|
Name |
Accession |
Description |
Interval |
E-value |
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
1-1147 |
0e+00 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 2436.44 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 1 MPEQYRYSLPAKAGDLRQLGELTGAACATLVAEMAERHKGPVVLVAPDMQNALRLNDEIRQFTDSMVMGLADWETLPYDS 80
Cdd:PRK10689 1 MPEQYRYTLPVKAGDQRQLGELTGAACATEVAEIAERHAGPVVLIAPDMQNALRLHDEIQQFTDQMVMNLADWETLPYDS 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 81 FSPHQDIISSRLATLYQLPTMQRGVLIVPVSTLMQRVCPHSFLHGHALVMKKGQRLSRDALRDQLEGAGYRHVDQVMEHG 160
Cdd:PRK10689 81 FSPHQDIISSRLSTLYQLPTMQRGVLILPVNTLMQRVCPHSFLHGHALVMKKGQRLSRDALRAQLEQAGYRHVDQVMEHG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 161 EYATRGALLDLFPMGSDQPYRLDFFDDEIDSLRLFDVDSQRTLEEVAAINLLPAHEFPTDQTAIELFRSQWRDRFEVKRD 240
Cdd:PRK10689 161 EYATRGALLDLFPMGSEEPYRIDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFEVKRD 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 241 AEHIYQQVSKGTLPAGIEYWQPLFFSEPLPPLFSYFPASTLIVNTGDLEASAERFQNEARARFENRGVDPMRPLLPPELL 320
Cdd:PRK10689 241 AEHIYQQVSKGTLPAGIEYWQPLFFSEPLPPLFSYFPANTLLVNTGDLETSAERFWADTLARFENRGVDPMRPLLPPESL 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 321 WLRSDELFGELKKWPRVQLKTERLADKAANTNLGYQTLPDLAVQAQNKAPLDNLRRFLESFTGPVIFSVESEGRREALSE 400
Cdd:PRK10689 321 WLRVDELFSELKNWPRVQLKTEHLPTKAANTNLGYQKLPDLAVQAQQKAPLDALRRFLESFDGPVVFSVESEGRREALGE 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 401 MLARIKIAPKHVLRLEEATGNGRYLMIGAAEHGFIDSQRGLALICESDLLGERVARRRQDSRRTINPDILIRNLAELHIG 480
Cdd:PRK10689 401 LLARIKIAPKRIMRLDEASDRGRYLMIGAAEHGFIDTVRNLALICESDLLGERVARRRQDSRRTINPDTLIRNLAELHPG 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 481 QPVVHLEHGVGRYAGMTTLEAGGITGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHKLGGDAWTRARQKAAEK 560
Cdd:PRK10689 481 QPVVHLEHGVGRYAGMTTLEAGGIKGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHKLGGDAWSRARQKAAEK 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 561 VRDVAAELLDIYAQRAAKAGFAFKHDREQYQLFCDGFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMR 640
Cdd:PRK10689 561 VRDVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMR 640
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 641 AAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQAQILEQAAEGKIDILIGTHKLLQSEVKL 720
Cdd:PRK10689 641 AAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKW 720
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 721 RDLGLLIVDEEHRFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDALVVRE 800
Cdd:PRK10689 721 KDLGLLIVDEEHRFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSLVVRE 800
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 801 AILRETLRGGQVYYLFNDVENIQKAADKLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTA 880
Cdd:PRK10689 801 AILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTA 880
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 881 NTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLG 960
Cdd:PRK10689 881 NTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLG 960
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 961 EDQSGQMETIGFSLYMELLENAVDALKAGREPSLEDLTSQQTEVELRMPSLLPDDFIPDVNTRLSFYKRIASAKNELDLE 1040
Cdd:PRK10689 961 EEQSGQMETIGFSLYMELLENAVDALKAGREPSLEDLTSQQTEVELRMPSLLPDDFIPDVNTRLSFYKRIASAKNENELE 1040
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 1041 EIKVELIDRFGRLPDAARNLLDIARLRQQAQKLGIRKLESNEKGGVIEFNEKNNVNPVWLIGLLQKQPQHFRLDGPTRLK 1120
Cdd:PRK10689 1041 EIKVELIDRFGLLPDPARNLLDIARLRQQAQKLGIRKLEGNEKGGFIEFAEKNHVDPAWLIGLLQKQPQHYRLDGPTRLK 1120
|
1130 1140
....*....|....*....|....*..
gi 1460644633 1121 FMQDLEERKTRMDWVRQFMRQLEENAV 1147
Cdd:PRK10689 1121 FIQDLSERKTRIEWVRQFMRELEENAI 1147
|
|
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
13-1148 |
0e+00 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 1834.31 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 13 AGDLRQLGELTGAACATLVAEMAERHKGPVVLVAPDMQNALRLNDEIRQFTDSM-VMGLADWETLPYDSFSPHQDIISSR 91
Cdd:COG1197 1 GGGRLTLSGLPGSARALLLAALARALGRPLLVVTADEREAERLAEDLRFFLPDLpVLLFPAWETLPYDRFSPSPDIVSER 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 92 LATLYQLPTMQRGVLIVPVSTLMQRVCPHSFLHGHALVMKKGQRLSRDALRDQLEGAGYRHVDQVMEHGEYATRGALLDL 171
Cdd:COG1197 81 LATLRRLASGKPGIVVTPVRALLQRLPPPELLAAASLSLKVGDELDLEELRERLVAAGYERVDQVEEPGEFAVRGGILDI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 172 FPMGSDQPYRLDFFDDEIDSLRLFDVDSQRTLEEVAAINLLPAHEFPTDQTAIELFRSQWRDRFEVKRDAEHIYQQVSKG 251
Cdd:COG1197 161 FPPGSEHPVRIEFFGDEIESIRTFDPETQRSLEKVDEVELLPAREFPLDEEAIERFRERLRELFGLDPKLDELYEALSEG 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 252 TLPAGIEYWQPLFFSEpLPPLFSYFPASTLIVNTG--DLEASAERFQNEARARFENRGVDPMRPLLPPELLWLRSDELFG 329
Cdd:COG1197 241 IAFAGIEYYLPLFYEE-LATLFDYLPEDALVVLDEpeRIEEAAEEFWEEIEERYEARRHDRGRPLLPPEELFLDPEELFA 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 330 ELKKWPRVQLKT-ERLADKAANTNLGYQTLPDlaVQAQNKAPLDNLRRFLESfTGPVIFSVESEGRREALSEMLARIKIA 408
Cdd:COG1197 320 ALKRRPRVTLSPfAALPEGAGVVNLGARPLPS--FAGQLEALLEELKRLLKD-GGRVLLAAESEGRRERLLELLRDHGIP 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 409 PKHVLRLEEATGNGRYLMIGAAEHGFIDSQRGLALICESDLLGERVARRRQdsRRTINPDILIRNLAELHIGQPVVHLEH 488
Cdd:COG1197 397 ARLVESLAELSPGGVAITVGPLEHGFELPDAKLAVITESELFGERVKRRRR--KKKRSADAFIRDLSELKPGDYVVHVDH 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 489 GVGRYAGMTTLEAGGITGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHKLGGDAWTRARQKAAEKVRDVAAEL 568
Cdd:COG1197 475 GIGRYLGLETLEVGGAERDYLVLEYAGGDKLYVPVDQLDLISRYVGSEGEAPKLDKLGGSDWQKAKAKAKKAVRDIAAEL 554
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 569 LDIYAQRAAKAGFAFKHDREQYQLFCDGFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVEN 648
Cdd:COG1197 555 LKLYAERAARKGFAFSPDTPWQREFEAAFPYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKTEVALRAAFKAVMD 634
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 649 HKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQAQILEQAAEGKIDILIGTHKLLQSEVKLRDLGLLIV 728
Cdd:COG1197 635 GKQVAVLVPTTLLAQQHYETFKERFAGFPVRVEVLSRFRTAKEQKETLEGLADGKVDIVIGTHRLLSKDVKFKDLGLLII 714
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 729 DEEHRFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDALVVREAILRETLR 808
Cdd:COG1197 715 DEEQRFGVRHKEKLKALRANVDVLTLTATPIPRTLQMSLSGIRDLSIIATPPEDRLPVKTFVGEYDDALIREAILRELLR 794
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 809 GGQVYYLFNDVENIQKAADKLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERA 888
Cdd:COG1197 795 GGQVFYVHNRVEDIEKVAARLQELVPEARIAVAHGQMSERELERVMLDFYEGEFDVLVCTTIIETGIDIPNANTIIIERA 874
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 889 DHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGEDQSGQME 968
Cdd:COG1197 875 DRFGLAQLYQLRGRVGRSHRRAYAYLLYPPDKVLTEDAEKRLEAIQEFTELGAGFKLAMHDLEIRGAGNLLGEEQSGHIA 954
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 969 TIGFSLYMELLENAVDALKAGREPSLEdltsQQTEVELRMPSLLPDDFIPDVNTRLSFYKRIASAKNELDLEEIKVELID 1048
Cdd:COG1197 955 EVGFDLYLQMLEEAVAALKGGKEPEEE----WEPEINLGVPALIPEDYIPDVRQRLELYKRIASAESEEELDELQEELID 1030
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 1049 RFGRLPDAARNLLDIARLRQQAQKLGIRKLESNEKGGVIEFNEKNNVNPVWLIGLLQKQPQHFRLDGPTRLKFMQDLEER 1128
Cdd:COG1197 1031 RFGPLPEEVENLLAVARLKLLARRLGIEKIDAGGKGIRIEFSPNTPLDPEKLIRLIQKQPGRYKLDGDDKLVITLDLEDP 1110
|
1130 1140
....*....|....*....|
gi 1460644633 1129 KTRMDWVRQFMRQLEENAVA 1148
Cdd:COG1197 1111 EERLEALEELLEALAKLAKE 1130
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
148-1079 |
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: 1321.59 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 148 AGYRHVDQVMEHGEYATRGALLDLFPMGSDQPYRLDFFDDEIDSLRLFDVDSQRTLEEVAAINLLPAHEFpTDQTAIELF 227
Cdd:TIGR00580 4 LGYERVDLVEEEGEFSVRGEILDIFPPGSELPVRIEFFGDEIESIREFDVDSQRSLEELLEITILPAKEF-ILLEEETIA 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 228 RSQWRDRFEVKRDAEHIYQQVSKGTLPAGIEYWQPLFFSEPlPPLFSYFPASTLIV-NTGDLEASAERFQNEARARFENR 306
Cdd:TIGR00580 83 RLKDNAARVEDAKHLETIEALSEGTLPAGEEMFLPLFFEDL-SSLFDYLPDNTPILlDDPERFHSAARFLQRELEEFYNA 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 307 GVDPMRPLLPPELLWlRSDELFGELKKW--PRVQLKTERLADKAANTNLGYQTLPDLAVQAQNKAPLDNLRRFLESFTGP 384
Cdd:TIGR00580 162 LEEAKKLINPPRLDL-DPSELAFEASAIslSRVQLENEHLSLKASEAIEGAQKHSRLEFGEILAFKEELFRWLKAGFKIT 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 385 VIFsvESEGRREALSEMLARIKIAPKHVLRLEEATGNGRYLMIGAAEHGFIDSQRGLALICESDLLGERVARRRQDSRRT 464
Cdd:TIGR00580 241 VAA--ESESQAERLKSLLAEHDIAAQVIDESCIIIPAVRYVMIGALSSGFILPTAGLAVITESELFGSRVLRRPKKSRLK 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 465 INPdilIRNLAELHIGQPVVHLEHGVGRYAGMTTLEAGGITGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHK 544
Cdd:TIGR00580 319 SKP---IESLNELNPGDYVVHLDHGIGRFLGLETLEVGGIERDYLVLEYAGEDKLYVPVEQLHLISRYVGGSGKNPALDK 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 545 LGGDAWTRARQKAAEKVRDVAAELLDIYAQRAAKAGFAFKHDREQYQLFCDGFPFETTPDQAQAINAVLSDMCQPLAMDR 624
Cdd:TIGR00580 396 LGGKSWEKTKAKVKKSVREIAAKLIELYAKRKAIKGHAFPPDLEWQQEFEDSFPFEETPDQLKAIEEIKADMESPRPMDR 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 625 LVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQAQILEQAAEGKI 704
Cdd:TIGR00580 476 LVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKI 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 705 DILIGTHKLLQSEVKLRDLGLLIVDEEHRFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRL 784
Cdd:TIGR00580 556 DILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPEDRL 635
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 785 AVKTFVREYDALVVREAILRETLRGGQVYYLFNDVENIQKAADKLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNV 864
Cdd:TIGR00580 636 PVRTFVMEYDPELVREAIRRELLRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQV 715
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 865 LVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFA 944
Cdd:TIGR00580 716 LVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDAQKRLEAIQEFSELGAGFK 795
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 945 LATHDLEIRGAGELLGEDQSGQMETIGFSLYMELLENAVDALKAGREPSLEdltsQQTEVELRMPSLLPDDFIPDVNTRL 1024
Cdd:TIGR00580 796 IALHDLEIRGAGNLLGEEQSGHIESIGFDLYMELLEEAIEELKGGKPPKLE----EETDIELPYSAFIPDDYIADDSLRL 871
|
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|....*
gi 1460644633 1025 SFYKRIASAKNELDLEEIKVELIDRFGRLPDAARNLLDIARLRQQAQKLGIRKLE 1079
Cdd:TIGR00580 872 EFYKRIASAETEEELEKIRDELIDRFGPLPEEARTLLDVARLKLLARKLGIRKLK 926
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
568-968 |
5.85e-125 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 399.04 E-value: 5.85e-125
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 568 LLDIYAQRAAKAGFAFKHDREQYQLFCDGFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVE 647
Cdd:COG1200 227 LLLRRARRRKRKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVE 306
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 648 NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQAQILEQAAEGKIDILIGTHKLLQSEVKLRDLGLLI 727
Cdd:COG1200 307 AGYQAALMAPTEILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVV 386
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 728 VDEEHRFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVR---EYDALVvrEAILR 804
Cdd:COG1200 387 IDEQHRFGVEQRLALREKGEAPHVLVMTATPIPRTLAMTLYGDLDVSVIDELPPGRKPIKTRVVpeeRRDEVY--ERIRE 464
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 805 ETLRGGQVYYLF--------NDVENIQKAADKLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGID 876
Cdd:COG1200 465 EIAKGRQAYVVCplieesekLDLQAAEETYEELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGVD 544
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 877 IPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPkaMTTDAQKRLEAIASLEDlgaGFALATHDLEIRGAG 956
Cdd:COG1200 545 VPNATVMVIENAERFGLSQLHQLRGRVGRGSAQSYCLLLYDAP--LSETARERLEVMRETND---GFEIAEEDLELRGPG 619
|
410
....*....|..
gi 1460644633 957 ELLGEDQSGQME 968
Cdd:COG1200 620 EFLGTRQSGLPD 631
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
586-778 |
3.84e-123 |
|
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: 376.14 E-value: 3.84e-123
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 586 DREQYQLFCDGFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQH 665
Cdd:cd17991 1 DGEEQEEFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 666 YDNFRDRFANWPVRIEMLSRFRSAKEQAQILEQAAEGKIDILIGTHKLLQSEVKLRDLGLLIVDEEHRFGVRHKERIKAM 745
Cdd:cd17991 81 YETFKERFANFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQKEKLKEL 160
|
170 180 190
....*....|....*....|....*....|...
gi 1460644633 746 RADVDILTLTATPIPRTLNMAMSGMRDLSIIAT 778
Cdd:cd17991 161 RPNVDVLTLSATPIPRTLHMALSGIRDLSVIAT 193
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
573-965 |
7.95e-122 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 390.67 E-value: 7.95e-122
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 573 AQRAAKAGFAFKHDREQYQLFCDGFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQV 652
Cdd:PRK10917 234 AGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGYQA 313
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 653 AVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQAQILEQAAEGKIDILIGTHKLLQSEVKLRDLGLLIVDEEH 732
Cdd:PRK10917 314 ALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIIDEQH 393
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 733 RFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVR---EYDALVvrEAILRETLRG 809
Cdd:PRK10917 394 RFGVEQRLALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIpdsRRDEVY--ERIREEIAKG 471
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 810 GQVY--Y--------LfnDVENIQKAADKLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPT 879
Cdd:PRK10917 472 RQAYvvCplieesekL--DLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPN 549
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 880 ANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKamTTDAQKRLEAIASLEDlgaGFALATHDLEIRGAGELL 959
Cdd:PRK10917 550 ATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPL--SETARERLKIMRETND---GFVIAEKDLELRGPGELL 624
|
....*.
gi 1460644633 960 GEDQSG 965
Cdd:PRK10917 625 GTRQSG 630
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
598-965 |
1.13e-113 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 367.44 E-value: 1.13e-113
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 598 PFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWP 677
Cdd:TIGR00643 233 PFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLAPLG 312
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 678 VRIEMLSRFRSAKEQAQILEQAAEGKIDILIGTHKLLQSEVKLRDLGLLIVDEEHRFGVRHKERIKAM---RADVDILTL 754
Cdd:TIGR00643 313 IEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLREKgqgGFTPHVLVM 392
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 755 TATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFV-REYDALVVREAILRETLRGGQVYY---LFNDVENIQ-KAAD-- 827
Cdd:TIGR00643 393 SATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLiKHDEKDIVYEFIEEEIAKGRQAYVvypLIEESEKLDlKAAEal 472
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 828 --KLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGR 905
Cdd:TIGR00643 473 yeRLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGR 552
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 906 SHHQAYAWLLTPHPKamTTDAQKRLEAIASLEDlgaGFALATHDLEIRGAGELLGEDQSG 965
Cdd:TIGR00643 553 GDHQSYCLLVYKNPK--SESAKKRLRVMADTLD---GFVIAEEDLELRGPGDLLGTKQSG 607
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
785-935 |
7.72e-84 |
|
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: 268.83 E-value: 7.72e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 785 AVKTFVREYDALVVREAILRETLRGGQVYYLFNDVENIQKAADKLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNV 864
Cdd:cd18810 1 PVRTYVMPYDDELIREAIERELLRGGQVFYVHNRIESIEKLATQLRQLVPEARIAIAHGQMTENELEEVMLEFAKGEYDI 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1460644633 865 LVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIAS 935
Cdd:cd18810 81 LVCTTIIESGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAYFLYPDQKKLTEDALKRLEAIQE 151
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
586-777 |
1.26e-82 |
|
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: 266.59 E-value: 1.26e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 586 DREQYQLFCDGFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQH 665
Cdd:cd17918 1 DRALIQELCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 666 YDNFRDRFAnwPVRIEMLSRFRsakeQAQILEQaaegkIDILIGTHKLLQSEVKLRDLGLLIVDEEHRFGVRHKERIKAM 745
Cdd:cd17918 81 YEEARKFLP--FINVELVTGGT----KAQILSG-----ISLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNL 149
|
170 180 190
....*....|....*....|....*....|..
gi 1460644633 746 RAdVDILTLTATPIPRTLNMAMSGMRDLSIIA 777
Cdd:cd17918 150 GA-THFLEATATPIPRTLALALSGLLDLSVID 180
|
|
| SF2_C_RecG_TRCF |
cd18792 |
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
785-935 |
3.12e-71 |
|
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: 234.08 E-value: 3.12e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 785 AVKTFVREYD-ALVVREAILRETLRGGQVYYLFN--------DVENIQKAADKLAELVPEARIAIGHGQMRERELERVMN 855
Cdd:cd18792 1 PIRTYVIPHDdLDLVYEAIERELARGGQVYYVYPrieeseklDLKSIEALAEELKELVPEARVALLHGKMTEDEKEAVML 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 856 DFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIAS 935
Cdd:cd18792 81 EFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYPDPKKLTETAKKRLRAIAE 160
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
568-780 |
2.49e-67 |
|
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: 225.87 E-value: 2.49e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 568 LLDIYAQRAAKAGFAFKHDREQYQLFCDGFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVE 647
Cdd:cd17992 13 LLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKTVVAALAMLAAVE 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 648 NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQAQILEQAAEGKIDILIGTHKLLQSEVKLRDLGLLI 727
Cdd:cd17992 93 NGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQEDVEFHNLGLVI 172
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 1460644633 728 VDEEHRFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPP 780
Cdd:cd17992 173 IDEQHRFGVEQRLKLREKGETPHVLVMTATPIPRTLALTLYGDLDVSIIDELP 225
|
|
| CarD_TRCF |
smart01058 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
476-573 |
5.45e-44 |
|
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: 154.53 E-value: 5.45e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 476 ELHIGQPVVHLEHGVGRYAGMTTLEAGGITGEYLMLTYANDAKLYVPVSSLHLISRYAGG-AEENAPLHKLGGDAWTRAR 554
Cdd:smart01058 1 ELKIGDYVVHPDHGVGRYEGIETIEVGGEKREYLVLEYAGGDKLYVPVDNLDLGSRYVGSeGEVEPVLDKLGGGSWSKRK 80
|
90
....*....|....*....
gi 1460644633 555 QKAAEKVRDVAAELLDIYA 573
Cdd:smart01058 81 RKAKSGIRDIAAELLRLYA 99
|
|
| TRCF |
smart00982 |
This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in ... |
1005-1104 |
2.37e-40 |
|
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: 144.14 E-value: 2.37e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 1005 ELRMPSLLPDDFIPDVNTRLSFYKRIASAKNELDLEEIKVELIDRFGRLPDAARNLLDIARLRQQAQKLGIRKLESNEKG 1084
Cdd:smart00982 1 DLPVPALIPEDYIPDVRQRLELYKRIASAETEEELDEIQEELIDRFGPLPEEVKNLLEVARLKLLAKKLGIEKIDAGGKG 80
|
90 100
....*....|....*....|
gi 1460644633 1085 GVIEFNEKNNVNPVWLIGLL 1104
Cdd:smart00982 81 IVIEFSPDTPIDPEKLILLI 100
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
798-935 |
9.71e-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: 139.02 E-value: 9.71e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 798 VREAILRETLRGGQVYYLFNDVENIQ----KAADKLAE-----LVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCT 868
Cdd:cd18811 15 VYEFVREEIAKGRQAYVIYPLIEESEkldlKAAVAMYEylkerFRPELNVGLLHGRLKSDEKDAVMAEFREGEVDILVST 94
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1460644633 869 TIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPkaMTTDAQKRLEAIAS 935
Cdd:cd18811 95 TVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKDP--LTETAKQRLRVMTE 159
|
|
| TRCF |
pfam03461 |
TRCF domain; |
1006-1100 |
2.05e-37 |
|
TRCF domain;
Pssm-ID: 460928 [Multi-domain] Cd Length: 95 Bit Score: 135.24 E-value: 2.05e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 1006 LRMPSLLPDDFIPDVNTRLSFYKRIASAKNELDLEEIKVELIDRFGRLPDAARNLLDIARLRQQAQKLGIRKLESNEKGG 1085
Cdd:pfam03461 1 LDVDAYIPDDYIPDESQRLELYKRLASIETEEELDDLQEELIDRFGPLPEEVENLLEIARLKLLAKKLGIEKIDLKGGGI 80
|
90
....*....|....*
gi 1460644633 1086 VIEFNEKNNVNPVWL 1100
Cdd:pfam03461 81 RITFSEDAKIDPEKL 95
|
|
| UvrB_inter |
pfam17757 |
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ... |
128-217 |
1.01e-32 |
|
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: 121.73 E-value: 1.01e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 128 LVMKKGQRLSRDALRDQLEGAGYRHVDQVMEHGEYATRGALLDLFPMGS-DQPYRLDFFDDEIDSLRLFDVDSQRTLEEV 206
Cdd:pfam17757 1 LSLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYSeDEAIRIEFFGDEIESIREFDPLTGRSLEKL 80
|
90
....*....|.
gi 1460644633 207 AAINLLPAHEF 217
Cdd:pfam17757 81 DEVTIYPASHY 91
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
602-765 |
1.55e-31 |
|
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: 121.20 E-value: 1.55e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 602 TPDQAQAINAVLSDMcqplamDRLVCGDVGFGKTEVAMRAAFLAVE---NHKQVAVLVPTTLLAQQHYDNFRDRFANWPV 678
Cdd:pfam00270 1 TPIQAEAIPAILEGR------DVLVQAPTGSGKTLAFLLPALEALDkldNGPQALVLAPTRELAEQIYEELKKLGKGLGL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 679 RIemlSRFRSAKEQAQILEQAAegKIDILIGTH----KLLQSEVKLRDLGLLIVDEEHR-----FGVRHKERIKAMRADV 749
Cdd:pfam00270 75 KV---ASLLGGDSRKEQLEKLK--GPDILVGTPgrllDLLQERKLLKNLKLLVLDEAHRlldmgFGPDLEEILRRLPKKR 149
|
170
....*....|....*.
gi 1460644633 750 DILTLTATPiPRTLNM 765
Cdd:pfam00270 150 QILLLSATL-PRNLED 164
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
621-757 |
4.90e-28 |
|
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: 110.57 E-value: 4.90e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 621 AMDRLVCGDVGFGKTEVAMRAAF-LAVENHKQVAVLVPTTLLAQQHYDNFRDRFaNWPVRIEMLSRFRSAKEQaqilEQA 699
Cdd:cd00046 1 GENVLITAPTGSGKTLAALLAALlLLLKKGKKVLVLVPTKALALQTAERLRELF-GPGIRVAVLVGGSSAEER----EKN 75
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1460644633 700 AEGKIDILIGTH----KLLQSEVKL--RDLGLLIVDEEHRFGVRHKER-------IKAMRADVDILTLTAT 757
Cdd:cd00046 76 KLGDADIIIATPdmllNLLLREDRLflKDLKLIIVDEAHALLIDSRGAlildlavRKAGLKNAQVILLSAT 146
|
|
| CarD_CdnL_TRCF |
pfam02559 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
477-572 |
3.87e-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: 3.87e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 477 LHIGQPVVHLEHGVGRYAGMTTLEaggiTGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEenapLHKLG-GDAWTRARQ 555
Cdd:pfam02559 1 LKVGDYVVHPDHGIGRIEGIEKLE----TKDYYVLEYAGGDKLYVPVDNLDLIRKYISKGE----LDKLGdGRRWRKYKE 72
|
90
....*....|....*..
gi 1460644633 556 KAAEKVRDVAAELLDIY 572
Cdd:pfam02559 73 KLKSGDIEEAAELIKLY 89
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
593-780 |
4.39e-27 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 109.89 E-value: 4.39e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 593 FCDGFPFETTPDQAQAINAVLSDMcqplaMDRLVCGDVGFGKTEVAMRAAFLAV--ENHKQVAVLVPTTLLAQQHYDNFR 670
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALLSGL-----RDVILAAPTGSGKTLAALLPALEALkrGKGGRVLVLVPTRELAEQWAEELK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 671 DRFANWPVRIEMLSRFRSAKEQaqiLEQAAEGKIDILIGT-----HKLLQSEVKLRDLGLLIVDEEHR-----FGVRHKE 740
Cdd:smart00487 76 KLGPSLGLKVVGLYGGDSKREQ---LRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRlldggFGDQLEK 152
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 1460644633 741 RIKAMRADVDILTLTATP---IPRTLNMAMSGMRDLSIIATPP 780
Cdd:smart00487 153 LLKLLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPL 195
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
523-1075 |
1.62e-18 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 90.85 E-value: 1.62e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 523 VSSLHLISRYAGGAEENAPLHKLGGDAWTRARQKAAEKVRDVAAELLDIYAQRAAKAGFAFKHDREQYQLFCDGFPFETT 602
Cdd:COG1061 1 VLLRGIAERGADKLRSSLLLLDLERLELSLLRNLVEARRLAIKEGTREDGRRLPEEDTERELAEAEALEAGDEASGTSFE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 603 --PDQAQAINAVLSDMCQplAMDR-LVCGDVGFGKTEVAMRAAfLAVENHKQVAVLVPTTLLAQQhydnFRDRFANWPVR 679
Cdd:COG1061 81 lrPYQQEALEALLAALER--GGGRgLVVAPTGTGKTVLALALA-AELLRGKRVLVLVPRRELLEQ----WAEELRRFLGD 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 680 IEMLSRFRSAKEqaqileqaaegkiDILIGTHKLLQSEVKLRDL----GLLIVDEEHRFGVRHKERIKAMRADVDILTLT 755
Cdd:COG1061 154 PLAGGGKKDSDA-------------PITVATYQSLARRAHLDELgdrfGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLT 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 756 ATPIpRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDALVVR--------------------------------EAIL 803
Cdd:COG1061 221 ATPF-RSDGREILLFLFDGIVYEYSLKEAIEDGYLAPPEYYGIRvdltderaeydalserlrealaadaerkdkilRELL 299
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 804 RETLRGGQVYYLFNDVENIQKAADKLAELVPEARIAigHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTI 883
Cdd:COG1061 300 REHPDDRKTLVFCSSVDHAEALAELLNEAGIRAAVV--TGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVA 377
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 884 IIerADHFG-LAQLHQLRGRVGRSH-HQAYAWLLTphpkaMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGE 961
Cdd:COG1061 378 IL--LRPTGsPREFIQRLGRGLRPApGKEDALVYD-----FVGNDVPVLEELAKDLRDLAGYRVEFLDEEESEELALLIA 450
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 962 DQSGQMETIG-FSLYMELLENAVDALKAGREPSLEDLTSQQTEVELRMPSLLPDDFIPDVNTRLSFYKRIASAKNELDLE 1040
Cdd:COG1061 451 VKPALEVKGElEEELLEELELLEDALLLVLAELLLLELLALALELLELAKAEGKAEEEEEEKELLLLLALAKLLKLLLLL 530
|
570 580 590
....*....|....*....|....*....|....*
gi 1460644633 1041 EIKVELIDRFGRLPDAARNLLDIARLRQQAQKLGI 1075
Cdd:COG1061 531 LLLLLLELLELLAALLRLEELAALLLKELLRAALA 565
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
625-769 |
2.91e-18 |
|
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' superfamily 2 DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350687 [Multi-domain] Cd Length: 178 Bit Score: 83.80 E-value: 2.91e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 625 LVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVriEMLSRFrSAKEQAQILEQAAEGKI 704
Cdd:cd17929 19 LLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRFGDKVA--VLHSKL-SDKERADEWRKIKRGEA 95
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1460644633 705 DILIGTHKLLQSEVKlrDLGLLIVDEEH----------RFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSG 769
Cdd:cd17929 96 KVVIGARSALFAPFK--NLGLIIVDEEHdssykqdsgpRYHARDVAIYRAKLENAPVVLGSATPSLESYYNAQQG 168
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
803-905 |
5.26e-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: 80.72 E-value: 5.26e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 803 LRETLRGGQVYYLfndVENIQKAADKLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANT 882
Cdd:pfam00271 9 LLKKERGGKVLIF---SQTKKTLEAELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDL 85
|
90 100
....*....|....*....|...
gi 1460644633 883 IIIERADhFGLAQLHQLRGRVGR 905
Cdd:pfam00271 86 VINYDLP-WNPASYIQRIGRAGR 107
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
625-919 |
9.06e-17 |
|
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: 84.74 E-value: 9.06e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 625 LVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANwpvRIEMLSRFRSAKEQAQILEQAAEGKI 704
Cdd:TIGR00595 1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGS---QVAVLHSGLSDSEKLQAWRKVKNGEI 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 705 DILIGTHKLLQSEVKlrDLGLLIVDEEH----------RFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLS 774
Cdd:TIGR00595 78 LVVIGTRSALFLPFK--NLGLIIVDEEHdssykqeegpRYHARDVAVYRAKKFNCPVVLGSATPSLESYHNAKQKAYRLL 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 775 II------ATPPA------RRLAVKTFVREydALVVReaiLRETLRGGQ------------------------------V 812
Cdd:TIGR00595 156 VLtrrvsgRKPPEvklidmRKEPRQSFLSP--ELITA---IEQTLAAGEqsilflnrrgysknllcrscgyilccpncdV 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 813 YYLFNDVEN-------------------------------IQKAADKLAELVPEARIAIGHGQM--RERELERVMNDFHH 859
Cdd:TIGR00595 231 SLTYHKKEGklrchycgyqepipktcpqcgsedlvykgygTEQVEEELAKLFPGARIARIDSDTtsRKGAHEALLNQFAN 310
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1460644633 860 QRFNVLVCTTIIETGIDIPTANTIIIERAD---HF--------GLAQLHQLRGRVGRSHHQAYAWLLTPHP 919
Cdd:TIGR00595 311 GKADILIGTQMIAKGHHFPNVTLVGVLDADsglHSpdfraaerGFQLLTQVAGRAGRAEDPGQVIIQTYNP 381
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
598-906 |
4.42e-16 |
|
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, recombination and repair];
Pssm-ID: 443274 [Multi-domain] Cd Length: 451 Bit Score: 82.23 E-value: 4.42e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 598 PFETTPDQAQAINAVLSDMCQplAMDRL---VCGDvgfGKTEVAMRAAFLAVENHKQVAVLVPTTllaqqhydnfrDrfa 674
Cdd:COG4098 108 EGTLTPAQQKASDELLEAIKK--KEEHLvwaVCGA---GKTEMLFPAIAEALKQGGRVCIATPRV-----------D--- 168
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 675 nwpVRIEMLSRFRSAKEQAQI--LEQAAEGKI---DILIGT-HKLLqsevklR-----DLglLIVDE---------EH-R 733
Cdd:COG4098 169 ---VVLELAPRLQQAFPGVDIaaLYGGSEEKYryaQLVIATtHQLL------RfyqafDL--LIIDEvdafpysgdPMlQ 237
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 734 FGVRhkeriKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIatpPAR----RLAVKTFVRE--YDALVVREAI----- 802
Cdd:COG4098 238 YAVK-----RARKPDGKLIYLTATPSKALQRQVKRGKLKVVKL---PARyhghPLPVPKFKWLgnWKKRLRRGKLprkll 309
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 803 --LRETL-RGGQVYYLFNDVENIQKAADKLAELVPEARIAIGHGQMRERElERVMnDFHHQRFNVLVCTTIIETGIDIPT 879
Cdd:COG4098 310 kwLKKRLkEGRQLLIFVPTIELLEQLVALLQKLFPEERIAGVHAEDPERK-EKVQ-AFRDGEIPILVTTTILERGVTFPN 387
|
330 340
....*....|....*....|....*....
gi 1460644633 880 ANTIIIErADH--FGLAQLHQLRGRVGRS 906
Cdd:COG4098 388 VDVAVLG-ADHpvFTEAALVQIAGRVGRS 415
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
827-905 |
7.31e-16 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 73.40 E-value: 7.31e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 827 DKLAELVPEARIAIG--HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADhFGLAQLHQLRGRVG 904
Cdd:smart00490 1 EELAELLKELGIKVArlHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-WSPASYIQRIGRAG 79
|
.
gi 1460644633 905 R 905
Cdd:smart00490 80 R 80
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
593-984 |
6.64e-14 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 75.70 E-value: 6.64e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 593 FCDGFPFET-TPDQAQAINAVLSDmcqplamDR--LVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNF 669
Cdd:COG1204 14 FLKERGIEElYPPQAEALEAGLLE-------GKnlVVSAPTASGKTLIAELAILKALLNGGKALYIVPLRALASEKYREF 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 670 RDRFANWPVRIEMLSR-FRSAKEqaqILEQAaegkiDILIGTHKLLQSEVK-----LRDLGLLIVDEEHRFGVRHK---- 739
Cdd:COG1204 87 KRDFEELGIKVGVSTGdYDSDDE---WLGRY-----DILVATPEKLDSLLRngpswLRDVDLVVVDEAHLIDDESRgptl 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 740 ----ERIKAMRADVDILTLTATpiprtlnmaMSGMRDLS------IIAT---PPARRLAV----------KTFVREYDAL 796
Cdd:COG1204 159 evllARLRRLNPEAQIVALSAT---------IGNAEEIAewldaeLVKSdwrPVPLNEGVlydgvlrfddGSRRSKDPTL 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 797 vvreAILRETLR-GGQVYYLFNDVENIQKAADKLAELVPE-------ARIAIGHGQMRERELERVMND-----------F 857
Cdd:COG1204 230 ----ALALDLLEeGGQVLVFVSSRRDAESLAKKLADELKRrltpeerEELEELAEELLEVSEETHTNEkladclekgvaF 305
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 858 HH------QR-----------FNVLVCTTIIETGIDIPtANTIIIERADHFGLAQL-----HQLRGRVGRSHH--QAYAW 913
Cdd:COG1204 306 HHaglpseLRrlvedafreglIKVLVATPTLAAGVNLP-ARRVIIRDTKRGGMVPIpvlefKQMAGRAGRPGYdpYGEAI 384
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 914 LLTPHPKAMTTDAQKRL----EAIASLedLGAGFALATHDLEIRGAGELLGEDqsGQMETIGFSLY-----MELLENAVD 984
Cdd:COG1204 385 LVAKSSDEADELFERYIlgepEPIRSK--LANESALRTHLLALIASGFANSRE--ELLDFLENTFYayqydKGDLEEVVD 460
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
584-732 |
2.01e-13 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 74.81 E-value: 2.01e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 584 KHDREQYQLFCDGFPFETTPDQAQAINAVLsdmcqplAMDR----LVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTT 659
Cdd:PRK05580 128 EVLRLRPPPDPAFEPPTLNPEQAAAVEAIR-------AAAGfspfLLDGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEI 200
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1460644633 660 LLAQQHYDNFRDRFANWPVriEMLSRFrSAKEQAQILEQAAEGKIDILIGThkllQSEV--KLRDLGLLIVDEEH 732
Cdd:PRK05580 201 ALTPQMLARFRARFGAPVA--VLHSGL-SDGERLDEWRKAKRGEAKVVIGA----RSALflPFKNLGLIIVDEEH 268
|
|
| PRK05298 |
PRK05298 |
excinuclease ABC subunit UvrB; |
119-225 |
2.58e-12 |
|
excinuclease ABC subunit UvrB;
Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 71.23 E-value: 2.58e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 119 PHSFlHGHALVMKKGQRLSRDALRDQLEGAGYRHVDQVMEHGEYATRGALLDLFPMGS-DQPYRLDFFDDEIDSLRLFDV 197
Cdd:PRK05298 151 PEEY-LKMVLSLRVGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPAYYeERAIRIEFFGDEIERISEFDP 229
|
90 100 110
....*....|....*....|....*....|..
gi 1460644633 198 DSQRTLEEVAAINLLPAHEFPTD----QTAIE 225
Cdd:PRK05298 230 LTGEVLGELDRVTIYPASHYVTPrerlERAIE 261
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
564-732 |
3.27e-11 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 67.45 E-value: 3.27e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 564 VAAELLDIYAQRAAKAGFAFKHDREQyqlfcdgfPFETTPDQAQAINAVLSdmcqplAMDR----LVCGDVGFGKTEVAM 639
Cdd:COG1198 167 VKKGLLEIEEREVDRDPFAPDVPAEP--------PPTLNEEQQAAVEAIRA------AAGGfsvfLLHGVTGSGKTEVYL 232
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 640 RAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFanwPVRIEML-SRFrSAKEQAQILEQAAEGKIDILIGThkllQSEV 718
Cdd:COG1198 233 QAIAEVLAQGKQALVLVPEIALTPQTVERFRARF---GARVAVLhSGL-SDGERLDEWRRARRGEARIVIGT----RSAL 304
|
170
....*....|....*.
gi 1460644633 719 --KLRDLGLLIVDEEH 732
Cdd:COG1198 305 faPFPNLGLIIVDEEH 320
|
|
| SrmB |
COG0513 |
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
599-905 |
3.41e-11 |
|
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 66.71 E-value: 3.41e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 599 FET-TPDQAQAInavlsdmcqPLAMDR---LVCGDVGFGKTevamrAAFL---------AVENHKQVAVLVPTTLLAQQH 665
Cdd:COG0513 22 YTTpTPIQAQAI---------PLILAGrdvLGQAQTGTGKT-----AAFLlpllqrldpSRPRAPQALILAPTRELALQV 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 666 YDNFRDRFANWPVRIEMLSRFRSAKEQAQILEQaaegKIDILIGT------HkLLQSEVKLRDLGLLIVDEehrfgvrhk 739
Cdd:COG0513 88 AEELRKLAKYLGLRVATVYGGVSIGRQIRALKR----GVDIVVATpgrlldL-IERGALDLSGVETLVLDE--------- 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 740 erikamrADvdiltltatpipRTLNMamsG-MRDLSII--ATPPARRL---------AVKTFVREY--DALVV---REAI 802
Cdd:COG0513 154 -------AD------------RMLDM---GfIEDIERIlkLLPKERQTllfsatmppEIRKLAKRYlkNPVRIevaPENA 211
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 803 LRETLRggQVYYLFN------------DVENIQKA---------ADKLAELVPEARIAIG--HGQMRERELERVMNDFHH 859
Cdd:COG0513 212 TAETIE--QRYYLVDkrdklellrrllRDEDPERAivfcntkrgADRLAEKLQKRGISAAalHGDLSQGQRERALDAFRN 289
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|..
gi 1460644633 860 QRFNVLVCTTIIETGIDIPTANTIIieradHFGLAQ-----LHqlR-GRVGR 905
Cdd:COG0513 290 GKIRVLVATDVAARGIDIDDVSHVI-----NYDLPEdpedyVH--RiGRTGR 334
|
|
| UvrB |
COG0556 |
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; |
119-225 |
9.18e-11 |
|
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
Pssm-ID: 440322 [Multi-domain] Cd Length: 657 Bit Score: 66.19 E-value: 9.18e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 119 PHSFlHGHALVMKKGQRLSRDALRDQLEGAGYRHVDQVMEHGEYATRGALLDLFPMGS-DQPYRLDFFDDEIDSLRLFDV 197
Cdd:COG0556 148 PEEY-LKMVLSLRVGEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAYSeERAIRIEFFGDEIERISEFDP 226
|
90 100
....*....|....*....|....*...
gi 1460644633 198 DSQRTLEEVAAINLLPAHEFPTDQTAIE 225
Cdd:COG0556 227 LTGEVLGELDRVTIYPASHYVTPRERLE 254
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
602-757 |
1.14e-10 |
|
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: 61.89 E-value: 1.14e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 602 TPDQAQAINAVLSDmcqplamDR--LVCGDVGFGKTEVAMRAAFLAVENHKQVAV-LVPTTLLAQQHYDNFRDRFANWPV 678
Cdd:cd17921 3 NPIQREALRALYLS-------GDsvLVSAPTSSGKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFGPLGK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 679 RIEML----SRFRSAKEQAQILEQAAEgKIDILIGTHkllqSEVKLRDLGLLIVDEEHRFGVRHK--------ERIKAMR 746
Cdd:cd17921 76 NVGLLtgdpSVNKLLLAEADILVATPE-KLDLLLRNG----GERLIQDVRLVVVDEAHLIGDGERgvvlelllSRLLRIN 150
|
170
....*....|.
gi 1460644633 747 ADVDILTLTAT 757
Cdd:cd17921 151 KNARFVGLSAT 161
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
631-758 |
1.81e-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: 60.40 E-value: 1.81e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 631 GFGKTEVAMRAAFLAVENHkqVAVLVPTTLLAQQHYDNFRDrfanwPVRIEMLSRFRSAKEQAQIleqaaegKIDILIGT 710
Cdd:cd17926 28 GSGKTLTALALIAYLKELR--TLIVVPTDALLDQWKERFED-----FLGDSSIGLIGGGKKKDFD-------DANVVVAT 93
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|...
gi 1460644633 711 HKLLQSEVK-----LRDLGLLIVDEEHRFGVRHKERIKAMRADVDILTLTATP 758
Cdd:cd17926 94 YQSLSNLAEeekdlFDQFGLLIVDEAHHLPAKTFSEILKELNAKYRLGLTATP 146
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
846-905 |
8.10e-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: 8.10e-09
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 846 RERELERVMNdfhhqRFNVLVCTTIIETGIDIPTANTIIIERAdHFGLAQLHQLRGRVGR 905
Cdd:cd18785 12 SIEHAEEIAS-----SLEILVATNVLGEGIDVPSLDTVIFFDP-PSSAASYIQRVGRAGR 65
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
631-759 |
1.24e-08 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 55.37 E-value: 1.24e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 631 GFGKTEVAMRAAFLAVENH--KQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEmlsrFRSAKEQAQILEQaaegkIDILI 708
Cdd:pfam04851 33 GSGKTLTAAKLIARLFKKGpiKKVLFLVPRKDLLEQALEEFKKFLPNYVEIGE----IISGDKKDESVDD-----NKIVV 103
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 1460644633 709 GT-HKL-----LQSEVKLRDL-GLLIVDEEHRFGVRHKERIKAMRADVDILTLTATPI 759
Cdd:pfam04851 104 TTiQSLykaleLASLELLPDFfDVIIIDEAHRSGASSYRNILEYFKPAFLLGLTATPE 161
|
|
| DEXHc_Hef |
cd18035 |
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
625-758 |
1.31e-08 |
|
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350793 [Multi-domain] Cd Length: 181 Bit Score: 55.98 E-value: 1.31e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 625 LVCGDVGFGKTEVAMRAAFLAVENHK-QVAVLVPTTLLAQQHYDNFRdRFANWPVRIEMLSRFRSAKEQAQILEQAAegk 703
Cdd:cd18035 20 LIVLPTGLGKTIIAILVAADRLTKKGgKVLILAPSRPLVEQHAENLK-RVLNIPDKITSLTGEVKPEERAERWDASK--- 95
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1460644633 704 idILIGT-----HKLLQSEVKLRDLGLLIVDEEHRFGVRHK-----ERIKAMRADVDILTLTATP 758
Cdd:cd18035 96 --IIVATpqvieNDLLAGRITLDDVSLLIFDEAHHAVGNYAyvyiaHRYKREANNPLILGLTASP 158
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
629-759 |
1.54e-08 |
|
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350769 [Multi-domain] Cd Length: 207 Bit Score: 56.14 E-value: 1.54e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 629 DVGFGKT-EVAMRAAFLAVEN-HKQVAVLVPTTLLAQ-QHYdnFRDRFANwpvRIEMLSRFRSAKEQAQILEQAAEGKID 705
Cdd:cd18011 25 EVGLGKTiEAGLIIKELLLRGdAKRVLILCPASLVEQwQDE--LQDKFGL---PFLILDRETAAQLRRLIGNPFEEFPIV 99
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1460644633 706 I----LIGTHKLLQSEVKLRDLGLLIVDEEHRF----GVRHKERIKAMRADVD----ILTLTATPI 759
Cdd:cd18011 100 IvsldLLKRSEERRGLLLSEEWDLVVVDEAHKLrnsgGGKETKRYKLGRLLAKrarhVLLLTATPH 165
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
631-907 |
4.96e-08 |
|
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: 56.28 E-value: 4.96e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 631 GFGKTEVAMRAAFLAVENHK--QVAVLVPTTLLAQQHYDNFRDRFANwPVRIEMLSRFRSAKEQAQILEQAAEGKIDIlI 708
Cdd:cd09639 9 GYGKTEAALLWALHSLKSQKadRVIIALPTRATINAMYRRAKEAFGE-TGLYHSSILSSRIKEMGDSEEFEHLFPLYI-H 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 709 GTHKLLQSEVKLRDL-----------------------GLLIVDEEHRFGVRHKERIKAM-----RADVDILTLTATpIP 760
Cdd:cd09639 87 SNDTLFLDPITVCTIdqvlksvfgefghyeftlasianSLLIFDEVHFYDEYTLALILAVlevlkDNDVPILLMSAT-LP 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 761 RTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDALVVREAILRETLR----GGQVYYLFNDVENIQKAADKLAELVPEA 836
Cdd:cd09639 166 KFLKEYAEKIGYVEENEPLDLKPNERAPFIKIESDKVGEISSLERLLEfikkGGSVAIIVNTVDRAQEFYQQLKEKGPEE 245
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1460644633 837 RIAIGHGQM----RERELERVMNDFHHQRFNVLVCTTIIETGIDIpTANTIIIERADhfgLAQLHQLRGRVGRSH 907
Cdd:cd09639 246 EIMLIHSRFtekdRAKKEAELLLEFKKSEKFVIVATQVIEASLDI-SVDVMITELAP---IDSLIQRLGRLHRYG 316
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
625-758 |
8.21e-08 |
|
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: 53.98 E-value: 8.21e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 625 LVCGDVGFGKTEVAMraafLAVENH---------KQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQAqi 695
Cdd:cd17927 21 IICLPTGSGKTFVAV----LICEHHlkkfpagrkGKVVFLANKVPLVEQQKEVFRKHFERPGYKVTGLSGDTSENVSV-- 94
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1460644633 696 lEQAAEGKiDILIGTHKLLQS------EVKLRDLGLLIVDEEHR--------FGVRH--KERIKAMRADVDILTLTATP 758
Cdd:cd17927 95 -EQIVESS-DVIIVTPQILVNdlksgtIVSLSDFSLLVFDECHNttknhpynEIMFRylDQKLGSSGPLPQILGLTASP 171
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
625-758 |
2.06e-07 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 55.12 E-value: 2.06e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 625 LVCGDVGFGKTEVAMR--AAFLAVENHKqVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQAQILEQAaeg 702
Cdd:COG1111 21 LVVLPTGLGKTAVALLviAERLHKKGGK-VLFLAPTKPLVEQHAEFFKEALNIPEDEIVVFTGEVSPEKRKELWEKA--- 96
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1460644633 703 kiDILIGT-----HKLLQSEVKLRDLGLLIVDEEHR-FG----VRHKERIKAMRADVDILTLTATP 758
Cdd:COG1111 97 --RIIVATpqvieNDLIAGRIDLDDVSLLIFDEAHRaVGnyayVYIAERYHEDAKDPLILGMTASP 160
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
823-905 |
6.39e-07 |
|
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350174 [Multi-domain] Cd Length: 131 Bit Score: 49.43 E-value: 6.39e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 823 QKAADKLAELVPEARIAIG--HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIieradHFGLAQ----- 895
Cdd:cd18787 37 KKRVDRLAELLEELGIKVAalHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGVDHVI-----NYDLPRdaedy 111
|
90
....*....|.
gi 1460644633 896 LHqlR-GRVGR 905
Cdd:cd18787 112 VH--RiGRTGR 120
|
|
| DEXHc_Snf |
cd17919 |
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
629-760 |
2.81e-06 |
|
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: 49.10 E-value: 2.81e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 629 DVGFGKTevAMRAAFLAVENHKQ-----VAVLVPTTLLaqqhyDNFRDRFANWPVRIEMLSRFRSAKEQAQILEQAAEGK 703
Cdd:cd17919 27 EMGLGKT--LQAIAFLAYLLKEGkergpVLVVCPLSVL-----ENWEREFEKWTPDLRVVVYHGSQRERAQIRAKEKLDK 99
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1460644633 704 IDILIGTHKLLQSEVKLR---DLGLLIVDEEHRF----GVRHKeRIKAMRADVDILtLTATPIP 760
Cdd:cd17919 100 FDVVLTTYETLRRDKASLrkfRWDLVVVDEAHRLknpkSQLSK-ALKALRAKRRLL-LTGTPLQ 161
|
|
| RecQ |
COG0514 |
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
678-915 |
2.94e-06 |
|
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 51.29 E-value: 2.94e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 678 VRIEMLSRFRSAKEQAQILEQAAEGKIDIL-IGTHKLLQSEV----KLRDLGLLIVDEEH-------------Rfgvrhk 739
Cdd:COG0514 82 IRAAFLNSSLSAEERREVLRALRAGELKLLyVAPERLLNPRFlellRRLKISLFAIDEAHcisqwghdfrpdyR------ 155
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 740 eRIKAMRA---DVDILTLTATPIPRTLN--MAMSGMRDLSIIATPPAR---RLAVKTFVRE--YDALVvreAILRETLRG 809
Cdd:COG0514 156 -RLGELRErlpNVPVLALTATATPRVRAdiAEQLGLEDPRVFVGSFDRpnlRLEVVPKPPDdkLAQLL---DFLKEHPGG 231
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 810 -GQVYYLFndveniQKAADKLAELVPEARIAIG--HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIie 886
Cdd:COG0514 232 sGIVYCLS------RKKVEELAEWLREAGIRAAayHAGLDAEEREANQDRFLRDEVDVIVATIAFGMGIDKPDVRFVI-- 303
|
250 260 270
....*....|....*....|....*....|...
gi 1460644633 887 radHFGLAQL----HQLRGRVGRSHHQAYAWLL 915
Cdd:COG0514 304 ---HYDLPKSieayYQEIGRAGRDGLPAEALLL 333
|
|
| UB2H |
pfam14814 |
Bifunctional transglycosylase second domain; UB2H is the second domain of the ... |
133-206 |
3.34e-06 |
|
Bifunctional transglycosylase second domain; UB2H is the second domain of the transglycosylases, or penicillin-binding proteins PBP1bs)), the multi-domain membrane proteins essential for cell wall synthesis that are targeted by penicillin antibiotics. The exact function of the UB2H domain is uncertain, but it may act as the binding component of PBP1b with different binding partners, or it may participate in the regulation between DNA repair and/or synthesis and cell wall formation during the bacterial cell cycle.
Pssm-ID: 434234 [Multi-domain] Cd Length: 85 Bit Score: 46.01 E-value: 3.34e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 133 GQRLSRDALRDQLEGAGYRHVDQVMEHGEYATRGALLDL------FPMGSD--QPYRLDFFDDEIDSLRlfDVDSQRTLE 204
Cdd:pfam14814 4 GQALSAAQLEQELKLLGYRKVSNPTRPGEYSVSGNRIELyrrgfdFPDGAEpaRRVRLRFAGGRVARLQ--DLDTGRDLA 81
|
..
gi 1460644633 205 EV 206
Cdd:pfam14814 82 LV 83
|
|
| PRK13766 |
PRK13766 |
Hef nuclease; Provisional |
625-758 |
6.15e-06 |
|
Hef nuclease; Provisional
Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 50.64 E-value: 6.15e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 625 LVCGDVGFGKTEVAM--RAAFLAVENHKqVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQAQILEQAaeg 702
Cdd:PRK13766 33 LVVLPTGLGKTAIALlvIAERLHKKGGK-VLILAPTKPLVEQHAEFFRKFLNIPEEKIVVFTGEVSPEKRAELWEKA--- 108
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1460644633 703 kiDILIGT-----HKLLQSEVKLRDLGLLIVDEEHR-FG----VRHKERIKAMRADVDILTLTATP 758
Cdd:PRK13766 109 --KVIVATpqvieNDLIAGRISLEDVSLLIFDEAHRaVGnyayVYIAERYHEDAKNPLVLGLTASP 172
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
603-757 |
9.08e-06 |
|
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: 47.33 E-value: 9.08e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 603 PDQAQAINAVLSDmcqplAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFanwPVRIEM 682
Cdd:cd18028 4 PPQAEAVRAGLLK-----GENLLISIPTASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEEFKKLE---EIGLKV 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 683 LSRFRSAKEQAQILeqaaeGKIDILIGTHKLLQSEVK-----LRDLGLLIVDEEHRFGVRHK--------ERIKAMRADV 749
Cdd:cd18028 76 GISTGDYDEDDEWL-----GDYDIIVATYEKFDSLLRhspswLRDVGVVVVDEIHLISDEERgptlesivARLRRLNPNT 150
|
....*...
gi 1460644633 750 DILTLTAT 757
Cdd:cd18028 151 QIIGLSAT 158
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
621-759 |
1.10e-05 |
|
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: 47.65 E-value: 1.10e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 621 AMDR--LVCGDVGFGKTEVA-MRAAFLAV------ENHKQVAVLVPTTLLAQQHYDNFRDrfaNWPVRIEMLSRFRSAKE 691
Cdd:cd18034 14 ALKRntIVVLPTGSGKTLIAvMLIKEMGElnrkekNPKKRAVFLVPTVPLVAQQAEAIRS---HTDLKVGEYSGEMGVDK 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 692 QAQILEQAAEGKIDILIGTHKLL-----QSEVKLRDLGLLIVDEEHRFGVRHKERiKAMR-----ADVD----ILTLTAT 757
Cdd:cd18034 91 WTKERWKEELEKYDVLVMTAQILldalrHGFLSLSDINLLIFDECHHATGDHPYA-RIMKefyhlEGRTsrprILGLTAS 169
|
..
gi 1460644633 758 PI 759
Cdd:cd18034 170 PV 171
|
|
| DEADc |
cd00268 |
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ... |
599-730 |
1.22e-05 |
|
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350669 [Multi-domain] Cd Length: 196 Bit Score: 47.44 E-value: 1.22e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 599 FET-TPDQAQAINAVLSDMcqplamDRLVCGDVGFGKTevamrAAFL------------AVENHKQVAVLVPTTLLAQQH 665
Cdd:cd00268 10 FEKpTPIQAQAIPLILSGR------DVIGQAQTGSGKT-----LAFLlpilekllpepkKKGRGPQALVLAPTRELAMQI 78
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 666 YDNFRdRFANwPVRIEMLSRFRSAKEQAQIleQAAEGKIDILIGT----HKLLQS-EVKLRDLGLLIVDE 730
Cdd:cd00268 79 AEVAR-KLGK-GTGLKVAAIYGGAPIKKQI--EALKKGPDIVVGTpgrlLDLIERgKLDLSNVKYLVLDE 144
|
|
| DEADc_DDX52 |
cd17957 |
DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ... |
600-730 |
2.43e-05 |
|
DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ubiquitously expressed in testis, endometrium, and other tissues in humans. DDX52 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: 350715 [Multi-domain] Cd Length: 198 Bit Score: 46.43 E-value: 2.43e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 600 ETTPDQAQAInavlsdmcqPLAMDR---LVCGDVGFGKTevamrAAFL-----AVENHKQVA-----VLVPTTLLAQQHY 666
Cdd:cd17957 12 EPTPIQMQAI---------PILLHGrdlLACAPTGSGKT-----LAFLipilqKLGKPRKKKglralILAPTRELASQIY 77
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1460644633 667 DNFRDRFANWPVRIEMLSrfrsaKEQAQILEQAAEG--KIDILIGTHKLL-----QSEVKLRDLGLLIVDE 730
Cdd:cd17957 78 RELLKLSKGTGLRIVLLS-----KSLEAKAKDGPKSitKYDILVSTPLRLvfllkQGPIDLSSVEYLVLDE 143
|
|
| SF2_C_dicer |
cd18802 |
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
840-902 |
2.76e-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: 45.27 E-value: 2.76e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1460644633 840 IGHG--------QMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIeradhFGLA----QLHQLRGR 902
Cdd:cd18802 61 IGRGnssqrkrsLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVIR-----FDLPktlrSYIQSRGR 130
|
|
| SF2_C_FANCM_Hef |
cd18801 |
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
817-905 |
2.95e-05 |
|
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: 45.04 E-value: 2.95e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 817 NDVENIQKAADKLAELVpEARIAIGHGQ------MRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADH 890
Cdd:cd18801 41 DSAEEIVNFLSKIRPGI-RATRFIGQASgksskgMSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASP 119
|
90
....*....|....*
gi 1460644633 891 FGLAQLhQLRGRVGR 905
Cdd:cd18801 120 SPIRMI-QRMGRTGR 133
|
|
| DEXHc_RLR |
cd18036 |
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
625-758 |
6.85e-05 |
|
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: 45.16 E-value: 6.85e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 625 LVCGDVGFGKTEVAMraafLAVENHKQ----------VAVLVPTTLLAQQHYDNFRDRFANWpVRIEMLSRFRSAKEQAQ 694
Cdd:cd18036 21 IICAPTGSGKTRVAV----YICRHHLEkrrsagekgrVVVLVNKVPLVEQQLEKFFKYFRKG-YKVTGLSGDSSHKVSFG 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 695 ileQAAEGKiDILIGTHKLLQS---------EVKLRDLGLLIVDEEHRFGVRH----------KERIKAMRADVDILTLT 755
Cdd:cd18036 96 ---QIVKAS-DVIICTPQILINnllsgreeeRVYLSDFSLLIFDECHHTQKEHpynkimrmylDKKLSSQGPLPQILGLT 171
|
...
gi 1460644633 756 ATP 758
Cdd:cd18036 172 ASP 174
|
|
| DDXDc_reverse_gyrase |
cd17924 |
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
631-789 |
1.09e-04 |
|
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: 44.24 E-value: 1.09e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 631 GFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRD--RFANWPVRIEMLSRFRSAKEQAQILEQAAEGKIDILI 708
Cdd:cd17924 42 GVGKTTFGLATSLYLASKGKRSYLIFPTKSLVKQAYERLSKyaEKAGVEVKILVYHSRLKKKEKEELLEKIEKGDFDILV 121
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 709 GTHKLLQ---SEVKLRDLGLLIVDeehrfgvrhkerikamraDVDILTLTATPIPRTLNMAmsGMRDLSII-ATPPARRL 784
Cdd:cd17924 122 TTNQFLSknfDLLSNKKFDFVFVD------------------DVDAVLKSSKNIDRLLKLL--GFGQLVVSsATGRPRGI 181
|
....*
gi 1460644633 785 AVKTF 789
Cdd:cd17924 182 RPLLF 186
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
822-919 |
1.17e-04 |
|
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: 44.93 E-value: 1.17e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 822 IQKAADKLAELVPEARIAIghgqM------RERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADhFGL-- 893
Cdd:cd18804 103 TERVEEELKTLFPEARIAR----IdrdttrKKGALEKLLDQFERGEIDILIGTQMIAKGLDFPNVTLVGILNAD-SGLns 177
|
90 100 110
....*....|....*....|....*....|....*.
gi 1460644633 894 ---------AQL-HQLRGRVGRSHHQAYAWLLTPHP 919
Cdd:cd18804 178 pdfraseraFQLlTQVSGRAGRGDKPGKVIIQTYNP 213
|
|
| SF2_C_XPB |
cd18789 |
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
770-905 |
2.48e-04 |
|
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: 42.62 E-value: 2.48e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 770 MRDLSIIATPPARRLAVKTfVREYDALvvrEAILRETLRGGQVYYLFNDVENIQKAADKLaeLVPeariAIgHGQMRERE 849
Cdd:cd18789 14 REYLGLGAHRKRRLLAAMN-PNKLRAL---EELLKRHEQGDKIIVFTDNVEALYRYAKRL--LKP----FI-TGETPQSE 82
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*.
gi 1460644633 850 LERVMNDFHHQRFNVLVCTTIIETGIDIPTANtIIIERADHFGLAQlhQLRGRVGR 905
Cdd:cd18789 83 REEILQNFREGEYNTLVVSKVGDEGIDLPEAN-VAIQISGHGGSRR--QEAQRLGR 135
|
|
| DEXHc_SKIV2L |
cd18027 |
DEXH-box helicase domain of SKIV2L; Superkiller viralicidic activity 2-like (SKIV2L, also ... |
597-779 |
9.68e-04 |
|
DEXH-box helicase domain of SKIV2L; Superkiller viralicidic activity 2-like (SKIV2L, also called SKI2 or DHX13) plays a role in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. SKIV2L 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: 350785 [Multi-domain] Cd Length: 179 Bit Score: 41.48 E-value: 9.68e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 597 FPFETTPDQAQAInavlsdMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANw 676
Cdd:cd18027 5 WPFELDVFQKQAI------LHLEAGDSVFVAAHTSAGKTVVAEYAIALAQKHMTRTIYTSPIKALSNQKFRDFKNTFGD- 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 677 pvrIEMLSrfrsakEQAQILEQAAegkidILIGTHKLLQSEVK-----LRDLGLLIVDEEHRF-----GVRHKERIKAMR 746
Cdd:cd18027 78 ---VGLIT------GDVQLNPEAS-----CLIMTTEILRSMLYngsdvIRDLEWVIFDEVHYIndaerGVVWEEVLIMLP 143
|
170 180 190
....*....|....*....|....*....|....*..
gi 1460644633 747 ADVDILTLTATpIPRTLNMA----MSGMRDLSIIATP 779
Cdd:cd18027 144 DHVSIILLSAT-VPNTVEFAdwigRIKKKNIYVISTP 179
|
|
| DEADc_MRH4 |
cd17965 |
DEAD-box helicase domain of ATP-dependent RNA helicase MRH4; Mitochondrial RNA helicase 4 ... |
654-779 |
1.12e-03 |
|
DEAD-box helicase domain of ATP-dependent RNA helicase MRH4; Mitochondrial RNA helicase 4 (MRH4) plays an essential role during the late stages of mitochondrial ribosome or mitoribosome assembly by promoting remodeling of the 21S rRNA-protein interactions. MRH4 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: 350723 [Multi-domain] Cd Length: 251 Bit Score: 41.98 E-value: 1.12e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 654 VLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQaQILEqAAEGKIDILIGTHKLLQSEVKLRDLGL-----LIV 728
Cdd:cd17965 114 ILVPTHELVEQVYSVLKKLSHTVKLGIKTFSSGFGPSYQ-RLQL-AFKGRIDILVTTPGKLASLAKSRPKILsrvthLVV 191
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*..
gi 1460644633 729 DE-----EHRFGVRHKERIKAMRADVDILTLTATpIPRTLNMAMSGM-RDLSIIATP 779
Cdd:cd17965 192 DEadtlfDRSFLQDTTSIIKRAPKLKHLILCSAT-IPKEFDKTLRKLfPDVVRIATP 247
|
|
| DEXHc_RLR-3 |
cd18075 |
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ... |
631-768 |
1.88e-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: 41.00 E-value: 1.88e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 631 GFGKTEVAMRAA--FLAVENHKQVAVLVPTTLLAQQHYDNFR----DRFanwpvRIEMLSRFRSAKEqaqILEQAAEGKi 704
Cdd:cd18075 27 GAGKTRAAVYVArrHLETKRGAKVAVLVNKVHLVDQHLEKEFhvllDKY-----TVTAISGDSSHKC---FFGQLARGS- 97
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1460644633 705 DILIGTHKLLQS---------EVKLRDLGLLIVDEEHRfgvRHKERI--KAMRADVDILTLTATPIPRTLNMAMS 768
Cdd:cd18075 98 DVVICTAQILQNallsgeeeaHVELTDFSLLVIDECHH---THKEAVynKIMLSYLEKKLSRQGDLPQILGLTAS 169
|
|
| DEADc_DDX56 |
cd17961 |
DEAD-box helicase domain of DEAD box protein 56; DDX56 is a helicase required for assembly of ... |
602-730 |
2.78e-03 |
|
DEAD-box helicase domain of DEAD box protein 56; DDX56 is a helicase required for assembly of infectious West Nile virus particles. New research suggests that DDX56 relocalizes to the site of virus assembly during WNV infection and that its interaction with WNV capsid in the cytoplasm may occur transiently during virion morphogenesis. DDX56 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: 350719 [Multi-domain] Cd Length: 206 Bit Score: 40.26 E-value: 2.78e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 602 TPDQAQAInavlsdmcqPLAM---DRLVCGDVGFGKTevamrAAFL--------------AVENHKQVAVLVPTTLLAQQ 664
Cdd:cd17961 18 TLIQSKAI---------PLALegkDILARARTGSGKT-----AAYAlpiiqkilkakaesGEEQGTRALILVPTRELAQQ 83
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1460644633 665 HYDNFRD--RFANWPVRIEMLSRFRSAKEQAQILeqaaEGKIDILIGT-----HKLLQSEVKLRD-LGLLIVDE 730
Cdd:cd17961 84 VSKVLEQltAYCRKDVRVVNLSASSSDSVQRALL----AEKPDIVVSTparllSHLESGSLLLLStLKYLVIDE 153
|
|
| SF2_C_EcoAI-like |
cd18799 |
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ... |
826-887 |
3.18e-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: 38.69 E-value: 3.18e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1460644633 826 ADKLAELVPEA---RIAIGHGQ-MRERELERVMNDFHHQ-RFNVLVCTTIIETGIDIPTANTIIIER 887
Cdd:cd18799 19 AEFMAEAFNEAgidAVALNSDYsDRERGDEALILLFFGElKPPILVTVDLLTTGVDIPEVDNVVFLR 85
|
|
| SF2_C_LHR |
cd18796 |
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ... |
827-909 |
4.98e-03 |
|
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases. LHR family helicases 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: 350183 [Multi-domain] Cd Length: 150 Bit Score: 38.78 E-value: 4.98e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 827 DKLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTII-IERAdhFGLAQLHQlrgRVGR 905
Cdd:cd18796 60 ELCPDRVPPDFIALHHGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIGDVDLVIqIGSP--KSVARLLQ---RLGR 134
|
....
gi 1460644633 906 SHHQ 909
Cdd:cd18796 135 SGHR 138
|
|
| DEADc_DDX51 |
cd17956 |
DEAD-box helicase domain of DEAD box protein 51; DDX51 aids cell cancer proliferation by ... |
603-734 |
6.36e-03 |
|
DEAD-box helicase domain of DEAD box protein 51; DDX51 aids cell cancer proliferation by regulating multiple signalling pathways. Mammalian DEAD box protein Ddx51 acts in 3' end maturation of 28S rRNA by promoting the release of U8 snoRNA.It 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: 350714 [Multi-domain] Cd Length: 231 Bit Score: 39.54 E-value: 6.36e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 603 PDQAQAINAVLSDMCQPLA---MDRLVCGDVGFGKTevamrAAFL---------AVENHKQVAVLVPTTLLAQQHYDNFR 670
Cdd:cd17956 15 PVQAAVIPWLLPSSKSTPPyrpGDLCVSAPTGSGKT-----LAYVlpivqalskRVVPRLRALIVVPTKELVQQVYKVFE 89
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1460644633 671 DRFANWPVRIEMLSRFRS-AKEQAQILEQAAEG---KIDILIGT------HKLLQSEVKLRDLGLLIVDEEHRF 734
Cdd:cd17956 90 SLCKGTGLKVVSLSGQKSfKKEQKLLLVDTSGRylsRVDILVATpgrlvdHLNSTPGFTLKHLRFLVIDEADRL 163
|
|
| DEXHc_RE_I_HsdR |
cd18030 |
DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of ... |
631-759 |
9.80e-03 |
|
DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of type I restriction-modification enzymes contains the DNA cleavage and ATP-dependent DNA translocation activities of the heteromeric complex. It 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: 350788 [Multi-domain] Cd Length: 208 Bit Score: 38.75 E-value: 9.80e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1460644633 631 GFGKTEVAMRAAFLAVENHKQ--VAVLVPTTLLAQQHYDNFRDRFANWPVRIEmlsrfrSAKEQAQILEQAAEGkidILI 708
Cdd:cd18030 57 GSGKSLTMFKAAKLLIEDPKNpkVVFVVDRKDLDYQTSSTFSRFAAEDVVRAN------STKELKELLKNLSGG---IIV 127
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1460644633 709 GT-HKLLQSEVKLRDLGLL-------IVDEEHR--FGVRHKERIKAMRaDVDILTLTATPI 759
Cdd:cd18030 128 TTiQKFNNAVKEESKPVLIyrknivvIVDEAHRsqFGELAKALKKALP-NATFIGFTGTPI 187
|
|
| |
