RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17934
(584 letters)
>1c4z_A E6AP, ubiquitin-protein ligase E3A; bilobal structure, elongated
shape, E3 ubiquitin ligase, E2 ubiquitin conjugating
enzyme; 2.60A {Homo sapiens} SCOP: d.148.1.1 PDB: 1d5f_A
Length = 358
Score = 374 bits (963), Expect = e-126
Identities = 170/244 (69%), Positives = 203/244 (83%), Gaps = 1/244 (0%)
Query: 340 NPYLRLKVRRDHIIEDALVELEMIAMENEKDLKKQLVVEFEGEQGIDEGGVSKEFFQLII 399
NPYLRLKVRRDHII+DALV LEMIAMEN DLKKQL VEFEGEQG+DEGGVSKEFFQL++
Sbjct: 3 NPYLRLKVRRDHIIDDALVRLEMIAMENPADLKKQLYVEFEGEQGVDEGGVSKEFFQLVV 62
Query: 400 EEIFNPDYGMFCVQSDTQHMWFNQMSFESDAQFTLVGIILGLAIYNNIILDVNFPMVVYK 459
EEIFNPD GMF T+ WFN SFE++ QFTL+GI+LGLAIYNN ILDV+FPMVVY+
Sbjct: 63 EEIFNPDIGMFTYDESTKLFWFNPSSFETEGQFTLIGIVLGLAIYNNCILDVHFPMVVYR 122
Query: 460 KLMGKRGSFYDLEDFNPVLFNGLRDLLDYEGQDMEDVFSQTFRICFTDPFGAFISHDLKP 519
KLMGK+G+F DL D +PVL+ L+DLL+YEG ++ED TF+I TD FG + +DLK
Sbjct: 123 KLMGKKGTFRDLGDSHPVLYQSLKDLLEYEG-NVEDDMMITFQISQTDLFGNPMMYDLKE 181
Query: 520 DGDNIAVTQENKQEFIDLYSDFLLNTSIEKQFKAFRRGFQMVTDESPLSLLFRPEEIEQL 579
+GD I +T EN++EF++LYSD++LN S+EKQFKAFRRGF MVT+ESPL LFRPEEIE L
Sbjct: 182 NGDKIPITNENRKEFVNLYSDYILNKSVEKQFKAFRRGFHMVTNESPLKYLFRPEEIELL 241
Query: 580 VCGS 583
+CGS
Sbjct: 242 ICGS 245
>2oni_A E3 ubiquitin-protein ligase NEDD4-like protein; alpha and beta
protein (A + B), E3 ligase, HECT domain, UBL-
conjugation pathway; HET: MSE; 2.20A {Homo sapiens} PDB:
3jvz_C 3jw0_C 2xbf_A 2xbb_A
Length = 392
Score = 328 bits (843), Expect = e-108
Identities = 80/282 (28%), Positives = 147/282 (52%), Gaps = 15/282 (5%)
Query: 308 ATKTLGLYYDSRIRMYSGRRISYLQSVVG-QPTNPYLRLKVRRDHIIEDALVELEMIAME 366
++ LY+ R + + + + + +K+ R++I E++ + ++++
Sbjct: 8 SSGRENLYFQGS-REFKQKYDYFRKKLKKPADIPNRFEMKLHRNNIFEESYRRI--MSVK 64
Query: 367 NEKDLKKQLVVEFEGEQGIDEGGVSKEFFQLIIEEIFNPDYGMF-CVQSDTQHMWFNQMS 425
LK +L +EFE E+G+D GGV++E+F L+ +E+FNP YG+F +D + N S
Sbjct: 65 RPDVLKARLWIEFESEKGLDYGGVAREWFFLLSKEMFNPYYGLFEYSATDNYTLQINPNS 124
Query: 426 F----ESDAQFTLVGIILGLAIYNNIILDVNFPMVVYKKLMGKRGSFYDLEDFNPVLFNG 481
+ + FT +G + GLA+++ +LD F YK ++GK+ + D+E + +N
Sbjct: 125 GLCNEDHLSYFTFIGRVAGLAVFHGKLLDGFFIRPFYKMMLGKQITLNDMESVDSEYYNS 184
Query: 482 LRDLLDYEGQDMEDVFSQTFRICFTDPFGAFISHDLKPDGDNIAVTQENKQEFIDLYSDF 541
L+ +L+ + +++ +F + FG DLKP+G I VT ENK+E+IDL +
Sbjct: 185 LKWILENDPTELDLMFCIDE-----ENFGQTYQVDLKPNGSEIMVTNENKREYIDLVIQW 239
Query: 542 LLNTSIEKQFKAFRRGFQMVTDESPLSLLFRPEEIEQLVCGS 583
++KQ AF GF + + +F E+E L+CG
Sbjct: 240 RFVNRVQKQMNAFLEGFTELLPIDLIK-IFDENELELLMCGL 280
>3h1d_A E3 ubiquitin-protein ligase HUWE1; E3ligase, HECT, LOBE,
alternative splicing, chromosomal rearrangement,
cytoplasm, differentiation; 1.89A {Homo sapiens} PDB:
3g1n_A
Length = 405
Score = 325 bits (836), Expect = e-106
Identities = 81/272 (29%), Positives = 138/272 (50%), Gaps = 15/272 (5%)
Query: 316 YDSRIRMYSGRRISYLQSVVGQPTNPYLRLKVRRDHIIEDALVELEMIAMENEKDLKKQL 375
+D + + + L+ + + + VRRDH+ ED+ E + ++ +++K +L
Sbjct: 25 FDVKRKYFR----QELERLDEGLRKEDMAVHVRRDHVFEDSYRE---LHRKSPEEMKNRL 77
Query: 376 VVEFEGEQGIDEGGVSKEFFQLIIEEIFNPDYGMF-CVQSDTQHMWFNQMSFESD---AQ 431
+ FEGE+G D GG+ +E++ +I E+FNP Y +F D N S + +
Sbjct: 78 YIVFEGEEGQDAGGLLREWYMIISREMFNPMYALFRTSPGDRVTYTINPSSHANPNHLSY 137
Query: 432 FTLVGIILGLAIYNNIILDVNFPMVVYKKLMGKRGSFYDLEDFNPVLFNGLRDLLDYEGQ 491
F VG I+ A+Y+N +L+ F YK ++GK + D+E + + GL LL+ +
Sbjct: 138 FKFVGRIVAKAVYDNRLLECYFTRSFYKHILGKSVRYTDMESEDYHFYQGLVYLLENDVS 197
Query: 492 DMEDVFSQTFRICFTDPFGAFISHDLKPDGDNIAVTQENKQEFIDLYSDFLLNTSIEKQF 551
+ + TF FG DLKP+G NI VT+ENK+E++ L + +I KQ
Sbjct: 198 TLG--YDLTFSTEV-QEFGVAEVRDLKPNGANILVTEENKKEYVHLVCQMRMTGAIRKQL 254
Query: 552 KAFRRGFQMVTDESPLSLLFRPEEIEQLVCGS 583
AF GF + + +S +F +E+E L+ G
Sbjct: 255 AAFLEGFYEIIPKRLIS-IFTEQELELLISGL 285
>1zvd_A SMAD ubiquitination regulatory factor 2; ubiquitin ligasecatalytic
mechanism,X-RAY ligase; 2.10A {Homo sapiens}
Length = 380
Score = 323 bits (830), Expect = e-106
Identities = 87/268 (32%), Positives = 145/268 (54%), Gaps = 13/268 (4%)
Query: 321 RMYSGRRISYLQSVV-GQPTNPYLRLKVRRDHIIEDALVELEMIAMENEKDLKKQLVVEF 379
R + Q + QP + R++V R+ I E++ + KDL K+L+++F
Sbjct: 2 RDLVQKLKILRQELSQQQPQAGHCRIEVSREEIFEESY---RQVMKMRPKDLWKRLMIKF 58
Query: 380 EGEQGIDEGGVSKEFFQLIIEEIFNPDYGMF-CVQSDTQHMWFNQMSF---ESDAQFTLV 435
GE+G+D GGV++E+ L+ E+ NP YG+F + D + N S E + F V
Sbjct: 59 RGEEGLDYGGVAREWLYLLSHEMLNPYYGLFQYSRDDIYTLQINPDSAVNPEHLSYFHFV 118
Query: 436 GIILGLAIYNNIILDVNFPMVVYKKLMGKRGSFYDLEDFNPVLFNGLRDLLDYEGQDMED 495
G I+G+A+++ +D F + YK+L+GK + D+E +P L N L +L+ D+
Sbjct: 119 GRIMGMAVFHGHYIDGGFTLPFYKQLLGKSITLDDMELVDPDLHNSLVWILEN---DITG 175
Query: 496 VFSQTFRICFTDPFGAFISHDLKPDGDNIAVTQENKQEFIDLYSDFLLNTSIEKQFKAFR 555
V TF + + +G I H+LKP+G +I V +ENK+E++ LY ++ IE QF A +
Sbjct: 176 VLDHTFCVEH-NAYGEIIQHELKPNGKSIPVNEENKKEYVRLYVNWRFLRGIEAQFLALQ 234
Query: 556 RGFQMVTDESPLSLLFRPEEIEQLVCGS 583
+GF V + L F +E+E ++CG
Sbjct: 235 KGFNEVIPQHLLK-TFDEKELELIICGL 261
>3olm_A E3 ubiquitin-protein ligase RSP5; ligase; 2.50A {Saccharomyces
cerevisiae}
Length = 429
Score = 315 bits (809), Expect = e-102
Identities = 88/286 (30%), Positives = 149/286 (52%), Gaps = 12/286 (4%)
Query: 302 SFILTPATKTLGLYYDSRIRMYSGRRISYLQSVVGQPTNPYLRLKVRRDHIIEDALVELE 361
++ +L R + + I + + +KVRR +I EDA +
Sbjct: 34 TWDDPRLPSSLDQNVPQYKRDFRRKVIYFRSQPALRILPGQCHIKVRRKNIFEDAY---Q 90
Query: 362 MIAMENEKDLKKQLVVEFEGEQGIDEGGVSKEFFQLIIEEIFNPDYGMF-CVQSDTQHMW 420
I + +DLKK+L+++F+GE+G+D GGVS+EFF L+ E+FNP Y +F D +
Sbjct: 91 EIMRQTPEDLKKRLMIKFDGEEGLDYGGVSREFFFLLSHEMFNPFYCLFEYSAYDNYTIQ 150
Query: 421 FNQMSF---ESDAQFTLVGIILGLAIYNNIILDVNFPMVVYKKLMGKRGSFYDLEDFNPV 477
N S E F +G ++GL +++ LD F +YK ++ K+ D+E +
Sbjct: 151 INPNSGINPEHLNYFKFIGRVVGLGVFHRRFLDAFFVGALYKMMLRKKVVLQDMEGVDAE 210
Query: 478 LFNGLRDLLDYEGQDMEDVFSQTFRICFTDPFGAFISHDLKPDGDNIAVTQENKQEFIDL 537
++N L +L+ ++ V TF + FG ++ DLKPDG NI VT NK+E+++L
Sbjct: 211 VYNSLNWMLEN---SIDGVLDLTFSADD-ERFGEVVTVDLKPDGRNIEVTDGNKKEYVEL 266
Query: 538 YSDFLLNTSIEKQFKAFRRGFQMVTDESPLSLLFRPEEIEQLVCGS 583
Y+ + + +++QFKAF GF + E ++ +F E+E L+ G
Sbjct: 267 YTQWRIVDRVQEQFKAFMDGFNELIPEDLVT-VFDERELELLIGGI 311
>1nd7_A WW domain-containing protein 1; HECT, ubiquitin, ligase, WWP1;
2.10A {Homo sapiens} SCOP: d.148.1.1 PDB: 3tug_A
Length = 374
Score = 307 bits (788), Expect = e-100
Identities = 71/264 (26%), Positives = 133/264 (50%), Gaps = 12/264 (4%)
Query: 326 RRISYLQSVVGQ-PTNPYLRLKVRRDHIIEDALVELEMIAMENEKDLKKQLVVEFEGEQG 384
++++ + + ++++ V R + ED+ + I DL+++L V F GE+G
Sbjct: 6 WKLAHFRYLCQSNALPSHVKINVSRQTLFEDSF---QQIMALKPYDLRRRLYVIFRGEEG 62
Query: 385 IDEGGVSKEFFQLIIEEIFNPDYGMF-CVQSDTQHMWFNQMSFESD---AQFTLVGIILG 440
+D GG+++E+F L+ E+ NP Y +F + + N S + + F +G +
Sbjct: 63 LDYGGLAREWFFLLSHEVLNPMYCLFEYAGKNNYCLQINPASTINPDHLSYFCFIGRFIA 122
Query: 441 LAIYNNIILDVNFPMVVYKKLMGKRGSFYDLEDFNPVLFNGLRDLLDYEGQDMEDVFSQT 500
+A+++ +D F + YK+++ K+ + DLE + +N L + D ++
Sbjct: 123 MALFHGKFIDTGFSLPFYKRMLSKKLTIKDLESIDTEFYNSLIWIRDNNIEECG--LEMY 180
Query: 501 FRICFTDPFGAFISHDLKPDGDNIAVTQENKQEFIDLYSDFLLNTSIEKQFKAFRRGFQM 560
F + + G SHDLK G NI VT+ENK E+I L +++ + +++Q KAF GF
Sbjct: 181 FSVDM-EILGKVTSHDLKLGGSNILVTEENKDEYIGLMTEWRFSRGVQEQTKAFLDGFNE 239
Query: 561 VTDESPLSLLFRPEEIEQLVCGSN 584
V L F +E+E ++CG
Sbjct: 240 VVPLQWLQ-YFDEKELEVMLCGMQ 262
>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 = 70.7 bits (172), Expect = 7e-13
Identities = 63/442 (14%), Positives = 130/442 (29%), Gaps = 127/442 (28%)
Query: 25 SPSSLSNGDLDTELTLDIKSVRRAYEQLFALPSSEFEHTLV------------------Q 66
P+ S D + + L I S++ +L +E+ L+ +
Sbjct: 210 DPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKP--YENCLLVLLNVQNAKAWNAFNLSCK 267
Query: 67 ALVT-----LSEYINVQLRCGSSL------LSTDSLINVFLVIFEIPSLGGCDYVERALP 115
L+T ++++++ SL L+ D + ++ L + + LP
Sbjct: 268 ILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCR--------PQDLP 319
Query: 116 K-ICK----AASQLPLTAQARIARI--WAAHCKQRLKTILEA-LQQLITIKTISNHYHKD 167
+ + S + + + +A W +L TI+E+ L L + +
Sbjct: 320 REVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVL-EPAEYRKMFDRL 378
Query: 168 YILQDEETITLPTKIMRILFYANILAGDLDPPCLRDETQDPEDNHESMFGVDISSSKSSV 227
+ I PT ++ ++++ D V+ S V
Sbjct: 379 SVFPPSAHI--PTILLSLIWFD-------------VIKSDVMVV------VNKLHKYSLV 417
Query: 228 QAN--------H--YEDSLAKLLQINVLDSRKPLIPFLEFYNEPL---SDAIEMDRDFGY 274
+ Y + KL L ++ YN P SD + Y
Sbjct: 418 EKQPKESTISIPSIYLELKVKLENEYALHRS-----IVDHYNIPKTFDSDDLIPPYLDQY 472
Query: 275 ------YRASEELTSETDCASSSRFLKFSFMYYSFILTPATKTLGLYYDSRIRMYSGRRI 328
+ E FL F F+ + +IR
Sbjct: 473 FYSHIGHHLKNIEHPERMTLFRMVFLDFRFL-----------------EQKIR-----HD 510
Query: 329 SYLQSVVGQPTNPYLRLKVRRDHIIEDALVELEMIAMENEKDLKKQLVVEFEGEQGIDEG 388
S + G N +LK + +I ++ ++ + L I+E
Sbjct: 511 STAWNASGSILNTLQQLKFYKPYICDNDPKYERLV-----NAILDFL-------PKIEEN 558
Query: 389 GVSKEFFQLIIEEIFNPDYGMF 410
+ ++ L+ + D +F
Sbjct: 559 LICSKYTDLLRIALMAEDEAIF 580
Score = 64.9 bits (157), Expect = 5e-11
Identities = 92/608 (15%), Positives = 184/608 (30%), Gaps = 180/608 (29%)
Query: 24 DSPSS-LSNGDLDTELTL--DIKSVRRAYEQLFALPSSEFEHTLVQALVTLSEYI--NVQ 78
D P S LS ++D + + R + L + + + + L +++ ++
Sbjct: 40 DMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIK 99
Query: 79 LRCGSSLLSTDSLINVFLVIFEIPSLGGCDYVERALP--KICKAASQL-P---------- 125
+ T I ++ + V R P K+ +A +L P
Sbjct: 100 TEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVL 159
Query: 126 ------LTAQA-RIARI---------WA--AHCKQRLKTILEALQQLITI----KTISNH 163
+ ++ W +C +T+LE LQ+L+ T +
Sbjct: 160 GSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNC-NSPETVLEMLQKLLYQIDPNWTSRSD 218
Query: 164 YHKDYILQDEETITLPTKIMRILFYANILAGDLDPPCLRDETQDPEDNHESMFGV----- 218
+ + L+ ++++ Y N L L L + Q+ + + F +
Sbjct: 219 HSSNIKLRIHSIQAELRRLLKSKPYENCL---LV---LLN-VQNAK--AWNAFNLSCKIL 269
Query: 219 ----DIS-------SSKSSVQANHYEDSL----AKLLQINVLDSRKPLIPFLEFYNEPLS 263
++ + + +H+ +L K L + LD R +P P
Sbjct: 270 LTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRR 329
Query: 264 DAI--EMDRDF----GYYR--ASEELTSETDCASSSRFLK---FSFMYYSFILTPA---- 308
+I E RD ++ ++LT+ + SS L+ + M+ + P
Sbjct: 330 LSIIAESIRDGLATWDNWKHVNCDKLTTIIE--SSLNVLEPAEYRKMFDRLSVFPPSAHI 387
Query: 309 -TKTLGL------YYDSRIRMYSGRRISYLQSVVGQPTNPYLRLKVRRDHIIEDALVELE 361
T L L D + + + S ++ QP + + +EL+
Sbjct: 388 PTILLSLIWFDVIKSDVMVVVNKLHKYSLVE---KQPKESTISI-----P---SIYLELK 436
Query: 362 MIAMENEKDLKKQLVVEFEGEQGIDEGGVSKE-----FFQLIIEEIFNPDYGMFCVQSDT 416
+ +ENE L + +V + + D + F+ I +
Sbjct: 437 V-KLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHI-------GH--------- 479
Query: 417 QHMWFNQMSFESDAQFTLVGIILGLAIYNNIILDVNFPMVVYKKLMGKRGSFYDLEDFNP 476
H+ + E F + LD F + +K+ R
Sbjct: 480 -HLKNIEHP-ERMTLFR------------MVFLDFRF---LEQKI---RHDSTAWNASGS 519
Query: 477 VLFNGLRDLLDYEGQDMEDVFSQTFRICFTDPFGAFISHDLKPDGDNIAVTQENKQEFID 536
+L N L+ L Y+ IC DP + ++
Sbjct: 520 IL-NTLQQLKFYKPY-----------ICDNDP---------------------KYERLVN 546
Query: 537 LYSDFLLN 544
DFL
Sbjct: 547 AILDFLPK 554
>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 = 52.4 bits (125), Expect = 4e-07
Identities = 110/605 (18%), Positives = 188/605 (31%), Gaps = 189/605 (31%)
Query: 26 PSSLSNGDLDTELTLDI-KSVRRAYEQLFALPSSEFEHTLVQALVTLSE----------- 73
P +LS+G L E L + + QL +F L + +
Sbjct: 8 PLTLSHGSL--EHVLLVPTASFFIASQL----QEQFNKILPEPTEGFAADDEPTTPAELV 61
Query: 74 -----YINVQLRCGSSLLSTDSLINVFLVIFEIPSLGGCDY--VERALPKICKAASQLPL 126
Y++ + D ++N+ L FE L G D + L + + L
Sbjct: 62 GKFLGYVSSLVEPSKVG-QFDQVLNLCLTEFENCYLEGNDIHALAAKLLQE----NDTTL 116
Query: 127 TAQARIARIW--AAHCKQRLKT------ILEALQ----QLITI----KTISNHYHKDYIL 170
+ + + A +R + A+ QL+ I DY
Sbjct: 117 VKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTD-----DYF- 170
Query: 171 QDEETITLPTKIMRILF--YANILAGDLDP--PCLRDETQDPEDNHESMF--GVDISS-- 222
+E +R L+ Y ++ + L + + D E +F G++I
Sbjct: 171 -EE---------LRDLYQTYHVLVGDLIKFSAETLSELIRTTLDA-EKVFTQGLNILEWL 219
Query: 223 -SKSSVQANHYEDSLAKLLQINVLDSRKPLIPFLEF--YNEPLSDAIEMDRDFGYYRASE 279
+ S+ Y LL I + S PLI ++ Y + A + G R+
Sbjct: 220 ENPSNTPDKDY------LLSIPI--SC-PLIGVIQLAHY---VVTAKLLGFTPGELRSY- 266
Query: 280 ELTSETDC-----------ASSS---------RFLKFSFMYYSFI------LTPATK-TL 312
L T + S + + F FI P T
Sbjct: 267 -LKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLF----FIGVRCYEAYPNTSLPP 321
Query: 313 GLYYDSRIR-------MYSGRRISY--LQSVVGQPTNPYLRLKVRRDHIIEDALVELEMI 363
+ DS M S ++ +Q V + TN +L ++ I +LV
Sbjct: 322 SILEDSLENNEGVPSPMLSISNLTQEQVQDYVNK-TNSHLPAG-KQVEI---SLV----- 371
Query: 364 AMENEKDLKKQLVVEFEGEQGIDEGG--VSKEFFQLIIEEIFNPDYGMFCVQSDTQHMWF 421
N LVV G S L + + P G+ QS F
Sbjct: 372 ---NGAK---NLVV----------SGPPQSLYGLNLTLRKAKAPS-GLD--QSRIP---F 409
Query: 422 NQMSFESDAQFTLVGIILGLAI---YNNIILDVNFPMVVYKKLMGKRGSFYDLEDFN-PV 477
++ + +F L + +++ +L ++ K + K ++ +D PV
Sbjct: 410 SERKLKFSNRF--------LPVASPFHSHLLVPASDLI--NKDLVKNNVSFNAKDIQIPV 459
Query: 478 L--FNGLRDLLDYEGQDMEDVFSQTFRICF----TDPFGAFISH--DLKPDGDN--IAVT 527
F+G DL G E + R+ T F A +H D P G + +T
Sbjct: 460 YDTFDG-SDLRVLSGSISERIVDCIIRLPVKWETTTQFKA--THILDFGPGGASGLGVLT 516
Query: 528 QENKQ 532
NK
Sbjct: 517 HRNKD 521
Score = 50.8 bits (121), Expect = 1e-06
Identities = 99/563 (17%), Positives = 162/563 (28%), Gaps = 209/563 (37%)
Query: 4 EQLT---QYTSPPPTLPSTEGSGDSPSSLSNGDLDTELTLDI---------KSVRRAYEQ 51
QL P PT + D P++ EL S ++Q
Sbjct: 31 SQLQEQFNKILPEPT--EGFAADDEPTT------PAELVGKFLGYVSSLVEPSKVGQFDQ 82
Query: 52 LFALPSSEFE---------HTLVQALVTLSE------------YINVQLRCG-------- 82
+ L +EFE H L L+ ++ YI ++
Sbjct: 83 VLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSN 142
Query: 83 SSLL--STDSLINVFLVIFEIPSLGG----CDYVE--RAL---------PKICKAASQL- 124
S+L + + IF GG DY E R L I +A L
Sbjct: 143 SALFRAVGEGNAQLVA-IF-----GGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLS 196
Query: 125 PLTAQARIARI----------W---------------------------AAH----CKQ- 142
L A W AH K
Sbjct: 197 ELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLL 256
Query: 143 ---------RLKTILEALQQLITIKTISNHYHKDYILQD--EETITLPTKIMRILFY--- 188
LK Q L+T I+ D E K + +LF+
Sbjct: 257 GFTPGELRSYLKGATGHSQGLVTAVAIA--------ETDSWESFFVSVRKAITVLFFIGV 308
Query: 189 -ANILAGDLD-PPCLRDETQDPEDNHE----SMFGVDISSSKSSVQA-----NHYEDSLA 237
+ PP +D +N+E M + + ++ VQ N + +
Sbjct: 309 RCYEAYPNTSLPP---SILEDSLENNEGVPSPMLSI-SNLTQEQVQDYVNKTNSHLPA-G 363
Query: 238 KLLQINVLDSRKPLI----PF----LEFYNEPLSDAIEMDRDFGYYRASEELTSETDCAS 289
K ++I++++ K L+ P L +D+ S SE
Sbjct: 364 KQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQ-------SRIPFSERKLKF 416
Query: 290 SSRFLKFSFMYYSFILTPATKTLGLYYDSRIRMYSGRRISYLQSVV-----GQPTNPYLR 344
S+RFL + ++S +L PA+ + ++ +Q V G
Sbjct: 417 SNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNA---KDIQIPVYDTFDGS------D 467
Query: 345 LKVRRDHIIEDALVELEMIA-----MENEKDLKKQLVVEFE--GEQGID-------EG-G 389
L+V I E +V + I E K +++F G G+ +G G
Sbjct: 468 LRVLSGSISER-IV--DCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTG 524
Query: 390 VSKEFFQLII----EEIFNPDYG 408
V ++I+ + + DYG
Sbjct: 525 V-----RVIVAGTLDINPDDDYG 542
Score = 43.1 bits (101), Expect = 3e-04
Identities = 74/476 (15%), Positives = 132/476 (27%), Gaps = 158/476 (33%)
Query: 173 EETITLPTKIMRILFYANIL----AGDLDPPCLRDETQD--PEDNHE--SMFGVDISSSK 224
E + +PT F A+ L L P D P E F +SS
Sbjct: 17 EHVLLVPT---ASFFIASQLQEQFNKILPEP-TEGFAADDEPTTPAELVGKFLGYVSSLV 72
Query: 225 SSVQANHYEDSLAKLLQ-----------INVLDSRKPLIPFLEFYNEPLSDAIEMDRDFG 273
+ ++ L L I+ L ++ L+ + L E+ ++
Sbjct: 73 EPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAK-----LLQENDTTLVKTKELIKN-- 125
Query: 274 YYRASEELTSETDCASSSRFLKFSFMYYSFILTPATKTLGLYYDSRIRMYS--GRRISYL 331
Y A D S+S + A + ++ + G
Sbjct: 126 YITARIMAKRPFDKKSNSALFR------------AVG------EGNAQLVAIFG------ 161
Query: 332 QSVVGQ-PTNPY---LRL-----KVRRDHIIEDALVELEMIAMENEKDLKKQLVVEFEGE 382
GQ T+ Y LR V +I+ + L + D +K
Sbjct: 162 ----GQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELI-RTTLDAEKVF------T 210
Query: 383 QGIDEGGVSKEFFQLIIEEIFNPDYGMFCVQSDTQHMWFNQMSFESDAQFTLVGI-ILGL 441
QG++ I+E + NP D ++ + I ++ L
Sbjct: 211 QGLN-----------ILEWLENPS-----NTPDKDYL--------LSIPISCPLIGVIQL 246
Query: 442 AIYNNI--ILDVNFPMVVYKKLMGKRGSFYDL------------EDFNPVLFNGLRDL-- 485
A Y +L P + L G G L E F + + L
Sbjct: 247 AHYVVTAKLLGFT-PGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFF 305
Query: 486 LDYEGQDMEDVFSQTFRICFTDPFGAFISHDLKPDGDNIA--------VTQENKQEFIDL 537
+ + + P I D + + + +TQE Q++++
Sbjct: 306 IGVRCY-------EAYPNTSLPP---SILEDSLENNEGVPSPMLSISNLTQEQVQDYVN- 354
Query: 538 YSDFLLNTSIEKQFKAF------RRGFQMVTDESPLSL-----LFR----PEEIEQ 578
N+ + + + +V P SL R P ++Q
Sbjct: 355 ----KTNSHLPAGKQVEISLVNGAK--NLVVSGPPQSLYGLNLTLRKAKAPSGLDQ 404
Score = 33.9 bits (77), Expect = 0.17
Identities = 28/137 (20%), Positives = 47/137 (34%), Gaps = 55/137 (40%)
Query: 373 KQLVVEFEGEQG---------------IDEGGVSKEFFQLIIEE----IFNPDYGMFCVQ 413
L + F GE+G +D +++ F+ I E F + G+
Sbjct: 1670 VNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLL--- 1726
Query: 414 SDTQHMWFNQ-----MSFESDAQFTLV---GII----------LG----LAIYNNIILDV 451
S TQ F Q M A F + G+I LG LA +++
Sbjct: 1727 SATQ---FTQPALTLMEK---AAFEDLKSKGLIPADATFAGHSLGEYAALASLADVM--- 1777
Query: 452 NFPMVVYKKLMGKRGSF 468
+ +V +++ RG
Sbjct: 1778 SIESLV--EVVFYRGMT 1792
Score = 33.5 bits (76), Expect = 0.24
Identities = 25/119 (21%), Positives = 35/119 (29%), Gaps = 25/119 (21%)
Query: 462 MGKRGSFYDLEDFNPVLFNGLRDLLDYEGQDMEDVFSQTF-----RICFTDPFGAFISHD 516
MG DL + +D+ + ++ F T+ I +P I H
Sbjct: 1631 MGM-----DLYKTSKAA----QDVWN----RADNHFKDTYGFSILDIVINNPVNLTI-HF 1676
Query: 517 LKPDGDNIAVTQENKQEFI-DLYSDFLLNTSIEKQFKAFRRGFQMVTDESPLSLLFRPE 574
G I EN I + D EK FK T S LL +
Sbjct: 1677 GGEKGKRIR---ENYSAMIFETIVDG--KLKTEKIFKEINEHSTSYTFRSEKGLLSATQ 1730
Score = 32.3 bits (73), Expect = 0.50
Identities = 20/130 (15%), Positives = 52/130 (40%), Gaps = 31/130 (23%)
Query: 383 QGIDEGGVSKEFFQL--IIEEIFNPDYGMFCVQSDTQHMWFNQMSFESDAQFTLVGIILG 440
QG E G+ + ++ ++++N ++D H F+ F+++ I++
Sbjct: 1624 QGSQEQGMGMDLYKTSKAAQDVWN--------RAD-NH-------FKDTYGFSILDIVIN 1667
Query: 441 LAIYNNIILDVNFPMVVYKKLMGKRGSFYDLEDFNPVLFNGLRDLLDYEGQDMEDVFSQT 500
N + L ++F G++G E+++ ++F + D + +++ +
Sbjct: 1668 ----NPVNLTIHFG--------GEKGK-RIRENYSAMIFETIVDGKLKTEKIFKEINEHS 1714
Query: 501 FRICFTDPFG 510
F G
Sbjct: 1715 TSYTFRSEKG 1724
>3hut_A Putative branched-chain amino acid ABC transporter; extracellular
ligand-binding receptor,transport protein; 1.93A
{Rhodospirillum rubrum atcc 11170}
Length = 358
Score = 32.2 bits (74), Expect = 0.40
Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 14/70 (20%)
Query: 500 TFRICFTDPF-GAFISHDLKPDGD-NIAVTQENKQEFIDLYSDF--LLNTSIEKQFKAFR 555
FR T F G + + DG ++AV I + +D+ + K F+
Sbjct: 116 QFRAITTPAFEGPNNAAWMIGDGFTSVAV--------IGVTTDWGLSSAQAFRKAFEL-- 165
Query: 556 RGFQMVTDES 565
RG +V +E
Sbjct: 166 RGGAVVVNEE 175
>3td9_A Branched chain amino acid ABC transporter, peripl amino
acid-binding protein; leucine binding, structural
genomics; HET: MSE PHE; 1.90A {Thermotoga maritima}
Length = 366
Score = 32.2 bits (74), Expect = 0.42
Identities = 13/60 (21%), Positives = 23/60 (38%), Gaps = 14/60 (23%)
Query: 500 TFRICFTDPF-----GAFISHDLKPDGDNIAVTQENKQEF-IDLYSDFLLNTSIEKQFKA 553
R+CF DPF F +L + V + +Q++ + L + F +F
Sbjct: 125 VSRVCFIDPFQGAAMAVFAYKNLGA--KRVVVFTDVEQDYSVGLSNFF------INKFTE 176
>3lkb_A Probable branched-chain amino acid ABC transporter, amino acid
binding protein; branched amino acid, PSI-II, NYSGXRC,
structural genomics; 2.40A {Thermus thermophilus}
Length = 392
Score = 32.0 bits (73), Expect = 0.59
Identities = 11/77 (14%), Positives = 21/77 (27%), Gaps = 19/77 (24%)
Query: 496 VFSQTFRICFTDPFGA-----FISHDLKPDGDNIAVTQENKQEFIDLYSDF--LLNTSIE 548
F + +I+ + K G +A+ + S F
Sbjct: 115 NNDYIFLPTTSYSEQVVALLEYIAREKK--GAKVAL--------VVHPSPFGRAPVEDAR 164
Query: 549 KQFKAFRRGFQMVTDES 565
K + G Q+V +
Sbjct: 165 KAARE--LGLQIVDVQE 179
>3snr_A Extracellular ligand-binding receptor; structural genomics,
APC102214, PSI-biology, midwest center structural
genomics, MCSG; HET: MSE TYR PHE; 1.49A
{Rhodopseudomonas palustris} PDB: 3uk0_A* 3t23_A*
3ukj_A* 3tx6_A*
Length = 362
Score = 31.9 bits (73), Expect = 0.61
Identities = 11/70 (15%), Positives = 24/70 (34%), Gaps = 14/70 (20%)
Query: 500 TFRICFTDPF-GAFISHDLKPDGD-NIAVTQENKQEFIDLYSDF--LLNTSIEKQFKAFR 555
+ + P G + +K + + I + L ++KQ +A
Sbjct: 112 SVVMPQPIPIMGKVLYEHMKKNNVKTVGY--------IGYSDSYGDLWFNDLKKQGEA-- 161
Query: 556 RGFQMVTDES 565
G ++V +E
Sbjct: 162 MGLKIVGEER 171
>3ipc_A ABC transporter, substrate binding protein (amino; venus flytrap
domain, transport protein; 1.30A {Agrobacterium
tumefaciens} PDB: 3ip5_A 3ip6_A 3ip7_A 3ip9_A 3ipa_A
Length = 356
Score = 31.5 bits (72), Expect = 0.68
Identities = 16/79 (20%), Positives = 24/79 (30%), Gaps = 19/79 (24%)
Query: 494 EDVFSQTFRICFTDPF-----GAFISHDLKPDGDNIAVTQENKQEFIDLYSDF--LLNTS 546
E TFR C D G +++ K +A+ I + + L
Sbjct: 108 ERGLWNTFRTCGRDDQQGGIAGKYLADHFKD--AKVAI--------IHDKTPYGQGLADE 157
Query: 547 IEKQFKAFRRGFQMVTDES 565
+K A G V E
Sbjct: 158 TKKAANA--AGVTEVMYEG 174
>1usg_A Leucine-specific binding protein; leucine-binding protein, X-RAY
crystallography, protein structure, ABC transport
systems, transport protein; 1.53A {Escherichia coli}
SCOP: c.93.1.1 PDB: 1usi_A* 1usk_A 2lbp_A 1z15_A 1z16_A
1z17_A 1z18_A 2liv_A
Length = 346
Score = 31.5 bits (72), Expect = 0.69
Identities = 13/73 (17%), Positives = 21/73 (28%), Gaps = 19/73 (26%)
Query: 500 TFRICFTDPF-----GAFISHDLKPDGDNIAVTQENKQEFIDLYSDF--LLNTSIEKQFK 552
R D +I +KP IA+ I + L S++ K
Sbjct: 114 IMRTAGLDSSQGPTAAKYILETVKP--QRIAI--------IHDKQQYGEGLARSVQDGLK 163
Query: 553 AFRRGFQMVTDES 565
A +V +
Sbjct: 164 A--ANANVVFFDG 174
>3sg0_A Extracellular ligand-binding receptor; structural genomics,
PSI-biology; HET: 173; 1.20A {Rhodopseudomonas
palustris} PDB: 4dqd_A*
Length = 386
Score = 30.4 bits (69), Expect = 1.8
Identities = 8/70 (11%), Positives = 17/70 (24%), Gaps = 14/70 (20%)
Query: 500 TFRICFTDPF-GAFISHDLKPDGD-NIAVTQENKQEFIDLYSDF--LLNTSIEKQFKAFR 555
+++ D I + G + I + +
Sbjct: 136 VYKVVPNDDIMAEAIGKYIAKTGAKKVGY--------IGFSDAYGEGYYKVLAAAAPK-- 185
Query: 556 RGFQMVTDES 565
GF++ T E
Sbjct: 186 LGFELTTHEV 195
>3eaf_A ABC transporter, substrate binding protein; PSI2, NYSGXRC,
substrate binding P structural genomics, protein
structure initiative; 2.00A {Aeropyrum pernix}
Length = 391
Score = 30.1 bits (68), Expect = 2.1
Identities = 10/72 (13%), Positives = 21/72 (29%), Gaps = 16/72 (22%)
Query: 500 TFRICFTDPF-----GAFISHDLKPDGDNIAVTQENKQEF-IDLYSDFLLNTSIEKQFKA 553
F AF++ + +A+ ++K + +K +
Sbjct: 117 NFYPAPDYSTQACSGLAFLASEFG--QGKLALAYDSKVAYSRSPIGAI------KKAAPS 168
Query: 554 FRRGFQMVTDES 565
G Q+V D
Sbjct: 169 --LGLQVVGDYD 178
>2jul_A Calsenilin; EF-hand, calcium, LXXLL, DNA binding protein, dimer,
alternative splicing, apoptosis, cytoplasm, endoplasmic
reticulum, golgi apparatus; NMR {Mus musculus}
Length = 256
Score = 28.9 bits (64), Expect = 4.1
Identities = 16/75 (21%), Positives = 25/75 (33%), Gaps = 8/75 (10%)
Query: 486 LDYEGQDMEDVFSQTFRICF----TDPFGAFISHDLKPDGDNIAVTQENKQEFIDLYSDF 541
G ED F + F + F+ + DG+ + ++F+ S
Sbjct: 103 ECPTGLVDEDTFKLIYSQFFPQGDATTYAHFLFNAFDADGNG----AIHFEDFVVGLSIL 158
Query: 542 LLNTSIEKQFKAFRR 556
L T EK AF
Sbjct: 159 LRGTVHEKLKWAFNL 173
>2xkj_E Topoisomerase IV; type IIA topoisomerase; 2.20A {Acinetobacter
baumannii} PDB: 2xkk_A*
Length = 767
Score = 28.9 bits (65), Expect = 5.3
Identities = 26/142 (18%), Positives = 51/142 (35%), Gaps = 23/142 (16%)
Query: 166 KDYILQDEETITL-----PTKIMRILFYANILAGDLDPPCLRDETQDPEDNHESMFGVDI 220
Y L DEE T+ K +I + + G+++ LR+ T DP + +D+
Sbjct: 167 VHYALDDEELETILKNVKGNKNPQITRFKGL--GEMNAIQLRETTMDPN--TRRLVQLDL 222
Query: 221 SSSKSSVQANHYEDSLAKLLQINVLDSRKPLIPFLEFYNEPLSDAIEMDRDFGYYRASEE 280
A+ L KLL RK + ++ ++ + A+E
Sbjct: 223 D------DAHLTAGLLDKLLAKKRAADRKQWLEQKG-NLADITVEDKLTMTSLAHHATEN 275
Query: 281 LTSETDCASSSRFLKFSFMYYS 302
+ F + +++ Y+
Sbjct: 276 RSVA-------EFTEQAYLNYA 290
>1s6c_A KV4 potassium channel-interacting protein kchip1B; EF-hand,
transport protein; 2.00A {Rattus norvegicus} SCOP:
a.39.1.5 PDB: 2nz0_A 2i2r_E
Length = 183
Score = 27.5 bits (61), Expect = 9.6
Identities = 9/66 (13%), Positives = 21/66 (31%), Gaps = 4/66 (6%)
Query: 491 QDMEDVFSQTFRICFTDPFGAFISHDLKPDGDNIAVTQENKQEFIDLYSDFLLNTSIEKQ 550
+ + +++Q F + ++ + ++F+ S L T EK
Sbjct: 39 ETFKQIYAQFFPHGDASTYAHYLFNAFDTTQTG----SVKFEDFVTALSILLRGTVHEKL 94
Query: 551 FKAFRR 556
F
Sbjct: 95 RWTFNL 100
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 0.137 0.396
Gapped
Lambda K H
0.267 0.0472 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 8,997,988
Number of extensions: 551740
Number of successful extensions: 1198
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1164
Number of HSP's successfully gapped: 36
Length of query: 584
Length of database: 6,701,793
Length adjustment: 99
Effective length of query: 485
Effective length of database: 3,937,614
Effective search space: 1909742790
Effective search space used: 1909742790
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: 60 (27.5 bits)