RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3251
(959 letters)
>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay,
zinc-finger, ATP-binding, metal-BIN UPF2, UPF1,
helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A
2iyk_A
Length = 800
Score = 1120 bits (2898), Expect = 0.0
Identities = 621/854 (72%), Positives = 704/854 (82%), Gaps = 55/854 (6%)
Query: 95 KELPPHACKYCGIHDPAYVIMCNICKKWFCNGRGHTSGSHIINHLVRAKHKEVTLHKDGP 154
K+LP HAC YCGIHDPA V+ CN KKWFCNGRG+TSGSHI+NHLVRAK KEVTLHKDGP
Sbjct: 2 KDLPIHACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGP 61
Query: 155 LGETVLECYTCGVRNIFVLGFIPAKADSVVVLLCRTPCAAQNSLKDMNWDQEQWKPLIAD 214
LGETVLECY CG RN+F+LGFIPAKADSVVVLLCR PCA+Q+SLKD+NWD QW+PLI D
Sbjct: 62 LGETVLECYNCGCRNVFLLGFIPAKADSVVVLLCRQPCASQSSLKDINWDSSQWQPLIQD 121
Query: 215 RSFLSWLVKVPTEQEQQRGRQVTSAQIAKLEEVWKDNAEATFQDLEKPGVDEDPHQVLLR 274
R FLSWLVK+P+EQEQ R RQ+T+ QI KLEE+WK+N AT +DLEKPGVDE+P
Sbjct: 122 RCFLSWLVKIPSEQEQLRARQITAQQINKLEELWKENPSATLEDLEKPGVDEEPQH---- 177
Query: 275 YEDGYQYQNIFGPLVKLEADYDKRLKESQTQENVTVRWDVGLNKKSIAYFSLAKTDGDGY 334
V +R++ D Y
Sbjct: 178 ---------------------------------VLLRYE------------------DAY 186
Query: 335 QYQNIFGPLVKLEADYDKRLKESQTQENVTVRWDVGLNKKSIAYFSLAKTDGDMRLMQGD 394
QYQNIFGPLVKLEADYDK+LKESQTQ+N+TVRWD+GLNKK IAYF+L KTD DMRLMQGD
Sbjct: 187 QYQNIFGPLVKLEADYDKKLKESQTQDNITVRWDLGLNKKRIAYFTLPKTDSDMRLMQGD 246
Query: 395 ELKLRYSYDASKTWSGLGHVIKIPDNFGDEVGLELKSSAGAPTEATTGFSVDFIWKSTSF 454
E+ LRY D + W G+GHVIK+PDN+GDE+ +EL+SS GAP E T F VDF+WKSTSF
Sbjct: 247 EICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAIELRSSVGAPVEVTHNFQVDFVWKSTSF 306
Query: 455 DRMQLALRKFAVDDQSVSAYIYHRLLGHNVDEVLFRCHLPKHFSAPNLPDLNRSQVYAVK 514
DRMQ AL+ FAVD+ SVS YIYH+LLGH V++V+ +C LPK F+A LPDLN SQVYAVK
Sbjct: 307 DRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVIIKCQLPKRFTAQGLPDLNHSQVYAVK 366
Query: 515 HAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHRTGLK 574
+QRPLSLIQGPPGTGKTVTSATIVY L +Q PVLVCAPSNIAVDQLTEKIH+TGLK
Sbjct: 367 TVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLK 426
Query: 575 VVRVCAKSREAIDSPVSFLALHNQIRNMEMNSELKKLLQLKEETGELSSADEKRYRMLKK 634
VVR+CAKSREAIDSPVSFLALHNQIRNM+ EL+KL QLK+ETGELSSADEKRYR LK+
Sbjct: 427 VVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALKR 486
Query: 635 NAEKSLLDNADVICCTCVGAGDPRLLKIKFHSILIDESMQATEPECMVPVILGAKQLILV 694
AE+ LL NADVICCTCVGAGDPRL K++F SILIDES QATEPECMVPV+LGAKQLILV
Sbjct: 487 TAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLGAKQLILV 546
Query: 695 GDHCQLGPVVMCKKAARAGLSQSLFERLVVLGIRPFRLEVQYRMHPELSKFPSNFFYEGS 754
GDHCQLGPVVMCKKAA+AGLSQSLFERLVVLGIRP RL+VQYRMHP LS FPSN FYEGS
Sbjct: 547 GDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSNIFYEGS 606
Query: 755 LQNGVCADERKLSKIDFPWPVPDKPMLFYVTQGQEEIAGSGTSYVNRTEASNVEKITTRF 814
LQNGV A +R DF WP PDKPM FYVTQGQEEIA SGTSY+NRTEA+NVEKITT+
Sbjct: 607 LQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKL 666
Query: 815 IRCGMKPEQIGVITPYEGQRAFLVQHMQYQGSLPAKIYQEIEVASVDAFQGREKDLIIMS 874
++ G KP+QIG+ITPYEGQR++LVQ+MQ+ GSL K+YQE+E+ASVDAFQGREKD II+S
Sbjct: 667 LKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILS 726
Query: 875 CVRSNDHQGIGFLNDPRRLNVALTRAKYGIIVIGNPKVLSKQPLWNNLLNFYKEQKVLVE 934
CVR+N+HQGIGFLNDPRRLNVALTRA+YG+I++GNPK LSKQPLWN+LLN+YKEQKVLVE
Sbjct: 727 CVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVE 786
Query: 935 GPLNNLKESLILFS 948
GPLNNL+ESL+ FS
Sbjct: 787 GPLNNLRESLMQFS 800
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA
degradation, allosteric REGU; HET: ADP 1PE; 2.40A
{Saccharomyces cerevisiae}
Length = 802
Score = 1065 bits (2756), Expect = 0.0
Identities = 446/860 (51%), Positives = 584/860 (67%), Gaps = 60/860 (6%)
Query: 89 GNEFFNKELPPHACKYCGIHDPAYVIMCNICKKWFCNGRGHTSGSHIINHLVRAKHKEVT 148
G + ++C YCGI VI CN CKKWFCN + TS SHI+NHLV + H V+
Sbjct: 1 GAASMSPSASDNSCAYCGIDSAKCVIKCNSCKKWFCNTKNGTSSSHIVNHLVLSHHNVVS 60
Query: 149 LHKDGPLGETVLECYTCGVRNIFVLGFIPAKADSVVVLLCRTPCAAQNSLKDMNWDQEQW 208
LH D LG+TVLECY CG +N+F+LGF+ AK+++VVVLLCR PCA K+ NWD +QW
Sbjct: 61 LHPDSDLGDTVLECYNCGRKNVFLLGFVSAKSEAVVVLLCRIPCA---QTKNANWDTDQW 117
Query: 209 KPLIADRSFLSWLVKVPTEQEQQRGRQVTSAQIAKLEEVWKDNAEATFQDLEKPGVDEDP 268
+PLI DR LSW+ + PTE+E+ + R +T +QI+KLE W+ N +AT D++ P E
Sbjct: 118 QPLIEDRQLLSWVAEQPTEEEKLKARLITPSQISKLEAKWRSNKDATINDIDAPEEQEAI 177
Query: 269 HQVLLRYEDGYQYQNIFGPLVKLEADYDKRLKESQTQENVTVRWDVGLNKKSIAYFSLAK 328
+LLRY+D Y+YQ +GPL+KLEADYDK+LKESQ E+++V W + LN + +A F+L+
Sbjct: 178 PPLLLRYQDAYEYQRSYGPLIKLEADYDKQLKESQALEHISVSWSLALNNRHLASFTLST 237
Query: 329 TDGDGYQYQNIFGPLVKLEADYDKRLKESQTQENVTVRWDVGLNKKSIAYFSLAKTDGDM 388
+ + + + G + L
Sbjct: 238 FESN--ELKVAIGDEMIL------------------------------------------ 253
Query: 389 RLMQGDELKLRYSYDASKTWSGLGHVIKIPDNFGDEVGLELKSSAGAP-TEATTGFSVDF 447
YS W G G+++++P++F D LELK S P T TTGF+ +F
Sbjct: 254 ----------WYSGMQHPDWEGRGYIVRLPNSFQDTFTLELKPSKTPPPTHLTTGFTAEF 303
Query: 448 IWKSTSFDRMQLALRKFAVDDQSVSAYIYHRLLGHNVDEVLFRCHLPKHFSAPNLPDLNR 507
IWK TS+DRMQ AL+KFA+D +S+S Y+Y+++LGH V ++ F LPK FS PN LN
Sbjct: 304 IWKGTSYDRMQDALKKFAIDKKSISGYLYYKILGHQVVDISFDVPLPKEFSIPNFAQLNS 363
Query: 508 SQVYAVKHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEK 567
SQ AV H +QRPLSLIQGPPGTGKTVTSATIVY L K +LVCAPSN+AVD L K
Sbjct: 364 SQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPSNVAVDHLAAK 423
Query: 568 IHRTGLKVVRVCAKSREAIDSPVSFLALHNQIRNMEMNSELKKLLQLKEETGELSSADEK 627
+ GLKVVR+ AKSRE ++S VS LALHN + ELK LL+LK+E GELS++D K
Sbjct: 424 LRDLGLKVVRLTAKSREDVESSVSNLALHNLVGR-GAKGELKNLLKLKDEVGELSASDTK 482
Query: 628 RYRMLKKNAEKSLLDNADVICCTCVGAGDPRLLKIKFHSILIDESMQATEPECMVPVILG 687
R+ L + E +L+ ADV+CCTCVGAGD R L KF ++LIDES QA+EPEC++P++ G
Sbjct: 483 RFVKLVRKTEAEILNKADVVCCTCVGAGDKR-LDTKFRTVLIDESTQASEPECLIPIVKG 541
Query: 688 AKQLILVGDHCQLGPVVMCKKAARAGLSQSLFERLVVLGIRPFRLEVQYRMHPELSKFPS 747
AKQ+ILVGDH QLGPV++ +KAA AGL QSLFERL+ LG P RLEVQYRM+P LS+FPS
Sbjct: 542 AKQVILVGDHQQLGPVILERKAADAGLKQSLFERLISLGHVPIRLEVQYRMNPYLSEFPS 601
Query: 748 NFFYEGSLQNGVCADERKLSKIDFPWPVPDKPMLFYVTQGQEEIAGSGTSYVNRTEASNV 807
N FYEGSLQNGV ++R + FPWP+ PM+F+ G+EEI+ +GTS++NR EA N
Sbjct: 602 NMFYEGSLQNGVTIEQRTVPNSKFPWPIRGIPMMFWANYGREEISANGTSFLNRIEAMNC 661
Query: 808 EKITTRFIRCGMKPEQIGVITPYEGQRAFLVQHMQYQGSLPAKIYQEIEVASVDAFQGRE 867
E+I T+ R G+KPEQIGVITPYEGQRA+++Q+MQ GSL +Y ++EVASVDAFQGRE
Sbjct: 662 ERIITKLFRDGVKPEQIGVITPYEGQRAYILQYMQMNGSLDKDLYIKVEVASVDAFQGRE 721
Query: 868 KDLIIMSCVRSNDHQGIGFLNDPRRLNVALTRAKYGIIVIGNPKVLSKQPLWNNLLNFYK 927
KD II+SCVR+N+ Q IGFL DPRRLNV LTRAKYG++++GNP+ L++ LWN+LL ++
Sbjct: 722 KDYIILSCVRANEQQAIGFLRDPRRLNVGLTRAKYGLVILGNPRSLARNTLWNHLLIHFR 781
Query: 928 EQKVLVEGPLNNLKESLILF 947
E+ LVEG L+NL+ +
Sbjct: 782 EKGCLVEGTLDNLQLCTVQL 801
>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD,
hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A*
2gk7_A 2xzo_A* 2xzp_A
Length = 624
Score = 877 bits (2268), Expect = 0.0
Identities = 484/617 (78%), Positives = 546/617 (88%)
Query: 332 DGYQYQNIFGPLVKLEADYDKRLKESQTQENVTVRWDVGLNKKSIAYFSLAKTDGDMRLM 391
D YQYQNIFGPLVKLEADYDK+LKESQTQ+N+TVRWD+GLNKK IAYF+L KTD DMRLM
Sbjct: 8 DAYQYQNIFGPLVKLEADYDKKLKESQTQDNITVRWDLGLNKKRIAYFTLPKTDSDMRLM 67
Query: 392 QGDELKLRYSYDASKTWSGLGHVIKIPDNFGDEVGLELKSSAGAPTEATTGFSVDFIWKS 451
QGDE+ LRY D + W G+GHVIK+PDN+GDE+ +EL+SS GAP E T F VDF+WKS
Sbjct: 68 QGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAIELRSSVGAPVEVTHNFQVDFVWKS 127
Query: 452 TSFDRMQLALRKFAVDDQSVSAYIYHRLLGHNVDEVLFRCHLPKHFSAPNLPDLNRSQVY 511
TSFDRMQ AL+ FAVD+ SVS YIYH+LLGH V++V+ +C LPK F+A LPDLN SQVY
Sbjct: 128 TSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVIIKCQLPKRFTAQGLPDLNHSQVY 187
Query: 512 AVKHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHRT 571
AVK +QRPLSLIQGPPGTGKTVTSATIVY L +Q PVLVCAPSNIAVDQLTEKIH+T
Sbjct: 188 AVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQT 247
Query: 572 GLKVVRVCAKSREAIDSPVSFLALHNQIRNMEMNSELKKLLQLKEETGELSSADEKRYRM 631
GLKVVR+CAKSREAIDSPVSFLALHNQIRNM+ EL+KL QLK+ETGELSSADEKRYR
Sbjct: 248 GLKVVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRA 307
Query: 632 LKKNAEKSLLDNADVICCTCVGAGDPRLLKIKFHSILIDESMQATEPECMVPVILGAKQL 691
LK+ AE+ LL NADVICCTCVGAGDPRL K++F SILIDES QATEPECMVPV+LGAKQL
Sbjct: 308 LKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLGAKQL 367
Query: 692 ILVGDHCQLGPVVMCKKAARAGLSQSLFERLVVLGIRPFRLEVQYRMHPELSKFPSNFFY 751
ILVGDHCQLGPVVMCKKAA+AGLSQSLFERLVVLGIRP RL+VQYRMHP LS FPSN FY
Sbjct: 368 ILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSNIFY 427
Query: 752 EGSLQNGVCADERKLSKIDFPWPVPDKPMLFYVTQGQEEIAGSGTSYVNRTEASNVEKIT 811
EGSLQNGV A +R DF WP PDKPM FYVTQGQEEIA SGTSY+NRTEA+NVEKIT
Sbjct: 428 EGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKIT 487
Query: 812 TRFIRCGMKPEQIGVITPYEGQRAFLVQHMQYQGSLPAKIYQEIEVASVDAFQGREKDLI 871
T+ ++ G KP+QIG+ITPYEGQR++LVQ+MQ+ GSL K+YQE+E+ASVDAFQGREKD I
Sbjct: 488 TKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFI 547
Query: 872 IMSCVRSNDHQGIGFLNDPRRLNVALTRAKYGIIVIGNPKVLSKQPLWNNLLNFYKEQKV 931
I+SCVR+N+HQGIGFLNDPRRLNVALTRA+YG+I++GNPK LSKQPLWN+LLN+YKEQKV
Sbjct: 548 ILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKV 607
Query: 932 LVEGPLNNLKESLILFS 948
LVEGPLNNL+ESL+ FS
Sbjct: 608 LVEGPLNNLRESLMQFS 624
>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase,
hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli}
SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*
Length = 608
Score = 69.7 bits (171), Expect = 3e-12
Identities = 53/262 (20%), Positives = 99/262 (37%), Gaps = 71/262 (27%)
Query: 454 FDRMQLALRKFAVDDQSVSAYIYHRLLGHNVDEVLFRCHLPKHFSAPNLPDLNRSQVYAV 513
+L L + ++++V+ + VDE L L K F + + Q A
Sbjct: 102 LCGDRLYLNRMWCNERTVARFFNEVNHAIEVDEALLAQTLDKLFPVSDEINW---QKVAA 158
Query: 514 KHAIQRPLSLIQGPPGTGKTVTSATIV---YQLVKQTGSPVLVCAPSNIAVDQLTEKIHR 570
A+ R +S+I G PGTGKT T A ++ Q+ + + AP+ A +LTE + +
Sbjct: 159 AVALTRRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLGK 218
Query: 571 TGLKVVRVCAKSREAIDSPVSFLALHNQIRNMEMNSELKKLLQLKEETGELSSADEKRYR 630
L+ + + + ++ I S LH +LL + +
Sbjct: 219 -ALRQLPLTDEQKKRIPEDAS--TLH-------------RLLGAQPGSQR---------- 252
Query: 631 MLKKNAEKSLLDNADVICCTCVGAGDPRLLKIKFHSILIDESMQATEPECMVPVILGAK- 689
L+ +A L + DV +++DE+ M+ + + ++
Sbjct: 253 -LRHHAGNPL--HLDV--------------------LVVDEA-------SMIDLPMMSRL 282
Query: 690 --------QLILVGDHCQLGPV 703
++I +GD QL V
Sbjct: 283 IDALPDHARVIFLGDRDQLASV 304
>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein,
ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus
radiodurans} PDB: 3gp8_A 3gpl_A*
Length = 574
Score = 63.6 bits (155), Expect = 2e-10
Identities = 25/120 (20%), Positives = 45/120 (37%), Gaps = 11/120 (9%)
Query: 458 QLALRKFAVDDQSVSAYIYHRLLGHNVDEVLFRCHLPKHFSAPNLPDLNRSQVYAVKHAI 517
++ L ++ +++ I L D + L + Q +
Sbjct: 146 RIYLPHVLRAEKKLASLIRTLLATPPADGAGNDDWAVPKKARKGLSE---EQASVLDQLA 202
Query: 518 QRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEK-------IHR 570
L ++ G PGTGK+ T+ + L + G V +CAP+ A +L E +HR
Sbjct: 203 GHRLVVLTGGPGTGKSTTTKAVA-DLAESLGLEVGLCAPTGKAARRLGEVTGRTASTVHR 261
Score = 29.3 bits (66), Expect = 7.9
Identities = 18/86 (20%), Positives = 27/86 (31%), Gaps = 27/86 (31%)
Query: 661 KIKFHSILIDESMQATEPECMVPVILGAK---------QLILVGDHCQLGPVVMCKKAAR 711
+ +++DE M+ L +++LVGD QL PV
Sbjct: 277 PAPYDLLIVDEV-------SMMGDALMLSLLAAVPPGARVLLVGDTDQLPPV-------D 322
Query: 712 AGLSQSLFERLVVLGIRPFRLEVQYR 737
AG L +L YR
Sbjct: 323 AG---LPLLAL-AQAAPTIKLTQVYR 344
>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 = 62.9 bits (152), Expect = 4e-10
Identities = 108/650 (16%), Positives = 190/650 (29%), Gaps = 152/650 (23%)
Query: 372 NKKSIAYFSLA-KTDGDMRLMQGDELKLRYS---YDASKTWSGLGHVIKIPDNFGDEVG- 426
K ++ F A + D + +Q D K S D H+I D G
Sbjct: 18 YKDILSVFEDAFVDNFDCKDVQ-DMPKSILSKEEID---------HIIMSKD---AVSGT 64
Query: 427 ------LELKSSAGAPTEATTGFSVDFIWKSTSFDRMQLALRKFAVDDQSVSAYIYHRLL 480
L K +++ + ++ R+ ++ + YI R
Sbjct: 65 LRLFWTLLSKQEEMVQKFVEEVLRINYKF---LMSPIKTEQRQPSMMTRM---YIEQRDR 118
Query: 481 GHNVDEVLFRCHLPKHFSAPNLPDLNRSQ-VYAVKHAIQ--RPLS--LIQGPPGTGKTVT 535
+N ++V K+ ++R Q ++ A+ RP LI G G+GKT
Sbjct: 119 LYNDNQVF-----AKYN-------VSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTW- 165
Query: 536 SATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHRTGLKVVRVCAKSREAIDSPVSFLAL 595
+ VC + ++ KI L + C ++ L
Sbjct: 166 -------VALD------VCLSYKV-QCKMDFKIF--WLNLKN-CNSPETVLE---MLQKL 205
Query: 596 HNQIRNMEMNSELKKLLQLKEETGELSSADEKRYRMLKKNAEKSL--LDNA--------- 644
QI S +K + E R + K E L L N
Sbjct: 206 LYQIDPN-WTSRSDHSSNIKLRIHSIQ--AELRRLLKSKPYENCLLVLLNVQNAKAWNAF 262
Query: 645 DVICCTCV-----GAGDPRLLKIKFHSILIDESMQATEPECMVPVILGAKQLIL--VGDH 697
++ C + D H L SM T E K L+L +
Sbjct: 263 NLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDE--------VKSLLLKYLDCR 314
Query: 698 CQLGPVVMCKKAARAGLSQSLFERLVVLGIRPFRLEVQYRMHPELSKFPSNFFYEGSLQN 757
Q P + S+ IR H K + E SL
Sbjct: 315 PQDLPREVLT---TNPRRLSIIAES----IRDGLATWDNWKHVNCDKLTTII--ESSLNV 365
Query: 758 GVCADERKLSK---IDFPW--PVPDK--PMLFY--VTQGQEEIAGS--GTSYVNRTEASN 806
A+ RK+ + FP +P ++++ + + S V + +
Sbjct: 366 LEPAEYRKMFDRLSV-FPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKES 424
Query: 807 VEKITTRFIRCGMKPEQIG-----VITPYEGQRAFLVQHM------QYQGSLPAKIYQ-- 853
I + ++ +K E ++ Y + F + QY Y
Sbjct: 425 TISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQY-------FYSHI 477
Query: 854 -----EIEVA-SVDAFQGREKDL-IIMSCVRSNDHQGIGFLNDPRRLNVALTRAKYGIIV 906
IE + F+ D + +R H + LN Y +
Sbjct: 478 GHHLKNIEHPERMTLFRMVFLDFRFLEQKIR---HDSTAWNASGSILNTLQQLKFYKPYI 534
Query: 907 IGNPKVLSKQPLWNNLLNF-YKEQKVLVEGPLNNLKESLILFSKPKQYFK 955
N + L N +L+F K ++ L+ +L + L ++ + F+
Sbjct: 535 CDNDPKYER--LVNAILDFLPKIEENLICSKYTDLLR-IALMAEDEAIFE 581
Score = 52.2 bits (124), Expect = 8e-07
Identities = 59/413 (14%), Positives = 120/413 (29%), Gaps = 130/413 (31%)
Query: 31 SEFDFTDF--TLPSQSQTQASQLDSVNQIQVNGKQNLDNSNLNLVSQKLHELQFEEEEDD 88
+ DF F L + + L+ + ++ N + + + + KL + +
Sbjct: 178 CKMDFKIFWLNL-KNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLR---IHSIQAE 233
Query: 89 GNEFFNKELPPHACKYCGIHDPAYVIMCNICKKW----F---CNGRGHTSGSHIINHLVR 141
+ + +++ N+ F C T + + L
Sbjct: 234 LRRLLKSKPYENC----------LLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSA 283
Query: 142 AKHKEVTLHKDGPLGETVLECYTCGVRNIF--VLGF----IPAKADSVVVLLCRTPCAAQ 195
A ++L + T E V+++ L +P + + A
Sbjct: 284 ATTTHISL-DHHSMTLTPDE-----VKSLLLKYLDCRPQDLPREVLTTNPRRLSI-IAE- 335
Query: 196 NSLKDMN--WDQEQWKPLIADR------SFLSWL------------------VKVPT--- 226
S++D WD WK + D+ S L+ L +PT
Sbjct: 336 -SIRDGLATWDN--WKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILL 392
Query: 227 -----EQEQQRGRQVTSAQIAKLEEVWKDNAEATF-----QDLEKPGVDEDP--HQVLL- 273
+ + V + ++ K V K E+T K ++ + H+ ++
Sbjct: 393 SLIWFDVIKSDVMVVVN-KLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVD 451
Query: 274 RY---------------EDGYQYQNIFGPLVKLEADYDKRLKESQTQENVTV-------- 310
Y D Y Y +I G + LK + E +T+
Sbjct: 452 HYNIPKTFDSDDLIPPYLDQYFYSHI-G--------H--HLKNIEHPERMTLFRMVFLDF 500
Query: 311 RWDVGLNKKSI-------AYFSLAKTDGDGYQYQNIFGPLVKLEADYDKRLKE 356
R+ L +K A S+ T Y+ + Y++ +
Sbjct: 501 RF---LEQKIRHDSTAWNASGSILNTLQQLKFYKPYI---CDNDPKYERLVNA 547
Score = 52.2 bits (124), Expect = 8e-07
Identities = 75/501 (14%), Positives = 140/501 (27%), Gaps = 167/501 (33%)
Query: 135 IINHLVRAK-HKEVTLHKDGPLGETVLECYTC---GVR-----NIFVLGFIPAKADSVVV 185
+ L+ + K V + G+T + C V+ IF L + V+
Sbjct: 140 LRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVL 199
Query: 186 L----LCRTPCAAQNSLKD--------MNWDQEQWKPLIADRSF---L--------SWLV 222
L S D ++ Q + + L+ + + L +
Sbjct: 200 EMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAW 259
Query: 223 K---------VPTEQEQQRGRQVTSAQIAKLE-EVWKDNAEATFQDLEKPG--------- 263
+ T R +QVT A + D+ T E
Sbjct: 260 NAFNLSCKILLTT-----RFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCR 314
Query: 264 VDEDPHQVLLRYEDGYQYQNIFGPL-VKLEADYDKRLKESQTQENVTVRWD----VGLNK 318
+ P +VL P + + A + +++ WD V +K
Sbjct: 315 PQDLPREVLTT-----------NPRRLSIIA---ESIRDG------LATWDNWKHVNCDK 354
Query: 319 -KSIAYFSLAKTDGDGYQ--YQN--IFGPLVKLEADYDKRL---KESQTQENVTVRWDVG 370
+I SL + Y+ + +F P + + V +
Sbjct: 355 LTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNK---- 410
Query: 371 LNKKSIA--------------YFSL-AKTDGDMRLMQGDELKLRYSYDASKTWSGLGHVI 415
L+K S+ Y L K + + L + + Y+ KT+ +
Sbjct: 411 LHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHR----SIVDHYNIPKTFDSDDLIP 466
Query: 416 KIPDN-FGDEVGLELKSSAGAPTEATTGFS---VDFIWKSTSFDRMQLALRKFAVDDQSV 471
D F +G LK+ E T F +DF + ++ +R + +
Sbjct: 467 PYLDQYFYSHIGHHLKNI--EHPERMTLFRMVFLDFRF-------LEQKIRHDSTAWNAS 517
Query: 472 SA-------------YI------YHRLLG------HNVDEVLFRCHLPKH-------FSA 499
+ YI Y RL+ ++E L K+ A
Sbjct: 518 GSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICS---KYTDLLRIALMA 574
Query: 500 PNLPDLNRSQVYAVKH-AIQR 519
+ ++ H +QR
Sbjct: 575 ED------EAIFEEAHKQVQR 589
Score = 46.4 bits (109), Expect = 5e-05
Identities = 93/688 (13%), Positives = 198/688 (28%), Gaps = 186/688 (27%)
Query: 237 TSAQIAKLEEVWKDNAEATFQDLEKPGVDEDPHQVLLR--YEDGYQYQN-------IFGP 287
T + +++ +A + + V + P +L + + ++ +F
Sbjct: 11 TGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWT 70
Query: 288 LVKLEADYDKRLKESQTQEN---VTVRWDVGLNKKS------IAYFSLAKTDGDGYQYQN 338
L+ + + ++ E + N + + S I D + N
Sbjct: 71 LLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYN 130
Query: 339 I--FGPLVKLEADYDKRLKESQTQENVTVRWDVGLNKKSIA------------------Y 378
+ P +KL + L E + +NV + +G K +A +
Sbjct: 131 VSRLQPYLKLR----QALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFW 186
Query: 379 FSLAKTDGDMRLMQGDELKLRYSYDASKTWSGLGHVIKIPDNFGDEVGLELKSSAGAPTE 438
+L + +++ + KL Y D + T S H I + EL+ +
Sbjct: 187 LNLKNCNSPETVLEMLQ-KLLYQIDPNWT-SRSDHSSNIKLRI-HSIQAELRRLLKSKPY 243
Query: 439 ATTGFSVDFIWKST---SFD---RMQLALRKFAVDDQSVSAYIYHRLLGHNV-----DEV 487
+ + + +F+ ++ L R V D +A H L H+ DEV
Sbjct: 244 ENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEV 303
Query: 488 --LFRCHLPKHFSAPNLPDLNRSQVYAVKHAIQRPL--SLIQGPPGTGKTVTSATIVYQL 543
L +L +LP + P S+I +++ +
Sbjct: 304 KSLLLKYL--DCRPQDLPRE------VLTTN---PRRLSII------AESIRDGLATWDN 346
Query: 544 VKQTGSPVLVCAPSNI---AVDQLTEKIHRTGLKVVRVCAKSREAIDSPVSFLALHNQIR 600
K L + I +++ L +R K+ + + P L+L
Sbjct: 347 WKHVNCDKL----TTIIESSLNVLEPAEYR---KMFDRLSVFPPSAHIPTILLSL----- 394
Query: 601 NMEMNSELKKL-LQLKEETGELSSADEKRYRMLKKNAEKSLLDNADVICCTCVGAGDPRL 659
+ + + + ++ K + SL++ P+
Sbjct: 395 ----------IWFDVIKSDVMV---------VVNKLHKYSLVE------------KQPKE 423
Query: 660 LKIKFHSILIDESMQATEPECMVPVILGAKQLILVGDHCQLGPVVMCKKAARAGLSQSLF 719
I SI ++ ++ + I+ + D L P L Q +
Sbjct: 424 STISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPY---------LDQYFY 474
Query: 720 ERLVVLGIRPFRLEVQYRMHPELSKFPSNFFYEGSLQNGVCAD----ERKLSKIDFPWPV 775
+ L+ ++ F F D E+K+ W
Sbjct: 475 SHIG------HHLK-NIEHPERMTLFRMVFL-----------DFRFLEQKIRHDSTAWNA 516
Query: 776 PDK--PML----FYVTQGQEEIAGSGTSYVNRTEASNVEKITT--RFIRCGMKPEQIGVI 827
L FY Y+ + + F+ K E+ +
Sbjct: 517 SGSILNTLQQLKFY------------KPYICDNDPKYERLVNAILDFL---PKIEENLIC 561
Query: 828 TPYEGQRAFLVQ-HMQYQGSLPAKIYQE 854
+ Y L++ + + I++E
Sbjct: 562 SKY----TDLLRIALMAEDE---AIFEE 582
>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase;
1.90A {Tomato mosaic virus}
Length = 446
Score = 61.7 bits (149), Expect = 5e-10
Identities = 40/313 (12%), Positives = 88/313 (28%), Gaps = 69/313 (22%)
Query: 622 SSADEKRYRMLKKNAEKSLLDNADVICCTCVGAGDPRLLKIKFHSILIDE-SMQATEPEC 680
+A+ R R + +V + + +F + IDE M T
Sbjct: 195 QAAEMIRRRANASGIIVA--TKDNVRTVDSFLMNYGKGARCQFKRLFIDEGLMLHTGCVN 252
Query: 681 MVPVILGAKQLILVGDHCQLGPVVMCKKAARAGLSQSLFERLVVLGIRPFRLEVQYRMHP 740
+ + + GD Q+ + + F +L V + R
Sbjct: 253 FLVEMSLCDIAYVYGDTQQIPYINRVT----GFPYPAHFAKLEVDEV--ETRRTTLRCPA 306
Query: 741 ELSKFPSNFFYEGSLQNGVCADERKLSKIDFPWPVPDKPMLFYVTQGQEEIAGSGTSYVN 800
+++ F + + + ++++ +S+
Sbjct: 307 DVTHFLNQRYEGHVMCTS--SEKKSVSQEMVSGAA------------------------- 339
Query: 801 RTEASNVEKITTRFIRCGMKPEQIGVITPYEGQRAFLVQHMQYQGSLPAKIYQEIEVASV 860
I KP + ++T + + L+ +V +V
Sbjct: 340 -------------SINPVSKPLKGKILTFTQSDKEALLSRGY------------ADVHTV 374
Query: 861 DAFQGREKDLIIMSCVRSNDHQGIGFLNDPRRLNVALTRAKYGII---VIGNP---KVLS 914
QG + VR D + V+L+R + V+ +P +
Sbjct: 375 HEVQGETYADVS--LVRLTPTPVSIIARDSPHVLVSLSRHTKSLKYYTVVMDPLVSIIRD 432
Query: 915 KQPLWNNLLNFYK 927
+ + + LL+ YK
Sbjct: 433 LERVSSYLLDMYK 445
Score = 45.6 bits (107), Expect = 7e-05
Identities = 17/82 (20%), Positives = 27/82 (32%), Gaps = 6/82 (7%)
Query: 497 FSAPNLPDLNRSQVYAVKHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAP 556
L L R H + L+ G PG GKT + V L+ P
Sbjct: 139 SDMAKLRTLRRLLKDGEPHVSSAKVVLVDGVPGCGKT----KEILSRVNF--EEDLILVP 192
Query: 557 SNIAVDQLTEKIHRTGLKVVRV 578
A + + + + +G+ V
Sbjct: 193 GRQAAEMIRRRANASGIIVATK 214
>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain,
PIN-tower interface, coupling hydrolysis to DNA
unwinding, ssDNA; 3.30A {Enterobacteria phage T4}
Length = 459
Score = 60.0 bits (145), Expect = 2e-09
Identities = 45/273 (16%), Positives = 80/273 (29%), Gaps = 100/273 (36%)
Query: 482 HNVDEVLFRCHLPKHFSAPNLPDLNRSQVYAVKHAIQ-----RPLSLIQGPPGTGKTVTS 536
H+ ++ R S DL Q A ++ + I GP GTG T +
Sbjct: 9 HHSSGLVPR------GSHMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLT 62
Query: 537 ATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHRTGLKVVRVCAKSREAIDSPVSFLALH 596
I+ L+ + +++ AP++ A L++ +G + A + +H
Sbjct: 63 KFIIEALISTGETGIILAAPTHAAKKILSKL---SGKE-----AST------------IH 102
Query: 597 NQIRNMEMNSELKKLLQLKEETGELSSADEKRYRMLKKNAEKSLLDNADVICCTCVGAGD 656
+L++ T E + E++ E L V+
Sbjct: 103 -------------SILKINPVTYEENVLFEQK--------EVPDLAKCRVL--------- 132
Query: 657 PRLLKIKFHSILIDE-SM----------QATEPECMVPVILGAKQLILVGDHCQLGPVVM 705
+ DE SM P C +I +GD+ Q+ PV
Sbjct: 133 -----------ICDEVSMYDRKLFKILLSTIPPWC---------TIIGIGDNKQIRPV-- 170
Query: 706 CKKAARAGLSQSLFERLVVLGIRP-FRLEVQYR 737
G + + L R
Sbjct: 171 -----DPGENTAYISPFFTHKDFYQCELTEVKR 198
>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 = 53.5 bits (128), Expect = 4e-07
Identities = 98/640 (15%), Positives = 153/640 (23%), Gaps = 263/640 (41%)
Query: 212 IADRSFL--------SWLVKVPTEQ----EQQRGRQVTSAQIAKLEEVWKDN-----AE- 253
+ R LV PT Q + Q E D+ AE
Sbjct: 4 YSTRPLTLSHGSLEHVLLV--PTASFFIASQLQ-EQFNKILPEPTEGFAADDEPTTPAEL 60
Query: 254 -ATF----QDLEKPGVDEDPHQVLL----RYEDGY-QYQNIFGPLVKLEADYDKRLKESQ 303
F L +P QVL +E+ Y + +I KL + D L +++
Sbjct: 61 VGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTK 120
Query: 304 TQENVTVRWDVGLNKKSIAYFSLAKTDGDGYQYQNIFGPLVKLEADYDKRLKESQTQENV 363
++ Y + P K S
Sbjct: 121 E----LIK----------NYITARIMAKR---------PFDKKS--------NS------ 143
Query: 364 TVRWDVGLNKKSIAYFSLAKTDGDMRLM-----QG------DELKLRY-SYDASKTWSGL 411
A F +G+ +L+ QG +EL+ Y +Y
Sbjct: 144 -------------ALFRAVG-EGNAQLVAIFGGQGNTDDYFEELRDLYQTY--------- 180
Query: 412 GHVIKIPDNFGDEVGLELKSSAGAPTEATTGFSVDFIWKSTSFDRMQLALRKFAVDDQSV 471
D I L +
Sbjct: 181 -----------------------------HVLVGDLI------KFSAETLSELIRTTLDA 205
Query: 472 SAYIYHRLLGHNVDEVLFRCHLPKHFSAPNLPDLNRSQVYAVKHAIQRPLSLIQGPPGTG 531
G N+ E L P + P+ L P+S P G
Sbjct: 206 EKVFTQ---GLNILEWL---ENPS--NTPDKDYLLSI-----------PISC----PLIG 242
Query: 532 KTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKI-----HRTGLKVVRVCAKSREAI 586
V QL V+ +L + H GL A++
Sbjct: 243 --------VIQLA----HYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAET---- 286
Query: 587 DSPVSFLAL---------------HNQIRNMEMNSELKKLLQLKEETGE-LSSADEKRYR 630
DS SF + N + + L+ E E + S
Sbjct: 287 DSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSI---LEDSLENNEGVPSP------ 337
Query: 631 MLKKNAEKSLLDNADVICCTCVGAGDPRLLKIKFHSILIDESMQATEPECMVPVIL--GA 688
ML + ++ ++++ V + L GA
Sbjct: 338 ML-----------------SISNLTQEQVQD------YVNKTNSHLPAGKQVEISLVNGA 374
Query: 689 KQLILVGDHCQLGPVVM--CKKAARAGLSQS--LF-ERLVVLGIR------PFRLEVQYR 737
K L++ G L + + K A +GL QS F ER + R PF
Sbjct: 375 KNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPF------- 427
Query: 738 MHPELSKFPSNFFYEGSLQNGVCADERKLSKIDFPWPVPD 777
H S + + D L K + + D
Sbjct: 428 -H---SH------LLVPASDLINKD---LVKNNVSFNAKD 454
Score = 49.3 bits (117), Expect = 6e-06
Identities = 82/520 (15%), Positives = 145/520 (27%), Gaps = 198/520 (38%)
Query: 519 RPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHRTGLKVVRV 578
RPL+L G ++ + L LV S QL E+ ++ +
Sbjct: 7 RPLTLSHG-----------SLEHVL--------LVPTASFFIASQLQEQFNKILPEPTEG 47
Query: 579 CAKSREAIDSPVSFLALHNQIRNMEMNSELKKLLQL---KEETGELSSADEKRYRMLK-- 633
A E +P + K L E ++ D+ +L
Sbjct: 48 FAADDEPT-TPAELVG---------------KFLGYVSSLVEPSKVGQFDQ----VLNLC 87
Query: 634 -KNAEKSLLDNADVICCTCVGAGDPRLLKIKFHSILIDESMQATEPECMVPVILGAKQLI 692
E L+ D+ H++ A + ++ K+LI
Sbjct: 88 LTEFENCYLEGNDI------------------HALA------AKLLQENDTTLVKTKELI 123
Query: 693 ---LVGDHCQLGPVVMCK-----KAARAGLSQSLFERLVVLG-----IRPFRLEVQ--YR 737
+ P +A G + L + G F E++ Y+
Sbjct: 124 KNYITARIMAKRPFDKKSNSALFRAVGEG-NAQLV---AIFGGQGNTDDYFE-ELRDLYQ 178
Query: 738 MHPELSKFPSNFFYEGS--LQNGVCADERKLSKIDFP-------W-----PVPDKPML-- 781
+ + + L + K+ F W PDK L
Sbjct: 179 TYHV---LVGDLIKFSAETLSE-LIRTTLDAEKV-FTQGLNILEWLENPSNTPDKDYLLS 233
Query: 782 ---------------FYVT---QGQ--EEIAG--SGTSYVNR------------TEAS-- 805
+ VT G E+ G + ++ + S
Sbjct: 234 IPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFF 293
Query: 806 -NVEK-ITTRFIRCGMKPEQIGVITPYEGQRAFLVQHMQYQGSLPAKIYQEIEVASVD-- 861
+V K IT F IGV A+ SLP I ++ S++
Sbjct: 294 VSVRKAITVLF--------FIGV----RCYEAYPNT------SLPPSILED----SLENN 331
Query: 862 --------AFQGREKDLIIMSCVRSNDHQGIGFLNDPRRLNVALTRAKYGIIVIGNPKVL 913
+ ++ + ++N H L +++ ++L ++V G P+ L
Sbjct: 332 EGVPSPMLSISNLTQEQVQDYVNKTNSH-----LPAGKQVEISLVNGAKNLVVSGPPQSL 386
Query: 914 SKQPLWNNLLNFYKEQKVLVEGPLNNLKESLILFS--KPK 951
L L +K + L +S I FS K K
Sbjct: 387 --YGLNLTL------RKAKAP---SGLDQSRIPFSERKLK 415
Score = 44.7 bits (105), Expect = 2e-04
Identities = 102/644 (15%), Positives = 189/644 (29%), Gaps = 218/644 (33%)
Query: 3 VDAYGPSSQTLTFLDTEETDLIGGDTQGSEFDFTDFTLPSQSQTQASQL-DSVNQIQVNG 61
+DAY S++ LT + GS + +P+ S ASQL + N+I
Sbjct: 1 MDAY--STRPLTL------------SHGS-LEHV-LLVPTASFFIASQLQEQFNKILPEP 44
Query: 62 KQNL--DN---SNLNLVSQKLHELQFEEEEDDG-----------NEF---F--NKELPPH 100
+ D+ + LV + L + E EF + ++ H
Sbjct: 45 TEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDI--H 102
Query: 101 --ACKYCGIHDPAYVIMCNICKKWFCNGRGHTSGSHIINHLVRAKHKEVTLHKDGPLGET 158
A K +D V + K + + + K L + G
Sbjct: 103 ALAAKLLQENDTTLVKTKELIKNYI-------TARIMAKRPFDKKSNS-ALFRAVGEGNA 154
Query: 159 VLECYTCGVRNIFVLGFIPAKADSVVVLLCRTPCAAQ-NS---LKDMNWDQEQWK---PL 211
L IF G Q N+ +++ ++ ++ L
Sbjct: 155 QL--VA-----IF--G-------------------GQGNTDDYFEEL---RDLYQTYHVL 183
Query: 212 IAD-----RSFLSWLVKVPTEQEQ--QRGRQVTSAQIAKLEEVWKDNAEATFQDLEKPGV 264
+ D LS L++ + E+ +G + W +N T P
Sbjct: 184 VGDLIKFSAETLSELIRTTLDAEKVFTQGLNILE---------WLENPSNT------PDK 228
Query: 265 DEDPHQVLLRYEDGYQYQNIFGPLVKLE--ADYD---KRLKESQTQENVTVRWDVGLNKK 319
D LL I PL+ + A Y K L + + ++ G ++
Sbjct: 229 D-----YLLSIP-------ISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQG 276
Query: 320 SI--AYFSLAKTDGD---------------GYQYQNIFGPLVKLEADYDKRLKESQTQEN 362
+ + + G + + P L L++S
Sbjct: 277 LVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAY-PNTSLPPSI---LEDSLENNE 332
Query: 363 ------VTVRWDVGLNKKSI----------------AYFSLAKTD------GDMRLMQGD 394
+++ L ++ + SL G + + G
Sbjct: 333 GVPSPMLSIS---NLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGL 389
Query: 395 ELKLRYSYDASKTWSGLGHVIKIPDNFGDEVGLELKSSA-----GAP------TEATTGF 443
L LR +K SGL +IP F + +LK S +P A+
Sbjct: 390 NLTLR----KAKAPSGLDQS-RIP--FSER---KLKFSNRFLPVASPFHSHLLVPASDLI 439
Query: 444 SVDFIWKSTSFDRMQLALRKFAVDD----QSVSAYIYHRLLGHNVDEVL-FRCHLPK--H 496
+ D + + SF+ + + + D + +S I R+ VD ++
Sbjct: 440 NKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERI----VDCIIRLPVKWETTTQ 495
Query: 497 FSAPNLPDLNRSQVYAVKHAIQRPLSLIQGPPGTG-KTVTSATI 539
F A ++ D + R GTG + + + T+
Sbjct: 496 FKATHILDFGPGGASGLGVLTHRNKD------GTGVRVIVAGTL 533
Score = 43.5 bits (102), Expect = 4e-04
Identities = 57/315 (18%), Positives = 96/315 (30%), Gaps = 134/315 (42%)
Query: 391 MQGDELKLRYSYDASKT----W--------SGLGHVIK--IPDN-------FGDEVGLEL 429
M G +L Y SK W G I + +N FG E G +
Sbjct: 1631 M-GMDL-----YKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRI 1684
Query: 430 K---------SSAGAPTEATTGF------SVDFIWKS-------TSFDRMQLALRKFAVD 467
+ + + F S + ++S T F Q AL +
Sbjct: 1685 RENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQF--TQPAL--TLM- 1739
Query: 468 DQSVSAYIYHRLL-------------GHNVDEVLFRCHLPKHFSAP-------NLPDLNR 507
+A+ L GH++ E ++A ++ L
Sbjct: 1740 --EKAAF---EDLKSKGLIPADATFAGHSLGE----------YAALASLADVMSIESL-- 1782
Query: 508 SQVYAVKHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCA--PSNI------ 559
V V R G T+ A + S + A P +
Sbjct: 1783 --VEVVF---YR-----------GMTMQVAV---PRDELGRSNYGMIAINPGRVAASFSQ 1823
Query: 560 -AVDQLTEKI-HRTGLKVVR-----------VCAKSREAIDSPVSFLALHNQIRNMEMNS 606
A+ + E++ RTG +V V A A+D+ + L +++ +++
Sbjct: 1824 EALQYVVERVGKRTG-WLVEIVNYNVENQQYVAAGDLRALDTVTNVLN-FIKLQKIDI-I 1880
Query: 607 ELKKLLQLKEETGEL 621
EL+K L L+E G L
Sbjct: 1881 ELQKSLSLEEVEGHL 1895
Score = 35.8 bits (82), Expect = 0.096
Identities = 27/120 (22%), Positives = 41/120 (34%), Gaps = 25/120 (20%)
Query: 833 QRAFLVQHMQYQGSLPAKIYQEIEV--ASVDAFQGREKDLIIMSCVRSNDHQGIGFL--- 887
R +Q + L Y I + V A +E + R G +
Sbjct: 1788 YRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYV--VERVGKRTG-WLVEIV 1844
Query: 888 NDPRRLNVALTRAKYGIIVI-GNPKVLSKQPLWNNLLNFYKEQKVLVEGPLNNLKESLIL 946
N NV V G+ + L + N+LNF K QK+ + L++SL L
Sbjct: 1845 NY----NVE-----NQQYVAAGDLRALDT--V-TNVLNFIKLQKI----DIIELQKSLSL 1888
Score = 30.8 bits (69), Expect = 2.6
Identities = 23/140 (16%), Positives = 41/140 (29%), Gaps = 44/140 (31%)
Query: 136 INHLVRAKHKEVTLHKDGPLGETVLECYTCGVRNIFVLGFIPAKADSVVVLLCRTPCAAQ 195
I +V +T+H G G+ + E Y+ + V G + + +
Sbjct: 1661 ILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTE---------KIFKEIN 1711
Query: 196 NSLKDMNWDQEQWKPLIADRSFLSWLVKVPTEQEQQRGRQVTSAQIA-KLEEVWKDNAEA 254
+ +++ LS T+ Q A L E A
Sbjct: 1712 EHSTSYTFR--------SEKGLLS-----ATQ----------FTQPALTLMEK------A 1742
Query: 255 TFQDLEKPGVDEDP-----H 269
F+DL+ G+ H
Sbjct: 1743 AFEDLKSKGLIPADATFAGH 1762
Score = 30.8 bits (69), Expect = 2.8
Identities = 26/131 (19%), Positives = 35/131 (26%), Gaps = 54/131 (41%)
Query: 844 QGSLPAKIYQEIEVASVDAFQGREKDLIIMSCV------RSNDHQGIGFLNDPRRLNVAL 897
QGS QE QG DL S R+++H
Sbjct: 1624 QGS------QE---------QGMGMDLYKTSKAAQDVWNRADNH---------------- 1652
Query: 898 TRAKYGI----IVIGNPKVL-------SKQPLWNNLLNF----YKEQKVLVEGPLNNLKE 942
+ YG IVI NP L + + N + K+ E + E
Sbjct: 1653 FKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINE 1712
Query: 943 SL--ILFSKPK 951
F K
Sbjct: 1713 HSTSYTFRSEK 1723
>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.70A {Anas platyrhynchos}
Length = 936
Score = 43.0 bits (100), Expect = 4e-04
Identities = 17/90 (18%), Positives = 26/90 (28%), Gaps = 5/90 (5%)
Query: 495 KHFSAPNLPDLNRSQVYAVKHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQ----TGSP 550
K Q+ + AI +LI P G+GKT S I + +
Sbjct: 239 KPPPVYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAK 298
Query: 551 VLVCAPSNIAVDQLTEKIHR-TGLKVVRVC 579
V+ A +Q + V
Sbjct: 299 VVFLATKVPVYEQQKNVFKHHFERQGYSVQ 328
>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein;
HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19
c.37.1.19 PDB: 2fzl_A*
Length = 472
Score = 42.9 bits (101), Expect = 5e-04
Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 4/68 (5%)
Query: 509 QVYAVKHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKI 568
Q A++ + I P G+GKT + + +L +P L+ P+ +Q E++
Sbjct: 98 QEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL----STPTLIVVPTLALAEQWKERL 153
Query: 569 HRTGLKVV 576
G + V
Sbjct: 154 GIFGEEYV 161
>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.40A {Anas platyrhynchos}
Length = 797
Score = 42.7 bits (99), Expect = 7e-04
Identities = 17/90 (18%), Positives = 26/90 (28%), Gaps = 5/90 (5%)
Query: 495 KHFSAPNLPDLNRSQVYAVKHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQT----GSP 550
K Q+ + AI +LI P G+GKT S I + +
Sbjct: 239 KPPPVYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAK 298
Query: 551 VLVCAPSNIAVDQLTEKIHR-TGLKVVRVC 579
V+ A +Q + V
Sbjct: 299 VVFLATKVPVYEQQKNVFKHHFERQGYSVQ 328
>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition
domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus
fulgidus} SCOP: c.37.1.19
Length = 237
Score = 38.9 bits (91), Expect = 0.004
Identities = 14/60 (23%), Positives = 27/60 (45%), Gaps = 4/60 (6%)
Query: 509 QVYAVKHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKI 568
Q A++ + I P G+GKT + + +L +P L+ P+ +Q E++
Sbjct: 98 QEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL----STPTLIVVPTLALAEQWKERL 153
>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP;
2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB:
3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A*
3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*
Length = 525
Score = 38.4 bits (89), Expect = 0.013
Identities = 12/97 (12%), Positives = 36/97 (37%), Gaps = 1/97 (1%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHRTGLKVVRVCAKS 582
L+ G GTGKT+ S +Y + + P + + + G + ++ +
Sbjct: 43 LVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEE-TPQDIIKNARSFGWDLAKLVDEG 101
Query: 583 REAIDSPVSFLALHNQIRNMEMNSELKKLLQLKEETG 619
+ I + ++++ ++++ ++
Sbjct: 102 KLFILDASPDPEGQEVVGGFDLSALIERINYAIQKYR 138
Score = 35.3 bits (81), Expect = 0.11
Identities = 13/64 (20%), Positives = 23/64 (35%), Gaps = 2/64 (3%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHRTGLKVVRVCAKS 582
L G GTGKT+ + V ++ A + QL + G+ + ++
Sbjct: 285 LATGATGTGKTLLVSRFVENACAN-KERAILFAYEE-SRAQLLRNAYSWGMDFEEMERQN 342
Query: 583 REAI 586
I
Sbjct: 343 LLKI 346
>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP,
translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A
Length = 504
Score = 38.0 bits (89), Expect = 0.014
Identities = 14/60 (23%), Positives = 23/60 (38%), Gaps = 15/60 (25%)
Query: 518 QRPLSLIQGPP---------GTGKTVTSATIVYQLVKQTGSPVLVCA----PSNIAVDQL 564
+ + +G G+GKT T + + Y ++ L+CA A DQL
Sbjct: 91 VKAWTPTKGKQNVIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLICADTFRAG--AFDQL 148
>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A
{Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB:
1j8y_F
Length = 297
Score = 37.5 bits (88), Expect = 0.016
Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 15/60 (25%)
Query: 518 QRPLSLIQGPP---------GTGKTVTSATIVYQLVKQTGSPVLVCA----PSNIAVDQL 564
+ P + P GTGKT T+ + Y K+ LV A P+ A++QL
Sbjct: 88 KEPKVIPDKIPYVIMLVGVQGTGKTTTAGKLAYFYKKKGFKVGLVGADVYRPA--ALEQL 145
>2ehv_A Hypothetical protein PH0186; KAIC, RECA ATPase, unknown function;
HET: ADP; 2.07A {Pyrococcus horikoshii} PDB: 2zts_A*
Length = 251
Score = 37.2 bits (86), Expect = 0.017
Identities = 17/88 (19%), Positives = 31/88 (35%), Gaps = 1/88 (1%)
Query: 521 LSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHRTGLKVVRVCA 580
L+ G GTGKT +A +Y+ ++ G P + L ++ G +
Sbjct: 32 TVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVTLEE-RARDLRREMASFGWDFEKYEK 90
Query: 581 KSREAIDSPVSFLALHNQIRNMEMNSEL 608
+ + AI VS + +
Sbjct: 91 EGKIAIVDGVSSVVGLPSEEKFVLEDRF 118
>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding,
signal recognition particle, GTP-binding, RNA-binding;
2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B
Length = 432
Score = 37.5 bits (88), Expect = 0.019
Identities = 16/60 (26%), Positives = 25/60 (41%), Gaps = 15/60 (25%)
Query: 518 QRPLSLIQGPP---------GTGKTVTSATIVYQLVKQTGSPVLVCA----PSNIAVDQL 564
+ L L G+GKT T+A + + K+ P L+ A P+ A +QL
Sbjct: 89 AKKLELNPKKQNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAADTYRPA--AYEQL 146
>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}
Length = 540
Score = 37.6 bits (87), Expect = 0.019
Identities = 35/175 (20%), Positives = 58/175 (33%), Gaps = 24/175 (13%)
Query: 512 AVKHAIQ-RPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHR 570
+A++ L+ PG GKTV L Q VL+ ++ +D + +
Sbjct: 18 EAINALKHGKTLLLNAKPGLGKTVFVE----VLGMQLKKKVLIFTRTHSQLDSIYKNAKL 73
Query: 571 TGLKVVRVCAKSREAIDSPVSFLALHNQIRNMEMNSELKKLLQLKEETGELSSADEKR-- 628
GLK + KS I + + ++K + + D
Sbjct: 74 LGLKTGFLIGKSASCIYAQGDEEPDEINCSKCRLKDKIKTIEDKEPSKLIEEFKDAVDYC 133
Query: 629 -YRMLKKNAEKSLLDNADVICCT-----------CVGAGDPRLLKIKFHSILIDE 671
Y L+ L + DVI T V LK++ + I+IDE
Sbjct: 134 PYYSLRA-----NLKDKDVIAMTYPYLFQKPIRNSVFCNKDDCLKLEDYLIVIDE 183
>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*
Length = 556
Score = 36.8 bits (84), Expect = 0.031
Identities = 17/86 (19%), Positives = 26/86 (30%), Gaps = 5/86 (5%)
Query: 499 APNLPDLNRSQVYAVKHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQ----TGSPVLVC 554
A Q+ + AI +LI P G+GKT S I + + V+
Sbjct: 2 AMETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFL 61
Query: 555 APSNIAVDQLTEKIHR-TGLKVVRVC 579
A +Q + V
Sbjct: 62 ATKVPVYEQQKNVFKHHFERQGYSVQ 87
>3ec2_A DNA replication protein DNAC; helicase loader, replication
initiation factor, ATP-binding, nucleotide-binding; HET:
DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*
Length = 180
Score = 35.8 bits (83), Expect = 0.032
Identities = 10/49 (20%), Positives = 18/49 (36%), Gaps = 1/49 (2%)
Query: 505 LNRSQVYAVKHAIQRPLSLI-QGPPGTGKTVTSATIVYQLVKQTGSPVL 552
L +V+ + L G PG GKT + + + ++ G
Sbjct: 23 LLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGY 71
>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}
Length = 235
Score = 36.1 bits (84), Expect = 0.033
Identities = 18/100 (18%), Positives = 39/100 (39%), Gaps = 2/100 (2%)
Query: 521 LSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHRTGLKVVRVCA 580
+ G PGTGKT+ S + + ++ G P + + D + + +
Sbjct: 25 FIALTGEPGTGKTIFSLHFIAKGLRD-GDPCIYVTTE-ESRDSIIRQAKQFNWDFEEYIE 82
Query: 581 KSREAIDSPVSFLALHNQIRNMEMNSELKKLLQLKEETGE 620
K ID+ + + N+ + K+++ K++ G
Sbjct: 83 KKLIIIDALMKEKEDQWSLVNLTPEELVNKVIEAKQKLGY 122
>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition
particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A
{Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A
Length = 433
Score = 36.4 bits (85), Expect = 0.038
Identities = 17/60 (28%), Positives = 23/60 (38%), Gaps = 15/60 (25%)
Query: 518 QRPLSLIQGPP---------GTGKTVTSATIVYQLVKQTGSPVLVCA----PSNIAVDQL 564
+ P P G+GKT T+ + Y K+ LV A P+ A DQL
Sbjct: 87 KEPNVNPTKLPFIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVAADVYRPA--AYDQL 144
>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H
RNA-binding helicase, innate immunity, IFIH1, S
genomics; 1.60A {Homo sapiens}
Length = 216
Score = 35.6 bits (82), Expect = 0.045
Identities = 20/94 (21%), Positives = 35/94 (37%), Gaps = 6/94 (6%)
Query: 492 HLPKHFSAPNLPDLNRSQVYAVKHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQ----- 546
++ S L Q+ + A++ +I P G+GKT + I + +
Sbjct: 21 NVAARASPEPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKAS 80
Query: 547 TGSPVLVCAPSNIAVDQLTEKIHR-TGLKVVRVC 579
V+V + V+QL K + K RV
Sbjct: 81 EPGKVIVLVNKVLLVEQLFRKEFQPFLKKWYRVI 114
>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase,
nucleotide excision repair,; 2.20A {Thermoplasma
acidophilum} PDB: 2vsf_A*
Length = 620
Score = 36.2 bits (84), Expect = 0.055
Identities = 13/76 (17%), Positives = 33/76 (43%), Gaps = 3/76 (3%)
Query: 512 AVKHAIQ-RPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHR 570
++ ++Q ++ P G+GKT+ + Q + VL +N +Q+ +++
Sbjct: 14 FLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSERKLKVLYLVRTNSQEEQVIKELRS 73
Query: 571 T--GLKVVRVCAKSRE 584
+K+ + + R
Sbjct: 74 LSSTMKIRAIPMQGRV 89
>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription
factor, RNA polymerase recycling, activator,
ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}
Length = 968
Score = 35.8 bits (82), Expect = 0.088
Identities = 29/150 (19%), Positives = 54/150 (36%), Gaps = 20/150 (13%)
Query: 509 QVYAVKHAIQRPLS--LIQGPPGTGKTVTSATIVYQLVKQT-GSPVLVCAPSNIAVDQ-L 564
Q+ +R L+ G GKT+ + I++Q + VL+ P + Q L
Sbjct: 158 QLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPETL-QHQWL 216
Query: 565 TEKIHRTGLKVVRVCAKSREAI--DSPVSFLALHNQIRNMEM-NSELKKLLQLKEETGEL 621
E + R L+ + D+ F I +++ ++L L E +L
Sbjct: 217 VEMLRRFNLRFALFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDL 276
Query: 622 SSADE------------KRYRMLKKNAEKS 639
DE + Y+ +++ AE
Sbjct: 277 LVVDEAHHLVWSEDAPSREYQAIEQLAEHV 306
>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA
sliding clamp, AAA+ at polymerase, DNA-binding protein;
HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP:
a.80.1.1 c.37.1.20
Length = 516
Score = 35.2 bits (81), Expect = 0.093
Identities = 10/30 (33%), Positives = 17/30 (56%), Gaps = 4/30 (13%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVL 552
++ GPPG GKT T + + ++ G +L
Sbjct: 81 MLYGPPGIGKT----TAAHLVAQELGYDIL 106
>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1;
winged-helix domain, helix-turn-helix, AAA+ ATPase
domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A
{Sulfolobus solfataricus}
Length = 386
Score = 35.0 bits (80), Expect = 0.11
Identities = 9/32 (28%), Positives = 13/32 (40%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVLVC 554
I G GTGKT ++ +L K+
Sbjct: 49 FIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHV 80
>2qgz_A Helicase loader, putative primosome component; structural genomics,
PSI-2, protein structure initiative; 2.40A
{Streptococcus pyogenes serotype M3}
Length = 308
Score = 34.8 bits (80), Expect = 0.12
Identities = 7/49 (14%), Positives = 17/49 (34%), Gaps = 5/49 (10%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHRT 571
+ G G GK+ A + ++L ++ G + + +
Sbjct: 156 YLYGDMGIGKSYLLAAMAHELSEKKGVSTTL-----LHFPSFAIDVKNA 199
>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate
immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*
Length = 696
Score = 35.0 bits (79), Expect = 0.14
Identities = 16/76 (21%), Positives = 26/76 (34%), Gaps = 5/76 (6%)
Query: 509 QVYAVKHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSP----VLVCAPSNIAVDQL 564
Q+ A++ ++I P G GKT S I +K+ V+ A +Q
Sbjct: 18 QLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQN 77
Query: 565 TEKIHR-TGLKVVRVC 579
+ RV
Sbjct: 78 KSVFSKYFERHGYRVT 93
>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA
repair, DNA recombina hydrolase; 2.90A {Pyrococcus
furiosus} SCOP: c.37.1.19 c.37.1.19
Length = 494
Score = 34.4 bits (78), Expect = 0.18
Identities = 19/72 (26%), Positives = 28/72 (38%), Gaps = 2/72 (2%)
Query: 509 QVYAVKHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKI 568
Q + LI P G GKT+ + I + + G VL+ AP+ V Q E
Sbjct: 14 QEVIYAKCKETN-CLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAESF 72
Query: 569 HR-TGLKVVRVC 579
R L ++
Sbjct: 73 RRLFNLPPEKIV 84
>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate
hydrolases fold, S genomics, joint center for structural
genomics, JCSG; HET: MSE; 1.70A {Chloroflexus
aurantiacus}
Length = 193
Score = 33.4 bits (76), Expect = 0.21
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 5/38 (13%)
Query: 516 AIQRP-LSLIQGPPGTGKTVTSATIVYQLVKQTGSPVL 552
+Q P L ++ G P TGKT T+ L P+L
Sbjct: 1 GMQTPALIIVTGHPATGKT----TLSQALATGLRLPLL 34
>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer,
structural genomics; HET: ADP; 2.00A {Pyrococcus
horikoshii}
Length = 247
Score = 33.5 bits (77), Expect = 0.22
Identities = 12/32 (37%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 521 LSLIQGPPGTGKTVTSATIVYQLVKQTGSPVL 552
+ L+ G PGTGKT+ S ++ +K G P +
Sbjct: 25 VVLLSGGPGTGKTIFSQQFLWNGLKM-GEPGI 55
>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA
helicase, acetyltransferase, GCN5 acetyltransferase;
HET: ACO ADP; 2.35A {Escherichia coli K12}
Length = 671
Score = 34.2 bits (78), Expect = 0.22
Identities = 15/80 (18%), Positives = 29/80 (36%), Gaps = 6/80 (7%)
Query: 494 PKHFSAPNLPDLNRSQVYAVKHAIQRP--LSLIQGPPGTGKTVTSATIVYQLVKQTGSPV 551
P+ P Q +K + P ++ + G GK+ + QL+ +
Sbjct: 165 PRTDWYPATGAPQPEQQQLLKQLMTMPPGVAAVTAARGRGKS----ALAGQLISRIAGRA 220
Query: 552 LVCAPSNIAVDQLTEKIHRT 571
+V AP+ + D L +
Sbjct: 221 IVTAPAKASTDVLAQFAGEK 240
>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase,
protein-targeting, transport protein; HET: GDP; 1.97A
{Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*
Length = 328
Score = 33.8 bits (78), Expect = 0.24
Identities = 30/106 (28%), Positives = 43/106 (40%), Gaps = 33/106 (31%)
Query: 529 GTGKTVTSATIVYQLVKQTGSPVLVCAPSNI---AVDQLTEKIHRTGLKVVR-------- 577
G+GKT T A + L K G V++ A A++QL E R G+KV++
Sbjct: 139 GSGKTTTIAKLANWL-KNHGFSVVIAASDTFRAGAIEQLEEHAKRIGVKVIKHSYGADPA 197
Query: 578 -VC------AKSREA----IDSPVSFLA--LHNQIRNMEMNSELKK 610
V AK+R ID+ A M+ E+KK
Sbjct: 198 AVAYDAIQHAKARGIDVVLIDT-----AGRSETNRNLMD---EMKK 235
>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain,
ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus}
SCOP: c.37.1.20 PDB: 1nsf_A*
Length = 272
Score = 33.6 bits (77), Expect = 0.26
Identities = 24/101 (23%), Positives = 44/101 (43%), Gaps = 24/101 (23%)
Query: 464 FAVDDQSVSAYIYHRL--LGHNVDEVLFRCHLPKHFSAPNLPDLNRSQVYAVKHAIQRPL 521
F + + ++YI + + G V VL L V K++ + PL
Sbjct: 20 FGTNQEDYASYIMNGIIKWGDPVTRVLDDGELL---------------VQQTKNSDRTPL 64
Query: 522 S--LIQGPPGTGKTVTSATIVYQLVKQTGSP-VLVCAPSNI 559
L++GPP +GKT +A I +++ P + +C+P +
Sbjct: 65 VSVLLEGPPHSGKTALAAKI----AEESNFPFIKICSPDKM 101
>3h1t_A Type I site-specific restriction-modification system, R
(restriction) subunit; hydrolase, restriction enzyme
HSDR, ATP-binding; 2.30A {Vibrio vulnificus}
Length = 590
Score = 34.0 bits (78), Expect = 0.28
Identities = 12/52 (23%), Positives = 20/52 (38%), Gaps = 2/52 (3%)
Query: 510 VYAVKHAIQ--RPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNI 559
+ ++ + SLI GTGKTV + I ++L + I
Sbjct: 187 INRAVQSVLQGKKRSLITMATGTGKTVVAFQISWKLWSARWNRTGDYRKPRI 238
>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal
recognition particle, SRP-GTPase, protein targeting,
cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus
furiosus}
Length = 443
Score = 33.7 bits (78), Expect = 0.31
Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 14/59 (23%)
Query: 518 QRPLSLIQGPP--------GTGKTVTSATIVYQLVKQTGSPVLVCA----PSNIAVDQL 564
+P+ + + P G+GKT T A + K+ +VC+ P A QL
Sbjct: 91 AKPIEIKEKPTILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVCSDTWRPG--AYHQL 147
>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS
protein structure initiative, PSI, joint center for
structu genomics; HET: CIT; 1.60A {Thermotoga maritima}
SCOP: a.24.13.1 c.37.1.10
Length = 306
Score = 33.3 bits (77), Expect = 0.34
Identities = 29/112 (25%), Positives = 43/112 (38%), Gaps = 33/112 (29%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNI---AVDQLTEKIHRTGLKVVR-- 577
++ G GTGKT + + V + G V++ A A++QL R G V+
Sbjct: 108 MVVGVNGTGKTTSCGKLAKMFVDE-GKSVVLAAADTFRAAAIEQLKIWGERVGATVISHS 166
Query: 578 -------VC------AKSREA----IDSPVSFLA--LHNQIRNMEMNSELKK 610
V A +R ID+ A LH + ME EL+K
Sbjct: 167 EGADPAAVAFDAVAHALARNKDVVIIDT-----AGRLHTKKNLME---ELRK 210
>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein
transport, biosynthetic protein; HET: GNP; 3.00A
{Bacillus subtilis} PDB: 2px3_A* 3syn_A*
Length = 296
Score = 33.1 bits (76), Expect = 0.39
Identities = 17/103 (16%), Positives = 37/103 (35%), Gaps = 20/103 (19%)
Query: 526 GPPGTGKTVTSATIVYQLVKQTG-SPVLVCA----PSNIAVDQLTE--KIHRTGLKVVRV 578
G G GKT T A + + + + + AV+QL ++ + L+V
Sbjct: 112 GSTGAGKTTTLAKLAAISMLEKHKKIAFITTDTYRIA--AVEQLKTYAELLQAPLEVCYT 169
Query: 579 CAKSREAIDSPVSF---LA-----LHNQIRNMEMNSELKKLLQ 613
+ ++A + + + ++ ELK+ +
Sbjct: 170 KEEFQQAKELFSEYDHVFVDTAGRNFKDPQYID---ELKETIP 209
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 32.7 bits (74), Expect = 0.41
Identities = 10/63 (15%), Positives = 19/63 (30%), Gaps = 19/63 (30%)
Query: 83 EEEEDDGNEFFNKELPPHACKYCGIHDPAYV-------IMCNICKKWFCNGRGHTSGSHI 135
+ G N L C C ++ P V ++C +C G +
Sbjct: 9 KRAGRRGPNL-NIVL---TCPECKVYPPKIVERFSEGDVVCALC--------GLVLSDKL 56
Query: 136 INH 138
++
Sbjct: 57 VDT 59
>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial
conjugation, F1-ATPase-like quaternary structure, ring
helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB:
1e9s_A 1gki_A* 1gl7_A* 1gl6_A*
Length = 437
Score = 32.9 bits (75), Expect = 0.46
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVLV 553
L+ G GTGK+V + Y + + V+V
Sbjct: 57 LVNGATGTGKSVLLRELAYTGLLRGDRMVIV 87
>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer,
nucleotide twinning, protein complex, protein transport;
HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1
c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D
2iyl_D* 2cnw_D* 2j7p_D*
Length = 304
Score = 32.9 bits (76), Expect = 0.50
Identities = 29/112 (25%), Positives = 41/112 (36%), Gaps = 33/112 (29%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNI---AVDQLTEKIHRTGLKVVR-- 577
L+ G G GKT T A + G V+ CA QL+E R + V++
Sbjct: 106 LVVGVNGVGKTTTIAKLGRYYQNL-GKKVMFCAGDTFRAAGGTQLSEWGKRLSIPVIQGP 164
Query: 578 -------VC------AKSREA----IDSPVSFLA--LHNQIRNMEMNSELKK 610
+ K+R +D+ A LH + ME ELKK
Sbjct: 165 EGTDSAALAYDAVQAMKARGYDLLFVDT-----AGRLHTKHNLME---ELKK 208
>3bbo_W Ribosomal protein L24; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 191
Score = 32.1 bits (73), Expect = 0.57
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 7/40 (17%)
Query: 557 SNIA-VDQLTEKIHRTGLKV------VRVCAKSREAIDSP 589
SN+ + + E R G K+ VR K+ E +D+P
Sbjct: 132 SNVMLILKEQEVADRVGHKILEDVRKVRYLIKTGEIVDTP 171
>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA
translocation, nucleotide-binding, DNA-binding; 3.00A
{Bovine papillomavirus type 1} PDB: 2gxa_A*
Length = 305
Score = 32.6 bits (74), Expect = 0.59
Identities = 14/84 (16%), Positives = 28/84 (33%)
Query: 457 MQLALRKFAVDDQSVSAYIYHRLLGHNVDEVLFRCHLPKHFSAPNLPDLNRSQVYAVKHA 516
M + S+ AYI R + ++ L + +K
Sbjct: 64 MVRHYLRAETQALSMPAYIKARCKLATGEGSWKSILTFFNYQNIELITFINALKLWLKGI 123
Query: 517 IQRPLSLIQGPPGTGKTVTSATIV 540
++ GPP TGK++ +++
Sbjct: 124 PKKNCLAFIGPPNTGKSMLCNSLI 147
>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase,
ultrahigh resolution, protein transport; 1.10A {Thermus
aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B*
1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B*
2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A
1ffh_A 2ng1_A*
Length = 295
Score = 31.7 bits (73), Expect = 0.90
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 6/40 (15%)
Query: 529 GTGKTVTSATIVYQLVKQTGSPVLVCA----PSNIAVDQL 564
G+GKT T+A + + P+LV A P+ A +QL
Sbjct: 108 GSGKTTTAAKLALYYKGKGRRPLLVAADTQRPA--AREQL 145
>1ypw_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD,
CDC48; HET: ADP ANP; 3.50A {Mus musculus} PDB: 1oz4_A*
1yq0_A* 1yqi_A* 1r7r_A* 3cf2_A* 3cf1_A* 3cf3_A*
Length = 806
Score = 32.5 bits (74), Expect = 0.91
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 4/31 (12%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVLV 553
L+ GPPGTGKT I + +TG+ +
Sbjct: 242 LLYGPPGTGKT----LIARAVANETGAFFFL 268
>3igf_A ALL4481 protein; two-domained protein consisting of the N-terminal
alpha-beta the C-terminal all beta domain., structural
genomics; 2.00A {Nostoc SP}
Length = 374
Score = 32.2 bits (73), Expect = 0.93
Identities = 27/145 (18%), Positives = 47/145 (32%), Gaps = 17/145 (11%)
Query: 526 GPPGTGKTVTSATIVYQLVKQTGSPVLVC---APS-NIAVDQ-LTEKIHR--TGLKVVRV 578
G G +T + L Q G VL+ P + ++Q LT + L+VV+
Sbjct: 9 GKSGVARTKIAIAAAKLLASQ-GKRVLLAGLAEPVLPLLLEQTLTPDPQQIAPNLEVVQF 67
Query: 579 CAKSREAIDSPVSFLALHNQIRNMEMNSELKKLLQLKEETGELSSADEKRYRMLKKNAEK 638
+S ++ + + +K++ +E L D L E
Sbjct: 68 --QSSVLLERN--WEEVKKLEAQYLRTPIIKEVYG--QELVVLPGMDS--ALALNAIREY 119
Query: 639 SLLDNADVICCTCVGAGDP-RLLKI 662
D I G R+L +
Sbjct: 120 DASGKYDTIVYDGTGDAFTLRMLGL 144
>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic
subunit]; helicase, flavivirus, DEAD-BOX, ATPase,
rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP:
c.37.1.14 c.37.1.14 PDB: 1ymf_A*
Length = 440
Score = 32.1 bits (73), Expect = 1.0
Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 16/80 (20%)
Query: 518 QRPLSLIQGPPGTGKTVTSATIVYQ-LVKQ---TGSPVLVCAPSNIAVDQLTEKIHRTGL 573
+ +++ PG GKT ++ + LV AP+ + + ++ E H GL
Sbjct: 7 KGMTTVLDFHPGAGKT----RRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFH--GL 60
Query: 574 KV------VRVCAKSREAID 587
V RE ID
Sbjct: 61 DVKFHTQAFSAHGSGREVID 80
>2k16_A Transcription initiation factor TFIID subunit 3; protein,
alternative splicing, metal-binding, nucleus,
phosphoprotein, transcription regulation; NMR {Mus
musculus} PDB: 2k17_A*
Length = 75
Score = 29.4 bits (66), Expect = 1.0
Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 11/48 (22%)
Query: 83 EEEEDDGNEFFNKELPPHACKYCG-IHDPAYVIMCNICKKWF---CNG 126
++ GN+ C C D + +I C+ C W+ C G
Sbjct: 9 VIRDEWGNQ-------IWICPGCNKPDDGSPMIGCDDCDDWYHWPCVG 49
>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3;
winged-helix domain, helix-turn-helix, AAA+ ATPase
domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A
{Sulfolobus solfataricus}
Length = 384
Score = 32.0 bits (72), Expect = 1.1
Identities = 24/136 (17%), Positives = 50/136 (36%), Gaps = 8/136 (5%)
Query: 512 AVKHAIQRPLS---LIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKI 568
A+++ ++ + L G GTGKT S I ++ + V+ ++
Sbjct: 35 AIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVN--CREV 92
Query: 569 HRTGLKVVRVCAKSREAIDSPVSFLALHNQIRNMEMNSELKKLLQLKEETGEL---SSAD 625
T V+ A P + L I ++ + + + +E L D
Sbjct: 93 GGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVKRRGGD 152
Query: 626 EKRYRMLKKNAEKSLL 641
Y++L+ +A S++
Sbjct: 153 IVLYQLLRSDANISVI 168
>3f6k_A Sortilin; protein sorting receptor, 10-bladed beta-propeller,
Cys-rich ssortilin, sortilin VPS10P-D, protein-peptide
complex, DEVE protein; HET: NAG BMA PGE; 2.00A {Homo
sapiens}
Length = 685
Score = 31.9 bits (71), Expect = 1.1
Identities = 19/114 (16%), Positives = 35/114 (30%), Gaps = 18/114 (15%)
Query: 348 ADYDKRLKESQTQENVTVRWDVGLNKKSIAYFSLAKTDGDMRLMQGDELKLRYSYDASKT 407
A+ + + +V++ W VG + I L + +M + KL S D K
Sbjct: 20 ANNTHQHVFDDLRGSVSLSW-VGDSTGVI--LVLTTFHVPLVIMTFGQSKLYRSEDYGKN 76
Query: 408 WSGLGHVIKIPDNFGDEVGLELKSSAGAPTEATTGFSVDF---------IWKST 452
+ I D + A P + I++S+
Sbjct: 77 FK------DITDLINNTFIRTEFGMAIGPENSGKVVLTAEVSGGSRGGRIFRSS 124
>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA
replication initation factor, cell cycle control factor;
HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11
c.37.1.20
Length = 389
Score = 31.7 bits (71), Expect = 1.1
Identities = 13/61 (21%), Positives = 22/61 (36%), Gaps = 2/61 (3%)
Query: 512 AVKHAIQRPLSL-IQGPPGTGKTVTSATIVYQLVKQTG-SPVLVCAPSNIAVDQLTEKIH 569
+++ + G PGTGKTVT + +T V + + +I
Sbjct: 36 WLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIA 95
Query: 570 R 570
R
Sbjct: 96 R 96
>3v2d_Y 50S ribosomal protein L24; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
1vsp_S 2hgj_X 2hgq_X 2hgu_X 1vsa_S 2j03_Y 2jl6_Y 2jl8_Y
2v47_Y 2v49_Y 2wdi_Y 2wdj_Y 2wdl_Y 2wdn_Y 2wh2_Y 2wh4_Y
2wrj_Y 2wrl_Y 2wro_Y 2wrr_Y ...
Length = 110
Score = 29.9 bits (68), Expect = 1.2
Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 7/40 (17%)
Query: 557 SNIA-VDQLTEKIHRTGLKV------VRVCAKSREAIDSP 589
S + + K R K +RVCAK A+D+
Sbjct: 70 SKVRPICPACGKPTRVRKKFLENGKKIRVCAKCGGALDTE 109
>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein
transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A
Length = 320
Score = 31.4 bits (72), Expect = 1.2
Identities = 25/110 (22%), Positives = 37/110 (33%), Gaps = 37/110 (33%)
Query: 529 GTGKTVTSATIVYQLVKQTGSPVLVCAPSNI---AVDQLT---EKIHRTGLKVVRV---- 578
GTGKT + A + + G VL+ A A QL + + +V+
Sbjct: 115 GTGKTTSLAKMANYY-AELGYKVLIAAADTFRAGATQQLEEWIKTRLNNKVDLVKANKLN 173
Query: 579 ------------CAKSREA----IDSPVSFLA--LHNQIRNMEMNSELKK 610
AK + ID+ A L N+ M EL+K
Sbjct: 174 ADPASVVFDAIKKAKEQNYDLLLIDT-----AGRLQNKTNLMA---ELEK 215
>2w58_A DNAI, primosome component (helicase loader); ATP-binding,
nucleotide-binding, hydrolase; HET: ADP; 2.50A
{Geobacillus kaustophilus HTA426}
Length = 202
Score = 30.8 bits (70), Expect = 1.3
Identities = 10/30 (33%), Positives = 13/30 (43%), Gaps = 1/30 (3%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVL 552
+ G G GKT A I +L K+ L
Sbjct: 58 YLHGSFGVGKTYLLAAIANELAKR-NVSSL 86
>3iox_A AGI/II, PA; alpha helix, PPII helix, supersandwich fold, surface
adhesin WALL, peptidoglycan-anchor, cell adhesion; HET:
PMS; 1.80A {Streptococcus mutans} PDB: 3ipk_A* 1jmm_A
Length = 497
Score = 31.8 bits (70), Expect = 1.4
Identities = 29/187 (15%), Positives = 53/187 (28%), Gaps = 2/187 (1%)
Query: 227 EQEQQRGRQVTSAQIAKLEEVWKD-NAEATFQDLEKPGVDEDPHQVLLRYEDGY-QYQNI 284
+ E R ++ + A E NA E + + YE +YQ
Sbjct: 15 QTELARVQKANADAKAAYEAAVAANNAANAALTAENTAIKKRNADAKADYEAKLAKYQAD 74
Query: 285 FGPLVKLEADYDKRLKESQTQENVTVRWDVGLNKKSIAYFSLAKTDGDGYQYQNIFGPLV 344
K ADY +LK + ++ L K +L + Y +
Sbjct: 75 LAKYQKDLADYPVKLKAYEDEQTSIKAALAELEKHKNEDGNLTEPSAQNLVYDLEPNANL 134
Query: 345 KLEADYDKRLKESQTQENVTVRWDVGLNKKSIAYFSLAKTDGDMRLMQGDELKLRYSYDA 404
L D + ++K + L T+ + ++L ++
Sbjct: 135 SLTTDGKFLKASAVDDAFSKSTSKAKYDQKILQLDDLDITNLEQSNDVASSMELYGNFGD 194
Query: 405 SKTWSGL 411
WS
Sbjct: 195 KAGWSTT 201
>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein
translocation, GTP-binding, nucleotide-binding, protein
transport; 1.75A {Arabidopsis thaliana}
Length = 302
Score = 31.4 bits (72), Expect = 1.5
Identities = 26/107 (24%), Positives = 37/107 (34%), Gaps = 34/107 (31%)
Query: 529 GTGKTVTSATIVYQLVKQTGSPVLVCAPSNI---AVDQLTEKIHRTGLKVVR-------- 577
G GKT + + ++L + G+ VL+ A A DQL RTG ++V
Sbjct: 110 GGGKTTSLGKLAHRLKNE-GTKVLMAAGDTFRAAASDQLEIWAERTGCEIVVAEGDKAKA 168
Query: 578 --VC------AKSREA----IDSPVSFLA--LHNQIRNMEMNSELKK 610
V K D+ + LH ME EL
Sbjct: 169 ATVLSKAVKRGKEEGYDVVLCDT-----SGRLHTNYSLME---ELIA 207
>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M
domain, RNA-binding, signal sequence-binding,
helix-turn-helix, protein targeting; 3.20A {Thermus
aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB:
2iy3_A
Length = 425
Score = 31.3 bits (72), Expect = 1.5
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 6/40 (15%)
Query: 529 GTGKTVTSATIVYQLVKQTGSPVLVCA----PSNIAVDQL 564
G+GKT T+A + + P+LV A P+ A +QL
Sbjct: 108 GSGKTTTAAKLALYYKGKGRRPLLVAADTQRPA--AREQL 145
>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET:
ANP; 2.14A {Mus musculus}
Length = 555
Score = 31.4 bits (70), Expect = 1.6
Identities = 16/79 (20%), Positives = 26/79 (32%), Gaps = 8/79 (10%)
Query: 509 QVYAVKHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSP----VLVCAPSNIAVDQL 564
Q+ A + ++I P G GKT S I +K+ V+ A +Q
Sbjct: 9 QLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQ 68
Query: 565 TEKIHR----TGLKVVRVC 579
R G + +
Sbjct: 69 ATVFSRYFERLGYNIASIS 87
>2og2_A Putative signal recognition particle receptor; nucleotide-binding,
protein transport; 2.00A {Arabidopsis thaliana}
Length = 359
Score = 31.1 bits (71), Expect = 1.8
Identities = 25/105 (23%), Positives = 36/105 (34%), Gaps = 30/105 (28%)
Query: 529 GTGKTVTSATIVYQLVKQTGSPVLVCAPSNI---AVDQLTEKIHRTGLKVVRVCAKSREA 585
G GKT + + ++L + G+ VL+ A A DQL RTG ++V +
Sbjct: 167 GGGKTTSLGKLAHRLKNE-GTKVLMAAGDTFRAAASDQLEIWAERTGCEIVV---AEGDK 222
Query: 586 IDS-PVSFLA-------------------LHNQIRNMEMNSELKK 610
+ V A LH ME EL
Sbjct: 223 AKAATVLSKAVKRGKEEGYDVVLCDTSGRLHTNYSLME---ELIA 264
>1nlf_A Regulatory protein REPA; replicative DNA helicase structural
changes, replication; 1.95A {Escherichia coli} SCOP:
c.37.1.11 PDB: 1g8y_A 1olo_A
Length = 279
Score = 30.8 bits (69), Expect = 1.8
Identities = 8/46 (17%), Positives = 19/46 (41%), Gaps = 2/46 (4%)
Query: 511 YAVKHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAP 556
Y + + + + + P G GK++ + + Q+ G +L
Sbjct: 22 YVLPNMVAGTVGALVSPGGAGKSMLALQLAAQIA--GGPDLLEVGE 65
>3kjh_A CO dehydrogenase/acetyl-COA synthase complex, accessory protein
COOC; Zn-bound dimer, nickel binding protein, ATPase;
1.90A {Carboxydothermus hydrogenoformans} PDB: 3kjg_A*
3kje_A 3kji_A*
Length = 254
Score = 30.9 bits (70), Expect = 1.9
Identities = 5/25 (20%), Positives = 10/25 (40%), Gaps = 1/25 (4%)
Query: 529 GTGKTVTSATIVYQLVKQTGSPVLV 553
G GKT +A ++ + +
Sbjct: 10 GVGKTTVAAGLIKIMASD-YDKIYA 33
>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding,
hydrolase, nucleotide- binding; 2.00A {Pyrococcus
furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*
Length = 720
Score = 31.4 bits (71), Expect = 2.0
Identities = 12/65 (18%), Positives = 22/65 (33%), Gaps = 1/65 (1%)
Query: 493 LPKHFSAPNLPDLNRSQVYAVKHAIQRPLS-LIQGPPGTGKTVTSATIVYQLVKQTGSPV 551
+ + Q A+K I + LI P +GKT+ + + + G
Sbjct: 12 IKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQGGKA 71
Query: 552 LVCAP 556
+ P
Sbjct: 72 VYIVP 76
>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding,
viral nucleoprotein, endoplasmic reticulum, helicase,
hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A*
2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A
2bhr_A
Length = 451
Score = 31.0 bits (70), Expect = 2.1
Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 12/76 (15%)
Query: 498 SAPNLPDLNRSQVYAVKHAIQR--PLSLIQGPPGTGKTVTSAT--IVYQLVKQTGSPVLV 553
SA P Y V I R L+++ PG GKT IV + + + L+
Sbjct: 2 SAMGEP------DYEVDEDIFRKKRLTIMDLHPGAGKT-KRILPSIVREALLRRLR-TLI 53
Query: 554 CAPSNIAVDQLTEKIH 569
AP+ + ++ E +
Sbjct: 54 LAPTRVVAAEMEEALR 69
>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding
protein; 2.30A {Archaeoglobus fulgidus}
Length = 221
Score = 30.3 bits (69), Expect = 2.1
Identities = 14/62 (22%), Positives = 28/62 (45%), Gaps = 17/62 (27%)
Query: 524 IQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAV---DQLT----EKIHRTGLKVV 576
I G G+GKT ++ + +++ G+ V I D ++ E++ R G+K
Sbjct: 35 IMGAIGSGKT----LLIERTIERIGNEV------KIGAMLGDVVSKADYERVRRFGIKAE 84
Query: 577 RV 578
+
Sbjct: 85 AI 86
>1obb_A Maltase, alpha-glucosidase; glycosidase, sulfinic acid, NAD+,
maltose, hydrolase; HET: MAL NAD; 1.90A {Thermotoga
maritima} SCOP: c.2.1.5 d.162.1.2
Length = 480
Score = 31.0 bits (69), Expect = 2.2
Identities = 17/130 (13%), Positives = 36/130 (27%), Gaps = 5/130 (3%)
Query: 184 VVLLCRTPCAAQNSLKDMNWDQEQWKPLIADRSFLSWLVKVPTEQEQQRGRQVTSAQIAK 243
V C ++ + ++E+ +A + WL + + G
Sbjct: 170 AVGFCHGHYGVMEIVEKLGLEEEKVDWQVAGVNHGIWLNRF-----RYNGGNAYPLLDKW 224
Query: 244 LEEVWKDNAEATFQDLEKPGVDEDPHQVLLRYEDGYQYQNIFGPLVKLEADYDKRLKESQ 303
+EE KD + + D ++ G +N + K E
Sbjct: 225 IEEKSKDWKPENPFNDQLSPAAIDMYRFYGVMPIGDTVRNSSWRYHRDLETKKKWYGEPW 284
Query: 304 TQENVTVRWD 313
+ + W
Sbjct: 285 GGADSEIGWK 294
>3dmn_A Putative DNA helicase; APC89291.2, lactobacillus plantarum WCFS1,
STR genomics, PSI-2, midwest center for structural
genomics; HET: MSE; 1.66A {Lactobacillus plantarum}
Length = 174
Score = 30.1 bits (68), Expect = 2.2
Identities = 12/114 (10%), Positives = 41/114 (35%), Gaps = 12/114 (10%)
Query: 802 TEASNVEKITTRFIRCGMKPEQIGVITPYEGQRAFLVQHMQ-------YQGSLPAKIYQE 854
+ V+++ + + + +I + L + ++ + ++
Sbjct: 42 NFEAGVDQVVDQLAMNDSERDTTAIIGKSLAECEALTKALKARGEQVTLIQTENQRLAPG 101
Query: 855 IEVASVDAFQGREKDL-IIMSCVRSNDHQGIGFLNDPRRLNVALTRAKYGIIVI 907
+ V +G E D I+ + + N + ++ + L +RA + + ++
Sbjct: 102 VIVVPSFLAKGLEFDAVIVWNANQENYQRE----DERQLLYTICSRAMHELTLV 151
>2chq_A Replication factor C small subunit; DNA-binding protein, DNA
replication, clamp loader, AAA+ ATP ATP-binding,
nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus
fulgidus} PDB: 2chv_A
Length = 319
Score = 30.8 bits (70), Expect = 2.3
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 523 LIQGPPGTGKTVTSATIVYQL 543
L GPPGTGKT T+ + L
Sbjct: 42 LFSGPPGTGKTATAIALARDL 62
>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural
genomics, PSI, protein struc initiative; 3.20A
{Agrobacterium tumefaciens str} SCOP: c.37.1.25
Length = 191
Score = 30.1 bits (67), Expect = 2.6
Identities = 14/71 (19%), Positives = 27/71 (38%), Gaps = 11/71 (15%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNI-------AVDQLTEKIHRTGLKV 575
L+ G PG+GK+ TI L G P + ++ +D + H+ +
Sbjct: 13 LLSGHPGSGKS----TIAEALANLPGVPKVHFHSDDLWGYIKHGRIDPWLPQSHQQNRMI 68
Query: 576 VRVCAKSREAI 586
+++ A
Sbjct: 69 MQIAADVAGRY 79
>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable
holliday junction DNA helicase; HET: ADP; 2.69A
{Campylobacter jejuni subsp}
Length = 338
Score = 30.6 bits (70), Expect = 2.6
Identities = 14/34 (41%), Positives = 21/34 (61%), Gaps = 5/34 (14%)
Query: 523 LIQGPPGTGKTVTSATIV-YQL---VKQTGSPVL 552
L GP G GKT T A I+ Y++ +K T +P++
Sbjct: 59 LFSGPAGLGKT-TLANIISYEMSANIKTTAAPMI 91
>3pvs_A Replication-associated recombination protein A; maintenance of
genome stability Pro recombination; 2.50A {Escherichia
coli}
Length = 447
Score = 30.6 bits (70), Expect = 2.7
Identities = 12/23 (52%), Positives = 15/23 (65%), Gaps = 2/23 (8%)
Query: 519 RPLSLIQ-GPPGTGKTVTSATIV 540
S+I GPPGTGKT T A ++
Sbjct: 49 HLHSMILWGPPGTGKT-TLAEVI 70
>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide,
hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP:
a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*
Length = 324
Score = 30.2 bits (69), Expect = 3.0
Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 5/34 (14%)
Query: 523 LIQGPPGTGKTVTSATIV-YQL---VKQTGSPVL 552
L+ GPPG GKT T A ++ ++L ++ T P +
Sbjct: 42 LLFGPPGLGKT-TLAHVIAHELGVNLRVTSGPAI 74
>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and
beta protein; HET: GSP; 1.90A {Methanocaldococcus
jannaschii} PDB: 2hf8_A*
Length = 226
Score = 29.9 bits (68), Expect = 3.1
Identities = 14/62 (22%), Positives = 24/62 (38%), Gaps = 17/62 (27%)
Query: 524 IQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAV---DQLT----EKIHRTGLKVV 576
G G+GKT ++ +L+ IA D + E++ + G KVV
Sbjct: 43 FMGAIGSGKT----LLIEKLIDNLKDKY------KIACIAGDVIAKFDAERMEKHGAKVV 92
Query: 577 RV 578
+
Sbjct: 93 PL 94
>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase,
winged-helix domain, ATP hydrolysis, walker A, walker B,
sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga
maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A*
1in8_A* 1in7_A* 1j7k_A*
Length = 334
Score = 30.2 bits (69), Expect = 3.2
Identities = 16/34 (47%), Positives = 20/34 (58%), Gaps = 5/34 (14%)
Query: 523 LIQGPPGTGKTVTSATIV-YQL---VKQTGSPVL 552
L+ GPPG GKT T A I+ +L + T PVL
Sbjct: 55 LLAGPPGLGKT-TLAHIIASELQTNIHVTSGPVL 87
>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein
struct initiative, northeast structural genomics
consortium, NESG, function; 2.40A {Bacillus halodurans}
SCOP: c.37.1.25
Length = 189
Score = 29.5 bits (66), Expect = 3.2
Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 4/31 (12%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVLV 553
+I GP G GK+ T +L Q + +
Sbjct: 6 IITGPAGVGKS----TTCKRLAAQLDNSAYI 32
>2zjr_R 50S ribosomal protein L24; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: b.34.5.1 PDB: 1nwx_S* 1nwy_S* 1sm1_S*
1xbp_S* 2d3o_S 2zjp_R* 2zjq_R 1nkw_S 3cf5_R* 3dll_R*
3pio_R* 3pip_R* 1pnu_S 1pny_S 1vor_V 1vou_V 1vow_V
1voy_V 1vp0_V
Length = 115
Score = 28.7 bits (65), Expect = 3.3
Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 6/37 (16%)
Query: 557 SNIA-VDQLTEKIHRTGLKV-----VRVCAKSREAID 587
S +A VD T K R ++ VRV S + ID
Sbjct: 79 SKVALVDPETGKATRVRKQIVDGKKVRVAVASGKTID 115
>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop,
rossman fold, AAA+, photosynthesis, metal transport;
2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB:
2x31_G
Length = 350
Score = 30.1 bits (68), Expect = 3.5
Identities = 6/13 (46%), Positives = 8/13 (61%)
Query: 523 LIQGPPGTGKTVT 535
L+ G GTGK+
Sbjct: 49 LVFGDRGTGKSTA 61
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR;
fatty acid synthase, acyl-carrier-protein, beta-ketoacyl
RED beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 30.6 bits (69), Expect = 3.5
Identities = 17/142 (11%), Positives = 37/142 (26%), Gaps = 44/142 (30%)
Query: 617 ETGELSSADE--KRY--RMLKK----NAEKSLLDNADVICCTCVGAGDPRLLKIKFHSIL 668
+T E + +Y +L+ E L + + K ++
Sbjct: 880 KTKEPVDDKDVKAKYETSILEHSGIRLIEPELFNGYNPEK------------KEMIQEVI 927
Query: 669 IDESMQATEPECMVPVILGAKQLIL-VGDHCQLGPVVMCKKAARAGLSQSLFERLVVLGI 727
++E ++ E A+Q GD + + + + L G
Sbjct: 928 VEEDLEPFEASKET-----AEQFKHQHGDKVDIFEIPETGEYSVKLLK----------GA 972
Query: 728 RPFRLEVQYRMHPELSKFPSNF 749
P+ +F
Sbjct: 973 T--------LYIPKALRFDRLV 986
>2r2a_A Uncharacterized protein; zonular occludens toxin, structural
genomics, APC84050.2, PS protein structure initiative;
HET: MSE; 1.82A {Neisseria meningitidis MC58}
Length = 199
Score = 29.7 bits (66), Expect = 3.6
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 519 RPLSLIQGPPGTGKT 533
+ LI G PG+GKT
Sbjct: 5 AEICLITGTPGSGKT 19
>2chg_A Replication factor C small subunit; DNA-binding protein, DNA
replication, clamp loader, AAA+ ATPase, ATP-binding,
nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus
fulgidus}
Length = 226
Score = 29.5 bits (67), Expect = 4.0
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 523 LIQGPPGTGKTVTSATIVYQL 543
L GPPGTGKT T+ + L
Sbjct: 42 LFSGPPGTGKTATAIALARDL 62
>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P;
hydrolase, type IV secretion, conjugation; 2.35A
{Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A
Length = 392
Score = 30.0 bits (67), Expect = 4.1
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSN 558
I PG GK+ T+ ++ + Q GS V++ P
Sbjct: 39 TILAKPGAGKSFTAKMLLLREYMQ-GSRVIIIDPER 73
>2yxl_A PH0851 protein, 450AA long hypothetical FMU protein; FMU-homolog,
methyltransferase, structural genomics, NPPSFA; HET:
SFG; 2.55A {Pyrococcus horikoshii}
Length = 450
Score = 29.9 bits (68), Expect = 4.2
Identities = 11/67 (16%), Positives = 26/67 (38%), Gaps = 13/67 (19%)
Query: 611 LLQLKEETGELSSAD--EKRYRMLKKNAEKSLLDNADVICCTCVGAGDPR-----LLKIK 663
L +L + G++ + D + R + LK ++ + + D R + +
Sbjct: 277 LAELMKNKGKIYAFDVDKMRMKRLKDFVKRMGIKIVKPLV------KDARKAPEIIGEEV 330
Query: 664 FHSILID 670
+L+D
Sbjct: 331 ADKVLLD 337
>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA
binding protein, hydrolase, gtpas; HET: GCP; 3.94A
{Escherichia coli} PDB: 2j28_9
Length = 433
Score = 29.8 bits (68), Expect = 4.5
Identities = 16/61 (26%), Positives = 25/61 (40%), Gaps = 16/61 (26%)
Query: 518 QRPLSLIQGPP---------GTGKTVTSATIVYQLVKQTGSPVLVCA-----PSNIAVDQ 563
+ L+L PP G GKT + + L ++ VLV + P+ A+ Q
Sbjct: 90 NQTLNLAAQPPAVVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSADVYRPA--AIKQ 147
Query: 564 L 564
L
Sbjct: 148 L 148
>2p51_A SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene regulation;
1.40A {Schizosaccharomyces pombe} PDB: 3g0z_A 3g10_A
Length = 333
Score = 29.7 bits (66), Expect = 4.5
Identities = 17/61 (27%), Positives = 24/61 (39%), Gaps = 15/61 (24%)
Query: 238 SAQIAKLEEVWKDNAEATFQ--------------DLEKPGVDEDPHQVLLRYEDGYQYQN 283
S+QI+ + +VW N + D E PGV P V +D Y YQ
Sbjct: 17 SSQISPIRDVWSTNLQQEMNLIMSLIERYPVVSMDTEFPGVVARPLGVFKSSDD-YHYQT 75
Query: 284 I 284
+
Sbjct: 76 L 76
>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling,
archaea, isomeras; 2.35A {Thermotoga maritima} PDB:
3p4y_A 3p4x_A*
Length = 414
Score = 29.7 bits (67), Expect = 4.5
Identities = 16/74 (21%), Positives = 29/74 (39%), Gaps = 5/74 (6%)
Query: 509 QVYAVKHAIQ-RPLSLIQGPPGTGKTVT-SATIVYQLVKQTGSPVLVCAPSNIAVDQLTE 566
Q K +Q + + P G GKT T ++ K G + P+ V Q E
Sbjct: 26 QRLWAKRIVQGKSF-TMVAPTGVGKTTFGMMTALWLARK--GKKSALVFPTVTLVKQTLE 82
Query: 567 KIHRTGLKVVRVCA 580
++ + + V++
Sbjct: 83 RLQKLADEKVKIFG 96
>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP,
replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP:
a.80.1.1 c.37.1.20
Length = 327
Score = 29.6 bits (67), Expect = 4.6
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 523 LIQGPPGTGKTVTSATIVYQL 543
L GPPG GKT + + +L
Sbjct: 50 LFAGPPGVGKTTAALALAREL 70
>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system
kinase, STRU genomics, joint center for structural
genomics, JCSG; 1.95A {Silicibacter SP}
Length = 208
Score = 29.3 bits (66), Expect = 4.7
Identities = 9/30 (30%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 524 IQGPPGTGKTVTSATIVYQLVKQTGSPVLV 553
+ G PG+GK+ T + + + G P V
Sbjct: 27 LSGAPGSGKS-TLSNPLAAALSAQGLPAEV 55
>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 = 28.8 bits (63), Expect = 5.1
Identities = 8/30 (26%), Positives = 12/30 (40%), Gaps = 12/30 (40%)
Query: 229 EQQRGRQVTSAQIAKLEEVWK----DNAEA 254
E+Q + KL+ K D+A A
Sbjct: 18 EKQ--------ALKKLQASLKLYADDSAPA 39
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 29.0 bits (64), Expect = 5.2
Identities = 8/55 (14%), Positives = 26/55 (47%), Gaps = 8/55 (14%)
Query: 598 QIRNMEMNSELKKLLQLKEETG-ELSSADEKRYRMLKKN------AEKSLLDNAD 645
+++ ++ S+ + +E+ +L ++++ ++KN A+K+ D
Sbjct: 97 RLQELDAASK-VMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKAFYQQPD 150
>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain,
TGF-beta, epigenetics, methylation, K9ME3, K14AC,
transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB:
3u5m_A* 3u5o_A* 3u5p_A*
Length = 207
Score = 29.1 bits (64), Expect = 5.5
Identities = 10/38 (26%), Positives = 15/38 (39%), Gaps = 10/38 (26%)
Query: 86 EDDGNEFFNKELPPHACKYCGIHDPAYVIMCNICKKWF 123
+DD NE + C C + ++ C C K F
Sbjct: 2 DDDPNEDW--------CAVC--QNGGDLLCCEKCPKVF 29
>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer
aging, hydrolase; HET: FLC; 2.00A {Sulfolobus
acidocaldarius} PDB: 3crw_1*
Length = 551
Score = 29.6 bits (66), Expect = 6.0
Identities = 31/182 (17%), Positives = 61/182 (33%), Gaps = 36/182 (19%)
Query: 512 AVKHAIQRPLSLI-QGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHR 570
V ++ + P G+GKT+ S + ++ + VL ++ + + +
Sbjct: 14 KVIEGLRNNFLVALNAPTGSGKTLFSLLVSLEVKPK----VLFVVRTHNEFYPIYRDLTK 69
Query: 571 T----GLKVVRVCAKSREAIDSPVSFLALHNQIRNMEMNSELKKLLQLKEETGELSSADE 626
+ + K L+ + + E K +LK E+ + D
Sbjct: 70 IREKRNITFSFLVGKPS---------SCLYAE-KGAESEDIPCKYCELKGSIVEVKTDDS 119
Query: 627 KRYRM--LKKNAEKS----------LLDNADVICCTCVGAGDPRLLK-----IKFHSILI 669
+ LKK+ + L ADVI T R + ++ + I+I
Sbjct: 120 PLSLVKKLKKDGLQDKFCPYYSLLNSLYKADVIALTYPYFFIDRYREFIDIDLREYMIVI 179
Query: 670 DE 671
DE
Sbjct: 180 DE 181
>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease,
double strand DNA repair, protein-DNA CO hydrolase-DNA
complex; HET: DNA; 2.80A {Bacillus subtilis} PDB:
3u44_A*
Length = 1232
Score = 29.6 bits (66), Expect = 6.3
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 895 VALTRAKYGIIVIGNPKVLSKQP 917
VALTRAK + +IG+ K KQ
Sbjct: 869 VALTRAKEKLFLIGSCKDHQKQL 891
>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET:
ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*
Length = 368
Score = 29.1 bits (65), Expect = 6.5
Identities = 18/88 (20%), Positives = 27/88 (30%), Gaps = 10/88 (11%)
Query: 509 QVYAVKHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKI 568
+ A+ LI G PGTGKT A + + G A + + L
Sbjct: 65 EGKIAGRAV-----LIAGQPGTGKT-AIAMGMA---QALGPDTPFTAIAGSEIFSLEMSK 115
Query: 569 HRTGLKVVRVCAKSREAIDSPVSFLALH 596
+ R V ++LH
Sbjct: 116 TEALTQAFRRSI-GVRIKAGAVHTVSLH 142
>2b9e_A NOL1/NOP2/SUN domain family, member 5 isoform 2; methytransferase,
structural genomics, structural genomics consortium,
SGC; HET: SAM; 1.65A {Homo sapiens} SCOP: c.66.1.38
Length = 309
Score = 29.2 bits (66), Expect = 6.9
Identities = 7/47 (14%), Positives = 16/47 (34%)
Query: 624 ADEKRYRMLKKNAEKSLLDNADVICCTCVGAGDPRLLKIKFHSILID 670
D KR + ++ + ++ + + H IL+D
Sbjct: 135 LDAKRLASMATLLARAGVSCCELAEEDFLAVSPSDPRYHEVHYILLD 181
>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase;
NMR {Homo sapiens} SCOP: c.37.1.11
Length = 189
Score = 28.5 bits (63), Expect = 6.9
Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 6/59 (10%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSNIAVDQLTEKIHRTGLKVVRVCAK 581
+ GPPG GKT T +++K +G PV +++ + R G VV +
Sbjct: 5 FLTGPPGVGKT-TLIHKASEVLKSSGVPV-----DGFYTEEVRQGGRRIGFDVVTLSGT 57
>2l8b_A Protein TRAI, DNA helicase I; RECD, hydrolase; NMR {Escherichia
coli}
Length = 189
Score = 28.7 bits (63), Expect = 7.0
Identities = 12/95 (12%), Positives = 31/95 (32%), Gaps = 4/95 (4%)
Query: 503 PDLNRSQVYA----VKHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLVCAPSN 558
+ R+ Y+ V + L+++ G G + + ++ G V + A
Sbjct: 31 KSVPRTAGYSDAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADR 90
Query: 559 IAVDQLTEKIHRTGLKVVRVCAKSREAIDSPVSFL 593
+ + + +G + +P S +
Sbjct: 91 RSQMNMKQDERLSGELITGRRQLLEGMAFTPGSTV 125
>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding,
nucleotide-binding, HY; HET: ADP; 3.11A
{Methanocaldococcus jannaschii}
Length = 285
Score = 29.2 bits (66), Expect = 7.1
Identities = 9/11 (81%), Positives = 10/11 (90%)
Query: 523 LIQGPPGTGKT 533
L+ GPPGTGKT
Sbjct: 55 LLYGPPGTGKT 65
>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins
(A/B), protein binding, transferase, phosphotransferase;
HET: ADP; 1.76A {Homo sapiens} PDB: 3iik_A 3iil_A*
3iim_A* 1rkb_A
Length = 180
Score = 28.5 bits (63), Expect = 7.3
Identities = 10/30 (33%), Positives = 16/30 (53%), Gaps = 4/30 (13%)
Query: 523 LIQGPPGTGKTVTSATIVYQLVKQTGSPVL 552
L+ G PG GKT T+ +L ++G +
Sbjct: 15 LLTGTPGVGKT----TLGKELASKSGLKYI 40
>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex,
transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}
Length = 460
Score = 29.0 bits (64), Expect = 7.7
Identities = 11/40 (27%), Positives = 15/40 (37%)
Query: 514 KHAIQRPLSLIQGPPGTGKTVTSATIVYQLVKQTGSPVLV 553
+ P +I G TGKT S T+ +K L
Sbjct: 133 MSNFEGPRVVIVGGSQTGKTSLSRTLCSYALKFNAYQPLY 172
>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus,
hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A
Length = 677
Score = 29.1 bits (64), Expect = 8.7
Identities = 18/89 (20%), Positives = 30/89 (33%), Gaps = 4/89 (4%)
Query: 446 DFIWKSTSFDRMQLALRKFAVDDQSVSAYIYHRLLGHNVDEVLFRCHLPKHFSAPNLPDL 505
++I +S S D + + + ++ L H L + DL
Sbjct: 84 NYIMQSHSLDVDIHIVLNDICFGAAHADDLFPFFLRHAKQIFP---VLDCKDDLRKISDL 140
Query: 506 NR-SQVYAVKHAIQRPLSLIQGPPGTGKT 533
Y A+QR + GP +GKT
Sbjct: 141 RIPPNWYPDARAMQRKIIFHSGPTNSGKT 169
>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET:
ADP; 3.90A {Thermus thermophilus}
Length = 499
Score = 28.7 bits (65), Expect = 9.9
Identities = 8/11 (72%), Positives = 9/11 (81%)
Query: 523 LIQGPPGTGKT 533
L+ GPPG GKT
Sbjct: 68 LLVGPPGVGKT 78
>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding,
chromatin regulator, growth regulation, hydrolase,
nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo
sapiens} PDB: 2xsz_A*
Length = 456
Score = 28.8 bits (64), Expect = 9.9
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 7/37 (18%)
Query: 504 DLNRSQVYAVKHAIQRPLSLIQGPPGTGKTVTSATIV 540
+L +S+ A + L+ GPPGTGKT A +
Sbjct: 54 ELIKSKKMAGRAV------LLAGPPGTGKT-ALALAI 83
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
0.318 0.135 0.400
Gapped
Lambda K H
0.267 0.0563 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 14,366,207
Number of extensions: 876124
Number of successful extensions: 2137
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2108
Number of HSP's successfully gapped: 143
Length of query: 959
Length of database: 6,701,793
Length adjustment: 103
Effective length of query: 856
Effective length of database: 3,825,930
Effective search space: 3274996080
Effective search space used: 3274996080
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 (21.7 bits)
S2: 62 (28.0 bits)