|
Name |
Accession |
Description |
Interval |
E-value |
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
24-1158 |
0e+00 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 1553.11 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 24 DRQLVMGLSGSSKALAMASAFLDSQEKIVVMTSTQNEVEKLASDLSSLLGEELVYQFFADDVAAAEFIFASMDKALSRIE 103
Cdd:COG1197 3 GRLTLSGLPGSARALLLAALARALGRPLLVVTADEREAERLAEDLRFFLPDLPVLLFPAWETLPYDRFSPSPDIVSERLA 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 104 TLQFLRNPKsQGVLIVSLSGLRTLLPNPDVFTKSQIQLTVGEDYDSDTLTKQLMTIGYQKVSQVISPGEFSRRGDILDIY 183
Cdd:COG1197 83 TLRRLASGK-PGIVVTPVRALLQRLPPPELLAAASLSLKVGDELDLEELRERLVAAGYERVDQVEEPGEFAVRGGILDIF 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 184 EITQELPYRLEFFGDDIDSIRQFHPETQKSFEQLEGIFINPASDLIFEASDFQRGIEQLEKALQtAQDDKKSYLEDVlav 263
Cdd:COG1197 162 PPGSEHPVRIEFFGDEIESIRTFDPETQRSLEKVDEVELLPAREFPLDEEAIERFRERLRELFG-LDPKLDELYEAL--- 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 264 sKNGFKHKDIRKFQSLFYEKEWSLLDYIPKGTPIFFDDFQKLVDKNARFDLEIANLLTEDLQ-QGKALSNLNYFADNYRE 342
Cdd:COG1197 238 -SEGIAFAGIEYYLPLFYEELATLFDYLPEDALVVLDEPERIEEAAEEFWEEIEERYEARRHdRGRPLLPPEELFLDPEE 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 343 LRHY---KPATFFSNFHKGLgniKFDQMHQLTQYAMQEFFNQFPLLIDEIKRYQKNQTTVIVQVESQYAYERLEKSFQDY 419
Cdd:COG1197 317 LFAAlkrRPRVTLSPFAALP---EGAGVVNLGARPLPSFAGQLEALLEELKRLLKDGGRVLLAAESEGRRERLLELLRDH 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 420 QFRLPLV-SANQIVSRESQIVIGAISSGFYFADEKLALITEHEIYHKKIKRRARRSNISNAERLKDYNELAVGDYVVHNV 498
Cdd:COG1197 394 GIPARLVeSLAELSPGGVAITVGPLEHGFELPDAKLAVITESELFGERVKRRRRKKKRSADAFIRDLSELKPGDYVVHVD 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 499 HGIGRFLGIETIQIQGIHRDYVTIQYQNSDRISLPIDQISSLSKYVSADGKEPKINKLNDGRFQKTKQKVARQVEDIADD 578
Cdd:COG1197 474 HGIGRYLGLETLEVGGAERDYLVLEYAGGDKLYVPVDQLDLISRYVGSEGEAPKLDKLGGSDWQKAKAKAKKAVRDIAAE 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 579 LLKLYAERSQQKGFSFSPDDDLQRAFDDDFAFVETEDQLRSIKEIKADMESMQPMDRLLVGDVGFGKTEVAMRAAFKAVN 658
Cdd:COG1197 554 LLKLYAERAARKGFAFSPDTPWQREFEAAFPYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKTEVALRAAFKAVM 633
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 659 DHKQVAVLVPTTVLAQQHYENFKARFENYPVEVDVLSRFRSKKEQAETLERVRKGQIDIIIGTHQLLSKDVVFSDLGLIV 738
Cdd:COG1197 634 DGKQVAVLVPTTLLAQQHYETFKERFAGFPVRVEVLSRFRTAKEQKETLEGLADGKVDIVIGTHRLLSKDVKFKDLGLLI 713
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 739 IDEEQRFGVKHKETLKELKTKVDVLTLTATPIPRTLHMSMLGIRDLSVIETPPTNRYPVQTYVLENNPGLVREAIIREMD 818
Cdd:COG1197 714 IDEEQRFGVRHKEKLKALRANVDVLTLTATPIPRTLQMSLSGIRDLSIIATPPEDRLPVKTFVGEYDDALIREAILRELL 793
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 819 RGGQVFYVYNKVDTIDKKVAELQELVPEASIGFVHGQMSEIQLENTLIDFINGDYDVLVATTIIETGVDISNVNTLFIEN 898
Cdd:COG1197 794 RGGQVFYVHNRVEDIEKVAARLQELVPEARIAVAHGQMSERELERVMLDFYEGEFDVLVCTTIIETGIDIPNANTIIIER 873
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 899 ADHMGLSTLYQLRGRVGRSNRIAYAYLMYRPDKVLTEVSEKRLEAIKGFTELGSGFKIAMRDLSIRGAGNILGASQSGFI 978
Cdd:COG1197 874 ADRFGLAQLYQLRGRVGRSHRRAYAYLLYPPDKVLTEDAEKRLEAIQEFTELGAGFKLAMHDLEIRGAGNLLGEEQSGHI 953
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 979 DSVGFEMYSQLLEQAIASKQGKTTVRQKGNTEINLQIDAYLPDDYIADERQKIDIYKRIREIQSREDYLNLQDELMDRFG 1058
Cdd:COG1197 954 AEVGFDLYLQMLEEAVAALKGGKEPEEEWEPEINLGVPALIPEDYIPDVRQRLELYKRIASAESEEELDELQEELIDRFG 1033
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 1059 EYPDQVAYLLEIALLKHYMDNAFAELVERKNNQVIVRF-EVTSLTyflTQDYFEALSKTHLKAKISEhQGKIDIVFDVRH 1137
Cdd:COG1197 1034 PLPEEVENLLAVARLKLLARRLGIEKIDAGGKGIRIEFsPNTPLD---PEKLIRLIQKQPGRYKLDG-DDKLVITLDLED 1109
|
1130 1140
....*....|....*....|.
gi 1797901375 1138 QKDytILEELMLFGESLSEIK 1158
Cdd:COG1197 1110 PEE--RLEALEELLEALAKLA 1128
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
156-1077 |
0e+00 |
|
transcription-repair coupling factor (mfd); All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273152 [Multi-domain] Cd Length: 926 Bit Score: 1078.15 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 156 LMTIGYQKVSQVISPGEFSRRGDILDIYEITQELPYRLEFFGDDIDSIRQFHPETQKSFEQLEGIFINPASDLIFEASDF 235
Cdd:TIGR00580 1 LVELGYERVDLVEEEGEFSVRGEILDIFPPGSELPVRIEFFGDEIESIREFDVDSQRSLEELLEITILPAKEFILLEEET 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 236 qrgIEQLEKALQTAQDDKKSYLEDVLavsKNGFKHKDIRKFQSLFYEKEWSLLDYIPKGTPIFfDDFQKLVDKNARFDLE 315
Cdd:TIGR00580 81 ---IARLKDNAARVEDAKHLETIEAL---SEGTLPAGEEMFLPLFFEDLSSLFDYLPDNTPIL-LDDPERFHSAARFLQR 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 316 IANLLTEDLQQGKALSNLNYFADNYRELRHYKPA-----TFFSNFHKGLGN---IKFDQMHQltqyamQEFFNQFPLLID 387
Cdd:TIGR00580 154 ELEEFYNALEEAKKLINPPRLDLDPSELAFEASAislsrVQLENEHLSLKAseaIEGAQKHS------RLEFGEILAFKE 227
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 388 EIKRYQKNQTTVIVQVESQYAYERLEKSFQDYQFRLP-LVSANQIVSRESQIVIGAISSGFYFADEKLALITEHEIYHKK 466
Cdd:TIGR00580 228 ELFRWLKAGFKITVAAESESQAERLKSLLAEHDIAAQvIDESCIIIPAVRYVMIGALSSGFILPTAGLAVITESELFGSR 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 467 IKRRARRSNISNAeRLKDYNELAVGDYVVHNVHGIGRFLGIETIQIQGIHRDYVTIQYQNSDRISLPIDQISSLSKYVSA 546
Cdd:TIGR00580 308 VLRRPKKSRLKSK-PIESLNELNPGDYVVHLDHGIGRFLGLETLEVGGIERDYLVLEYAGEDKLYVPVEQLHLISRYVGG 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 547 DGKEPKINKLNDGRFQKTKQKVARQVEDIADDLLKLYAERSQQKGFSFSPDDDLQRAFDDDFAFVETEDQLRSIKEIKAD 626
Cdd:TIGR00580 387 SGKNPALDKLGGKSWEKTKAKVKKSVREIAAKLIELYAKRKAIKGHAFPPDLEWQQEFEDSFPFEETPDQLKAIEEIKAD 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 627 MESMQPMDRLLVGDVGFGKTEVAMRAAFKAVNDHKQVAVLVPTTVLAQQHYENFKARFENYPVEVDVLSRFRSKKEQAET 706
Cdd:TIGR00580 467 MESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEI 546
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 707 LERVRKGQIDIIIGTHQLLSKDVVFSDLGLIVIDEEQRFGVKHKETLKELKTKVDVLTLTATPIPRTLHMSMLGIRDLSV 786
Cdd:TIGR00580 547 LKELASGKIDILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSI 626
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 787 IETPPTNRYPVQTYVLENNPGLVREAIIREMDRGGQVFYVYNKVDTIDKKVAELQELVPEASIGFVHGQMSEIQLENTLI 866
Cdd:TIGR00580 627 IATPPEDRLPVRTFVMEYDPELVREAIRRELLRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVML 706
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 867 DFINGDYDVLVATTIIETGVDISNVNTLFIENADHMGLSTLYQLRGRVGRSNRIAYAYLMYRPDKVLTEVSEKRLEAIKG 946
Cdd:TIGR00580 707 EFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDAQKRLEAIQE 786
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 947 FTELGSGFKIAMRDLSIRGAGNILGASQSGFIDSVGFEMYSQLLEQAIASKQGKTTVRQKGNTEINLQIDAYLPDDYIAD 1026
Cdd:TIGR00580 787 FSELGAGFKIALHDLEIRGAGNLLGEEQSGHIESIGFDLYMELLEEAIEELKGGKPPKLEEETDIELPYSAFIPDDYIAD 866
|
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|.
gi 1797901375 1027 ERQKIDIYKRIREIQSREDYLNLQDELMDRFGEYPDQVAYLLEIALLKHYM 1077
Cdd:TIGR00580 867 DSLRLEFYKRIASAETEEELEKIRDELIDRFGPLPEEARTLLDVARLKLLA 917
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
100-1074 |
0e+00 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 719.61 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 100 SRIETLQFLRNpKSQGVLIVSLSglrTLLPN--PDVFTKSQ-IQLTVGEDYDSDTLTKQLMTIGYQKVSQVISPGEFSRR 176
Cdd:PRK10689 90 SRLSTLYQLPT-MQRGVLILPVN---TLMQRvcPHSFLHGHaLVMKKGQRLSRDALRAQLEQAGYRHVDQVMEHGEYATR 165
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 177 GDILDIYEITQELPYRLEFFGDDIDSIRQFHPETQKSFEQLEGIFINPASDLIFEASDFQRGIEQLEKALQTAQDDKKSY 256
Cdd:PRK10689 166 GALLDLFPMGSEEPYRIDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFEVKRDAEHIY 245
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 257 LEdvlaVSKnGFKHKDIRKFQSLFYEKEW-SLLDYIPKGTPIFF--------DDFQKlvDKNARFDleiaNLLTEDLQQG 327
Cdd:PRK10689 246 QQ----VSK-GTLPAGIEYWQPLFFSEPLpPLFSYFPANTLLVNtgdletsaERFWA--DTLARFE----NRGVDPMRPL 314
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 328 KALSNLNYFADN-YRELRHYKPATFFSNF---HKGLGNIKFDQMHQLTQYAMQeffnQFPLliDEIKRYQKNQT-TVIVQ 402
Cdd:PRK10689 315 LPPESLWLRVDElFSELKNWPRVQLKTEHlptKAANTNLGYQKLPDLAVQAQQ----KAPL--DALRRFLESFDgPVVFS 388
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 403 VESQYAYERLEKSFQDYQFRLPLVSA-NQIVSRESQIVIGAISSGFYFADEKLALITEHEIYHKKIKRRAR--RSNISNA 479
Cdd:PRK10689 389 VESEGRREALGELLARIKIAPKRIMRlDEASDRGRYLMIGAAEHGFIDTVRNLALICESDLLGERVARRRQdsRRTINPD 468
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 480 ERLKDYNELAVGDYVVHNVHGIGRFLGIETIQIQGIHRDYVTIQYQNSDRISLPIDQISSLSKYVSADGKEPKINKLNDG 559
Cdd:PRK10689 469 TLIRNLAELHPGQPVVHLEHGVGRYAGMTTLEAGGIKGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHKLGGD 548
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 560 RFQKTKQKVARQVEDIADDLLKLYAERSQQKGFSFSPDDDLQRAFDDDFAFVETEDQLRSIKEIKADMESMQPMDRLLVG 639
Cdd:PRK10689 549 AWSRARQKAAEKVRDVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCG 628
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 640 DVGFGKTEVAMRAAFKAVNDHKQVAVLVPTTVLAQQHYENFKARFENYPVEVDVLSRFRSKKEQAETLERVRKGQIDIII 719
Cdd:PRK10689 629 DVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILI 708
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 720 GTHQLLSKDVVFSDLGLIVIDEEQRFGVKHKETLKELKTKVDVLTLTATPIPRTLHMSMLGIRDLSVIETPPTNRYPVQT 799
Cdd:PRK10689 709 GTHKLLQSDVKWKDLGLLIVDEEHRFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKT 788
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 800 YVLENNPGLVREAIIREMDRGGQVFYVYNKVDTIDKKVAELQELVPEASIGFVHGQMSEIQLENTLIDFINGDYDVLVAT 879
Cdd:PRK10689 789 FVREYDSLVVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCT 868
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 880 TIIETGVDISNVNTLFIENADHMGLSTLYQLRGRVGRSNRIAYAYLMYRPDKVLTEVSEKRLEAIKGFTELGSGFKIAMR 959
Cdd:PRK10689 869 TIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATH 948
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 960 DLSIRGAGNILGASQSGFIDSVGFEMYSQLLEQAI-ASKQGKT------TVRQkgnTEINLQIDAYLPDDYIADERQKID 1032
Cdd:PRK10689 949 DLEIRGAGELLGEEQSGQMETIGFSLYMELLENAVdALKAGREpsledlTSQQ---TEVELRMPSLLPDDFIPDVNTRLS 1025
|
970 980 990 1000
....*....|....*....|....*....|....*....|..
gi 1797901375 1033 IYKRIREIQSREDYLNLQDELMDRFGEYPDQVAYLLEIALLK 1074
Cdd:PRK10689 1026 FYKRIASAKNENELEEIKVELIDRFGLLPDPARNLLDIARLR 1067
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
579-979 |
8.86e-129 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 409.82 E-value: 8.86e-129
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 579 LLKLYAERSQQKGFSFSPDDDLQRAFDDDFAFVETEDQLRSIKEIKADMESMQPMDRLLVGDVGFGKTEVAMRAAFKAVN 658
Cdd:COG1200 227 LLLRRARRRKRKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVE 306
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 659 DHKQVAVLVPTTVLAQQHYENFKARFENYPVEVDVLSRFRSKKEQAETLERVRKGQIDIIIGTHQLLSKDVVFSDLGLIV 738
Cdd:COG1200 307 AGYQAALMAPTEILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVV 386
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 739 IDEEQRFGVKHKETLKELKTKVDVLTLTATPIPRTLHMSMLGIRDLSVI-ETPPtNRYPVQTYVL-ENNPGLVREAIIRE 816
Cdd:COG1200 387 IDEQHRFGVEQRLALREKGEAPHVLVMTATPIPRTLAMTLYGDLDVSVIdELPP-GRKPIKTRVVpEERRDEVYERIREE 465
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 817 MDRGGQVFYVYNKV---DTIDKK-----VAELQELVPEASIGFVHGQMSEIQLENTLIDFINGDYDVLVATTIIETGVDI 888
Cdd:COG1200 466 IAKGRQAYVVCPLIeesEKLDLQaaeetYEELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGVDV 545
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 889 SNVNTLFIENADHMGLSTLYQLRGRVGRSNRIAYAYLMYRPDkvLTEVSEKRLEAIkgfTELGSGFKIAMRDLSIRGAGN 968
Cdd:COG1200 546 PNATVMVIENAERFGLSQLHQLRGRVGRGSAQSYCLLLYDAP--LSETARERLEVM---RETNDGFEIAEEDLELRGPGE 620
|
410
....*....|.
gi 1797901375 969 ILGASQSGFID 979
Cdd:COG1200 621 FLGTRQSGLPD 631
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
579-993 |
9.78e-123 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 393.36 E-value: 9.78e-123
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 579 LLKLYAERSQQKGFSFSPDDDLQRAFDDDFAFVETEDQLRSIKEIKADMESMQPMDRLLVGDVGFGKTEVAMRAAFKAVN 658
Cdd:PRK10917 229 LLLLRAGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIE 308
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 659 DHKQVAVLVPTTVLAQQHYENFKARFENYPVEVDVLSRFRSKKEQAETLERVRKGQIDIIIGTHQLLSKDVVFSDLGLIV 738
Cdd:PRK10917 309 AGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVI 388
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 739 IDEEQRFGVKHKETLKELKTKVDVLTLTATPIPRTLHMSMLGIRDLSVI-ETPPtNRYPVQTYVL-ENNPGLVREAIIRE 816
Cdd:PRK10917 389 IDEQHRFGVEQRLALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIdELPP-GRKPITTVVIpDSRRDEVYERIREE 467
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 817 MDRGGQVFYVYNKV---DTIDKKVAE-----LQELVPEASIGFVHGQMSEIQLENTLIDFINGDYDVLVATTIIETGVDI 888
Cdd:PRK10917 468 IAKGRQAYVVCPLIeesEKLDLQSAEetyeeLQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDV 547
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 889 SNVNTLFIENADHMGLSTLYQLRGRVGRSNRIAYAYLMYRPDkvLTEVSEKRLEAIKGFTelgSGFKIAMRDLSIRGAGN 968
Cdd:PRK10917 548 PNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDP--LSETARERLKIMRETN---DGFVIAEKDLELRGPGE 622
|
410 420 430
....*....|....*....|....*....|
gi 1797901375 969 ILGASQSGFIDsvgFEMYS-----QLLEQA 993
Cdd:PRK10917 623 LLGTRQSGLPE---FKVADlvrdeELLEEA 649
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
597-789 |
7.50e-121 |
|
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350749 [Multi-domain] Cd Length: 193 Bit Score: 370.36 E-value: 7.50e-121
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 597 DDDLQRAFDDDFAFVETEDQLRSIKEIKADMESMQPMDRLLVGDVGFGKTEVAMRAAFKAVNDHKQVAVLVPTTVLAQQH 676
Cdd:cd17991 1 DGEEQEEFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 677 YENFKARFENYPVEVDVLSRFRSKKEQAETLERVRKGQIDIIIGTHQLLSKDVVFSDLGLIVIDEEQRFGVKHKETLKEL 756
Cdd:cd17991 81 YETFKERFANFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQKEKLKEL 160
|
170 180 190
....*....|....*....|....*....|...
gi 1797901375 757 KTKVDVLTLTATPIPRTLHMSMLGIRDLSVIET 789
Cdd:cd17991 161 RPNVDVLTLSATPIPRTLHMALSGIRDLSVIAT 193
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
579-979 |
1.06e-110 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 359.73 E-value: 1.06e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 579 LLKLYAERSQQKGFSFSPDDDLQRAFDDDFAFVETEDQLRSIKEIKADMESMQPMDRLLVGDVGFGKTEVAMRAAFKAVN 658
Cdd:TIGR00643 203 LARRLGEKQQFSAPPANPSEELLTKFLASLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIE 282
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 659 DHKQVAVLVPTTVLAQQHYENFKARFENYPVEVDVLSRFRSKKEQAETLERVRKGQIDIIIGTHQLLSKDVVFSDLGLIV 738
Cdd:TIGR00643 283 AGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVI 362
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 739 IDEEQRFGVKHKETLKE---LKTKVDVLTLTATPIPRTLHMSMLGIRDLSVIETPPTNRYPVQTYVL-ENNPGLVREAII 814
Cdd:TIGR00643 363 IDEQHRFGVEQRKKLREkgqGGFTPHVLVMSATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLIkHDEKDIVYEFIE 442
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 815 REMDRGGQVFYVYNKVDTIDK---KVAE-----LQELVPEASIGFVHGQMSEIQLENTLIDFINGDYDVLVATTIIETGV 886
Cdd:TIGR00643 443 EEIAKGRQAYVVYPLIEESEKldlKAAEalyerLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGV 522
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 887 DISNVNTLFIENADHMGLSTLYQLRGRVGRSNRIAYAYLMYRPDKvlTEVSEKRLEAIKGFTElgsGFKIAMRDLSIRGA 966
Cdd:TIGR00643 523 DVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKNPK--SESAKKRLRVMADTLD---GFVIAEEDLELRGP 597
|
410
....*....|...
gi 1797901375 967 GNILGASQSGFID 979
Cdd:TIGR00643 598 GDLLGTKQSGYPE 610
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
579-791 |
3.45e-69 |
|
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. It is a member of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350750 [Multi-domain] Cd Length: 225 Bit Score: 231.27 E-value: 3.45e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 579 LLKLYAERSQQKGFSFSPDDDLQRAFDDDFAFVETEDQLRSIKEIKADMESMQPMDRLLVGDVGFGKTEVAMRAAFKAVN 658
Cdd:cd17992 13 LLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKTVVAALAMLAAVE 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 659 DHKQVAVLVPTTVLAQQHYENFKARFENYPVEVDVLSRFRSKKEQAETLERVRKGQIDIIIGTHQLLSKDVVFSDLGLIV 738
Cdd:cd17992 93 NGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQEDVEFHNLGLVI 172
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 1797901375 739 IDEEQRFGVKHKETLKELKTKVDVLTLTATPIPRTLHMSMLGIRDLSVIETPP 791
Cdd:cd17992 173 IDEQHRFGVEQRLKLREKGETPHVLVMTATPIPRTLALTLYGDLDVSIIDELP 225
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
796-945 |
2.19e-68 |
|
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350197 [Multi-domain] Cd Length: 151 Bit Score: 226.07 E-value: 2.19e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 796 PVQTYVLENNPGLVREAIIREMDRGGQVFYVYNKVDTIDKKVAELQELVPEASIGFVHGQMSEIQLENTLIDFINGDYDV 875
Cdd:cd18810 1 PVRTYVMPYDDELIREAIERELLRGGQVFYVHNRIESIEKLATQLRQLVPEARIAIAHGQMTENELEEVMLEFAKGEYDI 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 876 LVATTIIETGVDISNVNTLFIENADHMGLSTLYQLRGRVGRSNRIAYAYLMYRPDKVLTEVSEKRLEAIK 945
Cdd:cd18810 81 LVCTTIIESGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAYFLYPDQKKLTEDALKRLEAIQ 150
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
597-787 |
1.32e-60 |
|
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase RecG family is part of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350676 [Multi-domain] Cd Length: 180 Bit Score: 204.96 E-value: 1.32e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 597 DDDLQRAFDDDFAFVETEDQLRSIKEIKADMESMQPMDRLLVGDVGFGKTEVAMRAAFKAVNDHKQVAVLVPTTVLAQQH 676
Cdd:cd17918 1 DRALIQELCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 677 YENFKARFENYPVEvdVLSRFRskKEQAETlervrkgQIDIIIGTHQLLSKDVVFSDLGLIVIDEEQRFGVKHKETLKEL 756
Cdd:cd17918 81 YEEARKFLPFINVE--LVTGGT--KAQILS-------GISLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNL 149
|
170 180 190
....*....|....*....|....*....|.
gi 1797901375 757 KtKVDVLTLTATPIPRTLHMSMLGIRDLSVI 787
Cdd:cd17918 150 G-ATHFLEATATPIPRTLALALSGLLDLSVI 179
|
|
| SF2_C_RecG_TRCF |
cd18792 |
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
796-946 |
1.10e-58 |
|
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family contains recombination factor RecG and transcription-repair coupling factor TrcF. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350179 [Multi-domain] Cd Length: 160 Bit Score: 198.65 E-value: 1.10e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 796 PVQTYVLENNPG-LVREAIIREMDRGGQVFYVYNKVDTIDKKVAE--------LQELVPEASIGFVHGQMSEIQLENTLI 866
Cdd:cd18792 1 PIRTYVIPHDDLdLVYEAIERELARGGQVYYVYPRIEESEKLDLKsiealaeeLKELVPEARVALLHGKMTEDEKEAVML 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 867 DFINGDYDVLVATTIIETGVDISNVNTLFIENADHMGLSTLYQLRGRVGRSNRIAYAYLMYRPDKVLTEVSEKRLEAIKG 946
Cdd:cd18792 81 EFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYPDPKKLTETAKKRLRAIAE 160
|
|
| CarD_TRCF |
smart01058 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
487-584 |
2.43e-37 |
|
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of light- and starvation-inducible genes. This family includes the presumed N-terminal domain. CarD interacts with the zinc-binding protein CarG, to form a complex that regulates multiple processes in Myxococcus xanthus. This family also includes a domain to the N-terminal side of the DEAD helicase of TRCF proteins. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription. This domain is involved in binding to the stalled RNA polymerase.
Pssm-ID: 215001 [Multi-domain] Cd Length: 99 Bit Score: 135.27 E-value: 2.43e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 487 ELAVGDYVVHNVHGIGRFLGIETIQIQGIHRDYVTIQYQNSDRISLPIDQISSLSKYVSADGK-EPKINKLNDGRFQKTK 565
Cdd:smart01058 1 ELKIGDYVVHPDHGVGRYEGIETIEVGGEKREYLVLEYAGGDKLYVPVDNLDLGSRYVGSEGEvEPVLDKLGGGSWSKRK 80
|
90
....*....|....*....
gi 1797901375 566 QKVARQVEDIADDLLKLYA 584
Cdd:smart01058 81 RKAKSGIRDIAAELLRLYA 99
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
796-946 |
1.21e-32 |
|
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350198 [Multi-domain] Cd Length: 159 Bit Score: 124.38 E-value: 1.21e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 796 PVQTYVL-ENNPGLVREAIIREMDRGGQVFYVYNKVDTIDK-----KVAELQEL----VPEASIGFVHGQMSEIQLENTL 865
Cdd:cd18811 1 PITTYLIfHTRLDKVYEFVREEIAKGRQAYVIYPLIEESEKldlkaAVAMYEYLkerfRPELNVGLLHGRLKSDEKDAVM 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 866 IDFINGDYDVLVATTIIETGVDISNVNTLFIENADHMGLSTLYQLRGRVGRSNRIAYAYLMYRPdkVLTEVSEKRLEAIK 945
Cdd:cd18811 81 AEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKD--PLTETAKQRLRVMT 158
|
.
gi 1797901375 946 G 946
Cdd:cd18811 159 E 159
|
|
| TRCF |
smart00982 |
This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in ... |
1012-1097 |
1.22e-30 |
|
This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; A lesion in the template strand blocks the RNA polymerase complex (RNAP). The RNAP-DNA-RNA complex is specifically recognised by the transcription-repair-coupling factor (TRCF) which releases RNAP and the truncated transcript.
Pssm-ID: 198050 [Multi-domain] Cd Length: 100 Bit Score: 116.41 E-value: 1.22e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 1012 NLQIDAYLPDDYIADERQKIDIYKRIREIQSREDYLNLQDELMDRFGEYPDQVAYLLEIALLKHYMDNAFAELVERKNNQ 1091
Cdd:smart00982 1 DLPVPALIPEDYIPDVRQRLELYKRIASAETEEELDEIQEELIDRFGPLPEEVKNLLEVARLKLLAKKLGIEKIDAGGKG 80
|
....*.
gi 1797901375 1092 VIVRFE 1097
Cdd:smart00982 81 IVIEFS 86
|
|
| UvrB_inter |
pfam17757 |
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ... |
139-227 |
8.45e-30 |
|
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the UvrA protein.
Pssm-ID: 465486 [Multi-domain] Cd Length: 91 Bit Score: 113.64 E-value: 8.45e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 139 IQLTVGEDYDSDTLTKQLMTIGYQKVSQVISPGEFSRRGDILDIYEITQE-LPYRLEFFGDDIDSIRQFHPETQKSFEQL 217
Cdd:pfam17757 1 LSLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYSEdEAIRIEFFGDEIESIREFDPLTGRSLEKL 80
|
90
....*....|
gi 1797901375 218 EGIFINPASD 227
Cdd:pfam17757 81 DEVTIYPASH 90
|
|
| TRCF |
pfam03461 |
TRCF domain; |
1013-1096 |
2.39e-29 |
|
TRCF domain;
Pssm-ID: 460928 [Multi-domain] Cd Length: 95 Bit Score: 112.52 E-value: 2.39e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 1013 LQIDAYLPDDYIADERQKIDIYKRIREIQSREDYLNLQDELMDRFGEYPDQVAYLLEIALLKHYMDNAFAELVERKNNQV 1092
Cdd:pfam03461 1 LDVDAYIPDDYIPDESQRLELYKRLASIETEEELDDLQEELIDRFGPLPEEVENLLEIARLKLLAKKLGIEKIDLKGGGI 80
|
....
gi 1797901375 1093 IVRF 1096
Cdd:pfam03461 81 RITF 84
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
613-776 |
6.77e-28 |
|
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.
Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 110.80 E-value: 6.77e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 613 TEDQLRSIKEIkadmesMQPMDRLLVGDVGFGKTEVAMRAAFKAVN---DHKQVAVLVPTTVLAQQHYENFKARFENYPV 689
Cdd:pfam00270 1 TPIQAEAIPAI------LEGRDVLVQAPTGSGKTLAFLLPALEALDkldNGPQALVLAPTRELAEQIYEELKKLGKGLGL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 690 EVdvlSRFRSKKEQAETLERVRKgqIDIIIGTH----QLLSKDVVFSDLGLIVIDEEQR-----FGVKHKETLKELKTKV 760
Cdd:pfam00270 75 KV---ASLLGGDSRKEQLEKLKG--PDILVGTPgrllDLLQERKLLKNLKLLVLDEAHRlldmgFGPDLEEILRRLPKKR 149
|
170
....*....|....*.
gi 1797901375 761 DVLTLTATPiPRTLHM 776
Cdd:pfam00270 150 QILLLSATL-PRNLED 164
|
|
| CarD_CdnL_TRCF |
pfam02559 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
488-583 |
3.78e-27 |
|
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of light- and starvation-inducible genes. This family includes the presumed N-terminal domain, CdnL. CarD interacts with the zinc-binding protein CarG to form a complex that regulates multiple processes in Myxococcus xanthus. This family also includes a domain to the N-terminal side of the DEAD helicase of TRCF (transcription-repair-coupling factor) proteins. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription. This domain is involved in binding to the stalled RNA polymerase. The family includes members otherwise referred to as CdnL, for CarD N-terminal like, which differ functionally from CarD. The TRCF domain mentioned above is the RNA polymerase-interacting domain or RID.
Pssm-ID: 460590 [Multi-domain] Cd Length: 89 Bit Score: 105.99 E-value: 3.78e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 488 LAVGDYVVHNVHGIGRFLGIETIQiqgiHRDYVTIQYQNSDRISLPIDQISSLSKYVSADgkepKINKLNDG-RFQKTKQ 566
Cdd:pfam02559 1 LKVGDYVVHPDHGIGRIEGIEKLE----TKDYYVLEYAGGDKLYVPVDNLDLIRKYISKG----ELDKLGDGrRWRKYKE 72
|
90
....*....|....*..
gi 1797901375 567 KVARQVEDIADDLLKLY 583
Cdd:pfam02559 73 KLKSGDIEEAAELIKLY 89
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
604-794 |
7.79e-26 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 106.42 E-value: 7.79e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 604 FDDDFAFVETEDQLRSIKEIKADMesmqpMDRLLVGDVGFGKTEVAMRAAFKAV--NDHKQVAVLVPTTVLAQQHYENFK 681
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALLSGL-----RDVILAAPTGSGKTLAALLPALEALkrGKGGRVLVLVPTRELAEQWAEELK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 682 ARFENYPVEVDVLSRFRSKKEQaetLERVRKGQIDIIIGT-----HQLLSKDVVFSDLGLIVIDEEQR-----FGVKHKE 751
Cdd:smart00487 76 KLGPSLGLKVVGLYGGDSKREQ---LRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRlldggFGDQLEK 152
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 1797901375 752 TLKELKTKVDVLTLTATP---IPRTLHMSMLGIRDLSVIETPPTNR 794
Cdd:smart00487 153 LLKLLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPLEPI 198
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
633-768 |
4.70e-23 |
|
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.
Pssm-ID: 350668 [Multi-domain] Cd Length: 146 Bit Score: 96.32 E-value: 4.70e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 633 MDRLLVGDVGFGKTEVAMRAAFKAVND-HKQVAVLVPTTVLAQQHYENFKARFeNYPVEVDVLSRFRSKKEQaetlERVR 711
Cdd:cd00046 2 ENVLITAPTGSGKTLAALLAALLLLLKkGKKVLVLVPTKALALQTAERLRELF-GPGIRVAVLVGGSSAEER----EKNK 76
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 712 KGQIDIIIGTHQLLSKDV------VFSDLGLIVIDEEQRFGVKHKETL-------KELKTKVDVLTLTAT 768
Cdd:cd00046 77 LGDADIIIATPDMLLNLLlredrlFLKDLKLIIVDEAHALLIDSRGALildlavrKAGLKNAQVILLSAT 146
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
616-742 |
1.66e-18 |
|
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' superfamily 2 DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350687 [Multi-domain] Cd Length: 178 Bit Score: 84.18 E-value: 1.66e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 616 QLRSIKEIKADMESMQPMdrLLVGDVGFGKTEVAMRAAFKAVNDHKQVAVLVPTTVLAQQHYENFKARFENypvEVDVLS 695
Cdd:cd17929 1 QRKAYEAIVSSLGGFKTF--LLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRFGD---KVAVLH 75
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 1797901375 696 RFRSKKEQAETLERVRKGQIDIIIGTHQLLSkdVVFSDLGLIVIDEE 742
Cdd:cd17929 76 SKLSDKERADEWRKIKRGEAKVVIGARSALF--APFKNLGLIIVDEE 120
|
|
| PRK05298 |
PRK05298 |
excinuclease ABC subunit UvrB; |
130-247 |
3.91e-18 |
|
excinuclease ABC subunit UvrB;
Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 89.72 E-value: 3.91e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 130 NPDVFTKSQIQLTVGEDYDSDTLTKQLMTIGYQKVSQVISPGEFSRRGDILDIYEI-TQELPYRLEFFGDDIDSIRQFHP 208
Cdd:PRK05298 150 SPEEYLKMVLSLRVGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPAyYEERAIRIEFFGDEIERISEFDP 229
|
90 100 110
....*....|....*....|....*....|....*....
gi 1797901375 209 ETQKSFEQLEGIFINPASDLIFEASDFQRGIEQLEKALQ 247
Cdd:PRK05298 230 LTGEVLGELDRVTIYPASHYVTPRERLERAIESIKEELE 268
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
811-918 |
3.02e-17 |
|
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.
Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 78.41 E-value: 3.02e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 811 EAIIREMD--RGGQVFYVYNKVDTIDKKVAELQElvpEASIGFVHGQMSEIQLENTLIDFINGDYDVLVATTIIETGVDI 888
Cdd:pfam00271 4 EALLELLKkeRGGKVLIFSQTKKTLEAELLLEKE---GIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDL 80
|
90 100 110
....*....|....*....|....*....|
gi 1797901375 889 SNVNTLFIENADHmGLSTLYQLRGRVGRSN 918
Cdd:pfam00271 81 PDVDLVINYDLPW-NPASYIQRIGRAGRAG 109
|
|
| UvrB |
COG0556 |
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; |
130-247 |
4.74e-17 |
|
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
Pssm-ID: 440322 [Multi-domain] Cd Length: 657 Bit Score: 86.22 E-value: 4.74e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 130 NPDVFTKSQIQLTVGEDYDSDTLTKQLMTIGYQKVSQVISPGEFSRRGDILDIYEI-TQELPYRLEFFGDDIDSIRQFHP 208
Cdd:COG0556 147 SPEEYLKMVLSLRVGEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAySEERAIRIEFFGDEIERISEFDP 226
|
90 100 110
....*....|....*....|....*....|....*....
gi 1797901375 209 ETQKSFEQLEGIFINPASDLIFEASDFQRGIEQLEKALQ 247
Cdd:COG0556 227 LTGEVLGELDRVTIYPASHYVTPRERLERAIESIKEELE 265
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
636-919 |
3.16e-16 |
|
primosomal protein N'; All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273162 [Multi-domain] Cd Length: 505 Bit Score: 83.20 E-value: 3.16e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 636 LLVGDVGFGKTEVAMRAAFKAVNDHKQVAVLVPTTVLAQQHYENFKARFENypvEVDVLSRFRSKKEQAETLERVRKGQI 715
Cdd:TIGR00595 1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGS---QVAVLHSGLSDSEKLQAWRKVKNGEI 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 716 DIIIGTHQLLSkdVVFSDLGLIVIDEEQ----------RFGVKHKETLKELKTKVDVLTLTATPIPRTLHMSMLGIRDLS 785
Cdd:TIGR00595 78 LVVIGTRSALF--LPFKNLGLIIVDEEHdssykqeegpRYHARDVAVYRAKKFNCPVVLGSATPSLESYHNAKQKAYRLL 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 786 VIETPPTNRYPVQTYVL-----ENNPGLVREAI--IRE-MDRGGQ-----------------------------VFYVYN 828
Cdd:TIGR00595 156 VLTRRVSGRKPPEVKLIdmrkePRQSFLSPELItaIEQtLAAGEQsilflnrrgysknllcrscgyilccpncdVSLTYH 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 829 KVDT-------------------------------IDKKVAELQELVPEASIGFVHGQMSEIQ--LENTLIDFINGDYDV 875
Cdd:TIGR00595 236 KKEGklrchycgyqepipktcpqcgsedlvykgygTEQVEEELAKLFPGARIARIDSDTTSRKgaHEALLNQFANGKADI 315
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*
gi 1797901375 876 LVATTIIETGVDISNVNTLFIENAD-----------HMGLSTLYQLRGRVGRSNR 919
Cdd:TIGR00595 316 LIGTQMIAKGHHFPNVTLVGVLDADsglhspdfraaERGFQLLTQVAGRAGRAED 370
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
642-917 |
3.20e-16 |
|
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, recombination and repair];
Pssm-ID: 443274 [Multi-domain] Cd Length: 451 Bit Score: 82.61 E-value: 3.20e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 642 GFGKTEVAMRAAFKAVNDHKQVAVLVPTTVLAQQHYENFKARFENYPVEVdvLSrfrskkeqAETLERVRKGQIdIIIGT 721
Cdd:COG4098 139 GAGKTEMLFPAIAEALKQGGRVCIATPRVDVVLELAPRLQQAFPGVDIAA--LY--------GGSEEKYRYAQL-VIATT 207
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 722 HQLLSkdvvFSD-LGLIVIDE---------EQ-RFGVKhketlKELKTKVDVLTLTATPiPRTLHMSM-LGIRDLSVIet 789
Cdd:COG4098 208 HQLLR----FYQaFDLLIIDEvdafpysgdPMlQYAVK-----RARKPDGKLIYLTATP-SKALQRQVkRGKLKVVKL-- 275
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 790 pPtNRY-----PVQTYVLENN----------PGLVREAIIREMDRGGQVFYVYNKVDTIDKKVAELQELVPEASIGFVHG 854
Cdd:COG4098 276 -P-ARYhghplPVPKFKWLGNwkkrlrrgklPRKLLKWLKKRLKEGRQLLIFVPTIELLEQLVALLQKLFPEERIAGVHA 353
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1797901375 855 QmSEIQLENTLiDFINGDYDVLVATTIIETGVDISNVNTlFIENADH--MGLSTLYQLRGRVGRS 917
Cdd:COG4098 354 E-DPERKEKVQ-AFRDGEIPILVTTTILERGVTFPNVDV-AVLGADHpvFTEAALVQIAGRVGRS 415
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
636-742 |
7.56e-16 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 82.51 E-value: 7.56e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 636 LLVGDVGFGKTEVAMRAAFKAVNDHKQVAVLVPTTVLAQQHYENFKARFenyPVEVDVL-SRFrSKKEQAETLERVRKGQ 714
Cdd:PRK05580 166 LLDGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQMLARFRARF---GAPVAVLhSGL-SDGERLDEWRKAKRGE 241
|
90 100 110
....*....|....*....|....*....|
gi 1797901375 715 IDIIIGTHQ--LLSkdvvFSDLGLIVIDEE 742
Cdd:PRK05580 242 AKVVIGARSalFLP----FKNLGLIIVDEE 267
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
636-914 |
2.87e-15 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 80.45 E-value: 2.87e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 636 LLVGDVGFGKTEVAMRAAfKAVNDHKQVAVLVPTTVLAQQHYENFKARFEnypvevDVLSRFRSKKEQAetlervrkgqi 715
Cdd:COG1061 104 LVVAPTGTGKTVLALALA-AELLRGKRVLVLVPRRELLEQWAEELRRFLG------DPLAGGGKKDSDA----------- 165
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 716 DIIIGTHQLLSKDVVFSDL----GLIVIDEEQRFGVK-HKETLKELKTKVdVLTLTATPI---PRTLHMSMLG------- 780
Cdd:COG1061 166 PITVATYQSLARRAHLDELgdrfGLVIIDEAHHAGAPsYRRILEAFPAAY-RLGLTATPFrsdGREILLFLFDgivyeys 244
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 781 ---------IRDLSVIE-----TPPTNRYPVQTYVLE-----NNPGLVR--EAIIREMDRGGQVFYVYNKVDTIDkkvaE 839
Cdd:COG1061 245 lkeaiedgyLAPPEYYGirvdlTDERAEYDALSERLRealaaDAERKDKilRELLREHPDDRKTLVFCSSVDHAE----A 320
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 840 LQELVPEA--SIGFVHGQMSEIQLENTLIDFINGDYDVLVATTIIETGVDISNVNTLFIenadHMGLSTL---YQLRGRV 914
Cdd:COG1061 321 LAELLNEAgiRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAIL----LRPTGSPrefIQRLGRG 396
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
598-742 |
1.16e-14 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 79.01 E-value: 1.16e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 598 DDLQRAFDDDFAFVETEDQLRSIKEIKADMESMQPMdrLLVGDVGFGKTEVAMRAAFKAVNDHKQVAVLVPTTVLAQQHY 677
Cdd:COG1198 182 DPFAPDVPAEPPPTLNEEQQAAVEAIRAAAGGFSVF--LLHGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQTV 259
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1797901375 678 ENFKARFenyPVEVDVL-SRFrSKKEQAETLERVRKGQIDIIIGThqllskdvvFSDLGLIVIDEE 742
Cdd:COG1198 260 ERFRARF---GARVAVLhSGL-SDGERLDEWRRARRGEARIVIGTrsal--fapFPNLGLIIVDEE 319
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
848-916 |
2.14e-13 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 66.47 E-value: 2.14e-13
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1797901375 848 SIGFVHGQMSEIQLENTLIDFINGDYDVLVATTIIETGVDISNVNTLFIENADhMGLSTLYQLRGRVGR 916
Cdd:smart00490 13 KVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-WSPASYIQRIGRAGR 80
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
642-769 |
1.01e-12 |
|
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350684 [Multi-domain] Cd Length: 146 Bit Score: 66.56 E-value: 1.01e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 642 GFGKTEVAMRAAFKAVNDHkqVAVLVPTTVLAQQhyenFKARFENYpVEVDVLSRFRSKKEQAetlervrKGQIDIIIGT 721
Cdd:cd17926 28 GSGKTLTALALIAYLKELR--TLIVVPTDALLDQ----WKERFEDF-LGDSSIGLIGGGKKKD-------FDDANVVVAT 93
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....
gi 1797901375 722 HQLLSKDV-----VFSDLGLIVIDEEQRFG-VKHKETLKELKTKVdVLTLTATP 769
Cdd:cd17926 94 YQSLSNLAeeekdLFDQFGLLIVDEAHHLPaKTFSEILKELNAKY-RLGLTATP 146
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
642-919 |
2.20e-10 |
|
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
Pssm-ID: 187770 [Multi-domain] Cd Length: 353 Bit Score: 63.60 E-value: 2.20e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 642 GFGKTEVAMRAAFKAVNDHK--QVAVLVPTTVLAQQHYENFKARF-ENYPVEVDVLSRFRSKKEQAETLERVRK------ 712
Cdd:cd09639 9 GYGKTEAALLWALHSLKSQKadRVIIALPTRATINAMYRRAKEAFgETGLYHSSILSSRIKEMGDSEEFEHLFPlyihsn 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 713 -----GQIDIIIGTHQLLSKDVVFSD---------LGLIVIDE-------EQRFGVKHKETLKELKTKVDVLTLTATPIP 771
Cdd:cd09639 89 dtlflDPITVCTIDQVLKSVFGEFGHyeftlasiaNSLLIFDEvhfydeyTLALILAVLEVLKDNDVPILLMSATLPKFL 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 772 RTLHMSMLGIRDLSVIETPPTNRYPVQTYVLENNPGL-VREAIIREMDRGGQVFYVYNKVDTIDKKVAELQELVPEASIG 850
Cdd:cd09639 169 KEYAEKIGYVEENEPLDLKPNERAPFIKIESDKVGEIsSLERLLEFIKKGGSVAIIVNTVDRAQEFYQQLKEKGPEEEIM 248
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1797901375 851 FVHGQMSE---IQLENTLI-DFINGDYDVLVATTIIETGVDISnVNTLFienADHMGLSTLYQLRGRVGRSNR 919
Cdd:cd09639 249 LIHSRFTEkdrAKKEAELLlEFKKSEKFVIVATQVIEASLDIS-VDVMI---TELAPIDSLIQRLGRLHRYGE 317
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
644-916 |
5.04e-10 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 63.38 E-value: 5.04e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 644 GKTEVAMRAAFKAVNDHKQVAVLVPTTVLAQQHYENFKARFENYPVEVDVLSR-FRSKKEqaetlervRKGQIDIIIGT- 721
Cdd:COG1204 50 GKTLIAELAILKALLNGGKALYIVPLRALASEKYREFKRDFEELGIKVGVSTGdYDSDDE--------WLGRYDILVATp 121
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 722 ---HQLLSKDV-VFSDLGLIVIDEEQRFGVKHK--------ETLKELKTKVDVLTLTAT--------------------- 768
Cdd:COG1204 122 eklDSLLRNGPsWLRDVDLVVVDEAHLIDDESRgptlevllARLRRLNPEAQIVALSATignaeeiaewldaelvksdwr 201
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 769 PIPRtlhmsMLGI---RDLSVIETPPTNRYPVQTYVL----ENNPGLV-----REA------IIREMDRgGQVFYVYNKV 830
Cdd:COG1204 202 PVPL-----NEGVlydGVLRFDDGSRRSKDPTLALALdlleEGGQVLVfvssrRDAeslakkLADELKR-RLTPEEREEL 275
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 831 DTIDKKVAELQELVPEAS---------IGFVHGQMSEIQLEntLID--FINGDYDVLVATTIIETGVdisN--VNTLFIE 897
Cdd:COG1204 276 EELAEELLEVSEETHTNEkladclekgVAFHHAGLPSELRR--LVEdaFREGLIKVLVATPTLAAGV---NlpARRVIIR 350
|
330 340
....*....|....*....|....
gi 1797901375 898 NA-----DHMGLSTLYQLRGRVGR 916
Cdd:COG1204 351 DTkrggmVPIPVLEFKQMAGRAGR 374
|
|
| cas3_core |
TIGR01587 |
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ... |
642-919 |
3.04e-09 |
|
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.
Pssm-ID: 273707 [Multi-domain] Cd Length: 359 Bit Score: 60.16 E-value: 3.04e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 642 GFGKTEVAMRAAFKAVNDHKQVAVLV--PTTVLAQQHYENFKARFENYPVEVDVLSRFRSKKEQAETLERVR------KG 713
Cdd:TIGR01587 9 GYGKTEAALLWALHSIKSQKADRVIIalPTRATINAMYRRAKELFGSELVGLHHSSSFSRIKEMGDSEEFEHlfplyiHS 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 714 QIDIIIGTHQLLSKDVVFSDLG----------------LIVIDE-------EQRFGVKHKETLKELKTKVDVLTLTATPI 770
Cdd:TIGR01587 89 NDKLFLDPITVCTIDQVLKSVFgefghyeftlasiansLLIFDEvhfydeyTLALILAVLEVLKDNDVPILLMSATLPKF 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 771 PRTLHMSMLGIRDLSVIETPPTNRYPVQTYVLENNPGLVR----EAIIREMDRGGQVFYVYNKVDTIDKKVAELQELVPE 846
Cdd:TIGR01587 169 LKEYAEKIGYVEFNEPLDLKEERRFENHRFILIESDKVGEisslERLLEFIKKGGSIAIIVNTVDRAQEFYQQLKEKAPE 248
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1797901375 847 ASIGFVHGQMSE---IQLENTLID--FINGDYDVLVATTIIETGVDISnVNTLFienADHMGLSTLYQLRGRVGRSNR 919
Cdd:TIGR01587 249 EEIILYHSRFTEkdrAKKEAELLRemKKSNEKFVIVATQVIEASLDIS-ADVMI---TELAPIDSLIQRLGRLHRYGR 322
|
|
| Cas3 |
COG1203 |
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
642-919 |
3.14e-09 |
|
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system
Pssm-ID: 440816 [Multi-domain] Cd Length: 535 Bit Score: 60.87 E-value: 3.14e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 642 GFGKTEVAMRAAFKAVNDHKQ--VAVLVPTTVLAQQHYENFKARFENYPVEVDVLSRFRSKKEQAETLERVRKGQI---- 715
Cdd:COG1203 157 GGGKTEAALLFALRLAAKHGGrrIIYALPFTSIINQTYDRLRDLFGEDVLLHHSLADLDLLEEEEEYESEARWLKLlkel 236
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 716 ---DIIIGTH-QLLskDVVFSD--------LGL----IVIDEEQRFGVKH----KETLKELKT-KVDVLTLTATpIPRTL 774
Cdd:COG1203 237 wdaPVVVTTIdQLF--ESLFSNrkgqerrlHNLansvIILDEVQAYPPYMlallLRLLEWLKNlGGSVILMTAT-LPPLL 313
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 775 HMSMLGIRDLSVIETPPTNRYPVQ----TYVLENNP---GLVREAIIREMDRGGQVFYVYNkvdTIDKKVA---ELQELV 844
Cdd:COG1203 314 REELLEAYELIPDEPEELPEYFRAfvrkRVELKEGPlsdEELAELILEALHKGKSVLVIVN---TVKDAQElyeALKEKL 390
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1797901375 845 PEASIGFVHGQMSEI---QLENTLID-FINGDYDVLVATTIIETGVDISnVNTLFIENAdhmGLSTLYQLRGRVGRSNR 919
Cdd:COG1203 391 PDEEVYLLHSRFCPAdrsEIEKEIKErLERGKPCILVSTQVVEAGVDID-FDVVIRDLA---PLDSLIQRAGRCNRHGR 465
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
635-770 |
4.55e-08 |
|
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350769 [Multi-domain] Cd Length: 207 Bit Score: 54.60 E-value: 4.55e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 635 RLLVGD-VGFGKT-EVAMRAA-FKAVNDHKQVAVLVPTTvLAQQHYENFKARFENYPVEVDvlsrfRSKKEQAETLERVR 711
Cdd:cd18011 19 RLLLADeVGLGKTiEAGLIIKeLLLRGDAKRVLILCPAS-LVEQWQDELQDKFGLPFLILD-----RETAAQLRRLIGNP 92
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1797901375 712 KGQIDIIIGTHQLL------SKDVVFSDLGLIVIDEEQRFGVKHK-------ETLKELKTKVD-VLTLTATPI 770
Cdd:cd18011 93 FEEFPIVIVSLDLLkrseerRGLLLSEEWDLVVVDEAHKLRNSGGgketkryKLGRLLAKRARhVLLLTATPH 165
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
636-770 |
5.84e-08 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 53.44 E-value: 5.84e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 636 LLVGDVGFGKTEVAMRAA--FKAVNDHKQVAVLVPTTVLAQQHYENFKARFENYPVEVDVLSRfRSKKEQaetlervrKG 713
Cdd:pfam04851 27 LIVMATGSGKTLTAAKLIarLFKKGPIKKVLFLVPRKDLLEQALEEFKKFLPNYVEIGEIISG-DKKDES--------VD 97
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1797901375 714 QIDIIIGTHQLLSKDVVFSDL-------GLIVIDEEQRFGVK-HKETLKELKTKVdVLTLTATPI 770
Cdd:pfam04851 98 DNKIVVTTIQSLYKALELASLellpdffDVIIIDEAHRSGASsYRNILEYFKPAF-LLGLTATPE 161
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
644-768 |
7.74e-08 |
|
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350679 [Multi-domain] Cd Length: 181 Bit Score: 53.42 E-value: 7.74e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 644 GKTEVAMRAAFKAVNDHKQVAV-LVPTTVLAQQHYENFKARFENYPVEVDVLSRFRSKKEQAEtlervrkGQIDIIIGT- 721
Cdd:cd17921 29 GKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFGPLGKNVGLLTGDPSVNKLLL-------AEADILVATp 101
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1797901375 722 ---HQLLSK--DVVFSDLGLIVIDE------EQRfGVKHKETLKELKT---KVDVLTLTAT 768
Cdd:cd17921 102 eklDLLLRNggERLIQDVRLVVVDEahligdGER-GVVLELLLSRLLRinkNARFVGLSAT 161
|
|
| DDXDc_reverse_gyrase |
cd17924 |
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
642-740 |
8.32e-08 |
|
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350682 [Multi-domain] Cd Length: 189 Bit Score: 53.48 E-value: 8.32e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 642 GFGKTEVAMRAAFKAVNDHKQVAVLVPTTVLAQQHYENFKARFENYPVEVDVL---SRFrSKKEQAETLERVRKGQIDII 718
Cdd:cd17924 42 GVGKTTFGLATSLYLASKGKRSYLIFPTKSLVKQAYERLSKYAEKAGVEVKILvyhSRL-KKKEKEELLEKIEKGDFDIL 120
|
90 100
....*....|....*....|....*
gi 1797901375 719 IGTHQLLSKDV---VFSDLGLIVID 740
Cdd:cd17924 121 VTTNQFLSKNFdllSNKKFDFVFVD 145
|
|
| DEXHc_Hef |
cd18035 |
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
636-769 |
9.14e-08 |
|
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350793 [Multi-domain] Cd Length: 181 Bit Score: 53.29 E-value: 9.14e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 636 LLVGDVGFGKTEVA-MRAAFKAVNDHKQVAVLVPTTVLAQQHYENFKaRFENYPVEVDVLSRFRSKKEQAETLERVRkgq 714
Cdd:cd18035 20 LIVLPTGLGKTIIAiLVAADRLTKKGGKVLILAPSRPLVEQHAENLK-RVLNIPDKITSLTGEVKPEERAERWDASK--- 95
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1797901375 715 idIIIGTHQLLSKDVV-----FSDLGLIVIDEEQRFGVKHK-----ETLKELKTKVDVLTLTATP 769
Cdd:cd18035 96 --IIVATPQVIENDLLagritLDDVSLLIFDEAHHAVGNYAyvyiaHRYKREANNPLILGLTASP 158
|
|
| RecQ |
COG0514 |
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
699-949 |
3.39e-07 |
|
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 54.38 E-value: 3.39e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 699 SKKEQAETLERVRKGQIDIII---------GTHQLLSKdvvfSDLGLIVIDE-------------E-QRFGvkhkeTLKE 755
Cdd:COG0514 92 SAEERREVLRALRAGELKLLYvaperllnpRFLELLRR----LKISLFAIDEahcisqwghdfrpDyRRLG-----ELRE 162
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 756 LKTKVDVLTLTATPIPRTLH--MSMLGIRD--------------LSVIETPPTNRYPVQTYVLENNPGlvrEAIIremdr 819
Cdd:COG0514 163 RLPNVPVLALTATATPRVRAdiAEQLGLEDprvfvgsfdrpnlrLEVVPKPPDDKLAQLLDFLKEHPG---GSGI----- 234
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 820 ggqvfyVY----NKVDtidkKVAE-LQELvpeasiGFV----HGQMSEIQLENTLIDFINGDYDVLVATTIIETGVDISN 890
Cdd:COG0514 235 ------VYclsrKKVE----ELAEwLREA------GIRaaayHAGLDAEEREANQDRFLRDEVDVIVATIAFGMGIDKPD 298
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1797901375 891 VNTLFienadHMGL-STL---YQLRGRVGRSNRIAYAYLMYRP-DKVL--------------TEVSEKRLEAIKGFTE 949
Cdd:COG0514 299 VRFVI-----HYDLpKSIeayYQEIGRAGRDGLPAEALLLYGPeDVAIqrffieqsppdeerKRVERAKLDAMLAYAE 371
|
|
| CdnL |
COG1329 |
RNA polymerase-interacting regulator, CarD/CdnL/TRCF family [Transcription]; |
490-595 |
1.71e-06 |
|
RNA polymerase-interacting regulator, CarD/CdnL/TRCF family [Transcription];
Pssm-ID: 440940 [Multi-domain] Cd Length: 155 Bit Score: 48.97 E-value: 1.71e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 490 VGDYVVHNVHGIGRFLGIETIQIQGIHRDYVTIQYQNSD-RISLPIDQISS--LSKYVSADGKEPKINKLNDG------- 559
Cdd:COG1329 3 VGDKVVYPMHGVGVIEAIEEKEIAGEKKEYYVLRFPYDDmTIMVPVDKAESvgLRPVISKEEVEKVLDVLKGRetvkptn 82
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 1797901375 560 ---RFQKTKQKVAR-QVEDIAdDLLK-LYAeRSQQKGFSFS 595
Cdd:COG1329 83 wsrRYREYEEKIKSgDIFEIA-EVVRdLYR-RDKEKKLSAG 121
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
836-918 |
3.07e-06 |
|
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350191 [Multi-domain] Cd Length: 238 Bit Score: 49.94 E-value: 3.07e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 836 KVAE-LQELVPEASIGFVHGQMSEIQ--LENTLIDFINGDYDVLVATTIIETGVDISNVNTLFIENADHM---------- 902
Cdd:cd18804 105 RVEEeLKTLFPEARIARIDRDTTRKKgaLEKLLDQFERGEIDILIGTQMIAKGLDFPNVTLVGILNADSGlnspdfrase 184
|
90
....*....|....*..
gi 1797901375 903 -GLSTLYQLRGRVGRSN 918
Cdd:cd18804 185 rAFQLLTQVSGRAGRGD 201
|
|
| DEXHc_RLR-3 |
cd18075 |
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ... |
642-769 |
1.15e-05 |
|
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of genetics and physiology 2 or LGP2 and DHX58) appears to positively and negatively regulate MDA5 and RIG-I signaling, respectively. RLR-3 resembles a chimera combining a MDA5-like helicase domain and RIG-I like CTD supporting both stem and end binding. RNA binding is required for RLR-3-mediated enhancement of MDA5 activation. RLR-3 end-binding may promote nucleation of MDA5 oligomerization on dsRNA. RLR-3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350833 [Multi-domain] Cd Length: 200 Bit Score: 47.54 E-value: 1.15e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 642 GFGKTEVAMRAAFKAVN--DHKQVAVLVPTTVLAQQHYENFkarFENYpvevdvLSRFRSKKEQAETLERVRKGQI---- 715
Cdd:cd18075 27 GAGKTRAAVYVARRHLEtkRGAKVAVLVNKVHLVDQHLEKE---FHVL------LDKYTVTAISGDSSHKCFFGQLargs 97
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1797901375 716 DIIIGTHQLLS---------KDVVFSDLGLIVIDE---EQRFGVKHKETLKELKTKV-------DVLTLTATP 769
Cdd:cd18075 98 DVVICTAQILQnallsgeeeAHVELTDFSLLVIDEchhTHKEAVYNKIMLSYLEKKLsrqgdlpQILGLTASP 170
|
|
| HepA |
COG0553 |
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
640-771 |
3.84e-05 |
|
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];
Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 47.91 E-value: 3.84e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 640 DVGFGKT-EV-AMRAAFKAVNDHKQVAVLVPTTVLAQQHYEnfKARFeNYPVEVDVLSRFRSKKEQAETLERVrkgqiDI 717
Cdd:COG0553 268 DMGLGKTiQAlALLLELKERGLARPVLIVAPTSLVGNWQRE--LAKF-APGLRVLVLDGTRERAKGANPFEDA-----DL 339
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1797901375 718 IIGTHQLLSKDV-VFSDL--GLIVIDEEQRfgVKHKET-----LKELKTKVdVLTLTATPIP 771
Cdd:COG0553 340 VITSYGLLRRDIeLLAAVdwDLVILDEAQH--IKNPATkrakaVRALKARH-RLALTGTPVE 398
|
|
| DEXHc_cas3 |
cd17930 |
DEXH/Q-box helicase domain of Cas3; CRISPR-associated (Cas) 3 is a nuclease-helicase ... |
642-768 |
4.92e-05 |
|
DEXH/Q-box helicase domain of Cas3; CRISPR-associated (Cas) 3 is a nuclease-helicase responsible for degradation of dsDNA. The two enzymatic units of Cas3, a histidine-aspartate (HD) nuclease and a Superfamily 2 (SF2) helicase, may be expressed from separate genes as Cas3' (SF2 helicase) and Cas3'' (HD nuclease) or may be fused as a single HD-SF2 polypeptide. The nucleolytic activity of most Cas3 enzymes is transition metal ion-dependent. Cas3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350688 [Multi-domain] Cd Length: 186 Bit Score: 45.36 E-value: 4.92e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 642 GFGKTEVAMRAAFKAVNDHKQ--VAVLVPTTVLAQQHYENFKARFENYPVEVDVLS---------RFRSKKEQAETLERV 710
Cdd:cd17930 11 GSGKTEAALLWALKLAARGGKrrIIYALPTRATINQMYERIREILGRLDDEDKVLLlhskaalelLESDEEPDDDPVEAV 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 711 RKGQI-------DIIIGT-HQLL-------SKDVVFSDLG--LIVIDEEQRFGVK----HKETLKELKTKVD--VLTLTA 767
Cdd:cd17930 91 DWALLlkrswlaPIVVTTiDQLLesllkykHFERRLHGLAnsVVVLDEVQAYDPEymalLLKALLELLGELGgpVVLMTA 170
|
.
gi 1797901375 768 T 768
Cdd:cd17930 171 T 171
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
642-769 |
7.27e-05 |
|
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350685 [Multi-domain] Cd Length: 201 Bit Score: 45.12 E-value: 7.27e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 642 GFGKTEVAMRAA------FKAVNDHKqVAVLVPTTVLAQQHYENFKARFENYPVEVDVLSrfrskkeqAETLERVRKGQI 715
Cdd:cd17927 27 GSGKTFVAVLICehhlkkFPAGRKGK-VVFLANKVPLVEQQKEVFRKHFERPGYKVTGLS--------GDTSENVSVEQI 97
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1797901375 716 ----DIIIGTHQLLSKD------VVFSDLGLIVIDEEQRFGVKH----------KETLKELKTKVDVLTLTATP 769
Cdd:cd17927 98 vessDVIIVTPQILVNDlksgtiVSLSDFSLLVFDECHNTTKNHpyneimfrylDQKLGSSGPLPQILGLTASP 171
|
|
| SrmB |
COG0513 |
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
644-891 |
1.19e-04 |
|
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 45.91 E-value: 1.19e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 644 GKTevamrAAF---------KAVNDHKQVAVLVPTTVLAQQHYENFKARFENYPVEVDVLSRFRSKKEQAETLERvrkgQ 714
Cdd:COG0513 51 GKT-----AAFllpllqrldPSRPRAPQALILAPTRELALQVAEELRKLAKYLGLRVATVYGGVSIGRQIRALKR----G 121
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 715 IDIIIGT------HqLLSKDVVFSDLGLIVIDEEQR-----FgvkhKETLKEL--KTKVDVLTL--TATpIPRtlhmsml 779
Cdd:COG0513 122 VDIVVATpgrlldL-IERGALDLSGVETLVLDEADRmldmgF----IEDIERIlkLLPKERQTLlfSAT-MPP------- 188
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 780 GIRDLS--------VIETPPTNRyPVQT---YVLENNPGLVREAIIR--EMDRGGQ--VFyVyNKVDTIDKKVAELQELv 844
Cdd:COG0513 189 EIRKLAkrylknpvRIEVAPENA-TAETieqRYYLVDKRDKLELLRRllRDEDPERaiVF-C-NTKRGADRLAEKLQKR- 264
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|.
gi 1797901375 845 peasiGF----VHGQMSEIQLENTLIDFINGDYDVLVATTIIETGVDISNV 891
Cdd:COG0513 265 -----GIsaaaLHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDV 310
|
|
| UB2H |
pfam14814 |
Bifunctional transglycosylase second domain; UB2H is the second domain of the ... |
141-183 |
1.22e-04 |
|
Bifunctional transglycosylase second domain; UB2H is the second domain of the transglycosylases, or penicillin-binding proteins PBP1bs)), the multi-domain membrane proteins essential for cell wall synthesis that are targeted by penicillin antibiotics. The exact function of the UB2H domain is uncertain, but it may act as the binding component of PBP1b with different binding partners, or it may participate in the regulation between DNA repair and/or synthesis and cell wall formation during the bacterial cell cycle.
Pssm-ID: 434234 [Multi-domain] Cd Length: 85 Bit Score: 41.77 E-value: 1.22e-04
10 20 30 40
....*....|....*....|....*....|....*....|...
gi 1797901375 141 LTVGEDYDSDTLTKQLMTIGYQKVSQVISPGEFSRRGDILDIY 183
Cdd:pfam14814 1 LYPGQALSAAQLEQELKLLGYRKVSNPTRPGEYSVSGNRIELY 43
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
636-770 |
1.31e-04 |
|
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350792 [Multi-domain] Cd Length: 200 Bit Score: 44.18 E-value: 1.31e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 636 LLVGDVGFGKTEVA---MRA----AFKAVNDHKQVAVLVPTTVLAQQHYENFKaRFENYPVEVDVLSRFRSKKEQAETLE 708
Cdd:cd18034 20 IVVLPTGSGKTLIAvmlIKEmgelNRKEKNPKKRAVFLVPTVPLVAQQAEAIR-SHTDLKVGEYSGEMGVDKWTKERWKE 98
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1797901375 709 RVRKgqIDIIIGTHQLL-----SKDVVFSDLGLIVIDEEQRFGVKH--KETLKELKTKVD------VLTLTATPI 770
Cdd:cd18034 99 ELEK--YDVLVMTAQILldalrHGFLSLSDINLLIFDECHHATGDHpyARIMKEFYHLEGrtsrprILGLTASPV 171
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
636-768 |
1.93e-04 |
|
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play an important role in RNA degradation, processing and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350786 [Multi-domain] Cd Length: 177 Bit Score: 43.48 E-value: 1.93e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 636 LLVGDVGFGKTEVAMRAAFKAVNDHKQVAVLVPTTVLAQQHYENFKARfenYPVEVDVLSRFRSKKEQAETLervrkGQI 715
Cdd:cd18028 21 LISIPTASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEEFKKL---EEIGLKVGISTGDYDEDDEWL-----GDY 92
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1797901375 716 DIIIGTHQ-----LLSKDVVFSDLGLIVIDE------EQRFGVKHKET--LKELKTKVDVLTLTAT 768
Cdd:cd18028 93 DIIVATYEkfdslLRHSPSWLRDVGVVVVDEihlisdEERGPTLESIVarLRRLNPNTQIIGLSAT 158
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
831-1159 |
3.12e-04 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 45.11 E-value: 3.12e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 831 DTIDKKVAELQElvPEASIGFVHGQ--------MSEIQLENTLIDFINGDYDVLVATTIIETGVDISNVNT-LFIENadh 901
Cdd:COG1111 364 DTAEMIVEFLSE--PGIKAGRFVGQaskegdkgLTQKEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLvIFYEP--- 438
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 902 mGLSTL--YQLRGRVGRSN--RI-----------AYAYLMYRPDKVLtevsEKRLEAIKG-FTELGSGFKIAMRDLSIRG 965
Cdd:COG1111 439 -VPSEIrsIQRKGRTGRKRegRVvvliakgtrdeAYYWSSRRKEKKM----KSILKKLKKlLDKQEKEKLKESAQATLDE 513
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 966 AGNILGASQSGFIDSVGFEMYSQLL---EQAIASKQGKTTVRQKGNTEINLQIDAYLPDDYIADERQKIDIYKRIREIQS 1042
Cdd:COG1111 514 FESIKELAEDEINEKDLDEIESSENgahVDWREPVLLQVIVSTLAESLELRELGEKVDDEVNLILEIDRVDVVDDGSVLR 593
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 1043 REDYLNLQDELMDRFGEYPDQVAYLLEIALLKHYMDNAFAELVERKNNQVIVRFEVTSLTYfLTQDYFEALSKTHLKAKI 1122
Cdd:COG1111 594 VSRLLVEIGELDGKTRVIIASYGDEYFDAILRLTSKIKLPSLVSDISVDIPDLPIVEIVGE-AVLCKKEDGSREARFIKK 672
|
330 340 350
....*....|....*....|....*....|....*..
gi 1797901375 1123 SEHQGKIDIVFDVRHQKDYTILEELMLFGESLSEIKF 1159
Cdd:COG1111 673 ERDLKGIRLAEGETLNDPLIELLRQQLYGEALREETE 709
|
|
| SNF2-rel_dom |
pfam00176 |
SNF2-related domain; This domain is found in proteins involved in a variety of processes ... |
636-775 |
3.36e-04 |
|
SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.
Pssm-ID: 425504 [Multi-domain] Cd Length: 289 Bit Score: 43.83 E-value: 3.36e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 636 LLVGDVGFGKT--EVAMRAAFKAV--NDHKQVAVLVPTTVLaqQHYENFKARFENYPvEVDVLSRFRSKKEQAETLE-RV 710
Cdd:pfam00176 21 ILADEMGLGKTlqTISLLLYLKHVdkNWGGPTLIVVPLSLL--HNWMNEFERWVSPP-ALRVVVLHGNKRPQERWKNdPN 97
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1797901375 711 RKGQIDIIIGTHQLLSKDVVFS---DLGLIVIDEEQRFG---VKHKETLKELKTKVDVLtLTATPIPRTLH 775
Cdd:pfam00176 98 FLADFDVVITTYETLRKHKELLkkvHWHRIVLDEGHRLKnskSKLSKALKSLKTRNRWI-LTGTPLQNNLE 167
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
875-927 |
4.36e-04 |
|
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350172 [Multi-domain] Cd Length: 77 Bit Score: 39.99 E-value: 4.36e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 1797901375 875 VLVATTIIETGVDISNVNTLFIENAdHMGLSTLYQLRGRVGRSNRIAYAYLMY 927
Cdd:cd18785 25 ILVATNVLGEGIDVPSLDTVIFFDP-PSSAASYIQRVGRAGRGGKDEGEVILF 76
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
674-739 |
1.79e-03 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 42.45 E-value: 1.79e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 674 QQHYENFKARFENYPVEVdvLSR--FRSKKEQAETLERVRKGQIDIIIGThQLLSK--DvvFSDLGLIVI 739
Cdd:PRK05580 440 ERLEEELAELFPEARILR--IDRdtTRRKGALEQLLAQFARGEADILIGT-QMLAKghD--FPNVTLVGV 504
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
835-892 |
1.84e-03 |
|
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350174 [Multi-domain] Cd Length: 131 Bit Score: 39.80 E-value: 1.84e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 835 KKVAELQELVPEASIGFV--HGQMSEIQLENTLIDFINGDYDVLVATTIIETGVDISNVN 892
Cdd:cd18787 38 KRVDRLAELLEELGIKVAalHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGVD 97
|
|
| DEXHc_RLR |
cd18036 |
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
642-769 |
1.91e-03 |
|
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprise RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). RIG-I-like receptors (RLRs) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350794 [Multi-domain] Cd Length: 204 Bit Score: 40.92 E-value: 1.91e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 642 GFGKTEVAMRAA------FKAVNDHKQVAVLVPTTVLAQQHyenfKARFENYPVEVDVLSRFRSKKEQAETLERVRKGQi 715
Cdd:cd18036 27 GSGKTRVAVYICrhhlekRRSAGEKGRVVVLVNKVPLVEQQ----LEKFFKYFRKGYKVTGLSGDSSHKVSFGQIVKAS- 101
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1797901375 716 DIIIGTHQLL---------SKDVVFSDLGLIVIDE---EQRFGVKH-------KETLKELKTKVDVLTLTATP 769
Cdd:cd18036 102 DVIICTPQILinnllsgreEERVYLSDFSLLIFDEchhTQKEHPYNkimrmylDKKLSSQGPLPQILGLTASP 174
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
678-739 |
2.86e-03 |
|
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350191 [Multi-domain] Cd Length: 238 Bit Score: 40.69 E-value: 2.86e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1797901375 678 ENFKARFENYPV---EVDVLsrfRSKKEQAETLERVRKGQIDIIIGThQLLSKDVVFSDLGLIVI 739
Cdd:cd18804 108 EELKTLFPEARIariDRDTT---RKKGALEKLLDQFERGEIDILIGT-QMIAKGLDFPNVTLVGI 168
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
681-739 |
2.87e-03 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 41.64 E-value: 2.87e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1797901375 681 KARFENYPVEVdvLSR--FRSKKEQAETLERVRKGQIDIIIGThQLLSK--DvvFSDLGLIVI 739
Cdd:COG1198 498 AELFPDARVLR--MDRdtTRRKGALEKLLEAFARGEADILVGT-QMLAKghD--FPNVTLVGV 555
|
|
| DEADc |
cd00268 |
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ... |
644-741 |
3.60e-03 |
|
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350669 [Multi-domain] Cd Length: 196 Bit Score: 40.12 E-value: 3.60e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1797901375 644 GKTevamrAAF------------KAVNDHKQVAVLVPTTVLAQQHYENFKARFENYPVEVDVLSRFRSKKEQAETLervr 711
Cdd:cd00268 39 GKT-----LAFllpilekllpepKKKGRGPQALVLAPTRELAMQIAEVARKLGKGTGLKVAAIYGGAPIKKQIEAL---- 109
|
90 100 110
....*....|....*....|....*....|....*
gi 1797901375 712 KGQIDIIIGT----HQLL-SKDVVFSDLGLIVIDE 741
Cdd:cd00268 110 KKGPDIVVGTpgrlLDLIeRGKLDLSNVKYLVLDE 144
|
|
| SF2_C_FANCM_Hef |
cd18801 |
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
854-918 |
4.18e-03 |
|
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350188 [Multi-domain] Cd Length: 143 Bit Score: 38.88 E-value: 4.18e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1797901375 854 GQMSEIQLEnTLIDFINGDYDVLVATTIIETGVDISNVNTLFIENADHMGLSTLyQLRGRVGRSN 918
Cdd:cd18801 73 GMSQKEQKE-VIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMI-QRMGRTGRKR 135
|
|
| |
