BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 000756
(1300 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4F91|B Chain B, Brr2 Helicase Region
Length = 1724
Score = 1235 bits (3196), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 573/876 (65%), Positives = 714/876 (81%)
Query: 418 LGQRQLLDLDTLAFQQGGLFMANRKCDLPEGSQRFTNKGYEEIHVPAMKHKPLDPNEKLI 477
L RQ+LDL+ L F QG FMAN++C LP+GS R KGYEE+HVPA+K KP E+L+
Sbjct: 2 LAPRQVLDLEDLVFTQGSHFMANKRCQLPDGSFRRQRKGYEEVHVPALKPKPFGSEEQLL 61
Query: 478 KISEMPEWAQPAFKGMTQLNRVQSRVYKSALSSADNILLCAPTGAGKTNVAVLTILQQLA 537
+ ++P++AQ F+G LNR+QS++Y++AL + +N+LLCAPTGAGKTNVA++ +L+++
Sbjct: 62 PVEKLPKYAQAGFEGFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIG 121
Query: 538 LNRNDDGSFNHSNYKIVYVAPMKALVAEVVGNLSNRLQMYDVKVRELSGDQTLTRQQIEE 597
+ N DG+ N ++KI+Y+APM++LV E+VG+ RL Y + V EL+GD L +++I
Sbjct: 122 KHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFGKRLATYGITVAELTGDHQLCKEEISA 181
Query: 598 TQIIVTTPEKWDIITRKSGDRTYTQLVKXXXXXXXXXXXXNRGPVLESIVARTVRQIETT 657
TQIIV TPEKWDIITRK G+RTYTQLV+ +RGPVLE++VAR +R IE T
Sbjct: 182 TQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHDDRGPVLEALVARAIRNIEMT 241
Query: 658 KEHIRLVGLSATLPNYEDVALFLRVNLEKGLFYFDNSYRPVPLSQQYIGIQVKKPLQRFQ 717
+E +RL+GLSATLPNYEDVA FLRV+ KGLFYFDNS+RPVPL Q Y+GI KK ++RFQ
Sbjct: 242 QEDVRLIGLSATLPNYEDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQ 301
Query: 718 LMNDLCYEKVVAVAGKHQVLIFVHSRKETAKTARAIRDTALENDTLGRFLKEDSVSREIL 777
+MN++ YEK++ AGK+QVL+FVHSRKET KTARAIRD LE DTLG FL+E S S E+L
Sbjct: 302 IMNEIVYEKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVL 361
Query: 778 QSHTDMVKSNDLKDLLPYGFAIHHAGMTRGDRQLVEDLFGDGHVQVLVSTATLAWGVNLP 837
++ + K+ +LKDLLPYGFAIHHAGMTR DR LVEDLF D H+QVLVSTATLAWGVNLP
Sbjct: 362 RTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLP 421
Query: 838 AHTVIIKGTQIYNPEKGAWTELSPLDIMQMLGRAGRPQYDSYGEGIIITGHSELRYYLSL 897
AHTVIIKGTQ+Y+PEKG WTEL LDI+QMLGRAGRPQYD+ GEGI+IT H EL+YYLSL
Sbjct: 422 AHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILITSHGELQYYLSL 481
Query: 898 MNQQLPIESQFVSKLADQLNAEIVLGTVQNAKEACNWIGYTYLYIRMLRNPALYGLAPEV 957
+NQQLPIESQ VSKL D LNAEIVLG VQNAK+A NW+GY YLYIRMLR+P LYG++ +
Sbjct: 482 LNQQLPIESQMVSKLPDMLNAEIVLGNVQNAKDAVNWLGYAYLYIRMLRSPTLYGISHDD 541
Query: 958 LKEDITLGERRADLVHTAATILDRNNLVKYDRKSGYFQVTDLGRIASYYYISHGTISTYN 1017
LK D L +RR DLVHTAA +LD+NNLVKYD+K+G FQVT+LGRIAS+YYI++ T+ TYN
Sbjct: 542 LKGDPLLDQRRLDLVHTAALMLDKNNLVKYDKKTGNFQVTELGRIASHYYITNDTVQTYN 601
Query: 1018 EHLKPTMGDIELCRLFSLSEEFKYVTVRQDEKMELAKLLDRVPIPVKESLEEPSAKINVL 1077
+ LKPT+ +IEL R+FSLS EFK +TVR++EK+EL KLL+RVPIPVKES+EEPSAKINVL
Sbjct: 602 QLLKPTLSEIELFRVFSLSSEFKNITVREEEKLELQKLLERVPIPVKESIEEPSAKINVL 661
Query: 1078 LQAYISQLKLEGLSLTSDMVFITQSAGRLLRALFEIVLKRGWAQLAEKALNLSKMVTKRM 1137
LQA+ISQLKLEG +L +DMV++TQSAGRL+RA+FEIVL RGWAQL +K LNL KM+ KRM
Sbjct: 662 LQAFISQLKLEGFALMADMVYVTQSAGRLMRAIFEIVLNRGWAQLTDKTLNLCKMIDKRM 721
Query: 1138 WSVQTPLRQFNGIPNEILMKLEKKDFAWERYYDLSPQELGELIRFPKMGRTLHKFVHQFP 1197
W PLRQF +P E++ K+EKK+F +ER YDL+ E+GELIR PKMG+T+HK+VH FP
Sbjct: 722 WQSMCPLRQFRKLPEEVVKKIEKKNFPFERLYDLNHNEIGELIRMPKMGKTIHKYVHLFP 781
Query: 1198 KLILAAHVQPITRTVLKVELTITPDFLWDDKVHGYVEPFWVIVEDNDGEYILHHEYFMLK 1257
KL L+ H+QPITR+ LKVELTITPDF WD+KVHG E FW++VED D E ILHHEYF+LK
Sbjct: 782 KLELSVHLQPITRSTLKVELTITPDFQWDEKVHGSSEAFWILVEDVDSEVILHHEYFLLK 841
Query: 1258 KQYIEEDHSLNFTVPIYEPLPPQYFIRVVSDKWLGV 1293
+Y +++H + F VP++EPLPPQYFIRVVSD+WL
Sbjct: 842 AKYAQDEHLITFFVPVFEPLPPQYFIRVVSDRWLSC 877
Score = 317 bits (813), Expect = 2e-86, Method: Compositional matrix adjust.
Identities = 219/714 (30%), Positives = 364/714 (50%), Gaps = 31/714 (4%)
Query: 472 PNEKLIKISEMPEWA--QPAFKGMTQ-----LNRVQSRVYKSALSSADNILLCAPTGAGK 524
P +L+ + +P A AF+ + Q N +Q++V+ + +S DN+ + APTG+GK
Sbjct: 896 PPTELLDLQPLPVSALRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGK 955
Query: 525 TNVAVLTILQQLALNRNDDGSFNHSNYKIVYVAPMKALVAEVVGNLSNRLQ-MYDVKVRE 583
T A IL+ L S + VY+ PM+AL +V + + Q + KV
Sbjct: 956 TICAEFAILRML---------LQSSEGRCVYITPMEALAEQVYMDWYEKFQDRLNKKVVL 1006
Query: 584 LSGDQTLTRQQIEETQIIVTTPEKWDIITRKSGDRTYTQLVKXXXXXXXXXXXXNRGPVL 643
L+G+ + + + + II++TPEKWDI++R+ R Q + GPVL
Sbjct: 1007 LTGETSTDLKLLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGGENGPVL 1066
Query: 644 ESIVARTVRQIETTKEH-IRLVGLSATLPNYEDVALFLRVNLEKGLFYFDNSYRPVPLSQ 702
E I +R +R I + E IR+V LS++L N +DVA +L + F F + RPVPL
Sbjct: 1067 EVICSR-MRYISSQIERPIRIVALSSSLSNAKDVAHWLGCS-ATSTFNFHPNVRPVPLEL 1124
Query: 703 QYIGIQVKKPLQRFQLMNDLCYEKVVAVAGKHQVLIFVHSRKETAKTARAIRDTALENDT 762
G + R M Y + + K V++FV SRK+T TA I T +
Sbjct: 1125 HIQGFNISHTQTRLLSMAKPVYHAITKHSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQ 1184
Query: 763 LGRFLKEDSVSREILQSHTDMVKSNDLKDLLPYGFAIHHAGMTRGDRQLVEDLFGDGHVQ 822
RFL + + L + + + + LK+ L G H G++ +R+LVE LF G +Q
Sbjct: 1185 RQRFLH---CTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQ 1241
Query: 823 VLVSTATLAWGVNLPAHTVIIKGTQIYNPEKGAWTELSPLDIMQMLGRAGRPQYDSYGEG 882
V+V++ +L WG+N+ AH VII TQ YN + A+ + D++QM+G A RP D G
Sbjct: 1242 VVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRC 1301
Query: 883 IIITGHSELRYYLSLMNQQLPIESQFVSKLADQLNAEIVLGTVQNAKEACNWIGYTYLYI 942
+I+ S+ ++ + + LP+ES + D NAEIV T++N ++A +++ +T+LY
Sbjct: 1302 VIMCQGSKKDFFKKFLYEPLPVESHLDHCMHDHFNAEIVTKTIENKQDAVDYLTWTFLYR 1361
Query: 943 RMLRNPALYGLAPEVLKEDITLGERRADLVHTAATILDRNNLVKYDRKSGYFQVTDLGRI 1002
RM +NP Y L + L + ++LV + L+++ + + + + +LG I
Sbjct: 1362 RMTQNPNYYNLQGISHRH---LSDHLSELVEQTLSDLEQSKCISIEDEMDVAPL-NLGMI 1417
Query: 1003 ASYYYISHGTISTYNEHLKPTMGDIELCRLFSLSEEFKYVTVRQDEKMELAKLLDRVPIP 1062
A+YYYI++ TI ++ L L + S + E++ + +R E L +L +VP
Sbjct: 1418 AAYYYINYTTIELFSMSLNAKTKVRGLIEIISNAAEYENIPIRHHEDNLLRQLAQKVPHK 1477
Query: 1063 VKE-SLEEPSAKINVLLQAYISQLKLEGLSLTSDMVFITQSAGRLLRALFEIVLKRGWAQ 1121
+ +P K N+LLQA++S+++L L SD I A RL++A +++ GW
Sbjct: 1478 LNNPKFNDPHVKTNLLLQAHLSRMQLSA-ELQSDTEEILSKAIRLIQACVDVLSSNGWLS 1536
Query: 1122 LAEKALNLSKMVTKRMWSVQTPLRQFNGIPNEILMKLEKKDFAWERYYDLSPQE 1175
A A+ L++MVT+ MWS + L+Q +E + + K E +D+ E
Sbjct: 1537 PALAAMELAQMVTQAMWSKDSYLKQLPHFTSEHIKRCTDKGV--ESVFDIMEME 1588
>pdb|4F92|B Chain B, Brr2 Helicase Region S1087l
pdb|4F93|B Chain B, Brr2 Helicase Region S1087l, Mg-Atp
Length = 1724
Score = 1233 bits (3191), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 572/876 (65%), Positives = 713/876 (81%)
Query: 418 LGQRQLLDLDTLAFQQGGLFMANRKCDLPEGSQRFTNKGYEEIHVPAMKHKPLDPNEKLI 477
L RQ+LDL+ L F QG FMAN++C LP+GS R KGYEE+HVPA+K KP E+L+
Sbjct: 2 LAPRQVLDLEDLVFTQGSHFMANKRCQLPDGSFRRQRKGYEEVHVPALKPKPFGSEEQLL 61
Query: 478 KISEMPEWAQPAFKGMTQLNRVQSRVYKSALSSADNILLCAPTGAGKTNVAVLTILQQLA 537
+ ++P++AQ F+G LNR+QS++Y++AL + +N+LLCAPTGAGKTNVA++ +L+++
Sbjct: 62 PVEKLPKYAQAGFEGFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIG 121
Query: 538 LNRNDDGSFNHSNYKIVYVAPMKALVAEVVGNLSNRLQMYDVKVRELSGDQTLTRQQIEE 597
+ N DG+ N ++KI+Y+APM++LV E+VG+ RL Y + V EL+GD L +++I
Sbjct: 122 KHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFGKRLATYGITVAELTGDHQLCKEEISA 181
Query: 598 TQIIVTTPEKWDIITRKSGDRTYTQLVKXXXXXXXXXXXXNRGPVLESIVARTVRQIETT 657
TQIIV TPEKWDIITRK G+RTYTQLV+ +RGPVLE++VAR +R IE T
Sbjct: 182 TQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHDDRGPVLEALVARAIRNIEMT 241
Query: 658 KEHIRLVGLSATLPNYEDVALFLRVNLEKGLFYFDNSYRPVPLSQQYIGIQVKKPLQRFQ 717
+E +RL+GLSATLPNYEDVA FLRV+ KGLFYFDNS+RPVPL Q Y+GI KK ++RFQ
Sbjct: 242 QEDVRLIGLSATLPNYEDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQ 301
Query: 718 LMNDLCYEKVVAVAGKHQVLIFVHSRKETAKTARAIRDTALENDTLGRFLKEDSVSREIL 777
+MN++ YEK++ AGK+QVL+FVHSRKET KTARAIRD LE DTLG FL+E S S E+L
Sbjct: 302 IMNEIVYEKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVL 361
Query: 778 QSHTDMVKSNDLKDLLPYGFAIHHAGMTRGDRQLVEDLFGDGHVQVLVSTATLAWGVNLP 837
++ + K+ +LKDLLPYGFAIHHAGMTR DR LVEDLF D H+QVLVSTATLAWGVNLP
Sbjct: 362 RTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLP 421
Query: 838 AHTVIIKGTQIYNPEKGAWTELSPLDIMQMLGRAGRPQYDSYGEGIIITGHSELRYYLSL 897
AHTVIIKGTQ+Y+PEKG WTEL LDI+QMLGRAGRPQYD+ GEGI+IT H EL+YYLSL
Sbjct: 422 AHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILITSHGELQYYLSL 481
Query: 898 MNQQLPIESQFVSKLADQLNAEIVLGTVQNAKEACNWIGYTYLYIRMLRNPALYGLAPEV 957
+NQQLPIESQ VSKL D LNAEIVLG VQNAK+A NW+GY YLYIRMLR+P LYG++ +
Sbjct: 482 LNQQLPIESQMVSKLPDMLNAEIVLGNVQNAKDAVNWLGYAYLYIRMLRSPTLYGISHDD 541
Query: 958 LKEDITLGERRADLVHTAATILDRNNLVKYDRKSGYFQVTDLGRIASYYYISHGTISTYN 1017
LK D L +RR DLVHTAA +LD+NNLVKYD+K+G FQVT+LGRIAS+YYI++ T+ TYN
Sbjct: 542 LKGDPLLDQRRLDLVHTAALMLDKNNLVKYDKKTGNFQVTELGRIASHYYITNDTVQTYN 601
Query: 1018 EHLKPTMGDIELCRLFSLSEEFKYVTVRQDEKMELAKLLDRVPIPVKESLEEPSAKINVL 1077
+ LKPT+ +IEL R+FSLS EFK +TVR++EK+EL KLL+RVPIPVKES+EEPSAKINVL
Sbjct: 602 QLLKPTLSEIELFRVFSLSSEFKNITVREEEKLELQKLLERVPIPVKESIEEPSAKINVL 661
Query: 1078 LQAYISQLKLEGLSLTSDMVFITQSAGRLLRALFEIVLKRGWAQLAEKALNLSKMVTKRM 1137
LQA+ISQLKLEG +L +DMV++TQ AGRL+RA+FEIVL RGWAQL +K LNL KM+ KRM
Sbjct: 662 LQAFISQLKLEGFALMADMVYVTQLAGRLMRAIFEIVLNRGWAQLTDKTLNLCKMIDKRM 721
Query: 1138 WSVQTPLRQFNGIPNEILMKLEKKDFAWERYYDLSPQELGELIRFPKMGRTLHKFVHQFP 1197
W PLRQF +P E++ K+EKK+F +ER YDL+ E+GELIR PKMG+T+HK+VH FP
Sbjct: 722 WQSMCPLRQFRKLPEEVVKKIEKKNFPFERLYDLNHNEIGELIRMPKMGKTIHKYVHLFP 781
Query: 1198 KLILAAHVQPITRTVLKVELTITPDFLWDDKVHGYVEPFWVIVEDNDGEYILHHEYFMLK 1257
KL L+ H+QPITR+ LKVELTITPDF WD+KVHG E FW++VED D E ILHHEYF+LK
Sbjct: 782 KLELSVHLQPITRSTLKVELTITPDFQWDEKVHGSSEAFWILVEDVDSEVILHHEYFLLK 841
Query: 1258 KQYIEEDHSLNFTVPIYEPLPPQYFIRVVSDKWLGV 1293
+Y +++H + F VP++EPLPPQYFIRVVSD+WL
Sbjct: 842 AKYAQDEHLITFFVPVFEPLPPQYFIRVVSDRWLSC 877
Score = 318 bits (814), Expect = 2e-86, Method: Compositional matrix adjust.
Identities = 219/714 (30%), Positives = 364/714 (50%), Gaps = 31/714 (4%)
Query: 472 PNEKLIKISEMPEWA--QPAFKGMTQ-----LNRVQSRVYKSALSSADNILLCAPTGAGK 524
P +L+ + +P A AF+ + Q N +Q++V+ + +S DN+ + APTG+GK
Sbjct: 896 PPTELLDLQPLPVSALRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGK 955
Query: 525 TNVAVLTILQQLALNRNDDGSFNHSNYKIVYVAPMKALVAEVVGNLSNRLQ-MYDVKVRE 583
T A IL+ L S + VY+ PM+AL +V + + Q + KV
Sbjct: 956 TICAEFAILRML---------LQSSEGRCVYITPMEALAEQVYMDWYEKFQDRLNKKVVL 1006
Query: 584 LSGDQTLTRQQIEETQIIVTTPEKWDIITRKSGDRTYTQLVKXXXXXXXXXXXXNRGPVL 643
L+G+ + + + + II++TPEKWDI++R+ R Q + GPVL
Sbjct: 1007 LTGETSTDLKLLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGGENGPVL 1066
Query: 644 ESIVARTVRQIETTKEH-IRLVGLSATLPNYEDVALFLRVNLEKGLFYFDNSYRPVPLSQ 702
E I +R +R I + E IR+V LS++L N +DVA +L + F F + RPVPL
Sbjct: 1067 EVICSR-MRYISSQIERPIRIVALSSSLSNAKDVAHWLGCS-ATSTFNFHPNVRPVPLEL 1124
Query: 703 QYIGIQVKKPLQRFQLMNDLCYEKVVAVAGKHQVLIFVHSRKETAKTARAIRDTALENDT 762
G + R M Y + + K V++FV SRK+T TA I T +
Sbjct: 1125 HIQGFNISHTQTRLLSMAKPVYHAITKHSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQ 1184
Query: 763 LGRFLKEDSVSREILQSHTDMVKSNDLKDLLPYGFAIHHAGMTRGDRQLVEDLFGDGHVQ 822
RFL + + L + + + + LK+ L G H G++ +R+LVE LF G +Q
Sbjct: 1185 RQRFLH---CTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQ 1241
Query: 823 VLVSTATLAWGVNLPAHTVIIKGTQIYNPEKGAWTELSPLDIMQMLGRAGRPQYDSYGEG 882
V+V++ +L WG+N+ AH VII TQ YN + A+ + D++QM+G A RP D G
Sbjct: 1242 VVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRC 1301
Query: 883 IIITGHSELRYYLSLMNQQLPIESQFVSKLADQLNAEIVLGTVQNAKEACNWIGYTYLYI 942
+I+ S+ ++ + + LP+ES + D NAEIV T++N ++A +++ +T+LY
Sbjct: 1302 VIMCQGSKKDFFKKFLYEPLPVESHLDHCMHDHFNAEIVTKTIENKQDAVDYLTWTFLYR 1361
Query: 943 RMLRNPALYGLAPEVLKEDITLGERRADLVHTAATILDRNNLVKYDRKSGYFQVTDLGRI 1002
RM +NP Y L + L + ++LV + L+++ + + + + +LG I
Sbjct: 1362 RMTQNPNYYNLQGISHRH---LSDHLSELVEQTLSDLEQSKCISIEDEMDVAPL-NLGMI 1417
Query: 1003 ASYYYISHGTISTYNEHLKPTMGDIELCRLFSLSEEFKYVTVRQDEKMELAKLLDRVPIP 1062
A+YYYI++ TI ++ L L + S + E++ + +R E L +L +VP
Sbjct: 1418 AAYYYINYTTIELFSMSLNAKTKVRGLIEIISNAAEYENIPIRHHEDNLLRQLAQKVPHK 1477
Query: 1063 VKE-SLEEPSAKINVLLQAYISQLKLEGLSLTSDMVFITQSAGRLLRALFEIVLKRGWAQ 1121
+ +P K N+LLQA++S+++L L SD I A RL++A +++ GW
Sbjct: 1478 LNNPKFNDPHVKTNLLLQAHLSRMQLSA-ELQSDTEEILSKAIRLIQACVDVLSSNGWLS 1536
Query: 1122 LAEKALNLSKMVTKRMWSVQTPLRQFNGIPNEILMKLEKKDFAWERYYDLSPQE 1175
A A+ L++MVT+ MWS + L+Q +E + + K E +D+ E
Sbjct: 1537 PALAAMELAQMVTQAMWSKDSYLKQLPHFTSEHIKRCTDKGV--ESVFDIMEME 1588
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 153 bits (387), Expect = 6e-37, Method: Compositional matrix adjust.
Identities = 136/445 (30%), Positives = 211/445 (47%), Gaps = 57/445 (12%)
Query: 491 KGMTQLNRVQSRVYKSALSSADNILLCAPTGAGKTNVAVLTILQQLALNRNDDGSFNHSN 550
+G+ +LN Q+ K L + +LL +PTG+GKT +A + I+ L N
Sbjct: 26 RGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKNGG--------- 76
Query: 551 YKIVYVAPMKALVAEVVGNLSNRLQMYDVKVRELSGDQTLTRQQIEETQIIVTTPEKWDI 610
K +YV P++AL E + ++ KV SGD ++ II+TT EK D
Sbjct: 77 -KAIYVTPLRALTNEKYLTFKD-WELIGFKVAMTSGDYDTDDAWLKNYDIIITTYEKLDS 134
Query: 611 ITRKSGDRTYTQLVKXXXXXXXXXXXXNRGPVLESIVARTVRQIETTKEHIRLVGLSATL 670
+ R + ++ RGPV+ES+ R R+ L+ LSAT+
Sbjct: 135 LWRHRPE-WLNEVNYFVLDELHYLNDPERGPVVESVTIRAKRR--------NLLALSATI 185
Query: 671 PNYEDVALFLRVNLEKGLFYFDNSYRPVPLSQQYIGIQVKKPLQRFQLMNDLCYEKVV-- 728
NY+ +A +L G ++RPVPL + I + KK + + D +KV
Sbjct: 186 SNYKQIAKWL------GAEPVATNWRPVPLIEGVIYPERKKK-EYNVIFKDNTTKKVHGD 238
Query: 729 ---------AVAGKHQVLIFVHSRKETAKTARAIRD----TALENDTLGRFLKEDSVSRE 775
+++ QVL+F +SRK TA I + +L+ + L LK+ E
Sbjct: 239 DAIIAYTLDSLSKNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEE 298
Query: 776 ILQSHTDMVKSNDLKDLLPYGFAIHHAGMTRGDRQLVEDLFGDGHVQVLVSTATLAWGVN 835
+++KS L+ G A HHAG+++ R L+E+ F ++V+V+T TLA GVN
Sbjct: 299 GGSDEKELLKS-----LISKGVAYHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVN 353
Query: 836 LPAHTVIIKGTQIYNPE-KGAWTELSPLDIMQMLGRAGRPQYDSYGEGIIITGHSE---- 890
LPA TVII +N + G + E+ ++ QM GRAGRP +D GE I++ E
Sbjct: 354 LPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRAGRPGFDQIGESIVVVRDKEDVDR 413
Query: 891 --LRYYLSLMNQQLPIESQFVSKLA 913
+Y LS + PIES+ S+ A
Sbjct: 414 VFKKYVLSDVE---PIESKLGSERA 435
>pdb|2P6R|A Chain A, Crystal Structure Of Superfamily 2 Helicase Hel308 In
Complex With Unwound Dna
pdb|2P6U|A Chain A, Apo Structure Of The Hel308 Superfamily 2 Helicase
Length = 702
Score = 145 bits (367), Expect = 1e-34, Method: Compositional matrix adjust.
Identities = 119/386 (30%), Positives = 193/386 (50%), Gaps = 46/386 (11%)
Query: 510 SADNILLCAPTGAGKTNVAVLTILQQLALNRNDDGSFNHSNYKIVYVAPMKALVAEVVGN 569
S N+LL PT AGKT +L ++A+ R K +YV P++AL E +
Sbjct: 39 SGKNLLLAMPTAAGKT------LLAEMAMVRE-----AIKGGKSLYVVPLRALAGEKYES 87
Query: 570 LSNRLQMYDVKVRELSGDQTLTRQQIEETQIIVTTPEKWD--IITRKSGDRTYTQLVKXX 627
+ + +++ +GD + + + IIVTT EK D I R S + + LV
Sbjct: 88 F-KKWEKIGLRIGISTGDYESRDEHLGDCDIIVTTSEKADSLIRNRASWIKAVSCLV--- 143
Query: 628 XXXXXXXXXXNRGPVLESIVARTVRQIETTKEHIRLVGLSATLPNYEDVALFLRVNLEKG 687
RG LE +V + R + +R++GLSAT PN ++A +L +
Sbjct: 144 VDEIHLLDSEKRGATLEILVTKMRRM----NKALRVIGLSATAPNVTEIAEWLDAD---- 195
Query: 688 LFYFDNSYRPVPLSQQYIGIQVKKPLQ----RFQLMNDLCYEKVV--AVAGKHQVLIFVH 741
Y+ + +RPVPL + G+ + L+ F + +E++V VA VL+F
Sbjct: 196 --YYVSDWRPVPLVE---GVLCEGTLELFDGAFSTSRRVKFEELVEECVAENGGVLVFES 250
Query: 742 SRKETAKTARAIRDTALENDTLGRFLKEDSVSREILQSHTDMVKSNDLKDLLPYGFAIHH 801
+R+ KTA ++ +A+ ++++ + + + IL+ + + S L + + G A HH
Sbjct: 251 TRRGAEKTA--VKLSAI----TAKYVENEGLEKAILEENEGEM-SRKLAECVRKGAAFHH 303
Query: 802 AGMTRGDRQLVEDLFGDGHVQVLVSTATLAWGVNLPAHTVIIKGTQIYNPEKGAWTELSP 861
AG+ G R++VED F G+++V+V+T TLA GVNLPA VI++ ++ G +
Sbjct: 304 AGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFD---GYSKRIKV 360
Query: 862 LDIMQMLGRAGRPQYDSYGEGIIITG 887
+ QM GRAGRP D GE III G
Sbjct: 361 SEYKQMAGRAGRPGMDERGEAIIIVG 386
>pdb|2ZJ2|A Chain A, Archaeal Dna Helicase Hjm Apo State In Form 1
pdb|2ZJ5|A Chain A, Archaeal Dna Helicase Hjm Complexed With Adp In Form 1
pdb|2ZJ8|A Chain A, Archaeal Dna Helicase Hjm Apo State In Form 2
pdb|2ZJA|A Chain A, Archaeal Dna Helicase Hjm Complexed With Amppcp In Form 2
Length = 720
Score = 133 bits (335), Expect = 5e-31, Method: Compositional matrix adjust.
Identities = 147/540 (27%), Positives = 243/540 (45%), Gaps = 68/540 (12%)
Query: 491 KGMTQLNRVQSRVYKSALSSADNILLCAPTGAGKTNVAVLTILQQLALNRNDDGSFNHSN 550
+G+ Q+ KS + N L+ PT +GKT +A + ++ ++
Sbjct: 19 RGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQGG--------- 69
Query: 551 YKIVYVAPMKALVAEVVGNLSNRLQMYDVKVRELSGDQTLTRQQIEETQIIVTTPEKWDI 610
K VY+ P+KAL E + + ++V +GD + + + II+ T EK+D
Sbjct: 70 -KAVYIVPLKALAEEKFQEFQD-WEKIGLRVAMATGDYDSKDEWLGKYDIIIATAEKFDS 127
Query: 611 ITRKSGDRTYTQLVKXXXXXXXXXX-XXNRGPVLESIVARTVRQIETTKEHIRLVGLSAT 669
+ R ++ + VK +RG LE I+A + + + ++GLSAT
Sbjct: 128 LLRHGS--SWIKDVKILVADEIHLIGSRDRGATLEVILAHMLGKAQ-------IIGLSAT 178
Query: 670 LPNYEDVALFLRVNLEKGLFYFDNSYRPVPLSQQ--YIGIQV--KKPLQRFQLMNDLCYE 725
+ N E++A +L L + +RPV L + Y G + RF +L Y+
Sbjct: 179 IGNPEELAEWLNAEL------IVSDWRPVKLRRGVFYQGFVTWEDGSIDRFSSWEELVYD 232
Query: 726 KVVAVAGKHQVLIFVHSRKETAKTARAI--RDTALENDTLGRFLKEDSVSREILQSHTDM 783
A+ K LIFV+ R++ + A + + +L R L E + S E ++ +
Sbjct: 233 ---AIRKKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKL 289
Query: 784 VKSNDLKDLLPYGFAIHHAGMTRGDRQLVEDLFGDGHVQVLVSTATLAWGVNLPAHTVII 843
K+ + G A HHAG+ R +R LVE+ F G ++ +V+T TL+ G+N PA VII
Sbjct: 290 AKA------IRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVII 343
Query: 844 KGTQIYNPEKGAWTELSPLDIMQMLGRAGRPQYDSYGEGIIITGHSELR----YYLSLMN 899
+ I+ + +++ QMLGRAGRP+YD GEGII++ + R +Y+
Sbjct: 344 R--DIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDDPREVMNHYIFGKP 401
Query: 900 QQLPIESQFVSKLADQLNAEIVLGTVQNAKEACNWIGYT-YLYIR--------MLRNPAL 950
++L + S L Q+ A I +E +I T Y Y R +RN
Sbjct: 402 EKLFSQLSNESNLRSQVLALIATFGYSTVEEILKFISNTFYAYQRKDTYSLEEKIRNILY 461
Query: 951 YGLAPEVLK---ED----ITLGERRADLV---HTAATILDR-NNLVKYDRKSGYFQVTDL 999
+ L E ++ ED ++LG R A L +TA D+ +VK G F + L
Sbjct: 462 FLLENEFIEISLEDKIRPLSLGIRTAKLYIDPYTAKMFKDKMEEVVKDPNPIGIFHLISL 521
>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2
Bound To Amppnp
Length = 997
Score = 78.6 bits (192), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 52/160 (32%), Positives = 84/160 (52%), Gaps = 8/160 (5%)
Query: 736 VLIFVHSRKETAKTARAIRDTALENDT----LGRFLKEDSVSREILQSHTDMVKSNDLKD 791
+++FV S+K + A + N+ + F+ E S++R + + D+ + +
Sbjct: 339 MVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFI-EKSITR-LKKEDRDLPQILKTRS 396
Query: 792 LLPYGFAIHHAGMTRGDRQLVEDLFGDGHVQVLVSTATLAWGVNLPAHTVIIKGTQIYNP 851
LL G A+HH G+ ++L+E LF G ++VL +T T A G+NLP TVI + I
Sbjct: 397 LLERGIAVHHGGLLPIVKELIEILFSKGFIKVLFATETFAMGLNLPTRTVIF--SSIRKH 454
Query: 852 EKGAWTELSPLDIMQMLGRAGRPQYDSYGEGIIITGHSEL 891
+ EL+P + QM GRAGR DS G I++ +S L
Sbjct: 455 DGNGLRELTPGEFTQMAGRAGRRGLDSTGTVIVMAYNSPL 494
Score = 43.9 bits (102), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 51/207 (24%), Positives = 85/207 (41%), Gaps = 30/207 (14%)
Query: 508 LSSADNILLCAPTGAGKTNVAVLTILQQLALNRNDDGSFNHSNY-KIVYVAPMKALVAEV 566
L D++ + A T AGKT VA I + H N K +Y +P+KAL +
Sbjct: 51 LEQGDSVFVAAHTSAGKTVVAEYAI------------AMAHRNMTKTIYTSPIKALSNQK 98
Query: 567 VGNLSNRLQMYDVKVRELSGDQTLTRQQIEETQIIVTTPEKWDIITRKSGDRTYTQLVKX 626
+ DV + ++GD + + +I+TT ++ R + + V
Sbjct: 99 FRDFKETFD--DVNIGLITGDVQINP---DANCLIMTTEILRSMLYRGADLIRDVEFV-- 151
Query: 627 XXXXXXXXXXXNRGPVLESIVARTVRQIETTKEHIRLVGLSATLPNYEDVALFLRVNLEK 686
+RG V E ++ +H++ + LSAT+PN + A ++ +K
Sbjct: 152 IFDEVHYVNDQDRGVVWEEVII-------MLPQHVKFILLSATVPNTYEFANWIGRTKQK 204
Query: 687 GLFYFDNSYRPVPLSQQYIGIQVKKPL 713
++ RPVPL I I KK L
Sbjct: 205 NIYVISTPKRPVPLE---INIWAKKEL 228
>pdb|3IM1|A Chain A, Structure Of The C-Terminal Sec63 Unit Of Yeast Brr2,
P212121 Form
pdb|3IM2|A Chain A, Structure Of The C-Terminal Sec63 Unit Of Yeast Brr2, P41212
Form
Length = 328
Score = 72.8 bits (177), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 62/209 (29%), Positives = 105/209 (50%), Gaps = 10/209 (4%)
Query: 1000 GRIASYYYISHGTISTYNEHLKPTMGDIELCRLFSLSEEFKYVTVRQDEKMELAKLLDRV 1059
G IAS+Y +S TI ++ L T + + S + EF+ V +R+ ++ L KL R+
Sbjct: 15 GLIASHYGVSFFTIQSFVSSLSNTSTLKNMLYVLSTAVEFESVPLRKGDRALLVKLSKRL 74
Query: 1060 PI--PVKESLEEPSAKINVLLQAYISQLKLEGLSLTSDMVFITQSAGRLLRALFEIVLKR 1117
P+ P S S K+ +LLQAY S+L+L + +D+ I + L+ + +I+
Sbjct: 75 PLRFPEHTSSGSVSFKVFLLLQAYFSRLEL-PVDFQNDLKDILEKVVPLINVVVDILSAN 133
Query: 1118 GWAQLAEKALNLSKMVTKRMWSVQTPLRQFNGIPNEILMKLEKKDFAWERYYD---LSPQ 1174
G+ A A++L++M+ + +W V PLRQ N+IL K K+ E YD L +
Sbjct: 134 GYLN-ATTAMDLAQMLIQGVWDVDNPLRQIPHFNNKILEKC--KEINVETVYDIMALEDE 190
Query: 1175 ELGELIRFPKMGRT-LHKFVHQFPKLILA 1202
E E++ + FV+ +P + L
Sbjct: 191 ERDEILTLTDSQLAQVAAFVNNYPNVELT 219
>pdb|2Q0Z|X Chain X, Crystal Structure Of Q9p172SEC63 FROM HOMO SAPIENS.
Northeast Structural Genomics Target Hr1979
Length = 339
Score = 72.0 bits (175), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 50/165 (30%), Positives = 84/165 (50%), Gaps = 2/165 (1%)
Query: 998 DLGRIASYYYISHGTISTYNEHLKPTMGDIELCRLFSLSEEFKYVTVRQDEKMELAKLLD 1057
+LG IA+YYYI++ TI ++ L L + S + E++ + +R E L +L
Sbjct: 17 NLGXIAAYYYINYTTIELFSXSLNAKTKVRGLIEIISNAAEYENIPIRHHEDNLLRQLAQ 76
Query: 1058 RVPIPVKE-SLEEPSAKINVLLQAYISQLKLEGLSLTSDMVFITQSAGRLLRALFEIVLK 1116
+VP + +P K N+LLQA++S+ +L L SD I A RL++A +++
Sbjct: 77 KVPHKLNNPKFNDPHVKTNLLLQAHLSRXQLSA-ELQSDTEEILSKAIRLIQACVDVLSS 135
Query: 1117 RGWAQLAEKALNLSKMVTKRMWSVQTPLRQFNGIPNEILMKLEKK 1161
GW A A L++ VT+ WS + L+Q +E + + K
Sbjct: 136 NGWLSPALAAXELAQXVTQAXWSKDSYLKQLPHFTSEHIKRCTDK 180
>pdb|3HIB|A Chain A, Crystal Structure Of The Second Sec63 Domain Of Yeast Brr2
Length = 318
Score = 66.2 bits (160), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 54/176 (30%), Positives = 89/176 (50%), Gaps = 6/176 (3%)
Query: 1002 IASYYYISHGTISTYNEHLKPTMGDIELCRLFSLSEEFKYVTVRQDEKMELAKLLDRVPI 1061
IAS+Y +S TI ++ L T + S + EF+ V +R+ ++ L KL R+P+
Sbjct: 7 IASHYGVSFFTIQSFVSSLSNTSTLKNXLYVLSTAVEFESVPLRKGDRALLVKLSKRLPL 66
Query: 1062 --PVKESLEEPSAKINVLLQAYISQLKLEGLSLTSDMVFITQSAGRLLRALFEIVLKRGW 1119
P S S K+ +LLQAY S+L+L + +D+ I + L+ + +I+ G+
Sbjct: 67 RFPEHTSSGSVSFKVFLLLQAYFSRLEL-PVDFQNDLKDILEKVVPLINVVVDILSANGY 125
Query: 1120 AQLAEKALNLSKMVTKRMWSVQTPLRQFNGIPNEILMKLEKKDFAWERYYDLSPQE 1175
A A +L++ + + +W V PLRQ N+IL K K+ E YD+ E
Sbjct: 126 LN-ATTAXDLAQXLIQGVWDVDNPLRQIPHFNNKILEKC--KEINVETVYDIXALE 178
>pdb|2XGJ|A Chain A, Structure Of Mtr4, A Dexh Helicase Involved In Nuclear Rna
Processing And Surveillance
pdb|2XGJ|B Chain B, Structure Of Mtr4, A Dexh Helicase Involved In Nuclear Rna
Processing And Surveillance
Length = 1010
Score = 63.5 bits (153), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 32/89 (35%), Positives = 54/89 (60%), Gaps = 2/89 (2%)
Query: 792 LLPYGFAIHHAGMTRGDRQLVEDLFGDGHVQVLVSTATLAWGVNLPAHTVIIKGTQIYNP 851
LL G IHH+G+ ++++E LF +G ++VL +T T + G+N+PA TV+ + ++
Sbjct: 404 LLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDG 463
Query: 852 EKGAWTELSPLDIMQMLGRAGRPQYDSYG 880
++ W +S + +QM GRAGR D G
Sbjct: 464 QQFRW--VSGGEYIQMSGRAGRRGLDDRG 490
>pdb|3L9O|A Chain A, Crystal Structure Of Mtr4, A Co-Factor Of The Nuclear
Exosome
Length = 1108
Score = 63.2 bits (152), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 32/89 (35%), Positives = 54/89 (60%), Gaps = 2/89 (2%)
Query: 792 LLPYGFAIHHAGMTRGDRQLVEDLFGDGHVQVLVSTATLAWGVNLPAHTVIIKGTQIYNP 851
LL G IHH+G+ ++++E LF +G ++VL +T T + G+N+PA TV+ + ++
Sbjct: 502 LLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDG 561
Query: 852 EKGAWTELSPLDIMQMLGRAGRPQYDSYG 880
++ W +S + +QM GRAGR D G
Sbjct: 562 QQFRW--VSGGEYIQMSGRAGRRGLDDRG 588
>pdb|4A2W|A Chain A, Structure Of Full-Length Duck Rig-I
pdb|4A2W|B Chain B, Structure Of Full-Length Duck Rig-I
Length = 936
Score = 38.1 bits (87), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 35/134 (26%), Positives = 60/134 (44%), Gaps = 22/134 (16%)
Query: 500 QSRVYKSALS----SADNILLCAPTGAGKTNVAVLTI---LQQLALNRNDDGSFNHSNYK 552
++R Y+ L+ + N L+CAPTG+GKT V++L Q + R K
Sbjct: 248 KARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGR---------KAK 298
Query: 553 IVYVAPMKALVAEVVGNLSNRLQMYDVKVRELSGD---QTLTRQQIEETQIIVTTPEKWD 609
+V++A + + + + V+ +SG+ + IE++ IIV TP+
Sbjct: 299 VVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQ--- 355
Query: 610 IITRKSGDRTYTQL 623
I+ D T T L
Sbjct: 356 ILVNSFEDGTLTSL 369
>pdb|4A2Q|A Chain A, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
pdb|4A2Q|B Chain B, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
pdb|4A2Q|D Chain D, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
pdb|4A2Q|E Chain E, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
Length = 797
Score = 38.1 bits (87), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 38/146 (26%), Positives = 58/146 (39%), Gaps = 37/146 (25%)
Query: 484 EWAQPAFKGMTQLNRVQSRVYKSALSSADNILLCAPTGAGKTNVAVLTI---LQQLALNR 540
E AQPA G N L+CAPTG+GKT V++L Q + R
Sbjct: 255 ELAQPAING-------------------KNALICAPTGSGKTFVSILICEHHFQNMPAGR 295
Query: 541 NDDGSFNHSNYKIVYVAPMKALVAEVVGNLSNRLQMYDVKVRELSGD---QTLTRQQIEE 597
K+V++A + + + + V+ +SG+ + IE+
Sbjct: 296 ---------KAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIED 346
Query: 598 TQIIVTTPEKWDIITRKSGDRTYTQL 623
+ IIV TP+ I+ D T T L
Sbjct: 347 SDIIVVTPQ---ILVNSFEDGTLTSL 369
>pdb|4A2P|A Chain A, Structure Of Duck Rig-I Helicase Domain
pdb|4A36|A Chain A, Structure Of Duck Rig-I Helicase Domain Bound To 19-Mer
Dsrna And Atp Transition State Analogue
pdb|4A36|B Chain B, Structure Of Duck Rig-I Helicase Domain Bound To 19-Mer
Dsrna And Atp Transition State Analogue
Length = 556
Score = 37.7 bits (86), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 38/146 (26%), Positives = 58/146 (39%), Gaps = 37/146 (25%)
Query: 484 EWAQPAFKGMTQLNRVQSRVYKSALSSADNILLCAPTGAGKTNVAVLTI---LQQLALNR 540
E AQPA G N L+CAPTG+GKT V++L Q + R
Sbjct: 14 ELAQPAING-------------------KNALICAPTGSGKTFVSILICEHHFQNMPAGR 54
Query: 541 NDDGSFNHSNYKIVYVAPMKALVAEVVGNLSNRLQMYDVKVRELSGD---QTLTRQQIEE 597
K+V++A + + + + V+ +SG+ + IE+
Sbjct: 55 ---------KAKVVFLATKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIED 105
Query: 598 TQIIVTTPEKWDIITRKSGDRTYTQL 623
+ IIV TP+ I+ D T T L
Sbjct: 106 SDIIVVTPQ---ILVNSFEDGTLTSL 128
>pdb|4GL2|A Chain A, Structural Basis For Dsrna Duplex Backbone Recognition By
Mda5
pdb|4GL2|B Chain B, Structural Basis For Dsrna Duplex Backbone Recognition By
Mda5
Length = 699
Score = 36.2 bits (82), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/38 (50%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 492 GMTQLNRVQSRVYKSALSSADNILLCAPTGAGKTNVAV 529
M QL Q V + AL NI++C PTG GKT VAV
Sbjct: 4 AMLQLRPYQMEVAQPALE-GKNIIICLPTGCGKTRVAV 40
>pdb|3TMI|A Chain A, Structural Basis For Rna Recognition And Activation Of
Rig-I
Length = 695
Score = 35.8 bits (81), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 43/98 (43%), Gaps = 11/98 (11%)
Query: 513 NILLCAPTGAGKTNVAVLTILQQL-ALNRNDDGSFNHSNYKIVYVAPMKALVAEVVGNLS 571
N ++CAPTG GKT V++L L + G K+V+ A + + S
Sbjct: 29 NTIICAPTGCGKTFVSLLICEHHLKKFPQGQKG-------KVVFFANQIPVYEQQKSVFS 81
Query: 572 NRLQMYDVKVRELSG---DQTLTRQQIEETQIIVTTPE 606
+ + +V +SG + Q +E II+ TP+
Sbjct: 82 KYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQ 119
>pdb|4AY2|A Chain A, Capturing 5' Tri-Phosphorylated Rna Duplex By Rig-I
Length = 687
Score = 35.8 bits (81), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 43/98 (43%), Gaps = 11/98 (11%)
Query: 513 NILLCAPTGAGKTNVAVLTILQQL-ALNRNDDGSFNHSNYKIVYVAPMKALVAEVVGNLS 571
N ++CAPTG GKT V++L L + G K+V+ A + + S
Sbjct: 21 NTIICAPTGCGKTFVSLLICEHHLKKFPQGQKG-------KVVFFANQIPVYEQNKSVFS 73
Query: 572 NRLQMYDVKVRELSG---DQTLTRQQIEETQIIVTTPE 606
+ + +V +SG + Q +E II+ TP+
Sbjct: 74 KYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQ 111
>pdb|2YKG|A Chain A, Structural Insights Into Rna Recognition By Rig-I
Length = 696
Score = 35.8 bits (81), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 43/98 (43%), Gaps = 11/98 (11%)
Query: 513 NILLCAPTGAGKTNVAVLTILQQL-ALNRNDDGSFNHSNYKIVYVAPMKALVAEVVGNLS 571
N ++CAPTG GKT V++L L + G K+V+ A + + S
Sbjct: 30 NTIICAPTGCGKTFVSLLICEHHLKKFPQGQKG-------KVVFFANQIPVYEQNKSVFS 82
Query: 572 NRLQMYDVKVRELSG---DQTLTRQQIEETQIIVTTPE 606
+ + +V +SG + Q +E II+ TP+
Sbjct: 83 KYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQ 120
>pdb|3TBK|A Chain A, Mouse Rig-I Atpase Domain
Length = 555
Score = 35.8 bits (81), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 28/98 (28%), Positives = 41/98 (41%), Gaps = 11/98 (11%)
Query: 513 NILLCAPTGAGKTNVAVLTILQQL-ALNRNDDGSFNHSNYKIVYVA---PMKALVAEVVG 568
N ++CAPTG GKT V++L L G K+V+ A P+ A V
Sbjct: 21 NTIICAPTGCGKTFVSLLICEHHLKKFPCGQKG-------KVVFFANQIPVYEQQATVFS 73
Query: 569 NLSNRLQMYDVKVRELSGDQTLTRQQIEETQIIVTTPE 606
RL + + D + IE+ II+ TP+
Sbjct: 74 RYFERLGYNIASISGATSDSVSVQHIIEDNDIIILTPQ 111
>pdb|3I32|A Chain A, Dimeric Structure Of A Hera Helicase Fragment Including
The C-Terminal Reca Domain, The Dimerization Domain, And
The Rna Binding Domain
Length = 300
Score = 34.7 bits (78), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 27/43 (62%)
Query: 801 HAGMTRGDRQLVEDLFGDGHVQVLVSTATLAWGVNLPAHTVII 843
H M++G+R+ V F G V+VLV+T A G+++P +++
Sbjct: 59 HGDMSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVV 101
>pdb|3B6E|A Chain A, Crystal Structure Of Human Dech-Box Rna Helicase Mda5
(Melanoma Differentiation-Associated Protein 5),
Dech-Domain
Length = 216
Score = 34.3 bits (77), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 18/35 (51%), Positives = 22/35 (62%), Gaps = 1/35 (2%)
Query: 495 QLNRVQSRVYKSALSSADNILLCAPTGAGKTNVAV 529
QL Q V + AL NI++C PTG+GKT VAV
Sbjct: 33 QLRPYQMEVAQPALE-GKNIIICLPTGSGKTRVAV 66
>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp
pdb|3I5Y|A Chain A, Structure Of Mss116p Bound To Ssrna Containing A Single
5-Bru And Amp- Pnp
pdb|3I61|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-beryllium
Fluoride
pdb|3I62|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-aluminum
Fluoride
Length = 563
Score = 33.1 bits (74), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 39/80 (48%), Gaps = 12/80 (15%)
Query: 490 FKGMTQLNRVQSRVYKSALSSAD-NILLCAPTGAGKTNVAVLTILQQLALNRNDDGSFNH 548
F G+T VQ + K LSS D +++ A TG GKT ++ I Q L + D
Sbjct: 92 FPGLTP---VQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFD------ 142
Query: 549 SNY--KIVYVAPMKALVAEV 566
S Y K V VAP + L ++
Sbjct: 143 SQYMVKAVIVAPTRDLALQI 162
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 33.1 bits (74), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 39/78 (50%), Gaps = 8/78 (10%)
Query: 490 FKGMTQLNRVQSRVYKSALSSAD-NILLCAPTGAGKTNVAVLTILQQLALNRNDDGSFNH 548
F G+T VQ + K LSS D +++ A TG GKT ++ I Q L +N D +
Sbjct: 41 FPGLTP---VQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHL-INTKFDSQY-- 94
Query: 549 SNYKIVYVAPMKALVAEV 566
K V VAP + L ++
Sbjct: 95 -MVKAVIVAPTRDLALQI 111
>pdb|3EAQ|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase Hera
Form 2, Complete Dimer, Symmetric
pdb|3EAQ|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase Hera
Form 2, Complete Dimer, Symmetric
pdb|3EAR|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Partial Dimer
pdb|3EAR|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Partial Dimer
pdb|3EAS|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Complete Dimer, Asymmetric
pdb|3EAS|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Complete Dimer, Asymmetric
Length = 212
Score = 32.7 bits (73), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 27/43 (62%)
Query: 801 HAGMTRGDRQLVEDLFGDGHVQVLVSTATLAWGVNLPAHTVII 843
H +++G+R+ V F G V+VLV+T A G+++P +++
Sbjct: 62 HGDLSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVV 104
>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|B Chain B, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|C Chain C, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|D Chain D, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|E Chain E, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|F Chain F, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
Length = 494
Score = 32.7 bits (73), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 26/115 (22%), Positives = 51/115 (44%), Gaps = 19/115 (16%)
Query: 499 VQSRVYKSAL---SSADNILLCAPTGAGKTNVAVLTILQQLALNRNDDGSFNHSNY--KI 553
+Q R+Y+ + N L+ PTG GKT +A++ + + Y K+
Sbjct: 8 IQPRIYQEVIYAKCKETNCLIVLPTGLGKTLIAMMI------------AEYRLTKYGGKV 55
Query: 554 VYVAPMKALVAEVVGNLSNRLQMYDVKVRELSGDQTLTRQQI--EETQIIVTTPE 606
+ +AP K LV + + + K+ L+G+++ + ++IV TP+
Sbjct: 56 LMLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWARAKVIVATPQ 110
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 32.7 bits (73), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 39/80 (48%), Gaps = 12/80 (15%)
Query: 490 FKGMTQLNRVQSRVYKSALSSAD-NILLCAPTGAGKTNVAVLTILQQLALNRNDDGSFNH 548
F G+T VQ + K LSS D +++ A TG GKT ++ I Q L + D
Sbjct: 41 FPGLTP---VQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFD------ 91
Query: 549 SNY--KIVYVAPMKALVAEV 566
S Y K V VAP + L ++
Sbjct: 92 SQYMVKAVIVAPTRDLALQI 111
>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna
Helicase From Sulfolobus Tokodaii
Length = 337
Score = 32.7 bits (73), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 29/116 (25%), Positives = 47/116 (40%), Gaps = 17/116 (14%)
Query: 492 GMTQLNRVQSRVYKSALSSADNILLCAPTGAGKTNVAVLTILQQLALNRNDDGSFNHSNY 551
G VQS+ L N+++ A TG+GKT + IL+
Sbjct: 13 GFKNFTEVQSKTIPLMLQ-GKNVVVRAKTGSGKTAAYAIPILEL--------------GM 57
Query: 552 KIVYVAPMKALVAEVVGNLSNRLQMYDVKVRELSGDQTLTRQ--QIEETQIIVTTP 605
K + V P + L +V ++ + + D KV E+ G Q ++ I+V TP
Sbjct: 58 KSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVRNADIVVATP 113
>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|B Chain B, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|C Chain C, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|D Chain D, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
Length = 434
Score = 32.7 bits (73), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 508 LSSADNILLCAPTGAGKTNVAVLTILQQLALNRNDDGSFNHSNYKIVYVAPMKALVAEV 566
+SS +++ CA TG+GKT +L IL +L D ++V V+P + L ++
Sbjct: 90 ISSGRDLMACAQTGSGKTAAFLLPILSKLL---EDPHELELGRPQVVIVSPTRELAIQI 145
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 31.6 bits (70), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 25/101 (24%), Positives = 43/101 (42%), Gaps = 7/101 (6%)
Query: 761 DTLGRFLKEDSVSREILQSHTDMVKSNDLKDLLPYGF--AIHHAGMTRGDRQLVEDLFGD 818
D L R+++E I+ ++ + L G A +HAG+ R V++ F
Sbjct: 225 DQLXRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQR 284
Query: 819 GHVQVLVSTATLAWGVNLP-----AHTVIIKGTQIYNPEKG 854
+Q++V+T G+N P H I + + Y E G
Sbjct: 285 DDLQIVVATVAFGXGINKPNVRFVVHFDIPRNIESYYQETG 325
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 31.2 bits (69), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 25/101 (24%), Positives = 43/101 (42%), Gaps = 7/101 (6%)
Query: 761 DTLGRFLKEDSVSREILQSHTDMVKSNDLKDLLPYGF--AIHHAGMTRGDRQLVEDLFGD 818
D L R+++E I+ ++ + L G A +HAG+ R V++ F
Sbjct: 225 DQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQR 284
Query: 819 GHVQVLVSTATLAWGVNLP-----AHTVIIKGTQIYNPEKG 854
+Q++V+T G+N P H I + + Y E G
Sbjct: 285 DDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETG 325
>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of
Djvlgb, A Pranarian Vasa-Like Rna Helicase
pdb|1WRB|B Chain B, Crystal Structure Of The N-Terminal Reca-Like Domain Of
Djvlgb, A Pranarian Vasa-Like Rna Helicase
Length = 253
Score = 31.2 bits (69), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 513 NILLCAPTGAGKTNVAVLTILQQLALNRNDDGSFNHSNY-KIVYVAPMKALVAEVVG 568
+I+ CA TG+GKT ++ I+ L + ++ + Y K + +AP + L +++
Sbjct: 62 DIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILS 118
>pdb|1K25|A Chain A, Pbp2x From A Highly Penicillin-Resistant Streptococcus
Pneumoniae Clinical Isolate
pdb|1K25|B Chain B, Pbp2x From A Highly Penicillin-Resistant Streptococcus
Pneumoniae Clinical Isolate
pdb|1K25|C Chain C, Pbp2x From A Highly Penicillin-Resistant Streptococcus
Pneumoniae Clinical Isolate
pdb|1K25|D Chain D, Pbp2x From A Highly Penicillin-Resistant Streptococcus
Pneumoniae Clinical Isolate
Length = 685
Score = 30.8 bits (68), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 25/43 (58%)
Query: 878 SYGEGIIITGHSELRYYLSLMNQQLPIESQFVSKLADQLNAEI 920
S+G+GI +T LR + ++ N + +E +F+S + D N +
Sbjct: 384 SFGQGISVTQTQMLRAFTAIANDGVMLEPKFISAIYDTNNQSV 426
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.319 0.135 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 34,642,895
Number of Sequences: 62578
Number of extensions: 1397732
Number of successful extensions: 3500
Number of sequences better than 100.0: 33
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 3433
Number of HSP's gapped (non-prelim): 39
length of query: 1300
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1190
effective length of database: 8,089,757
effective search space: 9626810830
effective search space used: 9626810830
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (26.6 bits)