ++KRI+YAK+ILQKE
Sbjct: 300 HICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKE 359
Query: 345 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRM 404
LPH+ + E++KA++ GY+I+RLLLCAL R+ +DDRDH+G KRLDLAGPLL LF+
Sbjct: 360 FLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKT 419
Query: 405 LFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWG-QANAAGTRAGV 463
LF+KLT+D+ Y+Q+ V+ D N++ AI AKTITSGLKY+LATGNWG Q A +RAGV
Sbjct: 420 LFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGV 479
Query: 464 SQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNL 523
SQVLNR TY+STLSHLRR N+PIGR+GKLAKPRQLHN+ WG++CPAETPEGQACGLVKNL
Sbjct: 480 SQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNL 539
Query: 524 ALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKT 583
+LM I+VG+ PI+ FL EWG E E+ P P AT++FVNG W G+HR+P L++T
Sbjct: 540 SLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMET 599
Query: 584 LRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVE------KQRLLIKKRDII 637
LR LRR+ D+N EV ++RDIR KEL+I+TD GR RPLFIVE + L ++K I
Sbjct: 600 LRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIA 659
Query: 638 ALQQR---------ESPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEE 688
L E E+ W L+ +G +EYID EEEE+ +I+M DL A + E
Sbjct: 660 KLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEEN 719
Query: 689 -------------AYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 735
+A T+THCEIHPS+ILGV ASIIPFPDHNQSPRNTYQSAMGKQAMG
Sbjct: 720 DLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMG 779
Query: 736 IYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSV 795
+++TNY RMDT+A +LYYPQKPL TTRAME+L FR+LPAG NAIVAIACYSGYNQEDS+
Sbjct: 780 VFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSM 839
Query: 796 IMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLA 855
IMNQSSIDRG FRSLFFRSY D+EKK G + E F +P R+NT+ M+HG+YDKLDDDGL
Sbjct: 840 IMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLI 899
Query: 856 PPGTRVSGEDVIIGKTTPISQDEAQ--GQASRYTRRDHSISLRHSETGMVDQVLLTTNAD 913
PG RVSGEDVIIGKTTPIS DE + + + +++RD S LR +E G+VDQVL+TTN D
Sbjct: 900 APGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQD 959
Query: 914 GLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPS 973
GL+FVKVRVR+ +IPQIGDKF+SRHGQKGT+G+TY +EDMP+T EGI PD+I+NPHAIPS
Sbjct: 960 GLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPS 1019
Query: 974 RMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGR 1033
RMT+ LIEC++ KVAA G EGDA+PFTD+TV+ ISK L + GYQ RGFE MYNGHTG+
Sbjct: 1020 RMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGK 1079
Query: 1034 RLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMI 1093
+L A IF GPTYYQRL+HMVDDKIH+R RGP+Q+LTRQP EGRSRDGGLRFGEMERDCMI
Sbjct: 1080 KLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMI 1139
Query: 1094 AHGASHFLKERLFDQSDAYRVHVCEHCGLIA-IANLKKNSFECRGCKNKTDIVQVHIPYA 1152
AHGA+ FLKERL + SDA+RVH+C CGL+ IA L N FEC+GC NK DI Q+HIPYA
Sbjct: 1140 AHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYA 1199
Query: 1153 CKLLFQELMAMAIAPRMLTKE 1173
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 = 1617 bits (4189), Expect = 0.0
Identities = 491/1175 (41%), Positives = 694/1175 (59%), Gaps = 62/1175 (5%)
Query: 17 EDEEEEITQEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHN 76
+ ++ ++ W VI AYF+ KGLVRQ LDS+++F++N +QEI+DE +I
Sbjct: 2 NELSSNLSIDERWKVIEAYFKSKGLVRQHLDSYNDFVRNKLQEIIDEQGEIPT-----EI 56
Query: 77 PGQQSDFAEIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEE 136
PG + +I + KP + ESD + P ARLRNLTY+APL++ + + E
Sbjct: 57 PGLKVRLGKIRIGKPRVRESDRGEREISPMEARLRNLTYAAPLWLTMIPVE-----NNIE 111
Query: 137 VTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQ 196
+ +V+IG +PIML+S+ + Q + L E+GE P D GGYFI+NGSE+V++ Q
Sbjct: 112 A----EPEEVYIGDLPIMLKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERVIVTQ 167
Query: 197 EKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRA 256
E ++ N V V + + + A++ S P + ++
Sbjct: 168 EDLAPNRVLVDTGKTGSNITHTAKIISSTAGYRVPVTIERLK------------DGTFHV 215
Query: 257 TLPYIRTEIPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVAL 316
+ P + +IP +I+ RALG + D+DI+ + D ++ L PSLE+A I N AL
Sbjct: 216 SFPAVPGKIPFVILMRALGILTDRDIVYAVSLD---PEIQNELFPSLEQASSIANVDDAL 272
Query: 317 DYIGKRGATVGVTRDKRIKYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALG 376
D+IG R A +G R+ RI+ A++I+ K LPH+GT KKAYY Y I +++ LG
Sbjct: 273 DFIGSRVA-IGQKRENRIEKAQQIIDKYFLPHLGTSADDRRKKAYYLAYAISKVIELYLG 331
Query: 377 RRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAK 436
RR DD+DHY NKRL LAG L LFR+ F+ +D+ ++K G+ + L+ ++
Sbjct: 332 RREPDDKDHYANKRLRLAGDLFASLFRVAFKAFVKDLTYQLEKSKVRGRKLALKALVRPD 391
Query: 437 TITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPR 496
+T ++++LATGNW R GVSQ+L+R + S LSHLRR+ S + R + R
Sbjct: 392 IVTERIRHALATGNWVG-----GRTGVSQLLDRTNWLSMLSHLRRVISSLARGQPNFEAR 446
Query: 497 QLHNSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPA 556
LH +QWG MCP ETPEG GLVKNLALM I VG + + L E G EE+
Sbjct: 447 DLHGTQWGRMCPFETPEGPNSGLVKNLALMAQIAVGINEKIVEKTLYEMGVVPVEEVIRR 506
Query: 557 VI---------PQATKIFVNGCWVGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDIR--L 605
V + +K+ +NG VG +RD E L K +R RR+ +++ EV V + +
Sbjct: 507 VTEGGEDQNEYLKWSKVILNGRLVGYYRDGEELAKKIRERRRKGEISDEVNVGHIVTDFI 566
Query: 606 KELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIEYIDTE 665
E+ + D GR RPL IV L+ + DI L + DLV +G IEY+D E
Sbjct: 567 NEVHVNCDSGRVRRPLIIVSNGNPLVTREDIEKLDSGSI----TFDDLVRQGKIEYLDAE 622
Query: 666 EEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTY 725
EEE +++ +DL +TH EI ILG+ ASIIP+P+HNQSPRNTY
Sbjct: 623 EEENAYVALEPSDL-----------TPEHTHLEIWSPAILGITASIIPYPEHNQSPRNTY 671
Query: 726 QSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIAC 785
QSAM KQA+G+Y NYQ R DT A++L+YPQ+PLV TRA++ + + PAG NAI+A+
Sbjct: 672 QSAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQTRALDIIGYTNRPAGNNAILAVIS 731
Query: 786 YSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGS 845
++GYN EDS+IMN+SS++RG +RS FFR Y EE K ++ P+
Sbjct: 732 FTGYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEVKYPGGQEDKIVMPEPGVRGYKGKEY 791
Query: 846 YDKLDDDGLAPPGTRVSGEDVIIGKTTPI-SQDEAQGQASRYTRRDHSISLRHSETGMVD 904
Y L+D+G+ P V G DV+IGK +P E + + +RD SI RH E G+VD
Sbjct: 792 YRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAKRDTSIVTRHGEMGIVD 851
Query: 905 QVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDI 964
VL+T A+G + VKVRVR +RIP IGDKF+SRHGQKG +GM Q DMP+TV+G+ PD+
Sbjct: 852 LVLITETAEGNKLVKVRVRDLRIPSIGDKFASRHGQKGVIGMLIPQVDMPYTVKGVVPDV 911
Query: 965 IVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFE 1024
I+NPHA+PSRMT+GQ++E I GK AA G DATPF ++ + + K GY E
Sbjct: 912 ILNPHALPSRMTLGQIMEGIAGKYAALSGNIVDATPFYKTPIEQLQNEILKYGYLPDATE 971
Query: 1025 TMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRF 1084
Y+G TG+++ + I+ G YYQ+L HMV DKIH+R RGPVQILTRQP EGR+R+GGLRF
Sbjct: 972 VTYDGRTGQKIKSRIYFGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRF 1031
Query: 1085 GEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDI 1144
GEMERDC+I G + LK+RL D SD ++VC+ CG I + KN + C +K+++
Sbjct: 1032 GEMERDCLIGFGTAMLLKDRLLDNSDRTTIYVCDQCGYIGWYDKNKNKYVCPIHGDKSNL 1091
Query: 1145 VQVHIPYACKLLFQELMAMAIAPRMLTKEDTKQSK 1179
V + YA KLL QELM+M I+PR++ ++ S
Sbjct: 1092 FPVTVSYAFKLLIQELMSMIISPRLILEDRVGLSG 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 = 172 bits (438), Expect = 1e-43
Identities = 115/404 (28%), Positives = 182/404 (45%), Gaps = 83/404 (20%)
Query: 776 GINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSY----RDEEKKMGTLVKEDFG 831
G N +VAI + GYN ED++++++ + R F+ S+ Y RD K+G E
Sbjct: 669 GQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDT--KLG---PERIT 723
Query: 832 R--PDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ--------- 880
R P S +R LD++G+ G V D+++G+T+ + E++
Sbjct: 724 RDIPHLSEAA-LRD-----LDEEGVVRIGAEVKPGDILVGRTSF--KGESEPTPEERLLR 775
Query: 881 ---GQASRYTRRDHSISLRHSETGMV-DQVLLTTNADG-------LRFVKVRVRSVRIPQ 929
G+ +R +D S+ + E G+V V L G V+V V R Q
Sbjct: 776 SIFGEKAR-DVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQ 834
Query: 930 IGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVA 989
+GDK ++RHG KG V EDMP +G D+I+NP +PSRM +GQ++E +G
Sbjct: 835 VGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAG 894
Query: 990 AHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFE------------------------- 1024
+G+ + F I + L + G
Sbjct: 895 YFLGQRYISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVT 954
Query: 1025 ------------------TMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQ 1066
+Y+G TG + I +G + +L HMV+DK+H+R GP
Sbjct: 955 PGKTPEEQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYS 1014
Query: 1067 ILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSD 1110
++T+QP G+++ GG RFGEME + A+GA+H L+E L +SD
Sbjct: 1015 LITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSD 1058
Score = 92.4 bits (230), Expect = 5e-19
Identities = 106/528 (20%), Positives = 184/528 (34%), Gaps = 141/528 (26%)
Query: 45 QLDSFDEFIQNTMQEIVDESADI-----EIRPESQHNPGQQS---DFAEIYLSKPMMTES 96
Q++S+ +Q + E+ I E P + + G+ DF E L +P +
Sbjct: 22 QVESYRRALQADVPPEKRENVGIQAAFRETFPIEEEDKGKGGLVLDFLEYRLGEPPFPQD 81
Query: 97 DGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLR 156
+ R ++LTY APLY ++I K D + E + VF+G +P+M
Sbjct: 82 E----------CREKDLTYQAPLYA--RLQLIHK--DTGLIKE-DE---VFLGHIPLM-- 121
Query: 157 SSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYA 216
TE G FIING+++V+++Q S + +P +Y
Sbjct: 122 --------------TEDGS--------FIINGADRVIVSQIHRSPGVYFTPDPARPGRYI 159
Query: 217 YVAEV------RSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIV 270
E + + +++ + + P++++
Sbjct: 160 ASIIPLPKRGPWIDLEVEPN--GVVSMKV---------------------NKRKFPLVLL 196
Query: 271 FRALGFVADKDILEHICYDFQD--TQMMELLRPSLEEAFVIQNQQV----------ALDY 318
R LG+ + E Y + EEA + + A+ Y
Sbjct: 197 LRVLGYDQETLARELGAYGELVQGLMDESVFAMRPEEALIRLFTLLRPGDPPKRDKAVAY 256
Query: 319 IGKRG--------ATVGVTRDKRIKYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRL 370
+ G R K ++ L + K F + L
Sbjct: 257 VYGLIADPRRYDLGEAG-----RYKAEEK-LGIRLSGRTLARFEDGEFKDEVFLPTLRYL 310
Query: 371 LLCALGRRAE--DDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVN 428
G DD DH GN+R+ G L+ FR+ +L R VR + + + +
Sbjct: 311 FALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGLARLARGVRE--RMLMGSEDSLT 368
Query: 429 LQFAIKAKTITSGLK-----YSLATGNWGQANAAGTRAGVSQVL---NRLTYASTLSHLR 480
+ ++ + + ++ L SQ N L S+L H R
Sbjct: 369 PAKLVNSRPLEAAIREFFSRSQL-----------------SQFKDETNPL---SSLRHKR 408
Query: 481 RLNS--PIG--REGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLA 524
R+++ P G RE R +H + +G +CP ETPEG GL+ +LA
Sbjct: 409 RISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLA 456
Score = 29.2 bits (66), Expect = 9.8
Identities = 26/121 (21%), Positives = 42/121 (34%), Gaps = 30/121 (24%)
Query: 659 IEYIDTEEEETTMISM---------TINDLVQARLHPE--EAYADTYTHCEIHPSLILGV 707
+ Y+ EE+ I+ + V AR E + ++ P + V
Sbjct: 483 VVYMTATEEDRYTIAQANTPLEGNRIAAERVVARRKGEPVIVSPEEVEFMDVSPKQVFSV 542
Query: 708 CASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYV-LYYPQKPLVTTRAME 766
++IPF +H+ + R S M QA V L Q P+V T +E
Sbjct: 543 NTNLIPFLEHDDANRALMGSNMQTQA-----------------VPLIRAQAPVVMT-GLE 584
Query: 767 H 767
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 = 108 bits (272), Expect = 6e-24
Identities = 74/245 (30%), Positives = 111/245 (45%), Gaps = 54/245 (22%)
Query: 915 LRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSR 974
L+ VKV + R Q GDK + RHG KG + EDMP+ G DI++NP +PSR
Sbjct: 1047 LKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSR 1106
Query: 975 MTIGQLIECIMG--------KVAAHMGKEGD----------------------------- 997
M IGQ++E +G K+ A + ++ +
Sbjct: 1107 MNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSD 1166
Query: 998 ----------------ATP-FTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIF 1040
ATP F I + L G +Y+G TG + +
Sbjct: 1167 EEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVT 1226
Query: 1041 LGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHF 1100
+G Y +L H+VDDK+H+R G ++T+QP G+++ GG RFGEME + A+GA++
Sbjct: 1227 VGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1286
Query: 1101 LKERL 1105
L+E L
Sbjct: 1287 LQEML 1291
Score = 75.9 bits (187), Expect = 7e-14
Identities = 43/163 (26%), Positives = 79/163 (48%), Gaps = 18/163 (11%)
Query: 366 IIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGK 425
++ +L+ G+ DD DH GN+R+ G + FR+ ++ R V+ + + +
Sbjct: 428 VMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLS--LGDLD 485
Query: 426 DVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS- 484
+ Q I AK I++ +K + +SQ + + S ++H RR+++
Sbjct: 486 TLMPQDMINAKPISAAVKEFFGSSQ------------LSQFMVQNNPLSEITHKRRISAL 533
Query: 485 -PIG--REGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLA 524
P G RE + R +H + +G +CP ETPEG GL+ +L+
Sbjct: 534 GPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLS 576
Score = 65.1 bits (159), Expect = 1e-10
Identities = 35/169 (20%), Positives = 68/169 (40%), Gaps = 60/169 (35%)
Query: 41 LVRQQLDSFDEFIQNTMQE-------------IVDESADIEIRPESQHNPGQQSDFAEIY 87
L+ QLDSF +FI+ + I S + E+ +
Sbjct: 27 LLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSEL------------QYVSYR 74
Query: 88 LSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVF 147
L +P+ + ++R +TYSAPL V + + ++ V + ++ +V+
Sbjct: 75 LGEPVFDVQE----------CQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKE-QEVY 123
Query: 148 IGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQ 196
+G++P+M T+ G F+ING+E+V+++Q
Sbjct: 124 MGEIPLM----------------TD--------NGTFVINGTERVIVSQ 148
Score = 47.0 bits (112), Expect = 4e-05
Identities = 33/140 (23%), Positives = 64/140 (45%), Gaps = 20/140 (14%)
Query: 776 GINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDE--EKKMGTLVKEDFGRP 833
G N VA ++GYN EDS+++++ + F ++ + + K+G E+
Sbjct: 797 GQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLG---PEEITA- 852
Query: 834 DRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ----------GQA 883
D N + + KLD+ G+ G V+G D+++GK TP + + G+
Sbjct: 853 DIPN---VGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFGEK 909
Query: 884 SRYTRRDHSISLRHSETGMV 903
+ +D S+ + + +G V
Sbjct: 910 ASDV-KDSSLRVPNGVSGTV 928
Score = 44.3 bits (105), Expect = 3e-04
Identities = 29/121 (23%), Positives = 45/121 (37%), Gaps = 29/121 (23%)
Query: 659 IEYIDTEEEETTMISMT----------INDLVQARLHPE--EAYADTYTHCEIHPSLILG 706
I Y+ EE +I+ + DLV R E D + ++ ++
Sbjct: 603 IHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVS 662
Query: 707 VCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAME 766
V AS+IPF +H+ + R + M +QA+ KPLV T ME
Sbjct: 663 VGASLIPFLEHDDANRALMGANMQRQAVP----------------TLRADKPLVGT-GME 705
Query: 767 H 767
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 = 76.0 bits (186), Expect = 5e-14
Identities = 92/688 (13%), Positives = 181/688 (26%), Gaps = 271/688 (39%)
Query: 403 RMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAG 462
LF L VQK V+ +N +F + S +K +
Sbjct: 65 LRLFWTLLSKQEEMVQKFVEEVLRINYKF------LMSPIKT--------EQRQPS---- 106
Query: 463 VSQVLNRLTYASTLSHLRRLNSP-----IGREGKLAKPR----QLHNSQW----GMMCPA 509
+ Y L N + R K R +L ++ G++
Sbjct: 107 ----MMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVL--- 159
Query: 510 ETPEGQACGLVKN-LALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNG 568
G G K +AL V +Y + + +F KIF
Sbjct: 160 ----G--SG--KTWVALDVC-----LSYKVQCKM------DF------------KIF--- 185
Query: 569 CW--VGIHRDPEMLVKTLRRLRRRVDVNTEVGVVRDI-----------RLKELRIYTDYG 615
W + PE +++ L++L ++D N L+ L Y
Sbjct: 186 -WLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYE 244
Query: 616 RCSRPLFIV----EKQ---------RLLIKKRD------IIALQQRESPEDGGWHDLVAK 656
C L ++ + ++L+ R + A D +
Sbjct: 245 NC---LLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDH-----HSM 296
Query: 657 GFIEYIDTEEEETTM----ISMTINDLVQARLHPEEAYADTYTHCEIHPSLILGVCASII 712
T +E ++ + DL P E +P + + SI
Sbjct: 297 TL-----TPDEVKSLLLKYLDCRPQDL------PREV-------LTTNPRRLSIIAESIR 338
Query: 713 PFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAM--EHL-- 768
N++ + L T L
Sbjct: 339 DGLATWD--------------------NWK----------HVNCDKLTTIIESSLNVLEP 368
Query: 769 -----HFRQL---PAGIN---AIVAIACYSGYNQEDSVIMNQ----SSIDRGFFRSLF-- 811
F +L P + ++++ + + V++N+ S +++ S
Sbjct: 369 AEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISI 428
Query: 812 ---FRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRH----GSY---DKLDDDGLAPPGTRV 861
+ + + + L H Y D D L PP
Sbjct: 429 PSIYLELKVKLENEYAL-----------------HRSIVDHYNIPKTFDSDDLIPP---- 467
Query: 862 SGED----VIIGKTTPISQDEAQGQASRYTRRDHSISLRHSE-TGMVDQVLLTTNADGLR 916
D IG + H ++ H E + V L D R
Sbjct: 468 -YLDQYFYSHIG----------------H----HLKNIEHPERMTLFRMVFL----D-FR 501
Query: 917 FVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMT 976
F++ ++R + + T + + + I + R+
Sbjct: 502 FLEQKIRHDSTA-----------WNASGSILNTLQQLKFYKPYICDN-----DPKYERL- 544
Query: 977 IGQLIECIMGKVAAHMGKEGDATPFTDV 1004
+ +++ + K+ ++ + +TD+
Sbjct: 545 VNAILDFLP-KIEENLIC----SKYTDL 567
Score = 70.3 bits (171), Expect = 3e-12
Identities = 105/774 (13%), Positives = 209/774 (27%), Gaps = 275/774 (35%)
Query: 8 YEEQHQQEEEDEEEEITQEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIV--DESA 65
+ H + E E + +D I + FE+ D D +Q+ + I+ +E
Sbjct: 1 HHHHHHMDFETGEHQYQYKD----ILSVFEDA--FVDNFDCKD--VQDMPKSILSKEEID 52
Query: 66 DIEIRP-------------ESQHNPGQQSDFAEI------YLSKPMMTESDGETATLFPK 106
I + S+ Q E+ +L P+ TE P
Sbjct: 53 HIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQ------PS 106
Query: 107 AARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNS 166
+ LY D +V K + V+ Q + K LR +
Sbjct: 107 MMTRMYIEQRDRLYNDN--QVFAKYN----VSRLQPYLK---------LRQA-------- 143
Query: 167 EKDLTELGECPYDQGGYFIING---SEK-VLIAQEKMSTNHVYVFKKRQPNKYAYVAEVR 222
L EL +I+G S K + +S Y + + K ++
Sbjct: 144 ---LLEL-----RPAKNVLIDGVLGSGKTWVALDVCLS----YKVQCKMDFKIFWL---- 187
Query: 223 SMAESQNRPPSTM-----FVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRA---- 273
++ N P + + + + I+ + I+ E+ ++ +
Sbjct: 188 NLKN-CNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC 246
Query: 274 ---LGFVADKDILEHICYDFQ--------DTQMMELLRPSLEEAFVIQNQQVALDYIGKR 322
L V + ++ Q+ + L + ++LD+
Sbjct: 247 LLVLLNVQNAKAWNA--FNLSCKILLTTRFKQVTDFLSAATT-------THISLDHHSM- 296
Query: 323 GATVGVTRDKRIKYAKEILQK------EMLPHVGTGDFCETKKAYYFGYIIHRLLLCALG 376
+T D+ K +L K + LP E + L +
Sbjct: 297 ----TLTPDE----VKSLLLKYLDCRPQDLPR-------EVLT-------TNPRRLSIIA 334
Query: 377 RRAEDDRDHYGN-KRLDLAGPLLGGLFRMLFRKLT-RDVRAYVQKCVDNGKDVNLQFAIK 434
D + N K ++ L + L + R + + I
Sbjct: 335 ESIRDGLATWDNWKHVNCDK--LTTIIESSLNVLEPAEYRKMFDRLSVFPPSAH----IP 388
Query: 435 AKT---------------ITSGL-KYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSH 478
+ + L KYSL T ++
Sbjct: 389 TILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQP----------------KESTI--SIPS 430
Query: 479 LRRLNSPIGREGKLAKPRQLHNS------------QWGMMCPAETPEGQACGLVKNLALM 526
+ KL LH S ++ P +
Sbjct: 431 IYLELKV-----KLENEYALHRSIVDHYNIPKTFDSDDLIPPYL--DQ------------ 471
Query: 527 VYITVGSAAYPI---LEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKT 583
Y ++ I L+ +E E +F++ ++
Sbjct: 472 -YF----YSH-IGHHLKNIEH--PERMTLFR--------MVFLDFRFLE----------- 504
Query: 584 LRRLRRRVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRE 643
+++R G + + L++L+ Y Y + P + +RL+ I+
Sbjct: 505 -QKIRHDSTAWNASGSILNT-LQQLKFYKPYICDNDPKY----ERLV---NAILD----- 550
Query: 644 SPEDGGWHDLVAKGFIEYIDTEEEETTMISMTINDLVQ-ARLHPEEA-YADTYT 695
F+ I E +I DL++ A + +EA + + +
Sbjct: 551 --------------FLPKI-----EENLICSKYTDLLRIALMAEDEAIFEEAHK 585
Score = 62.2 bits (150), Expect = 1e-09
Identities = 94/695 (13%), Positives = 192/695 (27%), Gaps = 248/695 (35%)
Query: 270 VFRALGFVADKDILEHICYDFQDTQMMELLRPS---LEEAFVIQNQQVALD---YIGKRG 323
R + K E + F + E+LR + L + +Q ++ YI +R
Sbjct: 64 TLRLFWTLLSKQ--EEMVQKF----VEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRD 117
Query: 324 ATVG---------VTRDKRIKYAKEILQKEMLPH--------VGTG------DFCETKK- 359
V+R + ++ L E+ P +G+G D C + K
Sbjct: 118 RLYNDNQVFAKYNVSRLQPYLKLRQALL-ELRPAKNVLIDGVLGSGKTWVALDVCLSYKV 176
Query: 360 -------AYY--FGY------IIHRLL-LCA-LGRRAEDDRDHYGNKRLDLAGPLLGGLF 402
++ ++ L L + DH N +L + +
Sbjct: 177 QCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIH--SIQAEL 234
Query: 403 RMLFRKLTRDVRAYVQKC---VDNGKDVNL--QFAIKAKTITSGLKYSLATGNWGQANAA 457
R L + + Y + C + N ++ F + K L T
Sbjct: 235 RRLLKS-----KPY-ENCLLVLLNVQNAKAWNAFNLSCKI--------LLT--------- 271
Query: 458 GTR-AGVSQVLNRLTYASTLSHLRRLNSPIG---REGK--LAKPRQLHNSQWGMMCPAET 511
TR V+ L+ A+T +H+ + + E K L K + P +
Sbjct: 272 -TRFKQVTDFLS----AATTTHISLDHHSMTLTPDEVKSLLLK--------YLDCRPQDL 318
Query: 512 PEGQACGLVKNLAL-MVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCW 570
P + L ++ A I + L W +N++ ++ + + +N
Sbjct: 319 PR-EVLT-TNPRRLSII------AES-IRDGLATW--DNWKHVNCDKLTTIIESSLN--- 364
Query: 571 VGIHRDPEMLVKTLRRLRR-----RVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVE 625
+P R++ + I L + S + +V
Sbjct: 365 ---VLEPA----EYRKMFDRLSVFPPSAH--------IPTILLSLIWFDVIKSDVMVVVN 409
Query: 626 K--QRLLIKKRDIIALQQRESPEDG--GWHDLVAKGFIEYIDTEEEETTMISMTINDLVQ 681
K + L++K+ P++ + Y++
Sbjct: 410 KLHKYSLVEKQ----------PKESTISIPSI-------YLEL----------------- 435
Query: 682 ARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNY 741
++ E YA +H S++ DH P+ + + Y Y
Sbjct: 436 -KVKLENEYA-------LHRSIV-----------DHYNIPKTFDSDDLIPPYLDQYF--Y 474
Query: 742 QFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSS 801
+ + L + FR + + + S + +
Sbjct: 475 SH----IGHHLKNIE------HPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTL 524
Query: 802 IDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRV 861
F++ + E+ + + DF +
Sbjct: 525 QQLKFYKPYICDNDPKYERLVNAI--LDF---------LPKI------------------ 555
Query: 862 SGEDVIIGKTTPISQ-----------DEAQGQASR 885
E++I K T + + +EA Q R
Sbjct: 556 -EENLICSKYTDLLRIALMAEDEAIFEEAHKQVQR 589
Score = 48.3 bits (114), Expect = 2e-05
Identities = 72/575 (12%), Positives = 148/575 (25%), Gaps = 185/575 (32%)
Query: 661 YIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHCEIHPSL--ILG--VCASIIPFPD 716
++D E T D++ E+A+ D + ++ IL II D
Sbjct: 6 HMDFE---TGEHQYQYKDILS---VFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKD 59
Query: 717 HNQ-----------SPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAM 765
Q + + NY+F M + ++P + TR
Sbjct: 60 AVSGTLRLFWTLLSKQEEMVQKFVE----EVLRINYKFLMSPIKTE---QRQPSMMTRMY 112
Query: 766 EHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRG-FFRSLFFRS--YRDEEKK- 821
R YN D+ + + ++ R + L R K
Sbjct: 113 IEQRDRL----------------YN--DNQVFAKYNVSRLQPYLKL--RQALLELRPAKN 152
Query: 822 -----MG-----TLVKE------------------DFGRPDRSNT-MGMRHGSYDKLDDD 852
+ + + + + T + M ++D +
Sbjct: 153 VLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPN 212
Query: 853 GLAPPGTRVSGEDVIIGKTTPISQDEAQGQASRY-TRRDHSISL------RHSETGMVD- 904
+ + Q + R + + L ++++ +
Sbjct: 213 WTSRSD---------HSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKA--WNA 261
Query: 905 -----QVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEG 959
++LLTT R Q+ D S T T +
Sbjct: 262 FNLSCKILLTT---------------RFKQVTDFLS---------AATTTHISLDHHSMT 297
Query: 960 ITPD---------IIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDAT--PFTDVTVDN 1008
+TPD + P +P + + +A + ++G AT + V D
Sbjct: 298 LTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSI--IAESI-RDGLATWDNWKHVNCDK 354
Query: 1009 ISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPT----YYQRLKHMVDD-KIHSRGRG 1063
++ + N L P + RL I
Sbjct: 355 LTTIIESS----------LN-----------VLEPAEYRKMFDRLSVFPPSAHI------ 387
Query: 1064 PVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCE----H 1119
P +L+ + D + ++ + ++ + +V + H
Sbjct: 388 PTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTI-SIPSIYLELKVKLENEYALH 446
Query: 1120 CGLIAIANLKKNSFECRGC-KNKTD--IVQVHIPY 1151
++ N+ K F+ D HI +
Sbjct: 447 RSIVDHYNIPKT-FDSDDLIPPYLDQYFYS-HIGH 479
Score = 45.6 bits (107), Expect = 1e-04
Identities = 84/575 (14%), Positives = 166/575 (28%), Gaps = 186/575 (32%)
Query: 1 MMEDDYDYEE--QHQQEE----------EDEEEEI-TQEDAWAVISAYFEEKGLVRQQLD 47
E Y Y++ ++ +D + I ++E+ +I + G +
Sbjct: 11 TGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSG-TLRLFW 69
Query: 48 SFDEFIQNTMQEIVDESADIE-------IRPESQHNPGQQSDFAEIYLSKPMMTESDGET 100
+ + +Q+ V+E I I+ E + Q S +Y+ + +D +
Sbjct: 70 TLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQR----QPSMMTRMYIEQRDRLYNDNQ- 124
Query: 101 ATLFPK--------AARLRNLTYSAPLYVDVTKRVIKKGHDG-------------EEVTE 139
+F K +LR + K V+ G G +V
Sbjct: 125 --VFAKYNVSRLQPYLKLRQALLE----LRPAKNVLIDGVLGSGKTWVALDVCLSYKVQC 178
Query: 140 TQDFTKVF---IGK------VPIMLRSSYCTLYQNSEKDLTELGECPYD----------- 179
DF K+F + V ML+ L + + T + +
Sbjct: 179 KMDF-KIFWLNLKNCNSPETVLEMLQ----KLLYQIDPNWTSRSDHSSNIKLRIHSIQAE 233
Query: 180 ------QGGY---FII-------------NGSEKVLIAQEKMSTNHVYVFKKRQPNKYAY 217
Y ++ N S K+L+ +T V +
Sbjct: 234 LRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILL-----TTRFKQVTDFLSAATTTH 288
Query: 218 VAEV---RSMAESQNRPPSTMFVRMLS------RTSAKGGSS------GQYIR---ATLP 259
++ ++ + + ++ ++ L + + IR AT
Sbjct: 289 ISLDHHSMTLTPDEVK---SLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWD 345
Query: 260 YIRT----EIPIII--------------VFRALG-FVADKDI----LEHICYD--FQDTQ 294
+ ++ II +F L F I L I +D D
Sbjct: 346 NWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVM 405
Query: 295 MM--ELLRPSLEEAFVIQNQQVALDYIGKRGATVGVTRDKRIKYAKEI-LQKEMLPHVGT 351
++ +L + SL V + + + I + + ++K E L + ++ H
Sbjct: 406 VVVNKLHKYSL----VEKQPKESTISI------PSIYLELKVKLENEYALHRSIVDHYNI 455
Query: 352 GD-FCETKKA------YYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRM 404
F Y++ +I H L R R + LD FR
Sbjct: 456 PKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVF----LD---------FRF 502
Query: 405 LFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTIT 439
L +K+ D A+ + + Q I
Sbjct: 503 LEQKIRHDSTAW--NASGSILNTLQQLKFYKPYIC 535
>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: 618 SRPLFI----VEKQRLLIKKRD-IIALQQRES-------PEDGGWHD--------LVAKG 657
+RPL + +E LL+ IA Q +E P +G D LV K
Sbjct: 6 TRPLTLSHGSLE-HVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGK- 63
Query: 658 FIEYIDTEEEETTMISMTINDLVQARL-HPEEAYADTYTHCEIHPSLILGVCASIIPFPD 716
F+ Y+ + E + + ++ L E Y +IH +L A ++ D
Sbjct: 64 FLGYVSSLVEPSKVGQFD--QVLNLCLTEFENCYL---EGNDIH-ALA----AKLLQEND 113
Query: 717 HNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAG 776
+ NY +A ++P + FR + G
Sbjct: 114 TTLVKTKEL------------IKNY-ITARIMA------KRPF--DKKSNSALFRAVGEG 152
Query: 777 INAIVAIACYSGYNQEDSVIMNQSSIDRGF--FRSLFFRSYRDEEKKMGTLVK------E 828
+VAI + G Q + D F R L+ ++Y +G L+K
Sbjct: 153 NAQLVAI--FGG----------QGNTDDYFEELRDLY-QTYHVL---VGDLIKFSAETLS 196
Query: 829 DFGRPDRSNTMGMRHGSYDK---LDDDGLAPPG-----TRVSGEDVIIGKTTPISQDEAQ 880
+ R G + L++ P +S +IG
Sbjct: 197 ELIRTTLDAEKVFTQG-LNILEWLENPSNTPDKDYLLSIPISC--PLIGVI--------- 244
Query: 881 GQASRYTRRDHSISLRHSETGMVDQVL-LTTNADGL-------------RFVKVRVRSVR 926
Q + Y + E + + T ++ GL F +++
Sbjct: 245 -QLAHYVVTAKLLGFTPGE--LRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAIT 301
Query: 927 IP-QIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRM------TIGQ 979
+ IG R + Y +P I D + N +PS M T Q
Sbjct: 302 VLFFIG----VR-CYE-----AYPNTSLP---PSILEDSLENNEGVPSPMLSISNLTQEQ 348
Query: 980 LIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMI 1039
+ + + K +H+ + +L NG ++
Sbjct: 349 V-QDYVNKTNSHLPAGKQ-----------VEISL-------------VNGAK-----NLV 378
Query: 1040 FLGPTYYQRLKHMVDD--KIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIA--- 1094
GP Q L + K + G Q +R P R RF +A
Sbjct: 379 VSGPP--QSLYGLNLTLRKAKAP-SGLDQ--SRIPFSERKLKFSNRFLP------VASPF 427
Query: 1095 HGASHFLKE 1103
H SH L
Sbjct: 428 H--SHLLVP 434
Score = 58.5 bits (141), Expect = 1e-08
Identities = 90/576 (15%), Positives = 174/576 (30%), Gaps = 196/576 (34%)
Query: 266 PIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSL---EEAFVIQN--QQVALDYIG 320
P +V + LG+V+ +E + Q ++L L E ++ N +A +
Sbjct: 57 PAELVGKFLGYVSSL--VE----PSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQ 110
Query: 321 KRGATVGVTRDKRIK-Y--AKEILQKEM--------LPHVGTGD---------------- 353
+ T+ V + IK Y A+ + ++ VG G+
Sbjct: 111 ENDTTL-VKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDY 169
Query: 354 FCETKKAY--YFGYI---IHRL--LLCALGRRAEDDRDHYGNKRLDL------------- 393
F E + Y Y + I L L R D + + L++
Sbjct: 170 FEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFT-QGLNILEWLENPSNTPDK 228
Query: 394 --------AGPLLG----GLFRMLFRKL---TRDVRAYVQKCVDNGKDVNLQFAIKAKTI 438
+ PL+G + + + L ++R+Y++ + + + + A I
Sbjct: 229 DYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGL-----VTAVAI 283
Query: 439 TSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQ- 497
T +W + +A + L + IG A P
Sbjct: 284 A-------ETDSWESFFVSVRKA-----ITVLFF-------------IGVRCYEAYPNTS 318
Query: 498 LHNSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAV 557
L S + E EG M+ I+ + +++ + N +
Sbjct: 319 LPPSI--LEDSLENNEGVPS-------PMLSIS-NLTQEQVQDYVNK---TN------SH 359
Query: 558 IPQATKIF---VNGCWVGIHRDPEMLV-----KTLRRLR---RRVDVNTEVGVVRDIRLK 606
+P ++ VNG + LV ++L L R+ + + R I
Sbjct: 360 LPAGKQVEISLVNG--------AKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSR-IPFS 410
Query: 607 E--LRIYTDYGRCSRPLF-----------IVE---KQRLLIKKRDI-IALQQRESPEDGG 649
E L+ + + P F I + K + +DI I + DG
Sbjct: 411 ERKLKFSNRFLPVASP-FHSHLLVPASDLINKDLVKNNVSFNAKDIQIPV---YDTFDG- 465
Query: 650 WHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADTYTHC-EIHPSLILGV- 707
DL ++ ++ +++ + E TH + P G+
Sbjct: 466 -SDL-----------RVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLG 513
Query: 708 ----------CASIIPFPDHNQSPRNTYQSAMG-KQ 732
+I + +P + Y G KQ
Sbjct: 514 VLTHRNKDGTGVRVIVAGTLDINPDDDY----GFKQ 545
Score = 53.9 bits (129), Expect = 3e-07
Identities = 75/471 (15%), Positives = 137/471 (29%), Gaps = 197/471 (41%)
Query: 605 LKELR-IYTDYGRCSRPLFIVEKQRL--LIKKR-----------DIIA-LQQRES-PEDG 648
+ELR +Y Y L + L LI+ +I+ L+ + P+
Sbjct: 170 FEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDK- 228
Query: 649 GWHDLVAKGFIEYIDTEEEETTMISMTINDLVQARLHPEEAYADT-----YTHCEIHPSL 703
+Y+ + IS + ++Q H Y T +T E+ L
Sbjct: 229 -----------DYLLSIP-----ISCPLIGVIQL-AH----YVVTAKLLGFTPGELRSYL 267
Query: 704 --ILGVCASIIP--FPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYV-----LYY 754
G ++ S + + S ++A+ + L ++ Y
Sbjct: 268 KGATGHSQGLVTAVAIAETDSWESFFVSV--RKAITV-----------LFFIGVRCYEAY 314
Query: 755 PQK---PLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLF 811
P P + ++E+ +P+ +++I S QE Q +++
Sbjct: 315 PNTSLPPSILEDSLENNE--GVPS---PMLSI---SNLTQEQV----QDYVNK------- 355
Query: 812 FRSYRDEEKKMG-TLVKEDFGRPDRSNTMGMRH----GSYDKLDDDGL--------APPG 858
S+ K++ +LV N G ++ G L GL AP G
Sbjct: 356 TNSHLPAGKQVEISLV----------N--GAKNLVVSGPPQSLY--GLNLTLRKAKAPSG 401
Query: 859 ---TRVSGEDVIIGKTTPISQDEAQGQASRYTRRDHSISLR--------HSE--TGMVDQ 905
+R+ P S+ R S R HS D
Sbjct: 402 LDQSRI-----------PFSE------------RKLKFSNRFLPVASPFHSHLLVPASDL 438
Query: 906 VLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDII 965
+ + + F + ++IP V T+ D+ I+ I+
Sbjct: 439 INKDLVKNNVSF---NAKDIQIP---------------VYDTFDGSDLRVLSGSISERIV 480
Query: 966 -------VN---------PHAI---PSRMT-IGQLIECIMGKVAAHMGKEG 996
V H + P + +G L H K+G
Sbjct: 481 DCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLT---------HRNKDG 522
Score = 53.1 bits (127), Expect = 5e-07
Identities = 92/497 (18%), Positives = 150/497 (30%), Gaps = 161/497 (32%)
Query: 32 ISAYFEEKGLVRQQL-DSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIY--- 87
YFEE L + L ++ + +++ SA+ + + + F +
Sbjct: 166 TDDYFEE--L--RDLYQTYHVLV----GDLIKFSAET-LSELIRTTLDAEKVFTQGLNIL 216
Query: 88 --LSKPMMTESDGETATLFPKAARLRNLTYSAPL--------YVDVTKRVIKKGHDGEEV 137
L P T P L ++ S PL YV VT +++ GE
Sbjct: 217 EWLENPSNT----------PDKDYLLSIPISCPLIGVIQLAHYV-VTAKLLGFTP-GELR 264
Query: 138 TETQDFTKVFIGKV---PIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLI 194
+ + T G V I S+ + + + K +T L F I G
Sbjct: 265 SYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVL----------FFI-GVR---- 309
Query: 195 AQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMF-VRMLSRTSAKGGSSGQY 253
E Y PN + + E+ PS M + L++ + Y
Sbjct: 310 CYE------AY------PNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQ-----DY 352
Query: 254 IRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSL---EEAFVIQ 310
+ T + +P A K + I SL + V+
Sbjct: 353 VNKT----NSHLP-----------AGKQV--EI---------------SLVNGAKNLVVS 380
Query: 311 NQQVALD----YIGKRGATVGVTRDKRIKYA--KEILQKEMLPHVGTGDFCETKKAYYFG 364
+L + K A G+ + RI ++ K LP V + F
Sbjct: 381 GPPQSLYGLNLTLRKAKAPSGLDQS-RIPFSERKLKFSNRFLP-VAS-PF---------- 427
Query: 365 YIIH-RLLLCALGRRAEDD-RDHYGNKRLDLAGPLL----GGLFRMLFRKLTRD-VRAYV 417
H LL+ A +D +++ D+ P+ G R+L ++ V +
Sbjct: 428 ---HSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCII 484
Query: 418 QKCVDNGKDVNLQFAIKAKTI-------TSGLKYSLATGNWGQANAAGTRAGVSQVLNRL 470
+ V KA I SGL G N GT GV R+
Sbjct: 485 RLPVKWETTTQF----KATHILDFGPGGASGL------GVLTHRNKDGT--GV-----RV 527
Query: 471 TYASTLSHLRRLNSPIG 487
A TL + G
Sbjct: 528 IVAGTLD--INPDDDYG 542
Score = 45.8 bits (108), Expect = 9e-05
Identities = 59/338 (17%), Positives = 96/338 (28%), Gaps = 135/338 (39%)
Query: 730 GKQA--MGIYVTNYQFRMDTLAYVLY--YPQKPLVTTRAMEHLHFRQLPAGINAIV---- 781
G Q MG MD LY V RA H I IV
Sbjct: 1625 GSQEQGMG---------MD-----LYKTSKAAQDVWNRADNHF-KDTYGFSILDIVINNP 1669
Query: 782 -AIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKE--------DFGR 832
+ + G + + N + ++ F + D + K + KE F
Sbjct: 1670 VNLTIHFGGEKGKRIREN--------YSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRS 1721
Query: 833 PDR-----SNT----MGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQGQA 883
T M +++ L GL P +G
Sbjct: 1722 EKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAG-------------------- 1761
Query: 884 SRYTRRDHSISLRHSETGMVDQVL-----LTTNADGLRF---VK-VRVR----SVRIPQI 930
HS L L + AD + V+ V R V +P+
Sbjct: 1762 -------------HS--------LGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPR- 1799
Query: 931 GDKFSSRHG----QKGTVGMTYTQEDMPWTVEGI---TPDI--IVNPHAIPSRMTIGQLI 981
+ S +G G V +++QE + + VE + T + IVN + + + Q +
Sbjct: 1800 DELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVN-YNVEN----QQYV 1854
Query: 982 ECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQ 1019
G + A +D ++ L+ Q
Sbjct: 1855 --AAGDLRA---------------LDTVTNVLNFIKLQ 1875
Score = 40.4 bits (94), Expect = 0.005
Identities = 55/341 (16%), Positives = 92/341 (26%), Gaps = 142/341 (41%)
Query: 180 QGGYFIINGSEKVLIAQEK-MSTNHVYVFKKRQPNKYAYVAEVRSMAES----------- 227
QG +QE+ M +Y +V + A++
Sbjct: 1624 QG-------------SQEQGMGM-DLY-------KTSKAAQDVWNRADNHFKDTYGFSIL 1662
Query: 228 ---QNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILE 284
N P + T GG G+ IR + E + + K+I E
Sbjct: 1663 DIVINNPVN--------LTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKI--FKEINE 1712
Query: 285 HIC-YDFQDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGATVGVTRDKRIKYAKEILQK 343
H Y F+ + LL + Q Q AL + A E L+
Sbjct: 1713 HSTSYTFRSEK--GLLSAT-------QFTQPAL-------TLMEKA-------AFEDLKS 1749
Query: 344 E-MLPHVGTGDFCETKKAYYFGYIIHRL-----LLCALGRRAEDDRDHYGNKRLDLAGPL 397
+ ++P A + G H L L LA +
Sbjct: 1750 KGLIP----------ADATFAG---HSLGEYAALAS-------------------LADVM 1777
Query: 398 -LGGLFRMLFRKLTRDVRA-YVQKCVDNGKDVNLQFAIKA---KTITSGL---------- 442
+ L ++F R +Q V + + + A + +
Sbjct: 1778 SIESLVEVVFY------RGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVE 1831
Query: 443 KYSLATGNWGQ-AN---------AAGTRAGV---SQVLNRL 470
+ TG + N AAG + + VLN +
Sbjct: 1832 RVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFI 1872
>3mlq_A DNA-directed RNA polymerase subunit beta; tudor,
transferase-transcription complex; 2.91A {Thermus
aquaticus}
Length = 188
Score = 56.8 bits (138), Expect = 4e-09
Identities = 40/167 (23%), Positives = 68/167 (40%), Gaps = 64/167 (38%)
Query: 45 QLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLF 104
Q++S+ + +Q ++ PE + N G Q+ F E + P+ E +
Sbjct: 7 QVESYKKALQA------------DVPPEKRENVGIQAAFKETF---PI--EEGDKGKGGL 49
Query: 105 -----------PKA----ARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIG 149
P R ++LTY APLY + ++I K D + E + VF+G
Sbjct: 50 VLDFLEYRIGDPPFSQDECREKDLTYQAPLYARL--QLIHK--DTGLIKE-DE---VFLG 101
Query: 150 KVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQ 196
+P+M TE G FIING+++V+++Q
Sbjct: 102 HLPLM----------------TEDGS--------FIINGADRVIVSQ 124
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 37.8 bits (87), Expect = 0.009
Identities = 10/61 (16%), Positives = 25/61 (40%), Gaps = 11/61 (18%)
Query: 9 EEQHQQ-EEEDEEEEITQEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADI 67
EEQ ++ +E D + E W EK ++ L+ +++ +++ +
Sbjct: 92 EEQRKRLQELDAASK-VMEQEW-------REKA--KKDLEEWNQRQSEQVEKNKINNRIA 141
Query: 68 E 68
+
Sbjct: 142 D 142
Score = 28.6 bits (63), Expect = 8.2
Identities = 11/70 (15%), Positives = 22/70 (31%), Gaps = 15/70 (21%)
Query: 625 EKQRLLIKKRDIIALQQRESPEDGGWHDLVAKGFIE--YIDTEEEETTMISMTINDLVQA 682
E+QR +++ D + + W + AK +E E+
Sbjct: 92 EEQRKRLQELDAASKVMEQE-----WRE-KAKKDLEEWNQRQSEQVEKNKI-------NN 138
Query: 683 RLHPEEAYAD 692
R+ + Y
Sbjct: 139 RIADKAFYQQ 148
>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 = 0.066
Identities = 25/64 (39%), Positives = 35/64 (54%)
Query: 1114 VHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKE 1173
V VCE+CG IA+ + ++ C C + I +V + YA KLL EL AM I P++ E
Sbjct: 5 VWVCENCGHIALEDKRRRRVYCPVCGEEERISKVEMSYAFKLLLDELKAMVIRPKLNLSE 64
Query: 1174 DTKQ 1177
K
Sbjct: 65 GGKV 68
>3tbi_B DNA-directed RNA polymerase subunit beta; transcription accessory
protein, transcription; 3.00A {Escherichia coli}
Length = 228
Score = 31.9 bits (73), Expect = 0.99
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 848 KLDDDGLAPPGTRVSGEDVIIGKTTP 873
KLD+ G+ G V+G D+++GK TP
Sbjct: 35 KLDESGIVYIGAEVTGGDILVGKVTP 60
>1twf_F ABC23, DNA-directed RNA polymerases I, II, and III 23 KD
polypeptide; transcription, mRNA, multiprotein complex;
HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP:
a.143.1.2 PDB: 1i3q_F 1i6h_F 1k83_F* 1nik_F 1nt9_F
1pqv_F 1r5u_F 1r9s_F* 1r9t_F* 1sfo_F* 1twa_F* 1twc_F*
1i50_F* 1twg_F* 1twh_F* 1wcm_F 1y1v_F 1y1w_F 1y1y_F
1y77_F* ...
Length = 155
Score = 30.0 bits (67), Expect = 2.4
Identities = 20/123 (16%), Positives = 41/123 (33%), Gaps = 22/123 (17%)
Query: 3 EDDYDYEEQHQQEEEDEEEEITQEDAWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVD 62
E+ D++ +H +EE EE+ +D + + T +
Sbjct: 13 ENFEDFDVEHFSDEETYEEKPQFKD----------------GETTDANGKTIVTGGNGPE 56
Query: 63 ESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVD 122
+ E + + P MT+ E A + R ++ +AP++VD
Sbjct: 57 DFQQHEQIRRKTLKEKAIPK--DQRATTPYMTKY--ERARIL--GTRALQISMNAPVFVD 110
Query: 123 VTK 125
+
Sbjct: 111 LEG 113
>3b98_A Prostaglandin I2 synthase; prostacyclin synthase, cytochrome P450
8A1, CYP8A1, isomerase; HET: HEM; 2.08A {Danio rerio}
PDB: 3b99_A*
Length = 475
Score = 31.1 bits (71), Expect = 2.7
Identities = 3/22 (13%), Positives = 10/22 (45%), Gaps = 1/22 (4%)
Query: 557 VIPQATKIFVNGCWVGIHRDPE 578
+ + ++ V ++ DP+
Sbjct: 347 HLRRGDRLCVF-PFISPQMDPQ 367
>3ecq_A Protein SPR0328, endo-alpha-N-acetylgalactosaminidase; distorted
(beta/alpha)8 (TIM) barrel glycoside hydrolase DOM WALL;
2.90A {Streptococcus pneumoniae}
Length = 1531
Score = 30.7 bits (68), Expect = 4.0
Identities = 29/121 (23%), Positives = 41/121 (33%), Gaps = 14/121 (11%)
Query: 94 TESDGETATLFPKAARLRNLTYSAPLY-VDVTKRVIKKGHDGEEVTETQDFTKVFIGKVP 152
T SD TL TY + + + HD + T QDF V G P
Sbjct: 1148 TGSDVSNVTLTLSREAGDEATYFDEIRTFENNSSMYGDKHDTGKGTFKQDFENVAQGIFP 1207
Query: 153 IMLRSSYCTLYQNSEKDLTELGE--CPYDQGGYF------IINGSEKVLIAQEKMSTNHV 204
++ + E + T L E PY Q G+ +I G+ + N V
Sbjct: 1208 FVVGGV-----EGVEDNRTHLSEKHDPYTQRGWNGKKVDDVIEGNWSLKTNGLVSRRNLV 1262
Query: 205 Y 205
Y
Sbjct: 1263 Y 1263
>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 = 4.8
Identities = 14/58 (24%), Positives = 16/58 (27%), Gaps = 17/58 (29%)
Query: 981 IECIMGKVAAHMG------------KEGDATPFTDVTVDN-----ISKALHKCGYQMR 1021
E M +VA G KEGD T F + L Y R
Sbjct: 353 AENWMSEVAVTCGLPAEEVRWKNMYKEGDLTHFNQRLEGFSVPRCWDECLKSSQYYAR 410
>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 = 30.0 bits (67), Expect = 5.5
Identities = 14/49 (28%), Positives = 19/49 (38%), Gaps = 7/49 (14%)
Query: 1112 YRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQEL 1160
R H C CG I N +N + + K++ V C F EL
Sbjct: 389 LRRHHCHACGKIVCRNCSRNKYPLKYLKDRMAKV-------CDGCFGEL 430
>1o5z_A Folylpolyglutamate synthase/dihydrofolate synthas; TM0166,
structural genomics, JC protein structure initiative;
2.10A {Thermotoga maritima} SCOP: c.59.1.2 c.72.2.2
Length = 442
Score = 29.8 bits (68), Expect = 6.0
Identities = 6/61 (9%), Positives = 17/61 (27%), Gaps = 16/61 (26%)
Query: 254 IRATLPYIRTEIP---IIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQ 310
+ + ++ + +V G + DK+ ++ E V +
Sbjct: 329 AESLVRSLKLYFNGEPLSLVI---GILDDKNR----------EDILRKYTGIFERVIVTR 375
Query: 311 N 311
Sbjct: 376 V 376
>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 = 29.5 bits (67), Expect = 7.0
Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 3/43 (6%)
Query: 536 YPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPE 578
+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
0.320 0.136 0.401
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: 18,569,847
Number of extensions: 1188279
Number of successful extensions: 2490
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2430
Number of HSP's successfully gapped: 50
Length of query: 1186
Length of database: 6,701,793
Length adjustment: 104
Effective length of query: 1082
Effective length of database: 3,798,009
Effective search space: 4109445738
Effective search space used: 4109445738
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 (21.8 bits)
S2: 63 (28.3 bits)