RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3476
(1417 letters)
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
and repair].
Length = 845
Score = 378 bits (974), Expect = e-114
Identities = 158/437 (36%), Positives = 237/437 (54%), Gaps = 25/437 (5%)
Query: 310 EVAADNFLSSYDVLVLDEIHERHLHGDFLLGVIKCLLHSTAE-VKIILMSATINIELFHT 368
E+ D LS Y V+++DE HER L+ D LLG++K LL + +K+I+MSAT++ E F
Sbjct: 153 EIQNDPLLSGYSVVIIDEAHERSLNTDILLGLLKDLLARRRDDLKLIIMSATLDAERFSA 212
Query: 369 YFNRIAKIIKVPGRLYPIQLEYHPIVELDRTKSEKLDPGPYIRILSIIDKKYPRTERGDV 428
YF A +I++ GR YP+++ Y P E D L I++ +D G +
Sbjct: 213 YFGN-APVIEIEGRTYPVEIRYLPEAEAD----YILLDA----IVAAVDIHLR-EGSGSI 262
Query: 429 LIFMSGISEISSIVRAAQEYNEKSQGWIVLPLHSTLSLEEQDRVFHYAPEGLRKCIVSTN 488
L+F+ G EI ++ E +LPL+ LS EEQ RVF AP G RK +++TN
Sbjct: 263 LVFLPGQREIERTAEWLEK-AELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATN 321
Query: 489 IAETSITIDGIRFVVDSGKVKEMSYDVTAKMSTLQEFWISKASAEQRKGRAGRTGPGVCY 548
IAETS+TI GIR+V+DSG KE YD ++ L+ ISKASA+QR GRAGRTGPG+CY
Sbjct: 322 IAETSLTIPGIRYVIDSGLAKEKRYDPRTGLTRLETEPISKASADQRAGRAGRTGPGICY 381
Query: 549 RLYSEEQYSLLAEYSTPEIRRVSIDSLLLSLVCMGLG-DVRKFPFLEAPPAENIESSVRS 607
RLYSEE + E++ PEI R + L+L L +G+G D+ FPFL+ PP I++++
Sbjct: 382 RLYSEEDFLAFPEFTLPEILRTDLSGLVLQLKSLGIGQDIAPFPFLDPPPEAAIQAALTL 441
Query: 608 LTQHGAIDSKERVTSLGRFLSDLPVDIPLGKMLVFGSMFHQIDTVLSLAAVLSVQ---SP 664
L + GA+D ++T LG+ +S LP+D L +ML+ + ++A++LS Q S
Sbjct: 442 LQELGALDDSGKLTPLGKQMSLLPLDPRLARMLLTAPEGGCLGEAATIASMLSEQDRESD 501
Query: 665 FTN-RAFRDPDCET------ARKELESNHGDPLTVLNAYKEWLGVKKDRVRS--KKWCKR 715
F+ R R+ GD L +L A+ + + K+ + C+
Sbjct: 502 FSRDVKLRKQRTAQDLLKRLKRRNAADPRGDHLLLLEAFPDRIARKRAKGEYLRANGCRA 561
Query: 716 RGIEEQRFYEVTKLRSQ 732
+ + +
Sbjct: 562 MLFPTKALSRAPWIIAA 578
Score = 131 bits (332), Expect = 6e-31
Identities = 49/124 (39%), Positives = 78/124 (62%), Gaps = 3/124 (2%)
Query: 19 FKQKEKFSTLMKIRETQNSLPVAQYKQEIIDTVLKERVVIIAGDTGCGKSTQIPQYLVQA 78
+ + + + I E ++ LPV + EI+ + + +VVII G+TG GK+TQ+PQ+L++
Sbjct: 30 MDARSRSANVPDILEYRSGLPVTAVRDEILKAIEQNQVVIIVGETGSGKTTQLPQFLLEE 89
Query: 79 GF---QRIACTQPRRIACISLSKRVAYETLSQYSNLVGYQIRFEKHRREKTKIVFITEGL 135
G +I CTQPRR+A S+++RVA E + VGY IRFE +T+I +T+G+
Sbjct: 90 GLGIAGKIGCTQPRRLAARSVAERVAEELGEKLGETVGYSIRFESKVSPRTRIKVMTDGI 149
Query: 136 LLRQ 139
LLR+
Sbjct: 150 LLRE 153
Score = 121 bits (305), Expect = 1e-27
Identities = 47/127 (37%), Positives = 74/127 (58%), Gaps = 1/127 (0%)
Query: 809 RTGPGVCYRLYSEEQYSLLAEYSTPEIRRVSIDSLLLSLVCMGLG-DVRKFPFLEAPPAE 867
RTGPG+CYRLYSEE + E++ PEI R + L+L L +G+G D+ FPFL+ PP
Sbjct: 374 RTGPGICYRLYSEEDFLAFPEFTLPEILRTDLSGLVLQLKSLGIGQDIAPFPFLDPPPEA 433
Query: 868 NIESSVRSLTQHGAIDSKERVTTLGRFLSDLPVDIPLGKMLVFGSMFHQIDTMLLLDLAL 927
I++++ L + GA+D ++T LG+ +S LP+D L +ML+ + + L
Sbjct: 434 AIQAALTLLQELGALDDSGKLTPLGKQMSLLPLDPRLARMLLTAPEGGCLGEAATIASML 493
Query: 928 NFGAIDS 934
+ +S
Sbjct: 494 SEQDRES 500
Score = 69.7 bits (171), Expect = 9e-12
Identities = 28/59 (47%), Positives = 40/59 (67%), Gaps = 1/59 (1%)
Query: 1119 DNFLSSYDVLVLDEIHERHLHGDFLLGVIKCLLHSTAE-VKIILMSATINIELFHTYFN 1176
D LS Y V+++DE HER L+ D LLG++K LL + +K+I+MSAT++ E F YF
Sbjct: 157 DPLLSGYSVVIIDEAHERSLNTDILLGLLKDLLARRRDDLKLIIMSATLDAERFSAYFG 215
Score = 50.4 bits (121), Expect = 7e-06
Identities = 15/55 (27%), Positives = 27/55 (49%)
Query: 980 GAIDSKERVTSLGRFLSDLPVDIPLGKMLVFGSMFHQIDTMLLLDLALNFGAIDS 1034
GA+D ++T LG+ +S LP+D L +ML+ + + L+ +S
Sbjct: 446 GALDDSGKLTPLGKQMSLLPLDPRLARMLLTAPEGGCLGEAATIASMLSEQDRES 500
Score = 47.7 bits (114), Expect = 5e-05
Identities = 15/28 (53%), Positives = 18/28 (64%)
Query: 230 TDNFLSSYDILILDEVHERHLYGDFLLG 257
D LS Y ++I+DE HER L D LLG
Sbjct: 156 NDPLLSGYSVVIIDEAHERSLNTDILLG 183
Score = 46.9 bits (112), Expect = 8e-05
Identities = 14/50 (28%), Positives = 25/50 (50%)
Query: 1030 GAIDSKERVTSLGRFLSDLPVDIPLGKMLVFGSMFHQIDTMLLLDLALNF 1079
GA+D ++T LG+ +S LP+D L +ML+ + + L+
Sbjct: 446 GALDDSGKLTPLGKQMSLLPLDPRLARMLLTAPEGGCLGEAATIASMLSE 495
>gnl|CDD|233659 TIGR01967, DEAH_box_HrpA, ATP-dependent helicase HrpA. This model
represents HrpA, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria
and a few high-GC Gram-positive bacteria. HrpA is about
1300 amino acids long, while its paralog HrpB, also
uncharacterized, is about 800 amino acids long. Related
characterized eukarotic proteins are RNA helicases
associated with pre-mRNA processing [Unknown function,
Enzymes of unknown specificity].
Length = 1283
Score = 287 bits (737), Expect = 2e-79
Identities = 165/444 (37%), Positives = 245/444 (55%), Gaps = 27/444 (6%)
Query: 310 EVAADNFLSSYDVLVLDEIHERHLHGDFLLGVIKCLLHSTAEVKIILMSATINIELFHTY 369
E D FLS YD +++DE HER L+ DFLLG +K LL ++KII+ SATI+ E F +
Sbjct: 170 ETQQDRFLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDLKIIITSATIDPERFSRH 229
Query: 370 FNRIAKIIKVPGRLYPIQLEYHPIVELDRTKSEKLDPGPYIRILSIIDKKYPRTERGDVL 429
FN A II+V GR YP+++ Y P+VE + E D IL +D+ + GD+L
Sbjct: 230 FNN-APIIEVSGRTYPVEVRYRPLVE----EQEDDDLDQLEAILDAVDELFAEGP-GDIL 283
Query: 430 IFMSGISEISSIVRAAQEYNEKSQ--GWIVLPLHSTLSLEEQDRVFHYAPEGLRKCIVST 487
IF+ G EI R A E K +LPL++ LS +EQ RVF P R+ +++T
Sbjct: 284 IFLPGEREI----RDAAEILRKRNLRHTEILPLYARLSNKEQQRVFQ--PHSGRRIVLAT 337
Query: 488 NIAETSITIDGIRFVVDSGKVKEMSYDVTAKMSTLQEFWISKASAEQRKGRAGRTGPGVC 547
N+AETS+T+ GI +V+D+G + Y K+ L IS+ASA QRKGR GR PG+C
Sbjct: 338 NVAETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVAPGIC 397
Query: 548 YRLYSEEQYSLLAEYSTPEIRRVSIDSLLLSLVCMGLGDVRKFPFLEAPPAENIESSVRS 607
RLYSEE ++ E++ PEI R ++ S++L ++ + LGD+ FPF+EAP I R
Sbjct: 398 IRLYSEEDFNSRPEFTDPEILRTNLASVILQMLALRLGDIAAFPFIEAPDPRAIRDGFRL 457
Query: 608 LTQHGAIDSKE---RVTSLGRFLSDLPVDIPLGKMLVFGSMFHQIDTVLSLAAVLSVQSP 664
L + GA+D E ++T +GR L+ LPVD L +ML+ + VL +A+ LS+Q P
Sbjct: 458 LEELGALDDDEAEPQLTPIGRQLAQLPVDPRLARMLLEAHRLGCLQEVLIIASALSIQDP 517
Query: 665 FTNRAFRDPDCETARKELESNHGDPLTVLNAY-KEWLGVKKDR-VRSK----KWCKRRGI 718
R + + A + + DP + + W +++ R S C+++ +
Sbjct: 518 RE----RPMEKQQAADQAHARFKDPRSDFLSRVNLWRHIEEQRQALSANQFRNACRKQYL 573
Query: 719 EEQRFYEVTKLRSQFKQVLGDSGL 742
R E + Q QV+ + GL
Sbjct: 574 NYLRVREWQDIYRQLTQVVKELGL 597
Score = 99.1 bits (247), Expect = 1e-20
Identities = 50/132 (37%), Positives = 78/132 (59%), Gaps = 5/132 (3%)
Query: 809 RTGPGVCYRLYSEEQYSLLAEYSTPEIRRVSIDSLLLSLVCMGLGDVRKFPFLEAPPAEN 868
R PG+C RLYSEE ++ E++ PEI R ++ S++L ++ + LGD+ FPF+EAP
Sbjct: 391 RVAPGICIRLYSEEDFNSRPEFTDPEILRTNLASVILQMLALRLGDIAAFPFIEAPDPRA 450
Query: 869 IESSVRSLTQHGAIDSKE---RVTTLGRFLSDLPVDIPLGKMLVFGSMFHQIDTMLLLDL 925
I R L + GA+D E ++T +GR L+ LPVD L +ML+ + +L++
Sbjct: 451 IRDGFRLLEELGALDDDEAEPQLTPIGRQLAQLPVDPRLARMLLEAHRLGCLQEVLIIAS 510
Query: 926 ALNFGAIDSKER 937
AL+ D +ER
Sbjct: 511 ALSIQ--DPRER 520
Score = 90.6 bits (225), Expect = 4e-18
Identities = 38/104 (36%), Positives = 66/104 (63%), Gaps = 3/104 (2%)
Query: 37 SLPVAQYKQEIIDTVLKERVVIIAGDTGCGKSTQIPQYLVQAGFQR---IACTQPRRIAC 93
+LPV+ +++I + + + +VVIIAG+TG GK+TQ+P+ ++ G I TQPRR+A
Sbjct: 65 NLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICLELGRGSHGLIGHTQPRRLAA 124
Query: 94 ISLSKRVAYETLSQYSNLVGYQIRFEKHRREKTKIVFITEGLLL 137
++++R+A E + VGY++RF T + +T+G+LL
Sbjct: 125 RTVAQRIAEELGTPLGEKVGYKVRFHDQVSSNTLVKLMTDGILL 168
Score = 70.2 bits (172), Expect = 6e-12
Identities = 31/58 (53%), Positives = 41/58 (70%)
Query: 1119 DNFLSSYDVLVLDEIHERHLHGDFLLGVIKCLLHSTAEVKIILMSATINIELFHTYFN 1176
D FLS YD +++DE HER L+ DFLLG +K LL ++KII+ SATI+ E F +FN
Sbjct: 174 DRFLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDLKIIITSATIDPERFSRHFN 231
Score = 42.8 bits (101), Expect = 0.001
Identities = 19/34 (55%), Positives = 22/34 (64%)
Query: 231 DNFLSSYDILILDEVHERHLYGDFLLGVISPPLH 264
D FLS YD +I+DE HER L DFLLG + L
Sbjct: 174 DRFLSRYDTIIIDEAHERSLNIDFLLGYLKQLLP 207
Score = 36.7 bits (85), Expect = 0.12
Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 1018 DTMLLLDLALNFGAIDSKE---RVTSLGRFLSDLPVDIPLGKMLVFGSMFHQIDTMLLLD 1074
D LL+ GA+D E ++T +GR L+ LPVD L +ML+ + +L++
Sbjct: 453 DGFRLLE---ELGALDDDEAEPQLTPIGRQLAQLPVDPRLARMLLEAHRLGCLQEVLIIA 509
Query: 1075 LALNFVHHSEEEEEEEAG 1092
AL+ E E++
Sbjct: 510 SALSIQDPRERPMEKQQA 527
Score = 35.1 bits (81), Expect = 0.31
Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 8/73 (10%)
Query: 968 DTMLLLDLALNFGAIDSKE---RVTSLGRFLSDLPVDIPLGKMLVFGSMFHQIDTMLLLD 1024
D LL+ GA+D E ++T +GR L+ LPVD L +ML+ + +L++
Sbjct: 453 DGFRLLE---ELGALDDDEAEPQLTPIGRQLAQLPVDPRLARMLLEAHRLGCLQEVLIIA 509
Query: 1025 LALNFGAIDSKER 1037
AL+ D +ER
Sbjct: 510 SALSIQ--DPRER 520
>gnl|CDD|182986 PRK11131, PRK11131, ATP-dependent RNA helicase HrpA; Provisional.
Length = 1294
Score = 280 bits (719), Expect = 4e-77
Identities = 146/361 (40%), Positives = 215/361 (59%), Gaps = 17/361 (4%)
Query: 310 EVAADNFLSSYDVLVLDEIHERHLHGDFLLGVIKCLLHSTAEVKIILMSATINIELFHTY 369
E+ D L YD +++DE HER L+ DF+LG +K LL ++K+I+ SATI+ E F +
Sbjct: 177 EIQQDRLLMQYDTIIIDEAHERSLNIDFILGYLKELLPRRPDLKVIITSATIDPERFSRH 236
Query: 370 FNRIAKIIKVPGRLYPIQLEYHPIVE-LDRTKSEKLDPGPYIRILSIIDKKYPRTERGDV 428
FN A II+V GR YP+++ Y PIVE D T+ ++L I +D+ R GD+
Sbjct: 237 FNN-APIIEVSGRTYPVEVRYRPIVEEADDTERDQLQA-----IFDAVDE-LGREGPGDI 289
Query: 429 LIFMSGISEISSIVRAAQEYNEKSQGWIVLPLHSTLSLEEQDRVFHYAPEGLRKCIVSTN 488
LIFMSG EI A + N + +LPL++ LS EQ+RVF R+ +++TN
Sbjct: 290 LIFMSGEREIRDTADALNKLNLRHTE--ILPLYARLSNSEQNRVFQ--SHSGRRIVLATN 345
Query: 489 IAETSITIDGIRFVVDSGKVKEMSYDVTAKMSTLQEFWISKASAEQRKGRAGRTGPGVCY 548
+AETS+T+ GI++V+D G + Y K+ L IS+ASA QRKGR GR G+C
Sbjct: 346 VAETSLTVPGIKYVIDPGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVSEGICI 405
Query: 549 RLYSEEQYSLLAEYSTPEIRRVSIDSLLLSLVCMGLGDVRKFPFLEAPPAENIESSVRSL 608
RLYSE+ + E++ PEI R ++ S++L + +GLGD+ FPF+EAP NI+ VR L
Sbjct: 406 RLYSEDDFLSRPEFTDPEILRTNLASVILQMTALGLGDIAAFPFVEAPDKRNIQDGVRLL 465
Query: 609 TQHGAIDSKE-----RVTSLGRFLSDLPVDIPLGKMLVFGSMFHQIDTVLSLAAVLSVQS 663
+ GAI + E ++T LGR L+ LPVD L +M++ + V+ + + LS+Q
Sbjct: 466 EELGAITTDEQASAYKLTPLGRQLAQLPVDPRLARMVLEAQKHGCVREVMIITSALSIQD 525
Query: 664 P 664
P
Sbjct: 526 P 526
Score = 95.5 bits (238), Expect = 1e-19
Identities = 45/106 (42%), Positives = 67/106 (63%), Gaps = 5/106 (4%)
Query: 809 RTGPGVCYRLYSEEQYSLLAEYSTPEIRRVSIDSLLLSLVCMGLGDVRKFPFLEAPPAEN 868
R G+C RLYSE+ + E++ PEI R ++ S++L + +GLGD+ FPF+EAP N
Sbjct: 398 RVSEGICIRLYSEDDFLSRPEFTDPEILRTNLASVILQMTALGLGDIAAFPFVEAPDKRN 457
Query: 869 IESSVRSLTQHGAIDSKE-----RVTTLGRFLSDLPVDIPLGKMLV 909
I+ VR L + GAI + E ++T LGR L+ LPVD L +M++
Sbjct: 458 IQDGVRLLEELGAITTDEQASAYKLTPLGRQLAQLPVDPRLARMVL 503
Score = 94.4 bits (235), Expect = 3e-19
Identities = 40/104 (38%), Positives = 68/104 (65%), Gaps = 3/104 (2%)
Query: 37 SLPVAQYKQEIIDTVLKERVVIIAGDTGCGKSTQIPQYLVQAGFQR---IACTQPRRIAC 93
+LPV+Q KQ+I++ + +VVI+AG+TG GK+TQ+P+ ++ G I TQPRR+A
Sbjct: 72 NLPVSQKKQDILEAIRDHQVVIVAGETGSGKTTQLPKICLELGRGVKGLIGHTQPRRLAA 131
Query: 94 ISLSKRVAYETLSQYSNLVGYQIRFEKHRREKTKIVFITEGLLL 137
+++ R+A E ++ VGY++RF + T + +T+G+LL
Sbjct: 132 RTVANRIAEELETELGGCVGYKVRFNDQVSDNTMVKLMTDGILL 175
Score = 66.2 bits (162), Expect = 1e-10
Identities = 27/58 (46%), Positives = 39/58 (67%)
Query: 1119 DNFLSSYDVLVLDEIHERHLHGDFLLGVIKCLLHSTAEVKIILMSATINIELFHTYFN 1176
D L YD +++DE HER L+ DF+LG +K LL ++K+I+ SATI+ E F +FN
Sbjct: 181 DRLLMQYDTIIIDEAHERSLNIDFILGYLKELLPRRPDLKVIITSATIDPERFSRHFN 238
Score = 43.1 bits (102), Expect = 0.001
Identities = 15/31 (48%), Positives = 20/31 (64%)
Query: 227 QVATDNFLSSYDILILDEVHERHLYGDFLLG 257
++ D L YD +I+DE HER L DF+LG
Sbjct: 177 EIQQDRLLMQYDTIIIDEAHERSLNIDFILG 207
Score = 35.4 bits (82), Expect = 0.28
Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 971 LLLDL-ALNFGAIDSKERVTSLGRFLSDLPVDIPLGKMLV 1009
LL +L A+ S ++T LGR L+ LPVD L +M++
Sbjct: 464 LLEELGAITTDEQASAYKLTPLGRQLAQLPVDPRLARMVL 503
Score = 35.4 bits (82), Expect = 0.28
Identities = 16/40 (40%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 1021 LLLDL-ALNFGAIDSKERVTSLGRFLSDLPVDIPLGKMLV 1059
LL +L A+ S ++T LGR L+ LPVD L +M++
Sbjct: 464 LLEELGAITTDEQASAYKLTPLGRQLAQLPVDPRLARMVL 503
>gnl|CDD|233660 TIGR01970, DEAH_box_HrpB, ATP-dependent helicase HrpB. This model
represents HrpB, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria,
but also in a few species of other lineages. The member
from Rhizobium meliloti has been designated HelO. HrpB
is typically about 800 residues in length, while its
paralog HrpA (TIGR01967), also uncharacterized, is about
1300 amino acids long. Related characterized eukarotic
proteins are RNA helicases associated with pre-mRNA
processing [Unknown function, Enzymes of unknown
specificity].
Length = 819
Score = 221 bits (564), Expect = 1e-59
Identities = 117/357 (32%), Positives = 184/357 (51%), Gaps = 22/357 (6%)
Query: 313 ADNFLSSYDVLVLDEIHERHLHGD----FLLGVIKCLLHSTAEVKIILMSATINIELFHT 368
D L L+ DE HER L D L V L ++KI+ MSAT++ E +
Sbjct: 107 DDPELDGVGALIFDEFHERSLDADLGLALALDVQSSL---REDLKILAMSATLDGERLSS 163
Query: 369 YFNRIAKIIKVPGRLYPIQLEYHPIVELDRTKSEKLDPGPYIRILSIIDKKYPRTERGDV 428
A +++ GR +P+++ Y P ++L+ + + +E G +
Sbjct: 164 LLPD-APVVESEGRSFPVEIRYLP-----LRGDQRLEDAVSRAVEHAL-----ASETGSI 212
Query: 429 LIFMSGISEISSIVRAAQEYNEKSQGWIVL-PLHSTLSLEEQDRVFHYAPEGLRKCIVST 487
L+F+ G +EI R ++ E+ +++ PL+ LSL QDR P+G RK +++T
Sbjct: 213 LVFLPGQAEIR---RVQEQLAERLDSDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLAT 269
Query: 488 NIAETSITIDGIRFVVDSGKVKEMSYDVTAKMSTLQEFWISKASAEQRKGRAGRTGPGVC 547
NIAETS+TI+GIR V+DSG + +D ++ L+ IS+ASA QR GRAGR PGVC
Sbjct: 270 NIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQASATQRAGRAGRLEPGVC 329
Query: 548 YRLYSEEQYSLLAEYSTPEIRRVSIDSLLLSLVCMGLGDVRKFPFLEAPPAENIESSVRS 607
YRL+SEEQ+ L PEI + + L L L G D +L+APP+ + ++ +
Sbjct: 330 YRLWSEEQHQRLPAQDEPEILQADLSGLALELAQWGAKDPSDLRWLDAPPSVALAAARQL 389
Query: 608 LTQHGAIDSKERVTSLGRFLSDLPVDIPLGKMLVFGSMFHQIDTVLSLAAVLSVQSP 664
L + GA+D++ R+T+ G+ ++ L L ML+ LAA+L +
Sbjct: 390 LQRLGALDAQGRLTAHGKAMAALGCHPRLAAMLLSAHSTGLAALACDLAALLEERGL 446
Score = 71.7 bits (176), Expect = 2e-12
Identities = 36/103 (34%), Positives = 56/103 (54%)
Query: 809 RTGPGVCYRLYSEEQYSLLAEYSTPEIRRVSIDSLLLSLVCMGLGDVRKFPFLEAPPAEN 868
R PGVCYRL+SEEQ+ L PEI + + L L L G D +L+APP+
Sbjct: 323 RLEPGVCYRLWSEEQHQRLPAQDEPEILQADLSGLALELAQWGAKDPSDLRWLDAPPSVA 382
Query: 869 IESSVRSLTQHGAIDSKERVTTLGRFLSDLPVDIPLGKMLVFG 911
+ ++ + L + GA+D++ R+T G+ ++ L L ML+
Sbjct: 383 LAAARQLLQRLGALDAQGRLTAHGKAMAALGCHPRLAAMLLSA 425
Score = 60.9 bits (148), Expect = 4e-09
Identities = 33/111 (29%), Positives = 54/111 (48%), Gaps = 5/111 (4%)
Query: 38 LPVAQYKQEIIDTVLKERVVIIAGDTGCGKSTQIPQYLVQAGF--QRIACTQPRRIACIS 95
LP+ + D + V++ G GKST +P L+ A +I +PRR+A S
Sbjct: 1 LPIHAVLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPGIGGKIIMLEPRRLAARS 60
Query: 96 LSKRVAYETLSQYSNLVGYQIRFEKHRREKTKIVFITEGLLLR---QDSGL 143
++R+A + VGY++R E +T++ +TEG+L R D L
Sbjct: 61 AAQRLASQLGEAVGQTVGYRVRGENKVSRRTRLEVVTEGILTRMIQDDPEL 111
Score = 41.7 bits (98), Expect = 0.003
Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 7/54 (12%)
Query: 1118 ADNFLSSYDVLVLDEIHERHLHGD----FLLGVIKCLLHSTAEVKIILMSATIN 1167
D L L+ DE HER L D L V L ++KI+ MSAT++
Sbjct: 107 DDPELDGVGALIFDEFHERSLDADLGLALALDVQSSL---REDLKILAMSATLD 157
Score = 32.4 bits (74), Expect = 2.1
Identities = 12/26 (46%), Positives = 12/26 (46%)
Query: 231 DNFLSSYDILILDEVHERHLYGDFLL 256
D L LI DE HER L D L
Sbjct: 108 DPELDGVGALIFDEFHERSLDADLGL 133
>gnl|CDD|236950 PRK11664, PRK11664, ATP-dependent RNA helicase HrpB; Provisional.
Length = 812
Score = 219 bits (561), Expect = 3e-59
Identities = 122/349 (34%), Positives = 182/349 (52%), Gaps = 22/349 (6%)
Query: 317 LSSYDVLVLDEIHERHLHGD----FLLGVIKCLLHSTAEVKIILMSATINIELFHTYFNR 372
LS +++LDE HER L D LL V + L ++K+++MSAT++ +
Sbjct: 114 LSGVGLVILDEFHERSLQADLALALLLDVQQGL---RDDLKLLIMSATLDNDRLQQLLPD 170
Query: 373 IAKIIKVPGRLYPIQLEYHPIVELDRTKSEKLDPGPYIRILSIIDKKYPRTERGDVLIFM 432
A +I GR +P++ Y P+ ++ D ++ R E G +L+F+
Sbjct: 171 -APVIVSEGRSFPVERRYQPL-----PAHQRFDEAVARATAELL-----RQESGSLLLFL 219
Query: 433 SGISEISSIVRAAQEYNEKSQGWIVLPLHSTLSLEEQDRVFHYAPEGLRKCIVSTNIAET 492
G+ EI + Q + + ++ PL+ LSL EQ + AP G RK +++TNIAET
Sbjct: 220 PGVGEIQRV--QEQLASRVASDVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAET 277
Query: 493 SITIDGIRFVVDSGKVKEMSYDVTAKMSTLQEFWISKASAEQRKGRAGRTGPGVCYRLYS 552
S+TI+GIR VVDSG + +D ++ L IS+AS QR GRAGR PG+C LYS
Sbjct: 278 SLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRLEPGICLHLYS 337
Query: 553 EEQYSLLAEYSTPEIRRVSIDSLLLSLVCMGLGDVRKFPFLEAPPAENIESSVRSLTQHG 612
+EQ A S PEI + LLL L+ G D + +L+ PPA + ++ R L Q G
Sbjct: 338 KEQAERAAAQSEPEILHSDLSGLLLELLQWGCHDPAQLSWLDQPPAAALAAAKRLLQQLG 397
Query: 613 AIDSKERVTSLGRFLSDLPVDIPLGKMLVFGSMF--HQIDTVLSLAAVL 659
A+D + R+T+ GR ++ L D L MLV + T LAA+L
Sbjct: 398 ALDGQGRLTARGRKMAALGNDPRLAAMLVAAKEDDEAALATAAKLAAIL 446
Score = 81.1 bits (201), Expect = 3e-15
Identities = 42/108 (38%), Positives = 57/108 (52%), Gaps = 4/108 (3%)
Query: 805 RLESRTGPGVCYRLYSEEQYSLLAEYSTPEIRRVSIDSLLLSLVCMGLGDVRKFPFLEAP 864
RLE PG+C LYS+EQ A S PEI + LLL L+ G D + +L+ P
Sbjct: 326 RLE----PGICLHLYSKEQAERAAAQSEPEILHSDLSGLLLELLQWGCHDPAQLSWLDQP 381
Query: 865 PAENIESSVRSLTQHGAIDSKERVTTLGRFLSDLPVDIPLGKMLVFGS 912
PA + ++ R L Q GA+D + R+T GR ++ L D L MLV
Sbjct: 382 PAAALAAAKRLLQQLGALDGQGRLTARGRKMAALGNDPRLAAMLVAAK 429
Score = 54.2 bits (131), Expect = 5e-07
Identities = 35/105 (33%), Positives = 58/105 (55%), Gaps = 2/105 (1%)
Query: 36 NSLPVAQYKQEIIDTVLKERVVIIAGDTGCGKSTQIP-QYLVQAGFQ-RIACTQPRRIAC 93
+SLPVA E++ + V++ TG GKST +P Q L G +I +PRR+A
Sbjct: 2 SSLPVAAVLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGINGKIIMLEPRRLAA 61
Query: 94 ISLSKRVAYETLSQYSNLVGYQIRFEKHRREKTKIVFITEGLLLR 138
++++R+A + + VGY++R E T++ +TEG+L R
Sbjct: 62 RNVAQRLAEQLGEKPGETVGYRMRAESKVGPNTRLEVVTEGILTR 106
Score = 38.0 bits (89), Expect = 0.040
Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 7/48 (14%)
Query: 1122 LSSYDVLVLDEIHERHLHGD----FLLGVIKCLLHSTAEVKIILMSAT 1165
LS +++LDE HER L D LL V + L ++K+++MSAT
Sbjct: 114 LSGVGLVILDEFHERSLQADLALALLLDVQQGL---RDDLKLLIMSAT 158
Score = 30.7 bits (70), Expect = 6.9
Identities = 15/33 (45%), Positives = 17/33 (51%), Gaps = 4/33 (12%)
Query: 230 TDNFLSSYDILILDEVHERHLYGD----FLLGV 258
D LS ++ILDE HER L D LL V
Sbjct: 110 RDPELSGVGLVILDEFHERSLQADLALALLLDV 142
>gnl|CDD|218070 pfam04408, HA2, Helicase associated domain (HA2). This presumed
domain is about 90 amino acid residues in length. It is
found is a diverse set of RNA helicases. Its function is
unknown, however it seems likely to be involved in
nucleic acid binding.
Length = 91
Score = 88.8 bits (221), Expect = 4e-21
Identities = 34/91 (37%), Positives = 57/91 (62%)
Query: 603 SSVRSLTQHGAIDSKERVTSLGRFLSDLPVDIPLGKMLVFGSMFHQIDTVLSLAAVLSVQ 662
++ L + GA+D +T LGR +++LP+D LGKML+ + F +D +L++AA+LSV
Sbjct: 1 KALELLYELGALDDDGELTPLGRQMAELPLDPRLGKMLLLSAEFGCLDEILTIAAMLSVP 60
Query: 663 SPFTNRAFRDPDCETARKELESNHGDPLTVL 693
SPF ++ + + AR++ S D LT+L
Sbjct: 61 SPFYRPKEKEEEADAARRKFASAESDHLTLL 91
Score = 54.9 bits (133), Expect = 3e-09
Identities = 19/53 (35%), Positives = 33/53 (62%)
Query: 871 SSVRSLTQHGAIDSKERVTTLGRFLSDLPVDIPLGKMLVFGSMFHQIDTMLLL 923
++ L + GA+D +T LGR +++LP+D LGKML+ + F +D +L +
Sbjct: 1 KALELLYELGALDDDGELTPLGRQMAELPLDPRLGKMLLLSAEFGCLDEILTI 53
Score = 54.2 bits (131), Expect = 7e-09
Identities = 24/65 (36%), Positives = 38/65 (58%), Gaps = 4/65 (6%)
Query: 1030 GAIDSKERVTSLGRFLSDLPVDIPLGKMLVFGSMFHQIDTMLLLDLALN----FVHHSEE 1085
GA+D +T LGR +++LP+D LGKML+ + F +D +L + L+ F E+
Sbjct: 10 GALDDDGELTPLGRQMAELPLDPRLGKMLLLSAEFGCLDEILTIAAMLSVPSPFYRPKEK 69
Query: 1086 EEEEE 1090
EEE +
Sbjct: 70 EEEAD 74
Score = 53.8 bits (130), Expect = 9e-09
Identities = 18/44 (40%), Positives = 29/44 (65%)
Query: 930 GAIDSKERVTSLGRFLSDLPVDIPLGKMLVFGSMFHQIDTMLLL 973
GA+D +T LGR +++LP+D LGKML+ + F +D +L +
Sbjct: 10 GALDDDGELTPLGRQMAELPLDPRLGKMLLLSAEFGCLDEILTI 53
Score = 53.8 bits (130), Expect = 9e-09
Identities = 18/44 (40%), Positives = 29/44 (65%)
Query: 980 GAIDSKERVTSLGRFLSDLPVDIPLGKMLVFGSMFHQIDTMLLL 1023
GA+D +T LGR +++LP+D LGKML+ + F +D +L +
Sbjct: 10 GALDDDGELTPLGRQMAELPLDPRLGKMLLLSAEFGCLDEILTI 53
>gnl|CDD|214852 smart00847, HA2, Helicase associated domain (HA2) Add an
annotation. This presumed domain is about 90 amino acid
residues in length. It is found is a diverse set of RNA
helicases. Its function is unknown, however it seems
likely to be involved in nucleic acid binding.
Length = 82
Score = 76.2 bits (188), Expect = 9e-17
Identities = 30/82 (36%), Positives = 47/82 (57%), Gaps = 2/82 (2%)
Query: 612 GAIDSKERVTSLGRFLSDLPVDIPLGKMLVFGSMFHQIDTVLSLAAVLSVQSPFTNRAFR 671
GA+D R+T LGR +++LP+D L KML+ + F +D +L++ A+LSV P +
Sbjct: 3 GALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGDPRPKE--K 60
Query: 672 DPDCETARKELESNHGDPLTVL 693
D + AR+ D LT+L
Sbjct: 61 REDADAARRRFADPESDHLTLL 82
Score = 53.8 bits (130), Expect = 6e-09
Identities = 23/73 (31%), Positives = 38/73 (52%)
Query: 1030 GAIDSKERVTSLGRFLSDLPVDIPLGKMLVFGSMFHQIDTMLLLDLALNFVHHSEEEEEE 1089
GA+D R+T LGR +++LP+D L KML+ + F +D +L + L+ +E+ E
Sbjct: 3 GALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGDPRPKEKRE 62
Query: 1090 EAGERLESMDANE 1102
+A E
Sbjct: 63 DADAARRRFADPE 75
Score = 51.5 bits (124), Expect = 4e-08
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 4/69 (5%)
Query: 930 GAIDSKERVTSLGRFLSDLPVDIPLGKMLVFGSMFHQIDTML----LLDLALNFGAIDSK 985
GA+D R+T LGR +++LP+D L KML+ + F +D +L +L + +
Sbjct: 3 GALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGDPRPKEKRE 62
Query: 986 ERVTSLGRF 994
+ + RF
Sbjct: 63 DADAARRRF 71
Score = 51.5 bits (124), Expect = 4e-08
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 4/69 (5%)
Query: 980 GAIDSKERVTSLGRFLSDLPVDIPLGKMLVFGSMFHQIDTML----LLDLALNFGAIDSK 1035
GA+D R+T LGR +++LP+D L KML+ + F +D +L +L + +
Sbjct: 3 GALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGDPRPKEKRE 62
Query: 1036 ERVTSLGRF 1044
+ + RF
Sbjct: 63 DADAARRRF 71
Score = 50.7 bits (122), Expect = 8e-08
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 4/69 (5%)
Query: 880 GAIDSKERVTTLGRFLSDLPVDIPLGKMLVFGSMFHQIDTML----LLDLALNFGAIDSK 935
GA+D R+T LGR +++LP+D L KML+ + F +D +L +L + +
Sbjct: 3 GALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGDPRPKEKRE 62
Query: 936 ERVTSLGRF 944
+ + RF
Sbjct: 63 DADAARRRF 71
>gnl|CDD|177443 PHA02653, PHA02653, RNA helicase NPH-II; Provisional.
Length = 675
Score = 80.0 bits (198), Expect = 4e-15
Identities = 59/251 (23%), Positives = 105/251 (41%), Gaps = 38/251 (15%)
Query: 315 NFLSSYDVLVLDEIHERHLHGDFLLGVIK---CLLHSTAEVKIILMSATI--NIELFHTY 369
N L Y +++DE+HE GD ++ V + + S + LM+AT+ + + +
Sbjct: 287 NKLFDYGTVIIDEVHEHDQIGDIIIAVARKHIDKIRS-----LFLMTATLEDDRDRIKEF 341
Query: 370 FNRIAKIIKVPG-RLYPIQLEYHPIVELDRTKSEKLDPGPYIR-----ILSIIDKKYPRT 423
F A + +PG L+PI Y + K + YI I++ + K P
Sbjct: 342 FPNPA-FVHIPGGTLFPISEVY------VKNKYNPKNKRAYIEEEKKNIVTALKKYTPPK 394
Query: 424 ERGDVLIFMSGISEISSIVRAAQEYNEKSQGWIVLPLHS-TLSLEEQDRVFHYAPEGLRK 482
++F++ +S+ + ++ +I+ H +++E +
Sbjct: 395 GSS-GIVFVASVSQCEEYKKYLEKRLPIYDFYII---HGKVPNIDE---ILEKVYSSKNP 447
Query: 483 CI-VSTNIAETSITIDGIRFVVDSGKVKEMSYDVTAKMSTLQEFWISKASAEQRKGRAGR 541
I +ST E+S+TI V D+G+V + +E +ISK+ QRKGR GR
Sbjct: 448 SIIISTPYLESSVTIRNATHVYDTGRV------YVPEPFGGKEMFISKSMRTQRKGRVGR 501
Query: 542 TGPGVCYRLYS 552
PG Y
Sbjct: 502 VSPGTYVYFYD 512
Score = 40.3 bits (95), Expect = 0.008
Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 10/65 (15%)
Query: 1120 NFLSSYDVLVLDEIHERHLHGDFLLGVIK---CLLHSTAEVKIILMSATI--NIELFHTY 1174
N L Y +++DE+HE GD ++ V + + S + LM+AT+ + + +
Sbjct: 287 NKLFDYGTVIIDEVHEHDQIGDIIIAVARKHIDKIRS-----LFLMTATLEDDRDRIKEF 341
Query: 1175 FNRIA 1179
F A
Sbjct: 342 FPNPA 346
Score = 35.7 bits (83), Expect = 0.22
Identities = 12/37 (32%), Positives = 22/37 (59%), Gaps = 2/37 (5%)
Query: 39 PVAQYKQEIIDTVLKERVVIIAGDTGCGKSTQIPQYL 75
P Q +I + + + V++ G TG GK++Q+P+ L
Sbjct: 166 PDVQ--LKIFEAWISRKPVVLTGGTGVGKTSQVPKLL 200
Score = 33.8 bits (78), Expect = 0.82
Identities = 13/29 (44%), Positives = 17/29 (58%)
Query: 230 TDNFLSSYDILILDEVHERHLYGDFLLGV 258
T N L Y +I+DEVHE GD ++ V
Sbjct: 285 TLNKLFDYGTVIIDEVHEHDQIGDIIIAV 313
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 70.7 bits (174), Expect = 7e-15
Identities = 28/93 (30%), Positives = 39/93 (41%), Gaps = 18/93 (19%)
Query: 451 KSQGWIVLPLHSTLSLEEQDRVFHYAPEGLRKCIVSTNIAETSITIDGIRFVVDSGKVKE 510
K G V LH LS EE++ + G K +V+T++AE + + G+ V+
Sbjct: 8 KELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYD---- 63
Query: 511 MSYDVTAKMSTLQEFWISKASAEQRKGRAGRTG 543
S AS QR GRAGR G
Sbjct: 64 --------------LPWSPASYIQRIGRAGRAG 82
>gnl|CDD|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain. The
Prosite family is restricted to DEAD/H helicases,
whereas this domain family is found in a wide variety of
helicases and helicase related proteins. It may be that
this is not an autonomously folding unit, but an
integral part of the helicase.
Length = 78
Score = 64.9 bits (159), Expect = 6e-13
Identities = 27/93 (29%), Positives = 40/93 (43%), Gaps = 18/93 (19%)
Query: 451 KSQGWIVLPLHSTLSLEEQDRVFHYAPEGLRKCIVSTNIAETSITIDGIRFVVDSGKVKE 510
+ G V LH LS EE++ + G K +V+T++A I + + V++
Sbjct: 4 RKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVIN------ 57
Query: 511 MSYDVTAKMSTLQEFWISKASAEQRKGRAGRTG 543
YD + AS QR GRAGR G
Sbjct: 58 --YD----------LPWNPASYIQRIGRAGRAG 78
>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated
with DEXDc-, DEAD-, and DEAH-box proteins, yeast
initiation factor 4A, Ski2p, and Hepatitis C virus NS3
helicases; this domain is found in a wide variety of
helicases and helicase related proteins; may not be an
autonomously folding unit, but an integral part of the
helicase; 4 helicase superfamilies at present according
to the organization of their signature motifs; all
helicases share the ability to unwind nucleic acid
duplexes with a distinct directional polarity; they
utilize the free energy from nucleoside triphosphate
hydrolysis to fuel their translocation along DNA,
unwinding the duplex in the process.
Length = 131
Score = 59.6 bits (145), Expect = 2e-10
Identities = 33/126 (26%), Positives = 48/126 (38%), Gaps = 24/126 (19%)
Query: 426 GDVLIFMSGISEISSIVRAAQEYNEKSQGWIVLPLHSTLSLEEQDRVFHYAPEGLRKCIV 485
G VLIF + + ++ G V LH S EE++ V EG +V
Sbjct: 29 GKVLIFCPSKKMLDELAELLRKP-----GIKVAALHGDGSQEEREEVLKDFREGEIVVLV 83
Query: 486 STNIAETSITIDGIRFVVDSGKVKEMSYDVTAKMSTLQEFWISKASAEQRKGRAGRTG-P 544
+T++ I + + V++ YD S +S QR GRAGR G
Sbjct: 84 ATDVIARGIDLPNVSVVIN--------YD----------LPWSPSSYLQRIGRAGRAGQK 125
Query: 545 GVCYRL 550
G L
Sbjct: 126 GTAILL 131
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 58.5 bits (142), Expect = 7e-10
Identities = 23/94 (24%), Positives = 36/94 (38%), Gaps = 12/94 (12%)
Query: 55 RVVIIAGDTGCGKSTQIPQYLVQAGFQ----RIACTQPRRIACISLSKRVAYETLSQYSN 110
R V++A TG GK+ +++ ++ P R +++R+ L
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLK--ELFGEGI 58
Query: 111 LVGYQIRFEKHR------REKTKIVFITEGLLLR 138
VGY I + KT IV T G LL
Sbjct: 59 KVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLD 92
Score = 41.2 bits (97), Expect = 8e-04
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 316 FLSSYDVLVLDEIHERHLHGDFLLGVIKCLLHSTAEVKIILMSATI 361
L D+L+LDE H G LLG+ L + +++L+SAT
Sbjct: 100 SLKKLDLLILDEAHRLLNQGFGLLGLKILLKLP-KDRQVLLLSATP 144
Score = 41.2 bits (97), Expect = 8e-04
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 1121 FLSSYDVLVLDEIHERHLHGDFLLGVIKCLLHSTAEVKIILMSATI 1166
L D+L+LDE H G LLG+ L + +++L+SAT
Sbjct: 100 SLKKLDLLILDEAHRLLNQGFGLLGLKILLKLP-KDRQVLLLSATP 144
Score = 31.5 bits (72), Expect = 1.4
Identities = 13/38 (34%), Positives = 17/38 (44%)
Query: 268 EIVAADYFLSSYDVLVLDEIHERHLHGDFLLGVIKCLL 305
E+ L D+L+LDE H G LLG+ L
Sbjct: 93 ELERLKLSLKKLDLLILDEAHRLLNQGFGLLGLKILLK 130
>gnl|CDD|219532 pfam07717, OB_NTP_bind, Oligonucleotide/oligosaccharide-binding
(OB)-fold. This family is found towards the C-terminus
of the DEAD-box helicases (pfam00270). In these helicases
it is apparently always found in association with
pfam04408. There do seem to be a couple of instances
where it occurs by itself - . The structure PDB:3i4u
adopts an OB-fold. helicases (pfam00270). In these
helicases it is apparently always found in association
with pfam04408. This C-terminal domain of the yeast
helicase contains an
oligonucleotide/oligosaccharide-binding (OB)-fold which
seems to be placed at the entrance of the putative
nucleic acid cavity. It also constitutes the binding site
for the G-patch-containing domain of Pfa1p. When found on
DEAH/RHA helicases, this domain is central to the
regulation of the helicase activity through its binding
of both RNA and G-patch domain proteins.
Length = 109
Score = 52.7 bits (127), Expect = 4e-08
Identities = 22/119 (18%), Positives = 38/119 (31%), Gaps = 33/119 (27%)
Query: 1190 SHKDVTILKVILASGLYPQVAIGDEFNTSETVKEALFHCKDKGFVSLHPFSVFTSQPDVL 1249
S D +++ L +GL+P VA + K+ V +HP SV
Sbjct: 23 SSNDYELIRKALCAGLFPNVARLVDEKGE------YKTLKEGQPVFIHPSSV-------- 68
Query: 1250 RISEDDIVDPPPGLKLPGRNVISSKHQLLVYMSLLETSKPFLVNCLRMPALQTLLLFSS 1308
+ +VY L+ET+K ++ + + L L
Sbjct: 69 -------------------LFGKKPPEWVVYHELVETTKEYMRDVTAIDPEWLLELAPH 108
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 53.3 bits (128), Expect = 1e-07
Identities = 27/107 (25%), Positives = 44/107 (41%), Gaps = 11/107 (10%)
Query: 43 YKQEIIDTVLK-ERVVIIAGDTGCGKSTQIPQYLVQAGFQ----RIACTQPRRIACISLS 97
Y++E I+ +L R VI+A TG GK+ ++A + R+ P R +
Sbjct: 12 YQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWA 71
Query: 98 KRVAYETLSQYSNLVGY------QIRFEKHRREKTKIVFITEGLLLR 138
+ + S +VG + + K KT I+ T G LL
Sbjct: 72 EELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLD 118
Score = 40.6 bits (95), Expect = 0.002
Identities = 22/78 (28%), Positives = 35/78 (44%), Gaps = 7/78 (8%)
Query: 1121 FLSSYDVLVLDEIHER--HLHGDFLLGVIKCLLHSTAEVKIILMSATI--NIELFHTYFN 1176
LS+ D+++LDE H GD L ++K L + V+++L+SAT IE F
Sbjct: 126 SLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKN---VQLLLLSATPPEEIENLLELFL 182
Query: 1177 RIAKDLLSGSTARSHKDV 1194
+ G T +
Sbjct: 183 NDPVFIDVGFTPLEPIEQ 200
Score = 40.2 bits (94), Expect = 0.004
Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 7/68 (10%)
Query: 316 FLSSYDVLVLDEIHER--HLHGDFLLGVIKCLLHSTAEVKIILMSATI--NIELFHTYFN 371
LS+ D+++LDE H GD L ++K L + V+++L+SAT IE F
Sbjct: 126 SLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKN---VQLLLLSATPPEEIENLLELFL 182
Query: 372 RIAKIIKV 379
I V
Sbjct: 183 NDPVFIDV 190
Score = 29.8 bits (67), Expect = 7.3
Identities = 15/73 (20%), Positives = 25/73 (34%), Gaps = 10/73 (13%)
Query: 275 FLSSYDVLVLDEIHER--HLHGDFLLGVIKCLLHS--------TVEVAADNFLSSYDVLV 324
LS+ D+++LDE H GD L ++K L + T +N L +
Sbjct: 126 SLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPEEIENLLELFLNDP 185
Query: 325 LDEIHERHLHGDF 337
+
Sbjct: 186 VFIDVGFTPLEPI 198
>gnl|CDD|187770 cd09639, Cas3_I, CRISPR/Cas system-associated protein Cas3. CRISPR
(Clustered Regularly Interspaced Short Palindromic
Repeats) and associated Cas proteins comprise a system
for heritable host defense by prokaryotic cells against
phage and other foreign DNA; DEAD/DEAH box helicase DNA
helicase cas3'; Often but not always is fused to HD
nuclease domain; signature gene for Type I.
Length = 353
Score = 38.2 bits (89), Expect = 0.029
Identities = 39/191 (20%), Positives = 73/191 (38%), Gaps = 34/191 (17%)
Query: 319 SYDVLVLDEIHERHLHGDFLLGVIKCLLHSTAE--VKIILMSATINIELFHTYFNRIAKI 376
+ +L+ DE+H + ++ L +I +L + V I+LMSAT+ + Y
Sbjct: 123 ANSLLIFDEVH---FYDEYTLALILAVLEVLKDNDVPILLMSATLP-KFLKEYA------ 172
Query: 377 IKVPGRLYPIQLEYHPI--VELDRTKSEKLDPGPYIRILSIIDKKYPRTERGDVLIFMSG 434
Y + E + E + D I L + + + G V I
Sbjct: 173 ---EKIGYVEENEPLDLKPNERAPFIKIESDKVGEISSLERLLEFIK--KGGSVAI---- 223
Query: 435 ISEISSIVRAAQEY----NEKSQGWIVLPLHSTLSL----EEQDRVFHYAPEGLRKCIVS 486
I + V AQE+ EK ++ +HS + +++ + + + IV+
Sbjct: 224 ---IVNTVDRAQEFYQQLKEKGPEEEIMLIHSRFTEKDRAKKEAELLLEFKKSEKFVIVA 280
Query: 487 TNIAETSITID 497
T + E S+ I
Sbjct: 281 TQVIEASLDIS 291
Score = 33.6 bits (77), Expect = 0.83
Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 15/80 (18%)
Query: 1110 DPKQVQVAADNFLSSYD---------VLVLDEIHERHLHGDFLLGVIKCLLHSTAE--VK 1158
QV + Y+ +L+ DE+H + ++ L +I +L + V
Sbjct: 100 TIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVH---FYDEYTLALILAVLEVLKDNDVP 156
Query: 1159 IILMSATINIELFHTYFNRI 1178
I+LMSAT+ + Y +I
Sbjct: 157 ILLMSATLP-KFLKEYAEKI 175
>gnl|CDD|233483 TIGR01587, cas3_core, CRISPR-associated helicase Cas3. This model
represents the highly conserved core region of an
alignment of Cas3, a protein found in association with
CRISPR repeat elements in a broad range of bacteria and
archaea. Cas3 appears to be a helicase, with regions
found by pfam00270 (DEAD/DEAH box helicase) and
pfam00271 (Helicase conserved C-terminal domain). Some
but not all members have an N-terminal HD domain region
(pfam01966) that is not included within this model
[Mobile and extrachromosomal element functions, Other].
Length = 358
Score = 37.8 bits (88), Expect = 0.032
Identities = 41/194 (21%), Positives = 76/194 (39%), Gaps = 37/194 (19%)
Query: 319 SYDVLVLDEIHERHLHGDFLLGVIKCLLHSTAE--VKIILMSATINIELFHTYFNRIAKI 376
+ +L+ DE+H + ++ L +I +L + V I+LMSAT+ + Y
Sbjct: 124 ANSLLIFDEVH---FYDEYTLALILAVLEVLKDNDVPILLMSATLP-KFLKEYA------ 173
Query: 377 IKVPGRLYPIQLEYHPIVELDRTKS-----EKLDPGPYIRILSIIDKKYPRTERGDVLIF 431
Y E + E R + + D I L + + + G + I
Sbjct: 174 ---EKIGYVEFNEPLDLKEERRFERHRFIKIESDKVGEISSLERLLEFIK--KGGKIAI- 227
Query: 432 MSGISEISSIVRAAQEY----NEKSQGWIVLPLHSTLSLEEQDRVFHYAPEGLRK----C 483
I + V AQE+ E + ++ LHS + +++ + E ++K
Sbjct: 228 ------IVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFV 281
Query: 484 IVSTNIAETSITID 497
IV+T + E S+ I
Sbjct: 282 IVATQVIEASLDIS 295
Score = 33.6 bits (77), Expect = 0.78
Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 15/80 (18%)
Query: 1110 DPKQVQVAADNFLSSYD---------VLVLDEIHERHLHGDFLLGVIKCLLHSTAE--VK 1158
QV + Y+ +L+ DE+H + ++ L +I +L + V
Sbjct: 101 TIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVH---FYDEYTLALILAVLEVLKDNDVP 157
Query: 1159 IILMSATINIELFHTYFNRI 1178
I+LMSAT+ + Y +I
Sbjct: 158 ILLMSATLP-KFLKEYAEKI 176
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 35.8 bits (82), Expect = 0.048
Identities = 15/84 (17%), Positives = 29/84 (34%), Gaps = 5/84 (5%)
Query: 55 RVVIIAGDTGCGKST---QIPQYLV--QAGFQRIACTQPRRIACISLSKRVAYETLSQYS 109
V++I G G GK+T + + L G I L + + S
Sbjct: 3 EVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGS 62
Query: 110 NLVGYQIRFEKHRREKTKIVFITE 133
+ ++ R+ K ++ + E
Sbjct: 63 GELRLRLALALARKLKPDVLILDE 86
>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
Length = 674
Score = 37.2 bits (86), Expect = 0.077
Identities = 95/412 (23%), Positives = 155/412 (37%), Gaps = 92/412 (22%)
Query: 275 FLSSYDVLVL-DEIHERHLHGDFLLGVIKCLLHSTVEVAADNFLSSYDVLVLDEIH--ER 331
F+ YDV++L E + +H D ++ ++V DEIH
Sbjct: 108 FIKRYDVVILTSEKADSLIHHD------------------PYIINDVGLIVADEIHIIGD 149
Query: 332 HLHGDFLLGVIKCLLHSTAEVKIILMSATI-NIELFHTYFNRIAKIIKVPGRLYPIQLE- 389
G L V+ + + +I+ +SAT+ N + N A +IK R P++L
Sbjct: 150 EDRGPTLETVLSSARYVNPDARILALSATVSNANELAQWLN--ASLIKSNFRPVPLKLGI 207
Query: 390 -YHPIVELDRTKSEKLDPGPYIRILSIIDKKYPRTERGDVLIFMSG-------------- 434
Y + LD + ++D I S+I K + G VL+F+S
Sbjct: 208 LYRKRLILDGYERSQVD------INSLI--KETVNDGGQVLVFVSSRKNAEDYAEMLIQH 259
Query: 435 ISEISSIVRAAQEYNEKSQGWI-VLPL-----HSTLSLEEQDRVFHYAPEGLRKCIVSTN 488
E + +++ N +LP H+ LS E++ + K IV+T
Sbjct: 260 FPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIKVIVATP 319
Query: 489 IAETSITIDGIRFVVDSGKVKEMSYDVTAKMSTLQEFWISKASAEQRKGRAGRT-----G 543
+ + R V+ V+ D+T + ++S +Q GRAGR G
Sbjct: 320 TLAAGVNLPA-RLVI----VR----DIT-RYGNGGIRYLSNMEIKQMIGRAGRPGYDQYG 369
Query: 544 PGVCYRLYSEEQYSLLAEY--STPEIRRVSIDSL------LLSLVCMGLG----DVRKF- 590
G Y S Y +Y PE + S L+ + MGL D+ F
Sbjct: 370 IGYIY-AASPASYDAAKKYLSGEPEPVISYMGSQRKVRFNTLAAISMGLASSMEDLILFY 428
Query: 591 --PFLEAPPAEN-----IESSVRSLTQHGAIDSKE--RVTSLGRFLSDLPVD 633
+ + IESS++ L ++G I R T LG+ SDL +D
Sbjct: 429 NETLMAIQNGVDEIDYYIESSLKFLKENGFIKGDVTLRATRLGKLTSDLYID 480
>gnl|CDD|223587 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA
replication, recombination, and repair / Transcription /
Translation, ribosomal structure and biogenesis].
Length = 513
Score = 36.3 bits (84), Expect = 0.11
Identities = 63/245 (25%), Positives = 100/245 (40%), Gaps = 43/245 (17%)
Query: 317 LSSYDVLVLDEIHERHLHGDFLLGVIKCLLHSTAEVKIILMSATIN---IELFHTYFNRI 373
LS + LVLDE +R L F+ + K L + + +L SAT+ EL Y N
Sbjct: 172 LSGVETLVLDEA-DRMLDMGFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDP 230
Query: 374 AKIIKVPGRLYP----IQLEYHPIVELDRTKSEKLDPGPYIRILSIIDKKYPRTERGDVL 429
+I +L I+ Y VE + K E L +++L D+ G V+
Sbjct: 231 VEIEVSVEKLERTLKKIKQFYLE-VESEEEKLELL-----LKLLKDEDE-------GRVI 277
Query: 430 IFMSGISEISSIVRAAQEYNEKSQGWIVLPLHSTLSLEEQDRVFHYAPEGLRKCIVSTNI 489
+F+ + A+ + +G+ V LH L EE+DR +G + +V+T++
Sbjct: 278 VFVRTKRLVE---ELAESLRK--RGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDV 332
Query: 490 AETSITIDGIRFVVDSGKVKEMSYDVTAKMSTLQEFWISKASAEQRKGRAGRTGPGVCYR 549
A + I + V+ +YD+ I R GRAGR GV
Sbjct: 333 AARGLDIPDVSHVI--------NYDLPLDPEDYVH-RIG------RTGRAGRK--GVAIS 375
Query: 550 LYSEE 554
+EE
Sbjct: 376 FVTEE 380
>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 169
Score = 34.9 bits (81), Expect = 0.13
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 305 LHSTVEVAADNFLSSYDVLVLDEIHERHLHGDFLLGVIKCLLHSTAEVKIILMSATINIE 364
L + L + +LVLDE H R L F + + L + +I+L+SAT+
Sbjct: 107 LLDLLRRGKLKLLKNLKLLVLDEAH-RLLDMGFGDDLEEILSRLPPDRQILLLSATLPRN 165
Query: 365 L 365
L
Sbjct: 166 L 166
Score = 33.8 bits (78), Expect = 0.26
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 1120 NFLSSYDVLVLDEIHERHLHGDFLLGVIKCLLHSTAEVKIILMSATINIEL 1170
L + +LVLDE H R L F + + L + +I+L+SAT+ L
Sbjct: 117 KLLKNLKLLVLDEAH-RLLDMGFGDDLEEILSRLPPDRQILLLSATLPRNL 166
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 35.9 bits (83), Expect = 0.19
Identities = 60/263 (22%), Positives = 105/263 (39%), Gaps = 43/263 (16%)
Query: 255 LLGVISPPLHCGGEIVAADYFLSSYDVLVLDEIHERHLHGDFLLGVIKCLLHSTVEVAAD 314
L VI LH + L D +L + + LL +I + +
Sbjct: 272 LFSVIGKSLH--SSSK--EPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVK 327
Query: 315 ----NFLSS--YDVLVLDEIHERHLHGD-----FLLGVIKCLLHSTAEVKIILMSATINI 363
FL+ +++LDE+H L+ D LL +++ L + A V ++LMSAT+
Sbjct: 328 GFKFEFLALLLTSLVILDEVH---LYADETMLAALLALLEAL--AEAGVPVLLMSATLP- 381
Query: 364 ELFHTYFNRIAKIIKVPGRLYPIQLEYHPIVE---LDRTKSEKLDPGPYIRILSIIDKKY 420
+ K GR ++ P + L R + ++ GP ++ +I ++
Sbjct: 382 ----PFLKEKLKKALGKGREVVENAKFCPKEDEPGLKRKERVDVEDGPQEELIELISEEV 437
Query: 421 PRTERGDVLIFMSGISEISSIVRAAQE-YNE-KSQGWIVLPLHSTLSL---EEQDRVFHY 475
+ ++I + V A E Y + K +G VL LHS +L EE++R
Sbjct: 438 KE-GKKVLVIVNT--------VDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKK 488
Query: 476 APEGLRKCI-VSTNIAETSITID 497
+ I V+T + E + ID
Sbjct: 489 LFKQNEGFIVVATQVIEAGVDID 511
>gnl|CDD|217269 pfam02887, PK_C, Pyruvate kinase, alpha/beta domain. As well as
being found in pyruvate kinase this family is found as an
isolated domain in some bacterial proteins.
Length = 117
Score = 32.9 bits (76), Expect = 0.28
Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 14/65 (21%)
Query: 1184 SGSTAR--------------SHKDVTILKVILASGLYPQVAIGDEFNTSETVKEALFHCK 1229
SGSTAR + + T ++ L G++P + +T E + EAL K
Sbjct: 26 SGSTARLVSKYRPGAPIIAVTPNERTARRLALYWGVHPVLGDERSISTDEIIAEALRMAK 85
Query: 1230 DKGFV 1234
D G V
Sbjct: 86 DAGLV 90
>gnl|CDD|216135 pfam00817, IMS, impB/mucB/samB family. These proteins are involved
in UV protection.
Length = 148
Score = 32.6 bits (75), Expect = 0.66
Identities = 10/30 (33%), Positives = 14/30 (46%)
Query: 548 YRLYSEEQYSLLAEYSTPEIRRVSIDSLLL 577
YR S +L +S P++ SID L
Sbjct: 72 YRRASRRIAEILRRFSPPKVEVYSIDEAFL 101
Score = 32.6 bits (75), Expect = 0.66
Identities = 10/30 (33%), Positives = 14/30 (46%)
Query: 816 YRLYSEEQYSLLAEYSTPEIRRVSIDSLLL 845
YR S +L +S P++ SID L
Sbjct: 72 YRRASRRIAEILRRFSPPKVEVYSIDEAFL 101
>gnl|CDD|222164 pfam13480, Acetyltransf_6, Acetyltransferase (GNAT) domain. This
family contains proteins with N-acetyltransferase
functions.
Length = 144
Score = 32.2 bits (74), Expect = 0.75
Identities = 27/145 (18%), Positives = 44/145 (30%), Gaps = 24/145 (16%)
Query: 182 KRRKMLKADNAYEIEEEEEEEEGERLESMDANEVEFRLKHDPKQVQVATDNFLSSYDILI 241
++R+ L+ E + + + L L + + A D F +
Sbjct: 9 RKRRRLEELGGVRFEVARDPADLDAL---------LDLFRAQWRRRGAPDLFADPWVRAF 59
Query: 242 LDEVHERHLYGDFLLGVISPPLHCGGEIVAADYFLSSYDVLVL-----DEIHERHLHGDF 296
L ++ R L + L GE VAA L L D R
Sbjct: 60 LRDLAARLAARGALRLYV---LRLDGEPVAAVLGLRDGGRLYYYLGGYDPEFARL----- 111
Query: 297 LLGVIKCLLHSTVEVAADNFLSSYD 321
LL +E AA+ + +D
Sbjct: 112 --SPGLLLLWELIEDAAEEGVRVFD 134
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 33.9 bits (78), Expect = 0.79
Identities = 75/399 (18%), Positives = 127/399 (31%), Gaps = 104/399 (26%)
Query: 314 DNFLSSYDVLVLDEIH---ERHLHGDFLLGVIKCLLHSTAEVKIILMSATI-NIELFHTY 369
+++ D++V+DEIH +R G L ++ + ++I+ +SAT+ N E
Sbjct: 141 PSWIEEVDLVVIDEIHLLGDRT-RGPVLESIVARMRRLNELIRIVGLSATLPNAEEV--- 196
Query: 370 FNRIAKIIKVP---GRLYPIQLEYHPIVELDRTKSEKLDPG--PYIRILSIIDKKYPRTE 424
A + P+ L + + P + ++
Sbjct: 197 ----ADWLNAKLVESDWRPVPL-RRGVPYVGAFLGADGKKKTWPLLIDNLALELVLESLA 251
Query: 425 RGD-VLIF-----------------MSG-ISEISSIVRAAQEYN------EKSQGWIVLP 459
G VL+F MS +S+ IV S+ +
Sbjct: 252 EGGQVLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAE 311
Query: 460 L--------HSTLSLEEQDRVFHYAPEGLRKCIVST-------NIAETSITIDGIRFVVD 504
L H+ L E++ V +G K +VST N+ ++ I R
Sbjct: 312 LVLRGVAFHHAGLPREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLPARTVIIKDTRR--- 368
Query: 505 SGKVKEMSYDVTAKMSTLQEFWISKASAEQRKGRAGR-----TGPG--VCYRLYSEEQYS 557
YD I Q GRAGR G + E +
Sbjct: 369 --------YD-----PKGGIVDIPVLDVLQMAGRAGRPGYDDYGEAIILATSHDELEYLA 415
Query: 558 LLAEYSTPEIRR------VSIDSLLLSLVCMG-----------LGDVRKFPFL--EAPPA 598
L S PE +++ + LL ++ +G P E
Sbjct: 416 ELYIQSEPEPIESKLGDELNLRTFLLGVISVGDAVSWLELTDFYERTFYNPQTYGEGMLR 475
Query: 599 ENIESSVRSLTQHGAIDSKERV----TSLGRFLSDLPVD 633
E I +S+R L ++G I + T LG+ +S L +D
Sbjct: 476 EEILASLRYLEENGLILDADWEALHATELGKLVSRLYID 514
>gnl|CDD|223466 COG0389, DinP, Nucleotidyltransferase/DNA polymerase involved in
DNA repair [DNA replication, recombination, and repair].
Length = 354
Score = 33.4 bits (77), Expect = 0.89
Identities = 20/69 (28%), Positives = 28/69 (40%), Gaps = 6/69 (8%)
Query: 528 SKASAEQRKGRAGR-TGPGVCYRLYSEEQYSLLAEYSTPEIRRVSIDSLLL----SLVCM 582
A + RA YRL S E ++L Y TP + +SID L +L +
Sbjct: 56 PLFEALKLCPRAIVAPPNFAAYRLASAEIRAILERY-TPLVEPLSIDEAFLDLTDALRLL 114
Query: 583 GLGDVRKFP 591
GL D +
Sbjct: 115 GLADAPRIA 123
Score = 31.5 bits (72), Expect = 3.5
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 5/48 (10%)
Query: 816 YRLYSEEQYSLLAEYSTPEIRRVSIDSLLL----SLVCMGLGDVRKFP 859
YRL S E ++L Y TP + +SID L +L +GL D +
Sbjct: 77 YRLASAEIRAILERY-TPLVEPLSIDEAFLDLTDALRLLGLADAPRIA 123
>gnl|CDD|217017 pfam02399, Herpes_ori_bp, Origin of replication binding protein.
This Pfam family represents the herpesvirus origin of
replication binding protein, probably involved in DNA
replication.
Length = 829
Score = 33.5 bits (77), Expect = 0.96
Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 18/64 (28%)
Query: 314 DNFLSSYDVLVLDEIHE----------RHLHGDFLLGVIKCLLHSTAEV--KIILMSATI 361
+N L++YDVL+LDE+ R L + LL +II M AT+
Sbjct: 137 ENLLNNYDVLILDEVMSTIGQLYSPTMRRLK------EVDALLLRLLRNCPRIIAMDATV 190
Query: 362 NIEL 365
N +L
Sbjct: 191 NAQL 194
Score = 33.5 bits (77), Expect = 0.96
Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 18/64 (28%)
Query: 1119 DNFLSSYDVLVLDEIHE----------RHLHGDFLLGVIKCLLHSTAEV--KIILMSATI 1166
+N L++YDVL+LDE+ R L + LL +II M AT+
Sbjct: 137 ENLLNNYDVLILDEVMSTIGQLYSPTMRRLK------EVDALLLRLLRNCPRIIAMDATV 190
Query: 1167 NIEL 1170
N +L
Sbjct: 191 NAQL 194
Score = 32.0 bits (73), Expect = 2.9
Identities = 10/16 (62%), Positives = 14/16 (87%)
Query: 230 TDNFLSSYDILILDEV 245
+N L++YD+LILDEV
Sbjct: 136 DENLLNNYDVLILDEV 151
>gnl|CDD|151096 pfam10554, Phage_ASH, Ash protein family. This family was identified
by Iyer and colleagues. It includes the Ash protein from
bacteriophage P4.
Length = 104
Score = 30.9 bits (70), Expect = 1.3
Identities = 22/83 (26%), Positives = 28/83 (33%), Gaps = 16/83 (19%)
Query: 1334 AKSTADVNQLEHSLTRDLVQ---FMSSATHLAYSIRRLLAADLKTMYRRTGAESGVPGS- 1389
AKS A + + + F + L+ L+ M R G SG P S
Sbjct: 7 AKSGAGIGNPSITKAPNRAPAVFFRRCVAPSSN-----LSWHLRIMVARAGQPSGWPVSL 61
Query: 1390 -----NPFVAEFPMVVEETLGGV 1407
NP A P V T GG
Sbjct: 62 LTGISNPVRATTPEV--STSGGS 82
>gnl|CDD|222160 pfam13476, AAA_23, AAA domain.
Length = 204
Score = 32.1 bits (73), Expect = 1.4
Identities = 29/192 (15%), Positives = 66/192 (34%), Gaps = 28/192 (14%)
Query: 40 VAQYKQEIIDTVLKERVVIIAGDTGCGKST-----------------QIPQYLVQAGFQR 82
+K ID + + +I G G GK+T + + G
Sbjct: 7 FGSFKDLEID--FSKGLTLIYGPNGSGKTTILDAIRWALYGKTSRLKKSKGRGIVKGDIE 64
Query: 83 IACTQPRRIACISLSKRVAYETLSQYSNLVGYQIRFEKHRREKTKIVFITEGLLLRQDSG 142
I + ++ + ++ L ++ +K ++ K I+ I E L++
Sbjct: 65 IEKDEGKKKTYVEITFENNKGKLKLRLIEESRELTKKKGKKVKKSILEIVEIDELQEFI- 123
Query: 143 LITDIPGPDASLSSRERALRHGEIKLLQAIKRKKAEEAPKRRKMLKADNAYEIEEEEEEE 202
D L S + L + ++ K + K+ ++ + + E E+E++
Sbjct: 124 --------DELLKSDKEILPLLLYLGQERLEELKFKRKEKKERLEELEKELEELEDEKDL 175
Query: 203 EGERLESMDANE 214
+ LE + +
Sbjct: 176 LEKLLEEKEKKK 187
>gnl|CDD|187612 cd05354, SDR_c7, classical (c) SDR, subgroup 7. These proteins are
members of the classical SDR family, with a canonical
active site triad (and also an active site Asn) and a
typical Gly-rich NAD-binding motif. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or additional
Ser, contributing to the active site. Substrates for
these enzymes include sugars, steroids, alcohols, and
aromatic compounds. The standard reaction mechanism is a
proton relay involving the conserved Tyr and Lys, as
well as Asn (or Ser). Some SDR family members, including
17 beta-hydroxysteroid dehydrogenase contain an
additional helix-turn-helix motif that is not generally
found among SDRs.
Length = 235
Score = 32.0 bits (73), Expect = 1.9
Identities = 12/55 (21%), Positives = 22/55 (40%), Gaps = 5/55 (9%)
Query: 647 HQIDTVLSLAAVLSVQSPFTNRAFRDPDCETARKELESNHGDPLTVLNAYKEWLG 701
+D V++ A VL + A E ++E++ N L + A+ L
Sbjct: 73 KDVDVVINNAGVLKPATLLEEGAL-----EALKQEMDVNVFGLLRLAQAFAPVLK 122
>gnl|CDD|193332 pfam12858, tRNA_iecd, TRNA-intron endonuclease catalytic domain. The
Sen15 subunit of the tRNA intron-splicing endonuclease is
one of the two structural subunits of this
heterotetrameric enzyme. Residues 36-157 of this subunit
possess a novel homodimeric fold. Each monomer consists
of three alpha-helices and a mixed antiparallel/parallel
beta-sheet. Two monomers of Sen15 fold with two monomers
of Sen34, one of the two catalytic subunits, to form an
alpha2-beta2 tetramer as part of the functional
endonuclease assembly.
Length = 69
Score = 29.3 bits (65), Expect = 2.5
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 1277 LLVYMSLLETSKPFLVNCLRMPALQTLLLFSSAI 1310
LVY+ L+E+ VNC+ +P LQ + L + I
Sbjct: 15 FLVYLDLMESKSWHEVNCVGLPELQLICLVGTEI 48
>gnl|CDD|151811 pfam11371, DUF3172, Protein of unknown function (DUF3172). This
family of proteins has no known function.
Length = 140
Score = 30.4 bits (69), Expect = 3.0
Identities = 12/23 (52%), Positives = 16/23 (69%), Gaps = 5/23 (21%)
Query: 1233 FVSLHPFSVFTSQPD-----VLR 1250
FV+L+PF+VF +QP VLR
Sbjct: 65 FVTLNPFNVFVTQPSMQPGCVLR 87
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 32.0 bits (72), Expect = 3.2
Identities = 23/89 (25%), Positives = 45/89 (50%), Gaps = 5/89 (5%)
Query: 165 EIKLLQAIKRKKAEEAPKRRKMLKADNAYEIEEEE----EEEEGERLESMDANEVE-FRL 219
E K + +K+K+AEE K ++ KA+ +I+ EE EE+ ++ E +E E ++
Sbjct: 1700 EAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKI 1759
Query: 220 KHDPKQVQVATDNFLSSYDILILDEVHER 248
H K+ + + + +I +E+ E
Sbjct: 1760 AHLKKEEEKKAEEIRKEKEAVIEEELDEE 1788
Score = 30.9 bits (69), Expect = 6.9
Identities = 24/89 (26%), Positives = 45/89 (50%), Gaps = 4/89 (4%)
Query: 716 RGIEEQRFYEVTKLRSQFKQVLGDSGLITDIPGPDASLSSRERALRHGEIKLLQAIKRKK 775
+ EE R EV KL + K++ + + +A + + E E K ++ +K+K+
Sbjct: 1587 KKAEEARIEEVMKLYEEEKKMKAEEAKKAE----EAKIKAEELKKAEEEKKKVEQLKKKE 1642
Query: 776 AEEAPKRRKMLKADNAYEIEEEEEEEEGE 804
AEE K ++ KA+ +I+ EE ++ E
Sbjct: 1643 AEEKKKAEELKKAEEENKIKAAEEAKKAE 1671
Score = 30.5 bits (68), Expect = 8.2
Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 5/61 (8%)
Query: 174 RKKAEEAPKRRKMLKADNAYEIEEEEEEEEGERLESM----DANEVEF-RLKHDPKQVQV 228
+KKAE+A K + KA++A + EE + E+ +R+E DA + E R D K+ +
Sbjct: 1121 KKKAEDARKAEEARKAEDARKAEEARKAEDAKRVEIARKAEDARKAEEARKAEDAKKAEA 1180
Query: 229 A 229
A
Sbjct: 1181 A 1181
>gnl|CDD|130456 TIGR01389, recQ, ATP-dependent DNA helicase RecQ. The
ATP-dependent DNA helicase RecQ of E. coli is about 600
residues long. This model represents bacterial proteins
with a high degree of similarity in domain architecture
and in primary sequence to E. coli RecQ. The model
excludes eukaryotic and archaeal proteins with RecQ-like
regions, as well as more distantly related bacterial
helicases related to RecQ [DNA metabolism, DNA
replication, recombination, and repair].
Length = 591
Score = 31.6 bits (72), Expect = 3.5
Identities = 44/149 (29%), Positives = 57/149 (38%), Gaps = 33/149 (22%)
Query: 419 KYPRTERGDVLIFMSGISEISS--IVRAAQEYNEKSQGWIVLPLHSTLSLEEQDRV---F 473
Y + RG SGI SS V E E SQG L H+ LS + + F
Sbjct: 217 DYLKKHRGQ-----SGIIYASSRKKVEELAERLE-SQGISALAYHAGLSNKVRAENQEDF 270
Query: 474 HYAPEGLRKCIVSTNIAETSITIDGIRFVVDSGKVKEMSYDVTAKMSTLQEFWISKASAE 533
Y K +V+TN I +RFV+ YD+ L+ ++
Sbjct: 271 LYDDV---KVMVATNAFGMGIDKPNVRFVI--------HYDMPG---NLESYY------- 309
Query: 534 QRKGRAGRTG-PGVCYRLYSEEQYSLLAE 561
Q GRAGR G P LYS +LL
Sbjct: 310 QEAGRAGRDGLPAEAILLYSPADIALLKR 338
>gnl|CDD|180975 PRK07429, PRK07429, phosphoribulokinase; Provisional.
Length = 327
Score = 31.1 bits (71), Expect = 3.8
Identities = 10/18 (55%), Positives = 15/18 (83%), Gaps = 2/18 (11%)
Query: 54 ERVVII--AGDTGCGKST 69
+R V++ AGD+GCGK+T
Sbjct: 6 DRPVLLGVAGDSGCGKTT 23
>gnl|CDD|219978 pfam08701, GN3L_Grn1, GNL3L/Grn1 putative GTPase. Grn1 (yeast) and
GNL3L (human) are putative GTPases which are required
for growth and play a role in processing of nucleolar
pre-rRNA. This family contains a potential nuclear
localisation signal.
Length = 80
Score = 28.4 bits (64), Expect = 5.1
Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 15/66 (22%)
Query: 759 ALRHGEIKLLQAIKRKKAEEA---PKRRKMLKAD----NAY--------EIEEEEEEEEG 803
LR+ K + RK +EA P + K D N++ EIEE++ ++E
Sbjct: 1 RLRYKIEKKVAEHHRKLRKEAKKNPTWKSKKKKDPGIPNSFPFKEEILEEIEEKKRKQEE 60
Query: 804 ERLESR 809
E+ +
Sbjct: 61 EKERRK 66
Score = 28.0 bits (63), Expect = 9.0
Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 15/64 (23%)
Query: 160 ALRHGEIKLLQAIKRKKAEEA---PKRRKMLKAD----NAY--------EIEEEEEEEEG 204
LR+ K + RK +EA P + K D N++ EIEE++ ++E
Sbjct: 1 RLRYKIEKKVAEHHRKLRKEAKKNPTWKSKKKKDPGIPNSFPFKEEILEEIEEKKRKQEE 60
Query: 205 ERLE 208
E+
Sbjct: 61 EKER 64
>gnl|CDD|146016 pfam03179, V-ATPase_G, Vacuolar (H+)-ATPase G subunit. This family
represents the eukaryotic vacuolar (H+)-ATPase
(V-ATPase) G subunit. V-ATPases generate an acidic
environment in several intracellular compartments.
Correspondingly, they are found as membrane-attached
proteins in several organelles. They are also found in
the plasma membranes of some specialised cells.
V-ATPases consist of peripheral (V1) and membrane
integral (V0) heteromultimeric complexes. The G subunit
is part of the V1 subunit, but is also thought to be
strongly attached to the V0 complex. It may be involved
in the coupling of ATP degradation to H+ translocation.
Length = 105
Score = 29.1 bits (66), Expect = 5.5
Identities = 19/45 (42%), Positives = 23/45 (51%), Gaps = 6/45 (13%)
Query: 167 KLLQAIKR--KKAEEAPKRR-KMLK---ADNAYEIEEEEEEEEGE 205
+LLQA K + EA KRR K LK + EIEE + E E
Sbjct: 8 QLLQAEKEAAEIVNEARKRRAKRLKQAKEEAEKEIEEYRAQREAE 52
Score = 29.1 bits (66), Expect = 5.5
Identities = 19/45 (42%), Positives = 23/45 (51%), Gaps = 6/45 (13%)
Query: 766 KLLQAIKR--KKAEEAPKRR-KMLK---ADNAYEIEEEEEEEEGE 804
+LLQA K + EA KRR K LK + EIEE + E E
Sbjct: 8 QLLQAEKEAAEIVNEARKRRAKRLKQAKEEAEKEIEEYRAQREAE 52
>gnl|CDD|179337 PRK01810, PRK01810, DNA polymerase IV; Validated.
Length = 407
Score = 30.8 bits (70), Expect = 5.8
Identities = 11/26 (42%), Positives = 18/26 (69%), Gaps = 1/26 (3%)
Query: 548 YRLYSEEQYSLLAEYSTPEIRRVSID 573
YR S + + +L+E+ TP ++ VSID
Sbjct: 83 YREASRQMFQILSEF-TPLVQPVSID 107
Score = 30.8 bits (70), Expect = 5.8
Identities = 11/26 (42%), Positives = 18/26 (69%), Gaps = 1/26 (3%)
Query: 816 YRLYSEEQYSLLAEYSTPEIRRVSID 841
YR S + + +L+E+ TP ++ VSID
Sbjct: 83 YREASRQMFQILSEF-TPLVQPVSID 107
>gnl|CDD|240235 PTZ00032, PTZ00032, 60S ribosomal protein L18; Provisional.
Length = 211
Score = 30.2 bits (68), Expect = 6.4
Identities = 19/56 (33%), Positives = 25/56 (44%), Gaps = 2/56 (3%)
Query: 148 PGPDASLSSRERALRHGEIKLLQAIKRKKAEEAPKRRKMLKADNAYEIEEEEEEEE 203
P+ S+ E+ LL KR K + PK RK+ K EI EE+ E E
Sbjct: 33 SSPNRKKSAPEQVPTGKNKLLLT--KRSKLKGIPKPRKLHKHGFWAEIFEEKVERE 86
Score = 30.2 bits (68), Expect = 6.4
Identities = 19/56 (33%), Positives = 25/56 (44%), Gaps = 2/56 (3%)
Query: 747 PGPDASLSSRERALRHGEIKLLQAIKRKKAEEAPKRRKMLKADNAYEIEEEEEEEE 802
P+ S+ E+ LL KR K + PK RK+ K EI EE+ E E
Sbjct: 33 SSPNRKKSAPEQVPTGKNKLLLT--KRSKLKGIPKPRKLHKHGFWAEIFEEKVERE 86
>gnl|CDD|224680 COG1766, fliF, Flagellar basal body M-ring protein [Cell motility
and secretion].
Length = 545
Score = 30.8 bits (70), Expect = 6.5
Identities = 19/62 (30%), Positives = 26/62 (41%), Gaps = 5/62 (8%)
Query: 395 ELDRTKSEKLDPGPYIRILSI---IDKKYPRTERGDVLIFMSG--ISEISSIVRAAQEYN 449
E+DRT S IR LS+ +D K +S + EI +VR A Y+
Sbjct: 346 EVDRTISHTKKEPGTIRRLSVAVVVDGKSLAGTGEKEYTPLSDEELKEIEDLVRDAVGYD 405
Query: 450 EK 451
K
Sbjct: 406 AK 407
>gnl|CDD|234981 PRK01766, PRK01766, multidrug efflux protein; Reviewed.
Length = 456
Score = 30.6 bits (70), Expect = 7.2
Identities = 21/91 (23%), Positives = 34/91 (37%), Gaps = 25/91 (27%)
Query: 842 SLLLSLVCMGLGDVRKFPFLEAPPAENIESSVRSLTQH-------GA------------I 882
+L LS++ M + P L N+E V + G I
Sbjct: 98 ALFLSVLIMLVLYNAVPPIL---NMMNLEPEVADIAVGYLHALLWGIPAYLLYQVLRSFI 154
Query: 883 D--SKERVTTLGRFLSDLPVDIPLGKMLVFG 911
D K + T + FL L ++IPL + ++G
Sbjct: 155 DGLGKTKPTMVIGFLG-LLINIPLNYIFIYG 184
Score = 30.2 bits (69), Expect = 9.2
Identities = 21/91 (23%), Positives = 34/91 (37%), Gaps = 25/91 (27%)
Query: 574 SLLLSLVCMGLGDVRKFPFLEAPPAENIESSVRSLTQH-------GA------------I 614
+L LS++ M + P L N+E V + G I
Sbjct: 98 ALFLSVLIMLVLYNAVPPIL---NMMNLEPEVADIAVGYLHALLWGIPAYLLYQVLRSFI 154
Query: 615 D--SKERVTSLGRFLSDLPVDIPLGKMLVFG 643
D K + T + FL L ++IPL + ++G
Sbjct: 155 DGLGKTKPTMVIGFLG-LLINIPLNYIFIYG 184
>gnl|CDD|216506 pfam01443, Viral_helicase1, Viral (Superfamily 1) RNA helicase.
Helicase activity for this family has been demonstrated
and NTPase activity. This helicase has multiple roles at
different stages of viral RNA replication, as dissected
by mutational analysis.
Length = 226
Score = 30.0 bits (68), Expect = 8.0
Identities = 18/85 (21%), Positives = 30/85 (35%), Gaps = 18/85 (21%)
Query: 57 VIIAGDTGCGKSTQIPQYLVQAGFQRIACTQPRRI--ACISLSKRVAYETLSQYSNLVGY 114
+++ G GCGKST I +++ T I ++ NL
Sbjct: 1 IVVHGVPGCGKSTLI---------RKLLRTDLTVIRPTAELRTEGKPDLP-----NLNVR 46
Query: 115 QIR-FEKHR-REKTKIVFITEGLLL 137
+ F + KI+ + E LL
Sbjct: 47 TVDTFLMALLKPTGKILILDEYTLL 71
>gnl|CDD|219925 pfam08598, Sds3, Sds3-like. Repression of gene transcription is
mediated by histone deacetylases containing
repressor-co-repressor complexes, which are recruited to
promoters of target genes via interactions with
sequence-specific transcription factors. The
co-repressor complex contains a core of at least seven
proteins. This family represents the conserved region
found in Sds3, Dep1 and BRMS1-homologue p40 proteins.
Length = 184
Score = 29.6 bits (67), Expect = 8.0
Identities = 33/137 (24%), Positives = 49/137 (35%), Gaps = 26/137 (18%)
Query: 680 KELESNHGDPLTVLNAYKEWLGVKKDRVRSKKWCKRRGIEEQRFYEVTKLRSQFKQVLGD 739
K+LE D L V +E K + + + +R+ +++ E LR + + L +
Sbjct: 49 KDLEERRDDRLKVAELRRE---YKLECIEREYEAERQAAKQEFEKEKRLLRERLLEELEE 105
Query: 740 -------SGLITDIPGPDASL-----SSRERALRHGEIKLLQAIKRKK--------AEEA 779
DI D L + R R LR KRKK + A
Sbjct: 106 KIYRLEEERRSLDITDSDYGLLGSHPNRRTRKLRRRVNSPELVAKRKKKNNESSDLSGLA 165
Query: 780 PKRRKMLKADNAYEIEE 796
P MLK + EI E
Sbjct: 166 PYILYMLKEE---EILE 179
>gnl|CDD|178493 PLN02905, PLN02905, beta-amylase.
Length = 702
Score = 30.3 bits (68), Expect = 8.0
Identities = 14/42 (33%), Positives = 20/42 (47%)
Query: 1083 SEEEEEEEAGERLESMDANEVEFRLKHDPKQVQVAADNFLSS 1124
SEE++EEE ++ D + R KH P V+ D S
Sbjct: 12 SEEDDEEEMDMDVKEEDDGDRRNREKHIPVTGMVSVDGAAVS 53
>gnl|CDD|129690 TIGR00602, rad24, checkpoint protein rad24. All proteins in this
family for which functions are known are involved in DNA
damage tolerance (likely cell cycle checkpoints).This
family is based on the phylogenomic analysis of JA Eisen
(1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 637
Score = 30.3 bits (68), Expect = 8.2
Identities = 20/47 (42%), Positives = 29/47 (61%), Gaps = 8/47 (17%)
Query: 33 ETQNSLPVAQYKQEIIDTVLK--------ERVVIIAGDTGCGKSTQI 71
ETQ+ L V + K E ++T LK +R+++I G +GCGKST I
Sbjct: 81 ETQHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTI 127
>gnl|CDD|234132 TIGR03167, tRNA_sel_U_synt, tRNA 2-selenouridine synthase. The
Escherichia coli YbbB protein was shown to encode a
selenophosphate-dependent tRNA 2-selenouridine synthase,
essential for modification of some tRNAs to replace a
sulfur atom with selenium. This enzyme works with SelD,
the selenium donor protein, which also acts in
selenocysteine incorporation. Although the members of
this protein family show a fairly deep split, sequences
from both sides of the split are supported by
co-occurence with, and often proximity to, the selD gene
[Protein synthesis, tRNA and rRNA base modification].
Length = 311
Score = 30.3 bits (69), Expect = 8.5
Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 5/45 (11%)
Query: 43 YKQEIIDTV----LKERVVIIAGDTGCGKSTQIPQYLVQAGFQRI 83
Y++ +ID + ++++ G TG GK T++ L AG Q +
Sbjct: 112 YRRFVIDQLEELPQPFPLIVLGGMTGSGK-TELLHALANAGAQVL 155
>gnl|CDD|153331 cd07647, F-BAR_PSTPIP, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Proline-Serine-Threonine
Phosphatase-Interacting Proteins. F-BAR domains are
dimerization modules that bind and bend membranes and
are found in proteins involved in membrane dynamics and
actin reorganization. Vetebrates contain two
Proline-Serine-Threonine Phosphatase-Interacting
Proteins (PSTPIPs), PSTPIP1 and PSTPIP2. PSTPIPs are
mainly expressed in hematopoietic cells and are involved
in the regulation of cell adhesion and motility.
Mutations in PSTPIPs have been shown to cause
autoinflammatory disorders. PSTPIP1 contains an
N-terminal F-BAR domain, PEST motifs, and a C-terminal
SH3 domain, while PSTPIP2 contains only the N-terminal
F-BAR domain. F-BAR domains form banana-shaped dimers
with a positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 239
Score = 29.8 bits (67), Expect = 9.0
Identities = 28/109 (25%), Positives = 49/109 (44%), Gaps = 14/109 (12%)
Query: 153 SLSSRERALRHGEIKLLQAIKRKKAEEAPKR---------RKMLKADNAYEI---EEEEE 200
+ S RE A + E + Q +RKK E+ KR +K +KA +YE E+++
Sbjct: 80 AQSLREEAEKLEEFREKQKEERKKTEDIMKRSQKNKKELYKKTMKAKKSYEQKCREKDKA 139
Query: 201 EEEGERLESMDANEVEFRLKHDPKQVQVATDNFLSSY--DILILDEVHE 247
E+ E+ S + +LK Q + + + S+Y I L++
Sbjct: 140 EQAYEKSSSGAQPKEAEKLKKKAAQCKTSAEEADSAYKSSIGCLEDARV 188
>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon.
Length = 431
Score = 30.0 bits (67), Expect = 9.1
Identities = 24/63 (38%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 158 ERALRHGEIKLLQAIKRKKAEEAPKRRKMLKADNAYEIEEEEEEEEGERLESMDANEVEF 217
E AL E+K + +RK EE +RRK +AD EEEE+ E +E A E
Sbjct: 211 EAALELEELKKKREERRKVLEEEEQRRKQEEADRKSR-EEEEKRRLKEEIERRRAEAAEK 269
Query: 218 RLK 220
R K
Sbjct: 270 RQK 272
>gnl|CDD|226425 COG3910, COG3910, Predicted ATPase [General function prediction
only].
Length = 233
Score = 29.7 bits (67), Expect = 9.2
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 37 SLPVAQYKQEIIDTVLKERVVIIAGDTGCGKSTQIPQYLVQAGF 80
SLP ++ +E ++ + + I G+ G GKST + GF
Sbjct: 22 SLPAFRHLEERLE--FRAPITFITGENGSGKSTLLEAIAAGMGF 63
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.137 0.392
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 73,947,604
Number of extensions: 7682761
Number of successful extensions: 10081
Number of sequences better than 10.0: 1
Number of HSP's gapped: 9975
Number of HSP's successfully gapped: 173
Length of query: 1417
Length of database: 10,937,602
Length adjustment: 109
Effective length of query: 1308
Effective length of database: 6,103,016
Effective search space: 7982744928
Effective search space used: 7982744928
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 65 (28.8 bits)