|
Name |
Accession |
Description |
Interval |
E-value |
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
12-1145 |
0e+00 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 1842.40 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 12 SAGKQHWGNLPGAALSLAVAEAASSAKRFTLLLTADSQNAERLEQELRFFAPDLPVLHFPDWETLPYDVFSPHQDIISQR 91
Cdd:COG1197 1 GGGRLTLSGLPGSARALLLAALARALGRPLLVVTADEREAERLAEDLRFFLPDLPVLLFPAWETLPYDRFSPSPDIVSER 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 92 IAALYQLPQLKHGVLVVPISTALHRLAPTRFLLGSSLVLDVGQKLDVERMRLRLEGAGYRCVDTVYEHGEFAVRGALIDL 171
Cdd:COG1197 81 LATLRRLASGKPGIVVTPVRALLQRLPPPELLAAASLSLKVGDELDLEELRERLVAAGYERVDQVEEPGEFAVRGGILDI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 172 FPMGSELPFRIDLFDDEIETLRTFDPETQRSIDKVESIRLLPAREFPLNKEAVTGFRGRFRERFDVDYRRCPIYQDLASG 251
Cdd:COG1197 161 FPPGSEHPVRIEFFGDEIESIRTFDPETQRSLEKVDEVELLPAREFPLDEEAIERFRERLRELFGLDPKLDELYEALSEG 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 252 LTPSGIEYYLPLFFEETATLFDYLPQDTQVF--SLPGIEQAAEQFWNDVRSRYEDRRVDPERPLLPPAEVFLPVEDCFAR 329
Cdd:COG1197 241 IAFAGIEYYLPLFYEELATLFDYLPEDALVVldEPERIEEAAEEFWEEIEERYEARRHDRGRPLLPPEELFLDPEELFAA 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 330 LKNWPRVVASQ-EDVEPGVGRERFPALPLPNlaIEAKAAEPLAALRRFIEEfPGRVLFCAESPGRREVLLELLARLKLRP 408
Cdd:COG1197 321 LKRRPRVTLSPfAALPEGAGVVNLGARPLPS--FAGQLEALLEELKRLLKD-GGRVLLAAESEGRRERLLELLRDHGIPA 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 409 EEVDGWPAflASKARLAISIAPLDEGLLLDHPALALVAESPLFGQRVmQRRRREKTRDGgDAVIKNLTELREGAPVVHID 488
Cdd:COG1197 398 RLVESLAE--LSPGGVAITVGPLEHGFELPDAKLAVITESELFGERV-KRRRRKKKRSA-DAFIRDLSELKPGDYVVHVD 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 489 HGVGRYLGLITLEVDNQQAEFLMLQYAEDAKLYVPVANLHLIARYTGADDALAPLHRLGSETWQKAKRKAAEQVRDVAAE 568
Cdd:COG1197 474 HGIGRYLGLETLEVGGAERDYLVLEYAGGDKLYVPVDQLDLISRYVGSEGEAPKLDKLGGSDWQKAKAKAKKAVRDIAAE 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 569 LLDIYARRAAREGFAFKDPQADYATFSAGFPFEETPDQQSAIEAVVADMLAPRPMDRLVCGDVGFGKTEVAMRAAFVAVH 648
Cdd:COG1197 554 LLKLYAERAARKGFAFSPDTPWQREFEAAFPYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKTEVALRAAFKAVM 633
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 649 SGKQVAVLVPTTLLAQQHYNSFRDRFADWPVSVEVMSRFKSAKEVENAARLLAEGKIDILIGTHKLLQEDVKFANLGLVV 728
Cdd:COG1197 634 DGKQVAVLVPTTLLAQQHYETFKERFAGFPVRVEVLSRFRTAKEQKETLEGLADGKVDIVIGTHRLLSKDVKFKDLGLLI 713
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 729 IDEEHRFGVRQKEQLKALRSEVDILTLTATPIPRTLNMAVSGMRDLSIIATPPARRLSVRTFVMEQQNAVIKEALLRELL 808
Cdd:COG1197 714 IDEEQRFGVRHKEKLKALRANVDVLTLTATPIPRTLQMSLSGIRDLSIIATPPEDRLPVKTFVGEYDDALIREAILRELL 793
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 809 RGGQVYYLHNEVKTIEKCARDLAELVPEARIGIGHGQMHERELEQVMSDFYHKRFNVLVASTIIETGIDVPSANTILIER 888
Cdd:COG1197 794 RGGQVFYVHNRVEDIEKVAARLQELVPEARIAVAHGQMSERELERVMLDFYEGEFDVLVCTTIIETGIDIPNANTIIIER 873
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 889 ADKFGLAQLHQLRGRVGRSHHQAYAYLLTPPRRQMTPDAEKRLEAIANAQDLGAGFVLATHDLEIRGAGELLGDGQSGQI 968
Cdd:COG1197 874 ADRFGLAQLYQLRGRVGRSHRRAYAYLLYPPDKVLTEDAEKRLEAIQEFTELGAGFKLAMHDLEIRGAGNLLGEEQSGHI 953
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 969 QAVGFTLYMEMLERAVKAIRKGEQPNLEQplggGPEVNLRVPALIPEDYLPDVHARLILYKRIANAPDEEGLRELQVEMI 1048
Cdd:COG1197 954 AEVGFDLYLQMLEEAVAALKGGKEPEEEW----EPEINLGVPALIPEDYIPDVRQRLELYKRIASAESEEELDELQEELI 1029
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 1049 DRFGLLPDPAKNLMRLTLLKLQAEKLGILKVDAGPQGGRIEFAADTQVDPLVLIKLIQGQPNRYKFEGATLFRFQVPMER 1128
Cdd:COG1197 1030 DRFGPLPEEVENLLAVARLKLLARRLGIEKIDAGGKGIRIEFSPNTPLDPEKLIRLIQKQPGRYKLDGDDKLVITLDLED 1109
|
1130
....*....|....*..
gi 730329923 1129 PEERFNTLEALFERLTP 1145
Cdd:COG1197 1110 PEERLEALEELLEALAK 1126
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
8-1143 |
0e+00 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 1496.94 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 8 SLPASAGKQ-HWGNLPGAALSLAVAEAASSAKRFTLLLTADSQNAERLEQELRFFApDLPVLHFPDWETLPYDVFSPHQD 86
Cdd:PRK10689 8 TLPVKAGDQrQLGELTGAACATEVAEIAERHAGPVVLIAPDMQNALRLHDEIQQFT-DQMVMNLADWETLPYDSFSPHQD 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 87 IISQRIAALYQLPQLKHGVLVVPISTALHRLAPTRFLLGSSLVLDVGQKLDVERMRLRLEGAGYRCVDTVYEHGEFAVRG 166
Cdd:PRK10689 87 IISSRLSTLYQLPTMQRGVLILPVNTLMQRVCPHSFLHGHALVMKKGQRLSRDALRAQLEQAGYRHVDQVMEHGEYATRG 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 167 ALIDLFPMGSELPFRIDLFDDEIETLRTFDPETQRSIDKVESIRLLPAREFPLNKEAVTGFRGRFRERFDVdyRRCP--I 244
Cdd:PRK10689 167 ALLDLFPMGSEEPYRIDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFEV--KRDAehI 244
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 245 YQDLASGLTPSGIEYYLPLFFEET-ATLFDYLPQDTQVFSLPGIEQAAEQFWNDVRSRYEDRRVDPERPLLPPAEVFLPV 323
Cdd:PRK10689 245 YQQVSKGTLPAGIEYWQPLFFSEPlPPLFSYFPANTLLVNTGDLETSAERFWADTLARFENRGVDPMRPLLPPESLWLRV 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 324 EDCFARLKNWPRVVASQEDVEPGVGRERFPALPLPNLAIEAKAAEPLAALRRFIEEFPGRVLFCAESPGRREVLLELLAR 403
Cdd:PRK10689 325 DELFSELKNWPRVQLKTEHLPTKAANTNLGYQKLPDLAVQAQQKAPLDALRRFLESFDGPVVFSVESEGRREALGELLAR 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 404 LKLRPEEVDGWPAflASKARLAISIAPLDEGLLLDHPALALVAESPLFGQRVMQRRRREKTRDGGDAVIKNLTELREGAP 483
Cdd:PRK10689 405 IKIAPKRIMRLDE--ASDRGRYLMIGAAEHGFIDTVRNLALICESDLLGERVARRRQDSRRTINPDTLIRNLAELHPGQP 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 484 VVHIDHGVGRYLGLITLEVDNQQAEFLMLQYAEDAKLYVPVANLHLIARYTGADDALAPLHRLGSETWQKAKRKAAEQVR 563
Cdd:PRK10689 483 VVHLEHGVGRYAGMTTLEAGGIKGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHKLGGDAWSRARQKAAEKVR 562
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 564 DVAAELLDIYARRAAREGFAFKDPQADYATFSAGFPFEETPDQQSAIEAVVADMLAPRPMDRLVCGDVGFGKTEVAMRAA 643
Cdd:PRK10689 563 DVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAA 642
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 644 FVAVHSGKQVAVLVPTTLLAQQHYNSFRDRFADWPVSVEVMSRFKSAKEVENAARLLAEGKIDILIGTHKLLQEDVKFAN 723
Cdd:PRK10689 643 FLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKD 722
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 724 LGLVVIDEEHRFGVRQKEQLKALRSEVDILTLTATPIPRTLNMAVSGMRDLSIIATPPARRLSVRTFVMEQQNAVIKEAL 803
Cdd:PRK10689 723 LGLLIVDEEHRFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSLVVREAI 802
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 804 LRELLRGGQVYYLHNEVKTIEKCARDLAELVPEARIGIGHGQMHERELEQVMSDFYHKRFNVLVASTIIETGIDVPSANT 883
Cdd:PRK10689 803 LREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANT 882
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 884 ILIERADKFGLAQLHQLRGRVGRSHHQAYAYLLTPPRRQMTPDAEKRLEAIANAQDLGAGFVLATHDLEIRGAGELLGDG 963
Cdd:PRK10689 883 IIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGEE 962
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 964 QSGQIQAVGFTLYMEMLERAVKAIRKGEQPNLEQPLGGGPEVNLRVPALIPEDYLPDVHARLILYKRIANAPDEEGLREL 1043
Cdd:PRK10689 963 QSGQMETIGFSLYMELLENAVDALKAGREPSLEDLTSQQTEVELRMPSLLPDDFIPDVNTRLSFYKRIASAKNENELEEI 1042
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 1044 QVEMIDRFGLLPDPAKNLMRLTLLKLQAEKLGILKVDAGPQGGRIEFAADTQVDPLVLIKLIQGQPNRYKFEGATLFRFQ 1123
Cdd:PRK10689 1043 KVELIDRFGLLPDPARNLLDIARLRQQAQKLGIRKLEGNEKGGFIEFAEKNHVDPAWLIGLLQKQPQHYRLDGPTRLKFI 1122
|
1130 1140
....*....|....*....|
gi 730329923 1124 VPMERPEERFNTLEALFERL 1143
Cdd:PRK10689 1123 QDLSERKTRIEWVRQFMREL 1142
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
148-1080 |
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: 1118.59 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 148 AGYRCVDTVYEHGEFAVRGALIDLFPMGSELPFRIDLFDDEIETLRTFDPETQRSIDKVESIRLLPAREFPLnKEAVTGF 227
Cdd:TIGR00580 4 LGYERVDLVEEEGEFSVRGEILDIFPPGSELPVRIEFFGDEIESIREFDVDSQRSLEELLEITILPAKEFIL-LEEETIA 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 228 RGRFRERFDVDYRRCPIYQDLASGLTPSGIEYYLPLFFEETATLFDYLPQDTQVF-SLP-GIEQAAEQFWNDVRsRYEDR 305
Cdd:TIGR00580 83 RLKDNAARVEDAKHLETIEALSEGTLPAGEEMFLPLFFEDLSSLFDYLPDNTPILlDDPeRFHSAARFLQRELE-EFYNA 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 306 RVDPERPLLPPAEVFLPVEDCF-ARLKNWPRVVASQEDVEPGVGRERFPALPLPNLAIEAKAAEPLAALRRFIEEFPGRV 384
Cdd:TIGR00580 162 LEEAKKLINPPRLDLDPSELAFeASAISLSRVQLENEHLSLKASEAIEGAQKHSRLEFGEILAFKEELFRWLKAGFKITV 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 385 LFCAESpgRREVLLELLARLKLRPEEVDgwPAFLASKARLAISIAPLDEGLLLDHPALALVAESPLFGQRVMQRRRREKT 464
Cdd:TIGR00580 242 AAESES--QAERLKSLLAEHDIAAQVID--ESCIIIPAVRYVMIGALSSGFILPTAGLAVITESELFGSRVLRRPKKSRL 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 465 RDggdAVIKNLTELREGAPVVHIDHGVGRYLGLITLEVDNQQAEFLMLQYAEDAKLYVPVANLHLIARYTGADDALAPLH 544
Cdd:TIGR00580 318 KS---KPIESLNELNPGDYVVHLDHGIGRFLGLETLEVGGIERDYLVLEYAGEDKLYVPVEQLHLISRYVGGSGKNPALD 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 545 RLGSETWQKAKRKAAEQVRDVAAELLDIYARRAAREGFAFKDPQADYATFSAGFPFEETPDQQSAIEAVVADMLAPRPMD 624
Cdd:TIGR00580 395 KLGGKSWEKTKAKVKKSVREIAAKLIELYAKRKAIKGHAFPPDLEWQQEFEDSFPFEETPDQLKAIEEIKADMESPRPMD 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 625 RLVCGDVGFGKTEVAMRAAFVAVHSGKQVAVLVPTTLLAQQHYNSFRDRFADWPVSVEVMSRFKSAKEVENAARLLAEGK 704
Cdd:TIGR00580 475 RLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGK 554
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 705 IDILIGTHKLLQEDVKFANLGLVVIDEEHRFGVRQKEQLKALRSEVDILTLTATPIPRTLNMAVSGMRDLSIIATPPARR 784
Cdd:TIGR00580 555 IDILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPEDR 634
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 785 LSVRTFVMEQQNAVIKEALLRELLRGGQVYYLHNEVKTIEKCARDLAELVPEARIGIGHGQMHERELEQVMSDFYHKRFN 864
Cdd:TIGR00580 635 LPVRTFVMEYDPELVREAIRRELLRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQ 714
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 865 VLVASTIIETGIDVPSANTILIERADKFGLAQLHQLRGRVGRSHHQAYAYLLTPPRRQMTPDAEKRLEAIANAQDLGAGF 944
Cdd:TIGR00580 715 VLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDAQKRLEAIQEFSELGAGF 794
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 945 VLATHDLEIRGAGELLGDGQSGQIQAVGFTLYMEMLERAVKAIRKGEQPNLEQPlgggPEVNLRVPALIPEDYLPDVHAR 1024
Cdd:TIGR00580 795 KIALHDLEIRGAGNLLGEEQSGHIESIGFDLYMELLEEAIEELKGGKPPKLEEE----TDIELPYSAFIPDDYIADDSLR 870
|
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|....*.
gi 730329923 1025 LILYKRIANAPDEEGLRELQVEMIDRFGLLPDPAKNLMRLTLLKLQAEKLGILKVD 1080
Cdd:TIGR00580 871 LEFYKRIASAETEEELEKIRDELIDRFGPLPEEARTLLDVARLKLLARKLGIRKLK 926
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
569-966 |
7.37e-130 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 412.14 E-value: 7.37e-130
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 569 LLDIYARRAAREGFAFKDPQADYATFSAGFPFEETPDQQSAIEAVVADMLAPRPMDRLVCGDVGFGKTEVAMRAAFVAVH 648
Cdd:COG1200 227 LLLRRARRRKRKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVE 306
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 649 SGKQVAVLVPTTLLAQQHYNSFRDRFADWPVSVEVMSRFKSAKEVENAARLLAEGKIDILIGTHKLLQEDVKFANLGLVV 728
Cdd:COG1200 307 AGYQAALMAPTEILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVV 386
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 729 IDEEHRFGVRQKEQLKALRSEVDILTLTATPIPRTLNMAVSGMRDLSIIATPPARRLSVRTFV--MEQQNAVIkEALLRE 806
Cdd:COG1200 387 IDEQHRFGVEQRLALREKGEAPHVLVMTATPIPRTLAMTLYGDLDVSVIDELPPGRKPIKTRVvpEERRDEVY-ERIREE 465
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 807 LLRGGQVYYL--------HNEVKTIEKCARDLAELVPEARIGIGHGQMHERELEQVMSDFYHKRFNVLVASTIIETGIDV 878
Cdd:COG1200 466 IAKGRQAYVVcplieeseKLDLQAAEETYEELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGVDV 545
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 879 PSANTILIERADKFGLAQLHQLRGRVGRSHHQAYAYLLTPPRrqMTPDAEKRLEAIANAQDlgaGFVLATHDLEIRGAGE 958
Cdd:COG1200 546 PNATVMVIENAERFGLSQLHQLRGRVGRGSAQSYCLLLYDAP--LSETARERLEVMRETND---GFEIAEEDLELRGPGE 620
|
....*...
gi 730329923 959 LLGDGQSG 966
Cdd:COG1200 621 FLGTRQSG 628
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
574-966 |
2.48e-127 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 405.30 E-value: 2.48e-127
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 574 ARRAAREGFAFKDPQADYATFSAGFPFEETPDQQSAIEAVVADMLAPRPMDRLVCGDVGFGKTEVAMRAAFVAVHSGKQV 653
Cdd:PRK10917 234 AGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGYQA 313
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 654 AVLVPTTLLAQQHYNSFRDRFADWPVSVEVMSRFKSAKEVENAARLLAEGKIDILIGTHKLLQEDVKFANLGLVVIDEEH 733
Cdd:PRK10917 314 ALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIIDEQH 393
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 734 RFGVRQKEQLKALRSEVDILTLTATPIPRTLNMAVSGMRDLSIIATPPARRLSVRTFV--MEQQNAVIkEALLRELLRGG 811
Cdd:PRK10917 394 RFGVEQRLALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVipDSRRDEVY-ERIREEIAKGR 472
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 812 QVYYL--------HNEVKTIEKCARDLAELVPEARIGIGHGQMHERELEQVMSDFYHKRFNVLVASTIIETGIDVPSANT 883
Cdd:PRK10917 473 QAYVVcplieeseKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATV 552
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 884 ILIERADKFGLAQLHQLRGRVGRSHHQAYAYLLTPPrrQMTPDAEKRLEAIANAQDlgaGFVLATHDLEIRGAGELLGDG 963
Cdd:PRK10917 553 MVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKD--PLSETARERLKIMRETND---GFVIAEKDLELRGPGELLGTR 627
|
...
gi 730329923 964 QSG 966
Cdd:PRK10917 628 QSG 630
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
587-779 |
2.52e-116 |
|
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: 358.04 E-value: 2.52e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 587 PQADYATFSAGFPFEETPDQQSAIEAVVADMLAPRPMDRLVCGDVGFGKTEVAMRAAFVAVHSGKQVAVLVPTTLLAQQH 666
Cdd:cd17991 1 DGEEQEEFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 667 YNSFRDRFADWPVSVEVMSRFKSAKEVENAARLLAEGKIDILIGTHKLLQEDVKFANLGLVVIDEEHRFGVRQKEQLKAL 746
Cdd:cd17991 81 YETFKERFANFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQKEKLKEL 160
|
170 180 190
....*....|....*....|....*....|...
gi 730329923 747 RSEVDILTLTATPIPRTLNMAVSGMRDLSIIAT 779
Cdd:cd17991 161 RPNVDVLTLSATPIPRTLHMALSGIRDLSVIAT 193
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
537-966 |
2.72e-116 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 374.37 E-value: 2.72e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 537 DDALAPLHRLGSETWQKAKRKaaeqvRDVAAELLDIYARRAAREGFAFKDPQADYATFSAGF--------PFEETPDQQS 608
Cdd:TIGR00643 168 EDALRAIHFPKTLSLLELARR-----RLIFDEFFYLQLAMLARRLGEKQQFSAPPANPSEELltkflaslPFKLTRAQKR 242
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 609 AIEAVVADMLAPRPMDRLVCGDVGFGKTEVAMRAAFVAVHSGKQVAVLVPTTLLAQQHYNSFRDRFADWPVSVEVM---S 685
Cdd:TIGR00643 243 VVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLtgsL 322
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 686 RFKSAKEVENAarlLAEGKIDILIGTHKLLQEDVKFANLGLVVIDEEHRFGVRQKEQLKALRSE---VDILTLTATPIPR 762
Cdd:TIGR00643 323 KGKRRKELLET---IASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLREKGQGgftPHVLVMSATPIPR 399
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 763 TLNMAVSGMRDLSIIATPPARRLSVRTFVMEQQNA-VIKEALLRELLRGGQVYYLHN--------EVKTIEKCARDLAEL 833
Cdd:TIGR00643 400 TLALTVYGDLDTSIIDELPPGRKPITTVLIKHDEKdIVYEFIEEEIAKGRQAYVVYPlieeseklDLKAAEALYERLKKA 479
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 834 VPEARIGIGHGQMHERELEQVMSDFYHKRFNVLVASTIIETGIDVPSANTILIERADKFGLAQLHQLRGRVGRSHHQAYA 913
Cdd:TIGR00643 480 FPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYC 559
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|...
gi 730329923 914 YLLTPPrrQMTPDAEKRLEAIANAQDlgaGFVLATHDLEIRGAGELLGDGQSG 966
Cdd:TIGR00643 560 LLVYKN--PKSESAKKRLRVMADTLD---GFVIAEEDLELRGPGDLLGTKQSG 607
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
787-936 |
2.30e-76 |
|
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: 248.03 E-value: 2.30e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 787 VRTFVMEQQNAVIKEALLRELLRGGQVYYLHNEVKTIEKCARDLAELVPEARIGIGHGQMHERELEQVMSDFYHKRFNVL 866
Cdd:cd18810 2 VRTYVMPYDDELIREAIERELLRGGQVFYVHNRIESIEKLATQLRQLVPEARIAIAHGQMTENELEEVMLEFAKGEYDIL 81
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 867 VASTIIETGIDVPSANTILIERADKFGLAQLHQLRGRVGRSHHQAYAYLLTPPRRQMTPDAEKRLEAIAN 936
Cdd:cd18810 82 VCTTIIESGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAYFLYPDQKKLTEDALKRLEAIQE 151
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
589-778 |
3.75e-70 |
|
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: 231.92 E-value: 3.75e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 589 ADYATFSAGFPFEETPDQQSAIEAVVADMLAPRPMDRLVCGDVGFGKTEVAMRAAFVAVHSGKQVAVLVPTTLLAQQHYN 668
Cdd:cd17918 3 ALIQELCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYE 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 669 SFRDRFAdwPVSVEVMSRFKSAKevenaarllAEGKIDILIGTHKLLQEDVKFANLGLVVIDEEHRFGVRQKEQLKALRS 748
Cdd:cd17918 83 EARKFLP--FINVELVTGGTKAQ---------ILSGISLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNLGA 151
|
170 180 190
....*....|....*....|....*....|
gi 730329923 749 eVDILTLTATPIPRTLNMAVSGMRDLSIIA 778
Cdd:cd17918 152 -THFLEATATPIPRTLALALSGLLDLSVID 180
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
572-781 |
8.72e-70 |
|
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: 232.81 E-value: 8.72e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 572 IYARRAARE--GFAFKDPQADYATFSAGFPFEETPDQQSAIEAVVADMLAPRPMDRLVCGDVGFGKTEVAMRAAFVAVHS 649
Cdd:cd17992 14 LLRRRKIEElkGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKTVVAALAMLAAVEN 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 650 GKQVAVLVPTTLLAQQHYNSFRDRFADWPVSVEVMSRFKSAKEVENAARLLAEGKIDILIGTHKLLQEDVKFANLGLVVI 729
Cdd:cd17992 94 GYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQEDVEFHNLGLVII 173
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 730329923 730 DEEHRFGVRQKEQLKALRSEVDILTLTATPIPRTLNMAVSGMRDLSIIATPP 781
Cdd:cd17992 174 DEQHRFGVEQRLKLREKGETPHVLVMTATPIPRTLALTLYGDLDVSIIDELP 225
|
|
| SF2_C_RecG_TRCF |
cd18792 |
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
787-936 |
3.36e-66 |
|
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: 220.22 E-value: 3.36e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 787 VRTFVME-QQNAVIKEALLRELLRGGQVYYLHN--------EVKTIEKCARDLAELVPEARIGIGHGQMHERELEQVMSD 857
Cdd:cd18792 2 IRTYVIPhDDLDLVYEAIERELARGGQVYYVYPrieeseklDLKSIEALAEELKELVPEARVALLHGKMTEDEKEAVMLE 81
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 730329923 858 FYHKRFNVLVASTIIETGIDVPSANTILIERADKFGLAQLHQLRGRVGRSHHQAYAYLLTPPRRQMTPDAEKRLEAIAN 936
Cdd:cd18792 82 FREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYPDPKKLTETAKKRLRAIAE 160
|
|
| CarD_TRCF |
smart01058 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
477-574 |
2.75e-42 |
|
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: 149.53 E-value: 2.75e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 477 ELREGAPVVHIDHGVGRYLGLITLEVDNQQAEFLMLQYAEDAKLYVPVANLHLIARYTGA-DDALAPLHRLGSETWQKAK 555
Cdd:smart01058 1 ELKIGDYVVHPDHGVGRYEGIETIEVGGEKREYLVLEYAGGDKLYVPVDNLDLGSRYVGSeGEVEPVLDKLGGGSWSKRK 80
|
90
....*....|....*....
gi 730329923 556 RKAAEQVRDVAAELLDIYA 574
Cdd:smart01058 81 RKAKSGIRDIAAELLRLYA 99
|
|
| TRCF |
smart00982 |
This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in ... |
1006-1105 |
1.92e-41 |
|
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: 147.23 E-value: 1.92e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 1006 NLRVPALIPEDYLPDVHARLILYKRIANAPDEEGLRELQVEMIDRFGLLPDPAKNLMRLTLLKLQAEKLGILKVDAGPQG 1085
Cdd:smart00982 1 DLPVPALIPEDYIPDVRQRLELYKRIASAETEEELDEIQEELIDRFGPLPEEVKNLLEVARLKLLAKKLGIEKIDAGGKG 80
|
90 100
....*....|....*....|
gi 730329923 1086 GRIEFAADTQVDPLVLIKLI 1105
Cdd:smart00982 81 IVIEFSPDTPIDPEKLILLI 100
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
799-935 |
6.92e-38 |
|
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: 139.40 E-value: 6.92e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 799 IKEALLRELLRGGQVYYLHNEVKTIE----KCARDLAE-----LVPEARIGIGHGQMHERELEQVMSDFYHKRFNVLVAS 869
Cdd:cd18811 15 VYEFVREEIAKGRQAYVIYPLIEESEkldlKAAVAMYEylkerFRPELNVGLLHGRLKSDEKDAVMAEFREGEVDILVST 94
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 730329923 870 TIIETGIDVPSANTILIERADKFGLAQLHQLRGRVGRSHHQAYAYLLTPPrrQMTPDAEKRLEAIA 935
Cdd:cd18811 95 TVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKD--PLTETAKQRLRVMT 158
|
|
| TRCF |
pfam03461 |
TRCF domain; |
1007-1098 |
9.82e-38 |
|
TRCF domain;
Pssm-ID: 460928 [Multi-domain] Cd Length: 95 Bit Score: 136.40 E-value: 9.82e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 1007 LRVPALIPEDYLPDVHARLILYKRIANAPDEEGLRELQVEMIDRFGLLPDPAKNLMRLTLLKLQAEKLGILKVDAGPQGG 1086
Cdd:pfam03461 1 LDVDAYIPDDYIPDESQRLELYKRLASIETEEELDDLQEELIDRFGPLPEEVENLLEIARLKLLAKKLGIEKIDLKGGGI 80
|
90
....*....|..
gi 730329923 1087 RIEFAADTQVDP 1098
Cdd:pfam03461 81 RITFSEDAKIDP 92
|
|
| UvrB_inter |
pfam17757 |
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ... |
128-217 |
7.64e-35 |
|
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: 127.90 E-value: 7.64e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 128 LVLDVGQKLDVERMRLRLEGAGYRCVDTVYEHGEFAVRGALIDLFPMGSE-LPFRIDLFDDEIETLRTFDPETQRSIDKV 206
Cdd:pfam17757 1 LSLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYSEdEAIRIEFFGDEIESIREFDPLTGRSLEKL 80
|
90
....*....|.
gi 730329923 207 ESIRLLPAREF 217
Cdd:pfam17757 81 DEVTIYPASHY 91
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
603-766 |
5.34e-30 |
|
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: 116.96 E-value: 5.34e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 603 TPDQQSAIEAVVADMlaprpmDRLVCGDVGFGKTEVAMRAAFVAVH---SGKQVAVLVPTTLLAQQHYNSFRDRFAdwPV 679
Cdd:pfam00270 1 TPIQAEAIPAILEGR------DVLVQAPTGSGKTLAFLLPALEALDkldNGPQALVLAPTRELAEQIYEELKKLGK--GL 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 680 SVEVMSRFKSAKEVENAARLlaeGKIDILIGTH----KLLQEDVKFANLGLVVIDEEHR-----FGVRQKEQLKALRSEV 750
Cdd:pfam00270 73 GLKVASLLGGDSRKEQLEKL---KGPDILVGTPgrllDLLQERKLLKNLKLLVLDEAHRlldmgFGPDLEEILRRLPKKR 149
|
170
....*....|....*.
gi 730329923 751 DILTLTATPiPRTLNM 766
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 ... |
478-573 |
3.22e-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: 3.22e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 478 LREGAPVVHIDHGVGRYLGLITLEVDnqqaEFLMLQYAEDAKLYVPVANLHLIARYTGADDalapLHRLG-SETWQKAKR 556
Cdd:pfam02559 1 LKVGDYVVHPDHGIGRIEGIEKLETK----DYYVLEYAGGDKLYVPVDNLDLIRKYISKGE----LDKLGdGRRWRKYKE 72
|
90
....*....|....*..
gi 730329923 557 KAAEQVRDVAAELLDIY 573
Cdd:pfam02559 73 KLKSGDIEEAAELIKLY 89
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
594-787 |
7.36e-26 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 106.42 E-value: 7.36e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 594 FSAGFPFEETPDQQSAIEAVVADMlaprpMDRLVCGDVGFGKTEVAMRAAFVAVHSG--KQVAVLVPTTLLAQQHYNSFR 671
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALLSGL-----RDVILAAPTGSGKTLAALLPALEALKRGkgGRVLVLVPTRELAEQWAEELK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 672 DRFADWPvsVEVMSRFKSAKEVENAARlLAEGKIDILIGT-----HKLLQEDVKFANLGLVVIDEEHRFGVR-QKEQL-- 743
Cdd:smart00487 76 KLGPSLG--LKVVGLYGGDSKREQLRK-LESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRLLDGgFGDQLek 152
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 730329923 744 --KALRSEVDILTLTATPIPRTLNMAVSGMRDLSIIATPPARRLSV 787
Cdd:smart00487 153 llKLLPKNVQLLLLSATPPEEIENLLELFLNDPVFIDVGFTPLEPI 198
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
623-758 |
3.35e-24 |
|
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: 99.79 E-value: 3.35e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 623 MDRLVCGDVGFGKTEVAMRAAF-VAVHSGKQVAVLVPTTLLAQQHYNSFRDRFaDWPVSVEVMSRFKSAKEVENAARLLA 701
Cdd:cd00046 2 ENVLITAPTGSGKTLAALLAALlLLLKKGKKVLVLVPTKALALQTAERLRELF-GPGIRVAVLVGGSSAEEREKNKLGDA 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 702 egkiDILIGTHKLLQEDVK------FANLGLVVIDEEHRFGVRQKEQL-------KALRSEVDILTLTAT 758
Cdd:cd00046 81 ----DIIIATPDMLLNLLLredrlfLKDLKLIIVDEAHALLIDSRGALildlavrKAGLKNAQVILLSAT 146
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
800-906 |
5.69e-18 |
|
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: 80.33 E-value: 5.69e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 800 KEALLRELL---RGGQVYYLHNEVKTIEKcarDLAELVPEARIGIGHGQMHERELEQVMSDFYHKRFNVLVASTIIETGI 876
Cdd:pfam00271 2 KLEALLELLkkeRGGKVLIFSQTKKTLEA---ELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGL 78
|
90 100 110
....*....|....*....|....*....|
gi 730329923 877 DVPSANTILIERADkFGLAQLHQLRGRVGR 906
Cdd:pfam00271 79 DLPDVDLVINYDLP-WNPASYIQRIGRAGR 107
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
606-733 |
3.98e-17 |
|
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: 80.33 E-value: 3.98e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 606 QQSAIEAVVADMLAPRPMdrLVCGDVGFGKTEVAMRAAFVAVHSGKQVAVLVPTTLLAQQHYNSFRDRFADwpvSVEVMS 685
Cdd:cd17929 1 QRKAYEAIVSSLGGFKTF--LLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRFGD---KVAVLH 75
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 730329923 686 RFKSAKEVENAARLLAEGKIDILIGTHKLLQedVKFANLGLVVIDEEH 733
Cdd:cd17929 76 SKLSDKERADEWRKIKRGEAKVVIGARSALF--APFKNLGLIIVDEEH 121
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
535-1047 |
3.08e-16 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 83.54 E-value: 3.08e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 535 GADDALAPLHRLGSETWQKAKRKAAEQVRDVAAELLDIYARRAAREGFAFKDPQA-DYATFSAGFPFEETPDQQSAIEAV 613
Cdd:COG1061 13 KLRSSLLLLDLERLELSLLRNLVEARRLAIKEGTREDGRRLPEEDTERELAEAEAlEAGDEASGTSFELRPYQQEALEAL 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 614 VADMLAPRpmDR-LVCGDVGFGKTEVAMRAAfVAVHSGKQVAVLVPTTLLAQQhynsFRDRFADWPVSVEVMSRFKSAKE 692
Cdd:COG1061 93 LAALERGG--GRgLVVAPTGTGKTVLALALA-AELLRGKRVLVLVPRRELLEQ----WAEELRRFLGDPLAGGGKKDSDA 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 693 venaarllaegkiDILIGTHKLLQEDVKFANL----GLVVIDEEHRFGVRQKEQLKALRSEVDILTLTATPIpRTLNMAV 768
Cdd:COG1061 166 -------------PITVATYQSLARRAHLDELgdrfGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLTATPF-RSDGREI 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 769 SGMRDLSIIATPPARRLSVRTFV--------------MEQQNAVIKEALLRELLRGGQ---------VYYLHNEVKTIEK 825
Cdd:COG1061 232 LLFLFDGIVYEYSLKEAIEDGYLappeyygirvdltdERAEYDALSERLREALAADAErkdkilrelLREHPDDRKTLVF 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 826 C-----ARDLAELVPEARIGIG--HGQMHERELEQVMSDFYHKRFNVLVASTIIETGIDVPSANTILIERADKFgLAQLH 898
Cdd:COG1061 312 CssvdhAEALAELLNEAGIRAAvvTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILLRPTGS-PREFI 390
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 899 QLRGRVGRSH---HQAYAYLLTPPRRqmtpdaeKRLEAIANAQDLGAGFVLATHDLEIRGAGELLGDGQ---SGQIQAVG 972
Cdd:COG1061 391 QRLGRGLRPApgkEDALVYDFVGNDV-------PVLEELAKDLRDLAGYRVEFLDEEESEELALLIAVKpalEVKGELEE 463
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 730329923 973 FTLYMEMLERAVKAIRKGEQPNLEQPLGGGPEVNLRVPALIPEDYLPDVHARLILYKRIANAPDEEGLRELQVEM 1047
Cdd:COG1061 464 ELLEELELLEDALLLVLAELLLLELLALALELLELAKAEGKAEEEEEEKELLLLLALAKLLKLLLLLLLLLLLEL 538
|
|
| PRK05298 |
PRK05298 |
excinuclease ABC subunit UvrB; |
124-278 |
1.32e-15 |
|
excinuclease ABC subunit UvrB;
Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 81.63 E-value: 1.32e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 124 LGSSLVLDVGQKLDVERMRLRLEGAGYRCVDTVYEHGEFAVRGALIDLFPMGSE-LPFRIDLFDDEIETLRTFDPETQRS 202
Cdd:PRK05298 155 LKMVLSLRVGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPAYYEeRAIRIEFFGDEIERISEFDPLTGEV 234
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 203 IDKVESIRLLPAREFPLNKE----AVTGFRGRFRERFD--------VDYRRcpIYQ----DL----ASGLTpSGIE-Y-- 259
Cdd:PRK05298 235 LGELDRVTIYPASHYVTPRErlerAIESIKEELEERLKelekegklLEAQR--LEQrtryDLemlrELGYC-SGIEnYsr 311
|
170 180
....*....|....*....|....*..
gi 730329923 260 YL--------PlffeetATLFDYLPQD 278
Cdd:PRK05298 312 HLdgrkpgepP------YTLLDYFPDD 332
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
828-906 |
4.05e-13 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 65.70 E-value: 4.05e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 828 RDLAELVPEARIGIG--HGQMHERELEQVMSDFYHKRFNVLVASTIIETGIDVPSANTILIERADkFGLAQLHQLRGRVG 905
Cdd:smart00490 1 EELAELLKELGIKVArlHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-WSPASYIQRIGRAG 79
|
.
gi 730329923 906 R 906
Cdd:smart00490 80 R 80
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
626-908 |
4.18e-13 |
|
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: 73.19 E-value: 4.18e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 626 LVCGDVGFGKTEVAMRAAFVAVHSGKQVAVLVPTTLLAQQHYNSFRDRFADwpvSVEVMSRFKSAKEVENAARLLAEGKI 705
Cdd:TIGR00595 1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGS---QVAVLHSGLSDSEKLQAWRKVKNGEI 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 706 DILIGTHKLLQedVKFANLGLVVIDEEHRFGVRQKE-------QLKALRSEVDILTL---TATPIPRTLNMAVSGMRDLS 775
Cdd:TIGR00595 78 LVVIGTRSALF--LPFKNLGLIIVDEEHDSSYKQEEgpryharDVAVYRAKKFNCPVvlgSATPSLESYHNAKQKAYRLL 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 776 II------ATPParRLSVRTFVMEQQNAVIKEALLREL------------------------------------------ 807
Cdd:TIGR00595 156 VLtrrvsgRKPP--EVKLIDMRKEPRQSFLSPELITAIeqtlaageqsilflnrrgysknllcrscgyilccpncdvslt 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 808 --LRGG--QVYYLHNEVKT------------------IEKCARDLAELVPEARIGIGHGQMHERE--LEQVMSDFYHKRF 863
Cdd:TIGR00595 234 yhKKEGklRCHYCGYQEPIpktcpqcgsedlvykgygTEQVEEELAKLFPGARIARIDSDTTSRKgaHEALLNQFANGKA 313
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*.
gi 730329923 864 NVLVASTIIETGIDVP--------SANTILIE---RADKFGLAQLHQLRGRVGRSH 908
Cdd:TIGR00595 314 DILIGTQMIAKGHHFPnvtlvgvlDADSGLHSpdfRAAERGFQLLTQVAGRAGRAE 369
|
|
| UvrB |
COG0556 |
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; |
124-217 |
6.00e-13 |
|
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
Pssm-ID: 440322 [Multi-domain] Cd Length: 657 Bit Score: 73.12 E-value: 6.00e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 124 LGSSLVLDVGQKLDVERMRLRLEGAGYRCVDTVYEHGEFAVRGALIDLFPMGS-ELPFRIDLFDDEIETLRTFDPETQRS 202
Cdd:COG0556 152 LKMVLSLRVGEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAYSeERAIRIEFFGDEIERISEFDPLTGEV 231
|
90
....*....|....*
gi 730329923 203 IDKVESIRLLPAREF 217
Cdd:COG0556 232 LGELDRVTIYPASHY 246
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
565-733 |
9.50e-13 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 72.46 E-value: 9.50e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 565 VAAELLDIYARRAAREGFAfkdpqadyATFSAGFPFEETPDQQSAIEAVVADMLAPRPMdrLVCGDVGFGKTEVAMRAAF 644
Cdd:COG1198 167 VKKGLLEIEEREVDRDPFA--------PDVPAEPPPTLNEEQQAAVEAIRAAAGGFSVF--LLHGVTGSGKTEVYLQAIA 236
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 645 VAVHSGKQVAVLVPTTLLAQQHYNSFRDRFADwpvSVEVM-SRFkSAKEVENAARLLAEGKIDILIGTHKLLqedvkFA- 722
Cdd:COG1198 237 EVLAQGKQALVLVPEIALTPQTVERFRARFGA---RVAVLhSGL-SDGERLDEWRRARRGEARIVIGTRSAL-----FAp 307
|
170
....*....|...
gi 730329923 723 --NLGLVVIDEEH 733
Cdd:COG1198 308 fpNLGLIIVDEEH 320
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
598-933 |
3.87e-11 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 66.84 E-value: 3.87e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 598 FPFEE-TPDQQSAIEAVVADmlaprpmDR--LVCGDVGFGKTEVAMRAAFVAVHSGKQVAVLVPTTLLAQQHYNSFRDRF 674
Cdd:COG1204 18 RGIEElYPPQAEALEAGLLE-------GKnlVVSAPTASGKTLIAELAILKALLNGGKALYIVPLRALASEKYREFKRDF 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 675 ADWPVSVEVMSRfksakEVENAARLLAEGkiDILIGT----HKLLQEDVKF-ANLGLVVIDEEHRFGVRQK--------E 741
Cdd:COG1204 91 EELGIKVGVSTG-----DYDSDDEWLGRY--DILVATpeklDSLLRNGPSWlRDVDLVVVDEAHLIDDESRgptlevllA 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 742 QLKALRSEVDILTLTAT---------------------PIPRTLNMAVSG---MRDLSIIATPPARRLSVRTFVMEQQNA 797
Cdd:COG1204 164 RLRRLNPEAQIVALSATignaeeiaewldaelvksdwrPVPLNEGVLYDGvlrFDDGSRRSKDPTLALALDLLEEGGQVL 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 798 VI----KEAL-----LRELLRGGQVYYLHNEVKTIEKCARDLAELVPEARI-------GIG--HGQMhERELEQVMSDFY 859
Cdd:COG1204 244 VFvssrRDAEslakkLADELKRRLTPEEREELEELAEELLEVSEETHTNEKladclekGVAfhHAGL-PSELRRLVEDAF 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 860 HKR-FNVLVA-STIIEtGIDVPsANTILIERADKFGLAQL-----HQLRGRVGRSHH--QAYAYLLTPPRRQMTPDAEKR 930
Cdd:COG1204 323 REGlIKVLVAtPTLAA-GVNLP-ARRVIIRDTKRGGMVPIpvlefKQMAGRAGRPGYdpYGEAILVAKSSDEADELFERY 400
|
...
gi 730329923 931 LEA 933
Cdd:COG1204 401 ILG 403
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
599-907 |
1.18e-10 |
|
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: 65.28 E-value: 1.18e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 599 PFEETPDQQSAIEAVVADMLAPRPMdrL---VCGDvgfGKTEVAMRAAFVAVHSGKQVAVLVPTTLLAQQHYNSFRDRFA 675
Cdd:COG4098 108 EGTLTPAQQKASDELLEAIKKKEEH--LvwaVCGA---GKTEMLFPAIAEALKQGGRVCIATPRVDVVLELAPRLQQAFP 182
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 676 DwpVSVEVMsRFKSAKEVENAARLLAEgkidiligTHKLLqedvKFAN-LGLVVIDEEHRFGVRQKEQL-----KALRSE 749
Cdd:COG4098 183 G--VDIAAL-YGGSEEKYRYAQLVIAT--------THQLL----RFYQaFDLLIIDEVDAFPYSGDPMLqyavkRARKPD 247
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 750 VDILTLTATPIPRTLNMAVSGMRDLSIIatpPAR----RLSVRTFVME-------QQNAVIK--EALLRELL-RGGQVYY 815
Cdd:COG4098 248 GKLIYLTATPSKALQRQVKRGKLKVVKL---PARyhghPLPVPKFKWLgnwkkrlRRGKLPRklLKWLKKRLkEGRQLLI 324
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 816 LHNEVKTIEKCARDLAELVPEARIGIGHGQMHERElEQVMsDFYHKRFNVLVASTIIETGIDVPSANTILIErADK--FG 893
Cdd:COG4098 325 FVPTIELLEQLVALLQKLFPEERIAGVHAEDPERK-EKVQ-AFRDGEIPILVTTTILERGVTFPNVDVAVLG-ADHpvFT 401
|
330
....*....|....
gi 730329923 894 LAQLHQLRGRVGRS 907
Cdd:COG4098 402 EAALVQIAGRVGRS 415
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
530-733 |
1.74e-10 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 65.18 E-value: 1.74e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 530 IARYTgaddaLAPL-----HRLGSETWQKAKRKAAEQVrdVAAELLDIYARRAARegfafkdpqADYATFSAGFPFEETP 604
Cdd:PRK05580 84 AADYY-----LSPLgevlrLALLAELALAASSAVLKGL--VKKGLIELEEVEVLR---------LRPPPDPAFEPPTLNP 147
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 605 DQQSAIEAVVADM------LAprpmdrlvcGDVGFGKTEVAMRAAFVAVHSGKQVAVLVPTTLLAQQHYNSFRDRFADWP 678
Cdd:PRK05580 148 EQAAAVEAIRAAAgfspflLD---------GVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQMLARFRARFGAPV 218
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*...
gi 730329923 679 VsveVM-SRFkSAKEVENAARLLAEGKIDILIGTHK--LLQedvkFANLGLVVIDEEH 733
Cdd:PRK05580 219 A---VLhSGL-SDGERLDEWRKAKRGEAKVVIGARSalFLP----FKNLGLIIVDEEH 268
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
606-759 |
3.59e-09 |
|
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: 56.55 E-value: 3.59e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 606 QQSAIEAvvadMLAPRPMDR-LVCGDVGFGKTEVAMrAAFVAVHSGKqVAVLVPTTLLAQQhynsFRDRFADWPVSVEVM 684
Cdd:cd17926 5 QEEALEA----WLAHKNNRRgILVLPTGSGKTLTAL-ALIAYLKELR-TLIVVPTDALLDQ----WKERFEDFLGDSSIG 74
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 730329923 685 sRFKSAKEVENAARLLAEGKIDILIGTHKLLQEdvKFANLGLVVIDEEHRFGVrqkEQLKALRSEVD---ILTLTATP 759
Cdd:cd17926 75 -LIGGGKKKDFDDANVVVATYQSLSNLAEEEKD--LFDQFGLLIVDEAHHLPA---KTFSEILKELNakyRLGLTATP 146
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
626-758 |
7.06e-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: 53.80 E-value: 7.06e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 626 LVCGDVGFGKTEVAMRAAFVAVHSGKQVAV-LVPTTLLAQQHYNSFRDRFADWPVSV-EVMSRFKSAKEVENAARLL--- 700
Cdd:cd17921 21 LVSAPTSSGKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFGPLGKNVgLLTGDPSVNKLLLAEADILvat 100
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 730329923 701 AEgKIDILIGTHkllqEDVKFANLGLVVIDEEHRF-----GVRQKEQLKALR---SEVDILTLTAT 758
Cdd:cd17921 101 PE-KLDLLLRNG----GERLIQDVRLVVVDEAHLIgdgerGVVLELLLSRLLrinKNARFVGLSAT 161
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
849-916 |
1.00e-07 |
|
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: 50.40 E-value: 1.00e-07
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 730329923 849 RELEQVMSdfyhkRFNVLVASTIIETGIDVPSANTILIERADKFgLAQLHQLRGRVGRSHHQAYAYLL 916
Cdd:cd18785 14 EHAEEIAS-----SLEILVATNVLGEGIDVPSLDTVIFFDPPSS-AASYIQRVGRAGRGGKDEGEVIL 75
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
600-760 |
1.13e-07 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 52.67 E-value: 1.13e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 600 FEETPDQQSAIEAVVAdMLAPRPMDRLVCGDVGFGKTEVAMRAAFVAVHSG--KQVAVLVPTTLLAQQHYNSFRDRFadw 677
Cdd:pfam04851 2 LELRPYQIEAIENLLE-SIKNGQKRGLIVMATGSGKTLTAAKLIARLFKKGpiKKVLFLVPRKDLLEQALEEFKKFL--- 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 678 PVSVEVMsrfksaKEVENAARLLAEGKIDILIGT-HKLLQEDVKFANL------GLVVIDEEHRFG----VRQKEQLKAL 746
Cdd:pfam04851 78 PNYVEIG------EIISGDKKDESVDDNKIVVTTiQSLYKALELASLEllpdffDVIIIDEAHRSGassyRNILEYFKPA 151
|
170
....*....|....
gi 730329923 747 RsevdILTLTATPI 760
Cdd:pfam04851 152 F----LLGLTATPE 161
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
610-760 |
1.89e-07 |
|
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: 53.06 E-value: 1.89e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 610 IEAVVADMLAPRPmdRLVCGD-VGFGKT-EVAMRAA-FVAVHSGKQVAVLVPTTLLAQ-QHYnsFRDRFADwpvSVEVMS 685
Cdd:cd18011 6 IDAVLRALRKPPV--RLLLADeVGLGKTiEAGLIIKeLLLRGDAKRVLILCPASLVEQwQDE--LQDKFGL---PFLILD 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 686 RFKSAKEVENAARLLAEGKIDI----LIGTHKLLQEDVKFANLGLVVIDEEHRFGVRQKEQ-------LKALRSEVD-IL 753
Cdd:cd18011 79 RETAAQLRRLIGNPFEEFPIVIvsldLLKRSEERRGLLLSEEWDLVVVDEAHKLRNSGGGKetkryklGRLLAKRARhVL 158
|
....*..
gi 730329923 754 TLTATPI 760
Cdd:cd18011 159 LLTATPH 165
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
632-908 |
1.97e-07 |
|
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: 54.36 E-value: 1.97e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 632 GFGKTEVAMRAAFVAVHSGK--QVAVLVPTTLLAQQHYNSFRDRFADWPV--SVEVMSRFKSAKEVENAARLLAE----- 702
Cdd:cd09639 9 GYGKTEAALLWALHSLKSQKadRVIIALPTRATINAMYRRAKEAFGETGLyhSSILSSRIKEMGDSEEFEHLFPLyihsn 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 703 ----------GKIDILIG--THKLLQEDVKFANLG--LVVIDEEHRFGVRQKEQLKAL-----RSEVDILTLTATpIPRT 763
Cdd:cd09639 89 dtlfldpitvCTIDQVLKsvFGEFGHYEFTLASIAnsLLIFDEVHFYDEYTLALILAVlevlkDNDVPILLMSAT-LPKF 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 764 LNMAVSGMR--------DLSIIATPPARRLSVRTFVMEQQnaviKEALLRELLRGGQVYYLHNEVKTIEKCARDLAELVP 835
Cdd:cd09639 168 LKEYAEKIGyveeneplDLKPNERAPFIKIESDKVGEISS----LERLLEFIKKGGSVAIIVNTVDRAQEFYQQLKEKGP 243
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 730329923 836 EARIGIGHGQM---HERELE-QVMSDFYHKRFNVLVASTIIETGIDVpSANTILIERADkfgLAQLHQLRGRVGRSH 908
Cdd:cd09639 244 EEEIMLIHSRFtekDRAKKEaELLLEFKKSEKFVIVATQVIEASLDI-SVDVMITELAP---IDSLIQRLGRLHRYG 316
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
626-759 |
6.64e-07 |
|
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: 51.28 E-value: 6.64e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 626 LVCGDVGFGKTEVAMraaFVAVH--------SGKQVAVLVPTTLLAQQHYNSFRDRFADWPVSVEVMSrfkSAKEVENAA 697
Cdd:cd17927 21 IICLPTGSGKTFVAV---LICEHhlkkfpagRKGKVVFLANKVPLVEQQKEVFRKHFERPGYKVTGLS---GDTSENVSV 94
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 730329923 698 RLLAEGKiDILIGTHKLLQEDVK------FANLGLVVIDEEHR--------FGVRQ--KEQLKALRSEVDILTLTATP 759
Cdd:cd17927 95 EQIVESS-DVIIVTPQILVNDLKsgtivsLSDFSLLVFDECHNttknhpynEIMFRylDQKLGSSGPLPQILGLTASP 171
|
|
| SF2_C_dicer |
cd18802 |
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
823-903 |
1.93e-05 |
|
C-terminal helicase domain of the 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. Dicer exists throughout eukaryotes, and a subset has 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 helicase domains 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: 350189 [Multi-domain] Cd Length: 142 Bit Score: 45.66 E-value: 1.93e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 823 IEKCARDLAELVPEARIGIGHGQ------MHERELEQVMSDFYHKRFNVLVASTIIETGIDVPSANTILieradKFGLA- 895
Cdd:cd18802 45 LKEHPSTLAFIRCGFLIGRGNSSqrkrslMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVI-----RFDLPk 119
|
90
....*....|.
gi 730329923 896 ---QLHQLRGR 903
Cdd:cd18802 120 tlrSYIQSRGR 130
|
|
| SF2_C_XPB |
cd18789 |
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
800-906 |
4.93e-05 |
|
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB 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: 350176 [Multi-domain] Cd Length: 153 Bit Score: 44.55 E-value: 4.93e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 800 KEALLRELLR----GGQVYYLHNEVKTIEKCARDLaeLVPeariGIgHGQMHERELEQVMSDFYHKRFNVLVASTIIETG 875
Cdd:cd18789 35 KLRALEELLKrheqGDKIIVFTDNVEALYRYAKRL--LKP----FI-TGETPQSEREEILQNFREGEYNTLVVSKVGDEG 107
|
90 100 110
....*....|....*....|....*....|.
gi 730329923 876 IDVPSANtILIERADKFGLAQlhQLRGRVGR 906
Cdd:cd18789 108 IDLPEAN-VAIQISGHGGSRR--QEAQRLGR 135
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
626-759 |
6.68e-05 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 47.03 E-value: 6.68e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 626 LVCGDVGFGKTEVA-MRAAFVAVHSGKQVAVLVPTTLLAQQHYNSFRDRFADWPVSVEVMSrfksaKEVENAARLLAEGK 704
Cdd:COG1111 21 LVVLPTGLGKTAVAlLVIAERLHKKGGKVLFLAPTKPLVEQHAEFFKEALNIPEDEIVVFT-----GEVSPEKRKELWEK 95
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 730329923 705 IDILIGTHKLLQED-----VKFANLGLVVIDEEHR-FG----VRQKEQLKALRSEVDILTLTATP 759
Cdd:COG1111 96 ARIIVATPQVIENDliagrIDLDDVSLLIFDEAHRaVGnyayVYIAERYHEDAKDPLILGMTASP 160
|
|
| DEXHc_Hef |
cd18035 |
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
626-759 |
2.13e-04 |
|
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: 43.27 E-value: 2.13e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 626 LVCGDVGFGKTEVA-MRAAFVAVHSGKQVAVLVPTTLLAQQHYNSFRdRFADWPVSVEVMSrfkSAKEVENAARLLAEGK 704
Cdd:cd18035 20 LIVLPTGLGKTIIAiLVAADRLTKKGGKVLILAPSRPLVEQHAENLK-RVLNIPDKITSLT---GEVKPEERAERWDASK 95
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 730329923 705 idILIGT-----HKLLQEDVKFANLGLVVIDEEHRFG-----VRQKEQLKALRSEVDILTLTATP 759
Cdd:cd18035 96 --IIVATpqvieNDLLAGRITLDDVSLLIFDEAHHAVgnyayVYIAHRYKREANNPLILGLTASP 158
|
|
| SF2_C_FANCM_Hef |
cd18801 |
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
822-916 |
3.35e-04 |
|
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: 41.96 E-value: 3.35e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 822 TIEKCARDLAELVP--EARIGIGHGQ------MHERELEQVMSDFYHKRFNVLVASTIIETGIDVPSANTILIERADKFG 893
Cdd:cd18801 42 SAEEIVNFLSKIRPgiRATRFIGQASgksskgMSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSP 121
|
90 100
....*....|....*....|...
gi 730329923 894 LAQLhQLRGRVGRsHHQAYAYLL 916
Cdd:cd18801 122 IRMI-QRMGRTGR-KRQGRVVVL 142
|
|
| DEXHc_RLR |
cd18036 |
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
626-759 |
7.77e-04 |
|
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: 42.08 E-value: 7.77e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 626 LVCGDVGFGKTEVAMRAA------FVAVHSGKQVAVLVPTTLLAQQHYNSFRDRFADWpvsVEVMSrFKSAKEVENAARL 699
Cdd:cd18036 21 IICAPTGSGKTRVAVYICrhhlekRRSAGEKGRVVVLVNKVPLVEQQLEKFFKYFRKG---YKVTG-LSGDSSHKVSFGQ 96
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 730329923 700 LAEGKiDILIGTHKLLQ---------EDVKFANLGLVVIDE------EHRFGV----RQKEQLKALRSEVDILTLTATP 759
Cdd:cd18036 97 IVKAS-DVIICTPQILInnllsgreeERVYLSDFSLLIFDEchhtqkEHPYNKimrmYLDKKLSSQGPLPQILGLTASP 174
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
604-758 |
9.05e-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: 41.55 E-value: 9.05e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 604 PDQQSAIEAVVADmlaprpmDR--LVCGDVGFGKTEVAMRAAFVAVHSGKQVAVLVPTTLLAQQHYNSFRDRFadwPVSV 681
Cdd:cd18028 4 PPQAEAVRAGLLK-------GEnlLISIPTASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEEFKKLE---EIGL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 682 EVMsrFKSAKEVENAARLlaeGKIDILIGTHKLLQEDVKFA-----NLGLVVIDEEHRFGVRQK--------EQLKALRS 748
Cdd:cd18028 74 KVG--ISTGDYDEDDEWL---GDYDIIVATYEKFDSLLRHSpswlrDVGVVVVDEIHLISDEERgptlesivARLRRLNP 148
|
170
....*....|
gi 730329923 749 EVDILTLTAT 758
Cdd:cd18028 149 NTQIIGLSAT 158
|
|
| RecQ |
COG0514 |
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
689-871 |
1.55e-03 |
|
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 42.44 E-value: 1.55e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 689 SAKEVENAARLLAEGKIDIL-IGTHKLLQEDV----KFANLGLVVIDEEH-------------RfgvrqkeQLKALRSE- 749
Cdd:COG0514 92 SAEERREVLRALRAGELKLLyVAPERLLNPRFlellRRLKISLFAIDEAHcisqwghdfrpdyR-------RLGELRERl 164
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 750 --VDILTLTATPIPRTLN--MAVSGMRDLSIIATPPAR---RLSVRTFVMEQQNAVIKEaLLRELLRG-GQVYYLhnEVK 821
Cdd:COG0514 165 pnVPVLALTATATPRVRAdiAEQLGLEDPRVFVGSFDRpnlRLEVVPKPPDDKLAQLLD-FLKEHPGGsGIVYCL--SRK 241
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 730329923 822 TIEKCARDLAELvpeariGIG----HGQMHERELEQVMSDFYHKRFNVLVAsTI 871
Cdd:COG0514 242 KVEELAEWLREA------GIRaaayHAGLDAEEREANQDRFLRDEVDVIVA-TI 288
|
|
| SNF2-rel_dom |
pfam00176 |
SNF2-related domain; This domain is found in proteins involved in a variety of processes ... |
626-765 |
1.58e-03 |
|
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: 41.90 E-value: 1.58e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 626 LVCGDVGFGKT--EVAMRAAFVAVHS--GKQVAVLVPTTLLaQQHYNSFrDRFADWP-VSVEVMSRFKSAKEVENAARLL 700
Cdd:pfam00176 21 ILADEMGLGKTlqTISLLLYLKHVDKnwGGPTLIVVPLSLL-HNWMNEF-ERWVSPPaLRVVVLHGNKRPQERWKNDPNF 98
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 730329923 701 AeGKIDILIGT-HKLLQEDVKFANLG--LVVIDEEHRF-GVRQK--EQLKALRSEVDILtLTATPIPRTLN 765
Cdd:pfam00176 99 L-ADFDVVITTyETLRKHKELLKKVHwhRIVLDEGHRLkNSKSKlsKALKSLKTRNRWI-LTGTPLQNNLE 167
|
|
| DDXDc_reverse_gyrase |
cd17924 |
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
632-711 |
1.69e-03 |
|
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: 40.77 E-value: 1.69e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 632 GFGKTEVAMRAAFVAVHSGKQVAVLVPTTLLAQQHYNSFRD--RFADWPVSVEVMSRFKSAKEVENAARLLAEGKIDILI 709
Cdd:cd17924 42 GVGKTTFGLATSLYLASKGKRSYLIFPTKSLVKQAYERLSKyaEKAGVEVKILVYHSRLKKKEKEELLEKIEKGDFDILV 121
|
..
gi 730329923 710 GT 711
Cdd:cd17924 122 TT 123
|
|
| DEAD-like_helicase_N |
cd17912 |
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ... |
626-667 |
3.86e-03 |
|
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region.
Pssm-ID: 350670 [Multi-domain] Cd Length: 81 Bit Score: 37.50 E-value: 3.86e-03
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 730329923 626 LVCGDVGFGKTEVAMRAAFVAVHSGKQVAVLVPTTLLAQQHY 667
Cdd:cd17912 3 LHLGPTGSGKTLVAIQKIASAMSSGKSVLVVTPTKLLAHEIL 44
|
|
| DEADc_DDX1 |
cd17938 |
DEAD-box helicase domain of DEAD box protein 1; DEAD box protein 1 (DDX1) acts as an ... |
736-809 |
8.18e-03 |
|
DEAD-box helicase domain of DEAD box protein 1; DEAD box protein 1 (DDX1) acts as an ATP-dependent RNA helicase, able to unwind both RNA-RNA and RNA-DNA duplexes. It possesses 5' single-stranded RNA overhang nuclease activity as well as ATPase activity on various RNA, but not DNA polynucleotides. DDX1 may play a role in RNA clearance at DNA double-strand breaks (DSBs), thereby facilitating the template-guided repair of transcriptionally active regions of the genome. It may also be involved in 3'-end cleavage and polyadenylation of pre-mRNAs. DDX1 is a member of the DEAD-box helicases, 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: 350696 [Multi-domain] Cd Length: 204 Bit Score: 38.84 E-value: 8.18e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 730329923 736 GVRQKEQLKALRSEVDIltLTATPIpRTLNMAVSGMRDLSiiatpparrlSVRTFVMEQQNAVIKEALLRELLR 809
Cdd:cd17938 100 GVKAREQLKRLESGVDI--VVGTPG-RLEDLIKTGKLDLS----------SVRFFVLDEADRLLSQGNLETINR 160
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
626-760 |
8.67e-03 |
|
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: 38.79 E-value: 8.67e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 730329923 626 LVCGDVGFGKTEVA---MRAAFVAVH----SGKQVAVLVPTTLLAQQHYNSFRDRFadwPVSVEVMSRfKSAKEVENAAR 698
Cdd:cd18034 20 IVVLPTGSGKTLIAvmlIKEMGELNRkeknPKKRAVFLVPTVPLVAQQAEAIRSHT---DLKVGEYSG-EMGVDKWTKER 95
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 730329923 699 LLAE-GKIDILIGTHKLL-----QEDVKFANLGLVVIDE------EHRFGVRQKEQLKALRSEV--DILTLTATPI 760
Cdd:cd18034 96 WKEElEKYDVLVMTAQILldalrHGFLSLSDINLLIFDEchhatgDHPYARIMKEFYHLEGRTSrpRILGLTASPV 171
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