|
Name |
Accession |
Description |
Interval |
E-value |
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
14-1149 |
0e+00 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 1834.69 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 14 GKQTWGNLPGAALSLAIAEAASSAGRFTLLLTADSQAADRLEQELRFFAPGLPVLPFPDWETLPYDLFSPHQDIISQRIA 93
Cdd:COG1197 3 GRLTLSGLPGSARALLLAALARALGRPLLVVTADEREAERLAEDLRFFLPDLPVLLFPAWETLPYDRFSPSPDIVSERLA 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 94 SLYRLPELSHGILVVPITTALHRLAPTRFLLGSSLVLDVGQTIDVEQMRSRLEATGYRCVDTVYEHGEFAVRGALIDLFP 173
Cdd:COG1197 83 TLRRLASGKPGIVVTPVRALLQRLPPPELLAAASLSLKVGDELDLEELRERLVAAGYERVDQVEEPGEFAVRGGILDIFP 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 174 MGSKLPYRIDLFDDEIETLRTFDPETQRSIDKVDSIRLLPAREFPMQKEEVTRFKARFRERFDVDFRRSAIFQDLASGII 253
Cdd:COG1197 163 PGSEHPVRIEFFGDEIESIRTFDPETQRSLEKVDEVELLPAREFPLDEEAIERFRERLRELFGLDPKLDELYEALSEGIA 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 254 PAGIEYYLPLFFEETSTLFDYLPSDTQVF--SLPGVEQAAEHFWNDVRGRYEDRRGDLSRPLLPPSELFLPVEDCFAQLK 331
Cdd:COG1197 243 FAGIEYYLPLFYEELATLFDYLPEDALVVldEPERIEEAAEEFWEEIEERYEARRHDRGRPLLPPEELFLDPEELFAALK 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 332 QWPRVVVSA-DDVEPGTGRERFPARTLPNlaIEAKANQPLAALSDFLDQfSGRVLFTAESAGRREVLLELLERLKLRPQT 410
Cdd:COG1197 323 RRPRVTLSPfAALPEGAGVVNLGARPLPS--FAGQLEALLEELKRLLKD-GGRVLLAAESEGRRERLLELLRDHGIPARL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 411 VEGWADFITGsqRLAITIAPLDEGLLLEDPAIALVAESPLFGQRVmqRRRRDKRgEAANDAVIKNLTELREGAPVVHIDH 490
Cdd:COG1197 400 VESLAELSPG--GVAITVGPLEHGFELPDAKLAVITESELFGERV--KRRRRKK-KRSADAFIRDLSELKPGDYVVHVDH 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 491 GVGRYLGLATLEIDGQAAEFLTLEYAEGAKLYVPVANLHLIARYTGSDDALAPLHRLGSEAWQKAKRKAAEQVRDVAAEL 570
Cdd:COG1197 475 GIGRYLGLETLEVGGAERDYLVLEYAGGDKLYVPVDQLDLISRYVGSEGEAPKLDKLGGSDWQKAKAKAKKAVRDIAAEL 554
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 571 LDIYARRAARKGYAFADPAADYATFSAGFPFEETPDQQNAIEAVRADMLAAKPMDRLVCGDVGFGKTEVAMRAAFIAVHS 650
Cdd:COG1197 555 LKLYAERAARKGFAFSPDTPWQREFEAAFPYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKTEVALRAAFKAVMD 634
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 651 GRQVAVLVPTTLLAQQHYNSFRDRFADWPVTVEVMSRFKSAKEVASAAADLAEGKIDILIGTHKLLQDDVRFKDLGLVVI 730
Cdd:COG1197 635 GKQVAVLVPTTLLAQQHYETFKERFAGFPVRVEVLSRFRTAKEQKETLEGLADGKVDIVIGTHRLLSKDVKFKDLGLLII 714
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 731 DEEHRFGVRQKEQLKALRSEVDILTLTATPIPRTLNMAVAGMRDLSIIATPPARRLSVRTFVMEHNNSTVKEALLRELLR 810
Cdd:COG1197 715 DEEQRFGVRHKEKLKALRANVDVLTLTATPIPRTLQMSLSGIRDLSIIATPPEDRLPVKTFVGEYDDALIREAILRELLR 794
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 811 GGQVYYLHNDVKTIEKCAADLAELVPEARIGIGHGQMRERELEQVMSDFYHKRFNVLIASTIIETGIDVPSANTIVIERA 890
Cdd:COG1197 795 GGQVFYVHNRVEDIEKVAARLQELVPEARIAVAHGQMSERELERVMLDFYEGEFDVLVCTTIIETGIDIPNANTIIIERA 874
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 891 DKFGLAQLHQLRGRVGRSHHQAYAYLLTPARQKVSADAEKRLEAIANTQDLGAGFVLATNDLEIRGAGELLGEGQSGQIQ 970
Cdd:COG1197 875 DRFGLAQLYQLRGRVGRSHRRAYAYLLYPPDKVLTEDAEKRLEAIQEFTELGAGFKLAMHDLEIRGAGNLLGEEQSGHIA 954
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 971 AVGFTLYMEMLERAVKAIRKGTQPNLEQplggGPEVNLRLPALIPEDYLPDVHARLILYKRIASATDEEGLKDLQVEMID 1050
Cdd:COG1197 955 EVGFDLYLQMLEEAVAALKGGKEPEEEW----EPEINLGVPALIPEDYIPDVRQRLELYKRIASAESEEELDELQEELID 1030
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 1051 RFGLLPEPTKNLMRLTQLKLQAEKLGIKKVDAGPNGGKLEFEAETPVDPLTLIKLIQGQPKRYKFEGATQFRFLVPMERP 1130
Cdd:COG1197 1031 RFGPLPEEVENLLAVARLKLLARRLGIEKIDAGGKGIRIEFSPNTPLDPEKLIRLIQKQPGRYKLDGDDKLVITLDLEDP 1110
|
1130
....*....|....*....
gi 1442975538 1131 DERFNTLEALFERLTPQTA 1149
Cdd:COG1197 1111 EERLEALEELLEALAKLAK 1129
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
8-1149 |
0e+00 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 1458.03 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 8 QMSATAGKQ-TWGNLPGAALSLAIAEAASSAGRFTLLLTADSQAADRLEQELRFFAPgLPVLPFPDWETLPYDLFSPHQD 86
Cdd:PRK10689 8 TLPVKAGDQrQLGELTGAACATEVAEIAERHAGPVVLIAPDMQNALRLHDEIQQFTD-QMVMNLADWETLPYDSFSPHQD 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 87 IISQRIASLYRLPELSHGILVVPITTALHRLAPTRFLLGSSLVLDVGQTIDVEQMRSRLEATGYRCVDTVYEHGEFAVRG 166
Cdd:PRK10689 87 IISSRLSTLYQLPTMQRGVLILPVNTLMQRVCPHSFLHGHALVMKKGQRLSRDALRAQLEQAGYRHVDQVMEHGEYATRG 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 167 ALIDLFPMGSKLPYRIDLFDDEIETLRTFDPETQRSIDKVDSIRLLPAREFPMQKEEVTRFKARFRERFDVdfRRSA--I 244
Cdd:PRK10689 167 ALLDLFPMGSEEPYRIDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFEV--KRDAehI 244
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 245 FQDLASGIIPAGIEYYLPLFFEET-STLFDYLPSDTQVFSLPGVEQAAEHFWNDVRGRYEDRRGDLSRPLLPPSELFLPV 323
Cdd:PRK10689 245 YQQVSKGTLPAGIEYWQPLFFSEPlPPLFSYFPANTLLVNTGDLETSAERFWADTLARFENRGVDPMRPLLPPESLWLRV 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 324 EDCFAQLKQWPRVVVSADDVEPGTGRERFPARTLPNLAIEAKANQPLAALSDFLDQFSGRVLFTAESAGRREVLLELLER 403
Cdd:PRK10689 325 DELFSELKNWPRVQLKTEHLPTKAANTNLGYQKLPDLAVQAQQKAPLDALRRFLESFDGPVVFSVESEGRREALGELLAR 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 404 LKLRPQTVEGWADFITGSQRLAITIAplDEGLLLEDPAIALVAESPLFGQRVmQRRRRDKRGEAANDAVIKNLTELREGA 483
Cdd:PRK10689 405 IKIAPKRIMRLDEASDRGRYLMIGAA--EHGFIDTVRNLALICESDLLGERV-ARRRQDSRRTINPDTLIRNLAELHPGQ 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 484 PVVHIDHGVGRYLGLATLEIDGQAAEFLTLEYAEGAKLYVPVANLHLIARYTGSDDALAPLHRLGSEAWQKAKRKAAEQV 563
Cdd:PRK10689 482 PVVHLEHGVGRYAGMTTLEAGGIKGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHKLGGDAWSRARQKAAEKV 561
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 564 RDVAAELLDIYARRAARKGYAFADPAADYATFSAGFPFEETPDQQNAIEAVRADMLAAKPMDRLVCGDVGFGKTEVAMRA 643
Cdd:PRK10689 562 RDVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRA 641
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 644 AFIAVHSGRQVAVLVPTTLLAQQHYNSFRDRFADWPVTVEVMSRFKSAKEVASAAADLAEGKIDILIGTHKLLQDDVRFK 723
Cdd:PRK10689 642 AFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWK 721
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 724 DLGLVVIDEEHRFGVRQKEQLKALRSEVDILTLTATPIPRTLNMAVAGMRDLSIIATPPARRLSVRTFVMEHNNSTVKEA 803
Cdd:PRK10689 722 DLGLLIVDEEHRFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSLVVREA 801
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 804 LLRELLRGGQVYYLHNDVKTIEKCAADLAELVPEARIGIGHGQMRERELEQVMSDFYHKRFNVLIASTIIETGIDVPSAN 883
Cdd:PRK10689 802 ILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTAN 881
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 884 TIVIERADKFGLAQLHQLRGRVGRSHHQAYAYLLTPARQKVSADAEKRLEAIANTQDLGAGFVLATNDLEIRGAGELLGE 963
Cdd:PRK10689 882 TIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGE 961
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 964 GQSGQIQAVGFTLYMEMLERAVKAIRKGTQPNLEQPLGGGPEVNLRLPALIPEDYLPDVHARLILYKRIASATDEEGLKD 1043
Cdd:PRK10689 962 EQSGQMETIGFSLYMELLENAVDALKAGREPSLEDLTSQQTEVELRMPSLLPDDFIPDVNTRLSFYKRIASAKNENELEE 1041
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 1044 LQVEMIDRFGLLPEPTKNLMRLTQLKLQAEKLGIKKVDAGPNGGKLEFEAETPVDPLTLIKLIQGQPKRYKFEGATQFRF 1123
Cdd:PRK10689 1042 IKVELIDRFGLLPDPARNLLDIARLRQQAQKLGIRKLEGNEKGGFIEFAEKNHVDPAWLIGLLQKQPQHYRLDGPTRLKF 1121
|
1130 1140
....*....|....*....|....*.
gi 1442975538 1124 LVPMERPDERFNTLEALFERLTPQTA 1149
Cdd:PRK10689 1122 IQDLSERKTRIEWVRQFMRELEENAI 1147
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
149-1081 |
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: 1108.19 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 149 GYRCVDTVYEHGEFAVRGALIDLFPMGSKLPYRIDLFDDEIETLRTFDPETQRSIDKVDSIRLLPAREFPMqKEEVTRFK 228
Cdd:TIGR00580 5 GYERVDLVEEEGEFSVRGEILDIFPPGSELPVRIEFFGDEIESIREFDVDSQRSLEELLEITILPAKEFIL-LEEETIAR 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 229 ARFRERFDVDFRRSAIFQDLASGIIPAGIEYYLPLFFEETSTLFDYLPSDTQVF-SLP-GVEQAAEHFWNDVRgRYEDRR 306
Cdd:TIGR00580 84 LKDNAARVEDAKHLETIEALSEGTLPAGEEMFLPLFFEDLSSLFDYLPDNTPILlDDPeRFHSAARFLQRELE-EFYNAL 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 307 GDLSRPLLPPSELFLPVEDCFAQLK-QWPRVVVSADDVEPGTGRERFPARTLPNLAIEAKANQPLAALSDFLDQFSGRVL 385
Cdd:TIGR00580 163 EEAKKLINPPRLDLDPSELAFEASAiSLSRVQLENEHLSLKASEAIEGAQKHSRLEFGEILAFKEELFRWLKAGFKITVA 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 386 ftAESAGRREVLLELLERLKLRPQtVEGWADFITGSQRLAITIaPLDEGLLLEDPAIALVAESPLFGQRVMqRRRRDKRg 465
Cdd:TIGR00580 243 --AESESQAERLKSLLAEHDIAAQ-VIDESCIIIPAVRYVMIG-ALSSGFILPTAGLAVITESELFGSRVL-RRPKKSR- 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 466 eaANDAVIKNLTELREGAPVVHIDHGVGRYLGLATLEIDGQAAEFLTLEYAEGAKLYVPVANLHLIARYTGSDDALAPLH 545
Cdd:TIGR00580 317 --LKSKPIESLNELNPGDYVVHLDHGIGRFLGLETLEVGGIERDYLVLEYAGEDKLYVPVEQLHLISRYVGGSGKNPALD 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 546 RLGSEAWQKAKRKAAEQVRDVAAELLDIYARRAARKGYAFADPAADYATFSAGFPFEETPDQQNAIEAVRADMLAAKPMD 625
Cdd:TIGR00580 395 KLGGKSWEKTKAKVKKSVREIAAKLIELYAKRKAIKGHAFPPDLEWQQEFEDSFPFEETPDQLKAIEEIKADMESPRPMD 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 626 RLVCGDVGFGKTEVAMRAAFIAVHSGRQVAVLVPTTLLAQQHYNSFRDRFADWPVTVEVMSRFKSAKEVASAAADLAEGK 705
Cdd:TIGR00580 475 RLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGK 554
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 706 IDILIGTHKLLQDDVRFKDLGLVVIDEEHRFGVRQKEQLKALRSEVDILTLTATPIPRTLNMAVAGMRDLSIIATPPARR 785
Cdd:TIGR00580 555 IDILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPEDR 634
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 786 LSVRTFVMEHNNSTVKEALLRELLRGGQVYYLHNDVKTIEKCAADLAELVPEARIGIGHGQMRERELEQVMSDFYHKRFN 865
Cdd:TIGR00580 635 LPVRTFVMEYDPELVREAIRRELLRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQ 714
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 866 VLIASTIIETGIDVPSANTIVIERADKFGLAQLHQLRGRVGRSHHQAYAYLLTPARQKVSADAEKRLEAIANTQDLGAGF 945
Cdd:TIGR00580 715 VLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDAQKRLEAIQEFSELGAGF 794
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 946 VLATNDLEIRGAGELLGEGQSGQIQAVGFTLYMEMLERAVKAIRKGTQPNLEQPlgggPEVNLRLPALIPEDYLPDVHAR 1025
Cdd:TIGR00580 795 KIALHDLEIRGAGNLLGEEQSGHIESIGFDLYMELLEEAIEELKGGKPPKLEEE----TDIELPYSAFIPDDYIADDSLR 870
|
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|....*.
gi 1442975538 1026 LILYKRIASATDEEGLKDLQVEMIDRFGLLPEPTKNLMRLTQLKLQAEKLGIKKVD 1081
Cdd:TIGR00580 871 LEFYKRIASAETEEELEKIRDELIDRFGPLPEEARTLLDVARLKLLARKLGIRKLK 926
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
570-967 |
3.64e-134 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 423.69 E-value: 3.64e-134
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 570 LLDIYARRAARKGYAFADPAADYATFSAGFPFEETPDQQNAIEAVRADMLAAKPMDRLVCGDVGFGKTEVAMRAAFIAVH 649
Cdd:COG1200 227 LLLRRARRRKRKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVE 306
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 650 SGRQVAVLVPTTLLAQQHYNSFRDRFADWPVTVEVMSRFKSAKEVASAAADLAEGKIDILIGTHKLLQDDVRFKDLGLVV 729
Cdd:COG1200 307 AGYQAALMAPTEILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVV 386
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 730 IDEEHRFGVRQKEQLKALRSEVDILTLTATPIPRTLNMAVAGMRDLSIIATPPARRLSVRTFVMEHNN-STVKEALLREL 808
Cdd:COG1200 387 IDEQHRFGVEQRLALREKGEAPHVLVMTATPIPRTLAMTLYGDLDVSVIDELPPGRKPIKTRVVPEERrDEVYERIREEI 466
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 809 LRGGQVYYL--------HNDVKTIEKCAADLAELVPEARIGIGHGQMRERELEQVMSDFYHKRFNVLIASTIIETGIDVP 880
Cdd:COG1200 467 AKGRQAYVVcplieeseKLDLQAAEETYEELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGVDVP 546
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 881 SANTIVIERADKFGLAQLHQLRGRVGRSHHQAYAYLLTPArqKVSADAEKRLEAIANTQDlgaGFVLATNDLEIRGAGEL 960
Cdd:COG1200 547 NATVMVIENAERFGLSQLHQLRGRVGRGSAQSYCLLLYDA--PLSETARERLEVMRETND---GFEIAEEDLELRGPGEF 621
|
....*..
gi 1442975538 961 LGEGQSG 967
Cdd:COG1200 622 LGTRQSG 628
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
575-967 |
2.79e-131 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 415.70 E-value: 2.79e-131
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 575 ARRAARKGYAFADPAADYATFSAGFPFEETPDQQNAIEAVRADMLAAKPMDRLVCGDVGFGKTEVAMRAAFIAVHSGRQV 654
Cdd:PRK10917 234 AGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGYQA 313
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 655 AVLVPTTLLAQQHYNSFRDRFADWPVTVEVMSRFKSAKEVASAAADLAEGKIDILIGTHKLLQDDVRFKDLGLVVIDEEH 734
Cdd:PRK10917 314 ALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIIDEQH 393
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 735 RFGVRQKEQLKALRSEVDILTLTATPIPRTLNMAVAGMRDLSIIATPPARRLSVRTFVMEHNN-STVKEALLRELLRGGQ 813
Cdd:PRK10917 394 RFGVEQRLALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRrDEVYERIREEIAKGRQ 473
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 814 VYYL--------HNDVKTIEKCAADLAELVPEARIGIGHGQMRERELEQVMSDFYHKRFNVLIASTIIETGIDVPSANTI 885
Cdd:PRK10917 474 AYVVcplieeseKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATVM 553
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 886 VIERADKFGLAQLHQLRGRVGRSHHQAYAYLLTPArqKVSADAEKRLEAIANTQDlgaGFVLATNDLEIRGAGELLGEGQ 965
Cdd:PRK10917 554 VIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKD--PLSETARERLKIMRETND---GFVIAEKDLELRGPGELLGTRQ 628
|
..
gi 1442975538 966 SG 967
Cdd:PRK10917 629 SG 630
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
595-967 |
2.60e-117 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 377.07 E-value: 2.60e-117
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 595 FSAGFPFEETPDQQNAIEAVRADMLAAKPMDRLVCGDVGFGKTEVAMRAAFIAVHSGRQVAVLVPTTLLAQQHYNSFRDR 674
Cdd:TIGR00643 228 FLASLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNL 307
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 675 FADWPVTVEVMSRFKSAKEVASAAADLAEGKIDILIGTHKLLQDDVRFKDLGLVVIDEEHRFGVRQKEQLKALRSE---V 751
Cdd:TIGR00643 308 LAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLREKGQGgftP 387
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 752 DILTLTATPIPRTLNMAVAGMRDLSIIATPPARRLSVRTFVMEHNNST-VKEALLRELLRGGQVYYLHN--------DVK 822
Cdd:TIGR00643 388 HVLVMSATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLIKHDEKDiVYEFIEEEIAKGRQAYVVYPlieeseklDLK 467
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 823 TIEKCAADLAELVPEARIGIGHGQMRERELEQVMSDFYHKRFNVLIASTIIETGIDVPSANTIVIERADKFGLAQLHQLR 902
Cdd:TIGR00643 468 AAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLR 547
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1442975538 903 GRVGRSHHQAYAYLLTpaRQKVSADAEKRLEAIANTQDlgaGFVLATNDLEIRGAGELLGEGQSG 967
Cdd:TIGR00643 548 GRVGRGDHQSYCLLVY--KNPKSESAKKRLRVMADTLD---GFVIAEEDLELRGPGDLLGTKQSG 607
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
591-780 |
2.45e-115 |
|
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: 355.34 E-value: 2.45e-115
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 591 DYATFSAGFPFEETPDQQNAIEAVRADMLAAKPMDRLVCGDVGFGKTEVAMRAAFIAVHSGRQVAVLVPTTLLAQQHYNS 670
Cdd:cd17991 4 EQEEFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQHYET 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 671 FRDRFADWPVTVEVMSRFKSAKEVASAAADLAEGKIDILIGTHKLLQDDVRFKDLGLVVIDEEHRFGVRQKEQLKALRSE 750
Cdd:cd17991 84 FKERFANFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQKEKLKELRPN 163
|
170 180 190
....*....|....*....|....*....|
gi 1442975538 751 VDILTLTATPIPRTLNMAVAGMRDLSIIAT 780
Cdd:cd17991 164 VDVLTLSATPIPRTLHMALSGIRDLSVIAT 193
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
788-937 |
2.27e-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: 248.41 E-value: 2.27e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 788 VRTFVMEHNNSTVKEALLRELLRGGQVYYLHNDVKTIEKCAADLAELVPEARIGIGHGQMRERELEQVMSDFYHKRFNVL 867
Cdd:cd18810 2 VRTYVMPYDDELIREAIERELLRGGQVFYVHNRIESIEKLATQLRQLVPEARIAIAHGQMTENELEEVMLEFAKGEYDIL 81
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 868 IASTIIETGIDVPSANTIVIERADKFGLAQLHQLRGRVGRSHHQAYAYLLTPARQKVSADAEKRLEAIAN 937
Cdd:cd18810 82 VCTTIIESGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAYFLYPDQKKLTEDALKRLEAIQE 151
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
570-782 |
2.89e-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: 2.89e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 570 LLDIYARRAARKGYAFADPAADYATFSAGFPFEETPDQQNAIEAVRADMLAAKPMDRLVCGDVGFGKTEVAMRAAFIAVH 649
Cdd:cd17992 13 LLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKTVVAALAMLAAVE 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 650 SGRQVAVLVPTTLLAQQHYNSFRDRFADWPVTVEVMSRFKSAKEVASAAADLAEGKIDILIGTHKLLQDDVRFKDLGLVV 729
Cdd:cd17992 93 NGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQEDVEFHNLGLVI 172
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 1442975538 730 IDEEHRFGVRQKEQLKALRSEVDILTLTATPIPRTLNMAVAGMRDLSIIATPP 782
Cdd:cd17992 173 IDEQHRFGVEQRLKLREKGETPHVLVMTATPIPRTLALTLYGDLDVSIIDELP 225
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
590-779 |
3.52e-68 |
|
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: 226.53 E-value: 3.52e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 590 ADYATFSAGFPFEETPDQQNAIEAVRADMLAAKPMDRLVCGDVGFGKTEVAMRAAFIAVHSGRQVAVLVPTTLLAQQHYN 669
Cdd:cd17918 3 ALIQELCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYE 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 670 SFRDRFAdwPVTVEVMSRFKSAKevasaaadlAEGKIDILIGTHKLLQDDVRFKDLGLVVIDEEHRFGVRQKEQLKALRS 749
Cdd:cd17918 83 EARKFLP--FINVELVTGGTKAQ---------ILSGISLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNLGA 151
|
170 180 190
....*....|....*....|....*....|
gi 1442975538 750 eVDILTLTATPIPRTLNMAVAGMRDLSIIA 779
Cdd:cd17918 152 -THFLEATATPIPRTLALALSGLLDLSVID 180
|
|
| SF2_C_RecG_TRCF |
cd18792 |
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
788-937 |
2.80e-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: 2.80e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 788 VRTFVMEHNNST-VKEALLRELLRGGQVYYLHN--------DVKTIEKCAADLAELVPEARIGIGHGQMRERELEQVMSD 858
Cdd:cd18792 2 IRTYVIPHDDLDlVYEAIERELARGGQVYYVYPrieeseklDLKSIEALAEELKELVPEARVALLHGKMTEDEKEAVMLE 81
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1442975538 859 FYHKRFNVLIASTIIETGIDVPSANTIVIERADKFGLAQLHQLRGRVGRSHHQAYAYLLTPARQKVSADAEKRLEAIAN 937
Cdd:cd18792 82 FREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYPDPKKLTETAKKRLRAIAE 160
|
|
| CarD_TRCF |
smart01058 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
478-575 |
1.15e-43 |
|
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: 153.38 E-value: 1.15e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 478 ELREGAPVVHIDHGVGRYLGLATLEIDGQAAEFLTLEYAEGAKLYVPVANLHLIARYTGS-DDALAPLHRLGSEAWQKAK 556
Cdd:smart01058 1 ELKIGDYVVHPDHGVGRYEGIETIEVGGEKREYLVLEYAGGDKLYVPVDNLDLGSRYVGSeGEVEPVLDKLGGGSWSKRK 80
|
90
....*....|....*....
gi 1442975538 557 RKAAEQVRDVAAELLDIYA 575
Cdd:smart01058 81 RKAKSGIRDIAAELLRLYA 99
|
|
| TRCF |
smart00982 |
This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in ... |
1007-1106 |
8.95e-43 |
|
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: 151.08 E-value: 8.95e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 1007 NLRLPALIPEDYLPDVHARLILYKRIASATDEEGLKDLQVEMIDRFGLLPEPTKNLMRLTQLKLQAEKLGIKKVDAGPNG 1086
Cdd:smart00982 1 DLPVPALIPEDYIPDVRQRLELYKRIASAETEEELDEIQEELIDRFGPLPEEVKNLLEVARLKLLAKKLGIEKIDAGGKG 80
|
90 100
....*....|....*....|
gi 1442975538 1087 GKLEFEAETPVDPLTLIKLI 1106
Cdd:smart00982 81 IVIEFSPDTPIDPEKLILLI 100
|
|
| TRCF |
pfam03461 |
TRCF domain; |
1008-1099 |
2.50e-38 |
|
TRCF domain;
Pssm-ID: 460928 [Multi-domain] Cd Length: 95 Bit Score: 137.94 E-value: 2.50e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 1008 LRLPALIPEDYLPDVHARLILYKRIASATDEEGLKDLQVEMIDRFGLLPEPTKNLMRLTQLKLQAEKLGIKKVDAGPNGG 1087
Cdd:pfam03461 1 LDVDAYIPDDYIPDESQRLELYKRLASIETEEELDDLQEELIDRFGPLPEEVENLLEIARLKLLAKKLGIEKIDLKGGGI 80
|
90
....*....|..
gi 1442975538 1088 KLEFEAETPVDP 1099
Cdd:pfam03461 81 RITFSEDAKIDP 92
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
788-936 |
3.59e-37 |
|
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: 137.09 E-value: 3.59e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 788 VRTFVMEHNN-STVKEALLRELLRGGQVYYLHNDVKTIE----KCAADLAE-----LVPEARIGIGHGQMRERELEQVMS 857
Cdd:cd18811 2 ITTYLIFHTRlDKVYEFVREEIAKGRQAYVIYPLIEESEkldlKAAVAMYEylkerFRPELNVGLLHGRLKSDEKDAVMA 81
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1442975538 858 DFYHKRFNVLIASTIIETGIDVPSANTIVIERADKFGLAQLHQLRGRVGRSHHQAYAYLLTParQKVSADAEKRLEAIA 936
Cdd:cd18811 82 EFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYK--DPLTETAKQRLRVMT 158
|
|
| UvrB_inter |
pfam17757 |
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ... |
128-217 |
5.78e-36 |
|
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: 130.98 E-value: 5.78e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 128 LVLDVGQTIDVEQMRSRLEATGYRCVDTVYEHGEFAVRGALIDLFPMGS-KLPYRIDLFDDEIETLRTFDPETQRSIDKV 206
Cdd:pfam17757 1 LSLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYSeDEAIRIEFFGDEIESIREFDPLTGRSLEKL 80
|
90
....*....|.
gi 1442975538 207 DSIRLLPAREF 217
Cdd:pfam17757 81 DEVTIYPASHY 91
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
604-767 |
2.11e-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: 112.34 E-value: 2.11e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 604 TPDQQNAIEAVRADMlaakpmDRLVCGDVGFGKTEVAMRAAFIAVH---SGRQVAVLVPTTLLAQQHYNSFRDRFADWPV 680
Cdd:pfam00270 1 TPIQAEAIPAILEGR------DVLVQAPTGSGKTLAFLLPALEALDkldNGPQALVLAPTRELAEQIYEELKKLGKGLGL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 681 TVevmSRFKSAKEVASAAADLAegKIDILIGTH----KLLQDDVRFKDLGLVVIDEEHR-----FGVRQKEQLKALRSEV 751
Cdd:pfam00270 75 KV---ASLLGGDSRKEQLEKLK--GPDILVGTPgrllDLLQERKLLKNLKLLVLDEAHRlldmgFGPDLEEILRRLPKKR 149
|
170
....*....|....*.
gi 1442975538 752 DILTLTATPiPRTLNM 767
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 ... |
479-574 |
6.05e-28 |
|
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: 108.30 E-value: 6.05e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 479 LREGAPVVHIDHGVGRYLGLATLEIDgqaaEFLTLEYAEGAKLYVPVANLHLIARYTGSDDalapLHRLG-SEAWQKAKR 557
Cdd:pfam02559 1 LKVGDYVVHPDHGIGRIEGIEKLETK----DYYVLEYAGGDKLYVPVDNLDLIRKYISKGE----LDKLGdGRRWRKYKE 72
|
90
....*....|....*..
gi 1442975538 558 KAAEQVRDVAAELLDIY 574
Cdd:pfam02559 73 KLKSGDIEEAAELIKLY 89
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
595-788 |
6.69e-26 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 106.42 E-value: 6.69e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 595 FSAGFPFEETPDQQNAIEAVRADMlaakpMDRLVCGDVGFGKTEVAMRAAFIAVHSGR--QVAVLVPTTLLAQQHYNSFR 672
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALLSGL-----RDVILAAPTGSGKTLAALLPALEALKRGKggRVLVLVPTRELAEQWAEELK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 673 DRFADWPV-TVEVMSRFKSAKEVasaaADLAEGKIDILIGT-----HKLLQDDVRFKDLGLVVIDEEHRFGVR-QKEQL- 744
Cdd:smart00487 76 KLGPSLGLkVVGLYGGDSKREQL----RKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRLLDGgFGDQLe 151
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 1442975538 745 ---KALRSEVDILTLTATPIPRTLNMAVAGMRDLSIIATPPARRLSV 788
Cdd:smart00487 152 kllKLLPKNVQLLLLSATPPEEIENLLELFLNDPVFIDVGFTPLEPI 198
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
624-759 |
1.52e-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: 100.56 E-value: 1.52e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 624 MDRLVCGDVGFGKTEVAMRAAFIAVHS-GRQVAVLVPTTLLAQQHYNSFRDRFaDWPVTVEVMSRFKSAKEVASAAADLA 702
Cdd:cd00046 2 ENVLITAPTGSGKTLAALLAALLLLLKkGKKVLVLVPTKALALQTAERLRELF-GPGIRVAVLVGGSSAEEREKNKLGDA 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 703 egkiDILIGTHKLLQDDV------RFKDLGLVVIDEEHRFGVRQKEQL-------KALRSEVDILTLTAT 759
Cdd:cd00046 81 ----DIIIATPDMLLNLLlredrlFLKDLKLIIVDEAHALLIDSRGALildlavrKAGLKNAQVILLSAT 146
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
801-907 |
1.79e-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: 81.87 E-value: 1.79e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 801 KEALLRELL---RGGQVYYLHNdvkTIEKCAADLAELVPEARIGIGHGQMRERELEQVMSDFYHKRFNVLIASTIIETGI 877
Cdd:pfam00271 2 KLEALLELLkkeRGGKVLIFSQ---TKKTLEAELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGL 78
|
90 100 110
....*....|....*....|....*....|
gi 1442975538 878 DVPSANTIVIERADkFGLAQLHQLRGRVGR 907
Cdd:pfam00271 79 DLPDVDLVINYDLP-WNPASYIQRIGRAGR 107
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
536-909 |
4.03e-17 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 86.23 E-value: 4.03e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 536 GSDDALAPLHRLGSEAWQKAKRKAAEQVRDVAAELLDIYARRAARKGYAFADPAA-DYATFSAGFPFEETPDQQNAIEAV 614
Cdd:COG1061 13 KLRSSLLLLDLERLELSLLRNLVEARRLAIKEGTREDGRRLPEEDTERELAEAEAlEAGDEASGTSFELRPYQQEALEAL 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 615 RAdMLAAKPMDRLVCGDVGFGKTEVAMRAAfIAVHSGRQVAVLVPTTLLAQQHYNSFRDRFADwpvtvevmsrfksakev 694
Cdd:COG1061 93 LA-ALERGGGRGLVVAPTGTGKTVLALALA-AELLRGKRVLVLVPRRELLEQWAEELRRFLGD----------------- 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 695 ASAAADLAEGKIDILIGTHKLLQDDVRFKDL----GLVVIDEEHRFGVRQKEQLKALRSEVDILTLTATPIpRTLNMAVA 770
Cdd:COG1061 154 PLAGGGKKDSDAPITVATYQSLARRAHLDELgdrfGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLTATPF-RSDGREIL 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 771 GMRDLSIIATPPARRLSVRTFVMEH----------------------------NNSTVKEALLRELLRggqvyYLHNDVK 822
Cdd:COG1061 233 LFLFDGIVYEYSLKEAIEDGYLAPPeyygirvdltderaeydalserlrealaADAERKDKILRELLR-----EHPDDRK 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 823 TIEKC-----AADLAELVPEARIGIG--HGQMRERELEQVMSDFYHKRFNVLIASTIIETGIDVPSANTIVIERADKFgL 895
Cdd:COG1061 308 TLVFCssvdhAEALAELLNEAGIRAAvvTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILLRPTGS-P 386
|
410
....*....|....
gi 1442975538 896 AQLHQLRGRVGRSH 909
Cdd:COG1061 387 REFIQRLGRGLRPA 400
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
607-734 |
1.73e-16 |
|
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: 78.40 E-value: 1.73e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 607 QQNAIEAVRADMLAAKPMdrLVCGDVGFGKTEVAMRAAFIAVHSGRQVAVLVPTTLLAQQHYNSFRDRFADwpvTVEVMS 686
Cdd:cd17929 1 QRKAYEAIVSSLGGFKTF--LLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRFGD---KVAVLH 75
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 1442975538 687 RFKSAKEVASAAADLAEGKIDILIGTHKLLQddVRFKDLGLVVIDEEH 734
Cdd:cd17929 76 SKLSDKERADEWRKIKRGEAKVVIGARSALF--APFKNLGLIIVDEEH 121
|
|
| PRK05298 |
PRK05298 |
excinuclease ABC subunit UvrB; |
124-311 |
4.07e-16 |
|
excinuclease ABC subunit UvrB;
Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 83.17 E-value: 4.07e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 124 LGSSLVLDVGQTIDVEQMRSRLEATGYRCVDTVYEHGEFAVRGALIDLFPMGS-KLPYRIDLFDDEIETLRTFDPETQRS 202
Cdd:PRK05298 155 LKMVLSLRVGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPAYYeERAIRIEFFGDEIERISEFDPLTGEV 234
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 203 IDKVDSIRLLPAREFPMQKEEVTR---------------FKA--------RFRER--FDVDFRRsaifqdlASGIIPaGI 257
Cdd:PRK05298 235 LGELDRVTIYPASHYVTPRERLERaiesikeeleerlkeLEKegklleaqRLEQRtrYDLEMLR-------ELGYCS-GI 306
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1442975538 258 E-Y--YL--------PlffeetSTLFDYLPSDTQVF------SLPgveQaaehfwndVRGRYedrRGDLSR 311
Cdd:PRK05298 307 EnYsrHLdgrkpgepP------YTLLDYFPDDFLLFideshvTVP---Q--------IGGMY---NGDRSR 357
|
|
| UvrB |
COG0556 |
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; |
124-226 |
3.13e-14 |
|
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
Pssm-ID: 440322 [Multi-domain] Cd Length: 657 Bit Score: 77.36 E-value: 3.13e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 124 LGSSLVLDVGQTIDVEQMRSRLEATGYRCVDTVYEHGEFAVRGALIDLFPMGS-KLPYRIDLFDDEIETLRTFDPETQRS 202
Cdd:COG0556 152 LKMVLSLRVGEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAYSeERAIRIEFFGDEIERISEFDPLTGEV 231
|
90 100
....*....|....*....|....
gi 1442975538 203 IDKVDSIRLLPAREFPMQKEEVTR 226
Cdd:COG0556 232 LGELDRVTIYPASHYVTPRERLER 255
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
831-907 |
1.36e-13 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 67.24 E-value: 1.36e-13
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1442975538 831 LAELVPEARIGIG--HGQMRERELEQVMSDFYHKRFNVLIASTIIETGIDVPSANTIVIERADkFGLAQLHQLRGRVGR 907
Cdd:smart00490 3 LAELLKELGIKVArlHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-WSPASYIQRIGRAGR 80
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
539-734 |
3.68e-13 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 74.00 E-value: 3.68e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 539 DALAPLHRLGSEAWQKAKRKAAEQVRDV-----AAELLDIYARRAARKGYAFADPAADyatfsagfPFEETPDQQNAIEA 613
Cdd:COG1198 135 RVLEALREHGGPLTLSELAKEAGVSRSVlkalvKKGLLEIEEREVDRDPFAPDVPAEP--------PPTLNEEQQAAVEA 206
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 614 VRADMLAAKPMdrLVCGDVGFGKTEVAMRAAFIAVHSGRQVAVLVPTTLLAQQHYNSFRDRFADWPVtveVM-SRFkSAK 692
Cdd:COG1198 207 IRAAAGGFSVF--LLHGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQTVERFRARFGARVA---VLhSGL-SDG 280
|
170 180 190 200
....*....|....*....|....*....|....*....|....*...
gi 1442975538 693 EVASAAADLAEGKIDILIGThkllqddvR------FKDLGLVVIDEEH 734
Cdd:COG1198 281 ERLDEWRRARRGEARIVIGT--------RsalfapFPNLGLIIVDEEH 320
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
627-909 |
3.73e-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: 73.57 E-value: 3.73e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 627 LVCGDVGFGKTEVAMRAAFIAVHSGRQVAVLVPTTLLAQQHYNSFRDRFADwpvTVEVMSRFKSAKEVASAAADLAEGKI 706
Cdd:TIGR00595 1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGS---QVAVLHSGLSDSEKLQAWRKVKNGEI 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 707 DILIGTHKLLQddVRFKDLGLVVIDEEHRFGVRQKE-------QLKALRSEVDILTL---TATPiprTLNmAVAGMRDLS 776
Cdd:TIGR00595 78 LVVIGTRSALF--LPFKNLGLIIVDEEHDSSYKQEEgpryharDVAVYRAKKFNCPVvlgSATP---SLE-SYHNAKQKA 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 777 IIATPPARRLSVRT--------FVMEHNNSTVKEALLREL---------------------------------------- 808
Cdd:TIGR00595 152 YRLLVLTRRVSGRKppevklidMRKEPRQSFLSPELITAIeqtlaageqsilflnrrgysknllcrscgyilccpncdvs 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 809 ----LRGG--QVYYLHNDVKTIEKCAA------------------DLAELVPEARIGIGHGQM--RERELEQVMSDFYHK 862
Cdd:TIGR00595 232 ltyhKKEGklRCHYCGYQEPIPKTCPQcgsedlvykgygteqveeELAKLFPGARIARIDSDTtsRKGAHEALLNQFANG 311
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*...
gi 1442975538 863 RFNVLIASTIIETGIDVPSANTIVIERAD-----------KFGLAQLHQLRGRVGRSH 909
Cdd:TIGR00595 312 KADILIGTQMIAKGHHFPNVTLVGVLDADsglhspdfraaERGFQLLTQVAGRAGRAE 369
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
600-908 |
8.95e-12 |
|
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: 68.75 E-value: 8.95e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 600 PFEETPDQQNAIEAVRADMLAAKPMdrL---VCGDvgfGKTEVAMRAAFIAVHSGRQVAVLVPTTllaqqhynsfrdrfa 676
Cdd:COG4098 108 EGTLTPAQQKASDELLEAIKKKEEH--LvwaVCGA---GKTEMLFPAIAEALKQGGRVCIATPRV--------------- 167
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 677 DwpVTVEVMSRFKSA-KEVASAA----ADLAEGKIDILIGT-HKLLqddvRFKD-LGLVVIDEEHRFGVRQKEQL----- 744
Cdd:COG4098 168 D--VVLELAPRLQQAfPGVDIAAlyggSEEKYRYAQLVIATtHQLL----RFYQaFDLLIIDEVDAFPYSGDPMLqyavk 241
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 745 KALRSEVDILTLTATPiPRTLNMAVA-GMRDLSIIatpPAR----RLSVRTFVMEHN------NSTVKEALLRELL---- 809
Cdd:COG4098 242 RARKPDGKLIYLTATP-SKALQRQVKrGKLKVVKL---PARyhghPLPVPKFKWLGNwkkrlrRGKLPRKLLKWLKkrlk 317
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 810 RGGQVYYLHNDVKTIEKCAADLAELVPEARIGIGHGQMRERElEQVMsDFYHKRFNVLIASTIIETGIDVPSANTIVIEr 889
Cdd:COG4098 318 EGRQLLIFVPTIELLEQLVALLQKLFPEERIAGVHAEDPERK-EKVQ-AFRDGEIPILVTTTILERGVTFPNVDVAVLG- 394
|
330 340
....*....|....*....|.
gi 1442975538 890 ADK--FGLAQLHQLRGRVGRS 908
Cdd:COG4098 395 ADHpvFTEAALVQIAGRVGRS 415
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
531-734 |
1.47e-11 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 68.64 E-value: 1.47e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 531 IARYTgsddaLAPL-----HRLGSEAWQKAKRKAAEQVrdVAAELLDIYARRAARkgyafadpaADYATFSAGFPFEETP 605
Cdd:PRK05580 84 AADYY-----LSPLgevlrLALLAELALAASSAVLKGL--VKKGLIELEEVEVLR---------LRPPPDPAFEPPTLNP 147
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 606 DQQNAIEAVRADmLAAKPMdrLVCGDVGFGKTEVAMRAafIA--VHSGRQVAVLVPTTLLAQQHYNSFRDRFADWPVtve 683
Cdd:PRK05580 148 EQAAAVEAIRAA-AGFSPF--LLDGVTGSGKTEVYLQA--IAevLAQGKQALVLVPEIALTPQMLARFRARFGAPVA--- 219
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*...
gi 1442975538 684 VM-SRFkSAKEVASAAADLAEGKIDILIGThkllqddvR------FKDLGLVVIDEEH 734
Cdd:PRK05580 220 VLhSGL-SDGERLDEWRKAKRGEAKVVIGA--------RsalflpFKNLGLIIVDEEH 268
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
599-934 |
1.58e-10 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 64.92 E-value: 1.58e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 599 FPFEE-TPDQQnaiEAVRADMLAAKPMdrLVCGDVGFGKTEVAMRAAFIAVHSGRQVAVLVPTTLLAQQHYNSFRDRFAD 677
Cdd:COG1204 18 RGIEElYPPQA---EALEAGLLEGKNL--VVSAPTASGKTLIAELAILKALLNGGKALYIVPLRALASEKYREFKRDFEE 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 678 WPVTVEVMS--RFKSAKEVASAaadlaegkiDILIGT----HKLLQDDVRF-KDLGLVVIDEEHRFGVRQK--------E 742
Cdd:COG1204 93 LGIKVGVSTgdYDSDDEWLGRY---------DILVATpeklDSLLRNGPSWlRDVDLVVVDEAHLIDDESRgptlevllA 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 743 QLKALRSEVDILTLTATpIPrtlNMA-VAGMRDLSIIATP--PARRlsvRTFVMEHNNSTVKE----------ALLRELL 809
Cdd:COG1204 164 RLRRLNPEAQIVALSAT-IG---NAEeIAEWLDAELVKSDwrPVPL---NEGVLYDGVLRFDDgsrrskdptlALALDLL 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 810 R-GGQVYYLHNDVKTIEKCAADLAELVPEARI---------------------------------GIG--HGQM--RERE 851
Cdd:COG1204 237 EeGGQVLVFVSSRRDAESLAKKLADELKRRLTpeereeleelaeellevseethtnekladclekGVAfhHAGLpsELRR 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 852 L-EQVmsdFYHKRFNVLIA-STIIEtGIDVPsANTIVIERADKFGLAQL-----HQLRGRVGRSHH--QAYAYLLTPARQ 922
Cdd:COG1204 317 LvEDA---FREGLIKVLVAtPTLAA-GVNLP-ARRVIIRDTKRGGMVPIpvlefKQMAGRAGRPGYdpYGEAILVAKSSD 391
|
410
....*....|..
gi 1442975538 923 KVSADAEKRLEA 934
Cdd:COG1204 392 EADELFERYILG 403
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
607-760 |
8.07e-10 |
|
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: 58.47 E-value: 8.07e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 607 QQNAIEAvradMLAAKPMDR-LVCGDVGFGKTEVAMrAAFIAVHSGRqVAVLVPTTLLAQQhynsFRDRFADWPVTVEVM 685
Cdd:cd17926 5 QEEALEA----WLAHKNNRRgILVLPTGSGKTLTAL-ALIAYLKELR-TLIVVPTDALLDQ----WKERFEDFLGDSSIG 74
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1442975538 686 sRFKSAKEVASAAADLAEGKIDILIGTHKLLQDdvRFKDLGLVVIDEEHRFGVrqkEQLKALRSEVD---ILTLTATP 760
Cdd:cd17926 75 -LIGGGKKKDFDDANVVVATYQSLSNLAEEEKD--LFDQFGLLIVDEAHHLPA---KTFSEILKELNakyRLGLTATP 146
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
848-917 |
6.73e-09 |
|
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: 53.48 E-value: 6.73e-09
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 848 RERELEQVMSdfyhkRFNVLIASTIIETGIDVPSANTIVIERADKFgLAQLHQLRGRVGRSHHQAYAYLL 917
Cdd:cd18785 12 SIEHAEEIAS-----SLEILVATNVLGEGIDVPSLDTVIFFDPPSS-AASYIQRVGRAGRGGKDEGEVIL 75
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
601-761 |
3.12e-08 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 54.22 E-value: 3.12e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 601 FEETPDQQNAIEAVRAdMLAAKPMDRLVCGDVGFGKTEVAMRAAFIAVHSG--RQVAVLVPTTLLAQQHYNSFRDRFadw 678
Cdd:pfam04851 2 LELRPYQIEAIENLLE-SIKNGQKRGLIVMATGSGKTLTAAKLIARLFKKGpiKKVLFLVPRKDLLEQALEEFKKFL--- 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 679 PVTVEVMsrfksaKEVASAAADLAEGKIDILIGT-HKLLQDDVRFKDL------GLVVIDEEHRFG----VRQKEQLKAL 747
Cdd:pfam04851 78 PNYVEIG------EIISGDKKDESVDDNKIVVTTiQSLYKALELASLEllpdffDVIIIDEAHRSGassyRNILEYFKPA 151
|
170
....*....|....
gi 1442975538 748 RsevdILTLTATPI 761
Cdd:pfam04851 152 F----LLGLTATPE 161
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
627-759 |
1.55e-07 |
|
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: 52.65 E-value: 1.55e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 627 LVCGDVGFGKTEVAMRAAFIAVHSGRQVAV-LVPTTLLAQQHYNSFRDRFADWPVTVEVMSRFKSakevasaAADLAEGK 705
Cdd:cd17921 21 LVSAPTSSGKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFGPLGKNVGLLTGDPS-------VNKLLLAE 93
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1442975538 706 IDILIGT----HKLLQD--DVRFKDLGLVVIDEEHRF-----GVRQKEQLKALR---SEVDILTLTAT 759
Cdd:cd17921 94 ADILVATpeklDLLLRNggERLIQDVRLVVVDEAHLIgdgerGVVLELLLSRLLrinKNARFVGLSAT 161
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
627-760 |
2.16e-06 |
|
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: 49.74 E-value: 2.16e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 627 LVCGDVGFGKTEVAMraaFIAVH------SGRQ--VAVLVPTTLLAQQHYNSFRDRFADWPVTVEVMSRFKSAKEVASAA 698
Cdd:cd17927 21 IICLPTGSGKTFVAV---LICEHhlkkfpAGRKgkVVFLANKVPLVEQQKEVFRKHFERPGYKVTGLSGDTSENVSVEQI 97
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1442975538 699 ADLAegkiDILIGTHKLLQDD------VRFKDLGLVVIDEEHR--------FGVRQ--KEQLKALRSEVDILTLTATP 760
Cdd:cd17927 98 VESS----DVIIVTPQILVNDlksgtiVSLSDFSLLVFDECHNttknhpynEIMFRylDQKLGSSGPLPQILGLTASP 171
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
631-807 |
2.38e-06 |
|
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: 49.59 E-value: 2.38e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 631 DVGFGKT-EVAMRAA-FIAVHSGRQVAVLVPTTLLAQ-QHYnsFRDRFADwpvTVEVMSRFKSAKEVASAAADLAEGKID 707
Cdd:cd18011 25 EVGLGKTiEAGLIIKeLLLRGDAKRVLILCPASLVEQwQDE--LQDKFGL---PFLILDRETAAQLRRLIGNPFEEFPIV 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 708 I----LIGTHKLLQDDVRFKDLGLVVIDEEHRFGVRQKEQ-------LKALRSEVD-ILTLTATPIprtlNMAVAGMRDL 775
Cdd:cd18011 100 IvsldLLKRSEERRGLLLSEEWDLVVVDEAHKLRNSGGGKetkryklGRLLAKRARhVLLLTATPH----NGKEEDFRAL 175
|
170 180 190
....*....|....*....|....*....|..
gi 1442975538 776 SIIATPPARRLSVRTFVMEHNNSTVKEALLRE 807
Cdd:cd18011 176 LSLLDPGRFAVLGRFLRLDGLREVLAKVLLRR 207
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
633-921 |
4.02e-06 |
|
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: 50.51 E-value: 4.02e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 633 GFGKTEVAMRAAFIAVHSGR--QVAVLVPTTLLAQQHYNSFRDRFADWPV--TVEVMSRFKS-------AKEVA----SA 697
Cdd:cd09639 9 GYGKTEAALLWALHSLKSQKadRVIIALPTRATINAMYRRAKEAFGETGLyhSSILSSRIKEmgdseefEHLFPlyihSN 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 698 AADLAEG----KIDILIG--THKLLQDDVRFKDLG--LVVIDEEHRFGVRQKEQLKAL-----RSEVDILTLTATpIP-- 762
Cdd:cd09639 89 DTLFLDPitvcTIDQVLKsvFGEFGHYEFTLASIAnsLLIFDEVHFYDEYTLALILAVlevlkDNDVPILLMSAT-LPkf 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 763 -RTLNMAVAGMRDLSIIATPPARRLSVRTFVMEHN-NSTVKEALLRELLRGGQVYYLHNDVKTIEKCAADLAELVPEARI 840
Cdd:cd09639 168 lKEYAEKIGYVEENEPLDLKPNERAPFIKIESDKVgEISSLERLLEFIKKGGSVAIIVNTVDRAQEFYQQLKEKGPEEEI 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 841 GIGHGQM----RERELEQVMSDFYHKRFNVLIASTIIETGIDVpSANTIVIERADkfgLAQLHQLRGRVGRsHHQAYA-- 914
Cdd:cd09639 248 MLIHSRFtekdRAKKEAELLLEFKKSEKFVIVATQVIEASLDI-SVDVMITELAP---IDSLIQRLGRLHR-YGEKNGee 322
|
....*...
gi 1442975538 915 -YLLTPAR 921
Cdd:cd09639 323 vYIITDAP 330
|
|
| SF2_C_dicer |
cd18802 |
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
840-904 |
5.46e-06 |
|
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: 47.20 E-value: 5.46e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1442975538 840 IGIGHGQ------MRERELEQVMSDFYHKRFNVLIASTIIETGIDVPSANTIVieradKFGLA----QLHQLRGR 904
Cdd:cd18802 61 IGRGNSSqrkrslMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVI-----RFDLPktlrSYIQSRGR 130
|
|
| DEXHc_RLR |
cd18036 |
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
627-760 |
7.82e-06 |
|
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: 48.24 E-value: 7.82e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 627 LVCGDVGFGKTEVAMRAA------FIAVHSGRQVAVLVPTTLLAQQHYNSFRDRFADWpvtVEVMSrFKSAKEVASAAAD 700
Cdd:cd18036 21 IICAPTGSGKTRVAVYICrhhlekRRSAGEKGRVVVLVNKVPLVEQQLEKFFKYFRKG---YKVTG-LSGDSSHKVSFGQ 96
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1442975538 701 LAEGKiDILIGTHKLLQ---------DDVRFKDLGLVVIDE------EHRFGV----RQKEQLKALRSEVDILTLTATP 760
Cdd:cd18036 97 IVKAS-DVIICTPQILInnllsgreeERVYLSDFSLLIFDEchhtqkEHPYNKimrmYLDKKLSSQGPLPQILGLTASP 174
|
|
| SF2_C_XPB |
cd18789 |
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
795-887 |
1.36e-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: 46.47 E-value: 1.36e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 795 HNNSTVKEALLRELLR----GGQVYYLHNDVKTIEKCAADLaeLVPeariGIgHGQMRERELEQVMSDFYHKRFNVLIAS 870
Cdd:cd18789 29 AAMNPNKLRALEELLKrheqGDKIIVFTDNVEALYRYAKRL--LKP----FI-TGETPQSEREEILQNFREGEYNTLVVS 101
|
90
....*....|....*..
gi 1442975538 871 TIIETGIDVPSANTIVI 887
Cdd:cd18789 102 KVGDEGIDLPEANVAIQ 118
|
|
| DEXHc_Hef |
cd18035 |
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
621-760 |
2.02e-05 |
|
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: 46.35 E-value: 2.02e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 621 AKPMDRLVCGDVGFGKTEVA-MRAAFIAVHSGRQVAVLVPTTLLAQQHYNSFRdRFADWPVTVEVMSRFKSAKEVASAAA 699
Cdd:cd18035 14 ALNGNTLIVLPTGLGKTIIAiLVAADRLTKKGGKVLILAPSRPLVEQHAENLK-RVLNIPDKITSLTGEVKPEERAERWD 92
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1442975538 700 dlaegKIDILIGTHKLLQDD-----VRFKDLGLVVIDEEHRFG-----VRQKEQLKALRSEVDILTLTATP 760
Cdd:cd18035 93 -----ASKIIVATPQVIENDllagrITLDDVSLLIFDEAHHAVgnyayVYIAHRYKREANNPLILGLTASP 158
|
|
| SNF2-rel_dom |
pfam00176 |
SNF2-related domain; This domain is found in proteins involved in a variety of processes ... |
627-766 |
7.29e-05 |
|
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: 46.14 E-value: 7.29e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 627 LVCGDVGFGKT--EVAMRAAFIAVHS--GRQVAVLVPTTLLaQQHYNSFrDRFADWP-VTVEVMSRFKSAKEVASAAADL 701
Cdd:pfam00176 21 ILADEMGLGKTlqTISLLLYLKHVDKnwGGPTLIVVPLSLL-HNWMNEF-ERWVSPPaLRVVVLHGNKRPQERWKNDPNF 98
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1442975538 702 AeGKIDILIGT-HKLLQDDVRFK--DLGLVVIDEEHRF-GVRQK--EQLKALRSEVDILtLTATPIPRTLN 766
Cdd:pfam00176 99 L-ADFDVVITTyETLRKHKELLKkvHWHRIVLDEGHRLkNSKSKlsKALKSLKTRNRWI-LTGTPLQNNLE 167
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
612-759 |
9.83e-05 |
|
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: 44.25 E-value: 9.83e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 612 EAVRADMLAAKPMdrLVCGDVGFGKTEVAMRAAFIAVHSGRQVAVLVPTTLLAQQHYNSFRDrfadwpvtvevmsRFKSA 691
Cdd:cd18028 8 EAVRAGLLKGENL--LISIPTASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEEFKK-------------LEEIG 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 692 KEVASAAADLAE-----GKIDILIGTHKLLQDDVRFK-----DLGLVVIDEEHRFGVRQK--------EQLKALRSEVDI 753
Cdd:cd18028 73 LKVGISTGDYDEddewlGDYDIIVATYEKFDSLLRHSpswlrDVGVVVVDEIHLISDEERgptlesivARLRRLNPNTQI 152
|
....*.
gi 1442975538 754 LTLTAT 759
Cdd:cd18028 153 IGLSAT 158
|
|
| PRK01172 |
PRK01172 |
ATP-dependent DNA helicase; |
598-931 |
1.48e-04 |
|
ATP-dependent DNA helicase;
Pssm-ID: 100801 [Multi-domain] Cd Length: 674 Bit Score: 46.03 E-value: 1.48e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 598 GFPFEETPDQQNAIEAVRadmlaaKPMDRLVCGDVGFGKTEVAMRAAFIAVHSGRQVAVLVPTTLLAQQHYNSF-RDRFA 676
Cdd:PRK01172 18 GNDFELYDHQRMAIEQLR------KGENVIVSVPTAAGKTLIAYSAIYETFLAGLKSIYIVPLRSLAMEKYEELsRLRSL 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 677 DWPVTVEVMSRFKSAKEVASA-AADLAEGKIDILIgtHkllQDDVRFKDLGLVVIDEEHRFGVRQK--------EQLKAL 747
Cdd:PRK01172 92 GMRVKISIGDYDDPPDFIKRYdVVILTSEKADSLI--H---HDPYIINDVGLIVADEIHIIGDEDRgptletvlSSARYV 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 748 RSEVDILTLTATPiprTLNMAVAGMRDLSIIAT---PPARRLSV----RTFVMEHNNSTVKE-ALLRELLR-GGQVYYLH 818
Cdd:PRK01172 167 NPDARILALSATV---SNANELAQWLNASLIKSnfrPVPLKLGIlyrkRLILDGYERSQVDInSLIKETVNdGGQVLVFV 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 819 NDVKTIEKCAADLAELVPE---------------------ARIGIG--HGQMRERELEQVMSDFYHKRFNVLIASTIIET 875
Cdd:PRK01172 244 SSRKNAEDYAEMLIQHFPEfndfkvssennnvyddslnemLPHGVAfhHAGLSNEQRRFIEEMFRNRYIKVIVATPTLAA 323
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1442975538 876 GIDVPSANTIV--IERADKFGLA-----QLHQLRGRVGRSHHQAYAYLLTPARQKVSADAEKR 931
Cdd:PRK01172 324 GVNLPARLVIVrdITRYGNGGIRylsnmEIKQMIGRAGRPGYDQYGIGYIYAASPASYDAAKK 386
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
619-760 |
2.30e-04 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 45.49 E-value: 2.30e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 619 LAAKPMDR--LVCGDVGFGKTEVA-MRAAFIAVHSGRQVAVLVPTTLLAQQHYNSFRDRFADWPVTVEVMSrfksaKEVA 695
Cdd:COG1111 11 LAASALRKntLVVLPTGLGKTAVAlLVIAERLHKKGGKVLFLAPTKPLVEQHAEFFKEALNIPEDEIVVFT-----GEVS 85
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1442975538 696 SAAADLAEGKIDILIGTHKLLQDD-----VRFKDLGLVVIDEEHR-FG----VRQKEQLKALRSEVDILTLTATP 760
Cdd:COG1111 86 PEKRKELWEKARIIVATPQVIENDliagrIDLDDVSLLIFDEAHRaVGnyayVYIAERYHEDAKDPLILGMTASP 160
|
|
| DEXHc_Snf |
cd17919 |
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
631-762 |
2.48e-04 |
|
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins 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: 350677 [Multi-domain] Cd Length: 182 Bit Score: 43.32 E-value: 2.48e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 631 DVGFGKTevAMRAAFIAV-----HSGRQVAVLVPTTLLAQqhynsFRDRFADWPVTVEVMSRFKSAKEVASAAADLAEGK 705
Cdd:cd17919 27 EMGLGKT--LQAIAFLAYllkegKERGPVLVVCPLSVLEN-----WEREFEKWTPDLRVVVYHGSQRERAQIRAKEKLDK 99
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1442975538 706 IDILIGTHKLLQDDVRF---KDLGLVVIDEEHRF---GVRQKEQLKALRSEVDILtLTATPIP 762
Cdd:cd17919 100 FDVVLTTYETLRRDKASlrkFRWDLVVVDEAHRLknpKSQLSKALKALRAKRRLL-LTGTPLQ 161
|
|
| SF2_C_FANCM_Hef |
cd18801 |
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
847-917 |
7.77e-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: 41.19 E-value: 7.77e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1442975538 847 MRERELEQVMSDFYHKRFNVLIASTIIETGIDVPSANTIVIERADKFGLAQLhQLRGRVGRsHHQAYAYLL 917
Cdd:cd18801 74 MSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMI-QRMGRTGR-KRQGRVVVL 142
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| DEXHc_RLR-3 |
cd18075 |
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ... |
633-760 |
2.60e-03 |
|
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: 40.61 E-value: 2.60e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 633 GFGKTEVAMRAA--FIAVHSGRQVAVLVPTTLLAQQHYNSFRdRFADWPVTVEVMSRFKSAKevaSAAADLAEGKiDILI 710
Cdd:cd18075 27 GAGKTRAAVYVArrHLETKRGAKVAVLVNKVHLVDQHLEKEF-HVLLDKYTVTAISGDSSHK---CFFGQLARGS-DVVI 101
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90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1442975538 711 GTHKLLQD---------DVRFKDLGLVVIDE---EHRFGVRQKEQLKALRSEV-------DILTLTATP 760
Cdd:cd18075 102 CTAQILQNallsgeeeaHVELTDFSLLVIDEchhTHKEAVYNKIMLSYLEKKLsrqgdlpQILGLTASP 170
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| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
620-761 |
3.70e-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: 39.94 E-value: 3.70e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 620 AAKPMDRLVCGDVGFGKTEVA------MRAAFIAVHSGRQVAV-LVPTTLLAQQHYNSFRDRFadwPVTVEVMSRFKSAK 692
Cdd:cd18034 13 AALKRNTIVVLPTGSGKTLIAvmlikeMGELNRKEKNPKKRAVfLVPTVPLVAQQAEAIRSHT---DLKVGEYSGEMGVD 89
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90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 693 EVASAAADLAEGKIDILIGTHKLLQD-----DVRFKDLGLVVIDE------EHRFGVRQKEQLKALRSEV--DILTLTAT 759
Cdd:cd18034 90 KWTKERWKEELEKYDVLVMTAQILLDalrhgFLSLSDINLLIFDEchhatgDHPYARIMKEFYHLEGRTSrpRILGLTAS 169
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..
gi 1442975538 760 PI 761
Cdd:cd18034 170 PV 171
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| SF2_C_EcoAI-like |
cd18799 |
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ... |
815-889 |
4.42e-03 |
|
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family is composed of helicase restriction enzymes, including the HsdR subunit of restriction-modification enzymes such as Escherichia coli type I restriction enzyme EcoAI R protein (R.EcoAI). The EcoAI enzyme recognizes 5'-GAGN(7)GTCA-3'. The HsdR or R subunit is required for both nuclease and ATPase activities, but not for modification. These proteins 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: 350186 [Multi-domain] Cd Length: 116 Bit Score: 38.31 E-value: 4.42e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 815 YYLHNDVKTIEKC-----AADLAELVPEA---RIGIGHGQ-MRERELEQVMSDFYHK-RFNVLIASTIIETGIDVPSANT 884
Cdd:cd18799 1 PYKYVEIKTLIFCvsiehAEFMAEAFNEAgidAVALNSDYsDRERGDEALILLFFGElKPPILVTVDLLTTGVDIPEVDN 80
|
....*
gi 1442975538 885 IVIER 889
Cdd:cd18799 81 VVFLR 85
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|
| DDXDc_reverse_gyrase |
cd17924 |
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
633-731 |
4.85e-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: 39.62 E-value: 4.85e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 633 GFGKTEVAMRAAFIAVHSGRQVAVLVPTTLLAQQHYNSFRD--RFADWPVTVEVMSRFKSAKEVASAAADLAEGKIDILI 710
Cdd:cd17924 42 GVGKTTFGLATSLYLASKGKRSYLIFPTKSLVKQAYERLSKyaEKAGVEVKILVYHSRLKKKEKEELLEKIEKGDFDILV 121
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90 100
....*....|....*....|....
gi 1442975538 711 GTHKLLQDDVRF---KDLGLVVID 731
Cdd:cd17924 122 TTNQFLSKNFDLlsnKKFDFVFVD 145
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
824-918 |
7.49e-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: 39.54 E-value: 7.49e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1442975538 824 IEKCAADLAELVPEARIGIghgqM------RERELEQVMSDFYHKRFNVLIASTIIETGIDVPSANTIVIERADkFGL-- 895
Cdd:cd18804 103 TERVEEELKTLFPEARIAR----IdrdttrKKGALEKLLDQFERGEIDILIGTQMIAKGLDFPNVTLVGILNAD-SGLns 177
|
90 100 110
....*....|....*....|....*....|...
gi 1442975538 896 ---------AQL-HQLRGRVGRSHHQAYAYLLT 918
Cdd:cd18804 178 pdfraseraFQLlTQVSGRAGRGDKPGKVIIQT 210
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