RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9877
(1447 letters)
>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 = 83.9 bits (207), Expect = 3e-16
Identities = 95/643 (14%), Positives = 180/643 (27%), Gaps = 271/643 (42%)
Query: 312 TRTFVNTKSSNVLLQTLVVKIRGKDGKQDKLARLMIDTGSQQSYVLEQTMNSLSYTPITK 371
++ + L L+ + K +L + +Y+ T ++ P K
Sbjct: 92 ENCYLEGNDIHALAAKLLQENDTTLVKTKELIK---------NYI---TARIMAKRPFDK 139
Query: 372 QS----MRH---------ALFGG--SITDAMD--HNLFKIVISNLDNTFACDFDVFGQSK 414
+S R A+FGG + D + +L++ + D + ++
Sbjct: 140 KSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQT-----YHVLVGDL-IKFSAE 193
Query: 415 ICSTIPSIPSGPWIDELKQHNIELTD-LQHPSTT--VDILVGADIAGKFYTGKRVELP-S 470
S + +++ + + + L++PS T D L+ I+ P
Sbjct: 194 TLSELIRTTLDA--EKVFTQGLNILEWLENPSNTPDKDYLLSIPIS----------CPLI 241
Query: 471 GLVAME----TC--MGWTLSGKMPTRYGSIDSSVATLVTSLLIKDANISDLWSLDVLGIQ 524
G++ + T +G+T G++ + LVT++ I A +D W
Sbjct: 242 GVIQLAHYVVTAKLLGFT-PGELRSYLKGATGHSQGLVTAVAI--A-ETDSW-------- 289
Query: 525 DPMDKSKADLAEAARK--HFLDTVQVNSDNRFEVHLPWI-----EGHPPLASNLLLSQKR 577
+ RK L F +I E +P + + +
Sbjct: 290 -------ESFFVSVRKAITVL----------F-----FIGVRCYEAYPNTSLPPSILEDS 327
Query: 578 L---EGT------VKKLRRDQYYADYKRVLDTWEMDKIIERV----PQEE-----LDNPG 619
L EG + L ++Q + + + P + L N G
Sbjct: 328 LENNEGVPSPMLSISNLTQEQ-------------VQDYVNKTNSHLPAGKQVEISLVN-G 373
Query: 620 YYMPHHHVVKPGSTTPVRPVFDASAKDNGVSLNDCLEKGPNLIETIPTSLAKFRINKIGI 679
+ VV + GP P SL +
Sbjct: 374 ---AKNLVV----S------------------------GP------PQSLYGLNL----- 391
Query: 680 SGDIAKAFLQISVSP---QDRDCLSMRQPRIMVSRDCLRFLWQDENGRVITYRHCRVVFG 736
+ Q R S R+ + RFL +
Sbjct: 392 ------TLRKAKAPSGLDQSRIPFSERKLKFSN-----RFL-------PVA--------- 424
Query: 737 VSSSPF---LLESCLKLHLELTLTDCREGKSSWPIHLVELLKDSFYVDNCLVSTDSQAEA 793
SPF LL +L D + S+ + ++
Sbjct: 425 ---SPFHSHLLVPA----SDLINKDLVKNNVSFN---AKDIQ------------------ 456
Query: 794 EQFIQVASSIMKEKGFDLRGWELTGDKDDKPTNVLGLLWDKSSDTLAINIDRLTSMHI-- 851
I V + G DLR L+G ++ + +D + + +
Sbjct: 457 ---IPVYDT---FDGSDLR--VLSG-------SISERI-----------VDCIIRLPVKW 490
Query: 852 EKITKKVMLSAAHRI-FDPIGVICAFALIPKLLIQKTWE-TGL 892
E T+ A H + F P G +L + + TG+
Sbjct: 491 ETTTQ---FKATHILDFGP-GGASGLG----VLTHRNKDGTGV 525
Score = 67.4 bits (164), Expect = 4e-11
Identities = 112/676 (16%), Positives = 184/676 (27%), Gaps = 269/676 (39%)
Query: 438 LTDLQHPSTTVDILVGADIAG-------KFYTGKRVELPSGLVAMETCMGWTLSGKMPTR 490
LT L H S +LV +F LP PT
Sbjct: 9 LT-LSHGSLEHVLLVPTASFFIASQLQEQFNK----ILPE-----------------PTE 46
Query: 491 YGSID---SSVATLVTSLLIKDANISDLWSLDVLGIQDPMDKSKADLAEAARKHFLDTVQ 547
+ D ++ A LV L +S L ++ + F +
Sbjct: 47 GFAADDEPTTPAELVGKFL---GYVSSL-------VEPSKVGQFDQVLNLCLTEFENCYL 96
Query: 548 VNSDNRFEVHLPWIEGHPPLASNLLLSQKRLEGTVKKLRRDQYYADY--KRVLDTWEMDK 605
+D +H LA+ LL K+L ++ A KR D
Sbjct: 97 EGND----IHA--------LAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSA 144
Query: 606 IIERVP------------Q-------EELDNPGY--YMPHHHVVKPGSTTPVRPVFDASA 644
+ V Q EEL + Y Y V + SA
Sbjct: 145 LFRAVGEGNAQLVAIFGGQGNTDDYFEELRDL-YQTYHVL-----------VGDLIKFSA 192
Query: 645 KDNGVSLNDCLEKGPNLIETIPTSLAKFRINKIGISGDIAKAFLQISVSPQDRDCL---- 700
+ L E I T+L ++ G+ +I +L+ + D+D L
Sbjct: 193 E--------------TLSELIRTTLDAEKVFTQGL--NI-LEWLENPSNTPDKDYLLSIP 235
Query: 701 -SMRQPRIMVSRDCLRFLWQDENGRVITYRHCRVVFGVSSSPFLLESCLKLHLELTLTDC 759
S P I + Q + V +++ G +P L S LK T
Sbjct: 236 ISC--PLI--------GVIQLAHYVVT----AKLL-GF--TPGELRSYLK-----GATGH 273
Query: 760 REG---------KSSWPIHLVELLKDSFYVDNCLVSTDSQAEAEQFIQVASSIMKEKGFD 810
+G SW +SF+ + + I V I G
Sbjct: 274 SQGLVTAVAIAETDSW---------ESFF-VS----------VRKAITVLFFI----G-- 307
Query: 811 LRGWELTGDKDDKPTNVLGLLWDKSSDTLAINIDRLTSM---------HIEKITKKV--M 859
+R +E + P+ + D+L N + M ++ K
Sbjct: 308 VRCYEAYPNTSLPPSIL--------EDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSH 359
Query: 860 LSAAHRIFDPIGVICAFALIPKLLIQKTWETGLAWNDEVDENTKTKFV------QWMAEV 913
L A ++ +L+ N V
Sbjct: 360 LPAGKQV--------EISLV---------------------NGAKNLVVSGPPQSLYGLN 390
Query: 914 PDIAEIRVPRWISEPNVESRESWSLHVFSDASKLAYAAAVFLRV---EHSKTKVSLHLLA 970
+ + + P + + + FS+ KL + + FL V HS HLL
Sbjct: 391 LTLRKAKAPSGLDQSRIP---------FSER-KLKF-SNRFLPVASPFHS------HLLV 433
Query: 971 -ARARVAPSSKSK------STLTIP--------RLELLAASIATRLCQTVVKDYKLQDVR 1015
A + + IP L +L+ SI+ R+ +++
Sbjct: 434 PASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRL------- 486
Query: 1016 TTFW-----TDATTVL 1026
W AT +L
Sbjct: 487 PVKWETTTQFKATHIL 502
Score = 60.8 bits (147), Expect = 4e-09
Identities = 85/524 (16%), Positives = 141/524 (26%), Gaps = 214/524 (40%)
Query: 38 TEVYIRELLKLVLANTASHDKLPIVILYDRLQSHLRNLESLGVSADRCAPILMPLVSSS- 96
T+ Y EL LY + +L A L L+ ++
Sbjct: 166 TDDYFEELRD----------------LYQTYHVLVGDL------IKFSAETLSELIRTTL 203
Query: 97 -----LPQ--DLLQMWERCSVTQLH--ATQPSAGCKEYLDS------------LMNFL-K 134
Q ++L+ W L + P K+YL S L +++
Sbjct: 204 DAEKVFTQGLNILE-W-------LENPSNTPD---KDYLLSIPISCPLIGVIQLAHYVVT 252
Query: 135 AEVEGVQKLELAKS-------GFGVVSSANKVESNNRRKDKHVKSPEKMNFLKAEVEGVQ 187
A++ G EL G+V++ + S E +F + + +
Sbjct: 253 AKLLGFTPGELRSYLKGATGHSQGLVTAV--AIA-------ETDSWE--SFFVSVRKAIT 301
Query: 188 KLELAKSGF--GVVSSANKVESNNRRKDKHVKSPEKVPTATGLVNSTPKGE---SCIFCS 242
L F GV + P + L +S E S +
Sbjct: 302 VL------FFIGVRC--------------YEAYPNTSLPPSILEDSLENNEGVPSPMLSI 341
Query: 243 QGHYSGDCQKDMTLSQRQDIIR--NKQVCYACLKFGHRVSRCRTKSRLKCEKCGSRHLTI 300
+T Q QD + N HL
Sbjct: 342 SN---------LTQEQVQDYVNKTNS------------------------------HL-- 360
Query: 301 LCPRDSKSDIVTRTFVNTKSSNVL------LQTLVVKIRGKDGKQDKLARLMIDTGSQQS 354
P + +I + VN + V+ L L + +R + +G QS
Sbjct: 361 --PAGKQVEI---SLVNGAKNLVVSGPPQSLYGLNLTLR----------KAKAPSGLDQS 405
Query: 355 YVL---EQTMNSLSYTPIT-----------KQSMRHALFGGSIT-DAMDHNLFKI-VISN 398
+ + S + P+ + L +++ +A D +I V
Sbjct: 406 RIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKD---IQIPVYDT 462
Query: 399 LDNTFACDFDVFGQSKICSTIPSIPSGP--WIDELKQHNIELTDLQH-----PSTTVDI- 450
D + D V S + I P W E + T H P +
Sbjct: 463 FDGS---DLRVLSGSISERIVDCIIRLPVKW--E-TTTQFKAT---HILDFGPGGASGLG 513
Query: 451 -LVGADIAGKFYTGKRVELPSGLVAMETCMGWTLSGKMPTRYGS 493
L + G TG RV + +G TL YG
Sbjct: 514 VLTHRNKDG---TGVRV-IVAG----------TLDINPDDDYGF 543
Score = 37.7 bits (87), Expect = 0.033
Identities = 31/221 (14%), Positives = 67/221 (30%), Gaps = 67/221 (30%)
Query: 831 LWDK----SSDTLAINIDRL-----TSMHI-------EKITKKVMLSAAHRIFDPIGVIC 874
+W++ DT +I + ++ I ++I + I D G +
Sbjct: 1645 VWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVD--GKLK 1702
Query: 875 AFALIPKLLIQKTWETGLAWNDEVDENTKTKFVQWMAEVP-----DIAEIRVPRWISEPN 929
+ ++ T + E + T+F Q P + A S+
Sbjct: 1703 TEKIFKEINEHST---SYTFRSEKGLLSATQFTQ-----PALTLMEKAAFED--LKSKGL 1752
Query: 930 VESRESW---SL-------HV-----FSDASKLAYAAAVFLR-------VEHSKTKVSLH 967
+ + ++ SL + ++ VF R V + S +
Sbjct: 1753 IPADATFAGHSLGEYAALASLADVMSIESLVEV-----VFYRGMTMQVAVPRDELGRSNY 1807
Query: 968 LLAARARVAPSSKSKSTLTIPRLELLAASIATR---LCQTV 1005
+ A + P + S + L+ + + R L + V
Sbjct: 1808 GMIA---INPGRVAAS-FSQEALQYVVERVGKRTGWLVEIV 1844
>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 = 59.1 bits (142), Expect = 1e-08
Identities = 108/705 (15%), Positives = 204/705 (28%), Gaps = 224/705 (31%)
Query: 99 QDLLQMWERCSVTQLHATQPSAGCKEYLDSLMNFL-KAEVEGVQKLELAKSG----FGVV 153
+D+L ++E V CK+ D + L K E++ + + A SG F +
Sbjct: 19 KDILSVFEDAFVDNFD-------CKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTL 71
Query: 154 SSANKVESNNRRKDKHVKSPEKMN--FLKAEVEGVQKLELAKSGFGV--VSSANKVESNN 209
S K V+ ++N FL + ++ + S + +++ ++N
Sbjct: 72 LS-----KQEEMVQKFVEEVLRINYKFL---MSPIKTEQRQPSMMTRMYIEQRDRLYNDN 123
Query: 210 RRKDK-HVKSPEKVPTA-TGLVNSTPKGESCIFCSQGHYSGDCQK-----DMTLSQRQDI 262
+ K +V + L+ P I K D+ LS +
Sbjct: 124 QVFAKYNVSRLQPYLKLRQALLELRPAKNVLI-----DGVLGSGKTWVALDVCLSYKVQC 178
Query: 263 IRNKQVCYACLKFGHRVSRCRTKSRLKCEKCGSRHLTILCPRDSKSDIVTRTFVNTKSSN 322
+ ++ + L + ++ L E I S+SD + + S
Sbjct: 179 KMDFKIFW--LNLKN---CNSPETVL--EMLQKLLYQIDPNWTSRSDHSSNIKLRIHSI- 230
Query: 323 VLLQTLVVKIRGKDGKQDKLARLMIDTGSQQSYVLEQTMNSLSYTPITKQSMRHALFGGS 382
Q +L RL+ + Y N L
Sbjct: 231 ----------------QAELRRLL----KSKPYE-----NCL------------------ 247
Query: 383 ITDAMDHNLFKIVISNLDNTFACD------FDVFGQSKICSTIPSIPSGPWIDELKQHNI 436
+V L N + F++ KI T
Sbjct: 248 -----------LV---LLNV--QNAKAWNAFNL--SCKILLT--------------TRFK 275
Query: 437 ELTDLQHPSTTVDILVGADIAGKFYTGKRVELPSGLVAMETCMGWTLSGKMPTRYGSIDS 496
++TD +TT I + + L + +P + +
Sbjct: 276 QVTDFLSAATTTHISLDHHSMT-LTPDEVKSLLLKYLDCRP-------QDLPREVLTTNP 327
Query: 497 SVATLVTSLLIKDANISDLW--------------SLDVLGIQDPMDKSKADLAEAARKHF 542
+++ + D W SL+VL +P + RK F
Sbjct: 328 RRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVL---EPAE---------YRKMF 375
Query: 543 LDTVQVNSDNRFEVHLP-------WIEGHP--------PLASNLLLSQKRLEGTV----- 582
H+P W + L L+ ++ E T+
Sbjct: 376 DRLSVFPPS----AHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSI 431
Query: 583 ---KKLRRDQYYADYKRVLDTWEMDKIIERVPQEELDNP---GYYMPH--HHVVK---PG 631
K++ + YA ++ ++D + I + ++L P Y+ H HH+ P
Sbjct: 432 YLELKVKLENEYALHRSIVDHY---NIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPE 488
Query: 632 STTPVRPVFDASAKDNGVSLNDCLEKGPNLIETIPTSLAKFRINKI--GISGDIAKAFLQ 689
T R VF L+ +E K R + SG I Q
Sbjct: 489 RMTLFRMVF----------LDF------RFLE------QKIRHDSTAWNASGSILNTLQQ 526
Query: 690 ISVSPQDRDCLSMRQPRIMVSRDCLRFLWQDENGRVITYRHCRVV 734
+ + C + + +V L FL + E +I ++ ++
Sbjct: 527 LKFY-KPYICDNDPKYERLV-NAILDFLPKIEE-NLICSKYTDLL 568
Score = 54.9 bits (131), Expect = 2e-07
Identities = 74/521 (14%), Positives = 145/521 (27%), Gaps = 137/521 (26%)
Query: 384 TDAMDHNLFKIVISNLDNTFACDFDVFGQSKICSTIPSIPSGPWIDELKQHNIELTDLQH 443
T + I+ D F +FD C + D K L+
Sbjct: 11 TGEHQYQYKDILSVFEDA-FVDNFD-------CKDVQ--------DMPKS---ILS---- 47
Query: 444 PSTTVDILVGADIAGKFYTGKRVELPSGLVAMETCMGWTLSGKMPTRYGSIDSSVATLVT 503
+D ++ + V L WTL K + V V
Sbjct: 48 -KEEIDHIIMS--------KDAVSGTLRLF-------WTLLSKQ-------EEMVQKFVE 84
Query: 504 SLLIKDANISDLWSLDVLGIQDPMDKSKADLAEAARKHFLDTVQVNSD---NRFEVHLPW 560
+L + + + + + + R + QV + +R + +L
Sbjct: 85 EVLRINYK----FLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYL-- 138
Query: 561 IEGHPPLASNLLLSQKRLEGTVKKLRRDQYYADY------KRVL--DTWEMDKIIERVPQ 612
+L + +LR + K + D K+ Q
Sbjct: 139 ----------------KLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKV-----Q 177
Query: 613 EELDNPGYYMPHHHVVKPGSTTPVRPVFDASAKDNGVSLNDCLEKGPNLIETIPTSLAKF 672
++D +++ + P + + N S +D I +I L +
Sbjct: 178 CKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRL 237
Query: 673 RINKIG-----I-----SGDIAKAFLQISVSPQDRDCLSMRQPRIMV-SRDC--LRFLWQ 719
+K + + AF + C +I++ +R FL
Sbjct: 238 LKSKPYENCLLVLLNVQNAKAWNAF--------NLSC------KILLTTRFKQVTDFL-S 282
Query: 720 DENGRVITYRHCRVVFGVSSSPFLLESCLKLHLELTLTDCREGKSSWPIHL---VELLKD 776
I+ H + LL L + L RE ++ P L E ++D
Sbjct: 283 AATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQ-DLP--REVLTTNPRRLSIIAESIRD 339
Query: 777 -----SFYVDNCLVSTDSQAEAEQFIQVASSIMKEKGFDLRG--WELTG-DKDDK-PTNV 827
+ V+ D + SS+ + + R L+ PT +
Sbjct: 340 GLATWDNWKH---VNCDKLTTI-----IESSLNVLEPAEYRKMFDRLSVFPPSAHIPTIL 391
Query: 828 LGLLWDKSSDTLAINIDRLTSMHIEKITKKVMLSAAHRIFD 868
L L+W + + + + +H + +K + I
Sbjct: 392 LSLIWFDVIKSDVMVV--VNKLHKYSLVEKQPKESTISIPS 430
Score = 43.3 bits (101), Expect = 7e-04
Identities = 71/496 (14%), Positives = 148/496 (29%), Gaps = 142/496 (28%)
Query: 20 YNQVVEALKARFGREDLLTEVYIRELLKLVLANTASHDKLPIVI--LYDRLQSHLRNLES 77
Y ++ +K + ++T +YI + +L + K + Y +L+ L L
Sbjct: 91 YKFLMSPIKTEQRQPSMMTRMYIEQRDRL-YNDNQVFAKYNVSRLQPYLKLRQALLELRP 149
Query: 78 ----------------LGVSADRCAPIL--MP-------LVSSSLPQDLLQMWER-CS-V 110
+ + + M L + + P+ +L+M ++ +
Sbjct: 150 AKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQI 209
Query: 111 TQLHATQPSAGCKEYLDSLMNFLKAEVEGVQKLELAKSGFGV---VSSANKVESNNRR-- 165
++ L ++ ++AE+ + K + ++ V V +A + N
Sbjct: 210 DPNWTSRSDHSSNIKLR--IHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCK 267
Query: 166 -----KDKHVKSPEKMNFLKAEVEGVQKLELAKSGFGVVSSANKVES--------NNRRK 212
+ K V +FL A L+ E + R +
Sbjct: 268 ILLTTRFKQV-----TDFLSAATTTHISLDHHSMTL------TPDEVKSLLLKYLDCRPQ 316
Query: 213 DKHVKSPEKV----PTATGLVNSTPKGESCIFCSQGHYSGDCQKDMTLSQRQDIIRNKQV 268
D P +V P ++ ES G + D K + + II +
Sbjct: 317 D----LPREVLTTNPRRLSII-----AES---IRDGLATWDNWKHVNCDKLTTII---ES 361
Query: 269 CYACLKFGHRVSRCRTKSRLKCEKCGSRHLTILCPRDSK-------------SDIVTRTF 315
L+ + L++ P +
Sbjct: 362 SLNVLEPAE------YRKMFD-------RLSVF-PPSAHIPTILLSLIWFDVIKSDVMVV 407
Query: 316 VNT-----------KSSNVLLQTLVVKIRGKDGKQDKLARLMIDTGSQQSYVLEQTMNSL 364
VN K S + + ++ ++++ K + L R ++D Y + +T +S
Sbjct: 408 VNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVD-----HYNIPKTFDSD 462
Query: 365 SYTPITKQS------MRHALFGGSITDAMDHNLFKIVISNLDNTFACDFDVFGQSKIC-S 417
P H L + M LF++V + F + KI
Sbjct: 463 DLIPPYLDQYFYSHIGHH-LKNIEHPERMT--LFRMVFLDFR---------FLEQKIRHD 510
Query: 418 TIPSIPSGPWIDELKQ 433
+ SG ++ L+Q
Sbjct: 511 STAWNASGSILNTLQQ 526
Score = 42.5 bits (99), Expect = 0.001
Identities = 66/488 (13%), Positives = 129/488 (26%), Gaps = 132/488 (27%)
Query: 915 DIAEIRVPRWISEPNVESRESWSLHVFSDASKLAYAAAVFLRVEH---SKTKVS-LHLLA 970
DI + ++ + + + + S ++H SK VS L
Sbjct: 20 DILSVFEDAFVDNFDCKDVQDMPKSILSKEE-----------IDHIIMSKDAVSGTLRLF 68
Query: 971 ARARVAPSSKSK---STLTIPRLELLAASIATRLCQTVVKDYKLQDVRTTFWTDATTVLA 1027
+ + + L + I T Q + + R + D
Sbjct: 69 WTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVF-- 126
Query: 1028 WIRRNEPWNVFVMNRITEIRNLSQE---HEWRHVPGEMNPADLPSRGC---------TMK 1075
+NV + ++R E + + G + G +
Sbjct: 127 -----AKYNVSRLQPYLKLRQALLELRPAKNVLIDG-V-------LGSGKTWVALDVCLS 173
Query: 1076 KLVQCRWWEGPEWLK-GSPEQWPHHEEIEDEDEVCREKKKTVVSSVTLSQPMDVDWHKYF 1134
VQC+ WL + C + + L +D +W
Sbjct: 174 YKVQCKMDFKIFWLNLKN----------------CNSPETVLEMLQKLLYQIDPNWTSRS 217
Query: 1135 SKYNKLVRMVGWMK-RFKTNCEFKKYNK--LV-RMVGWMKR----FKTNCE------FKK 1180
+ + + ++ + + K Y LV V + F +C+ FK+
Sbjct: 218 DHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNV-QNAKAWNAFNLSCKILLTTRFKQ 276
Query: 1181 VHGHLP--TPQDLTVEE----LCTAETQVL--KWVQ-------EESCKEEDPRFSSLVTF 1225
V L T ++++ L E + L K++ E +PR S++
Sbjct: 277 VTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTT-NPRRLSIIAE 335
Query: 1226 LDEDGLIRVKT-KISNRQDLED--SCCPVVLPRHPVVLK-----LVMFHHLNNCHAGTQI 1277
DGL K N L VL P + L +F I
Sbjct: 336 SIRDGLATWDNWKHVNCDKLTTIIESSLNVLE--PAEYRKMFDRLSVFP------PSAHI 387
Query: 1278 LMSILRQKYWILGETGVPEYEMDAS----------------------DLRAHYKLRRELK 1315
+L W ++ +L+ + L
Sbjct: 388 PTILL-SLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALH 446
Query: 1316 KQLRERFR 1323
+ + + +
Sbjct: 447 RSIVDHYN 454
Score = 39.5 bits (91), Expect = 0.009
Identities = 39/221 (17%), Positives = 73/221 (33%), Gaps = 54/221 (24%)
Query: 1242 QDLEDSCCPVVLPRHPVVLKLVMFHHLNNCHA--GTQILMSILRQKYWILGETGVPEYEM 1299
+D++D P+ ++ K + H + + A GT L L K E V ++
Sbjct: 36 KDVQDM------PK-SILSKEEIDHIIMSKDAVSGTLRLFWTLLSK----QEEMVQKFVE 84
Query: 1300 DASDLRAHYKLRRELKKQLRERFRSEYLGQLKLTAKKKREHIIKVGDVVLIGDDNVKRLD 1359
+ LR +YK L ++E +T + D + NV RL
Sbjct: 85 EV--LRINYKF-------LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQ 135
Query: 1360 W------------PMGRVINLC--PGADGHVRVVKLRTSSGVLTRPIQRIYPLEF-HCSS 1404
P V+ + G+ + + S V + +I+ L +C+S
Sbjct: 136 PYLKLRQALLELRPAKNVL-IDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNS 194
Query: 1405 DD------------MTPNLHEEKTKVSDLDTVPKSDLQEVE 1433
+ + PN SD + K + ++
Sbjct: 195 PETVLEMLQKLLYQIDPNWTSR----SDHSSNIKLRIHSIQ 231
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding,
exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Length = 124
Score = 40.1 bits (93), Expect = 6e-04
Identities = 11/46 (23%), Positives = 16/46 (34%), Gaps = 5/46 (10%)
Query: 264 RNKQVCYACLKFGHRVSRCRTKSRLKCEKCGSR--HLTILCPRDSK 307
C C + GH C C CG+ H + CP+ +
Sbjct: 2 EAAPKCNNCSQRGHLKKDCPHI---ICSYCGATDDHYSRHCPKAIQ 44
Score = 36.7 bits (84), Expect = 0.013
Identities = 20/93 (21%), Positives = 24/93 (25%), Gaps = 32/93 (34%)
Query: 233 PKGESCIFCSQ-GHYSGDCQKDMTLSQRQDIIRNKQVCYACLKFGHRVSRCRTKSR---- 287
PK C C + GHY C K C C H RC + R
Sbjct: 40 PKAIQCSKCDEVGHYRSQCPHK----------WKKVQCTLCKSKKHSKERCPSIWRAYIL 89
Query: 288 ----------------LKCEKCGSR-HLTILCP 303
+ C CG + H C
Sbjct: 90 VDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCK 122
Score = 36.3 bits (83), Expect = 0.016
Identities = 18/76 (23%), Positives = 20/76 (26%), Gaps = 17/76 (22%)
Query: 234 KGESCIFCSQ-GHYSGDCQKDMTLSQRQDIIRNKQVCYACLKFGHRVSRCRTKSRLKCEK 292
C CSQ GH DC + Y H C + C K
Sbjct: 3 AAPKCNNCSQRGHLKKDC-------------PHIICSYCGATDDHYSRHCPKAIQ--CSK 47
Query: 293 CG-SRHLTILCPRDSK 307
C H CP K
Sbjct: 48 CDEVGHYRSQCPHKWK 63
Score = 31.7 bits (71), Expect = 0.55
Identities = 14/63 (22%), Positives = 21/63 (33%), Gaps = 10/63 (15%)
Query: 233 PKGESCIFC-SQGHYSGDC---------QKDMTLSQRQDIIRNKQVCYACLKFGHRVSRC 282
K C C S+ H C D ++ + + + CY C GH C
Sbjct: 62 WKKVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDC 121
Query: 283 RTK 285
+ K
Sbjct: 122 KEK 124
>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding
protein, retrovirus, viral protein; NMR {Mason-pfizer
monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A
Length = 60
Score = 38.0 bits (88), Expect = 0.001
Identities = 12/56 (21%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 235 GESCIFCSQ-GHYSGDCQKDMTLSQRQDIIRNKQVCYACLKFGHRVSRCRTKSRLK 289
G SC C + GH++ +C + + + +C C + H + C++K+ +
Sbjct: 1 GGSCFKCGKKGHFAKNCHEH---AHNNAEPKVPGLCPRCKRGKHWANECKSKTDNQ 53
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA
complex; NMR {Homo sapiens}
Length = 74
Score = 38.0 bits (88), Expect = 0.001
Identities = 12/42 (28%), Positives = 15/42 (35%), Gaps = 2/42 (4%)
Query: 264 RNKQVCYACLKFGHRVSRCRTKSRLK-CEKCGSR-HLTILCP 303
CY C H C+ + K C C S H+ CP
Sbjct: 22 SKGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCP 63
Score = 33.8 bits (77), Expect = 0.034
Identities = 15/82 (18%), Positives = 27/82 (32%), Gaps = 11/82 (13%)
Query: 214 KHVKSPEKVPTATGLVNSTPKGESCIFCSQ-GHYSGDCQKDMTLSQRQDIIRNKQVCYAC 272
V +P + KG+ C C H++ +C+ + C+ C
Sbjct: 3 GLVPRGSHMPKGKSMQKRRSKGDRCYNCGGLDHHAKECKLP----------PQPKKCHFC 52
Query: 273 LKFGHRVSRCRTKSRLKCEKCG 294
H V+ C K++ G
Sbjct: 53 QSISHMVASCPLKAQQGPSAQG 74
>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 63
Score = 37.6 bits (87), Expect = 0.001
Identities = 13/62 (20%), Positives = 17/62 (27%), Gaps = 18/62 (29%)
Query: 244 GHYSGDCQKDMTLSQRQDIIRNKQVCYACLKFGHRVSRCRTKSRLK-CEKCGSR-HLTIL 301
G + CY C H C+ + K C C S H+
Sbjct: 1 GSSGSSGDR----------------CYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVAS 44
Query: 302 CP 303
CP
Sbjct: 45 CP 46
Score = 35.3 bits (81), Expect = 0.010
Identities = 12/58 (20%), Positives = 22/58 (37%), Gaps = 11/58 (18%)
Query: 231 STPKGESCIFCSQ-GHYSGDCQKDMTLSQRQDIIRNKQVCYACLKFGHRVSRCRTKSR 287
S G+ C C H++ +C+ + C+ C H V+ C K++
Sbjct: 3 SGSSGDRCYNCGGLDHHAKECKLP----------PQPKKCHFCQSISHMVASCPLKAQ 50
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA
complex; NMR {Rous sarcoma virus}
Length = 61
Score = 35.6 bits (82), Expect = 0.007
Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 6/52 (11%)
Query: 264 RNKQVCYACLKFGHRVSRCRTK-----SRLKCEKCGSR-HLTILCPRDSKSD 309
R + +CY C GH ++C K SR +C+ C H C + +
Sbjct: 2 RARGLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQCRKRDGNQ 53
Score = 32.2 bits (73), Expect = 0.12
Identities = 14/62 (22%), Positives = 22/62 (35%), Gaps = 7/62 (11%)
Query: 234 KGESCIFCSQ-GHYSGDCQKDMTLSQRQDIIRNKQVCYACLKFGHRVSRCRTKSRLKCEK 292
C C GHY C K +++ C C GH +CR + + ++
Sbjct: 3 ARGLCYTCGSPGHYQAQCPKKRKSG------NSRERCQLCNGMGHNAKQCRKRDGNQGQR 56
Query: 293 CG 294
G
Sbjct: 57 PG 58
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein,
retrovirus zinc finger-like domains; NMR {Equine
infectious anemia virus}
Length = 37
Score = 33.0 bits (75), Expect = 0.028
Identities = 15/37 (40%), Positives = 17/37 (45%), Gaps = 3/37 (8%)
Query: 267 QVCYACLKFGHRVSRCRTKSRLKCEKCGSR-HLTILC 302
Q CY C K GH S+CR C KC H + C
Sbjct: 1 QTCYNCGKPGHLSSQCRAPK--VCFKCKQPGHFSKQC 35
Score = 28.0 bits (62), Expect = 2.2
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 14/50 (28%)
Query: 236 ESCIFCSQ-GHYSGDCQKDMTLSQRQDIIRNKQVCYACLKFGHRVSRCRT 284
++C C + GH S C R +VC+ C + GH +CR+
Sbjct: 1 QTCYNCGKPGHLSSQC-------------RAPKVCFKCKQPGHFSKQCRS 37
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein,
metal binding protein; NMR {Synthetic}
Length = 39
Score = 31.8 bits (72), Expect = 0.099
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 269 CYACLKFGHRVSRCRTKSRLKCEKCGSR-HLTILCPR 304
C+ C K GH CR + C CGS+ H CP+
Sbjct: 3 CFNCGKPGHTARMCRQPRQEGCWNCGSKEHRFAQCPK 39
>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex,
PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus
musculus} PDB: 3trz_A* 3ts0_A*
Length = 148
Score = 33.8 bits (77), Expect = 0.15
Identities = 17/103 (16%), Positives = 29/103 (28%), Gaps = 15/103 (14%)
Query: 190 ELAKSGFGVVSSANKVE-----SNNRRKDKHVKSPEKVPTATGLVNSTPKGESCIFCSQG 244
+L GF + VE S + V P V
Sbjct: 48 KLHMEGFRSLKEGEAVEFTFKKSAKGLESIRVTGPGGVFCIGSERRPKGGDRCYNCGGLD 107
Query: 245 HYSGDCQKDMTLSQRQDIIRNKQVCYACLKFGHRVSRCRTKSR 287
H++ +C+ + C+ C H V+ C K++
Sbjct: 108 HHAKECKLP----------PQPKKCHFCQSINHMVASCPLKAQ 140
>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 = 32.6 bits (73), Expect = 0.39
Identities = 10/30 (33%), Positives = 18/30 (60%), Gaps = 4/30 (13%)
Query: 69 QSHLRNLE-SLGVSADRCAPILMPLVSSSL 97
Q+ L+ L+ SL + AD AP L + +++
Sbjct: 20 QA-LKKLQASLKLYADDSAPALA--IKATM 46
Score = 30.7 bits (68), Expect = 2.0
Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 12/40 (30%)
Query: 852 EK--ITKKVMLSAAHRIFDPIGVICAFALIPKLLIQKTWE 889
EK + KK L A+ +++ P L I+ T E
Sbjct: 18 EKQAL-KK--LQASLKLYADDSA-------PALAIKATME 47
>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA
recognition, zinc finger, viral protein; NMR {Human
immunodeficiency virus type 2} SCOP: g.40.1.1
Length = 49
Score = 30.3 bits (68), Expect = 0.41
Identities = 12/26 (46%), Positives = 14/26 (53%)
Query: 269 CYACLKFGHRVSRCRTKSRLKCEKCG 294
C+ C K GH +CR R C KCG
Sbjct: 9 CWNCGKEGHSARQCRAPRRQGCWKCG 34
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 31.7 bits (71), Expect = 1.1
Identities = 15/111 (13%), Positives = 36/111 (32%), Gaps = 46/111 (41%)
Query: 1043 ITEIRNLSQEHEWRHVPGEMNPADLPSRGCTMKKLVQCRWWEGPEWLKGSPEQWPHHEEI 1102
I + L+QE E +++K W E EQ + +
Sbjct: 74 IAQADRLTQEPE------------------SIRK-----WRE---------EQ---RKRL 98
Query: 1103 EDEDEVCREKKKTVVSSVTLSQPMDVDWHKYFSKYNKLVRMVGWMKRFKTN 1153
++ D + ++ + ++ +W++ + ++ V K N
Sbjct: 99 QELDAASKVMEQEWREKA--KKDLE-EWNQ---RQSEQVE-----KNKINN 138
Score = 31.3 bits (70), Expect = 1.8
Identities = 11/48 (22%), Positives = 23/48 (47%), Gaps = 2/48 (4%)
Query: 1298 EMDASDLRAHYKLRRELKKQLRE--RFRSEYLGQLKLTAKKKREHIIK 1343
E+DA+ + R + KK L E + +SE + + K+ + + +
Sbjct: 100 ELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKAFYQ 147
>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR
{Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB:
1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A*
1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A
Length = 55
Score = 29.2 bits (65), Expect = 1.3
Identities = 11/26 (42%), Positives = 13/26 (50%)
Query: 269 CYACLKFGHRVSRCRTKSRLKCEKCG 294
C+ C K GH CR + C KCG
Sbjct: 15 CFNCGKEGHIAKNCRAPRKKGCWKCG 40
>3blz_A NTF2-like protein of unknown function; structural genomics, joint
center for structural genomics, J protein structure
initiative, PSI-2; 1.75A {Shewanella baltica} SCOP:
d.17.4.14
Length = 128
Score = 30.3 bits (68), Expect = 1.8
Identities = 23/81 (28%), Positives = 35/81 (43%), Gaps = 9/81 (11%)
Query: 631 GSTTPVRPVFDASAKDNGVSLNDCLEKGP--NLIETI-----PTSLAKFRINKIGISGDI 683
+T +RP F + A GV +++ L GP L + I P+ AK I +I I G
Sbjct: 28 ADSTIMRPAFSSQATIFGVDVDNKLTGGPIQGLFDVIDNVFHPSPEAKAAIARIDIVGTA 87
Query: 684 AKAFLQISVSPQDR--DCLSM 702
A A + R D ++
Sbjct: 88 ASARIDTDDISGFRFTDFFNL 108
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA
surveillance binds to TRF4P/AIR2P heterodimer; 2.70A
{Saccharomyces cerevisiae}
Length = 83
Score = 28.5 bits (63), Expect = 3.5
Identities = 13/67 (19%), Positives = 17/67 (25%), Gaps = 21/67 (31%)
Query: 265 NKQVCYACLKFGHRVSRCRTKSR--------------------LKCEKCGSR-HLTILCP 303
K C C H RC + R + C CG + H C
Sbjct: 4 KKVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCK 63
Query: 304 RDSKSDI 310
S +
Sbjct: 64 EKRSSRV 70
>2con_A RUH-035 protein, NIN one binding protein; ribosome, RNA binding
protein, unknown function, structural genomics, NPPSFA;
NMR {Mus musculus} SCOP: g.41.15.1
Length = 79
Score = 27.8 bits (62), Expect = 5.2
Identities = 8/31 (25%), Positives = 13/31 (41%), Gaps = 6/31 (19%)
Query: 269 CYACLKFGHRVSRCRTKSRLKCEKCGSRHLT 299
C+ C K +R+ C CG++ L
Sbjct: 18 CHGCFKT------TSDMNRVFCGHCGNKTLK 42
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA
degradation, allosteric REGU; HET: ADP 1PE; 2.40A
{Saccharomyces cerevisiae}
Length = 802
Score = 30.3 bits (68), Expect = 5.7
Identities = 13/89 (14%), Positives = 31/89 (34%)
Query: 1312 RELKKQLRERFRSEYLGQLKLTAKKKREHIIKVGDVVLIGDDNVKRLDWPMGRVINLCPG 1371
+ + +L L+ + E + +GD +++ ++ DW I P
Sbjct: 215 EHISVSWSLALNNRHLASFTLSTFESNELKVAIGDEMILWYSGMQHPDWEGRGYIVRLPN 274
Query: 1372 ADGHVRVVKLRTSSGVLTRPIQRIYPLEF 1400
+ ++L+ S + + EF
Sbjct: 275 SFQDTFTLELKPSKTPPPTHLTTGFTAEF 303
>1yy9_A Epidermal growth factor receptor; cell surface receptor, tyrosine
kinase, glycoprotein, antigen:antibody complex, FAB
fragment, antitumor, drug; HET: NDG NAG BMA MAN; 2.60A
{Homo sapiens} SCOP: c.10.2.5 c.10.2.5 g.3.9.1 g.3.9.1
PDB: 3qwq_A* 1nql_A* 3b2v_A* 1ivo_A* 3njp_A*
Length = 624
Score = 30.0 bits (66), Expect = 6.9
Identities = 18/131 (13%), Positives = 31/131 (23%), Gaps = 12/131 (9%)
Query: 203 NKVESNNRRKDKHVKSPEKVPTATGLVNSTPKGESCIFCSQGHYSGDCQKDMTLSQRQD- 261
K+ SN + P+ C+ C +C L + +
Sbjct: 464 TKIISNRGENKCKATGQVCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCKLLEGEPR 523
Query: 262 IIRNKQVCYAC---LKFGHRVSRCRTKSRLKCEKCGSRHLTIL------CPRDSKSDIVT 312
C C C + C +C H CP + T
Sbjct: 524 EFVENSECIQCHPECLPQAMNITCTGRGPDNCIQC--AHYIDGPHCVKTCPAGVMGENNT 581
Query: 313 RTFVNTKSSNV 323
+ + +V
Sbjct: 582 LVWKYADAGHV 592
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 29.3 bits (65), Expect = 8.1
Identities = 15/77 (19%), Positives = 27/77 (35%), Gaps = 19/77 (24%)
Query: 856 KKVMLSAAHRIFDPIGVICAFALIPKLLI----QKTWETGLAWNDEV-------DENTKT 904
KK ++ A +P I A +P I + DE+ D +K
Sbjct: 161 KKFLVIAY----EPFENI-AIE-LPPNEILFSENNDMDNNNDGVDELNKKCTFWDAISKL 214
Query: 905 KFVQWM--AEVPDIAEI 919
+VQ+ + A++
Sbjct: 215 YYVQFFFKQAEQEQADV 231
>3q9d_A Protein CPN_0803/CP_1068/CPJ0803/CPB0832; coiled-coil, needle TIP
TYPEIII secretion system, unknown FU; 2.00A
{Chlamydophila pneumoniae}
Length = 220
Score = 28.9 bits (64), Expect = 9.0
Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 3/58 (5%)
Query: 1262 LVMFHHLNNCHAGTQILMSILRQKYWILGETGVPEYEMDASDLRAHYKLRRELKKQLR 1319
L+M N CH +L +L + +GE + E + + + L+ H+ EL K L+
Sbjct: 166 LLMTDVQNTCHLIRHLLARLLEAQKNPVGEKNLQEIQEEITSLKNHFD---ELTKALQ 220
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
0.319 0.133 0.403
Gapped
Lambda K H
0.267 0.0515 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 22,111,612
Number of extensions: 1356041
Number of successful extensions: 3027
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2999
Number of HSP's successfully gapped: 47
Length of query: 1447
Length of database: 6,701,793
Length adjustment: 106
Effective length of query: 1341
Effective length of database: 3,742,167
Effective search space: 5018245947
Effective search space used: 5018245947
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: 64 (28.9 bits)