|
Name |
Accession |
Description |
Interval |
E-value |
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
23-1142 |
0e+00 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 1337.02 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 23 GQLYGSSINLALAERIKNDLDFKIVIAPEINSAEILCNEINYFSeTGLSIELLPDLEILPYDVSSPSNQVIANRSEILFQ 102
Cdd:COG1197 8 SGLPGSARALLLAALARALGRPLLVVTADEREAERLAEDLRFFL-PDLPVLLFPAWETLPYDRFSPSPDIVSERLATLRR 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 103 LLKGNIDVLVLNASSLLWKLPPRKYFEKESFTLSVGELFSMQQIGEKLRINGYERVSTVIKPGEFCIRGSLIDLFSPLYT 182
Cdd:COG1197 87 LASGKPGIVVTPVRALLQRLPPPELLAAASLSLKVGDELDLEELRERLVAAGYERVDQVEEPGEFAVRGGILDIFPPGSE 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 183 NPIRIDFDDEKIDLIKLFDVDSQLTLNTINSVTIIPSEHYPKSSLAFDFFKTNMRNAFDGNQLEWPLYNFIETYAESHGV 262
Cdd:COG1197 167 HPVRIEFFGDEIESIRTFDPETQRSLEKVDEVELLPAREFPLDEEAIERFRERLRELFGLDPKLDELYEALSEGIAFAGI 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 263 YNYLPLFFESMSSIWDYCKPGTKLFCVG--DIKTSIKEYQKLINQRFNS-QDNLSQPNLKPSELFFSATEQINKINEMHP 339
Cdd:COG1197 247 EYYLPLFYEELATLFDYLPEDALVVLDEpeRIEEAAEEFWEEIEERYEArRHDRGRPLLPPEELFLDPEELFAALKRRPR 326
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 340 INLQHQKCwKSRAHNSINFDTRPLTAFKtSSMDKIIHGLLE--TSTNKILLSAGSKNRIAFIENQLREFSIAARRVSNWN 417
Cdd:COG1197 327 VTLSPFAA-LPEGAGVVNLGARPLPSFA-GQLEALLEELKRllKDGGRVLLAAESEGRRERLLELLRDHGIPARLVESLA 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 418 EFleRRAGVFVTEKSISESFITAKSGIAVIGEIELFGRRSSTRKYRSPagKDPESIIQDLKDLQVGSLVVHGEHGIGKYK 497
Cdd:COG1197 405 EL--SPGGVAITVGPLEHGFELPDAKLAVITESELFGERVKRRRRKKK--RSADAFIRDLSELKPGDYVVHVDHGIGRYL 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 498 GLSVMMVDNVNSEFLTIEYALGDLLHVPVTLMDQVSRFIGQSSDESILSHLGSNQWKKLCKKTKKQAYDVAAELLEIYAN 577
Cdd:COG1197 481 GLETLEVGGAERDYLVLEYAGGDKLYVPVDQLDLISRYVGSEGEAPKLDKLGGSDWQKAKAKAKKAVRDIAAELLKLYAE 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 578 RAIAVGKSHVANQKDYENFCDGFEYVLTQDQAKVIEDVLDDMAASKSMDRLVCGDVGFGKTEVALRAAFTCAINGYQVAL 657
Cdd:COG1197 561 RAARKGFAFSPDTPWQREFEAAFPYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKTEVALRAAFKAVMDGKQVAV 640
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 658 LVPTTILAQQHFETFNERFSEWPIAINILSRLQTSKNNNQVRTDIEKGKADIIIGTHALLSDKVVYKNLGLVIVDEEHRF 737
Cdd:COG1197 641 LVPTTLLAQQHYETFKERFAGFPVRVEVLSRFRTAKEQKETLEGLADGKVDIVIGTHRLLSKDVKFKDLGLLIIDEEQRF 720
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 738 GVRHKEKLKALRKDVDYLALTATPIPRTLNMAIGELKDISMIATPPEGRIPVKTYISQWDKSLIHEACQREISRGGQVLF 817
Cdd:COG1197 721 GVRHKEKLKALRANVDVLTLTATPIPRTLQMSLSGIRDLSIIATPPEDRLPVKTFVGEYDDALIREAILRELLRGGQVFY 800
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 818 VHNRIDDIENMAETIRQIMPVGSLEIAHGRMKERSLERVMMKFYNNEFDVLLATSIIESGLDIPNANTIIINRADRFGLA 897
Cdd:COG1197 801 VHNRVEDIEKVAARLQELVPEARIAVAHGQMSERELERVMLDFYEGEFDVLVCTTIIETGIDIPNANTIIIERADRFGLA 880
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 898 QLHQLRGRVGRSERQSYAYLMIPPKHTLTNEGRQRLEAIEAIEDLGVGFILATHDLEIRGAGEILGDEQSGQIQKIGFSL 977
Cdd:COG1197 881 QLYQLRGRVGRSHRRAYAYLLYPPDKVLTEDAEKRLEAIQEFTELGAGFKLAMHDLEIRGAGNLLGEEQSGHIAEVGFDL 960
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 978 YKDMLAQAIDSLRDGPQmQSTTISSDINLNIPALIPENYMPDVNLRLTMYKRISSTKSKIEIKHIESELIDRFGELPEQT 1057
Cdd:COG1197 961 YLQMLEEAVAALKGGKE-PEEEWEPEINLGVPALIPEDYIPDVRQRLELYKRIASAESEEELDELQEELIDRFGPLPEEV 1039
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 1058 TNLLLMAHLKNQASTLGIKKIRMDRRYGRFYFDQSTTIEAQNIIDLIEREPDVFKMYPDQSLGFKGDFPLVLNRINQVNT 1137
Cdd:COG1197 1040 ENLLAVARLKLLARRLGIEKIDAGGKGIRIEFSPNTPLDPEKLIRLIQKQPGRYKLDGDDKLVITLDLEDPEERLEALEE 1119
|
....*
gi 167041424 1138 ILGYL 1142
Cdd:COG1197 1120 LLEAL 1124
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
23-1143 |
0e+00 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 931.46 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 23 GQLYGSSINLALAERIKNDLDFKIVIAPEINSAEILCNEINYFseTGLSIELLPDLEILPYDVSSPSNQVIANRSEILFQ 102
Cdd:PRK10689 20 GELTGAACATEVAEIAERHAGPVVLIAPDMQNALRLHDEIQQF--TDQMVMNLADWETLPYDSFSPHQDIISSRLSTLYQ 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 103 LLKGNIDVLVLNASSLLWKLPPRKYFEKESFTLSVGELFSMQQIGEKLRINGYERVSTVIKPGEFCIRGSLIDLFSPLYT 182
Cdd:PRK10689 98 LPTMQRGVLILPVNTLMQRVCPHSFLHGHALVMKKGQRLSRDALRAQLEQAGYRHVDQVMEHGEYATRGALLDLFPMGSE 177
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 183 NPIRIDFDDEKIDLIKLFDVDSQLTLNTINSVTIIPSEHYPKSSLAFDFFKTNMRNAFDGNQLEWPLYNFIETYAESHGV 262
Cdd:PRK10689 178 EPYRIDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFEVKRDAEHIYQQVSKGTLPAGI 257
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 263 YNYLPLFF-ESMSSIWDYCKPGTKLFCVGDIKTSIKEYQKLINQRFNSQ--DNLsQPNLKPSELFFSATEQINKINEMHP 339
Cdd:PRK10689 258 EYWQPLFFsEPLPPLFSYFPANTLLVNTGDLETSAERFWADTLARFENRgvDPM-RPLLPPESLWLRVDELFSELKNWPR 336
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 340 INLQHQKCWKSRAHNSINFDTRP---LTAFKTSSMDKIIHgLLETSTNKILLSAGSKNRIAFIENQLREFSIAARRVSNW 416
Cdd:PRK10689 337 VQLKTEHLPTKAANTNLGYQKLPdlaVQAQQKAPLDALRR-FLESFDGPVVFSVESEGRREALGELLARIKIAPKRIMRL 415
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 417 NEFLErrAGVFVTEKSISESFITAKSGIAVIGEIELFGRRSSTRKYRSPAGKDPESIIQDLKDLQVGSLVVHGEHGIGKY 496
Cdd:PRK10689 416 DEASD--RGRYLMIGAAEHGFIDTVRNLALICESDLLGERVARRRQDSRRTINPDTLIRNLAELHPGQPVVHLEHGVGRY 493
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 497 KGLSVMMVDNVNSEFLTIEYALGDLLHVPVTLMDQVSRFIGQSSDESILSHLGSNQWKKLCKKTKKQAYDVAAELLEIYA 576
Cdd:PRK10689 494 AGMTTLEAGGIKGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHKLGGDAWSRARQKAAEKVRDVAAELLDIYA 573
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 577 NRAIAVGKSHVANQKDYENFCDGFEYVLTQDQAKVIEDVLDDMAASKSMDRLVCGDVGFGKTEVALRAAFTCAINGYQVA 656
Cdd:PRK10689 574 QRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVA 653
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 657 LLVPTTILAQQHFETFNERFSEWPIAINILSRLQTSKNNNQVRTDIEKGKADIIIGTHALLSDKVVYKNLGLVIVDEEHR 736
Cdd:PRK10689 654 VLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEHR 733
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 737 FGVRHKEKLKALRKDVDYLALTATPIPRTLNMAIGELKDISMIATPPEGRIPVKTYISQWDKSLIHEACQREISRGGQVL 816
Cdd:PRK10689 734 FGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSLVVREAILREILRGGQVY 813
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 817 FVHNRIDDIENMAETIRQIMPVGSLEIAHGRMKERSLERVMMKFYNNEFDVLLATSIIESGLDIPNANTIIINRADRFGL 896
Cdd:PRK10689 814 YLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGL 893
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 897 AQLHQLRGRVGRSERQSYAYLMIPPKHTLTNEGRQRLEAIEAIEDLGVGFILATHDLEIRGAGEILGDEQSGQIQKIGFS 976
Cdd:PRK10689 894 AQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGEEQSGQMETIGFS 973
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 977 LYKDMLAQAIDSLRDG--PQMQSTTIS-SDINLNIPALIPENYMPDVNLRLTMYKRISSTKSKIEIKHIESELIDRFGEL 1053
Cdd:PRK10689 974 LYMELLENAVDALKAGrePSLEDLTSQqTEVELRMPSLLPDDFIPDVNTRLSFYKRIASAKNENELEEIKVELIDRFGLL 1053
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 1054 PEQTTNLLLMAHLKNQASTLGIKKIRMDRRYGRFYFDQSTTIEAQNIIDLIEREPDVFKMYPDQSLGFKGDFPLVLNRIN 1133
Cdd:PRK10689 1054 PDPARNLLDIARLRQQAQKLGIRKLEGNEKGGFIEFAEKNHVDPAWLIGLLQKQPQHYRLDGPTRLKFIQDLSERKTRIE 1133
|
1130
....*....|
gi 167041424 1134 QVNTILGYLV 1143
Cdd:PRK10689 1134 WVRQFMRELE 1143
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
153-1078 |
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: 922.91 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 153 NGYERVSTVIKPGEFCIRGSLIDLFSPLYTNPIRIDFDDEKIDLIKLFDVDSQLTLNTINSVTIIP-SEHYPKSSLAFDF 231
Cdd:TIGR00580 4 LGYERVDLVEEEGEFSVRGEILDIFPPGSELPVRIEFFGDEIESIREFDVDSQRSLEELLEITILPaKEFILLEEETIAR 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 232 FKTNMRNAFDGNQLewPLYNFIETYAESHGVYNYLPLFFESMSSIWDYCKPGTKLF------CVGDIKTSIKEYQKLINQ 305
Cdd:TIGR00580 84 LKDNAARVEDAKHL--ETIEALSEGTLPAGEEMFLPLFFEDLSSLFDYLPDNTPILlddperFHSAARFLQRELEEFYNA 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 306 RFNSQDNLS--QPNLKPSELFFSATEqinkinemhpINLQHQKCwkSRAHNSINFDTRPLTAFKTSSMDKI-IHGLLET- 381
Cdd:TIGR00580 162 LEEAKKLINppRLDLDPSELAFEASA----------ISLSRVQL--ENEHLSLKASEAIEGAQKHSRLEFGeILAFKEEl 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 382 -----STNKILLSAGSKNRIAFIENQLREFSIAARRVSNWNEFLERRAGVFVTEksISESFITAKSGIAVIGEIELFGRR 456
Cdd:TIGR00580 230 frwlkAGFKITVAAESESQAERLKSLLAEHDIAAQVIDESCIIIPAVRYVMIGA--LSSGFILPTAGLAVITESELFGSR 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 457 SSTRKYRSPAGKDPesiIQDLKDLQVGSLVVHGEHGIGKYKGLSVMMVDNVNSEFLTIEYALGDLLHVPVTLMDQVSRFI 536
Cdd:TIGR00580 308 VLRRPKKSRLKSKP---IESLNELNPGDYVVHLDHGIGRFLGLETLEVGGIERDYLVLEYAGEDKLYVPVEQLHLISRYV 384
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 537 GQSSDESILSHLGSNQWKKLCKKTKKQAYDVAAELLEIYANRAIAVGKSHVANQKDYENFCDGFEYVLTQDQAKVIEDVL 616
Cdd:TIGR00580 385 GGSGKNPALDKLGGKSWEKTKAKVKKSVREIAAKLIELYAKRKAIKGHAFPPDLEWQQEFEDSFPFEETPDQLKAIEEIK 464
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 617 DDMAASKSMDRLVCGDVGFGKTEVALRAAFTCAINGYQVALLVPTTILAQQHFETFNERFSEWPIAINILSRLQTSKNNN 696
Cdd:TIGR00580 465 ADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQN 544
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 697 QVRTDIEKGKADIIIGTHALLSDKVVYKNLGLVIVDEEHRFGVRHKEKLKALRKDVDYLALTATPIPRTLNMAIGELKDI 776
Cdd:TIGR00580 545 EILKELASGKIDILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDL 624
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 777 SMIATPPEGRIPVKTYISQWDKSLIHEACQREISRGGQVLFVHNRIDDIENMAETIRQIMPVGSLEIAHGRMKERSLERV 856
Cdd:TIGR00580 625 SIIATPPEDRLPVRTFVMEYDPELVREAIRRELLRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEV 704
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 857 MMKFYNNEFDVLLATSIIESGLDIPNANTIIINRADRFGLAQLHQLRGRVGRSERQSYAYLMIPPKHTLTNEGRQRLEAI 936
Cdd:TIGR00580 705 MLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDAQKRLEAI 784
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 937 EAIEDLGVGFILATHDLEIRGAGEILGDEQSGQIQKIGFSLYKDMLAQAIDSLRDGpQMQSTTISSDINLNIPALIPENY 1016
Cdd:TIGR00580 785 QEFSELGAGFKIALHDLEIRGAGNLLGEEQSGHIESIGFDLYMELLEEAIEELKGG-KPPKLEEETDIELPYSAFIPDDY 863
|
890 900 910 920 930 940
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 167041424 1017 MPDVNLRLTMYKRISSTKSKIEIKHIESELIDRFGELPEQTTNLLLMAHLKNQASTLGIKKI 1078
Cdd:TIGR00580 864 IADDSLRLEFYKRIASAETEEELEKIRDELIDRFGPLPEEARTLLDVARLKLLARKLGIRKL 925
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
571-985 |
4.82e-138 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 433.71 E-value: 4.82e-138
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 571 LLEIYANRAIAVGKSHVANQKDYENFCDGFEYVLTQDQAKVIEDVLDDMAASKSMDRLVCGDVGFGKTEVALRAAFTCAI 650
Cdd:COG1200 227 LLLRRARRRKRKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVE 306
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 651 NGYQVALLVPTTILAQQHFETFNERFSEWPIAINILSRLQTSKNNNQVRTDIEKGKADIIIGTHALLSDKVVYKNLGLVI 730
Cdd:COG1200 307 AGYQAALMAPTEILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVV 386
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 731 VDEEHRFGVRHKEKLKALRKDVDYLALTATPIPRTLNMAI-GELkDISMIATPPEGRIPVKTYI---SQWDKslIHEACQ 806
Cdd:COG1200 387 IDEQHRFGVEQRLALREKGEAPHVLVMTATPIPRTLAMTLyGDL-DVSVIDELPPGRKPIKTRVvpeERRDE--VYERIR 463
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 807 REISRGGQVLFVHNRIDD--------IENMAETIRQIMPVGSLEIAHGRMK--ERslERVMMKFYNNEFDVLLATSIIES 876
Cdd:COG1200 464 EEIAKGRQAYVVCPLIEEsekldlqaAEETYEELREAFPGLRVGLLHGRMKpaEK--DAVMAAFKAGEIDVLVATTVIEV 541
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 877 GLDIPNANTIIINRADRFGLAQLHQLRGRVGRSERQSYAYLMIPPKhtLTNEGRQRLEAIEAIEDlgvGFILATHDLEIR 956
Cdd:COG1200 542 GVDVPNATVMVIENAERFGLSQLHQLRGRVGRGSAQSYCLLLYDAP--LSETARERLEVMRETND---GFEIAEEDLELR 616
|
410 420 430
....*....|....*....|....*....|..
gi 167041424 957 GAGEILGDEQSGQIQ-KIGfSLYKD--MLAQA 985
Cdd:COG1200 617 GPGEFLGTRQSGLPDlRIA-DLVRDadLLEAA 647
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
604-985 |
3.53e-134 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 423.41 E-value: 3.53e-134
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 604 LTQDQAKVIEDVLDDMAASKSMDRLVCGDVGFGKTEVALRAAFTCAINGYQVALLVPTTILAQQHFETFNERFSEWPIAI 683
Cdd:PRK10917 262 LTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGYQAALMAPTEILAEQHYENLKKLLEPLGIRV 341
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 684 NILSRLQTSKNNNQVRTDIEKGKADIIIGTHALLSDKVVYKNLGLVIVDEEHRFGVRHKEKLKALRKDVDYLALTATPIP 763
Cdd:PRK10917 342 ALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIIDEQHRFGVEQRLALREKGENPHVLVMTATPIP 421
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 764 RTLNMAI-GELkDISMIATPPEGRIPVKTY-ISQWDKSLIHEACQREISRGGQVLFVHNRIDDIEN--------MAETIR 833
Cdd:PRK10917 422 RTLAMTAyGDL-DVSVIDELPPGRKPITTVvIPDSRRDEVYERIREEIAKGRQAYVVCPLIEESEKldlqsaeeTYEELQ 500
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 834 QIMPVGSLEIAHGRMKERSLERVMMKFYNNEFDVLLATSIIESGLDIPNANTIIINRADRFGLAQLHQLRGRVGRSERQS 913
Cdd:PRK10917 501 EAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQS 580
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 167041424 914 YAYLMIPPKhtLTNEGRQRLEAIEAIEDlgvGFILATHDLEIRGAGEILGDEQSGQIQ-KIgFSLYKD--MLAQA 985
Cdd:PRK10917 581 YCVLLYKDP--LSETARERLKIMRETND---GFVIAEKDLELRGPGELLGTRQSGLPEfKV-ADLVRDeeLLEEA 649
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
582-968 |
2.43e-120 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 385.16 E-value: 2.43e-120
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 582 VGKSHVANQKDYENFCDGFEYVLTQDQAKVIEDVLDDMAASKSMDRLVCGDVGFGKTEVALRAAFTCAINGYQVALLVPT 661
Cdd:TIGR00643 214 SAPPANPSEELLTKFLASLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPT 293
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 662 TILAQQHFETFNERFSEWPIAINILSRLQTSKNNNQVRTDIEKGKADIIIGTHALLSDKVVYKNLGLVIVDEEHRFGVRH 741
Cdd:TIGR00643 294 EILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQ 373
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 742 KEKLKA---LRKDVDYLALTATPIPRTLNMAI-GELkDISMIATPPEGRIPVKTY-ISQWDKSLIHEACQREISRGGQVL 816
Cdd:TIGR00643 374 RKKLREkgqGGFTPHVLVMSATPIPRTLALTVyGDL-DTSIIDELPPGRKPITTVlIKHDEKDIVYEFIEEEIAKGRQAY 452
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 817 FVHNRIDDIE--------NMAETIRQIMPVGSLEIAHGRMKERSLERVMMKFYNNEFDVLLATSIIESGLDIPNANTIII 888
Cdd:TIGR00643 453 VVYPLIEESEkldlkaaeALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVI 532
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 889 NRADRFGLAQLHQLRGRVGRSERQSYAYLMIppKHTLTNEGRQRLEAIEAIEDlgvGFILATHDLEIRGAGEILGDEQSG 968
Cdd:TIGR00643 533 EDAERFGLSQLHQLRGRVGRGDHQSYCLLVY--KNPKSESAKKRLRVMADTLD---GFVIAEEDLELRGPGDLLGTKQSG 607
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
592-781 |
1.33e-107 |
|
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: 334.93 E-value: 1.33e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 592 DYENFCDGFEYVLTQDQAKVIEDVLDDMAASKSMDRLVCGDVGFGKTEVALRAAFTCAINGYQVALLVPTTILAQQHFET 671
Cdd:cd17991 4 EQEEFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQHYET 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 672 FNERFSEWPIAINILSRLQTSKNNNQVRTDIEKGKADIIIGTHALLSDKVVYKNLGLVIVDEEHRFGVRHKEKLKALRKD 751
Cdd:cd17991 84 FKERFANFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQKEKLKELRPN 163
|
170 180 190
....*....|....*....|....*....|
gi 167041424 752 VDYLALTATPIPRTLNMAIGELKDISMIAT 781
Cdd:cd17991 164 VDVLTLSATPIPRTLHMALSGIRDLSVIAT 193
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
571-783 |
2.52e-69 |
|
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. It is a member of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350750 [Multi-domain] Cd Length: 225 Bit Score: 231.65 E-value: 2.52e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 571 LLEIYANRAIAVGKSHVANQKDYENFCDGFEYVLTQDQAKVIEDVLDDMAASKSMDRLVCGDVGFGKTEVALRAAFTCAI 650
Cdd:cd17992 13 LLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKTVVAALAMLAAVE 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 651 NGYQVALLVPTTILAQQHFETFNERFSEWPIAINILSRLQTSKNNNQVRTDIEKGKADIIIGTHALLSDKVVYKNLGLVI 730
Cdd:cd17992 93 NGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQEDVEFHNLGLVI 172
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 167041424 731 VDEEHRFGVRHKEKLKALRKDVDYLALTATPIPRTLNMAI-GELkDISMIATPP 783
Cdd:cd17992 173 IDEQHRFGVEQRLKLREKGETPHVLVMTATPIPRTLALTLyGDL-DVSIIDELP 225
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
788-937 |
8.90e-65 |
|
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: 215.67 E-value: 8.90e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 788 PVKTYISQWDKSLIHEACQREISRGGQVLFVHNRIDDIENMAETIRQIMPVGSLEIAHGRMKERSLERVMMKFYNNEFDV 867
Cdd:cd18810 1 PVRTYVMPYDDELIREAIERELLRGGQVFYVHNRIESIEKLATQLRQLVPEARIAIAHGQMTENELEEVMLEFAKGEYDI 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 868 LLATSIIESGLDIPNANTIIINRADRFGLAQLHQLRGRVGRSERQSYAYLMIPPKHTLTNEGRQRLEAIE 937
Cdd:cd18810 81 LVCTTIIESGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAYFLYPDQKKLTEDALKRLEAIQ 150
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
589-780 |
7.67e-64 |
|
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: 214.20 E-value: 7.67e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 589 NQKDYENFCDGFEYVLTQDQAKVIEDVLDDMAASKSMDRLVCGDVGFGKTEVALRAAFTCAINGYQVALLVPTTILAQQH 668
Cdd:cd17918 1 DRALIQELCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 669 FETFNERFSEWPIAINILSRlqtsknnnqvRTDIEKGkADIIIGTHALLSDKVVYKNLGLVIVDEEHRFGVRHKEKLKAL 748
Cdd:cd17918 81 YEEARKFLPFINVELVTGGT----------KAQILSG-ISLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNL 149
|
170 180 190
....*....|....*....|....*....|..
gi 167041424 749 RKdVDYLALTATPIPRTLNMAIGELKDISMIA 780
Cdd:cd17918 150 GA-THFLEATATPIPRTLALALSGLLDLSVID 180
|
|
| SF2_C_RecG_TRCF |
cd18792 |
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
788-937 |
1.92e-62 |
|
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: 209.43 E-value: 1.92e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 788 PVKTYISQWDKS-LIHEACQREISRGGQVLFVHNRID--------DIENMAETIRQIMPVGSLEIAHGRMKERSLERVMM 858
Cdd:cd18792 1 PIRTYVIPHDDLdLVYEAIERELARGGQVYYVYPRIEesekldlkSIEALAEELKELVPEARVALLHGKMTEDEKEAVML 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 167041424 859 KFYNNEFDVLLATSIIESGLDIPNANTIIINRADRFGLAQLHQLRGRVGRSERQSYAYLMIPPKHTLTNEGRQRLEAIE 937
Cdd:cd18792 81 EFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYPDPKKLTETAKKRLRAIA 159
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
788-937 |
1.09e-41 |
|
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: 150.19 E-value: 1.09e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 788 PVKTYI---SQWDKslIHEACQREISRGGQVLFVHNRIDDIE--------NMAETIRQIMPvGSLEIA--HGRMKERSLE 854
Cdd:cd18811 1 PITTYLifhTRLDK--VYEFVREEIAKGRQAYVIYPLIEESEkldlkaavAMYEYLKERFR-PELNVGllHGRLKSDEKD 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 855 RVMMKFYNNEFDVLLATSIIESGLDIPNANTIIINRADRFGLAQLHQLRGRVGRSERQSYAYLMIPPKhtLTNEGRQRLE 934
Cdd:cd18811 78 AVMAEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKDP--LTETAKQRLR 155
|
...
gi 167041424 935 AIE 937
Cdd:cd18811 156 VMT 158
|
|
| TRCF |
smart00982 |
This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in ... |
1005-1104 |
1.28e-33 |
|
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: 124.88 E-value: 1.28e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 1005 NLNIPALIPENYMPDVNLRLTMYKRISSTKSKIEIKHIESELIDRFGELPEQTTNLLLMAHLKNQASTLGIKKIRMDRRY 1084
Cdd:smart00982 1 DLPVPALIPEDYIPDVRQRLELYKRIASAETEEELDEIQEELIDRFGPLPEEVKNLLEVARLKLLAKKLGIEKIDAGGKG 80
|
90 100
....*....|....*....|
gi 167041424 1085 GRFYFDQSTTIEAQNIIDLI 1104
Cdd:smart00982 81 IVIEFSPDTPIDPEKLILLI 100
|
|
| TRCF |
pfam03461 |
TRCF domain; |
1006-1100 |
1.37e-31 |
|
TRCF domain;
Pssm-ID: 460928 [Multi-domain] Cd Length: 95 Bit Score: 118.68 E-value: 1.37e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 1006 LNIPALIPENYMPDVNLRLTMYKRISSTKSKIEIKHIESELIDRFGELPEQTTNLLLMAHLKNQASTLGIKKIRMDRRYG 1085
Cdd:pfam03461 1 LDVDAYIPDDYIPDESQRLELYKRLASIETEEELDDLQEELIDRFGPLPEEVENLLEIARLKLLAKKLGIEKIDLKGGGI 80
|
90
....*....|....*
gi 167041424 1086 RFYFDQSTTIEAQNI 1100
Cdd:pfam03461 81 RITFSEDAKIDPEKL 95
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
605-768 |
2.06e-27 |
|
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: 109.64 E-value: 2.06e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 605 TQDQAKVIEDVLDDmaasKSMdrLVCGDVGFGKTEVALRAAFTC---AINGYQVALLVPTTILAQQHFETFNERFSEWPI 681
Cdd:pfam00270 1 TPIQAEAIPAILEG----RDV--LVQAPTGSGKTLAFLLPALEAldkLDNGPQALVLAPTRELAEQIYEELKKLGKGLGL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 682 ainILSRLQTSKNNNQVRTDIEkgKADIIIGTHALLSD----KVVYKNLGLVIVDEEHR-----FGVRHKEKLKALRKDV 752
Cdd:pfam00270 75 ---KVASLLGGDSRKEQLEKLK--GPDILVGTPGRLLDllqeRKLLKNLKLLVLDEAHRlldmgFGPDLEEILRRLPKKR 149
|
170
....*....|....*.
gi 167041424 753 DYLALTATPiPRTLNM 768
Cdd:pfam00270 150 QILLLSATL-PRNLED 164
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
596-786 |
1.48e-24 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 102.57 E-value: 1.48e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 596 FCDGFEYVLTQDQAKVIEDVLDDMaasksMDRLVCGDVGFGKTEVALRAAFTCAINGY--QVALLVPTTILAQQHFETFN 673
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALLSGL-----RDVILAAPTGSGKTLAALLPALEALKRGKggRVLVLVPTRELAEQWAEELK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 674 ERFSEWPIainILSRLQTSKNNNQVRTDIEKGKADIIIGT-----HALLSDKVVYKNLGLVIVDEEHR-----FGVRHKE 743
Cdd:smart00487 76 KLGPSLGL---KVVGLYGGDSKREQLRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRlldggFGDQLEK 152
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 167041424 744 KLKALRKDVDYLALTATP---IPRTLNMAIGELKDISMIATPPEGR 786
Cdd:smart00487 153 LLKLLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPLEPI 198
|
|
| CarD_TRCF |
smart01058 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
479-576 |
1.56e-23 |
|
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: 95.98 E-value: 1.56e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 479 DLQVGSLVVHGEHGIGKYKGLSVMMVDNVNSEFLTIEYALGDLLHVPVTLMDQVSRFIGQSSD-ESILSHLGSNQWKKLC 557
Cdd:smart01058 1 ELKIGDYVVHPDHGVGRYEGIETIEVGGEKREYLVLEYAGGDKLYVPVDNLDLGSRYVGSEGEvEPVLDKLGGGSWSKRK 80
|
90
....*....|....*....
gi 167041424 558 KKTKKQAYDVAAELLEIYA 576
Cdd:smart01058 81 RKAKSGIRDIAAELLRLYA 99
|
|
| UvrB_inter |
pfam17757 |
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ... |
134-222 |
6.59e-21 |
|
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: 88.22 E-value: 6.59e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 134 TLSVGELFSMQQIGEKLRINGYERVSTVIKPGEFCIRGSLIDLFsPLYT--NPIRIDFDDEKIDLIKLFDVDSQLTLNTI 211
Cdd:pfam17757 2 SLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIF-PAYSedEAIRIEFFGDEIESIREFDPLTGRSLEKL 80
|
90
....*....|.
gi 167041424 212 NSVTIIPSEHY 222
Cdd:pfam17757 81 DEVTIYPASHY 91
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
625-760 |
8.86e-20 |
|
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: 87.07 E-value: 8.86e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 625 MDRLVCGDVGFGKTEVALRAAFTCAI-NGYQVALLVPTTILAQQHFETFNERFSeWPIAINILSRLQTSKNnnqvRTDIE 703
Cdd:cd00046 2 ENVLITAPTGSGKTLAALLAALLLLLkKGKKVLVLVPTKALALQTAERLRELFG-PGIRVAVLVGGSSAEE----REKNK 76
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 704 KGKADIIIGTHALLSDKV------VYKNLGLVIVDEEHRFGVRHKEKL-------KALRKDVDYLALTAT 760
Cdd:cd00046 77 LGDADIIIATPDMLLNLLlredrlFLKDLKLIIVDEAHALLIDSRGALildlavrKAGLKNAQVILLSAT 146
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
808-908 |
1.95e-18 |
|
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 81.87 E-value: 1.95e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 808 EISRGGQVLFVHNRIDDIENMAETIRQIMPVGSLeiaHGRMKERSLERVMMKFYNNEFDVLLATSIIESGLDIPNANTII 887
Cdd:pfam00271 11 KKERGGKVLIFSQTKKTLEAELLLEKEGIKVARL---HGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVI 87
|
90 100
....*....|....*....|.
gi 167041424 888 INRADrFGLAQLHQLRGRVGR 908
Cdd:pfam00271 88 NYDLP-WNPASYIQRIGRAGR 107
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
533-906 |
5.22e-17 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 85.85 E-value: 5.22e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 533 SRFIGQSSDESILSHLGSNQWKKLCKKTKKQAYDVAAELLEIYANRAIAVGKSHVANQKDYENFC--DGFEYVLTQDQAK 610
Cdd:COG1061 8 ERGADKLRSSLLLLDLERLELSLLRNLVEARRLAIKEGTREDGRRLPEEDTERELAEAEALEAGDeaSGTSFELRPYQQE 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 611 VIEDVLDDMAASKsmDR-LVCGDVGFGKTEVALRAAfTCAINGYQVALLVPTTILAQQHFETFNERFSEwpiainilsrl 689
Cdd:COG1061 88 ALEALLAALERGG--GRgLVVAPTGTGKTVLALALA-AELLRGKRVLVLVPRRELLEQWAEELRRFLGD----------- 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 690 qtsKNNNQVRTDIEkgkADIIIGTHALLSDKVVYKNL----GLVIVDEEHRFGvrhKEKLKALRKDVDY---LALTATPI 762
Cdd:COG1061 154 ---PLAGGGKKDSD---APITVATYQSLARRAHLDELgdrfGLVIIDEAHHAG---APSYRRILEAFPAayrLGLTATPF 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 763 pR------------------TLNMAI--GELKDISMIATPPEGRIPVKTYI---SQWDKSLIH---------EACQREIS 810
Cdd:COG1061 225 -RsdgreillflfdgivyeySLKEAIedGYLAPPEYYGIRVDLTDERAEYDalsERLREALAAdaerkdkilRELLREHP 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 811 RGGQVLFVHNRIDDIENMAETIRQImpVGSLEIAHGRMKERSLERVMMKFYNNEFDVLLATSIIESGLDIPNANTIIINR 890
Cdd:COG1061 304 DDRKTLVFCSSVDHAEALAELLNEA--GIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILLR 381
|
410
....*....|....*.
gi 167041424 891 ADRFgLAQLHQLRGRV 906
Cdd:COG1061 382 PTGS-PREFIQRLGRG 396
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
601-909 |
7.45e-15 |
|
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: 78.38 E-value: 7.45e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 601 EYVLTQDQAKVIEDVLDdmAASKSMDRL---VCGDvgfGKTEVALRAAFTCAINGYQVALLVPTTILAQQHFETFNERFS 677
Cdd:COG4098 108 EGTLTPAQQKASDELLE--AIKKKEEHLvwaVCGA---GKTEMLFPAIAEALKQGGRVCIATPRVDVVLELAPRLQQAFP 182
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 678 EWPIAInilsrL-QTSKnnnqvrtdiEKGK-ADIIIGT-HALLSdkvVYKNLGLVIVDEEHRFGVRHKEKL-----KALR 749
Cdd:COG4098 183 GVDIAA-----LyGGSE---------EKYRyAQLVIATtHQLLR---FYQAFDLLIIDEVDAFPYSGDPMLqyavkRARK 245
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 750 KDVDYLALTATPiPRTLNMAI--GELKdISMIATPPEGR-IPVKTYISQWD-----------KSLIHEACQReISRGGQV 815
Cdd:COG4098 246 PDGKLIYLTATP-SKALQRQVkrGKLK-VVKLPARYHGHpLPVPKFKWLGNwkkrlrrgklpRKLLKWLKKR-LKEGRQL 322
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 816 L-FVHNrIDDIENMAETIRQIMPVGSLEIAHGRMKERSlERVMmKFYNNEFDVLLATSIIESGLDIPNANTIIINRADR- 893
Cdd:COG4098 323 LiFVPT-IELLEQLVALLQKLFPEERIAGVHAEDPERK-EKVQ-AFRDGEIPILVTTTILERGVTFPNVDVAVLGADHPv 399
|
330
....*....|....*.
gi 167041424 894 FGLAQLHQLRGRVGRS 909
Cdd:COG4098 400 FTEAALVQIAGRVGRS 415
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
826-908 |
1.15e-14 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 70.32 E-value: 1.15e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 826 ENMAETIRQI-MPVGSLeiaHGRMKERSLERVMMKFYNNEFDVLLATSIIESGLDIPNANTIIINRADrFGLAQLHQLRG 904
Cdd:smart00490 1 EELAELLKELgIKVARL---HGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-WSPASYIQRIG 76
|
....
gi 167041424 905 RVGR 908
Cdd:smart00490 77 RAGR 80
|
|
| CarD_CdnL_TRCF |
pfam02559 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
480-575 |
1.54e-14 |
|
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: 70.17 E-value: 1.54e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 480 LQVGSLVVHGEHGIGKYKGLSVMmvdnVNSEFLTIEYALGDLLHVPVTLMDQVSRFIGqssdESILSHLGSNQ-WKKLCK 558
Cdd:pfam02559 1 LKVGDYVVHPDHGIGRIEGIEKL----ETKDYYVLEYAGGDKLYVPVDNLDLIRKYIS----KGELDKLGDGRrWRKYKE 72
|
90
....*....|....*..
gi 167041424 559 KTKKQAYDVAAELLEIY 575
Cdd:pfam02559 73 KLKSGDIEEAAELIKLY 89
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
608-908 |
5.98e-14 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 76.09 E-value: 5.98e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 608 QAKVIEDVLDDmaaSKSMdrLVCGDVGFGKTEVALRAAFTCAINGYQVALLVPTTILAQQHFETFNERFSEWPIAINILS 687
Cdd:COG1204 27 QAEALEAGLLE---GKNL--VVSAPTASGKTLIAELAILKALLNGGKALYIVPLRALASEKYREFKRDFEELGIKVGVST 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 688 RlqtsknnNQVRTDIEKGKADIIIGT----HALLSDKV-VYKNLGLVIVDEEHRFGVRHK--------EKLKALRKDVDY 754
Cdd:COG1204 102 G-------DYDSDDEWLGRYDILVATpeklDSLLRNGPsWLRDVDLVVVDEAHLIDDESRgptlevllARLRRLNPEAQI 174
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 755 LALTATpiprtlnmaIGELKDIS--MIATPpegripvktYISQW------------------DKSLIHE-----ACQREI 809
Cdd:COG1204 175 VALSAT---------IGNAEEIAewLDAEL---------VKSDWrpvplnegvlydgvlrfdDGSRRSKdptlaLALDLL 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 810 SRGGQVLFVHNRIDDIENMAETIRQIMPVGSLEIAHGRMKERS---------------LERVMMK--------------- 859
Cdd:COG1204 237 EEGGQVLVFVSSRRDAESLAKKLADELKRRLTPEEREELEELAeellevseethtnekLADCLEKgvafhhaglpselrr 316
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*....
gi 167041424 860 -----FYNNEFDVLLATSIIESGLDIPnANTIIINRADRFGLAQL-----HQLRGRVGR 908
Cdd:COG1204 317 lvedaFREGLIKVLVATPTLAAGVNLP-ARRVIIRDTKRGGMVPIpvlefKQMAGRAGR 374
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
608-735 |
1.92e-12 |
|
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: 66.85 E-value: 1.92e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 608 QAKVIEDVLDDMAASKSMdrLVCGDVGFGKTEVALRAAFTCAINGYQVALLVPTTILAQQHFETFNERFSEwPIAInILS 687
Cdd:cd17929 1 QRKAYEAIVSSLGGFKTF--LLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRFGD-KVAV-LHS 76
|
90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 167041424 688 RLQTSKNNNQVRTdIEKGKADIIIGTH-ALLsdkVVYKNLGLVIVDEEH 735
Cdd:cd17929 77 KLSDKERADEWRK-IKRGEAKVVIGARsALF---APFKNLGLIIVDEEH 121
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
628-912 |
3.07e-11 |
|
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: 67.41 E-value: 3.07e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 628 LVCGDVGFGKTEVALRAAFTCAINGYQVALLVPTTILAQQHFETFNERFSEwPIAInILSRLQTSKNNNQVRTdIEKGKA 707
Cdd:TIGR00595 1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGS-QVAV-LHSGLSDSEKLQAWRK-VKNGEI 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 708 DIIIGTHALLSdkVVYKNLGLVIVDEEH----------RFGVRHKEKLKALRKDVDYLALTATPIPRTL-NMAIGELKDI 776
Cdd:TIGR00595 78 LVVIGTRSALF--LPFKNLGLIIVDEEHdssykqeegpRYHARDVAVYRAKKFNCPVVLGSATPSLESYhNAKQKAYRLL 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 777 SMI-----ATPPEGRI------PVKTYISQwdkSLIhEACQREISRGGQV-LFVHNR----------------------- 821
Cdd:TIGR00595 156 VLTrrvsgRKPPEVKLidmrkePRQSFLSP---ELI-TAIEQTLAAGEQSiLFLNRRgysknllcrscgyilccpncdvs 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 822 -----------------------------IDDI-------ENMAETIRQIMPvgSLEIAhgRM------KERSLERVMMK 859
Cdd:TIGR00595 232 ltyhkkegklrchycgyqepipktcpqcgSEDLvykgygtEQVEEELAKLFP--GARIA--RIdsdttsRKGAHEALLNQ 307
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 167041424 860 FYNNEFDVLLATSIIESGLDIPNANTI-IIN----------RADRFGLAQLHQLRGRVGRSERQ 912
Cdd:TIGR00595 308 FANGKADILIGTQMIAKGHHFPNVTLVgVLDadsglhspdfRAAERGFQLLTQVAGRAGRAEDP 371
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
603-735 |
5.40e-11 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 67.07 E-value: 5.40e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 603 VLTQDQAKVIEDVLDDMAASKSMdrLVCGDVGFGKTEVALRAAFTCAINGYQVALLVPTTILAQQHFETFNERFSEwPIA 682
Cdd:COG1198 195 TLNEEQQAAVEAIRAAAGGFSVF--LLHGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQTVERFRARFGA-RVA 271
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 167041424 683 IniL-SRLqtsknNNQVRTD----IEKGKADIIIGTH-ALLSDkvvYKNLGLVIVDEEH 735
Cdd:COG1198 272 V--LhSGL-----SDGERLDewrrARRGEARIVIGTRsALFAP---FPNLGLIIVDEEH 320
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
603-735 |
4.77e-10 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 63.64 E-value: 4.77e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 603 VLTQDQAKVIEDVLDDMAASKSmdrLVCGDVGFGKTEVALRAAFTCAINGYQVALLVPTTILAQQHFETFNERFSEWPIA 682
Cdd:PRK05580 144 TLNPEQAAAVEAIRAAAGFSPF---LLDGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQMLARFRARFGAPVAV 220
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....
gi 167041424 683 INilSRLqTSKNNNQVRTDIEKGKADIIIGTH-ALLSDkvvYKNLGLVIVDEEH 735
Cdd:PRK05580 221 LH--SGL-SDGERLDEWRKAKRGEAKVVIGARsALFLP---FKNLGLIIVDEEH 268
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
634-762 |
3.83e-09 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 56.91 E-value: 3.83e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 634 GFGKTEVALRAAFTCAINGYQ--VALLVPTTILAQQHFETFNERFSEWPIAINILSRLqtsknnnqvRTDIEKGKADIII 711
Cdd:pfam04851 33 GSGKTLTAAKLIARLFKKGPIkkVLFLVPRKDLLEQALEEFKKFLPNYVEIGEIISGD---------KKDESVDDNKIVV 103
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 167041424 712 GT-HALLSDKVVYKNL------GLVIVDEEHRFG----VRHKEKLKALRKdvdyLALTATPI 762
Cdd:pfam04851 104 TTiQSLYKALELASLEllpdffDVIIIDEAHRSGassyRNILEYFKPAFL----LGLTATPE 161
|
|
| Cas3 |
COG1203 |
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
634-880 |
1.55e-08 |
|
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system
Pssm-ID: 440816 [Multi-domain] Cd Length: 535 Bit Score: 58.55 E-value: 1.55e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 634 GFGKTEVALRAAFTCAINGYQ----VALlvPTTILAQQHFETFNERFSEwpiaiNIL-----SRLQTSKNNNQVRTDIEK 704
Cdd:COG1203 157 GGGKTEAALLFALRLAAKHGGrriiYAL--PFTSIINQTYDRLRDLFGE-----DVLlhhslADLDLLEEEEEYESEARW 229
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 705 GK-------ADIIIGT--HALLSdkvVYKN--------LGL----VIVDEEHRFGVrhkEKLKALRKDVDYLA------- 756
Cdd:COG1203 230 LKllkelwdAPVVVTTidQLFES---LFSNrkgqerrlHNLansvIILDEVQAYPP---YMLALLLRLLEWLKnlggsvi 303
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 757 -LTATpIPRTLnmaIGELKDISMIATPPEGRIP----------VKTYISQWDKSLIHEACQREISRGGQVLFVHNRIDDI 825
Cdd:COG1203 304 lMTAT-LPPLL---REELLEAYELIPDEPEELPeyfrafvrkrVELKEGPLSDEELAELILEALHKGKSVLVIVNTVKDA 379
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*....
gi 167041424 826 ENMAETIRQIMPVGSLEIAHGRM--KERS--LERVMMKFYNNEFDVLLATSIIESGLDI 880
Cdd:COG1203 380 QELYEALKEKLPDEEVYLLHSRFcpADRSeiEKEIKERLERGKPCILVSTQVVEAGVDI 438
|
|
| PRK05298 |
PRK05298 |
excinuclease ABC subunit UvrB; |
128-222 |
1.90e-08 |
|
excinuclease ABC subunit UvrB;
Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 58.52 E-value: 1.90e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 128 FEKESFTLSVGELFSMQQIGEKLRINGYERVSTVIKPGEFCIRGSLIDLFSPLY-TNPIRIDFDDEKIDLIKLFDVdsqL 206
Cdd:PRK05298 154 YLKMVLSLRVGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPAYYeERAIRIEFFGDEIERISEFDP---L 230
|
90
....*....|....*....
gi 167041424 207 T---LNTINSVTIIPSEHY 222
Cdd:PRK05298 231 TgevLGELDRVTIYPASHY 249
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
634-761 |
3.43e-08 |
|
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: 53.85 E-value: 3.43e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 634 GFGKTEVALRAAFTCAINGyqVALLVPTTILAQQ---HFETFNErfsewPIAINILsrlqTSKNNnqvrtdIEKGKADII 710
Cdd:cd17926 28 GSGKTLTALALIAYLKELR--TLIVVPTDALLDQwkeRFEDFLG-----DSSIGLI----GGGKK------KDFDDANVV 90
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 167041424 711 IGTHALLS-----DKVVYKNLGLVIVDEEHRFGVrhkEKLKALRKDVDY---LALTATP 761
Cdd:cd17926 91 VATYQSLSnlaeeEKDLFDQFGLLIVDEAHHLPA---KTFSEILKELNAkyrLGLTATP 146
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
628-760 |
5.72e-08 |
|
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350679 [Multi-domain] Cd Length: 181 Bit Score: 53.80 E-value: 5.72e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 628 LVCGDVGFGKTEVALRAAFTCAINGYQVAL-LVPTTILAQQHFETFNERFSEWPIAINILSRLQTSKNNnqvrtdiEKGK 706
Cdd:cd17921 21 LVSAPTSSGKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFGPLGKNVGLLTGDPSVNKL-------LLAE 93
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 167041424 707 ADIIIGT----HALLSD--KVVYKNLGLVIVDEEHRFGVRHK--------EKLKALRKDVDYLALTAT 760
Cdd:cd17921 94 ADILVATpeklDLLLRNggERLIQDVRLVVVDEAHLIGDGERgvvlelllSRLLRINKNARFVGLSAT 161
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
628-761 |
8.17e-07 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 53.20 E-value: 8.17e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 628 LVCGDVGFGKTEVALR-AAFTCAINGYQVALLVPTTILAQQHFETFNERFSEWPIAINILsrlqTSKNNNQVRTDIEKgK 706
Cdd:COG1111 21 LVVLPTGLGKTAVALLvIAERLHKKGGKVLFLAPTKPLVEQHAEFFKEALNIPEDEIVVF----TGEVSPEKRKELWE-K 95
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 167041424 707 ADIIIGT-----HALLSDKVVYKNLGLVIVDEEHR-FG----VRHKEKLKALRKDVDYLALTATP 761
Cdd:COG1111 96 ARIIVATpqvieNDLIAGRIDLDDVSLLIFDEAHRaVGnyayVYIAERYHEDAKDPLILGMTASP 160
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
863-908 |
1.66e-06 |
|
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: 46.93 E-value: 1.66e-06
10 20 30 40
....*....|....*....|....*....|....*....|....*.
gi 167041424 863 NEFDVLLATSIIESGLDIPNANTIIINRADRFgLAQLHQLRGRVGR 908
Cdd:cd18785 21 SSLEILVATNVLGEGIDVPSLDTVIFFDPPSS-AASYIQRVGRAGR 65
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
808-919 |
1.81e-06 |
|
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: 48.27 E-value: 1.81e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 808 EISRGGQVL-FVhNRIDDIENMAETIRQI-MPVGSLeiaHGRMKERSLERVMMKFYNNEFDVLLATSIIESGLDIPNANT 885
Cdd:cd18787 23 EKLKPGKAIiFV-NTKKRVDRLAELLEELgIKVAAL---HGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGVDH 98
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 167041424 886 iIINradrFGLAQ-----LHqlR-GRVGRSERQSYAYLMI 919
Cdd:cd18787 99 -VIN----YDLPRdaedyVH--RiGRTGRAGRKGTAITFV 131
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
628-760 |
2.46e-06 |
|
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play an important role in RNA degradation, processing and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350786 [Multi-domain] Cd Length: 177 Bit Score: 48.87 E-value: 2.46e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 628 LVCGDVGFGKTEVALRAAFTCAINGYQVALLVPTTILAQQHFETFNeRFSEWPIAINIlsrlQTSKNNnqvRTDIEKGKA 707
Cdd:cd18028 21 LISIPTASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEEFK-KLEEIGLKVGI----STGDYD---EDDEWLGDY 92
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 167041424 708 DIIIGTH----ALLSDKVVY-KNLGLVIVDEEHRFGVRHK--------EKLKALRKDVDYLALTAT 760
Cdd:cd18028 93 DIIVATYekfdSLLRHSPSWlRDVGVVVVDEIHLISDEERgptlesivARLRRLNPNTQIIGLSAT 158
|
|
| DEXHc_RLR |
cd18036 |
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
620-761 |
5.28e-06 |
|
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprise RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). RIG-I-like receptors (RLRs) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350794 [Multi-domain] Cd Length: 204 Bit Score: 48.63 E-value: 5.28e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 620 AASKSMDRLVCGDVGFGKTEVALRAA------FTCAINGYQVALLVPTTILAQQHFETFNERFSE--WPIAINILSRLQT 691
Cdd:cd18036 13 PALRGKNTIICAPTGSGKTRVAVYICrhhlekRRSAGEKGRVVVLVNKVPLVEQQLEKFFKYFRKgyKVTGLSGDSSHKV 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 692 SKNNNQVRTDIEKGKADIIIgtHALLS----DKVVYKNLGLVIVDEEHRFGVRH----------KEKLKALRKDVDYLAL 757
Cdd:cd18036 93 SFGQIVKASDVIICTPQILI--NNLLSgreeERVYLSDFSLLIFDECHHTQKEHpynkimrmylDKKLSSQGPLPQILGL 170
|
....
gi 167041424 758 TATP 761
Cdd:cd18036 171 TASP 174
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
632-762 |
2.78e-05 |
|
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: 46.51 E-value: 2.78e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 632 DVGFGKT--------EVALRAaftcaiNGYQVALLVPTTILAQQHFEtFNERFsewpiaiNILSRLQTSKNNNQVRTDIE 703
Cdd:cd18011 25 EVGLGKTieagliikELLLRG------DAKRVLILCPASLVEQWQDE-LQDKF-------GLPFLILDRETAAQLRRLIG 90
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 167041424 704 KGKA--DIIIGTHALL-----SDKVVYK-NLGLVIVDEEHRFGVRHKEK-------LKALRKDVDY-LALTATPI 762
Cdd:cd18011 91 NPFEefPIVIVSLDLLkrseeRRGLLLSeEWDLVVVDEAHKLRNSGGGKetkryklGRLLAKRARHvLLLTATPH 165
|
|
| SrmB |
COG0513 |
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
599-937 |
3.21e-05 |
|
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 47.83 E-value: 3.21e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 599 GFEYvLTQDQAKVIEDVLD--DMaasksmdrLVCGDVGFGKTevalrAAFTCAI---------NGYQVALLVPTTILAQQ 667
Cdd:COG0513 21 GYTT-PTPIQAQAIPLILAgrDV--------LGQAQTGTGKT-----AAFLLPLlqrldpsrpRAPQALILAPTRELALQ 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 668 HFETFnERFSEwPIAINILSrL--QTSKNNnQVRtDIEKGkADIIIGT----HALLSDKVVY-KNLGLVIVDEEHR---- 736
Cdd:COG0513 87 VAEEL-RKLAK-YLGLRVAT-VygGVSIGR-QIR-ALKRG-VDIVVATpgrlLDLIERGALDlSGVETLVLDEADRmldm 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 737 -FgvrhkeklkalRKDVDYLaLTATPIPR-------TLNMAIGEL-----KDISMIATPPEGRIPVKtyISQW------- 796
Cdd:COG0513 161 gF-----------IEDIERI-LKLLPKERqtllfsaTMPPEIRKLakrylKNPVRIEVAPENATAET--IEQRyylvdkr 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 797 DKS--LIHEACQREISRGgqVLFVhNRIDDIENMAET-IRQIMPVGSLeiaHGRM--KERslERVMMKFYNNEFDVLLAT 871
Cdd:COG0513 227 DKLelLRRLLRDEDPERA--IVFC-NTKRGADRLAEKlQKRGISAAAL---HGDLsqGQR--ERALDAFRNGKIRVLVAT 298
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 167041424 872 SIIESGLDIPNAnTIIINradrFGLAQ-----LHqlR-GRVGRSERQSYAYLMIPPKhtltnEgRQRLEAIE 937
Cdd:COG0513 299 DVAARGIDIDDV-SHVIN----YDLPEdpedyVH--RiGRTGRAGAEGTAISLVTPD-----E-RRLLRAIE 357
|
|
| SF2_C_FANCM_Hef |
cd18801 |
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
848-919 |
4.54e-05 |
|
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350188 [Multi-domain] Cd Length: 143 Bit Score: 44.65 E-value: 4.54e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 167041424 848 MKERSLERVMMKFYNNEFDVLLATSIIESGLDIPNANTIIINRADRFGLAQLhQLRGRVGRsERQSYAYLMI 919
Cdd:cd18801 74 MSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMI-QRMGRTGR-KRQGRVVVLL 143
|
|
| SF2_C_dicer |
cd18802 |
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
848-919 |
7.39e-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: 44.12 E-value: 7.39e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 167041424 848 MKERSLERVMMKFYNNEFDVLLATSIIESGLDIPNANTIIinradRFGLA----QLHQLRGRvGRsERQSYAYLMI 919
Cdd:cd18802 74 MTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVI-----RFDLPktlrSYIQSRGR-AR-APNSKYILMV 142
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
848-910 |
1.44e-04 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 45.88 E-value: 1.44e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 167041424 848 MKERSLERVMMKFYNNEFDVLLATSIIESGLDIPNANTII-----------INRadrfglaqlhqlRGRVGRSE 910
Cdd:COG1111 395 LTQKEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVIfyepvpseirsIQR------------KGRTGRKR 456
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
728-908 |
1.58e-04 |
|
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: 45.50 E-value: 1.58e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 728 LVIVDEEHRFGVRHKEKLKAL-----RKDVDYLALTATpIP---RTLNMAIGELKDISMIATPPEGRIPVKTYISQWDKS 799
Cdd:cd09639 126 LLIFDEVHFYDEYTLALILAVlevlkDNDVPILLMSAT-LPkflKEYAEKIGYVEENEPLDLKPNERAPFIKIESDKVGE 204
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 800 L-IHEACQREISRGGQVLFVHNRIDDIENMAETIRQIMPVGSLEIAHGRM----KERSLERVMMKFYNNEFDVLLATSII 874
Cdd:cd09639 205 IsSLERLLEFIKKGGSVAIIVNTVDRAQEFYQQLKEKGPEEEIMLIHSRFtekdRAKKEAELLLEFKKSEKFVIVATQVI 284
|
170 180 190
....*....|....*....|....*....|....*.
gi 167041424 875 ESGLDIpNANTII--INRADRfglaqLHQLRGRVGR 908
Cdd:cd09639 285 EASLDI-SVDVMIteLAPIDS-----LIQRLGRLHR 314
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
825-912 |
1.70e-04 |
|
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350191 [Multi-domain] Cd Length: 238 Bit Score: 44.54 E-value: 1.70e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 825 IENMAETIRQIMPvgSLEIAhgRM------KERSLERVMMKFYNNEFDVLLATSIIESGLDIPNANTIIINRADrFGL-- 896
Cdd:cd18804 103 TERVEEELKTLFP--EARIA--RIdrdttrKKGALEKLLDQFERGEIDILIGTQMIAKGLDFPNVTLVGILNAD-SGLns 177
|
90 100
....*....|....*....|....*.
gi 167041424 897 ---------AQL-HQLRGRVGRSERQ 912
Cdd:cd18804 178 pdfraseraFQLlTQVSGRAGRGDKP 203
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
620-761 |
2.58e-04 |
|
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: 43.58 E-value: 2.58e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 620 AASKSMDRLVCGDVGFGKTEVAL-----RAAFTCAINGYQVALLVPTTILAQQHFETFNERFSEWPIAINILSrlqtSKN 694
Cdd:cd17927 13 PALKGKNTIICLPTGSGKTFVAVlicehHLKKFPAGRKGKVVFLANKVPLVEQQKEVFRKHFERPGYKVTGLS----GDT 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 695 NNQVRTDIEKGKADIIIGT-HALLSD-----KVVYKNLGLVIVDEEHRFGVRH----------KEKLKALRKDVDYLALT 758
Cdd:cd17927 89 SENVSVEQIVESSDVIIVTpQILVNDlksgtIVSLSDFSLLVFDECHNTTKNHpyneimfrylDQKLGSSGPLPQILGLT 168
|
...
gi 167041424 759 ATP 761
Cdd:cd17927 169 ASP 171
|
|
| DEXHc_Hef |
cd18035 |
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
620-761 |
3.21e-04 |
|
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350793 [Multi-domain] Cd Length: 181 Bit Score: 42.89 E-value: 3.21e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 620 AASKSMDRLVCGDVGFGKTEVA-LRAAFTCAINGYQVALLVPTTILAQQHFETFNERFSEWPIAINILSRLQTSKnnnqv 698
Cdd:cd18035 12 AVALNGNTLIVLPTGLGKTIIAiLVAADRLTKKGGKVLILAPSRPLVEQHAENLKRVLNIPDKITSLTGEVKPEE----- 86
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 167041424 699 RTDIEKgKADIIIGT-----HALLSDKVVYKNLGLVIVDEEHRFGVRHK-----EKLKALRKDVDYLALTATP 761
Cdd:cd18035 87 RAERWD-ASKIIVATpqvieNDLLAGRITLDDVSLLIFDEAHHAVGNYAyvyiaHRYKREANNPLILGLTASP 158
|
|
| DDXDc_reverse_gyrase |
cd17924 |
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
634-782 |
6.48e-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: 41.93 E-value: 6.48e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 634 GFGKTEVALRAAFTCAINGYQVALLVPTTILAQQ---HFETFNERFSEWPIAINILSRLQTSKNNNqVRTDIEKGKADII 710
Cdd:cd17924 42 GVGKTTFGLATSLYLASKGKRSYLIFPTKSLVKQayeRLSKYAEKAGVEVKILVYHSRLKKKEKEE-LLEKIEKGDFDIL 120
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 167041424 711 IGTHALLS---DKVVYKNLGLVIVDeehrfgvrhkeklkalrkDVDYLALTATPIPRTLNMA-IGELKDISMIATP 782
Cdd:cd17924 121 VTTNQFLSknfDLLSNKKFDFVFVD------------------DVDAVLKSSKNIDRLLKLLgFGQLVVSSATGRP 178
|
|
| PRK13766 |
PRK13766 |
Hef nuclease; Provisional |
859-910 |
1.35e-03 |
|
Hef nuclease; Provisional
Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 42.94 E-value: 1.35e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*.
gi 167041424 859 KFYNNEFDVLLATSIIESGLDIPNANTII----INRADRFglaqlHQLRGRVGRSE 910
Cdd:PRK13766 418 KFRAGEFNVLVSTSVAEEGLDIPSVDLVIfyepVPSEIRS-----IQRKGRTGRQE 468
|
|
| SNF2-rel_dom |
pfam00176 |
SNF2-related domain; This domain is found in proteins involved in a variety of processes ... |
628-767 |
1.68e-03 |
|
SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.
Pssm-ID: 425504 [Multi-domain] Cd Length: 289 Bit Score: 41.90 E-value: 1.68e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 628 LVCGDVGFGKT--EVALRAA-FTCAIN-GYQVALLVPTTILaqQHFETFNERFSEWPiAINILSRLQTSKNNNQVRTD-I 702
Cdd:pfam00176 21 ILADEMGLGKTlqTISLLLYlKHVDKNwGGPTLIVVPLSLL--HNWMNEFERWVSPP-ALRVVVLHGNKRPQERWKNDpN 97
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 703 EKGKADIIIGT-HALLSDKVVYKNLG--LVIVDEEHRFGVRHKEKLKALRK-DVDY-LALTATPIPRTLN 767
Cdd:pfam00176 98 FLADFDVVITTyETLRKHKELLKKVHwhRIVLDEGHRLKNSKSKLSKALKSlKTRNrWILTGTPLQNNLE 167
|
|
| RecG_dom3_C |
pfam19833 |
ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent ... |
945-1017 |
3.74e-03 |
|
ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent DNA helicase RecG from bacteria the homolog from Arabidopsis, which has a critical role in recombination and DNA repair. This protein comprises three structural domains, the largest N-terminal Domain 1 which interacts with DNA junctions, and Domains 2 and 3 at the C-terminal which contain the characteriztic motifs that identify RecG as an SF2 helicase. This domain represents the C-terminal of Domain 3. Around 50 residues that extend from its end cross back to Domain 1 forming a hook that wraps around the extended alpha-helix. This interaction provides a link between Domain 1 and 3 and it is likely that these residues are involved in conformational changes associated with domain movements arising from ATP binding and hydrolysis.
Pssm-ID: 437665 [Multi-domain] Cd Length: 87 Bit Score: 37.84 E-value: 3.74e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 167041424 945 GFILATHDLEIRGAGEILGDEQSGqiqkIGFSLykdmlaQAIDSLRDGPQMQ-STTISSDINLNIPALI-PENYM 1017
Cdd:pfam19833 4 GFEIAEADLKLRGPGDLEGTQQSG----IAFDL------KIADIARDGQLLQlARTEAEEIIDNDPECSlPENAV 68
|
|
| UB2H |
pfam14814 |
Bifunctional transglycosylase second domain; UB2H is the second domain of the ... |
135-209 |
6.44e-03 |
|
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: 36.77 E-value: 6.44e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 135 LSVGELFSMQQIGEKLRINGYERVSTVIKPGEFCIRGSLIDLFSPLYTNP--------IRIDFDDEKIDLIKlfDVDSQL 206
Cdd:pfam14814 1 LYPGQALSAAQLEQELKLLGYRKVSNPTRPGEYSVSGNRIELYRRGFDFPdgaeparrVRLRFAGGRVARLQ--DLDTGR 78
|
...
gi 167041424 207 TLN 209
Cdd:pfam14814 79 DLA 81
|
|
| PRK13766 |
PRK13766 |
Hef nuclease; Provisional |
628-761 |
7.44e-03 |
|
Hef nuclease; Provisional
Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 40.63 E-value: 7.44e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167041424 628 LVCGDVGFGKTEVA-LRAAFTCAINGYQVALLVPTTILAQQHFETFNERFSEWPIAINILS-RLQTSKnnnqvRTDIEKg 705
Cdd:PRK13766 33 LVVLPTGLGKTAIAlLVIAERLHKKGGKVLILAPTKPLVEQHAEFFRKFLNIPEEKIVVFTgEVSPEK-----RAELWE- 106
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 167041424 706 KADIIIGT-----HALLSDKVVYKNLGLVIVDEEHR-FG----VRHKEKLKALRKDVDYLALTATP 761
Cdd:PRK13766 107 KAKVIVATpqvieNDLIAGRISLEDVSLLIFDEAHRaVGnyayVYIAERYHEDAKNPLVLGLTASP 172
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