RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1643
(962 letters)
>1yke_B RNA polymerase II holoenzyme component SRB7; gene regulation; 3.30A
{Saccharomyces cerevisiae} SCOP: a.252.1.1
Length = 151
Score = 102 bits (254), Expect = 2e-25
Identities = 22/123 (17%), Positives = 51/123 (41%), Gaps = 3/123 (2%)
Query: 840 EQADNFCNSVGILQQTAIPSKFSGFDRGGSQTPQQQTQQEDYAH---LFATLISRCARDI 896
+ + FC ++ + + + + + S E++++ +T I R I
Sbjct: 14 QMTEQFCATLNYIDKNHGFERLTVNEPQMSDKHATVVPPEEFSNTIDELSTDIILKTRQI 73
Query: 897 DALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAALTDIAQSQ 956
+ LI+SLP D + E QL + L++ + + +++ E LL + + + D
Sbjct: 74 NKLIDSLPGVDVSAEEQLRKIDMLQKKLVEVEDEKIEAIKKKEKLLRHVDSLIEDFVDGI 133
Query: 957 LET 959
+
Sbjct: 134 ANS 136
>1ykh_B RNA polymerase II holoenzyme component SRB7; gene regulation; 3.00A
{Saccharomyces cerevisiae} SCOP: a.252.1.1
Length = 132
Score = 97.4 bits (242), Expect = 6e-24
Identities = 21/117 (17%), Positives = 50/117 (42%), Gaps = 3/117 (2%)
Query: 840 EQADNFCNSVGILQQTAIPSKFSGFDRGGSQTPQQQTQQEDYAHL---FATLISRCARDI 896
+ + FC ++ + + + + + S E++++ +T I R I
Sbjct: 14 QMTEQFCATLNYIDKNHGFERLTVNEPQMSDKHATVVPPEEFSNTIDELSTDIILKTRQI 73
Query: 897 DALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAALTDIA 953
+ LI+SLP D + E QL + L++ + + +++ E L+ + + + D
Sbjct: 74 NKLIDSLPGVDVSAEEQLRKIDMLQKKLVEVEDEKIEAIKKKEKLMRHVDSMIEDFV 130
>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 = 89.7 bits (222), Expect = 3e-18
Identities = 118/677 (17%), Positives = 218/677 (32%), Gaps = 232/677 (34%)
Query: 125 VEAIRLRRRVKMKPLK----NTQCSIHLKHLPAPKSTHAPAEFRLKCILLFKQEYPM--- 177
++A R PL + + + + P ++ A +L+ F + P
Sbjct: 1 MDAYSTR------PLTLSHGSLEHVLLV-----PTASFFIAS-QLQEQ--FNKILPEPTE 46
Query: 178 -FYHDNVKTPPVNFYYKFSTTKDRKAPAEMAIFNCVDQLVAQDKK---DTILTTITSEGG 233
F D+ T P KF + + V LV K D +L +E
Sbjct: 47 GFAADDEPTTPAELVGKF-----------LG-Y--VSSLVEPSKVGQFDQVLNLCLTE-- 90
Query: 234 EQNFIMFQLKYL----IKCLIVKVL-DNSNPLLINYDIVL-YVLAKCLQLVQQDPKAKLP 287
F+ YL I L K+L +N L+ +++ Y+ A+ + ++ K
Sbjct: 91 ------FENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITAR--IMAKRPFDKKSN 142
Query: 288 STTIIEFRTKVLELAVDRVA-------GQ-NSERFL-----MFVLY-------------- 320
S + + A GQ N++ + ++ Y
Sbjct: 143 S--------ALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAET 194
Query: 321 MLNFSPKSLRPDAVRKQ---LQKWYMGKES--DQLVVLVAKCS-----VYQGLSHANVLK 370
+ +L + V Q + +W + D+ +L S V Q
Sbjct: 195 LSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQ--------- 245
Query: 371 LIHFDVFHQ----SPDKKLALYAIAFGFAYVSHRLISGKFLATPRVPPFVTSDDCFDKAS 426
L H+ V + +P + L + G S L++ +A S + F +
Sbjct: 246 LAHYVVTAKLLGFTPGE---LRSYLKGATGHSQGLVTAVAIAE------TDSWESFFVSV 296
Query: 427 DKVKTIVKDVAVVRCNTSHQ---------KVVAAAVKTHSLGIESVCPKFAKSFKVNTAC 477
K T++ + V RC ++ ++ +++ ++ G+ S P +
Sbjct: 297 RKAITVLFFIGV-RC---YEAYPNTSLPPSILEDSLE-NNEGVPS--PMLS--------- 340
Query: 478 LEGMTQRGLLQSMHRLRKDNV-LSSEDHAIVDESTTCG--TYVKQLGASPVTEPPLHPAE 534
+ +TQ + + K N L + + S G V V+ PP +
Sbjct: 341 ISNLTQEQVQD---YVNKTNSHLPAGKQVEI--SLVNGAKNLV-------VSGPP----Q 384
Query: 535 VLAAYAEYVLAPVTKMASFQKKAVKPPPSEGGGGDQAQEKSEDETPV-----LTAKAP-- 587
L Y L + +K K P G DQ++ + L +P
Sbjct: 385 SL-----YGLN-----LTLRK--AKAPS----GLDQSRIPFSERKLKFSNRFLPVASPFH 428
Query: 588 ----EPAIVSALQELYKSSFSNLKTHDSLKISVCLDLQPRFESQPCRDYRPLSGSHVAVL 643
PA ++L K++ S D ++I V +++ D R LSGS
Sbjct: 429 SHLLVPASDLINKDLVKNNVS-FNAKD-IQIPV-------YDTFDGSDLRVLSGS----- 474
Query: 644 VLESLLRMVDYKMDNIRL-VGFKDAKVRPIVRLKTHNCD---DNLEGLDDLVDE------ 693
+ E ++ + IRL V ++ TH D GL L
Sbjct: 475 ISERIVDCI------IRLPVKWETTTQFKA----THILDFGPGGASGLGVLTHRNKDGTG 524
Query: 694 ----LATVKLEDAPEAE 706
+A L+ P+ +
Sbjct: 525 VRVIVAGT-LDINPDDD 540
Score = 59.7 bits (144), Expect = 5e-09
Identities = 105/654 (16%), Positives = 181/654 (27%), Gaps = 252/654 (38%)
Query: 259 PLLINYDIV---------LYVLAKCLQLVQQDPKAKLPSTTIIEFRTKVLELAVDRVAGQ 309
PL +++ + + +A QL Q+ +F K+L + A
Sbjct: 8 PLTLSHGSLEHVLLVPTASFFIA--SQL--QE-----------QF-NKILPEPTEGFAAD 51
Query: 310 N---SE-----RFLMFVLYMLNFSPKSLRPDAVRKQLQKW---YM-GKE---------SD 348
+ + +FL +V ++ S + L ++ Y+ G + +
Sbjct: 52 DEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQE 111
Query: 349 QLVVLVAKCSVYQGLSHANVLKLIHFDVFHQSP------DKKLALYAIAFG-----FAYV 397
LV + + A ++ FD S + L AI FG Y
Sbjct: 112 NDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAI-FGGQGNTDDYF 170
Query: 398 SH-RLISGKFLATPRVPPFVTSDDCFDKASDKVKTIVKDVAVVRCNTSHQKVV------A 450
R + T V D +++ + +++ + +
Sbjct: 171 EELRDLY----QTY--HVLV--GDLIKFSAETLSELIRTTL--DAEKVFTQGLNILEWLE 220
Query: 451 AAVKTHSLGIESVCPKFAKSFKVNTACLEGMTQRGLLQSMHRLRKDNVLSSEDHAIVDES 510
T P S + G++Q L+ H +V
Sbjct: 221 NPSNTPDKDYLLSIP---ISCPLI----------GVIQ----------LA---HYVV--- 251
Query: 511 TTCGTYVKQLGASP---------VTEPPLHPAEVLAAYAEYVLAPVTKMASFQKKAVKPP 561
T K LG +P T H ++ A A +A SF K
Sbjct: 252 -TA----KLLGFTPGELRSYLKGAT---GHSQGLVTAVA---IAETDSWESFFVSVRK-- 298
Query: 562 PSEGGG-------GDQAQEKSEDETPVLTAKAPEPAIVSALQELYKSSFSNLKTHDSLKI 614
G + E P + P+I+ DSL+
Sbjct: 299 -----AITVLFFIGVRCYE----AYPNT---SLPPSILE----------------DSLEN 330
Query: 615 SVCLDLQPRFESQPCRDYRP-LSGSHVAVLVLESLLRMVDYKMDNIRLVGFKDAKVRPIV 673
+ E P P LS ++ L E + V+ N L +V +
Sbjct: 331 N---------EGVPS----PMLS---ISNLTQEQVQDYVNK--TNSHL--PAGKQVE--I 368
Query: 674 RLKTHNCDDNL------EGLDDLVDELATVKLEDAPEAEKEEESGKDSADSIIKNYEKIW 727
L N NL + L L L K AP SG D S I E+
Sbjct: 369 SL--VNGAKNLVVSGPPQSLYGLNLTLRKAK---AP-------SGLDQ--SRIPFSERKL 414
Query: 728 RYYKRQIPKARGITI--H-KLL----------------SWSIKQMWHPDVYVVICSQENL 768
++ R +P + H LL S++ K + P VY +L
Sbjct: 415 KFSNRFLP----VASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIP-VYDT-FDGSDL 468
Query: 769 SLYKTNVIFAEYMEKTKRKNTNQENLSLYKTNVIFAE--YMEKTKRKNTNSSHL 820
+ ++ E + + I E T ++H+
Sbjct: 469 RVLSGSIS---------------ERI----VDCIIRLPVKWETT--TQFKATHI 501
Score = 44.7 bits (105), Expect = 2e-04
Identities = 84/535 (15%), Positives = 151/535 (28%), Gaps = 200/535 (37%)
Query: 527 EPPLHPAEVLAAYAEYV-----------LAPVTKMA--SFQKK----------AVKPPPS 563
+ P PAE++ + YV V + F+ A K
Sbjct: 52 DEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQE 111
Query: 564 EGGGGDQAQE------KSEDETPVLTAKAPEPAIVSA----------------------- 594
+ +E + K A+ A
Sbjct: 112 NDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFE 171
Query: 595 -LQELYKSSFSNLK-----THDSLK--ISVCLDLQPRF-------------ESQPCRDYR 633
L++LY++ + + ++L I LD + F + P +DY
Sbjct: 172 ELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDY- 230
Query: 634 PLSGSHVAVLVLESLLRMVDYKMDNIRLVGFKDAKVRPIVR-LKTHNCDDNLEGLDDLVD 692
L ++ L ++++ Y + +L+GF ++R ++ H LV
Sbjct: 231 -LLSIPIS-CPLIGVIQLAHY-VVTAKLLGFTPGELRSYLKGATGH--------SQGLV- 278
Query: 693 ELATVKLEDAPEAEKEEESGKDSADSIIKNYEKI-WR----YYKRQIPKA---------- 737
A A ES S I I R Y +P +
Sbjct: 279 -TAV-----AIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNE 332
Query: 738 ---------RGITIHKLLSWSIKQM-----WHPDVYV-VICSQENL-------SLYKTNV 775
+T ++ + + + V + ++ +NL SLY N+
Sbjct: 333 GVPSPMLSISNLTQEQVQDY-VNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNL 391
Query: 776 IFAEYMEKTKRK-NTNQENLSLYKTNVIFAEYMEKTKRKNTNSS---------HLKYMPK 825
K K +Q + + F ++RK S+ H +
Sbjct: 392 TL----RKAKAPSGLDQ-------SRIPF------SERKLKFSNRFLPVASPFHSHLL-- 432
Query: 826 LKAKTPIQQLLSSAEQADNFCNSVGILQQTAIP--SKFSGFD-R--GGSQTPQ------- 873
P L++ +N + +Q IP F G D R GS + +
Sbjct: 433 ----VPASDLINKDLVKNNVSFNAKDIQ---IPVYDTFDGSDLRVLSGSISERIVDCIIR 485
Query: 874 -----QQTQQEDYAHL--F--------ATLISR-----CARDIDA-LIESLPNED 907
+ T Q H+ F L R R I A ++ P++D
Sbjct: 486 LPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVRVIVAGTLDINPDDD 540
Score = 43.1 bits (101), Expect = 5e-04
Identities = 42/272 (15%), Positives = 85/272 (31%), Gaps = 101/272 (37%)
Query: 483 QRGLLQSMHRLRKDNVLSSEDHAIVDESTTCGTYVKQLGASPVTEPPLHPAEVLAA--YA 540
++G R+R +N + IVD K++ + +L+A +
Sbjct: 1679 EKG-----KRIR-ENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFT 1732
Query: 541 EYVLAP---VTKMASFQKKAVKPPPSEGGGGDQAQEKSEDETPVLTAKAPEPAIV----- 592
+ P + + A+F+ +K S+G P A
Sbjct: 1733 Q----PALTLMEKAAFE--DLK---SKGL-------------------IPADATFAGHSL 1764
Query: 593 ---SALQELYKSSFSN-LKTHDSLKISVCLDLQPRFESQPCRDYRPLSGSHVAVLVLESL 648
+AL +S ++ + +++ V YR G + V V
Sbjct: 1765 GEYAAL-----ASLADVMSIESLVEV-VF--------------YR---GMTMQVAVPRDE 1801
Query: 649 LRMVDYKMDNIR----LVGFKDAKVRPIVRL---KT--------HNCDD-------NLEG 686
L +Y M I F ++ +V +T +N ++ +L
Sbjct: 1802 LGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRA 1861
Query: 687 LDDLVDEL--------ATVKLEDAPEAEKEEE 710
LD + + L ++L+ + E+ E
Sbjct: 1862 LDTVTNVLNFIKLQKIDIIELQKSLSLEEVEG 1893
Score = 42.3 bits (99), Expect = 0.001
Identities = 38/267 (14%), Positives = 80/267 (29%), Gaps = 91/267 (34%)
Query: 275 LQLVQQDPKAKLPSTTIIEFRTKVLELAVDRVAGQNSERFLMFVLYML-------NFSPK 327
L +V +P I F G+ +R M+ +
Sbjct: 1662 LDIVINNPVNL-----TIHF------------GGEKGKRIRENYSAMIFETIVDGKLKTE 1704
Query: 328 SLRPDAVRKQLQKWYMGKESD-------QLVVLVAKCSVYQGLSHANVLKLIHFDVF--H 378
+ + + ++ Q + + + + ++ L ++ F H
Sbjct: 1705 KIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPAD--ATFAGH 1762
Query: 379 QSPDKKL----ALYAIA--FGFA----YVSHRLISGKFL--ATPR------------VPP 414
S L AL ++A V +R G + A PR + P
Sbjct: 1763 -S----LGEYAALASLADVMSIESLVEVVFYR---GMTMQVAVPRDELGRSNYGMIAINP 1814
Query: 415 FVTSDDCFDKASDKVKTIVKDVA--------VVRCNTSHQKVVAAAVKTHSLGIESVCP- 465
+ + + ++ +V+ V +V N +Q+ VAA +++V
Sbjct: 1815 GRVAASF---SQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAG---DLRALDTVTNV 1868
Query: 466 -KFAKSFKVNTACLEGMTQRGLLQSMH 491
F K K++ L+ +S+
Sbjct: 1869 LNFIKLQKIDIIELQ--------KSLS 1887
Score = 39.6 bits (92), Expect = 0.006
Identities = 43/299 (14%), Positives = 80/299 (26%), Gaps = 121/299 (40%)
Query: 633 RPLSGSH----VAVLVLESLLRMVDYKMDNIRLVGFKDAKVRPIVRLKTHNCDDNLEGLD 688
RPL+ SH +LV + F A +L+ + + L
Sbjct: 7 RPLTLSHGSLEHVLLVPTAS---------------FFIAS-----QLQ----EQFNKILP 42
Query: 689 DLVDELATVKLEDAPEAEKE-------------EESGKDSADSIIKNYEKIWRYYKRQIP 735
+ + A +D P E E S D ++ ++
Sbjct: 43 EPTEGFA---ADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNL---CLTEFENCY- 95
Query: 736 KARGITIHKLLSWSIKQMWHPDVYVVICSQENLSLYKTNVIFAEYMEKTKRKNTNQENLS 795
G IH L + + + + +L KT + Y
Sbjct: 96 -LEGNDIHALAA-------------KLLQENDTTLVKTKELIKNY--------------- 126
Query: 796 LYKTNVIFAEYMEKTKRKNTNSSHLKYMPKLKAKTPIQQLLSSAEQADNFCNSVGILQQT 855
++ ++ K +NS+ L + + + ++
Sbjct: 127 -ITARIM----AKRPFDKKSNSA----------------LFRAVGE-----GNAQLV--- 157
Query: 856 AIPSKFSGFDRGGSQ-TPQQ-----QTQQEDYAHLFATLISRCARDIDALIESLPNEDS 908
AI F GG Q + + Y L LI A + LI + + +
Sbjct: 158 AI------F--GG-QGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEK 207
Score = 37.3 bits (86), Expect = 0.031
Identities = 38/225 (16%), Positives = 60/225 (26%), Gaps = 75/225 (33%)
Query: 6 KKGGKNTNNSAPGAASTSQCSGG--SA-------------KPANQA-------GP-SKQN 42
K G + S G +A +A G +
Sbjct: 254 KLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEA 313
Query: 43 VPANQAGPS--KQNVPVNQGGAAKQ-NIQGSSSKQ---NVSA-NQAGPSKQ-------NG 88
P PS + ++ N+G + +I + +Q V+ N P+ + NG
Sbjct: 314 YPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNG 373
Query: 89 P----VKQTG--AS---------KQNGPVKQTSKETPRSRRKPS--------SLP----- 120
V +G S K P P S RK + P
Sbjct: 374 AKNLVV--SGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHL 431
Query: 121 LQKEVEAIRLRRRVKMKPLKNTQCSIHLKHLPAP-KSTHAPAEFR 164
L + I K L S + K + P T ++ R
Sbjct: 432 LVPASDLI-------NKDLVKNNVSFNAKDIQIPVYDTFDGSDLR 469
Score = 35.0 bits (80), Expect = 0.17
Identities = 16/102 (15%), Positives = 31/102 (30%), Gaps = 22/102 (21%)
Query: 834 QLLSSAEQ-ADNFCNSVGI----LQQTAIPS-------KFSGFDRGGSQTPQQQTQQEDY 881
A Q + F + P+ KF G+ + + ++ +
Sbjct: 25 ASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGY----VSSLVEPSKVGQF 80
Query: 882 AHLFATLISR------CARDIDALIESLPNEDSTTELQLASL 917
+ ++ DI AL L E+ TT ++ L
Sbjct: 81 DQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKEL 122
>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 = 88.8 bits (219), Expect = 5e-18
Identities = 98/642 (15%), Positives = 198/642 (30%), Gaps = 189/642 (29%)
Query: 445 HQKVVAAAVKTHSLGIESVCPKFAKSFKVNTACLEGMTQRGLLQSMHRLRKDNVLSSE-- 502
H + H + + F +F N C + +Q M + ++LS E
Sbjct: 3 HHHHMDFETGEHQYQYKDILSVFEDAFVDNFDCKD-------VQDMPK----SILSKEEI 51
Query: 503 DHAIVDESTTCGTY-------------VKQ-LG----------ASPVTEPPLHPAEVLAA 538
DH I+ + GT V++ + SP+ P+ +
Sbjct: 52 DHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRM 111
Query: 539 YAEY---------VLAP--VT---KMASFQKKAVKPPPSE-------GGGGDQAQEKSED 577
Y E V A V+ ++ ++ P++ G G K+
Sbjct: 112 YIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSG-----KT-- 164
Query: 578 ETPVLTAKA-PEPAIVSALQ-ELYKSSFSNLKTHDS-LKI--SVCLDLQPRFESQPCRDY 632
+ + + +++ + N + ++ L++ + + P + S+
Sbjct: 165 ---WVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSS 221
Query: 633 RPLSGSHVAVLVLESLLRMVDYK-----MDNIR--------------LVGFKDAKVRPIV 673
H L LL+ Y+ + N++ L+ + +V +
Sbjct: 222 NIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFL 281
Query: 674 --RLKTHNC-DDNLEGL--DDLVDELATV---KLEDAPEAEKEEESGKDSADSII----K 721
TH D + L D++ L + +D P E + SII +
Sbjct: 282 SAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPR---EVLTTNPRRLSIIAESIR 338
Query: 722 NYEKIWRYYKR-QIPKARGITIHKLLSWSIKQMWHPDVYVVICSQENLSLYKTNVIFAEY 780
+ W +K K + ++ S+ + P E ++ +F
Sbjct: 339 DGLATWDNWKHVNCDK-----LTTIIESSLNVL-EPA--------EYRKMFDRLSVF--- 381
Query: 781 MEKTKRKNTN--QENLSLYKTNVIFAEYM------------EKTKRKNTNSSHLKYMPKL 826
+ + LSL +VI ++ M EK +++T S Y+ +L
Sbjct: 382 -----PPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYL-EL 435
Query: 827 KAKTPIQQLLSSAEQADNFCNSVGILQQTAIPSKFSGFDRGGSQTPQ----------QQT 876
K K + L + I+ IP F D Q +
Sbjct: 436 KVKLENEYALHRS-----------IVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNI 484
Query: 877 QQEDYAHLFATLISRCARD---IDA-LIESLPNEDSTTELQ--LASLRKLEQ---DNQGA 927
+ + LF + D ++ + +++ + L L+ + DN
Sbjct: 485 EHPERMTLFRMVF----LDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPK 540
Query: 928 AERLEDTVRRGELLLEQIQAAL-----TDIAQSQL--ETNGV 962
ERL + + L +I+ L TD+ + L E +
Sbjct: 541 YERLVNAILD---FLPKIEENLICSKYTDLLRIALMAEDEAI 579
Score = 70.7 bits (172), Expect = 2e-12
Identities = 65/330 (19%), Positives = 104/330 (31%), Gaps = 99/330 (30%)
Query: 116 PSSLPLQKEVEAIRLRRRVKMKPLKNTQCSIHLKHLPAPKSTHAPAEFRLKC-ILLFKQE 174
S++ L+ LRR +K KP +N C + L ++ K+ +A F L C ILL
Sbjct: 220 SSNIKLRIHSIQAELRRLLKSKPYEN--CLLVLLNVQNAKAWNA---FNLSCKILL---- 270
Query: 175 YPMFYHDNVKTPPVNFYYKFSTTKDRKAPAEMAIFNCVDQLVAQDKKDTILTTITSEGGE 234
TT+ + D L A I+ +
Sbjct: 271 ---------------------TTRFK---------QVTDFLSAATTTH-----ISLDHHS 295
Query: 235 QNFIMFQ-LKYLIKCLIVKVLD------NSNPLLINYDIVLYVLAKCL-------QLVQQ 280
+ L+K L + D +NP ++ ++A+ + +
Sbjct: 296 MTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLS------IIAESIRDGLATWDNWKH 349
Query: 281 DPKAKLPSTTIIEFRTKVLELAVDRVAGQNSERFLMFVLYMLNFSPKSLR-PDAVRKQLQ 339
KL TTIIE VLE A R + F + F P S P + +
Sbjct: 350 VNCDKL--TTIIESSLNVLEPAEYR------KMFDRLSV----F-PPSAHIPTILLSLI- 395
Query: 340 KWYMGKESDQLVVLVAKCSVY-----QGLSHANVLKLIHFDVFHQSPDKKLALYAIAFGF 394
W+ +SD +VV V K Y Q + I+ + + + AL
Sbjct: 396 -WFDVIKSDVMVV-VNKLHKYSLVEKQPKESTISIPSIYLE-LKVKLENEYAL------- 445
Query: 395 AYVSHRLISGKFLATPRVPPFVTSDDCFDK 424
HR I + D+
Sbjct: 446 ----HRSIVDHYNIPKTFDSDDLIPPYLDQ 471
Score = 58.7 bits (141), Expect = 8e-09
Identities = 86/614 (14%), Positives = 168/614 (27%), Gaps = 188/614 (30%)
Query: 123 KEVEAIRLRRRVKMKPLKNTQCSIHLKHLPAPKSTHAPAEFRLKCILLFKQEYPMFYHDN 182
K+V+ + + + L + H+ S RL LL KQE
Sbjct: 36 KDVQ--DMPKSI----LSKEEID-HIIMSKDAVS----GTLRLFWTLLSKQE-------- 76
Query: 183 VKTPPVNFYYKFSTTKDRKAPAEMAIFNCVDQLVAQDKKDTILTTITSEGGEQNFIMFQL 242
KF V++++ + +++ I +E + + +
Sbjct: 77 ------EMVQKF-----------------VEEVLRINY-KFLMSPIKTEQRQPSMMT--R 110
Query: 243 KYLIKCLIVKVLDNSNPLLINYDIV----LYVLAKCLQLVQQDPKAKLPSTTIIEFRTKV 298
Y I+ L N N + Y++ L + L + P + +
Sbjct: 111 MY-IEQ--RDRLYNDNQVFAKYNVSRLQPYLKLRQALL--ELRPAKNV-----------L 154
Query: 299 LE---------LAVDRVAGQNSERFLMFVLYMLNFSPKSLRPDAVRKQLQKWYM------ 343
++ +A+D + + F ++ LN P+ V + LQK
Sbjct: 155 IDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLK-NCNSPETVLEMLQKLLYQIDPNW 213
Query: 344 GKESDQLVVLVAKC-SVYQGLS-------HANVLKLIHFDVFHQSPDKKLALYAIAFGF- 394
SD + + S+ L + N L L+ +V + K AF
Sbjct: 214 TSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL-LVLLNVQ----NAKAWN---AFNLS 265
Query: 395 ---------AYVSHRLISGKFLATPRVPPFVTSDDCFDKA------SDKVKTIVKDVAVV 439
V+ L + AT + +D+
Sbjct: 266 CKILLTTRFKQVTDFLSA----ATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPRE 321
Query: 440 RCNTS--HQKVVAAAVKTHSLGIE----SVCPKFAKSFKVNTACLEGMTQRGLLQSMHRL 493
T+ ++A +++ + C K + + LE R + +
Sbjct: 322 VLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVF 381
Query: 494 RKD-----NVLS--------SEDHAIVDE------------STTCGTYVKQLG--ASPVT 526
+LS S+ +V++ +T L
Sbjct: 382 PPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLEN 441
Query: 527 EPPLHPAEVLAAYAEYVLAPVTKMASFQKKAVKPPPSEG----------GGGDQAQEKSE 576
E LH ++ Y +F + PP + + + +
Sbjct: 442 EYALH-RSIVDHYN--------IPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTL 492
Query: 577 DETPVL-------------TAKAPEPAIVSALQEL--YKSSFSNLKTHDSLKISVCLDLQ 621
L TA +I++ LQ+L YK + ++ LD
Sbjct: 493 FRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFL 552
Query: 622 PRFESQ----PCRD 631
P+ E D
Sbjct: 553 PKIEENLICSKYTD 566
Score = 41.8 bits (97), Expect = 0.001
Identities = 49/335 (14%), Positives = 96/335 (28%), Gaps = 108/335 (32%)
Query: 115 KPSSLPLQKEVEAI----------RLR---------RRVKMKPLKNTQCSIHLKHLPAPK 155
+P LP +EV +R + V L L L
Sbjct: 314 RPQDLP--REVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTII-ESSLNVLE--- 367
Query: 156 STHAPAEFRLKCILLFKQEYPMF--YHDNVKTPP--VNFYYKFSTTKDRKAPAEMAIFN- 210
PAE+R + + + + P ++ + D M + N
Sbjct: 368 ----PAEYR--------KMFDRLSVFPPSAHIPTILLSLIWFDVIKSD-----VMVVVNK 410
Query: 211 CVDQ-LVAQDKKDTILTTITSEGGEQNFIM-FQLKYLIKCLIVKVLDNSNPLLINYDIVL 268
LV + K++ ++ I L+ +K L S ++++
Sbjct: 411 LHKYSLVEKQPKESTIS-----------IPSIYLELKVKLENEYALHRS---IVDH---- 452
Query: 269 YVLAKCLQLVQQDPKAKLPSTT---IIEFRTKVLELAVDRVAGQNSERFLMF-VLYM-LN 323
Y + K D +P + ++ ER +F ++++
Sbjct: 453 YNIPKTF-----DSDDLIPPYLDQYFYSH------IGHHLKNIEHPERMTLFRMVFLDFR 501
Query: 324 FSPKSLRPDAVRKQLQKWYM-GKESDQLVVL-------VAKCSVYQGLSHANVLKLIHF- 374
F + +R D+ W G + L L Y+ L V ++ F
Sbjct: 502 FLEQKIRHDST-----AWNASGSILNTLQQLKFYKPYICDNDPKYERL----VNAILDFL 552
Query: 375 ----DVFHQSPDK---KLALYAIAFGFAYVSHRLI 402
+ S ++AL A +H+ +
Sbjct: 553 PKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQV 587
>1yvr_A RO autoantigen, 60-kDa SS-A/RO ribonucleoprotein, 60 kDa; heat
repeat, VON willebrand factor A, rossmann fold, midas
motif', RNA binding protein; 1.95A {Xenopus laevis}
SCOP: a.118.25.1 c.62.1.5 PDB: 1yvp_A 2i91_A
Length = 538
Score = 63.0 bits (152), Expect = 3e-10
Identities = 68/394 (17%), Positives = 138/394 (35%), Gaps = 72/394 (18%)
Query: 302 AVDRVAGQNSERFLMFVLYMLNFSPKSLRPD---AVRKQLQKWYMGKESDQLVVLVAKCS 358
AV V + F+ + + A+RK + WY K++ L + V K
Sbjct: 114 AVPEVC-RIPTHLFTFIQFKKDLKEGMKCGMWGRALRKAVSDWYNTKDALNLAMAVTKYK 172
Query: 359 VYQGLSHANVLKLIHFDVFHQSPDKKLALYAIAFGFAYVSHRLISGKFLATPRVPPFVTS 418
G SH ++L+L H + + + YVS + +
Sbjct: 173 QRNGWSHKDLLRLSH--IKPANEGLTMV-------AKYVSKGWKEVQEAYKEKELS---- 219
Query: 419 DDCFDKASDKVKTIVKDVAVVRCNTSHQKVVAAAVKTHSLGIESVCPKFAKSFKVNTACL 478
++KV ++ V+ + + + + L E + KS ++ + L
Sbjct: 220 -----PETEKVLKYLEATERVKRTKD-ELEIIHLIDEYRLVREHLLTIHLKSKEIWKSLL 273
Query: 479 EGMTQRGLLQSMHRLRKDNVL--SSEDHAIVDESTTCGTYVKQLGASPVTEPPLHPAEVL 536
+ M LL+++ ++ D+VL +S + + V E T +K+ +HP +L
Sbjct: 274 QDMPLTALLRNLGKMTADSVLAPASSEVSSVCERLTNEKLLKK--------ARIHPFHIL 325
Query: 537 AAYAEYVLAPVTKMASFQKKAVKPPPSEGGGGDQAQEKSEDETPVLTAKAPEPAIVSALQ 596
A Y + G G++ + + P+ +IV AL
Sbjct: 326 VALETY---------------------KKGHGNRGKLR----------WIPDTSIVEALD 354
Query: 597 ELYKSSFSNLKTHDSLKISVCLDLQPRFESQPCRDYRPLSGSHVAVLVLESLLRMVDYKM 656
+ SF ++ + + +D+ +Q L+ S VA + + R
Sbjct: 355 NAFYKSFKLVEPTG-KRFLLAIDVSAS-MNQRVLG-SILNASVVAAAMCMLVAR----TE 407
Query: 657 DNIRLVGFKDAKVRPIVRLKTHNCDDNLEGLDDL 690
+ +V F D ++ P + +E + D+
Sbjct: 408 KDSHMVAFSD-EMLPCPITVNMLLHEVVEKMSDI 440
>2nvo_A RO sixty-related protein, RSR; alpha helical repeats, VON
willebrand factor A domain, beta- RNA binding protein;
1.89A {Deinococcus radiodurans}
Length = 535
Score = 61.8 bits (149), Expect = 7e-10
Identities = 60/399 (15%), Positives = 123/399 (30%), Gaps = 79/399 (19%)
Query: 293 EFRTKVLELAVDRVAGQNSERFLMFVLYMLNFSPKSLRPDAVRKQLQKWYMGKESDQLVV 352
K A+ VA + L F+ + R+ + Y + D+L +
Sbjct: 116 AADRKAAWDALPEVA-RTGTMLLHFLAFADALGG---WGRLTRRGVANVYETADVDKLAL 171
Query: 353 LVAKCSVYQGLSHANVLKLIHFDVFHQSPDKKLALYAIAFGFAYVSHRLISGKFLATPRV 412
K G S A+ L+ H A ++ +
Sbjct: 172 WAVKYKARDGWSQADALRKAHPKTDD---------AARNAVLKFMVDGV----------- 211
Query: 413 PPFVTSDDCFDKASDKVKTIVKDVAVVRCNTSHQKVVAAAVKTHSLGIESVCPKFAKSFK 472
K +++ + AA ++ + L +E+V P + +
Sbjct: 212 ---------LPKVDSPALRVIEGHLKATEAQTDAA-AAALMQEYRLPLEAV-PTHVRGAE 260
Query: 473 VNTACLEGMTQRGLLQSMHRLRKDNVLSSEDHAIVDESTTCGTYVKQLG-ASPVTEPPLH 531
V A ++ LL+++ L + VL+ D A V +++L + + +H
Sbjct: 261 VYRAAMQTNGLTWLLRNLGNLGRVGVLTPNDSATVQA------VIERLTDPAALKRGRIH 314
Query: 532 PAEVLAAYAEYVLAPVTKMASFQKKAVKPPPSEGGGGDQAQEKSEDETPVLTAKAPEPAI 591
P + L A Y G G + + P P +
Sbjct: 315 PLDALKARLVY---------------------AQGQGVRGKGTWL----------PVPRV 343
Query: 592 VSALQELYKSSFSNLKTHDSLKISVCLDLQPRFESQPCRDYRPLSGSHVAVLVLESLLRM 651
V AL+E + +F N++ + + + LD+ L+ + A + LR
Sbjct: 344 VDALEEAFTLAFGNVQ-PANTRHLLALDVSGSMTCGDVAGVPGLTPNMAAAAMSLIALR- 401
Query: 652 VDYKMDNIRLVGFKDAKVRPIVRLKTHNCDDNLEGLDDL 690
+ +GF + + RP+ + ++ +
Sbjct: 402 ---TEPDALTMGFAE-QFRPLGITPRDTLESAMQKAQSV 436
>2xs1_A Programmed cell death 6-interacting protein; protein
transport-viral protein complex, cell cycle; 2.30A {Homo
sapiens} PDB: 2xs8_A 2oev_A 2r05_A 2r02_A 2r03_A 2oex_A
2ojq_A
Length = 704
Score = 33.0 bits (74), Expect = 0.50
Identities = 36/283 (12%), Positives = 94/283 (33%), Gaps = 18/283 (6%)
Query: 676 KTHNCDDNLEGLDDLVDELATVKLEDAPEAEKEEESGKDSADSIIKNYEKIWRYYKRQIP 735
K + ++ + + V A E+ SG SI+ + Q
Sbjct: 380 KADLVNRSIAQMREATTLANGVLASLNLPAAIEDVSGDTVPQSILTKSRSVIEQGGIQTV 439
Query: 736 KARGITIHKLLSWSIKQMWHPDVYVVICSQENLSLYKT--NVIFAEYMEKTKRKNTNQEN 793
+ +LL + + + S L + N + A++ E+ +R +N+
Sbjct: 440 DQLIKELPELLQRNREIL--------DESLRLLDEEEATDNDLRAKFKERWQRTPSNELY 491
Query: 794 LSLYKTNVIFAEYMEKTKRKNTNSSHLKYMPKLKAKTPIQQLLSSAEQADNFCNSVGILQ 853
L F ++K + + + I L + + S +
Sbjct: 492 KPLRAEGTNFRTVLDKAVQADGQVKECYQ----SHRDTIVLLCKPEPELNAAIPSANPAK 547
Query: 854 QTAIPSKFSGFDRGGSQTPQQQTQQEDYAHLFATLISRCARDIDALIESLPNEDSTTELQ 913
+ S + + ++E + D+ + + +D +
Sbjct: 548 TMQGSEVVNVLKSLLSNLDEVKKEREG----LENDLKSVNFDMTSKFLTALAQDGVINEE 603
Query: 914 LASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAALTDIAQSQ 956
S+ +L++ G ++++++++ E LL+ IQ + + ++ +
Sbjct: 604 ALSVTELDRVYGGLTTKVQESLKKQEGLLKNIQVSHQEFSKMK 646
>1dx0_A Prion protein; brain, repeat; NMR {Bos taurus} SCOP: d.6.1.1 PDB:
1dx1_A 1qlx_A 1qlz_A
Length = 219
Score = 31.7 bits (71), Expect = 0.75
Identities = 16/98 (16%), Positives = 27/98 (27%)
Query: 5 NKKGGKNTNNSAPGAASTSQCSGGSAKPANQAGPSKQNVPANQAGPSKQNVPVNQGGAAK 64
N G + +PG GG + G + + + GG +
Sbjct: 13 NTGGSRYPGQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQ 72
Query: 65 QNIQGSSSKQNVSANQAGPSKQNGPVKQTGASKQNGPV 102
+ G + PSK +K + G V
Sbjct: 73 PHGGGGWGQGGTHGQWNKPSKPKTNMKHVAGAAAAGAV 110
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 30.1 bits (67), Expect = 2.5
Identities = 8/43 (18%), Positives = 19/43 (44%), Gaps = 6/43 (13%)
Query: 698 KLE--DAPEAEKEEESGKDSADSIIKNYEKIWRYYKRQIPKAR 738
+L+ DA E+E ++ A ++ + + Q+ K +
Sbjct: 97 RLQELDAASKVMEQEW-REKAKKDLEEW---NQRQSEQVEKNK 135
>3nix_A Flavoprotein/dehydrogenase; structural genomics, PSI-2, NES protein
structure initiative, northeast structural genomics
consortium; HET: FAD; 2.60A {Cytophaga hutchinsonii}
Length = 421
Score = 30.1 bits (68), Expect = 3.4
Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 6/56 (10%)
Query: 235 QNFIMFQLKYL-IKCLIVKVL-----DNSNPLLINYDIVLYVLAKCLQLVQQDPKA 284
+ K +I VL D +NP + ++ +L LAK +Q+ ++ +
Sbjct: 361 HAVFFAKNPDPDHKRMICSVLAGYVWDKNNPFVKKHNTILKTLAKVIQMGEEALEH 416
>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 = 28.4 bits (62), Expect = 6.7
Identities = 10/31 (32%), Positives = 13/31 (41%), Gaps = 6/31 (19%)
Query: 808 EKTKRKNTNSSHLK-Y----MPKLKAKTPIQ 833
EK K +S LK Y P L K ++
Sbjct: 18 EKQALKKLQAS-LKLYADDSAPALAIKATME 47
>1ky3_A GTP-binding protein YPT7P; vesicular traffic, GTP hydrolysis,
YPT/RAB protein, endocytosis, hydrolase,
endocytosis/exocytosis complex; HET: GDP; 1.35A
{Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ky2_A*
Length = 182
Score = 28.3 bits (64), Expect = 9.2
Identities = 13/35 (37%), Positives = 17/35 (48%), Gaps = 11/35 (31%)
Query: 289 TTI-IEFRTKVLELAVDRV--------AGQNSERF 314
TI +F TK + + D+V AGQ ERF
Sbjct: 39 ATIGADFLTKEVTVDGDKVATMQVWDTAGQ--ERF 71
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 0.130 0.368
Gapped
Lambda K H
0.267 0.0649 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 13,384,854
Number of extensions: 779655
Number of successful extensions: 1455
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1442
Number of HSP's successfully gapped: 28
Length of query: 962
Length of database: 6,701,793
Length adjustment: 103
Effective length of query: 859
Effective length of database: 3,825,930
Effective search space: 3286473870
Effective search space used: 3286473870
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 (21.6 bits)
S2: 62 (27.8 bits)