RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 000291
(1714 letters)
>4ayb_A DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_A
2y0s_A 2waq_A 4b1o_A 4b1p_W 2pmz_A 3hkz_A
Length = 880
Score = 310 bits (796), Expect = 5e-89
Identities = 217/883 (24%), Positives = 338/883 (38%), Gaps = 184/883 (20%)
Query: 13 QIVGIRFGLATQKEICTASISDCSISHASQ-----------LANPFLGLPLEFGKCESCG 61
I GI+FG+ + EI +S +I + +P LG+ KC +CG
Sbjct: 5 NIKGIKFGILSPDEI--RKMSVTAIITPDVYDEDGTPIEGSVMDPRLGVIEPGQKCPTCG 62
Query: 62 TSEPGKCEGHFGYIELPIPIYHPSHISELKLTM-------YAFQLQIKNDGVAQRLLSSC 114
+ G C GHFG+IEL P+ H + + + ++ R+ ++
Sbjct: 63 NTL-GNCPGHFGHIELVRPVIHVGFVKHVYEFLKATCRRCGRVKISEDEIEKYSRIYNAI 121
Query: 115 --------------------------------------------CEVKEMLKRI-PEETR 129
E KE + ++ P + R
Sbjct: 122 KKRWPSAARRLTEYVKKTAMKAQVCPHCGEKQFKIKLEKPYNFYEERKEGVAKLTPSDIR 181
Query: 130 KKLAGKGYFPQDGYIL--------------EYLPVPPNCL--SVPDISDGVSTMSSDLSI 173
++L + D IL LPVPP + S+ + + DL+
Sbjct: 182 ERL--EKVPESDVEILGYDPTTSRPEWMILTVLPVPPITIRPSI--MIESGIRAEDDLTH 237
Query: 174 AMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYL--EVRGTAKSSRDVDARF 230
L +++ E ++ S +G P +++ + LQ V Y E+ G S
Sbjct: 238 -KLVDIVRINERLKESIDAGAPQLIIEDLW-DLLQYHVATYFDNEIPGLPPSKHR----- 290
Query: 231 GVSQDPNSTTKAWLEK----MRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRIT 286
S P T L+ R K FSSR+VI+ D ++E+GVP IA+ +T
Sbjct: 291 --SGRPLRTLAQRLKGKEGRFRGNLSGKRVDFSSRTVISPDPNISIDEVGVPEIIARTLT 348
Query: 287 FEERVNVHNINYLQELVDN-------KLCLTYSDGS--SSYSLREGSKGHTFLRPGQVVH 337
ER+ NI L++ V N + DG +++ + + L PG VV
Sbjct: 349 VPERITPWNIEKLRQFVINGPDKWPGANYVIRPDGRRIDLRYVKDRKELASTLAPGYVVE 408
Query: 338 RRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQ 397
R + DGD V NR P+ H+ S+ A V V T ++N L+C P +ADFDGD ++L PQ
Sbjct: 409 RHLTDGDVVLFNRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPYNADFDGDEMNLHVPQ 468
Query: 398 SLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMFKK-YFLDKAFTQQLAMFA 456
S A AE E+ V K +++ G + A D + ++ K L K QQ+ A
Sbjct: 469 SEEAIAEAKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLTKEEAQQILGVA 528
Query: 457 LSP--LPRPALSKARCSARWTALQILQSVLPPGF------------------DSCGDRY- 495
L PA+ R +T Q++ + LP F D D Y
Sbjct: 529 DVKIDLGEPAILAPR--EYYTGKQVVSAFLPKDFNFHGQANVSSGPRLCKNEDCPHDSYV 586
Query: 496 LIKKSEVLKGDFDRDTI-PSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSV 554
+IK +L+G FD+ I I+ + E E D+L + + + GF++
Sbjct: 587 VIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDEYGKWLMDNLFRVFIRFVELQGFTM 646
Query: 555 SLEDFSLSKAALWNIQKEIQALYS------LLYHRMSTQN----------ELVDLQIENH 598
LED SL I EI Y + E L +
Sbjct: 647 RLEDVSLGDDVKKEIYNEIDRAKVEVDNLIQKYKNGELEPIPGRTLEESLENYILDTLDK 706
Query: 599 IRHVKMLVAKFILKSS-TLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGK-----FYSKT 652
+R +A L + + + +V + Q A LG Q S RG+ + ++T
Sbjct: 707 LRSTAGDIASKYLDPFNFAYVMARTGARGSVLNITQMAAMLGQQ-SVRGERIKRGYMTRT 765
Query: 653 LVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGL-- 710
L HF+ P D++ P A+ G I F GL P E H+ RE GL
Sbjct: 766 L-----PHFK---PYDIS-PEAR-GFIYSSFRTGLKPTELFFHAAGGRE-------GLVD 808
Query: 711 -----SEPGTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDY 748
S+ G + + L+ L D+ YDGTVR+ +IQ Y
Sbjct: 809 TAVRTSQSGYMQRRLINALSDLRAEYDGTVRS-LYGEVIQVAY 850
>1twf_A B220, DNA-directed RNA polymerase II largest subunit;
transcription, mRNA, multiprotein complex; HET: UTP;
2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB:
1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A
1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A*
1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 298 bits (764), Expect = 6e-82
Identities = 181/752 (24%), Positives = 313/752 (41%), Gaps = 89/752 (11%)
Query: 56 KCESCGTSE--PGKCEGHFGYIELPIPIYHPSHISELKLTMYAFQLQIKNDGVAQRLLSS 113
CE+ SE P + G I +L + + D R+LS+
Sbjct: 147 VCETDVPSEDDPTQLVSRGGCGNTQPTIRKDG--LKLVGSWKKDRATGDADEPELRVLST 204
Query: 114 CCEVKEMLKRIPEETRKKLAGKGYFPQ----DGYILEYLPVPPNCLSVPDISDGVSTMSS 169
E+ + K I + L G+ + IL LPVPP + +
Sbjct: 205 E-EILNIFKHISVKDFTSL---GFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGED 260
Query: 170 DLSIAMLKKVLKQVEIIRSS-RSGTPNFESQEVESNDLQLAVGQYL--EVRGTAKSSRDV 226
DL+ L +LK + + +G P+ +E E + LQ V Y+ ++ G ++ +
Sbjct: 261 DLTF-KLADILKANISLETLEHNGAPHHAIEEAE-SLLQFHVATYMDNDIAGQPQALQK- 317
Query: 227 DARFGVSQDPNSTTKAWLEK----MRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIA 282
S P + +A L+ +R + K FS+R+VI+GD ++++GVP IA
Sbjct: 318 ------SGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIA 371
Query: 283 QRITFEERVNVHNINYLQELVDN-------KLCLTYSDGSSSYSLREGSK-GHTFLRPGQ 334
+ +T+ E V +NI+ L +LV N + G LR + G L+ G
Sbjct: 372 KTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDR-IDLRYSKRAGDIQLQYGW 430
Query: 335 VVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLF 394
V R IMD D V NR P+ HK S+ A V V T ++N + P +ADFDGD ++L
Sbjct: 431 KVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLH 490
Query: 395 YPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMFKK-YFLDKAFTQQLA 453
PQS +AE+ +L +V Q++S + + + D L ++ + + F++ +
Sbjct: 491 VPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNML 550
Query: 454 MFALS---PLPRPALSKARCSARWTALQILQSVLPPG-----------FDSCGDRY-LIK 498
+ +P PA+ K + W+ QIL +P G S D LI
Sbjct: 551 YWVPDWDGVIPTPAIIKPKP--LWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLII 608
Query: 499 KSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLED 558
+++ G ++ T+ S ++ + EKGP+ + F ++Q ++ L +GFS + D
Sbjct: 609 DGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGD 668
Query: 559 FSLSKAALWNIQKEIQALYS------LLYHRMSTQNELVD----------LQIENHIRHV 602
+ I + I + ++ N R
Sbjct: 669 TIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDK 728
Query: 603 KMLVAKFILKSS-TLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGK-----FYSKTLVED 656
+A+ LK + ++ + S + + Q + +G Q S GK F +TL
Sbjct: 729 AGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQ-SVEGKRIAFGFVDRTL--- 784
Query: 657 IASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTL 716
HF + D P +K G ++ + GL P E H++ RE ++ ++ +E G +
Sbjct: 785 --PHFSK----DDYSPESK-GFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYI 837
Query: 717 FKNLMAVLRDVVICYDGTVRNVCSNSIIQFDY 748
+ L+ L D+++ YD T RN ++IQF Y
Sbjct: 838 QRRLVKALEDIMVHYDNTTRN-SLGNVIQFIY 868
Score = 63.6 bits (154), Expect = 5e-10
Identities = 27/137 (19%), Positives = 53/137 (38%), Gaps = 22/137 (16%)
Query: 13 QIVGIRFGLATQKEICTASISDCSISHASQLANPFLGLPLEFG-------------KCES 59
+ ++FGL + +E+ +IS I + + G KC++
Sbjct: 13 TVKEVQFGLFSPEEV--RAISVAKIRFP-ETMDETQTRAKIGGLNDPRLGSIDRNLKCQT 69
Query: 60 CGTSEPGKCEGHFGYIELPIPIYHPSHISELKLTM-----YAFQLQIKNDGVAQRLLSSC 114
C +C GHFG+I+L P++H I+++K + +L + R +
Sbjct: 70 CQEGM-NECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQALAI 128
Query: 115 CEVKEMLKRIPEETRKK 131
+ K+ I + K
Sbjct: 129 KDSKKRFAAIWTLCKTK 145
Score = 49.7 bits (118), Expect = 1e-05
Identities = 82/572 (14%), Positives = 177/572 (30%), Gaps = 99/572 (17%)
Query: 597 NHIRHVKMLVAKFILKSSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTLVED 656
V +L L S L + D + ++ + QL KF + V+
Sbjct: 894 EKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEY---KQLVKDRKFLREVFVDG 950
Query: 657 IASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYE--EMTHSISTREVIVRSSRGLS-EP 713
A+ + + + I L + + +++R +
Sbjct: 951 EANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNA 1010
Query: 714 GTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYAVNA---RKSHSLFPAGEPVGVLAA 770
L L + V + FD+ ++ + S+ GE VGVLAA
Sbjct: 1011 QRDAVTLFCCLLRSRLATR-RVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAA 1069
Query: 771 TAMSNPAYKAVLDS-----SPSSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGR 825
++ PA + L++ S + L ++ + + +YL
Sbjct: 1070 QSIGEPATQMTLNTFHFAGVASKKVT--SGVPRLKEILNVAKNMKTPSLTVYLEP----G 1123
Query: 826 KYCQERAAYMVKNQLKRVSLKDAAVEFLIEYK---KPEIISDDEGLVG------------ 870
+ A ++++ ++ +LK + I Y + +I +DE ++
Sbjct: 1124 HAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQ 1183
Query: 871 ----------HIHLNKILLEDLRISMHDILPKCQETLKSF----CKKKKMKKVVQFFKNT 916
+ L++ + D ++M + + ++T K+ + +K++ +
Sbjct: 1184 SFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVV 1243
Query: 917 SLSISECCSFQQSCADKRSNMPCLM--FVLRG----------ASDSYLDKLSGVLANMIY 964
+ + + + ++ LRG D + +G
Sbjct: 1244 RPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPE 1303
Query: 965 PVL------LETIIKENWWVRQRL-SASVTMVA---------KGVLKE------------ 996
VL L ++ R+ + S + + KE
Sbjct: 1304 WVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYV 1363
Query: 997 ---HLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHT 1053
H+ LL + MT G L G+ + ++ F E + +A
Sbjct: 1364 NYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEIL-----FEAGASAEL 1418
Query: 1054 DNLSSVVAACSWGKHVAVGTGSRFDLLWQTEN 1085
D+ V G+ +GTG+ FD++ E+
Sbjct: 1419 DDCRGVSENVILGQMAPIGTGA-FDVMIDEES 1449
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 296 bits (760), Expect = 2e-81
Identities = 187/751 (24%), Positives = 317/751 (42%), Gaps = 83/751 (11%)
Query: 56 KCESCGTSEPGKCEGHFGYIELPIPIYHPSH--ISELKLTMYAFQLQIKND-GVAQRLLS 112
C++ ++ + + + I + L ++ + K++ + ++ L
Sbjct: 149 VCDTGLSAGSDNFDLSNPSANMGHGGCGAAQPTIRKDGLRLWGSWKRGKDESDLPEKRLL 208
Query: 113 SCCEVKEMLKRIPEETRKKLA-GKGYFPQDGYILEYLPVPPNCLSVPDISDGVSTMSSDL 171
S EV + I E L + Y D I+ LPVPP + DG S DL
Sbjct: 209 SPLEVHTIFTHISSEDLAHLGLNEQYARPDWMIITVLPVPPPSVRPSISVDGTSRGEDDL 268
Query: 172 SIAMLKKVLKQVEIIR-SSRSGTPNFESQEVESNDLQLAVGQYL--EVRGTAKSSRDVDA 228
+ L ++K +R + G P E E LQ V Y+ E+ G ++ +
Sbjct: 269 TH-KLSDIIKANANVRRCEQEGAPAHIVSEYE-QLLQFHVATYMDNEIAGQPQALQK--- 323
Query: 229 RFGVSQDPNSTTKAWLE----KMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQR 284
S P + +A L+ ++R + K FS+R+VITGD ++E+GVP IA+
Sbjct: 324 ----SGRPLKSIRARLKGKEGRLRGNLMGKRVDFSARTVITGDPNLSLDELGVPRSIAKT 379
Query: 285 ITFEERVNVHNINYLQELVDN-------KLCLTYSDGSSSYSLREGSKGH-TFLRPGQVV 336
+T+ E V +NI LQELV N + G LR + LR G V
Sbjct: 380 LTYPETVTPYNIYQLQELVRNGPDEHPGAKYIIRDTGER-IDLRYHKRAGDIPLRYGWRV 438
Query: 337 HRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYP 396
R I DGD V NR P+ HK S+ + V T ++N + P +ADFDGD +++ P
Sbjct: 439 ERHIRDGDVVIFNRQPSLHKMSMMGHRIRVMPYSTFRLNLSVTSPYNADFDGDEMNMHVP 498
Query: 397 QSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSLKVMFKK-YFLDKAFTQQLAMF 455
QS +AE+ E+ V KQ++S + + + D L ++ + FL + + ++
Sbjct: 499 QSEETRAEIQEITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTRNAVMNIMLW 558
Query: 456 ALS---PLPRPALSKARCSARWTALQILQSVLPPG-----------FDSCGDRY-LIKKS 500
LP P + K + WT QIL ++P G + D LI+
Sbjct: 559 VPDWDGILPPPVILKPK--VLWTGKQILSLIIPKGINLIRDDDKQSLSNPTDSGMLIENG 616
Query: 501 EVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFS 560
E++ G D+ T+ + +V +I+ EKGPE FF+ +Q ++ L +GFS+ + D
Sbjct: 617 EIIYGVVDKKTVGASQGGLVHTIWKEKGPEICKGFFNGIQRVVNYWLLHNGFSIGIGDTI 676
Query: 561 LSKAALWNIQKEIQALYS------LLYHRMSTQNEL---VDLQIENHIRHVKMLVAKFIL 611
+ + + ++ + E + E + +
Sbjct: 677 ADADTMKEVTRTVKEARRQVAECIQDAQHNRLKPEPGMTLRESFEAKVSRILNQARDNAG 736
Query: 612 KSSTLGYL---------IDSKSDSAVSKVVQQAGFLGLQLSDRGK-----FYSKTLVEDI 657
+ S L + + S + + Q + +G Q GK F +TL
Sbjct: 737 R-SAEHSLKDSNNVKQMVAAGSKGSFINISQMSACVGQQ-IVEGKRIPFGFKYRTL---- 790
Query: 658 ASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLF 717
HF + D + P ++ G I+ + GL P E H+++ RE ++ ++ +E G +
Sbjct: 791 -PHFPK----DDDSPESR-GFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQ 844
Query: 718 KNLMAVLRDVVICYDGTVRNVCSNSIIQFDY 748
+ L+ + DV++ YDGTVRN IIQF Y
Sbjct: 845 RRLVKAMEDVMVRYDGTVRN-AMGDIIQFAY 874
Score = 63.2 bits (153), Expect = 7e-10
Identities = 32/147 (21%), Positives = 58/147 (39%), Gaps = 20/147 (13%)
Query: 13 QIVGIRFGLATQKEICTASISDCSISHASQ------------LANPFLGLPLEFGKCESC 60
++ ++FG+ + +EI S+S I L +P LG KC++C
Sbjct: 15 RVEEVQFGILSPEEI--RSMSVAKIEFPETMDESGQRPRVGGLLDPRLGTIDRQFKCQTC 72
Query: 61 GTSEPGKCEGHFGYIELPIPIYHPSHISELKLTM-----YAFQLQIKNDGVAQRLLSSCC 115
G + C GHFG+IEL P++H +S++K + +L+I +
Sbjct: 73 GETM-ADCPGHFGHIELAKPVFHIGFLSKIKKILECVCWNCGKLKIDSSNPKFNDTQRYR 131
Query: 116 EVKEMLKRIPEETRKKLAGKGYFPQDG 142
+ K L + + K+
Sbjct: 132 DPKNRLNAVWNVCKTKMVCDTGLSAGS 158
Score = 50.1 bits (119), Expect = 7e-06
Identities = 18/88 (20%), Positives = 29/88 (32%), Gaps = 6/88 (6%)
Query: 997 HLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHTDNL 1056
HL LL + MT G L+ G + + AA D+
Sbjct: 1373 HLALLCDVMTSRGHLMAITRHGINRAETG-----ALMRCSFEETVEILMDAAASGEKDDC 1427
Query: 1057 SSVVAACSWGKHVAVGTGSRFDLLWQTE 1084
+ G+ +GTG+ FD+ +
Sbjct: 1428 KGISENIMLGQLAPMGTGA-FDIYLDQD 1454
Score = 34.7 bits (79), Expect = 0.33
Identities = 44/270 (16%), Positives = 90/270 (33%), Gaps = 20/270 (7%)
Query: 690 YEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYA 749
+ + + I R S ++ L+ + V + + F++
Sbjct: 989 IINGLNELIAKLTIFRGSDRITRDVQNNATLLFQILLRSKFAVKRVIMEYRLNKVAFEWI 1048
Query: 750 VNA---RKSHSLFPAGEPVGVLAATAMSNPAYKAVLDS---SPSSNNSWELMKEILLCRV 803
+ R ++ GE VG LAA ++ PA + L++ + S+ + L L +
Sbjct: 1049 MGEVEARFQQAVVSPGEMVGTLAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEIL 1108
Query: 804 SFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPE--- 860
+ + + +YL A V+ Q++ +L I Y P+
Sbjct: 1109 NVAKNIKTPSLTIYLMPWIAA----NMDLAKNVQTQIEHTTLSTVTSATEIHY-DPDPQD 1163
Query: 861 -IISDDEGLVGHIHLNKILLEDLRISMHDILPKCQETLKSFCKKKKMKKVVQFFKNTSLS 919
+I +D+ V I E++ +++ P L+ + KM + +
Sbjct: 1164 TVIEEDKDFV--EAFFAIPDEEVEENLYKQSPWL---LRLELDRAKMLDKKLSMSDVAGK 1218
Query: 920 ISECCSFQQSCADKRSNMPCLMFVLRGASD 949
I+E N L+ R D
Sbjct: 1219 IAESFERDLFTIWSEDNADKLIIRCRIIRD 1248
>2k0m_A Uncharacterized protein; structural genomics, unknown function,
PSI-2, protein structure initiative; NMR {Rhodospirillum
rubrum atcc 11170}
Length = 104
Score = 106 bits (265), Expect = 3e-27
Identities = 24/90 (26%), Positives = 49/90 (54%), Gaps = 5/90 (5%)
Query: 1588 IMRSIRRIMHQSGYNDGDRLSADDKSFIFDNVFNYHPDKAMKMGAGIDHFKVDKHGSFQD 1647
+ ++ ++++ Y GD +S D +F+ + HPD K+G G+ +F+V
Sbjct: 20 ALAFMKVMLNR--YRPGDIVSTVDGAFLVE-ALKRHPDATSKIGPGVRNFEVRSA--DYG 74
Query: 1648 SRCLFVVSTDGSQQDFSYRKCLESFIRGKY 1677
++C +++ TDGS++ FSY+KC+ +
Sbjct: 75 TQCFWILRTDGSEERFSYKKCVLEHHHHHH 104
>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 = 89.3 bits (221), Expect = 1e-17
Identities = 112/663 (16%), Positives = 184/663 (27%), Gaps = 231/663 (34%)
Query: 538 SLQPLLMENLFADGFSVSLE-DFSLSKAALW----NIQKEIQALYSLLYHRMSTQNELVD 592
S +PL + + G SLE + A + +Q++ + + +E
Sbjct: 5 STRPLTLSH----G---SLEHVLLVP-TASFFIASQLQEQFNKILPEPTEGFAADDEPTT 56
Query: 593 LQIENHIRHVKMLVAKFILKSSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKT 652
E LV KF LGY+ S V Q L L L++ F +
Sbjct: 57 -PAE--------LVGKF------LGYVSSLVEPSKVG---QFDQVLNLCLTE---FENCY 95
Query: 653 LV-EDI---ASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSR 708
L DI A+ + L LIK + R + R
Sbjct: 96 LEGNDIHALAAKLLQENDTTL---VKTKELIK-NYITA-------------RIMAKRPFD 138
Query: 709 GLSEPGTLFK-------NLMAV-------------LRDVVICYDGTVRNVCSNSIIQF-D 747
S LF+ L+A+ LRD+ Y V ++ S +
Sbjct: 139 KKSNSA-LFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSE 197
Query: 748 YAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDSSPSSNNSWELMKEILLCRVSFNN 807
+ +F G + + P K L S P +S
Sbjct: 198 LIRTTLDAEKVFTQGLNILEWLENPSNTPD-KDYLLSIP----------------ISC-- 238
Query: 808 DPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEG 867
P+ + + Y V+ K L+ + E+ S +G
Sbjct: 239 -PL-----IGVIQLAH---YV--------------VTAK------LLGFTPGELRSYLKG 269
Query: 868 LVGHIHLNKILLEDLRISMHDILPKCQETLKSFCKKKKMKKVVQF-----------FKNT 916
GH + L+ + I+ D + +SF ++K + + NT
Sbjct: 270 ATGHS---QGLVTAVAIAETD-------SWESF--FVSVRKAITVLFFIGVRCYEAYPNT 317
Query: 917 SLSISECCSFQQSCADKRSNMPCLMFVLRGASDSYLDKLSGVLANMIYPVLLETIIKENW 976
SL S + + +P M + + ++ + +
Sbjct: 318 SLPPSI----LEDSLENNEGVPSPMLSISNLTQE----------------QVQDYVNK-- 355
Query: 977 WVRQRLSASVTMVAKGVLKEHL-ILLANS---MTCAG---DLVGFNSG--GYKALSRSLN 1027
L A + + I L N + +G L G N KA S
Sbjct: 356 -TNSHLPAG----------KQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQ 404
Query: 1028 VQVPFTE-----ATLFMPRKC-FEKAAEKRHTDNLSSVVAACSWGKHVAVGTGSRFDLLW 1081
++PF+E + F+P F H+ L DL
Sbjct: 405 SRIPFSERKLKFSNRFLPVASPF-------HSHLLVPASDLI------------NKDL-- 443
Query: 1082 QTENEEFNQDD-GVDVYDFLHMVRSSTG--IEELDTGCLGEEVDGL-EDEFDW----SLS 1133
N FN D + VYD + G + L VD + W
Sbjct: 444 VKNNVSFNAKDIQIPVYD------TFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFK 497
Query: 1134 PEH 1136
H
Sbjct: 498 ATH 500
Score = 67.8 bits (165), Expect = 3e-11
Identities = 103/616 (16%), Positives = 182/616 (29%), Gaps = 222/616 (36%)
Query: 313 DGSS--SYSLREGSKGHTFLRP-GQVVH-RRIMDGDTVFINRPPTTHKHSLQALSVYVHD 368
D S +L GS H L P ++ + F P + + D
Sbjct: 2 DAYSTRPLTLSHGSLEHVLLVPTASFFIASQLQEQ---FNKILP-------EPTEGFAAD 51
Query: 369 DHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLEL----FSVEKQLLSS---HNG 421
D P L F G L P + +VL L F E L H
Sbjct: 52 D-----EPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEF--ENCYLEGNDIH-- 102
Query: 422 NLNLQLATD---ALLSLKVMFKKYFLDKAFTQQLAMFALSPLPRPALSKA--RCSARWTA 476
L +L + L+ K + K Y + ++ AL +A +A+ A
Sbjct: 103 ALAAKLLQENDTTLVKTKELIKNYITARIMAKR----PFDKKSNSALFRAVGEGNAQLVA 158
Query: 477 L---QILQSVLPPGFDSCGDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVL 533
+ Q G D Y F+ E+ ++ V
Sbjct: 159 IFGGQ--------G---NTDDY-----------FE---------ELRD--LYQTYHVLVG 185
Query: 534 EFFDS----LQPLL-----MENLFADGFSVS--LE--------DFSLSKAALWNIQKEIQ 574
+ L L+ E +F G ++ LE D+ LS + I
Sbjct: 186 DLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPL---IG 242
Query: 575 ALYSLL-YHRMSTQNELVDLQIENHIR----HVK-MLVAKFILKSST-----------LG 617
+ L Y + ++ ++++ H + ++ A I ++ + +
Sbjct: 243 -VIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAIT 301
Query: 618 YL--IDSKSDSAV------SKVVQQA-----GFLGLQLSDRGKFYSKTLVEDIASHFERI 664
L I + A +++ + G LS ++ V+D +
Sbjct: 302 VLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISN--LTQEQVQDYVNKTNSH 359
Query: 665 YPMD-------LN---------YPTAKYGLI----KGCFFHGLD----PYEEMTHSISTR 700
P +N P + YGL K GLD P+ E R
Sbjct: 360 LPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSE-------R 412
Query: 701 EVIVRSSRGL--SEPGTLF-KNLMA-----VLRDV---------------VIC-YDGT-V 735
++ S+R L + P F +L+ + +D+ V +DG+ +
Sbjct: 413 KLKF-SNRFLPVASP---FHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDL 468
Query: 736 RNVCSN---SIIQ--------FDYAVNARKSHSL-F-PAGEP--------------VGVL 768
R + + I+ ++ + +H L F P G V V+
Sbjct: 469 RVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVRVI 528
Query: 769 AATAM-SNPA----YK 779
A + NP +K
Sbjct: 529 VAGTLDINPDDDYGFK 544
Score = 64.7 bits (157), Expect = 3e-10
Identities = 119/664 (17%), Positives = 190/664 (28%), Gaps = 255/664 (38%)
Query: 462 RP-ALSKARCSARW---TALQILQSVLPPGFDSCGDRYLIKKSEVLKGDFDRDTIPSVIN 517
RP LS TA + S L F+ L + +E D + P+
Sbjct: 7 RPLTLSHGSLEHVLLVPTASFFIASQLQEQFNK----ILPEPTEGFAADDE----PTTPA 58
Query: 518 EIVTSIF--F---EKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDFSLSKAALWNIQKE 572
E+V F + P +V +F L L E F + + L +
Sbjct: 59 ELVGK-FLGYVSSLVEPSKVGQFDQVLNLCLTE--FENCY-------------LEG--ND 100
Query: 573 IQAL-YSLLYHRMSTQNELVDLQIENHIRHVKMLVAKFILKSSTLGYLIDSKSDSAVSKV 631
I AL LL +T + +L I+N+I A+ + K D KS+SA+ +
Sbjct: 101 IHALAAKLLQENDTTLVKTKEL-IKNYIT------ARIMAKRP-----FDKKSNSALFRA 148
Query: 632 VQQ------AGFLGLQ---------LSDRGKFYSKTLVED-IASHFERIYPMDLNYPTAK 675
V + A F G Q L D + Y LV D I E + + A+
Sbjct: 149 VGEGNAQLVAIFGG-QGNTDDYFEELRDLYQTY-HVLVGDLIKFSAETLSELIRTTLDAE 206
Query: 676 YGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAVLRDVVICYDGTV 735
F GL+ E + + +T + S +S P +I
Sbjct: 207 K-----VFTQGLNILEWLENPSNTPDKDYLLSIPISCP--------------LIG----- 242
Query: 736 RNVCSNSIIQF-DYAVNARKSHSLFPA----------GEPVGVLAATAMSNPAYKAVLDS 784
+IQ Y V K P G G++ A A+
Sbjct: 243 -------VIQLAHYVV-TAKLLGFTPGELRSYLKGATGHSQGLVTAVAI----------- 283
Query: 785 SPSSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERA------------ 832
+ +SWE SF R+ I L G R C E
Sbjct: 284 --AETDSWE----------SFFV--SVRKAITVLFFIGV-R--CYEAYPNTSLPPSILED 326
Query: 833 ---------AYM--VKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGLVGHIHL------- 874
+ M + N L V+ + + + + +
Sbjct: 327 SLENNEGVPSPMLSISN------LTQEQVQDYVNKTNSHLPAGK-----QVEISLVNGAK 375
Query: 875 NKIL------LEDLRISMHDILPKCQETLKS----FCKKKKMKKVVQFFKNTSLSISECC 924
N ++ L L +++ K L F ++K K +F L ++
Sbjct: 376 NLVVSGPPQSLYGLNLTLRKA--KAPSGLDQSRIPFSERKL-KFSNRF-----LPVAS-- 425
Query: 925 SFQQSCADKRSNMPCLMF---VLRGASDSYLDKLSG------------------------ 957
P F +L ASD L
Sbjct: 426 -------------P---FHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLR 469
Query: 958 VLANMIYPVLLETIIKE--NWWVRQRLSASVTMVAKGVLKEHLILL-ANSMTCAGDLVGF 1014
VL+ I +++ II+ W + A+ H++ + G L
Sbjct: 470 VLSGSISERIVDCIIRLPVKWETTTQFKAT-----------HILDFGPGGASGLGVLTHR 518
Query: 1015 NSGG 1018
N G
Sbjct: 519 NKDG 522
Score = 54.3 bits (130), Expect = 5e-07
Identities = 107/666 (16%), Positives = 202/666 (30%), Gaps = 231/666 (34%)
Query: 71 HFGYIELPIPIYHPSHISELKLTMYAFQLQIKNDGVAQRLLSSCCEVKEMLKRIPEETRK 130
H G +E + + S A QLQ ++ K +PE
Sbjct: 13 H-GSLEHVLLVPTASFF-------IASQLQ-----------------EQFNKILPE---- 43
Query: 131 KLAGKGYFPQDGYILEYLPVPPNCLSVPD--------ISDGVSTMSSDLSIAMLKKVLKQ 182
P +G+ + P + + +S V +L L +
Sbjct: 44 --------PTEGFAADDEPT-----TPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTE 90
Query: 183 VEIIRSSRSGTPNFESQEVESNDLQLAVGQYL-EVRGTAKSSRDV-----DARFGVSQDP 236
FE+ +E ND+ + L E T ++++ AR +
Sbjct: 91 -------------FENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPF 137
Query: 237 NSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEI----GVPFEIAQRITFEERVN 292
+ + + LF R+V G+A ++ I G + FEE
Sbjct: 138 DKKSNS------ALF---------RAVGEGNA--QLVAIFGGQGNTDD-----YFEE--- 172
Query: 293 VHNINYLQELVDNKLCLTYSD------GSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTV 346
L++L TY S+ +L E + V + ++
Sbjct: 173 ------LRDLYQ-----TYHVLVGDLIKFSAETLSELIRTTLDAEK---VFTQGLNILE- 217
Query: 347 FINRPPTTHKHS-------------LQALSVYVHDDHTVKINPLICGPLSADFDGDCIHL 393
++ P T + L+ YV + P G L + G H
Sbjct: 218 WLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTP---GELRSYLKGATGHS 274
Query: 394 -----------------FYPQSLAAKAEVLE-LFSVEKQLLSSHNGNLNLQLATDALLSL 435
F+ KA + LF + + + + + L
Sbjct: 275 QGLVTAVAIAETDSWESFF--VSVRKA--ITVLFFIG---VRCY------EAYPNTSLPP 321
Query: 436 KVMFKKYFLDKAFTQQLAMFALSPLPRPALSK--ARCSARW---TALQI-L-----QSVL 484
++ + L+ M ++S L + + + ++ ++I L V+
Sbjct: 322 SIL--EDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVV 379
Query: 485 --PP----GFDSCGDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEF--- 535
PP G + ++K++ G D+ IP F E+ + F
Sbjct: 380 SGPPQSLYGLNL-----TLRKAKAPSGL-DQSRIP----------FSERKLKFSNRFLPV 423
Query: 536 ---FDS--LQP---LLMENLFADGFSVSLEDFSLSKAALWNIQ--KEIQALYSLLYHRMS 585
F S L P L+ ++L + S + +D + +++ +++ L + R
Sbjct: 424 ASPFHSHLLVPASDLINKDLVKNNVSFNAKDI---QIPVYDTFDGSDLRVLSGSISER-- 478
Query: 586 TQNELVDLQIENHIR--HVKMLVAKFIL-----KSSTLGYLIDSKSDSAVSKVVQQAGFL 638
+VD I ++ A IL +S LG L D +V+ AG L
Sbjct: 479 ----IVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVRVI-VAGTL 533
Query: 639 GLQLSD 644
+ D
Sbjct: 534 DINPDD 539
Score = 53.1 bits (127), Expect = 1e-06
Identities = 104/639 (16%), Positives = 170/639 (26%), Gaps = 249/639 (38%)
Query: 28 CTASISDCSISHASQLANPF---LGLPLEFGKCESCGTSEPG-KCE--GHF-GYIELPIP 80
+ S ASQL F L P E EP E G F GY+ +
Sbjct: 18 HVLLVPTASFFIASQLQEQFNKILPEPTE----GFAADDEPTTPAELVGKFLGYVSSLVE 73
Query: 81 IYHPSHISE-LKLTMYAFQLQI--KND--GVAQRLLSS----CCEVKEMLK--------- 122
+ L L + F+ ND +A +LL + KE++K
Sbjct: 74 PSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMA 133
Query: 123 --RIPEETRKKL---AGKG----Y--FPQDGYILEYLP-------VPPNCLSVPDISDGV 164
+++ L G+G F G +Y + D +
Sbjct: 134 KRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYH-----VLVGDLI 188
Query: 165 STMSSDLSIAMLKKVLKQVEIIRSSRSGTPNF-----------ESQEVESND-------- 205
+ LS E+IR++ F D
Sbjct: 189 KFSAETLS-----------ELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPIS 237
Query: 206 ------LQLAVGQYL-----------EVR----GTAKSSRD-VDARF-GVSQDPNSTTKA 242
+QLA Y+ E+R G S+ V A + S +
Sbjct: 238 CPLIGVIQLA--HYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVS 295
Query: 243 WLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPF-EIAQRITFEERVNVHNINYLQE 301
+ + LF IGV E + + L++
Sbjct: 296 VRKAITVLFF----------------------IGVRCYEAYPNTSLPPSI-------LED 326
Query: 302 LVDNKLCLTYSDGSSSY--SLREGSKGHTFLRPGQVVHRRIMDGDTVFINR--PPTTHKH 357
++N ++G S S+ ++ V + N P
Sbjct: 327 SLEN------NEGVPSPMLSISNLTQEQ--------VQDYVNK-----TNSHLPAGKQVE 367
Query: 358 SLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLS 417
+S+ + V + GP PQSL
Sbjct: 368 ----ISLVNGAKNLV-----VSGP--------------PQSLYG---------------- 388
Query: 418 SHNGNLNLQL----ATDALLSLKVMF--KKYFLDKAFTQQLAMFAL--SPLPRPALSK-- 467
LNL L A L ++ F +K F L + + S L PA
Sbjct: 389 -----LNLTLRKAKAPSGLDQSRIPFSERKLKFSNRF---LPVASPFHSHLLVPASDLIN 440
Query: 468 ---ARCSARWTA--LQILQSVLPPGFDSC-GDRYLIKKSEVLKGDFDRDTIPSVINEIVT 521
+ + + A +QI P +D+ G L+ +++ I+
Sbjct: 441 KDLVKNNVSFNAKDIQI------PVYDTFDG--------SDLR-VLSGSISERIVDCIIR 485
Query: 522 S-IFFEK----GPEEVLEF----FDSLQPLLMENLFADG 551
+ +E +L+F L L N DG
Sbjct: 486 LPVKWETTTQFKATHILDFGPGGASGLGVLTHRNK--DG 522
Score = 43.5 bits (102), Expect = 7e-04
Identities = 52/319 (16%), Positives = 99/319 (31%), Gaps = 124/319 (38%)
Query: 667 MDL--NYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTL---F---- 717
MDL A+ ++ D + + T+ S + IV ++ P L F
Sbjct: 1633 MDLYKTSKAAQ------DVWNRADNHFKDTYGFSILD-IVINN-----PVNLTIHFGGEK 1680
Query: 718 -----KNLMAVLRDVVICYDGTVRNVCSNSIIQFDYAVNARKSHSLFPAGEPVGVLAATA 772
+N A++ + DG ++ + I + +N + F G+L+AT
Sbjct: 1681 GKRIRENYSAMIFET--IVDGKLK---TEKIFK---EINEHSTSYTF--RSEKGLLSATQ 1730
Query: 773 MSNPAYKAVLDSSPSSNNSWELMKE---I----------------LLCR---VSFNNDPI 810
+ PA + ++E +K I L +S +
Sbjct: 1731 FTQPALTLM------EKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSI-ESLV 1783
Query: 811 DRRVILYLNDCGCGR-KYCQE--------RAAY-MVKNQLKRV--SLKDAAVEFLIEYKK 858
+ +++ R Q R+ Y M+ RV S A+++++E
Sbjct: 1784 E---VVFY------RGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVE--- 1831
Query: 859 PEIISDDEGLV---------------GHIHLNKILLEDLRISMHDILPKCQETLKSFCKK 903
+ LV G L L D + +K +K
Sbjct: 1832 -RVGKRTGWLVEIVNYNVENQQYVAAGD-------LRAL-----DTVTNVLNFIKL--QK 1876
Query: 904 KKMKKVVQFFKNTSLSISE 922
+ ++ SLS+ E
Sbjct: 1877 IDIIEL-----QKSLSLEE 1890
Score = 40.8 bits (95), Expect = 0.005
Identities = 62/321 (19%), Positives = 113/321 (35%), Gaps = 97/321 (30%)
Query: 267 DAYKRVNEIGVPFEIAQRITFEERVNVHNI-NY---LQELV-DNKLCLT-YSDGSSSYSL 320
D YK + AQ + + R + H Y + ++V +N + LT + G +
Sbjct: 1634 DLYKT-------SKAAQDV-WN-RADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRI 1684
Query: 321 REGSKGHTF--LRPGQVVHRRIMD------------GDTVFINRPPTTHKHSLQ-AL--- 362
RE F + G++ +I + ++ T Q AL
Sbjct: 1685 RENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFT-----QPALTLM 1739
Query: 363 SVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQS------LAAKAEVLELFSVEKQLL 416
+D +K LI P A F G H S LA+ A+V+ + S+ + +
Sbjct: 1740 EKAAFED--LKSKGLI--PADATFAG---H-----SLGEYAALASLADVMSIESLVE--V 1785
Query: 417 SSHNGNLNLQLATDALLSLKVMFKKYFLDKAFTQQLAMFALSP------LPRPALSK-AR 469
+ G +Q+A D+ M A++P + AL
Sbjct: 1786 VFYRGMT-MQVAVPR-------------DELGRSNYGMIAINPGRVAASFSQEALQYVVE 1831
Query: 470 CSARWTALQILQSVLPPGFDSCGDRYLIKKSEVLKGDF-DRDTIPSVINEI-VTSIFFEK 527
+ T +++ V ++ +Y V GD DT+ +V+N I + I +
Sbjct: 1832 RVGKRTG-WLVEIV---NYNVENQQY------VAAGDLRALDTVTNVLNFIKLQKIDIIE 1881
Query: 528 GPEEVLEFFDSLQPLLMENLF 548
+ + SL+ + +LF
Sbjct: 1882 LQKSL-----SLEE-VEGHLF 1896
Score = 39.3 bits (91), Expect = 0.016
Identities = 78/581 (13%), Positives = 152/581 (26%), Gaps = 218/581 (37%)
Query: 724 LRDVVICYDGTVRNVCSNSIIQFDYAVNARKSHSLFPAGEPVGVLA---ATAMSNPAYKA 780
R + + + G++ + + F L + P
Sbjct: 6 TRPLTLSH-GSLE--HVLLV-----------PTASFFIAS---QLQEQFNKILPEPTEGF 48
Query: 781 VLDSSPSSNNSWELMKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQL 840
D P++ EL+ + L + + ++ + + +Q+
Sbjct: 49 AADDEPTT--PAELVGKFL----GYVSSLVEP----------------SKVGQF---DQV 83
Query: 841 KRVSLKDAAVEFLIEYKKPEIISDDEGLVGHIHLNKILLEDLRISMHDILPKCQETLKSF 900
+ L + +L ++ IH L L L K +E +K++
Sbjct: 84 LNLCLTEFENCYL---------EGND-----IHA---LAAKLLQENDTTLVKTKELIKNY 126
Query: 901 CKKKKMKKVVQFFKNTSLSISECCSFQQSCADKRSNMPCLMFVLRGASDSYLDKLSGVLA 960
+ M K + F S S + ++ + + + +F +G +D Y ++L +
Sbjct: 127 ITARIMAK--RPFDKKSNS-----ALFRAVGEGNAQL-VAIFGGQGNTDDYFEELRDLYQ 178
Query: 961 NMIYPVLLETIIKE-------------------------NWWVRQR---------LSASV 986
Y VL+ +IK W+ LS +
Sbjct: 179 --TYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPI 236
Query: 987 TMVAKGVL----------------KEHLILLANSMTCAGDLV------------GFNSGG 1018
+ GV+ E L + + LV F
Sbjct: 237 SCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSV 296
Query: 1019 YKALSRSLNVQVPF---TEATLFMPRKCFEKAAEKRHTDN--------LS---------- 1057
KA+ V F P + + +N LS
Sbjct: 297 RKAI------TVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQ 350
Query: 1058 SVVAAC----SWGKHVAVG----------TGSRFDL---------------LWQTENEEF 1088
V GK V + +G L L Q+ F
Sbjct: 351 DYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSR-IPF 409
Query: 1089 NQDDGVDVYDFL------H---MVRSSTGIEELDTGCLGEEVDGLE------DEFDWSLS 1133
++ FL H +V +S I + D + + D FD S
Sbjct: 410 SERKLKFSNRFLPVASPFHSHLLVPASDLINK-DLVKNNVSFNAKDIQIPVYDTFDGS-- 466
Query: 1134 PEHNLCS-DKPVFEDLVEDQSWLENKQENANWDSEADCRKS 1173
+L + E +V+ + W++ + +
Sbjct: 467 ---DLRVLSGSISERIVDCII-----RLPVKWETTTQFKAT 499
Score = 35.8 bits (82), Expect = 0.19
Identities = 47/321 (14%), Positives = 88/321 (27%), Gaps = 151/321 (47%)
Query: 773 MSNPAYKAVLDSSPSSNNSWELMKEILLCRVSFN------NDPIDRRVILYLNDCGCGRK 826
M Y +S ++ + W F+ N+P + ++ G K
Sbjct: 1631 MGMDLY----KTSKAAQDVWNRADNHFKDTYGFSILDIVINNP--VNLTIHFG----GEK 1680
Query: 827 YCQERAAYMVKNQLKRVSLKDAAVE----------------------------------F 852
+ R Y + ++ D ++
Sbjct: 1681 GKRIRENYS---AMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALT 1737
Query: 853 LIEY------KKPEIISDDEGLVGH--------IHLNKIL-LEDL------R-ISMHDIL 890
L+E K +I D GH L ++ +E L R ++M +
Sbjct: 1738 LMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAV 1797
Query: 891 PK----------------------CQETLKSFCKK--KKMKKVVQ---FFKNTSLSISEC 923
P+ QE L+ ++ K+ +V+ + N
Sbjct: 1798 PRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNY--N-------- 1847
Query: 924 CSFQQ-SCA-DKRSNMPCLMFVLRGASDSYLDKLSGVLANM----IYPVLLETIIKENWW 977
QQ A D R+ LD ++ VL + I II+
Sbjct: 1848 VENQQYVAAGDLRA----------------LDTVTNVLNFIKLQKI------DIIE---- 1881
Query: 978 VRQRLSASVTMVAKGVLKEHL 998
L S+++ ++ HL
Sbjct: 1882 ----LQKSLSLEE---VEGHL 1895
>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 = 85.9 bits (213), Expect = 2e-17
Identities = 38/206 (18%), Positives = 72/206 (34%), Gaps = 40/206 (19%)
Query: 116 EVKEMLKRIPEETRKKLA-GKGYFPQDGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIA 174
EV++ L++IP++ L + +L LPVPP + DL+
Sbjct: 246 EVRDWLEKIPDKDLPLLGLDPEKSRPEWMVLTVLPVPPVTARPSITLETGIRAEDDLTH- 304
Query: 175 MLKKVLKQVEIIR-SSRSGTPNFESQEVESNDLQLAVGQYLEVRGTAKSSRDVDARFGVS 233
L +++ ++ + +G P +++ LQ V Y+ + +A GV
Sbjct: 305 KLVDIIRINNRLKQNIEAGAPQLIIEDLWDL-LQYHVTTYI----------NNEAP-GVP 352
Query: 234 QDPNSTTKAWLEKMRTLFIR-KG---------SG----FSSRSVITGDAYKRVNEIGVPF 279
+ + + ++TL R KG SG + + A
Sbjct: 353 PAKHKSGRP----LKTLAQRLKGKEGRFRGNLSGGAGSGAGSGSVLARA-------AFEI 401
Query: 280 EIAQRITFEERVNVHNINYLQELVDN 305
+ E+ V N+N + E V
Sbjct: 402 TVQHLFEAAEKGEVDNLNGVIENVLI 427
Score = 53.5 bits (129), Expect = 4e-07
Identities = 24/91 (26%), Positives = 41/91 (45%), Gaps = 16/91 (17%)
Query: 13 QIVGIRFGLATQKEICTASISDCSISHASQ-----------LANPFLGLPLEFG-KCESC 60
I I FG+ + +EI +S ++ + + +G ++ G +CE+C
Sbjct: 68 VIGSIEFGILSPQEI--RKMSAVEVTVPDTYDDDGYPIEGGVMDKRMG-VIDPGLRCETC 124
Query: 61 GTSEPGKCEGHFGYIELPIPIYHPSHISELK 91
G G+C GHFG+IEL P+ H +
Sbjct: 125 G-GRAGECPGHFGHIELARPVIHVGFAKTIY 154
>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 = 74.9 bits (183), Expect = 2e-13
Identities = 90/689 (13%), Positives = 195/689 (28%), Gaps = 206/689 (29%)
Query: 69 EGHFGYIELPIPIYHPSHISELKLTMYAFQLQIKNDGVAQRLLSSCCEVKEMLKRIPEET 128
E + Y ++ + ++ + + F + D + + +LS E+ ++ +
Sbjct: 13 EHQYQYKDI-LSVFEDAFVDN-------FDCKDVQD-MPKSILSKE-EIDHIIMSKDAVS 62
Query: 129 RKK-----LAGKG-----YFPQDGYILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKK 178
L K F ++ + Y + + T S+
Sbjct: 63 GTLRLFWTLLSKQEEMVQKFVEEVLRINY----------KFLMSPIKTEQRQPSMMTRMY 112
Query: 179 VLKQVEIIRSSRSGTPNFESQEVESNDL-----QLAVGQYLEV---RGTAKSS------R 224
+ ++ + ++ S+ L +L + + + G+ K+
Sbjct: 113 IEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCL 172
Query: 225 D--VDARFG-------VSQDPNSTTKAWLEKMRTLFIRKGSGFSSRSVITGDAYKRVNEI 275
V + + ++ + LE ++ L + ++SRS + + R++ I
Sbjct: 173 SYKVQCKMDFKIFWLNLKNC--NSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSI 230
Query: 276 GVPFEIAQRITFEERV---------NVHNINYLQELVDNKLC---LTYSDGSSSYSLREG 323
+ R + + NV N + C LT +
Sbjct: 231 ----QAELRRLLKSKPYENCLLVLLNVQNAKAW-NAFNLS-CKILLTTRFKQVT------ 278
Query: 324 SKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVH---DD---HTVKINPL 377
FL H + T L Y+ D + NP
Sbjct: 279 ----DFLSAATTTHISLDHHSMTL------TPDEVKSLLLKYLDCRPQDLPREVLTTNPR 328
Query: 378 ICGPLSADFDGDCIHL-FYPQSLAAK-AEVLELFSVEKQLLSSHNGNLNLQLATDALLSL 435
++ + K ++E LN+ +
Sbjct: 329 RLSIIAESIRDGLATWDNWKHVNCDKLTTIIESS-------------LNVLEPAE----- 370
Query: 436 KVMFKKYFLDKAFTQQLAMFALS-PLPRPALSKARCSARWTAL--QILQSVLPPGFDSCG 492
++K F L++F S +P LS W + + V+ +
Sbjct: 371 ---YRKMFDR------LSVFPPSAHIPTILLSLI-----WFDVIKSDVMVVV----NKLH 412
Query: 493 DRYLIKKSEVLKGDFDRDT--IPSVINEIVTSIFFEKGPE---EVLEFF--------DSL 539
L++K T IPS+ E+ + E +++ + D L
Sbjct: 413 KYSLVEK------QPKESTISIPSIYLELKVKL--ENEYALHRSIVDHYNIPKTFDSDDL 464
Query: 540 QPLLMENLF----------------ADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHR 583
P ++ F F + DF + ++++I+ +
Sbjct: 465 IPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFR------F-LEQKIRHDSTAWNAS 517
Query: 584 MSTQNELVDLQI-ENHI--------RHVKMLVAKFILKSSTLGYLIDSKSDSAVSKVVQQ 634
S N L L+ + +I R V ++ F+ K LI SK + +++
Sbjct: 518 GSILNTLQQLKFYKPYICDNDPKYERLVNAIL-DFLPKIEE--NLICSKY----TDLLRI 570
Query: 635 AGFLGLQLSDRGKFYSKTLVEDIASHFER 663
A L + E+ +R
Sbjct: 571 A------LMAEDEAI----FEEAHKQVQR 589
Score = 71.0 bits (173), Expect = 3e-12
Identities = 103/647 (15%), Positives = 183/647 (28%), Gaps = 167/647 (25%)
Query: 355 HKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLF-YPQSLAAKAEVLELF---S 410
H H H I + +FD C + P+S+ +K E+ +
Sbjct: 2 HHHHHMDFETGEHQYQYKDILSVFEDAFVDNFD--CKDVQDMPKSILSKEEIDHIIMSKD 59
Query: 411 VEKQ------LLSSHNGNLNLQLATDALLS----LKVMFKKYFLDKA-----FTQQL--- 452
L S + + + L L K + + +Q
Sbjct: 60 AVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRL 119
Query: 453 ----AMFALSPLPRP-ALSKARCSARWTALQILQS---VLPPGFDSCGDRYLIKKSEVLK 504
+FA + R K R AL L+ VL G G K+ +
Sbjct: 120 YNDNQVFAKYNVSRLQPYLKLR-----QALLELRPAKNVLIDGVLGSG------KT-WVA 167
Query: 505 GDFDRDTIPSVINEIVTSIFF-----EKGPEEVLEFFDSLQPLLMENLFADGFSVSLEDF 559
D V ++ IF+ PE VLE L + N S D
Sbjct: 168 LDVCLSY--KVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNW------TSRSDH 219
Query: 560 SLSKAALWNIQKEIQALYSLLYHRMSTQNELVDLQIENHIRHVKMLVAKFILKSSTL--- 616
S I L LL + +N L+ L ++++ K A F L L
Sbjct: 220 S--SNIKLRIHSIQAELRRLLKSKPY-ENCLLVL---LNVQNAKAWNA-FNLSCKILLTT 272
Query: 617 --GYLIDSKSDSAVSKVVQQAGFLGLQLSDRGKFYSKTL---VEDIASHFERIYPMDLNY 671
+ D S + + + + L + K L +D+ P L
Sbjct: 273 RFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRL-- 330
Query: 672 PTAKYGLIKGCFFHG----LDPYEEMTHSISTREVIVRSSRGLSEPG---TLFKNLMAVL 724
+I D ++ + +I S L EP +F L +V
Sbjct: 331 -----SII-AESIRDGLATWDNWKHVNCD-KLTTIIESSLNVL-EPAEYRKMFDRL-SVF 381
Query: 725 R-DV-----VIC---YDGTVRNV-------CSNSIIQFDYAVNARKSHSLFPAGEPVGVL 768
++ +D +V S+++ + S++
Sbjct: 382 PPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIY--------- 432
Query: 769 AATAMSNPAYKAVLDSSPSSNNSWELMKEIL----LCRVSFNNDPIDRRVILY------- 817
L+ N + L + I+ + + ++D I + Y
Sbjct: 433 -------------LELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGH 479
Query: 818 -LNDCGCGRKYCQERAAYM----VKNQLKRVSLKDAAVEF-------LIEYKKPEIISDD 865
L + + R ++ ++ +++ S A L YK
Sbjct: 480 HLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKP------- 532
Query: 866 EGLVGHIHLNKILLEDLRISMHDILPKCQETLKSFCKKKKMKKVVQF 912
+I N E L ++ D LPK +E L K +++
Sbjct: 533 -----YICDNDPKYERLVNAILDFLPKIEENL----ICSKYTDLLRI 570
Score = 61.8 bits (149), Expect = 2e-09
Identities = 108/791 (13%), Positives = 207/791 (26%), Gaps = 304/791 (38%)
Query: 153 NCLSVPDISDGVSTMSSDLSIAMLKKVLKQ----------VEIIRSSRSGT--------- 193
+C V D+ + LS + ++ + S +
Sbjct: 34 DCKDVQDMPKSI------LSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVL 87
Query: 194 -PNF----ESQEVESNDLQLAVGQYLEVRGTAKSSRDVDARFGVS-QDPNSTTKAWLEKM 247
N+ + E + Y+E R + V A++ VS P + L ++
Sbjct: 88 RINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLEL 147
Query: 248 R-----TLFIRKGSGFSSRSVITGDAYK--RVNEIGVPFEI-----AQRITFEERVNVHN 295
R + GSG ++ + D +V + + F+I + E +
Sbjct: 148 RPAKNVLIDGVLGSG---KTWVALDVCLSYKV-QCKMDFKIFWLNLKNCNSPETVLE--M 201
Query: 296 INYLQELVDNKLCLTYSDGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTH 355
+ L +D + SD SS+ LR S Q RR+ ++P +
Sbjct: 202 LQKLLYQIDPNWT-SRSDHSSNIKLRIHS--------IQAELRRL------LKSKP---Y 243
Query: 356 KHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQL 415
++ L L + V+ N +A F+ C K L
Sbjct: 244 ENCLLVL-----LN--VQ-NAKA---WNA-FNLSC----------------------KIL 269
Query: 416 LSSHNGNLNLQLATDALLSLKVMFKKYFLD---KAFT--QQLAMFALSPLPRPALSKARC 470
L++ + TD L + LD T + ++
Sbjct: 270 LTTRFKQV-----TDFLSAATT--THISLDHHSMTLTPDEVKSLLL-------------- 308
Query: 471 SARWTALQILQSVLPPGFDSCGDRYLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPE 530
++ L LP EVL + P ++ I E
Sbjct: 309 --KY--LDCRPQDLPR--------------EVLTTN------PRRLSII---------AE 335
Query: 531 EVLEFFDSLQPLLMENL--FADGFSVSLEDFSLSKAALWNIQKEIQALYSLLYHRMSTQN 588
+ + + N SL E + ++
Sbjct: 336 SIRDGLATWDNWKHVNCDKLTTIIESSLNVLE---------PAEYRKMF----------- 375
Query: 589 ELVDLQI--ENHIRHVKMLVAKFILKSSTLGYLIDSKSDSAVSKVVQQAGFLGLQLSDRG 646
L + + + + L + S V VV
Sbjct: 376 --DRLSVFPPS----AH-------IPTILLSLIWFDVIKSDVMVVVN------------- 409
Query: 647 KFYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRS 706
K + +LVE + + + Y E+ +
Sbjct: 410 KLHKYSLVE-------------KQPKESTISI------PSI--YLELKVKLE-------- 440
Query: 707 SRGLSEPGTLFKNLMAVLRDVVICYDGTVRNVCSNSII---QFDYAVNARKSHSLFPAGE 763
N A+ R +V Y+ + S+ +I Y + H
Sbjct: 441 ------------NEYALHRSIVDHYNIP-KTFDSDDLIPPYLDQYFYSHIGHH------- 480
Query: 764 PVGVLAATAMSNPAYKAVLDSSPSSNNSWELMKEILLCRVSFNNDPIDRRVILY-LNDCG 822
L L + + L F +++++
Sbjct: 481 ----LKNIEHPE---------------RMTLFRMVFL-DFRF----LEQKIRHDSTAWNA 516
Query: 823 CG---------RKYCQERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGLVGHIH 873
G + Y Y+ N K L +A ++FL + ++ I S L+ I
Sbjct: 517 SGSILNTLQQLKFY----KPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLL-RIA 571
Query: 874 L---NKILLED 881
L ++ + E+
Sbjct: 572 LMAEDEAIFEE 582
Score = 52.5 bits (125), Expect = 1e-06
Identities = 51/329 (15%), Positives = 86/329 (26%), Gaps = 90/329 (27%)
Query: 1427 EDFSTKGWEDSSKPSANEKSIVHQIGGWNVPDAK-GTDDSCW--------GKQKLTENAK 1477
++F K +D K +++ I H I DA GT W QK E
Sbjct: 31 DNFDCKDVQDMPKSILSKEEIDHII---MSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVL 87
Query: 1478 GTDDSSWGKQK-HTENESPQPASSNAWDLPDATGGSE---TEMQVWGQSRKEPFKKNRGW 1533
+ + TE P + + D + V R +P+ K R
Sbjct: 88 -RINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVS---RLQPYLKLRQA 143
Query: 1534 ASS--SGEW--------KGK-------------KNRPPR-----SPGVVNDDSTV----N 1561
+ GK + + + N TV
Sbjct: 144 LLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQ 203
Query: 1562 AMYTVTRQRLDMFTSEEQDILSDVEPIMRSIRRIMHQSGYNDGDRLSADDKSFIFDNVFN 1621
+ + +I + I +RR++ Y + L + NV
Sbjct: 204 KLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC--L------LVLLNVQ- 254
Query: 1622 YHPDKAMKMGAGIDHFKVDKHGSFQDSRCLFVVST-DGSQQDF-----SYRKCLESFIRG 1675
+ + F + C +++T DF + L+
Sbjct: 255 ---NAKA-----WNAF---------NLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMT 297
Query: 1676 KYPDLVDEFIGKYFRRPRSGGNREPSLPP 1704
PD V + KY R LP
Sbjct: 298 LTPDEVKSLLLKYL------DCRPQDLPR 320
Score = 47.2 bits (111), Expect = 5e-05
Identities = 94/689 (13%), Positives = 196/689 (28%), Gaps = 224/689 (32%)
Query: 581 YHRMSTQNELVDLQIENHIRH-VKMLVAKF-----------ILKSSTLGYLIDSKSDSAV 628
+H M + Q ++ + V F IL + ++I SK
Sbjct: 4 HHHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDA--- 60
Query: 629 SKVVQQAGFLGLQLSDRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLD 688
V L L + + + VE++ + +NY +
Sbjct: 61 ---VSGTLRLFWTLLSKQEEMVQKFVEEV---------LRINYKFLMSPIKTEQ----RQ 104
Query: 689 PYEEMTHSISTREVIVRSSRGLS-------EPGTLFKNLMAVLRD---VVICYDG----- 733
P I R+ + ++ + +P + + LR V+I G
Sbjct: 105 PSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLID--GVLGSG 162
Query: 734 -TV--RNVCSNSIIQ--FDYAV------NARKSHSLFPAGEPVGVLAATAMSNPAYKAVL 782
T +VC + +Q D+ + N ++ E + L N + +
Sbjct: 163 KTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVL---EMLQKLLYQIDPN--WTSRS 217
Query: 783 DSS---PSSNNSWELMKEILLCRVSFNN-----DPI-DRRVILYLNDCGC-----GRKYC 828
D S +S + LL + N + + + + C R
Sbjct: 218 DHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAF-NLSCKILLTTRF-- 274
Query: 829 QERAAYMVKNQLKRVSLKDAAVEFLIEYKKPEIISDDEGLVGHIHLNKIL---LEDLRIS 885
++ ++ +SL ++ + DE + L K L +DL
Sbjct: 275 KQVTDFLSAATTTHISLDHHSMTL----------TPDEVK--SL-LLKYLDCRPQDLPRE 321
Query: 886 MHDILPKCQETLKSFCKKKK-MKKVVQFFKNTSL----SISECCSFQQSCADKRSNMPCL 940
+ P+ L + + +K+ + +I E A+ R
Sbjct: 322 VLTTNPR---RLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRK----- 373
Query: 941 MFVLRGASDSYLDKLSGVLANMIYP-------VLLETIIKENWWVRQRLSASVTMVAKGV 993
D+LS ++P +LL I W+ V
Sbjct: 374 ----------MFDRLS------VFPPSAHIPTILLSLI----WF--------------DV 399
Query: 994 LKEHLILLANSMTCAGDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEKAAEKRHT 1053
+K ++++ N + SL V+ E+T+ +P E K
Sbjct: 400 IKSDVMVVVNKL----------------HKYSL-VEKQPKESTISIPSIYLE---LKVKL 439
Query: 1054 DNLSSVVAACSWGKHVAVGTGSRFDLLWQTENEEFNQDDGVDVYDFLHMVRSSTGIEELD 1113
+N ++ H ++ + +++ D Y + H+ IE
Sbjct: 440 ENEYAL--------HRSIVDHYNIPKTFDSDDLIPPYLDQ---YFYSHIGHHLKNIE--- 485
Query: 1114 TGCLGEEVDGLEDEFDWSLSPEHNLCSDKPVFEDLVEDQSWLENK--QENANWDSEA--- 1168
+ +F + D +LE K ++ W++
Sbjct: 486 ----------HPERMT--------------LFRMVFLDFRFLEQKIRHDSTAWNASGSIL 521
Query: 1169 ----DCRK------SSEDKWEKLGTSLEK 1187
+ ++ K+E+L ++
Sbjct: 522 NTLQQLKFYKPYICDNDPKYERLVNAILD 550
Score = 43.3 bits (101), Expect = 7e-04
Identities = 30/177 (16%), Positives = 55/177 (31%), Gaps = 45/177 (25%)
Query: 1078 DLLWQTENEEFNQD-DGVDVYDFLHMVRSSTGIEEL----DT--------GCL---GEEV 1121
D+L + F + D DV D + S I+ + D L EE+
Sbjct: 20 DIL-SVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEM 78
Query: 1122 ------DGLEDEFDWSLSPEHNLCSDKPVFEDLVEDQSWLENKQENANWDSEADCRKSSE 1175
+ L + + +SP + + +Q ++ N N A S
Sbjct: 79 VQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQ---RDRLYNDN-QVFAKYNVSRL 134
Query: 1176 DKWEKLGTSLE--KPSSGWRTEG--AWGKSS-------DDKLEKAGSPSRKPSG--W 1219
+ KL +L +P+ +G GK+ K++ + W
Sbjct: 135 QPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQC-----KMDFKIFW 186
Score = 38.3 bits (88), Expect = 0.029
Identities = 45/329 (13%), Positives = 83/329 (25%), Gaps = 115/329 (34%)
Query: 1454 WNVPDAKGTDDSCWGKQKL--TENAKGTDDSSWGKQKH----------TENESPQPASSN 1501
N + SC + L T + TD S H T +E
Sbjct: 254 QNAKAWNAFNLSC---KILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKY 310
Query: 1502 AW----DLP-DATGGSETEMQVWGQSRKEPFKKNRGWASSSGEWKGKKNR---------- 1546
DLP + + + + +S ++ W + + K
Sbjct: 311 LDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCD---KLTTIIESSLNVLE 367
Query: 1547 PP------RSPGVVNDDSTVNAMYTVTRQRL-----DMFTSEEQDILS----------DV 1585
P V + + L D+ S+ +++
Sbjct: 368 PAEYRKMFDRLSVFPPS--AH----IPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQP 421
Query: 1586 EPIMRSI-------------RRIMHQS---GYNDGDRLSADDKSFIF-DN-VFN---YHP 1624
+ SI +H+S YN +DD + D ++ +H
Sbjct: 422 KESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHL 481
Query: 1625 DKAMKMGAGIDHF------------KVDKHGS-----------FQDSRCL--FVVSTDGS 1659
+ + F K+ + Q + ++ D
Sbjct: 482 KNI-EHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPK 540
Query: 1660 QQ-------DFSYRKCLESFIRGKYPDLV 1681
+ DF K E+ I KY DL+
Sbjct: 541 YERLVNAILDFL-PKIEENLICSKYTDLL 568
>4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C
4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C
Length = 395
Score = 57.1 bits (137), Expect = 3e-08
Identities = 59/381 (15%), Positives = 117/381 (30%), Gaps = 68/381 (17%)
Query: 738 VCSNSIIQFDYAVNARKSHSLFPAGEPVGVLAATAMSNPAYKAVLDS-----SPSSNNSW 792
V + I + S L GE +G++AA ++ P + L + N +
Sbjct: 43 VTRDEIDKIFDLAIKEYSEGLIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTL 102
Query: 793 EL--MKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAV 850
L + EI+ + P + +YL D + A V +L+ +++
Sbjct: 103 GLPRLIEIVDAK----KVPSTPMMTIYLTDE----YKHDKEKALEVARKLEYTKIENVVS 154
Query: 851 EFLIEYKKPEIISDDEGLVGHIHLNKILLEDLRISMHDILPKCQETLKSFCKKKKM---K 907
I+ I + L+ +L+D +++ D+ +
Sbjct: 155 STSIDIASMSI---------ILQLDNEMLKDKGVTVDDVKKAINRLKLGEFVIDESEGNT 205
Query: 908 KVVQFFKNTSLSISECCSFQQSCADKRSNMPCLMFVLRGASDSYLDKLSGVLANMIYPV- 966
+ F S++ + + +++ D Y+ G + + V
Sbjct: 206 LNISFANIDSIAALFKLRDKILNTKIKGIKGIKRAIVQKKGDEYIILTDGSNLSGVLSVK 265
Query: 967 --------------LLETIIKENWWVRQRLSASVTMVAKG----VLKEHLILLANSMTCA 1008
+ E E R+ + ++ V V H++L+A+ MT
Sbjct: 266 GVDIAKVETNNIREIEEVFGIEA--AREIIIREISKVLAEQGLDVDMRHILLVADVMTRT 323
Query: 1009 GDLVGFNSGGYKALSRSLNVQVPFTEATLFMPRKCFEK-------AAEKRHTDNLSSVVA 1061
G + G S A FE AA + + VV
Sbjct: 324 GVVRQIGRHGVTGEKNS-----VLARAA-------FEVTVKHLLDAAARGDVEEFKGVVE 371
Query: 1062 ACSWGKHVAVGTGSRFDLLWQ 1082
G + +GTG +L +
Sbjct: 372 NIIIGHPIKLGTGM-VELTMR 391
>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D-
structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB:
1i6v_D* 2gho_D
Length = 1265
Score = 55.4 bits (134), Expect = 2e-07
Identities = 42/176 (23%), Positives = 78/176 (44%), Gaps = 45/176 (25%)
Query: 258 FSSRSVITGDAYKRVNEIGVPFEIA---------QRITFEERVNVHNINYLQELVDNKLC 308
+S RSVI ++++ G+P +A +++ EE+ N+ + +++ +
Sbjct: 365 YSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKM--EEKAFAPNVKAARRMLERQRD 422
Query: 309 LTYS--DGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYV 366
+ D +L E G V +NR PT H+ +QA +
Sbjct: 423 IKDEVWD-----ALEEVIHGK----V-------------VLLNRAPTLHRLGIQAFQPVL 460
Query: 367 HDDHTVKINPLICGPLSADFDGD--CIHLFYPQSLAAKAEVLELFSVEKQLLSSHN 420
+ +++++PL+C +ADFDGD +H+ P S A+AE +LS+HN
Sbjct: 461 VEGQSIQLHPLVCEAFNADFDGDQMAVHV--PLSSFAQAEARIQ------MLSAHN 508
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2
PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D*
2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D*
3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D
Length = 1524
Score = 54.4 bits (131), Expect = 3e-07
Identities = 42/176 (23%), Positives = 78/176 (44%), Gaps = 45/176 (25%)
Query: 258 FSSRSVITGDAYKRVNEIGVPFEIA---------QRITFEERVNVHNINYLQELVDNKLC 308
+S RSVI ++++ G+P +A +++ EE+ N+ + +++ +
Sbjct: 625 YSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKM--EEKGIAPNVKAARRMLERQRD 682
Query: 309 LTYS--DGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYV 366
+ D +L E G V +NR PT H+ +QA +
Sbjct: 683 IKDEVWD-----ALEEVIHGK----V-------------VLLNRAPTLHRLGIQAFQPVL 720
Query: 367 HDDHTVKINPLICGPLSADFDGD--CIHLFYPQSLAAKAEVLELFSVEKQLLSSHN 420
+ +++++PL+C +ADFDGD +H+ P S A+AE +LS+HN
Sbjct: 721 VEGQSIQLHPLVCEAFNADFDGDQMAVHV--PLSSFAQAEARIQ------MLSAHN 768
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase,
nucleotidyltransferase, transcription, transferase;
11.20A {Escherichia coli} PDB: 3iyd_D*
Length = 1407
Score = 48.0 bits (115), Expect = 3e-05
Identities = 25/78 (32%), Positives = 44/78 (56%), Gaps = 10/78 (12%)
Query: 346 VFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGD--CIHLFYPQSLAAKA 403
V +NR PT H+ +QA + + ++++PL+C +ADFDGD +H+ P +L A+
Sbjct: 421 VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHV--PLTLEAQL 478
Query: 404 EVLELFSVEKQLLSSHNG 421
E L ++S++N
Sbjct: 479 EARAL------MMSTNNI 490
>1c1l_A Protein (congerin I); galectin, lectin, beta-galactose-binding,
sugar binding PROT; HET: GAL BGC; 1.50A {Conger
myriaster} SCOP: b.29.1.3 PDB: 1c1f_A* 3ajy_A*
Length = 137
Score = 32.2 bits (73), Expect = 0.62
Identities = 18/130 (13%), Positives = 36/130 (27%), Gaps = 34/130 (26%)
Query: 198 SQEVESNDLQLAVGQYLEVRGTAKSSRD----------------VDARFGVSQDPNSTTK 241
S ++ + VG++L V G +S +D RF D N+
Sbjct: 2 SGGLQVKNFDFTVGKFLTVGGFINNSPQRFSVNVGESMNSLSLHLDHRFNYGADQNTIVM 61
Query: 242 AWL----------EKMRTLFIRKGSGFSSRSVITGDAYK-RVNEIGVPFEIAQRITFEER 290
++ + G F + + + P + F R
Sbjct: 62 NSTLKGDNGWETEQRSTNFTLSAGQYFEITLSYDINKFYIDIL--DGPN-----LEFPNR 114
Query: 291 VNVHNINYLQ 300
+ + +L
Sbjct: 115 YSKEFLPFLS 124
>1ur4_A Galactanase; hydrolase, beta-1, glycoside hydrolase, substrate
specificity, pectin, GH-A, family 53, plant cell WALL
degradation; HET: B2G PGE; 2.2A {Bacillus licheniformis}
SCOP: c.1.8.3 PDB: 1r8l_A* 1ur0_A* 2ccr_A* 2j74_A*
2gft_A*
Length = 399
Score = 32.5 bits (73), Expect = 1.3
Identities = 19/133 (14%), Positives = 34/133 (25%), Gaps = 1/133 (0%)
Query: 1163 NWDSEADCRKSSEDKWEKLGTSLEKPSSGWRTEGAWGKSSDDKLEKAGSPSRKPSGWGTE 1222
+ + + G + + + G + K G P +
Sbjct: 237 WHGTLKNLTSVLTSVADTYGKKVMVAETSYTYTAEDGDGHGNTAPKNGQTLNNPVTVQGQ 296
Query: 1223 ASWGESSCDKWENVGSPAAKSFSEWGTEASWGKSFGDKPENVSPAAKTSSGWGSEASWGK 1282
A+ +VG F W +N + SGW + +
Sbjct: 297 ANAVRDVIQAVSDVGEAGIGVFY-WEPAWIPVGPAHRLEKNKALWETYGSGWATSYAAEY 355
Query: 1283 SSGDRQENVGGSA 1295
D + GGSA
Sbjct: 356 DPEDAGKWFGGSA 368
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 31.1 bits (69), Expect = 1.8
Identities = 9/29 (31%), Positives = 15/29 (51%), Gaps = 10/29 (34%)
Query: 837 KNQLKRV--SLK----DA----AVEFLIE 855
K LK++ SLK D+ A++ +E
Sbjct: 19 KQALKKLQASLKLYADDSAPALAIKATME 47
Score = 29.9 bits (66), Expect = 3.7
Identities = 16/58 (27%), Positives = 19/58 (32%), Gaps = 32/58 (55%)
Query: 412 EKQLLSSHNGNLNLQLATDALLSLKVMFKKYFLDKAFTQQLAMFALSPLPRPALS-KA 468
EKQ L +L SLK+ Y D A PAL+ KA
Sbjct: 18 EKQALK--------KLQA----SLKL----YADDSA---------------PALAIKA 44
>1a78_A Galectin-1; S-lectin, carbohydrate binding, complex
(lectin/saccharide); HET: TDG; 2.00A {Bufo arenarum}
SCOP: b.29.1.3 PDB: 1gan_A*
Length = 134
Score = 30.6 bits (69), Expect = 2.0
Identities = 16/125 (12%), Positives = 34/125 (27%), Gaps = 32/125 (25%)
Query: 201 VESNDLQLAVGQYLEVRGTAKSSRD----------------VDARFGVSQDPNSTTKAWL 244
V +L L G +E++G+ +ARF + D N
Sbjct: 5 VAVTNLNLKPGHCVEIKGSIPPDCKGFAVNLGEDASNFLLHFNARFDLHGDVNKIVCNSK 64
Query: 245 --------EKMRTLFIRKGSGFSSRSVITGDAYK-RVNEIGVPFEIAQRITFEERVNVHN 295
++ ++G+ + + +F R + +
Sbjct: 65 EADAWGSEQREEVFPFQQGAEVMVCFEYQTQKIIIKFS--SGDQ-----FSFPVRKVLPS 117
Query: 296 INYLQ 300
I +L
Sbjct: 118 IPFLS 122
>1vq8_U 50S ribosomal protein L24E; ribosome 50S, protein-protein complex,
RNA-RNA complex, PROT complex, peptidyl transferase
reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A
{Haloarcula marismortui} SCOP: g.39.1.6 PDB: 1giy_R
1jj2_T 1k73_V* 1k8a_V* 1k9m_V* 1kc8_V* 1kd1_V* 1kqs_T*
1m1k_V* 1m90_V* 1ml5_r* 1n8r_V* 1nji_V* 1q7y_V* 1q81_V*
1q82_V* 1q86_V* 1qvf_T 1qvg_T 1s72_U* ...
Length = 66
Score = 28.2 bits (63), Expect = 3.3
Identities = 10/41 (24%), Positives = 13/41 (31%), Gaps = 5/41 (12%)
Query: 101 IKNDGVAQRLLSSCCEVKEMLKRIPEETR-----KKLAGKG 136
+ DG SS CE L R + AG+
Sbjct: 22 VHKDGATTHFCSSKCENNADLGREARNLEWTDTARGEAGEA 62
>3grl_A General vesicular transport factor P115; vesicle transport,
membrane trafficking, membrane tethering, fusion, snare,
RAB GTPase, armadillo repeats; 2.00A {Bos taurus} PDB:
3gq2_A 2w3c_A
Length = 651
Score = 31.2 bits (70), Expect = 3.6
Identities = 16/102 (15%), Positives = 36/102 (35%), Gaps = 5/102 (4%)
Query: 397 QSLAAKAEVLE-LFSVEKQLLSSHNGNLN---LQLATDALLSLKVMFKKYFLDKAFTQQL 452
Q + A E L + + +S G + L L LL + +F + ++ Q++
Sbjct: 201 QKIVAFENAFERLLDIITEEGNSDGGIVVEDCLIL-LQNLLKNNNSNQNFFKEGSYIQRM 259
Query: 453 AMFALSPLPRPALSKARCSARWTALQILQSVLPPGFDSCGDR 494
+ S + + LQ+++ ++ P
Sbjct: 260 KPWFEVGDENSGWSAQKVTNLHLMLQLVRVLVSPNNPPGATS 301
>3iz6_A 40S ribosomal protein SA (S2P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum}
Length = 305
Score = 30.5 bits (68), Expect = 4.5
Identities = 14/91 (15%), Positives = 24/91 (26%), Gaps = 3/91 (3%)
Query: 1313 EDKLEEVETTVAKPSSAWGTEASWDKSSEVTLEKVAAPAENPLSGWGTEAQDSGKSS--D 1370
+ EE E + P E + + E A P + D +
Sbjct: 214 AKEQEEEEAALVAPDYGAVAEYAAPAADTWGGEWGTDAAAQPAAIPAQAGADWTAAPAPA 273
Query: 1371 WSEWKDHANATASWGRNGSEENSGWDTKASW 1401
W A W + + + T +W
Sbjct: 274 AGGWDTAAAPAPGWEQGSAPVPAAAPT-PNW 303
Score = 29.7 bits (66), Expect = 7.5
Identities = 16/82 (19%), Positives = 28/82 (34%), Gaps = 2/82 (2%)
Query: 1304 AKASWGKSSEDKLEEVETTVAKPSSAWGTEASWDKSSEVTLEKVAAPAENPLSGWGTEAQ 1363
+G +E +T + + + + ++ + AAPA GW T A
Sbjct: 225 VAPDYGAVAEYAAPAADTWGGEWGTDAAAQPA-AIPAQAGADWTAAPAPAA-GGWDTAAA 282
Query: 1364 DSGKSSDWSEWKDHANATASWG 1385
+ S A T +WG
Sbjct: 283 PAPGWEQGSAPVPAAAPTPNWG 304
>2gig_A Type II restriction enzyme hincii; protein DNA complex, indirect
readout, DNA intercalation, endonuclease, hydrolase/DNA
complex; 1.83A {Haemophilus influenzae} PDB: 2gih_A
2gii_A 2gij_A 3e3y_A 3e40_A 3e41_A 3e42_A 3e43_A 3e44_A
3e45_A 1tx3_A 1tw8_A 1kc6_A 1xhu_A 1xhv_A 2gie_A 2aud_A
Length = 257
Score = 30.1 bits (67), Expect = 6.0
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 1671 SFIRGKYPDLVDEFIGKYFRRPRSG 1695
SFI+ Y D+ IG+ +RP+SG
Sbjct: 1 SFIKPIYQDINSILIGQKVKRPKSG 25
>1io1_A Phase 1 flagellin; beta-folium, structural protein; 2.00A {Salmonella
typhimurium} SCOP: e.32.1.1
Length = 398
Score = 30.3 bits (67), Expect = 6.8
Identities = 21/186 (11%), Positives = 46/186 (24%)
Query: 1240 AAKSFSEWGTEASWGKSFGDKPENVSPAAKTSSGWGSEASWGKSSGDRQENVGGSASKPL 1299
G ++ ++ + ++ + +A+
Sbjct: 190 DGYYEVSVDKTNGEVTLAGGATSPLTGGLPATATEDVKNVQVANADLTEAKAALTAAGVT 249
Query: 1300 SGWGAKASWGKSSEDKLEEVETTVAKPSSAWGTEASWDKSSEVTLEKVAAPAENPLSGWG 1359
+ K + V + + D S + K A +
Sbjct: 250 GTASVVKMSYTDNNGKTIDGGLAVKVGDDYYSATQNKDGSISINTTKYTADDGTSKTALN 309
Query: 1360 TEAQDSGKSSDWSEWKDHANATASWGRNGSEENSGWDTKASWKTKALDKLDDVGSAVENS 1419
GK+ S A+ + G N + + A+ L K+D + V+
Sbjct: 310 KLGGADGKTEVVSIGGKTYAASKAEGHNFKAQPDLAEAAATTTENPLQKIDAALAQVDTL 369
Query: 1420 SSVWGA 1425
S A
Sbjct: 370 RSDLAA 375
>2c20_A UDP-glucose 4-epimerase; carbohydrate metabolism, galactose
metabolism, isomerase, NAD, spine; HET: NAD; 2.7A
{Bacillus anthracis}
Length = 330
Score = 30.1 bits (69), Expect = 7.0
Identities = 11/30 (36%), Positives = 18/30 (60%), Gaps = 2/30 (6%)
Query: 255 GSGFSSRSVITGDAYKRVNEIGVPFEIAQR 284
G+GFS + ++ DA + V +P E+A R
Sbjct: 255 GNGFSVKEIV--DAVREVTNHEIPAEVAPR 282
>3gbg_A TCP pilus virulence regulatory protein; cupin, helix-turn-helix,
ARAC family, activator, DNA-binding transcription,
transcription regulation; HET: PAM; 1.90A {Vibrio
cholerae}
Length = 276
Score = 29.9 bits (67), Expect = 7.3
Identities = 19/147 (12%), Positives = 39/147 (26%), Gaps = 17/147 (11%)
Query: 795 MKEILLCRVSFNNDPIDRRVILYLNDCGCGRKYCQERAAYMVKNQLKRVSLKDAAVEFLI 854
+K +L + N + + +L N E + LK F
Sbjct: 94 LKSYILGDLMIRNLYSENKDLLLWNCEHNDIAVLSEVVNGFREINYSDEFLKVFFSGFFS 153
Query: 855 EYKK---PEIISDDEGLVGHI------HL-NKILLEDL-------RISMHDILPKCQETL 897
+ +K I+DD + I + D+ R+ + L
Sbjct: 154 KVEKKYNSIFITDDLDAMEKISCLVKSDITRNWRWADICGELRTNRMILKKELESRGVKF 213
Query: 898 KSFCKKKKMKKVVQFFKNTSLSISECC 924
+ ++ + K I +
Sbjct: 214 RELINSIRISYSISLMKTGEFKIKQIA 240
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
0.315 0.131 0.394
Gapped
Lambda K H
0.267 0.0510 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 25,834,869
Number of extensions: 1562411
Number of successful extensions: 3136
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3068
Number of HSP's successfully gapped: 58
Length of query: 1714
Length of database: 6,701,793
Length adjustment: 107
Effective length of query: 1607
Effective length of database: 3,714,246
Effective search space: 5968793322
Effective search space used: 5968793322
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 64 (28.9 bits)