|
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: 2463.79 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 1 MPEQYRYTLPVKAGEQRLLGELTGAACATLVAEIAERHAGPVVLIAPDMQNALRLHDEISQFTDQMVMNLADWETLPYDS 80
Cdd:PRK10689 1 MPEQYRYTLPVKAGDQRQLGELTGAACATEVAEIAERHAGPVVLIAPDMQNALRLHDEIQQFTDQMVMNLADWETLPYDS 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 81 FSPHQDIISSRLSTLYQLPTMQRGVLIVPVNTLMQRVCPHSFLHGHALVMKKGQRLSRDALRTQLDSAGYRHVDQVMEHG 160
Cdd:PRK10689 81 FSPHQDIISSRLSTLYQLPTMQRGVLILPVNTLMQRVCPHSFLHGHALVMKKGQRLSRDALRAQLEQAGYRHVDQVMEHG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 161 EYATRGALLDLFPMGSELPYRLDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFEVKRD 240
Cdd:PRK10689 161 EYATRGALLDLFPMGSEEPYRIDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFEVKRD 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 241 PEHIYQQVSKGTLPAGIEYWQPLFFSEPLPPLFSYFPANTLLVNTGDLETSAERFQADTLARFENRGVDPMRPLLPPQSL 320
Cdd:PRK10689 241 AEHIYQQVSKGTLPAGIEYWQPLFFSEPLPPLFSYFPANTLLVNTGDLETSAERFWADTLARFENRGVDPMRPLLPPESL 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 321 WLRVDELFSELKNWPRVQLKTEHLPTKAANANLGFQKLPDLAVQAQQKAPLDALRKFLETFDGPVVFSVESEGRREALGE 400
Cdd:PRK10689 321 WLRVDELFSELKNWPRVQLKTEHLPTKAANTNLGYQKLPDLAVQAQQKAPLDALRRFLESFDGPVVFSVESEGRREALGE 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 401 LLARIKIAPQRIMRLDEASDRGRYLMIGAAEHGFVDKVRNLALICESDLLGERVARRRQDSRRTINPDTLIRNLAELHIG 480
Cdd:PRK10689 401 LLARIKIAPKRIMRLDEASDRGRYLMIGAAEHGFIDTVRNLALICESDLLGERVARRRQDSRRTINPDTLIRNLAELHPG 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 481 QPVVHLEHGVGRYAGMTTLEAGGITGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHKLGGDAWSRARQKAAEK 560
Cdd:PRK10689 481 QPVVHLEHGVGRYAGMTTLEAGGIKGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHKLGGDAWSRARQKAAEK 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 561 VRDVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMR 640
Cdd:PRK10689 561 VRDVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMR 640
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 641 AAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKF 720
Cdd:PRK10689 641 AAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKW 720
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 721 KDLGLLIVDEEHRFGVRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSLVVRE 800
Cdd:PRK10689 721 KDLGLLIVDEEHRFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSLVVRE 800
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 801 AILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTA 880
Cdd:PRK10689 801 AILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTA 880
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 881 NTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLG 960
Cdd:PRK10689 881 NTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLG 960
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 961 EEQSGSMETIGFSLYMELLENAVDALKAGREPSLEDLTSQQTEVELRMPSLLPDDFIPDVNTRLSFYKRIASAKTENELE 1040
Cdd:PRK10689 961 EEQSGQMETIGFSLYMELLENAVDALKAGREPSLEDLTSQQTEVELRMPSLLPDDFIPDVNTRLSFYKRIASAKNENELE 1040
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 1041 EIKVELIDRFGLLPDPARILLDVARLRQQAQKLGIRKLEGNEKGGVIEFAEKNHVNPAWLIGLLQKQPQHYRLDGPTRLK 1120
Cdd:PRK10689 1041 EIKVELIDRFGLLPDPARNLLDIARLRQQAQKLGIRKLEGNEKGGFIEFAEKNHVDPAWLIGLLQKQPQHYRLDGPTRLK 1120
|
1130 1140
....*....|....*....|....*..
gi 1910937583 1121 FIQDLSERKTRIEWVRQFMRELEENAI 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: 1882.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 13 AGEQRLLGELTGAACATLVAEIAERHAGPVVLIAPDMQNALRLHDEISQF-TDQMVMNLADWETLPYDSFSPHQDIISSR 91
Cdd:COG1197 1 GGGRLTLSGLPGSARALLLAALARALGRPLLVVTADEREAERLAEDLRFFlPDLPVLLFPAWETLPYDRFSPSPDIVSER 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 92 LSTLYQLPTMQRGVLIVPVNTLMQRVCPHSFLHGHALVMKKGQRLSRDALRTQLDSAGYRHVDQVMEHGEYATRGALLDL 171
Cdd:COG1197 81 LATLRRLASGKPGIVVTPVRALLQRLPPPELLAAASLSLKVGDELDLEELRERLVAAGYERVDQVEEPGEFAVRGGILDI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 172 FPMGSELPYRLDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFEVKRDPEHIYQQVSKG 251
Cdd:COG1197 161 FPPGSEHPVRIEFFGDEIESIRTFDPETQRSLEKVDEVELLPAREFPLDEEAIERFRERLRELFGLDPKLDELYEALSEG 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 252 TLPAGIEYWQPLFFSEpLPPLFSYFPANTLLVNTG--DLETSAERFQADTLARFENRGVDPMRPLLPPQSLWLRVDELFS 329
Cdd:COG1197 241 IAFAGIEYYLPLFYEE-LATLFDYLPEDALVVLDEpeRIEEAAEEFWEEIEERYEARRHDRGRPLLPPEELFLDPEELFA 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 330 ELKNWPRVQLKT-EHLPTKAANANLGFQKLPDlaVQAQQKAPLDALRKFLETfDGPVVFSVESEGRREALGELLARIKIA 408
Cdd:COG1197 320 ALKRRPRVTLSPfAALPEGAGVVNLGARPLPS--FAGQLEALLEELKRLLKD-GGRVLLAAESEGRRERLLELLRDHGIP 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 409 PQRIMRLDEASDRGRYLMIGAAEHGFVDKVRNLALICESDLLGERVARRRQdsRRTINPDTLIRNLAELHIGQPVVHLEH 488
Cdd:COG1197 397 ARLVESLAELSPGGVAITVGPLEHGFELPDAKLAVITESELFGERVKRRRR--KKKRSADAFIRDLSELKPGDYVVHVDH 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 489 GVGRYAGMTTLEAGGITGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHKLGGDAWSRARQKAAEKVRDVAAEL 568
Cdd:COG1197 475 GIGRYLGLETLEVGGAERDYLVLEYAGGDKLYVPVDQLDLISRYVGSEGEAPKLDKLGGSDWQKAKAKAKKAVRDIAAEL 554
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 569 LDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN 648
Cdd:COG1197 555 LKLYAERAARKGFAFSPDTPWQREFEAAFPYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKTEVALRAAFKAVMD 634
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 649 HKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLIV 728
Cdd:COG1197 635 GKQVAVLVPTTLLAQQHYETFKERFAGFPVRVEVLSRFRTAKEQKETLEGLADGKVDIVIGTHRLLSKDVKFKDLGLLII 714
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 729 DEEHRFGVRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSLVVREAILREILR 808
Cdd:COG1197 715 DEEQRFGVRHKEKLKALRANVDVLTLTATPIPRTLQMSLSGIRDLSIIATPPEDRLPVKTFVGEYDDALIREAILRELLR 794
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 809 GGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERA 888
Cdd:COG1197 795 GGQVFYVHNRVEDIEKVAARLQELVPEARIAVAHGQMSERELERVMLDFYEGEFDVLVCTTIIETGIDIPNANTIIIERA 874
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 889 DHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGEEQSGSME 968
Cdd:COG1197 875 DRFGLAQLYQLRGRVGRSHRRAYAYLLYPPDKVLTEDAEKRLEAIQEFTELGAGFKLAMHDLEIRGAGNLLGEEQSGHIA 954
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 969 TIGFSLYMELLENAVDALKAGREPSLEdltsQQTEVELRMPSLLPDDFIPDVNTRLSFYKRIASAKTENELEEIKVELID 1048
Cdd:COG1197 955 EVGFDLYLQMLEEAVAALKGGKEPEEE----WEPEINLGVPALIPEDYIPDVRQRLELYKRIASAESEEELDELQEELID 1030
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 1049 RFGLLPDPARILLDVARLRQQAQKLGIRKLEGNEKGGVIEFAEKNHVNPAWLIGLLQKQPQHYRLDGPTRLKFIQDLSER 1128
Cdd:COG1197 1031 RFGPLPEEVENLLAVARLKLLARRLGIEKIDAGGKGIRIEFSPNTPLDPEKLIRLIQKQPGRYKLDGDDKLVITLDLEDP 1110
|
1130 1140
....*....|....*....|
gi 1910937583 1129 KTRIEWVRQFMRELEENAIA 1148
Cdd:COG1197 1111 EERLEALEELLEALAKLAKE 1130
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
145-1079 |
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: 1410.19 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 145 LDSAGYRHVDQVMEHGEYATRGALLDLFPMGSELPYRLDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFpTDKAAI 224
Cdd:TIGR00580 1 LVELGYERVDLVEEEGEFSVRGEILDIFPPGSELPVRIEFFGDEIESIREFDVDSQRSLEELLEITILPAKEF-ILLEEE 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 225 ELFRSQWRDTFEVKRDPEHIYQQVSKGTLPAGIEYWQPLFFSEPlPPLFSYFPANTL-LVNTGDLETSAERFQADTLARF 303
Cdd:TIGR00580 80 TIARLKDNAARVEDAKHLETIEALSEGTLPAGEEMFLPLFFEDL-SSLFDYLPDNTPiLLDDPERFHSAARFLQRELEEF 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 304 ENRGVDPMRPLLPPQsLWLRVDELFSE--LKNWPRVQLKTEHLPTKAANANLGFQKLPDLAVQAQQKAPLDALRKFLETF 381
Cdd:TIGR00580 159 YNALEEAKKLINPPR-LDLDPSELAFEasAISLSRVQLENEHLSLKASEAIEGAQKHSRLEFGEILAFKEELFRWLKAGF 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 382 DGPVVFsvESEGRREALGELLARIKIAPQRIMRLDEASDRGRYLMIGAAEHGFVDKVRNLALICESDLLGERVARRRQDS 461
Cdd:TIGR00580 238 KITVAA--ESESQAERLKSLLAEHDIAAQVIDESCIIIPAVRYVMIGALSSGFILPTAGLAVITESELFGSRVLRRPKKS 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 462 RRTinpDTLIRNLAELHIGQPVVHLEHGVGRYAGMTTLEAGGITGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAP 541
Cdd:TIGR00580 316 RLK---SKPIESLNELNPGDYVVHLDHGIGRFLGLETLEVGGIERDYLVLEYAGEDKLYVPVEQLHLISRYVGGSGKNPA 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 542 LHKLGGDAWSRARQKAAEKVRDVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLA 621
Cdd:TIGR00580 393 LDKLGGKSWEKTKAKVKKSVREIAAKLIELYAKRKAIKGHAFPPDLEWQQEFEDSFPFEETPDQLKAIEEIKADMESPRP 472
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 622 MDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAE 701
Cdd:TIGR00580 473 MDRLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELAS 552
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 702 GKIDILIGTHKLLQSDVKFKDLGLLIVDEEHRFGVRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIATPPA 781
Cdd:TIGR00580 553 GKIDILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPE 632
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 782 RRLAVKTFVREYDSLVVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQR 861
Cdd:TIGR00580 633 DRLPVRTFVMEYDPELVREAIRRELLRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGE 712
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 862 FNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGA 941
Cdd:TIGR00580 713 FQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDAQKRLEAIQEFSELGA 792
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 942 GFALATHDLEIRGAGELLGEEQSGSMETIGFSLYMELLENAVDALKAGREPSLEdltsQQTEVELRMPSLLPDDFIPDVN 1021
Cdd:TIGR00580 793 GFKIALHDLEIRGAGNLLGEEQSGHIESIGFDLYMELLEEAIEELKGGKPPKLE----EETDIELPYSAFIPDDYIADDS 868
|
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|....*...
gi 1910937583 1022 TRLSFYKRIASAKTENELEEIKVELIDRFGLLPDPARILLDVARLRQQAQKLGIRKLE 1079
Cdd:TIGR00580 869 LRLEFYKRIASAETEEELEKIRDELIDRFGPLPEEARTLLDVARLKLLARKLGIRKLK 926
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
568-968 |
5.23e-131 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 415.22 E-value: 5.23e-131
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 568 LLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVD 647
Cdd:COG1200 227 LLLRRARRRKRKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVE 306
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 648 NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLI 727
Cdd:COG1200 307 AGYQAALMAPTEILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVV 386
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 728 VDEEHRFGVRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSL--VVrEAILRE 805
Cdd:COG1200 387 IDEQHRFGVEQRLALREKGEAPHVLVMTATPIPRTLAMTLYGDLDVSVIDELPPGRKPIKTRVVPEERRdeVY-ERIREE 465
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 806 ILRGGQVYYLY--------NDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDI 877
Cdd:COG1200 466 IAKGRQAYVVCplieesekLDLQAAEETYEELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGVDV 545
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 878 PTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPkaMTTDAQKRLEAIASLEDlgaGFALATHDLEIRGAGE 957
Cdd:COG1200 546 PNATVMVIENAERFGLSQLHQLRGRVGRGSAQSYCLLLYDAP--LSETARERLEVMRETND---GFEIAEEDLELRGPGE 620
|
410
....*....|.
gi 1910937583 958 LLGEEQSGSME 968
Cdd:COG1200 621 FLGTRQSGLPD 631
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
573-965 |
1.14e-128 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 408.77 E-value: 1.14e-128
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 573 AQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQV 652
Cdd:PRK10917 234 AGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGYQA 313
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 653 AVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLIVDEEH 732
Cdd:PRK10917 314 ALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIIDEQH 393
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 733 RFGVRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVR---EYDSLVvrEAILREILRG 809
Cdd:PRK10917 394 RFGVEQRLALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIpdsRRDEVY--ERIREEIAKG 471
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 810 GQVYYLYN--------DVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTAN 881
Cdd:PRK10917 472 RQAYVVCPlieeseklDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNAT 551
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 882 TIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKamTTDAQKRLEAIASLEDlgaGFALATHDLEIRGAGELLGE 961
Cdd:PRK10917 552 VMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPL--SETARERLKIMRETND---GFVIAEKDLELRGPGELLGT 626
|
....
gi 1910937583 962 EQSG 965
Cdd:PRK10917 627 RQSG 630
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
586-778 |
4.79e-127 |
|
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: 386.16 E-value: 4.79e-127
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 586 DREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQH 665
Cdd:cd17991 1 DGEEQEEFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 666 YDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLIVDEEHRFGVRHKERIKAM 745
Cdd:cd17991 81 YETFKERFANFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQKEKLKEL 160
|
170 180 190
....*....|....*....|....*....|...
gi 1910937583 746 RANVDILTLTATPIPRTLNMAMSGMRDLSIIAT 778
Cdd:cd17991 161 RPNVDVLTLSATPIPRTLHMALSGIRDLSVIAT 193
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
593-965 |
1.69e-117 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 377.45 E-value: 1.69e-117
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 593 FCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDR 672
Cdd:TIGR00643 228 FLASLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNL 307
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 673 FANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLIVDEEHRFGVRHKERIKAM---RANV 749
Cdd:TIGR00643 308 LAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLREKgqgGFTP 387
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 750 DILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSL-VVREAILREILRGGQVYYLY---NDVENIQ-K 824
Cdd:TIGR00643 388 HVLVMSATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLIKHDEKdIVYEFIEEEIAKGRQAYVVYpliEESEKLDlK 467
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 825 AA----ERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLR 900
Cdd:TIGR00643 468 AAealyERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLR 547
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1910937583 901 GRVGRSHHQAYAWLLTPHPKamTTDAQKRLEAIASLEDlgaGFALATHDLEIRGAGELLGEEQSG 965
Cdd:TIGR00643 548 GRVGRGDHQSYCLLVYKNPK--SESAKKRLRVMADTLD---GFVIAEEDLELRGPGDLLGTKQSG 607
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
785-935 |
9.30e-86 |
|
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: 274.22 E-value: 9.30e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 785 AVKTFVREYDSLVVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNV 864
Cdd:cd18810 1 PVRTYVMPYDDELIREAIERELLRGGQVFYVHNRIESIEKLATQLRQLVPEARIAIAHGQMTENELEEVMLEFAKGEYDI 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1910937583 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 |
1.13e-85 |
|
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: 275.06 E-value: 1.13e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 586 DREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQH 665
Cdd:cd17918 1 DRALIQELCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 666 YDNFRDRFAnwPVRIEMISRFRsakeQTQILAEvaegkIDILIGTHKLLQSDVKFKDLGLLIVDEEHRFGVRHKERIKAM 745
Cdd:cd17918 81 YEEARKFLP--FINVELVTGGT----KAQILSG-----ISLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNL 149
|
170 180 190
....*....|....*....|....*....|..
gi 1910937583 746 RaNVDILTLTATPIPRTLNMAMSGMRDLSIIA 777
Cdd:cd17918 150 G-ATHFLEATATPIPRTLALALSGLLDLSVID 180
|
|
| SF2_C_RecG_TRCF |
cd18792 |
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
785-935 |
1.33e-73 |
|
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: 241.02 E-value: 1.33e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 785 AVKTFVREYDSL-VVREAILREILRGGQVYYLYN--------DVENIQKAAERLAELVPEARIAIGHGQMRERELERVMN 855
Cdd:cd18792 1 PIRTYVIPHDDLdLVYEAIERELARGGQVYYVYPrieeseklDLKSIEALAEELKELVPEARVALLHGKMTEDEKEAVML 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 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 |
1.21e-68 |
|
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: 229.73 E-value: 1.21e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 568 LLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVD 647
Cdd:cd17992 13 LLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKTVVAALAMLAAVE 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 648 NHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLI 727
Cdd:cd17992 93 NGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQEDVEFHNLGLVI 172
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 1910937583 728 VDEEHRFGVRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIATPP 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 |
1.53e-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: 156.07 E-value: 1.53e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 476 ELHIGQPVVHLEHGVGRYAGMTTLEAGGITGEYLMLTYANDAKLYVPVSSLHLISRYAGG-AEENAPLHKLGGDAWSRAR 554
Cdd:smart01058 1 ELKIGDYVVHPDHGVGRYEGIETIEVGGEKREYLVLEYAGGDKLYVPVDNLDLGSRYVGSeGEVEPVLDKLGGGSWSKRK 80
|
90
....*....|....*....
gi 1910937583 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 |
1.08e-39 |
|
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: 142.22 E-value: 1.08e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 1005 ELRMPSLLPDDFIPDVNTRLSFYKRIASAKTENELEEIKVELIDRFGLLPDPARILLDVARLRQQAQKLGIRKLEGNEKG 1084
Cdd:smart00982 1 DLPVPALIPEDYIPDVRQRLELYKRIASAETEEELDEIQEELIDRFGPLPEEVKNLLEVARLKLLAKKLGIEKIDAGGKG 80
|
90 100
....*....|....*....|
gi 1910937583 1085 GVIEFAEKNHVNPAWLIGLL 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 |
1.51e-39 |
|
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: 144.02 E-value: 1.51e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 798 VREAILREILRGGQVYYLYN--------DVENIQKAAERLAELV-PEARIAIGHGQMRERELERVMNDFHHQRFNVLVCT 868
Cdd:cd18811 15 VYEFVREEIAKGRQAYVIYPlieeseklDLKAAVAMYEYLKERFrPELNVGLLHGRLKSDEKDAVMAEFREGEVDILVST 94
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1910937583 869 TIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPkaMTTDAQKRLEAIAS 935
Cdd:cd18811 95 TVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKDP--LTETAKQRLRVMTE 159
|
|
| TRCF |
pfam03461 |
TRCF domain; |
1006-1100 |
1.71e-37 |
|
TRCF domain;
Pssm-ID: 460928 [Multi-domain] Cd Length: 95 Bit Score: 135.63 E-value: 1.71e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 1006 LRMPSLLPDDFIPDVNTRLSFYKRIASAKTENELEEIKVELIDRFGLLPDPARILLDVARLRQQAQKLGIRKLEGNEKGG 1085
Cdd:pfam03461 1 LDVDAYIPDDYIPDESQRLELYKRLASIETEEELDDLQEELIDRFGPLPEEVENLLEIARLKLLAKKLGIEKIDLKGGGI 80
|
90
....*....|....*
gi 1910937583 1086 VIEFAEKNHVNPAWL 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 |
6.66e-33 |
|
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: 122.50 E-value: 6.66e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 128 LVMKKGQRLSRDALRTQLDSAGYRHVDQVMEHGEYATRGALLDLFPMGSE-LPYRLDFFDDEIDSLRVFDVDSQRTLEEV 206
Cdd:pfam17757 1 LSLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYSEdEAIRIEFFGDEIESIREFDPLTGRSLEKL 80
|
90
....*....|.
gi 1910937583 207 EAINLLPAHEF 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 |
7.29e-32 |
|
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: 122.35 E-value: 7.29e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 602 TPDQAQAINAVLSDMcqplamDRLVCGDVGFGKTEVAMRAAFLAV---DNHKQVAVLVPTTLLAQQHYDNFRDRFANWPV 678
Cdd:pfam00270 1 TPIQAEAIPAILEGR------DVLVQAPTGSGKTLAFLLPALEALdklDNGPQALVLAPTRELAEQIYEELKKLGKGLGL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 679 RiemISRFRSAKEQTQILAEVAegKIDILIGTH----KLLQSDVKFKDLGLLIVDEEHR-----FGVRHKERIKAMRANV 749
Cdd:pfam00270 75 K---VASLLGGDSRKEQLEKLK--GPDILVGTPgrllDLLQERKLLKNLKLLVLDEAHRlldmgFGPDLEEILRRLPKKR 149
|
170
....*....|....*.
gi 1910937583 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 |
1.05e-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: 112.50 E-value: 1.05e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 621 AMDRLVCGDVGFGKTEVAMRAAFLAVD-NHKQVAVLVPTTLLAQQHYDNFRDRFaNWPVRIEMISRFRSAKEQtqilAEV 699
Cdd:cd00046 1 GENVLITAPTGSGKTLAALLAALLLLLkKGKKVLVLVPTKALALQTAERLRELF-GPGIRVAVLVGGSSAEER----EKN 75
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1910937583 700 AEGKIDILIGTHKLLQSDVK------FKDLGLLIVDEEHRFGVRHKER-------IKAMRANVDILTLTAT 757
Cdd:cd00046 76 KLGDADIIIATPDMLLNLLLredrlfLKDLKLIIVDEAHALLIDSRGAlildlavRKAGLKNAQVILLSAT 146
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
593-780 |
2.85e-27 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 110.27 E-value: 2.85e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 593 FCDSFPFETTPDQAQAINAVLSDMcqplaMDRLVCGDVGFGKTEVAMRAAFLAVDNH--KQVAVLVPTTLLAQQHYDNFR 670
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALLSGL-----RDVILAAPTGSGKTLAALLPALEALKRGkgGRVLVLVPTRELAEQWAEELK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 671 DRFANWPVRIEMISRFRSAKEQtqiLAEVAEGKIDILIGT-----HKLLQSDVKFKDLGLLIVDEEHR-----FGVRHKE 740
Cdd:smart00487 76 KLGPSLGLKVVGLYGGDSKREQ---LRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRlldggFGDQLEK 152
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 1910937583 741 RIKAMRANVDILTLTATP---IPRTLNMAMSGMRDLSIIATPP 780
Cdd:smart00487 153 LLKLLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPL 195
|
|
| CarD_CdnL_TRCF |
pfam02559 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
477-572 |
4.52e-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: 105.61 E-value: 4.52e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 477 LHIGQPVVHLEHGVGRYAGMTTLEaggiTGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEenapLHKLG-GDAWSRARQ 555
Cdd:pfam02559 1 LKVGDYVVHPDHGIGRIEGIEKLE----TKDYYVLEYAGGDKLYVPVDNLDLIRKYISKGE----LDKLGdGRRWRKYKE 72
|
90
....*....|....*..
gi 1910937583 556 KAAEKVRDVAAELLDIY 572
Cdd:pfam02559 73 KLKSGDIEEAAELIKLY 89
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
523-1075 |
7.57e-20 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 95.09 E-value: 7.57e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 523 VSSLHLISRYAGGAEENAPLHKLGGDAWSRARQKAAEKVRDVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETT 602
Cdd:COG1061 1 VLLRGIAERGADKLRSSLLLLDLERLELSLLRNLVEARRLAIKEGTREDGRRLPEEDTERELAEAEALEAGDEASGTSFE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 603 --PDQAQAINAVLSDMCQplAMDR-LVCGDVGFGKTEVAMRAAfLAVDNHKQVAVLVPTTLLAQQhydnFRDRFANWPVR 679
Cdd:COG1061 81 lrPYQQEALEALLAALER--GGGRgLVVAPTGTGKTVLALALA-AELLRGKRVLVLVPRRELLEQ----WAEELRRFLGD 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 680 IEMISRFRSAKEqtqilaevaegkiDILIGTHKLLQSDVKFKDL----GLLIVDEEHRFG-VRHKERIKAMRANVdILTL 754
Cdd:COG1061 154 PLAGGGKKDSDA-------------PITVATYQSLARRAHLDELgdrfGLVIIDEAHHAGaPSYRRILEAFPAAY-RLGL 219
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 755 TATPIpRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSLVVR----------------------------EAILREI 806
Cdd:COG1061 220 TATPF-RSDGREILLFLFDGIVYEYSLKEAIEDGYLAPPEYYGIRvdltderaeydalserlrealaadaerkDKILREL 298
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 807 LRGgqvyylYNDVENI------QKAAERLAELVPEARIAIG--HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIP 878
Cdd:COG1061 299 LRE------HPDDRKTlvfcssVDHAEALAELLNEAGIRAAvvTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVP 372
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 879 TANTIIIerADHFG-LAQLHQLRGRVGRSH-HQAYAWLLTphpkaMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAG 956
Cdd:COG1061 373 RLDVAIL--LRPTGsPREFIQRLGRGLRPApGKEDALVYD-----FVGNDVPVLEELAKDLRDLAGYRVEFLDEEESEEL 445
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 957 ELLGEEQSGSMETIG-FSLYMELLENAVDALKAGREPSLEDLTSQQTEVELRMPSLLPDDFIPDVNTRLSFYKRIASAKT 1035
Cdd:COG1061 446 ALLIAVKPALEVKGElEEELLEELELLEDALLLVLAELLLLELLALALELLELAKAEGKAEEEEEEKELLLLLALAKLLK 525
|
570 580 590 600
....*....|....*....|....*....|....*....|
gi 1910937583 1036 ENELEEIKVELIDRFGLLPDPARILLDVARLRQQAQKLGI 1075
Cdd:COG1061 526 LLLLLLLLLLLELLELLAALLRLEELAALLLKELLRAALA 565
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
801-905 |
2.09e-18 |
|
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 81.87 E-value: 2.09e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 801 AILREIL---RGGQVYYLyndVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDI 877
Cdd:pfam00271 4 EALLELLkkeRGGKVLIF---SQTKKTLEAELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDL 80
|
90 100
....*....|....*....|....*...
gi 1910937583 878 PTANTIIIERADhFGLAQLHQLRGRVGR 905
Cdd:pfam00271 81 PDVDLVINYDLP-WNPASYIQRIGRAGR 107
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
625-919 |
1.10e-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: 87.82 E-value: 1.10e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 625 LVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEmiSRFrSAKEQTQILAEVAEGKI 704
Cdd:TIGR00595 1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLH--SGL-SDSEKLQAWRKVKNGEI 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 705 DILIGTHKLLQsdVKFKDLGLLIVDEEH----------RFGVRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLS 774
Cdd:TIGR00595 78 LVVIGTRSALF--LPFKNLGLIIVDEEHdssykqeegpRYHARDVAVYRAKKFNCPVVLGSATPSLESYHNAKQKAYRLL 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 775 II------ATPParRLAVKTFVRE-YDSLVVREAI--LREILRGGQ------------------------------VYYL 815
Cdd:TIGR00595 156 VLtrrvsgRKPP--EVKLIDMRKEpRQSFLSPELItaIEQTLAAGEqsilflnrrgysknllcrscgyilccpncdVSLT 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 816 YNDVEN-------------------------------IQKAAERLAELVPEARIAIGHGQM--RERELERVMNDFHHQRF 862
Cdd:TIGR00595 234 YHKKEGklrchycgyqepipktcpqcgsedlvykgygTEQVEEELAKLFPGARIARIDSDTtsRKGAHEALLNQFANGKA 313
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1910937583 863 NVLVCTTIIETGIDIPTANTIIIERAD---HF--------GLAQLHQLRGRVGRSHHQAYAWLLTPHP 919
Cdd:TIGR00595 314 DILIGTQMIAKGHHFPNVTLVGVLDADsglHSpdfraaerGFQLLTQVAGRAGRAEDPGQVIIQTYNP 381
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
625-769 |
8.92e-17 |
|
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' superfamily 2 DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350687 [Multi-domain] Cd Length: 178 Bit Score: 79.17 E-value: 8.92e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 625 LVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVriEMISRFrSAKEQTQILAEVAEGKI 704
Cdd:cd17929 19 LLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRFGDKVA--VLHSKL-SDKERADEWRKIKRGEA 95
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1910937583 705 DILIGTHKLLQsdVKFKDLGLLIVDEEH----------RFGVRHKERIKAMRANVDILTLTATPIPRTLNMAMSG 769
Cdd:cd17929 96 KVVIGARSALF--APFKNLGLIIVDEEHdssykqdsgpRYHARDVAIYRAKLENAPVVLGSATPSLESYYNAQQG 168
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
598-906 |
1.47e-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: 83.77 E-value: 1.47e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 598 PFETTPDQAQAINAVLSDMCQplAMDRL---VCGDvgfGKTEVAMRAAFLAVDNHKQVAVLVPTTllaqqhydnfrDrfa 674
Cdd:COG4098 108 EGTLTPAQQKASDELLEAIKK--KEEHLvwaVCGA---GKTEMLFPAIAEALKQGGRVCIATPRV-----------D--- 168
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 675 nwpVRIEMISRFRSAKEQTQILA-----EVAEGKIDILIGT-HKLLqsdvKFKD-LGLLIVDE---------EH-RFGVR 737
Cdd:COG4098 169 ---VVLELAPRLQQAFPGVDIAAlyggsEEKYRYAQLVIATtHQLL----RFYQaFDLLIIDEvdafpysgdPMlQYAVK 241
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 738 hkeriKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIatpPAR----RLAVKTFVREYD----------SLVVREAIL 803
Cdd:COG4098 242 -----RARKPDGKLIYLTATPSKALQRQVKRGKLKVVKL---PARyhghPLPVPKFKWLGNwkkrlrrgklPRKLLKWLK 313
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 804 REILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERElERVMnDFHHQRFNVLVCTTIIETGIDIPTANTI 883
Cdd:COG4098 314 KRLKEGRQLLIFVPTIELLEQLVALLQKLFPEERIAGVHAEDPERK-EKVQ-AFRDGEIPILVTTTILERGVTFPNVDVA 391
|
330 340
....*....|....*....|....*
gi 1910937583 884 IIErADH--FGLAQLHQLRGRVGRS 906
Cdd:COG4098 392 VLG-ADHpvFTEAALVQIAGRVGRS 415
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
827-905 |
3.69e-16 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 74.56 E-value: 3.69e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 827 ERLAELVPEARIAIG--HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADhFGLAQLHQLRGRVG 904
Cdd:smart00490 1 EELAELLKELGIKVArlHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-WSPASYIQRIGRAG 79
|
.
gi 1910937583 905 R 905
Cdd:smart00490 80 R 80
|
|
| PRK05298 |
PRK05298 |
excinuclease ABC subunit UvrB; |
119-225 |
8.24e-13 |
|
excinuclease ABC subunit UvrB;
Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 72.77 E-value: 8.24e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 119 PHSFlHGHALVMKKGQRLSRDALRTQLDSAGYRHVDQVMEHGEYATRGALLDLFPMGSE-LPYRLDFFDDEIDSLRVFDV 197
Cdd:PRK05298 151 PEEY-LKMVLSLRVGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPAYYEeRAIRIEFFGDEIERISEFDP 229
|
90 100
....*....|....*....|....*...
gi 1910937583 198 DSQRTLEEVEAINLLPAHEFPTDKAAIE 225
Cdd:PRK05298 230 LTGEVLGELDRVTIYPASHYVTPRERLE 257
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
593-984 |
1.51e-12 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 71.46 E-value: 1.51e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 593 FCDSFPFET-TPDQAQAINAVLSDmcqplamDR--LVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNF 669
Cdd:COG1204 14 FLKERGIEElYPPQAEALEAGLLE-------GKnlVVSAPTASGKTLIAELAILKALLNGGKALYIVPLRALASEKYREF 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 670 RDRFANWPVRIEMISR-FRSAKEQTqilaevaeGKIDILIGT----HKLLQSDVKF-KDLGLLIVDEEHRFGVRHK---- 739
Cdd:COG1204 87 KRDFEELGIKVGVSTGdYDSDDEWL--------GRYDILVATpeklDSLLRNGPSWlRDVDLVVVDEAHLIDDESRgptl 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 740 ----ERIKAMRANVDILTLTATpiprtlnmaMSGMRDLS------IIAT---PPARRLAV----------KTFVREYDSL 796
Cdd:COG1204 159 evllARLRRLNPEAQIVALSAT---------IGNAEEIAewldaeLVKSdwrPVPLNEGVlydgvlrfddGSRRSKDPTL 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 797 vvrEAILREILRGGQVYYLYNDVENIQKAAERLAELVPE-------ARIAIGHGQMRERELERVMND-----------FH 858
Cdd:COG1204 230 ---ALALDLLEEGGQVLVFVSSRRDAESLAKKLADELKRrltpeerEELEELAEELLEVSEETHTNEkladclekgvaFH 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 859 H------QR-----------FNVLVCTTIIETGIDIPtANTIIIERADHFGLAQL-----HQLRGRVGRSHH--QAYAWL 914
Cdd:COG1204 307 HaglpseLRrlvedafreglIKVLVATPTLAAGVNLP-ARRVIIRDTKRGGMVPIpvlefKQMAGRAGRPGYdpYGEAIL 385
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1910937583 915 LTPHPKAMTTDAQKRL----EAIASLedLGAGFALATHDLEIRGAGELLGEEqsGSMETIGFSLY-----MELLENAVD 984
Cdd:COG1204 386 VAKSSDEADELFERYIlgepEPIRSK--LANESALRTHLLALIASGFANSRE--ELLDFLENTFYayqydKGDLEEVVD 460
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
584-732 |
1.68e-12 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 71.73 E-value: 1.68e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 584 KHDREQYQLFCDSFPFETTPDQAQAINAVLsdmcqplAMDR----LVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTT 659
Cdd:PRK05580 128 EVLRLRPPPDPAFEPPTLNPEQAAAVEAIR-------AAAGfspfLLDGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEI 200
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1910937583 660 LLAQQHYDNFRDRFANWPVriEMISRFrSAKEQTQILAEVAEGKIDILIGThkllQSDV--KFKDLGLLIVDEEH 732
Cdd:PRK05580 201 ALTPQMLARFRARFGAPVA--VLHSGL-SDGERLDEWRKAKRGEAKVVIGA----RSALflPFKNLGLIIVDEEH 268
|
|
| UvrB |
COG0556 |
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; |
119-225 |
5.48e-12 |
|
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
Pssm-ID: 440322 [Multi-domain] Cd Length: 657 Bit Score: 70.04 E-value: 5.48e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 119 PHSFlHGHALVMKKGQRLSRDALRTQLDSAGYRHVDQVMEHGEYATRGALLDLFPMGS-ELPYRLDFFDDEIDSLRVFDV 197
Cdd:COG0556 148 PEEY-LKMVLSLRVGEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAYSeERAIRIEFFGDEIERISEFDP 226
|
90 100
....*....|....*....|....*...
gi 1910937583 198 DSQRTLEEVEAINLLPAHEFPTDKAAIE 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 |
1.24e-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: 61.51 E-value: 1.24e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 602 TPDQAQAINAVLSDmcqplamDR--LVCGDVGFGKTEVAMRAAFLAVDNHKQVAV-LVPTTLLAQQHYDNFRDRFANWPV 678
Cdd:cd17921 3 NPIQREALRALYLS-------GDsvLVSAPTSSGKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFGPLGK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 679 RIEM----ISRFRSAKEQTQILAEVAEgKIDILIGTHkllqSDVKFKDLGLLIVDEEHRFGVRHK--------ERIKAMR 746
Cdd:cd17921 76 NVGLltgdPSVNKLLLAEADILVATPE-KLDLLLRNG----GERLIQDVRLVVVDEAHLIGDGERgvvlelllSRLLRIN 150
|
170
....*....|.
gi 1910937583 747 ANVDILTLTAT 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 |
1.63e-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: 1.63e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 631 GFGKTEVAMrAAFLAVDNHKqVAVLVPTTLLAQQHYDNFRDrfanwPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGT 710
Cdd:cd17926 28 GSGKTLTAL-ALIAYLKELR-TLIVVPTDALLDQWKERFED-----FLGDSSIGLIGGGKKKDFDDANVVVATYQSLSNL 100
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 1910937583 711 HKLLQSdvKFKDLGLLIVDEEHRFGVRHKERIKAMRANVDILTLTATP 758
Cdd:cd17926 101 AEEEKD--LFDQFGLLIVDEAHHLPAKTFSEILKELNAKYRLGLTATP 146
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
564-732 |
3.48e-10 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 64.37 E-value: 3.48e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 564 VAAELLDIYAQRAAKEGFAFKHDREQyqlfcdsfPFETTPDQAQAINAVLSdmcqplAMDR----LVCGDVGFGKTEVAM 639
Cdd:COG1198 167 VKKGLLEIEEREVDRDPFAPDVPAEP--------PPTLNEEQQAAVEAIRA------AAGGfsvfLLHGVTGSGKTEVYL 232
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 640 RAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVriEMISRFrSAKEQTQILAEVAEGKIDILIGThkllQSDV- 718
Cdd:COG1198 233 QAIAEVLAQGKQALVLVPEIALTPQTVERFRARFGARVA--VLHSGL-SDGERLDEWRRARRGEARIVIGT----RSALf 305
|
170
....*....|....*
gi 1910937583 719 -KFKDLGLLIVDEEH 732
Cdd:COG1198 306 aPFPNLGLIIVDEEH 320
|
|
| SrmB |
COG0513 |
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
599-905 |
2.29e-09 |
|
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 60.93 E-value: 2.29e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 599 FET-TPDQAQAInavlsdmcqPLAMDR---LVCGDVGFGKTevamrAAFL---------AVDNHKQVAVLVPTTLLAQQH 665
Cdd:COG0513 22 YTTpTPIQAQAI---------PLILAGrdvLGQAQTGTGKT-----AAFLlpllqrldpSRPRAPQALILAPTRELALQV 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 666 YDNFRDRFANWPVRIEMISRFRSAKEQTQILAEvaegKIDILIGT------HkLLQSDVKFKDLGLLIVDEEHR---FGV 736
Cdd:COG0513 88 AEELRKLAKYLGLRVATVYGGVSIGRQIRALKR----GVDIVVATpgrlldL-IERGALDLSGVETLVLDEADRmldMGF 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 737 RHK-ERI-KAMRANVDILTLTATpIPRTL-NMAMSGMRDLSIIATPPARRLAVKT-----FVREYDslvvREAILREILR 808
Cdd:COG0513 163 IEDiERIlKLLPKERQTLLFSAT-MPPEIrKLAKRYLKNPVRIEVAPENATAETIeqryyLVDKRD----KLELLRRLLR 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 809 ggqvyylyndVENIQKA---------AERLAELVPEARIAIG--HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDI 877
Cdd:COG0513 238 ----------DEDPERAivfcntkrgADRLAEKLQKRGISAAalHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDI 307
|
330 340 350
....*....|....*....|....*....|....
gi 1910937583 878 PTANTIIieradHFGLAQ-----LHqlR-GRVGR 905
Cdd:COG0513 308 DDVSHVI-----NYDLPEdpedyVH--RiGRTGR 334
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
846-905 |
8.02e-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: 8.02e-09
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 846 RERELERVMNdfhhqRFNVLVCTTIIETGIDIPTANTIIIERAdHFGLAQLHQLRGRVGR 905
Cdd:cd18785 12 SIEHAEEIAS-----SLEILVATNVLGEGIDVPSLDTVIFFDP-PSSAASYIQRVGRAGR 65
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
631-759 |
3.08e-08 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 54.22 E-value: 3.08e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 631 GFGKTEVAMRAAFLAVDNH--KQVAVLVPTTLLAQQHYDNFRDRFANWpvriEMISRFRSAKEQTQILaevaeGKIDILI 708
Cdd:pfam04851 33 GSGKTLTAAKLIARLFKKGpiKKVLFLVPRKDLLEQALEEFKKFLPNY----VEIGEIISGDKKDESV-----DDNKIVV 103
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 1910937583 709 GT-HKLLQSDVKFKDL------GLLIVDEEHRFGVRHKERIKAMRANVDILTLTATPI 759
Cdd:pfam04851 104 TTiQSLYKALELASLEllpdffDVIIIDEAHRSGASSYRNILEYFKPAFLLGLTATPE 161
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
629-759 |
4.69e-08 |
|
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350769 [Multi-domain] Cd Length: 207 Bit Score: 54.60 E-value: 4.69e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 629 DVGFGKT-EVAMRAAFLAVDN-HKQVAVLVPTTLLAQ-QHYdnFRDRFANwpvRIEMISRFRSAKEQTQILAEVAEGKID 705
Cdd:cd18011 25 EVGLGKTiEAGLIIKELLLRGdAKRVLILCPASLVEQwQDE--LQDKFGL---PFLILDRETAAQLRRLIGNPFEEFPIV 99
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1910937583 706 I----LIGTHKLLQSDVKFKDLGLLIVDEEHRF----GVRHKERIKAMRANVD----ILTLTATPI 759
Cdd:cd18011 100 IvsldLLKRSEERRGLLLSEEWDLVVVDEAHKLrnsgGGKETKRYKLGRLLAKrarhVLLLTATPH 165
|
|
| DEXHc_Hef |
cd18035 |
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
625-758 |
3.05e-07 |
|
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: 51.75 E-value: 3.05e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 625 LVCGDVGFGKTEVAMRAAFLAVDNHK-QVAVLVPTTLLAQQHYDNFRdRFANWPVRIEMISRFRSAKEQTQILAevaegK 703
Cdd:cd18035 20 LIVLPTGLGKTIIAILVAADRLTKKGgKVLILAPSRPLVEQHAENLK-RVLNIPDKITSLTGEVKPEERAERWD-----A 93
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1910937583 704 IDILIGTHKLLQSD-----VKFKDLGLLIVDEEHRFGVRHK-----ERIKAMRANVDILTLTATP 758
Cdd:cd18035 94 SKIIVATPQVIENDllagrITLDDVSLLIFDEAHHAVGNYAyvyiaHRYKREANNPLILGLTASP 158
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
823-905 |
3.76e-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: 50.20 E-value: 3.76e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 823 QKAAERLAELVPEARIAIG--HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIieradHFGLAQ----- 895
Cdd:cd18787 37 KKRVDRLAELLEELGIKVAalHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGVDHVI-----NYDLPRdaedy 111
|
90
....*....|.
gi 1910937583 896 LHqlR-GRVGR 905
Cdd:cd18787 112 VH--RiGRTGR 120
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
625-758 |
4.28e-07 |
|
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350685 [Multi-domain] Cd Length: 201 Bit Score: 51.66 E-value: 4.28e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 625 LVCGDVGFGKTEVAMraafLAVDNH---------KQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQI 695
Cdd:cd17927 21 IICLPTGSGKTFVAV----LICEHHlkkfpagrkGKVVFLANKVPLVEQQKEVFRKHFERPGYKVTGLSGDTSENVSVEQ 96
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1910937583 696 LAEVAegkiDILIGTHKLLQSDVK------FKDLGLLIVDEEHR--------FGVRH--KERIKAMRANVDILTLTATP 758
Cdd:cd17927 97 IVESS----DVIIVTPQILVNDLKsgtivsLSDFSLLVFDECHNttknhpynEIMFRylDQKLGSSGPLPQILGLTASP 171
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
631-907 |
7.05e-07 |
|
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I
Pssm-ID: 187770 [Multi-domain] Cd Length: 353 Bit Score: 52.82 E-value: 7.05e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 631 GFGKTEVAMRAAFLAVDNHK--QVAVLVPTTLLAQQHYDNFRDRFANwPVRIEMISRFRSAKEQTQILAEVAEGKIDIlI 708
Cdd:cd09639 9 GYGKTEAALLWALHSLKSQKadRVIIALPTRATINAMYRRAKEAFGE-TGLYHSSILSSRIKEMGDSEEFEHLFPLYI-H 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 709 GTHKLLQSDVK-----------FKDLG------------LLIVDEEHRFGVRHKERIKAM-----RANVDILTLTATpIP 760
Cdd:cd09639 87 SNDTLFLDPITvctidqvlksvFGEFGhyeftlasiansLLIFDEVHFYDEYTLALILAVlevlkDNDVPILLMSAT-LP 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 761 RTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSLVVREAILREILR----GGQVYYLYNDVENIQKAAERLAELVPEA 836
Cdd:cd09639 166 KFLKEYAEKIGYVEENEPLDLKPNERAPFIKIESDKVGEISSLERLLEfikkGGSVAIIVNTVDRAQEFYQQLKEKGPEE 245
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1910937583 837 RIAIGHGQM----RERELERVMNDFHHQRFNVLVCTTIIETGIDIpTANTIIIERADhfgLAQLHQLRGRVGRSH 907
Cdd:cd09639 246 EIMLIHSRFtekdRAKKEAELLLEFKKSEKFVIVATQVIEASLDI-SVDVMITELAP---IDSLIQRLGRLHRYG 316
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
603-757 |
8.16e-07 |
|
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: 50.41 E-value: 8.16e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 603 PDQAQAINAVLSDmcqplAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDrFANWPVRIEM 682
Cdd:cd18028 4 PPQAEAVRAGLLK-----GENLLISIPTASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEEFKK-LEEIGLKVGI 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 683 -ISRFRSAKEQTqilaevaeGKIDILIGTHKLLQSDVKFK-----DLGLLIVDEEHRFGVRHK--------ERIKAMRAN 748
Cdd:cd18028 78 sTGDYDEDDEWL--------GDYDIIVATYEKFDSLLRHSpswlrDVGVVVVDEIHLISDEERgptlesivARLRRLNPN 149
|
....*....
gi 1910937583 749 VDILTLTAT 757
Cdd:cd18028 150 TQIIGLSAT 158
|
|
| UB2H |
pfam14814 |
Bifunctional transglycosylase second domain; UB2H is the second domain of the ... |
133-207 |
4.48e-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: 4.48e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 133 GQRLSRDALRTQLDSAGYRHVDQVMEHGEYATRGALLDL------FPMGSE--LPYRLDFFDDEIDSLRvfDVDSQRTLE 204
Cdd:pfam14814 4 GQALSAAQLEQELKLLGYRKVSNPTRPGEYSVSGNRIELyrrgfdFPDGAEpaRRVRLRFAGGRVARLQ--DLDTGRDLA 81
|
...
gi 1910937583 205 EVE 207
Cdd:pfam14814 82 LVR 84
|
|
| RecQ |
COG0514 |
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
678-915 |
5.80e-06 |
|
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 50.14 E-value: 5.80e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 678 VRIEMISRFRSAKEQTQILAEVAEGKIDILI---------GTHKLLQSDvkfkDLGLLIVDEEH-------------Rfg 735
Cdd:COG0514 82 IRAAFLNSSLSAEERREVLRALRAGELKLLYvaperllnpRFLELLRRL----KISLFAIDEAHcisqwghdfrpdyR-- 155
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 736 vrhkeRIKAMRA---NVDILTLTATPIPRTLN--MAMSGMRDLSIIATPPAR---RLAVKTFVREYdslvVREAILREI- 806
Cdd:COG0514 156 -----RLGELRErlpNVPVLALTATATPRVRAdiAEQLGLEDPRVFVGSFDRpnlRLEVVPKPPDD----KLAQLLDFLk 226
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 807 -LRGGQ--VYYLyndvenIQKAAERLAELVPEARIAIG--HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTAN 881
Cdd:COG0514 227 eHPGGSgiVYCL------SRKKVEELAEWLREAGIRAAayHAGLDAEEREANQDRFLRDEVDVIVATIAFGMGIDKPDVR 300
|
250 260 270
....*....|....*....|....*....|....*...
gi 1910937583 882 TIIieradHFGLAQL----HQLRGRVGRSHHQAYAWLL 915
Cdd:COG0514 301 FVI-----HYDLPKSieayYQEIGRAGRDGLPAEALLL 333
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
625-758 |
8.16e-06 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 50.11 E-value: 8.16e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 625 LVCGDVGFGKTEVAMR--AAFLAVDNHKqVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVaeg 702
Cdd:COG1111 21 LVVLPTGLGKTAVALLviAERLHKKGGK-VLFLAPTKPLVEQHAEFFKEALNIPEDEIVVFTGEVSPEKRKELWEKA--- 96
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1910937583 703 kiDILIGTHKLLQSD-----VKFKDLGLLIVDEEHR-FG----VRHKERIKAMRANVDILTLTATP 758
Cdd:COG1111 97 --RIIVATPQVIENDliagrIDLDDVSLLIFDEAHRaVGnyayVYIAERYHEDAKDPLILGMTASP 160
|
|
| SF2_C_XPB |
cd18789 |
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
789-905 |
1.17e-05 |
|
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350176 [Multi-domain] Cd Length: 153 Bit Score: 46.47 E-value: 1.17e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 789 FVREYDSLVVR-------------EAILREILR----GGQVYYLYNDVENIQKAAERLaeLVPeariAIgHGQMRERELE 851
Cdd:cd18789 12 FYREYLGLGAHrkrrllaamnpnkLRALEELLKrheqGDKIIVFTDNVEALYRYAKRL--LKP----FI-TGETPQSERE 84
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....
gi 1910937583 852 RVMNDFHHQRFNVLVCTTIIETGIDIPTANtIIIERADHFGLAQlhQLRGRVGR 905
Cdd:cd18789 85 EILQNFREGEYNTLVVSKVGDEGIDLPEAN-VAIQISGHGGSRR--QEAQRLGR 135
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
822-919 |
1.55e-05 |
|
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: 47.62 E-value: 1.55e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 822 IQKAAERLAELVPEARIAIghgqM------RERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADhFGL-- 893
Cdd:cd18804 103 TERVEEELKTLFPEARIAR----IdrdttrKKGALEKLLDQFERGEIDILIGTQMIAKGLDFPNVTLVGILNAD-SGLns 177
|
90 100 110
....*....|....*....|....*....|....*.
gi 1910937583 894 ---------AQL-HQLRGRVGRSHHQAYAWLLTPHP 919
Cdd:cd18804 178 pdfraseraFQLlTQVSGRAGRGDKPGKVIIQTYNP 213
|
|
| DEXHc_Snf |
cd17919 |
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
629-760 |
2.29e-05 |
|
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: 46.41 E-value: 2.29e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 629 DVGFGKTevAMRAAFLAVDNHKQ-----VAVLVPTTLLaqqhyDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGK 703
Cdd:cd17919 27 EMGLGKT--LQAIAFLAYLLKEGkergpVLVVCPLSVL-----ENWEREFEKWTPDLRVVVYHGSQRERAQIRAKEKLDK 99
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1910937583 704 IDILIGTHKLLQSDVKF---KDLGLLIVDEEHRF----GVRHKeRIKAMRANVDILtLTATPIP 760
Cdd:cd17919 100 FDVVLTTYETLRRDKASlrkFRWDLVVVDEAHRLknpkSQLSK-ALKALRAKRRLL-LTGTPLQ 161
|
|
| SF2_C_dicer |
cd18802 |
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
840-902 |
2.73e-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: 2.73e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1910937583 840 IGHG--------QMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIeradhFGLA----QLHQLRGR 902
Cdd:cd18802 61 IGRGnssqrkrsLMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVIR-----FDLPktlrSYIQSRGR 130
|
|
| DEXHc_RLR |
cd18036 |
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
625-758 |
3.33e-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: 46.31 E-value: 3.33e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 625 LVCGDVGFGKTEVAMRAAFLAVDNHKQ------VAVLVPTTLLAQQHYDNFRDRFANWpVRIEMISRFRSAKEQTQilaE 698
Cdd:cd18036 21 IICAPTGSGKTRVAVYICRHHLEKRRSagekgrVVVLVNKVPLVEQQLEKFFKYFRKG-YKVTGLSGDSSHKVSFG---Q 96
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1910937583 699 VAEGKiDILIGTHKLLQS---------DVKFKDLGLLIVDEEHRFGVRH----------KERIKAMRANVDILTLTATP 758
Cdd:cd18036 97 IVKAS-DVIICTPQILINnllsgreeeRVYLSDFSLLIFDECHHTQKEHpynkimrmylDKKLSSQGPLPQILGLTASP 174
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
826-1067 |
5.74e-05 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 47.42 E-value: 5.74e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 826 AERLAELVPEARIAIGHGQ------MRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTII-----------IERa 888
Cdd:COG1111 370 VEFLSEPGIKAGRFVGQASkegdkgLTQKEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVIfyepvpseirsIQR- 448
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 889 dhfglaqlhqlRGRVGRSHH-------------QAYAWLLTPHPKAMtTDAQKRLEAIASLEDLGAGFALATHDLEirga 955
Cdd:COG1111 449 -----------KGRTGRKREgrvvvliakgtrdEAYYWSSRRKEKKM-KSILKKLKKLLDKQEKEKLKESAQATLD---- 512
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 956 gELLGEEQSGSMETIGFSLYmELLENAVDALKAGREPSLE--DLTSQQTEVELRMPS-LLPDDFIPDVNTRLSFYKRIAS 1032
Cdd:COG1111 513 -EFESIKELAEDEINEKDLD-EIESSENGAHVDWREPVLLqvIVSTLAESLELRELGeKVDDEVNLILEIDRVDVVDDGS 590
|
250 260 270
....*....|....*....|....*....|....*
gi 1910937583 1033 AKTENELEEIKVELIDRFGLLPDPARILLDVARLR 1067
Cdd:COG1111 591 VLRVSRLLVEIGELDGKTRVIIASYGDEYFDAILR 625
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
621-759 |
7.15e-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: 44.95 E-value: 7.15e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 621 AMDR--LVCGDVGFGKTEVA-MRAAFLAVD------NHKQVAVLVPTTLLAQQHYDNFRDrfaNWPVRIEMISRFRSAKE 691
Cdd:cd18034 14 ALKRntIVVLPTGSGKTLIAvMLIKEMGELnrkeknPKKRAVFLVPTVPLVAQQAEAIRS---HTDLKVGEYSGEMGVDK 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 692 QTQILAEVAEGKIDILIGTHKLL-----QSDVKFKDLGLLIVDEEHRFGVRH------KE-RIKAMRANV-DILTLTATP 758
Cdd:cd18034 91 WTKERWKEELEKYDVLVMTAQILldalrHGFLSLSDINLLIFDECHHATGDHpyarimKEfYHLEGRTSRpRILGLTASP 170
|
.
gi 1910937583 759 I 759
Cdd:cd18034 171 V 171
|
|
| DEADc |
cd00268 |
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ... |
599-730 |
7.59e-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: 45.13 E-value: 7.59e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 599 FET-TPDQAQAINAVLSDMcqplamDRLVCGDVGFGKTevamrAAFL------------AVDNHKQVAVLVPTTLLAQQH 665
Cdd:cd00268 10 FEKpTPIQAQAIPLILSGR------DVIGQAQTGSGKT-----LAFLlpilekllpepkKKGRGPQALVLAPTRELAMQI 78
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 666 YDNFRdRFANwPVRIEMISRFRSAKEQTQILAEvaEGKIDILIGT----HKLLQS-DVKFKDLGLLIVDE 730
Cdd:cd00268 79 AEVAR-KLGK-GTGLKVAAIYGGAPIKKQIEAL--KKGPDIVVGTpgrlLDLIERgKLDLSNVKYLVLDE 144
|
|
| SF2_C_FANCM_Hef |
cd18801 |
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
817-905 |
1.55e-04 |
|
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350188 [Multi-domain] Cd Length: 143 Bit Score: 43.11 E-value: 1.55e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 817 NDVENIQKAAERLAELVpEARIAIGHGQ------MRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADH 890
Cdd:cd18801 41 DSAEEIVNFLSKIRPGI-RATRFIGQASgksskgMSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASP 119
|
90
....*....|....*
gi 1910937583 891 FGLAQLhQLRGRVGR 905
Cdd:cd18801 120 SPIRMI-QRMGRTGR 133
|
|
| DDXDc_reverse_gyrase |
cd17924 |
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
631-729 |
3.05e-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: 43.08 E-value: 3.05e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 631 GFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRD--RFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILI 708
Cdd:cd17924 42 GVGKTTFGLATSLYLASKGKRSYLIFPTKSLVKQAYERLSKyaEKAGVEVKILVYHSRLKKKEKEELLEKIEKGDFDILV 121
|
90 100
....*....|....*....|....
gi 1910937583 709 GTHKLLQSDV---KFKDLGLLIVD 729
Cdd:cd17924 122 TTNQFLSKNFdllSNKKFDFVFVD 145
|
|
| DEXHc_RecQ |
cd17920 |
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ... |
603-763 |
5.63e-04 |
|
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box helicase superfamily is a family of highly conserved DNA repair helicases. This domain contains the ATP-binding region.
Pssm-ID: 350678 [Multi-domain] Cd Length: 200 Bit Score: 42.52 E-value: 5.63e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 603 PDQAQAINAVLSdmcqplAMDRLVCGDVGFGKTEVAMRAAFLAvdnHKQVAVLVPttLLA----QQhydnfrDRFANWPV 678
Cdd:cd17920 15 PGQLEAINAVLA------GRDVLVVMPTGGGKSLCYQLPALLL---DGVTLVVSP--LISlmqdQV------DRLQQLGI 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 679 RIEMISRFRSAKEQTQILAEVAEGKIDILI---------GTHKLLQSDVKFKDLGLLIVDEEH--------------RFG 735
Cdd:cd17920 78 RAAALNSTLSPEEKREVLLRIKNGQYKLLYvtperllspDFLELLQRLPERKRLALIVVDEAHcvsqwghdfrpdylRLG 157
|
170 180
....*....|....*....|....*...
gi 1910937583 736 vrhkeRIKAMRANVDILTLTATPIPRTL 763
Cdd:cd17920 158 -----RLRRALPGVPILALTATATPEVR 180
|
|
| SF2_C_EcoAI-like |
cd18799 |
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ... |
826-887 |
7.39e-04 |
|
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: 40.24 E-value: 7.39e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1910937583 826 AERLAELVPEA---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 ... |
821-909 |
8.21e-04 |
|
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: 41.10 E-value: 8.21e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 821 NIQKAAERLA--------ELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTII-IERAdhF 891
Cdd:cd18796 46 NTRSQAERLAqrlrelcpDRVPPDFIALHHGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIGDVDLVIqIGSP--K 123
|
90
....*....|....*...
gi 1910937583 892 GLAQLHQlrgRVGRSHHQ 909
Cdd:cd18796 124 SVARLLQ---RLGRSGHR 138
|
|
| DEADc_DDX52 |
cd17957 |
DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ... |
600-730 |
1.06e-03 |
|
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: 41.42 E-value: 1.06e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 600 ETTPDQAQAInavlsdmcqPLAMDR---LVCGDVGFGKTevamrAAFL-----AVDNHKQVA-----VLVPTTLLAQQHY 666
Cdd:cd17957 12 EPTPIQMQAI---------PILLHGrdlLACAPTGSGKT-----LAFLipilqKLGKPRKKKglralILAPTRELASQIY 77
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1910937583 667 DNFRDRFANWPVRIEMISrfrsaKEQTQILAEVAEG--KIDILIGTHKLL-----QSDVKFKDLGLLIVDE 730
Cdd:cd17957 78 RELLKLSKGTGLRIVLLS-----KSLEAKAKDGPKSitKYDILVSTPLRLvfllkQGPIDLSSVEYLVLDE 143
|
|
| DEXHc_Brr2_1 |
cd18019 |
N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD ... |
598-741 |
1.21e-03 |
|
N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD box helicase that mediates spliceosome catalytic activation. It is a stable subunit of the spliceosome, required during splicing catalysis and spliceosome disassembly. Brr2 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: 350777 [Multi-domain] Cd Length: 214 Bit Score: 41.59 E-value: 1.21e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 598 PFETTpdqaQAINAVLSDMCqPLAMDR----LVCGDVGFGKTEVAMRAAFLAVDNHK-----------QVAVLVPTTLLA 662
Cdd:cd18019 11 AFEGF----KSLNRIQSKLF-PAAFETdenlLLCAPTGAGKTNVALLTILREIGKHRnpdgtinldafKIVYIAPMKALV 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 663 QQHYDNFRDRFANWPVRI-EMISRFRSAKEQ---TQILAEVAEgKIDILigTHKllQSDVKFKDL-GLLIVDEEHrfgVR 737
Cdd:cd18019 86 QEMVGNFSKRLAPYGITVaELTGDQQLTKEQiseTQIIVTTPE-KWDII--TRK--SGDRTYTQLvRLIIIDEIH---LL 157
|
....
gi 1910937583 738 HKER 741
Cdd:cd18019 158 HDDR 161
|
|
| 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 |
2.16e-03 |
|
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of genetics and physiology 2 or LGP2 and DHX58) appears to positively and negatively regulate MDA5 and RIG-I signaling, respectively. RLR-3 resembles a chimera combining a MDA5-like helicase domain and RIG-I like CTD supporting both stem and end binding. RNA binding is required for RLR-3-mediated enhancement of MDA5 activation. RLR-3 end-binding may promote nucleation of MDA5 oligomerization on dsRNA. RLR-3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350833 [Multi-domain] Cd Length: 200 Bit Score: 40.61 E-value: 2.16e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 631 GFGKTEVAMRAA--FLAVDNHKQVAVLVPTTLLAQQHYDNFR----DRFanwpvRIEMISRFRSAKEQTQILAEVAegki 704
Cdd:cd18075 27 GAGKTRAAVYVArrHLETKRGAKVAVLVNKVHLVDQHLEKEFhvllDKY-----TVTAISGDSSHKCFFGQLARGS---- 97
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1910937583 705 DILIGTHKLLQS---------DVKFKDLGLLIVDEEHRfgvRHKERI--KAMRANVDILTLTATPIPRTLNMAMS 768
Cdd:cd18075 98 DVVICTAQILQNallsgeeeaHVELTDFSLLVIDECHH---THKEAVynKIMLSYLEKKLSRQGDLPQILGLTAS 169
|
|
| DEXHc_SKIV2L |
cd18027 |
DEXH-box helicase domain of SKIV2L; Superkiller viralicidic activity 2-like (SKIV2L, also ... |
596-779 |
2.37e-03 |
|
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: 40.33 E-value: 2.37e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 596 SFPFETTPDQAQAInavlsdMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFAN 675
Cdd:cd18027 4 KWPFELDVFQKQAI------LHLEAGDSVFVAAHTSAGKTVVAEYAIALAQKHMTRTIYTSPIKALSNQKFRDFKNTFGD 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 676 wpvrIEMISrfrsakEQTQILAEVAegkidILIGTHKLLQS------DVkFKDLGLLIVDEEHRF-----GVRHKERIKA 744
Cdd:cd18027 78 ----VGLIT------GDVQLNPEAS-----CLIMTTEILRSmlyngsDV-IRDLEWVIFDEVHYIndaerGVVWEEVLIM 141
|
170 180 190
....*....|....*....|....*....|....*....
gi 1910937583 745 MRANVDILTLTATpIPRTLNMA----MSGMRDLSIIATP 779
Cdd:cd18027 142 LPDHVSIILLSAT-VPNTVEFAdwigRIKKKNIYVISTP 179
|
|
| DEADc_MRH4 |
cd17965 |
DEAD-box helicase domain of ATP-dependent RNA helicase MRH4; Mitochondrial RNA helicase 4 ... |
654-779 |
3.01e-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: 40.82 E-value: 3.01e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 654 VLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAevAEGKIDILIGTHKLLQSDVK-----FKDLGLLIV 728
Cdd:cd17965 114 ILVPTHELVEQVYSVLKKLSHTVKLGIKTFSSGFGPSYQRLQLA--FKGRIDILVTTPGKLASLAKsrpkiLSRVTHLVV 191
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*..
gi 1910937583 729 DE-----EHRFGVRHKERIKAMRANVDILTLTATpIPRTLNMAMSGM-RDLSIIATP 779
Cdd:cd17965 192 DEadtlfDRSFLQDTTSIIKRAPKLKHLILCSAT-IPKEFDKTLRKLfPDVVRIATP 247
|
|
| PRK13766 |
PRK13766 |
Hef nuclease; Provisional |
625-758 |
4.14e-03 |
|
Hef nuclease; Provisional
Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 41.40 E-value: 4.14e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 625 LVCGDVGFGKTEVAM--RAAFLAVDNHKqVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMIS-RFRSAKEQtqilAEVAE 701
Cdd:PRK13766 33 LVVLPTGLGKTAIALlvIAERLHKKGGK-VLILAPTKPLVEQHAEFFRKFLNIPEEKIVVFTgEVSPEKRA----ELWEK 107
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1910937583 702 GKIdiLIGTHKLLQSD-----VKFKDLGLLIVDEEHR-FG----VRHKERIKAMRANVDILTLTATP 758
Cdd:PRK13766 108 AKV--IVATPQVIENDliagrISLEDVSLLIFDEAHRaVGnyayVYIAERYHEDAKNPLVLGLTASP 172
|
|
| DEADc_DDX51 |
cd17956 |
DEAD-box helicase domain of DEAD box protein 51; DDX51 aids cell cancer proliferation by ... |
603-734 |
9.12e-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: 39.15 E-value: 9.12e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1910937583 603 PDQAQAINAVLSDMCQPLA---MDRLVCGDVGFGKTevamrAAFL---------AVDNHKQVAVLVPTTLLAQQHYDNFR 670
Cdd:cd17956 15 PVQAAVIPWLLPSSKSTPPyrpGDLCVSAPTGSGKT-----LAYVlpivqalskRVVPRLRALIVVPTKELVQQVYKVFE 89
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1910937583 671 DRFANWPVRIEMISRFRSAKEQTQILAEVAEG----KIDILIGT------HklLQSDVKF--KDLGLLIVDEEHRF 734
Cdd:cd17956 90 SLCKGTGLKVVSLSGQKSFKKEQKLLLVDTSGrylsRVDILVATpgrlvdH--LNSTPGFtlKHLRFLVIDEADRL 163
|
|
| |
