|
Name |
Accession |
Description |
Interval |
E-value |
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
23-1151 |
0e+00 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 1765.36 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 23 PGARFTQPRPPGSGDGWLLADLARQAGKPLVVLTADPLEAQRLADEIPQFAPELRVRQLPDWETLPYDAFSPHQDLISQR 102
Cdd:COG1197 1 GGGRLTLSGLPGSARALLLAALARALGRPLLVVTADEREAERLAEDLRFFLPDLPVLLFPAWETLPYDRFSPSPDIVSER 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 103 LRTLHALMNQGVDILTVPVTTALYRLAPPAFLAAYTFSFKQKDRLDEAALRAQLTLANYSHVTQVTAPGEFCLRGGLIDL 182
Cdd:COG1197 81 LATLRRLASGKPGIVVTPVRALLQRLPPPELLAAASLSLKVGDELDLEELRERLVAAGYERVDQVEEPGEFAVRGGILDI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 183 FPMGSVVPYRLDLFDDEIESIRSFDVDTQRSLYPVGEVQLLPGREFPMDEEARNRFRARFREVFEGDPSRALPYKDIGNG 262
Cdd:COG1197 161 FPPGSEHPVRIEFFGDEIESIRTFDPETQRSLEKVDEVELLPAREFPLDEEAIERFRERLRELFGLDPKLDELYEALSEG 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 263 IAFAGIEYYLPLFFEQTATLFDYLAADTITVTVG--DIDDAMQRFAHDTRSRYDFLKVDRERPVLPPDTLFLDHEALFAR 340
Cdd:COG1197 241 IAFAGIEYYLPLFYEELATLFDYLPEDALVVLDEpeRIEEAAEEFWEEIEERYEARRHDRGRPLLPPEELFLDPEELFAA 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 341 LKDFPRLAL--MAERPHP----DFAAAPDVAVARRADDPVARLRALLAQtGDRVLLCADSAGRRETLAQMLGEHGLAPeA 414
Cdd:COG1197 321 LKRRPRVTLspFAALPEGagvvNLGARPLPSFAGQLEALLEELKRLLKD-GGRVLLAAESEGRRERLLELLRDHGIPA-R 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 415 QADSIQAFldDGARFGLAVAPLSAGFCVPGGALLFLTENDLYPghagvTRRGKRTQERTSNVEAMVRDLAELRAGDPVVH 494
Cdd:COG1197 399 LVESLAEL--SPGGVAITVGPLEHGFELPDAKLAVITESELFG-----ERVKRRRRKKKRSADAFIRDLSELKPGDYVVH 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 495 AQHGIGRYHGLVNMDMGEGEMEFLHLEYASGSTLYVPVSQLHVIARYSGADPDAAPLHQLGSGQWDKARRKAARQVRDTA 574
Cdd:COG1197 472 VDHGIGRYLGLETLEVGGAERDYLVLEYAGGDKLYVPVDQLDLISRYVGSEGEAPKLDKLGGSDWQKAKAKAKKAVRDIA 551
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 575 AELLALYAQRAAREGYAFKLPMSDYEAFAEGFGFEETPDQAAAIQAVIMDMTSGRPMDRLVCGDVGFGKTEVALRAAFLA 654
Cdd:COG1197 552 AELLKLYAERAARKGFAFSPDTPWQREFEAAFPYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKTEVALRAAFKA 631
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 655 VANGKQVALLCPTTLLAEQHAQTFSDRFADWPVRVVELSRFRSAKEVAAAVEGINDGRVDIVIGTHKILSKDVRFKRLGL 734
Cdd:COG1197 632 VMDGKQVAVLVPTTLLAQQHYETFKERFAGFPVRVEVLSRFRTAKEQKETLEGLADGKVDIVIGTHRLLSKDVKFKDLGL 711
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 735 VIIDEEHRFGVRQKETLKALRAEVDVLTLTATPIPRTLGMSLEGIRDFSVIATAPQKRLAIKTFVRREDGSTIREALLRE 814
Cdd:COG1197 712 LIIDEEQRFGVRHKEKLKALRANVDVLTLTATPIPRTLQMSLSGIRDLSIIATPPEDRLPVKTFVGEYDDALIREAILRE 791
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 815 LKRGGQVYFLHNEVETIHNRRARLEELVPEARIAVAHGQMPERELEQVMKGFYQQRHNVLLCTTIIETGIDIPTANTIVI 894
Cdd:COG1197 792 LLRGGQVFYVHNRVEDIEKVAARLQELVPEARIAVAHGQMSERELERVMLDFYEGEFDVLVCTTIIETGIDIPNANTIII 871
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 895 HRADRFGLAQLHQLRGRVGRSHHQAYAYLLTPGEDAITNNAKKRLEAIQAMEELGSGFYLAMHDLEIRGTGEILGDSQSG 974
Cdd:COG1197 872 ERADRFGLAQLYQLRGRVGRSHRRAYAYLLYPPDKVLTEDAEKRLEAIQEFTELGAGFKLAMHDLEIRGAGNLLGEEQSG 951
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 975 NIQEVGFSMYNEMLNEAVRALKAGEEPDLDApfnlACEVNLHAPALLPSDYCPDVHGRLAIYKRLSHADGEDDLIRIQEE 1054
Cdd:COG1197 952 HIAEVGFDLYLQMLEEAVAALKGGKEPEEEW----EPEINLGVPALIPEDYIPDVRQRLELYKRIASAESEEELDELQEE 1027
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 1055 LIDRFGKLPEAAQTLLATHRLRLAAQPLGIVKIDASETQALLQFGAKTTVDPLRIIELVQRQ-RHIKLSGQDKLRVEIKA 1133
Cdd:COG1197 1028 LIDRFGPLPEEVENLLAVARLKLLARRLGIEKIDAGGKGIRIEFSPNTPLDPEKLIRLIQKQpGRYKLDGDDKLVITLDL 1107
|
1130
....*....|....*...
gi 499229419 1134 PQIAARADAVRAVLRALK 1151
Cdd:COG1197 1108 EDPEERLEALEELLEALA 1125
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
46-1128 |
0e+00 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 1227.68 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 46 RQAGkPLVVLTADPLEAQRLADEIPQFAPELrVRQLPDWETLPYDAFSPHQDLISQRLRTLHAL--MNQGVDILtvPVTT 123
Cdd:PRK10689 37 RHAG-PVVLIAPDMQNALRLHDEIQQFTDQM-VMNLADWETLPYDSFSPHQDIISSRLSTLYQLptMQRGVLIL--PVNT 112
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 124 ALYRLAPPAFLAAYTFSFKQKDRLDEAALRAQLTLANYSHVTQVTAPGEFCLRGGLIDLFPMGSVVPYRLDLFDDEIESI 203
Cdd:PRK10689 113 LMQRVCPHSFLHGHALVMKKGQRLSRDALRAQLEQAGYRHVDQVMEHGEYATRGALLDLFPMGSEEPYRIDFFDDEIDSL 192
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 204 RSFDVDTQRSLYPVGEVQLLPGREFPMDEEARNRFRARFREVFEGDPSRALPYKDIGNGIAFAGIEYYLPLFFEQT-ATL 282
Cdd:PRK10689 193 RVFDVDSQRTLEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFEVKRDAEHIYQQVSKGTLPAGIEYWQPLFFSEPlPPL 272
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 283 FDYLAADTITVTVGDIDDAMQRFAHDTRSRYDFLKVDRERPVLPPDTLFLDHEALFARLKDFPRLALMAER-------PH 355
Cdd:PRK10689 273 FSYFPANTLLVNTGDLETSAERFWADTLARFENRGVDPMRPLLPPESLWLRVDELFSELKNWPRVQLKTEHlptkaanTN 352
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 356 PDFAAAPDVAVARRADDPVARLRALLAQTGDRVLLCADSAGRRETLAQMLGEHGLAPEAQADSIQAfldDGARFGLAVAP 435
Cdd:PRK10689 353 LGYQKLPDLAVQAQQKAPLDALRRFLESFDGPVVFSVESEGRREALGELLARIKIAPKRIMRLDEA---SDRGRYLMIGA 429
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 436 LSAGFCVPGGALLFLTENDLYPGHagVTRRgKRTQERTSNVEAMVRDLAELRAGDPVVHAQHGIGRYHGLVNMDMGEGEM 515
Cdd:PRK10689 430 AEHGFIDTVRNLALICESDLLGER--VARR-RQDSRRTINPDTLIRNLAELHPGQPVVHLEHGVGRYAGMTTLEAGGIKG 506
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 516 EFLHLEYASGSTLYVPVSQLHVIARYSGADPDAAPLHQLGSGQWDKARRKAARQVRDTAAELLALYAQRAAREGYAFKLP 595
Cdd:PRK10689 507 EYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHKLGGDAWSRARQKAAEKVRDVAAELLDIYAQRAAKEGFAFKHD 586
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 596 MSDYEAFAEGFGFEETPDQAAAIQAVIMDMTSGRPMDRLVCGDVGFGKTEVALRAAFLAVANGKQVALLCPTTLLAEQHA 675
Cdd:PRK10689 587 REQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHY 666
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 676 QTFSDRFADWPVRVVELSRFRSAKEVAAAVEGINDGRVDIVIGTHKILSKDVRFKRLGLVIIDEEHRFGVRQKETLKALR 755
Cdd:PRK10689 667 DNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEHRFGVRHKERIKAMR 746
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 756 AEVDVLTLTATPIPRTLGMSLEGIRDFSVIATAPQKRLAIKTFVRREDGSTIREALLRELKRGGQVYFLHNEVETIHNRR 835
Cdd:PRK10689 747 ADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSLVVREAILREILRGGQVYYLYNDVENIQKAA 826
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 836 ARLEELVPEARIAVAHGQMPERELEQVMKGFYQQRHNVLLCTTIIETGIDIPTANTIVIHRADRFGLAQLHQLRGRVGRS 915
Cdd:PRK10689 827 ERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRS 906
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 916 HHQAYAYLLTPGEDAITNNAKKRLEAIQAMEELGSGFYLAMHDLEIRGTGEILGDSQSGNIQEVGFSMYNEMLNEAVRAL 995
Cdd:PRK10689 907 HHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGEEQSGQMETIGFSLYMELLENAVDAL 986
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 996 KAGEEPDLDAPFNLACEVNLHAPALLPSDYCPDVHGRLAIYKRLSHADGEDDLIRIQEELIDRFGKLPEAAQTLLATHRL 1075
Cdd:PRK10689 987 KAGREPSLEDLTSQQTEVELRMPSLLPDDFIPDVNTRLSFYKRIASAKNENELEEIKVELIDRFGLLPDPARNLLDIARL 1066
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|....
gi 499229419 1076 RLAAQPLGIVKIDASETQALLQFGAKTTVDPLRIIELVQRQ-RHIKLSGQDKLR 1128
Cdd:PRK10689 1067 RQQAQKLGIRKLEGNEKGGFIEFAEKNHVDPAWLIGLLQKQpQHYRLDGPTRLK 1120
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
161-1088 |
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: 1045.40 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 161 YSHVTQVTAPGEFCLRGGLIDLFPMGSVVPYRLDLFDDEIESIRSFDVDTQRSLYPVGEVQLLPGREFPMDEEARNRFRA 240
Cdd:TIGR00580 6 YERVDLVEEEGEFSVRGEILDIFPPGSELPVRIEFFGDEIESIREFDVDSQRSLEELLEITILPAKEFILLEEETIARLK 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 241 RFrEVFEGDPSRALPYKDIGNGIAFAGIEYYLPLFFEQTATLFDYLAADT-ITVTVGDIDDAMQRFAHDTRSRYDFLKVD 319
Cdd:TIGR00580 86 DN-AARVEDAKHLETIEALSEGTLPAGEEMFLPLFFEDLSSLFDYLPDNTpILLDDPERFHSAARFLQRELEEFYNALEE 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 320 RERPVLPPDTLF-LDHEALFARLKDFPRLALMAERPHPDFAAAPDVA--VARRADDPVA----RLRALLAQTGDRVLLCA 392
Cdd:TIGR00580 165 AKKLINPPRLDLdPSELAFEASAISLSRVQLENEHLSLKASEAIEGAqkHSRLEFGEILafkeELFRWLKAGFKITVAAE 244
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 393 dSAGRRETLAQMLGEHGLAPEAQADSiqAFLDDGARfGLAVAPLSAGFCVPGGALLFLTENDLYpghagvTRRGKRTQER 472
Cdd:TIGR00580 245 -SESQAERLKSLLAEHDIAAQVIDES--CIIIPAVR-YVMIGALSSGFILPTAGLAVITESELF------GSRVLRRPKK 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 473 TSNVEAMVRDLAELRAGDPVVHAQHGIGRYHGLVNMDMGEGEMEFLHLEYASGSTLYVPVSQLHVIARYSGADPDAAPLH 552
Cdd:TIGR00580 315 SRLKSKPIESLNELNPGDYVVHLDHGIGRFLGLETLEVGGIERDYLVLEYAGEDKLYVPVEQLHLISRYVGGSGKNPALD 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 553 QLGSGQWDKARRKAARQVRDTAAELLALYAQRAAREGYAFKLPMSDYEAFAEGFGFEETPDQAAAIQAVIMDMTSGRPMD 632
Cdd:TIGR00580 395 KLGGKSWEKTKAKVKKSVREIAAKLIELYAKRKAIKGHAFPPDLEWQQEFEDSFPFEETPDQLKAIEEIKADMESPRPMD 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 633 RLVCGDVGFGKTEVALRAAFLAVANGKQVALLCPTTLLAEQHAQTFSDRFADWPVRVVELSRFRSAKEVAAAVEGINDGR 712
Cdd:TIGR00580 475 RLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGK 554
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 713 VDIVIGTHKILSKDVRFKRLGLVIIDEEHRFGVRQKETLKALRAEVDVLTLTATPIPRTLGMSLEGIRDFSVIATAPQKR 792
Cdd:TIGR00580 555 IDILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPEDR 634
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 793 LAIKTFVRREDGSTIREALLRELKRGGQVYFLHNEVETIHNRRARLEELVPEARIAVAHGQMPERELEQVMKGFYQQRHN 872
Cdd:TIGR00580 635 LPVRTFVMEYDPELVREAIRRELLRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQ 714
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 873 VLLCTTIIETGIDIPTANTIVIHRADRFGLAQLHQLRGRVGRSHHQAYAYLLTPGEDAITNNAKKRLEAIQAMEELGSGF 952
Cdd:TIGR00580 715 VLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDAQKRLEAIQEFSELGAGF 794
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 953 YLAMHDLEIRGTGEILGDSQSGNIQEVGFSMYNEMLNEAVRALKAGEEPDLDApfnlACEVNLHAPALLPSDYCPDVHGR 1032
Cdd:TIGR00580 795 KIALHDLEIRGAGNLLGEEQSGHIESIGFDLYMELLEEAIEELKGGKPPKLEE----ETDIELPYSAFIPDDYIADDSLR 870
|
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|....*.
gi 499229419 1033 LAIYKRLSHADGEDDLIRIQEELIDRFGKLPEAAQTLLATHRLRLAAQPLGIVKID 1088
Cdd:TIGR00580 871 LEFYKRIASAETEEELEKIRDELIDRFGPLPEEARTLLDVARLKLLARKLGIRKLK 926
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
577-974 |
3.20e-127 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 405.20 E-value: 3.20e-127
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 577 LLALYAQRAAREGYAFKLPMSDYEAFAEGFGFEETPDQAAAIQAVIMDMTSGRPMDRLVCGDVGFGKTEVALRAAFLAVA 656
Cdd:COG1200 227 LLLRRARRRKRKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVE 306
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 657 NGKQVALLCPTTLLAEQHAQTFSDRFADWPVRVVELSRFRSAKEVAAAVEGINDGRVDIVIGTHKILSKDVRFKRLGLVI 736
Cdd:COG1200 307 AGYQAALMAPTEILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVV 386
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 737 IDEEHRFGVRQKETLKALRAEVDVLTLTATPIPRTLGMSLEGIRDFSVIATAPQKRLAIKTFV----RREDgstIREALL 812
Cdd:COG1200 387 IDEQHRFGVEQRLALREKGEAPHVLVMTATPIPRTLAMTLYGDLDVSVIDELPPGRKPIKTRVvpeeRRDE---VYERIR 463
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 813 RELKRGGQVYFL--------HNEVETIHNRRARLEELVPEARIAVAHGQMPERELEQVMKGFYQQRHNVLLCTTIIETGI 884
Cdd:COG1200 464 EEIAKGRQAYVVcplieeseKLDLQAAEETYEELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGV 543
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 885 DIPTANTIVIHRADRFGLAQLHQLRGRVGRSHHQAYAYLLTpgEDAITNNAKKRLEaiqAMEELGSGFYLAMHDLEIRGT 964
Cdd:COG1200 544 DVPNATVMVIENAERFGLSQLHQLRGRVGRGSAQSYCLLLY--DAPLSETARERLE---VMRETNDGFEIAEEDLELRGP 618
|
410
....*....|
gi 499229419 965 GEILGDSQSG 974
Cdd:COG1200 619 GEFLGTRQSG 628
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
577-975 |
1.01e-124 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 398.37 E-value: 1.01e-124
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 577 LLALYAQRAAREGYAFKLPMSDYEAFAEGFGFEETPDQAAAIQAVIMDMTSGRPMDRLVCGDVGFGKTEVALRAAFLAVA 656
Cdd:PRK10917 229 LLLLRAGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIE 308
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 657 NGKQVALLCPTTLLAEQHAQTFSDRFADWPVRVVELSRFRSAKEVAAAVEGINDGRVDIVIGTHKILSKDVRFKRLGLVI 736
Cdd:PRK10917 309 AGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVI 388
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 737 IDEEHRFGVRQKETLKALRAEVDVLTLTATPIPRTLGMSLEGIRDFSVIATAPQKRLAIKTFVRREDG-STIREALLREL 815
Cdd:PRK10917 389 IDEQHRFGVEQRLALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRrDEVYERIREEI 468
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 816 KRGGQVYF---LHNEVETIH-----NRRARLEELVPEARIAVAHGQMPERELEQVMKGFYQQRHNVLLCTTIIETGIDIP 887
Cdd:PRK10917 469 AKGRQAYVvcpLIEESEKLDlqsaeETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVP 548
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 888 TANTIVIHRADRFGLAQLHQLRGRVGRSHHQAYAYLLTpgEDAITNNAKKRLEaiqAMEELGSGFYLAMHDLEIRGTGEI 967
Cdd:PRK10917 549 NATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLY--KDPLSETARERLK---IMRETNDGFVIAEKDLELRGPGEL 623
|
....*...
gi 499229419 968 LGDSQSGN 975
Cdd:PRK10917 624 LGTRQSGL 631
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
600-976 |
2.45e-116 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 374.37 E-value: 2.45e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 600 EAFAEGFGFEETPDQAAAIQAVIMDMTSGRPMDRLVCGDVGFGKTEVALRAAFLAVANGKQVALLCPTTLLAEQHAQTFS 679
Cdd:TIGR00643 226 TKFLASLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLR 305
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 680 DRFADWPVRVVELSRFRSAKEVAAAVEGINDGRVDIVIGTHKILSKDVRFKRLGLVIIDEEHRFGVRQKETLKALRAE-- 757
Cdd:TIGR00643 306 NLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLREKGQGgf 385
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 758 -VDVLTLTATPIPRTLGMSLEGIRDFSVIATAPQKRLAIKTFV-RREDGSTIREALLRELKRGGQVYF---LHNEVETIH 832
Cdd:TIGR00643 386 tPHVLVMSATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLiKHDEKDIVYEFIEEEIAKGRQAYVvypLIEESEKLD 465
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 833 NRRA-----RLEELVPEARIAVAHGQMPERELEQVMKGFYQQRHNVLLCTTIIETGIDIPTANTIVIHRADRFGLAQLHQ 907
Cdd:TIGR00643 466 LKAAealyeRLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQ 545
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499229419 908 LRGRVGRSHHQAYAYLLTpgEDAITNNAKKRLeaiQAMEELGSGFYLAMHDLEIRGTGEILGDSQSGNI 976
Cdd:TIGR00643 546 LRGRVGRGDHQSYCLLVY--KNPKSESAKKRL---RVMADTLDGFVIAEEDLELRGPGDLLGTKQSGYP 609
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
595-787 |
2.77e-116 |
|
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350749 [Multi-domain] Cd Length: 193 Bit Score: 358.04 E-value: 2.77e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 595 PMSDYEAFAEGFGFEETPDQAAAIQAVIMDMTSGRPMDRLVCGDVGFGKTEVALRAAFLAVANGKQVALLCPTTLLAEQH 674
Cdd:cd17991 1 DGEEQEEFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 675 AQTFSDRFADWPVRVVELSRFRSAKEVAAAVEGINDGRVDIVIGTHKILSKDVRFKRLGLVIIDEEHRFGVRQKETLKAL 754
Cdd:cd17991 81 YETFKERFANFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQKEKLKEL 160
|
170 180 190
....*....|....*....|....*....|...
gi 499229419 755 RAEVDVLTLTATPIPRTLGMSLEGIRDFSVIAT 787
Cdd:cd17991 161 RPNVDVLTLSATPIPRTLHMALSGIRDLSVIAT 193
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
794-943 |
2.19e-73 |
|
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: 239.94 E-value: 2.19e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 794 AIKTFVRREDGSTIREALLRELKRGGQVYFLHNEVETIHNRRARLEELVPEARIAVAHGQMPERELEQVMKGFYQQRHNV 873
Cdd:cd18810 1 PVRTYVMPYDDELIREAIERELLRGGQVFYVHNRIESIEKLATQLRQLVPEARIAIAHGQMTENELEEVMLEFAKGEYDI 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 874 LLCTTIIETGIDIPTANTIVIHRADRFGLAQLHQLRGRVGRSHHQAYAYLLTPGEDAITNNAKKRLEAIQ 943
Cdd:cd18810 81 LVCTTIIESGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAYFLYPDQKKLTEDALKRLEAIQ 150
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
577-789 |
8.37e-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: 230.11 E-value: 8.37e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 577 LLALYAQRAAREGYAFKLPMSDYEAFAEGFGFEETPDQAAAIQAVIMDMTSGRPMDRLVCGDVGFGKTEVALRAAFLAVA 656
Cdd:cd17992 13 LLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKTVVAALAMLAAVE 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 657 NGKQVALLCPTTLLAEQHAQTFSDRFADWPVRVVELSRFRSAKEVAAAVEGINDGRVDIVIGTHKILSKDVRFKRLGLVI 736
Cdd:cd17992 93 NGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQEDVEFHNLGLVI 172
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 499229419 737 IDEEHRFGVRQKETLKALRAEVDVLTLTATPIPRTLGMSLEGIRDFSVIATAP 789
Cdd:cd17992 173 IDEQHRFGVEQRLKLREKGETPHVLVMTATPIPRTLALTLYGDLDVSIIDELP 225
|
|
| SF2_C_RecG_TRCF |
cd18792 |
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
794-943 |
5.44e-66 |
|
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family contains recombination factor RecG and transcription-repair coupling factor TrcF. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350179 [Multi-domain] Cd Length: 160 Bit Score: 219.45 E-value: 5.44e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 794 AIKTFVRREDGST-IREALLRELKRGGQVYFLHN--------EVETIHNRRARLEELVPEARIAVAHGQMPERELEQVMK 864
Cdd:cd18792 1 PIRTYVIPHDDLDlVYEAIERELARGGQVYYVYPrieeseklDLKSIEALAEELKELVPEARVALLHGKMTEDEKEAVML 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499229419 865 GFYQQRHNVLLCTTIIETGIDIPTANTIVIHRADRFGLAQLHQLRGRVGRSHHQAYAYLLTPGEDAITNNAKKRLEAIQ 943
Cdd:cd18792 81 EFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYPDPKKLTETAKKRLRAIA 159
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
598-786 |
8.14e-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: 8.14e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 598 DYEAFAEGFGFEETPDQAAAIQAVIMDMTSGRPMDRLVCGDVGFGKTEVALRAAFLAVANGKQVALLCPTTLLAEQHAQT 677
Cdd:cd17918 4 LIQELCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 678 FSDRFAdwPVRVVELSRFRSAKevaaAVEGIndgrvDIVIGTHKILSKDVRFKRLGLVIIDEEHRFGVRQKETLKALRAe 757
Cdd:cd17918 84 ARKFLP--FINVELVTGGTKAQ----ILSGI-----SLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNLGA- 151
|
170 180
....*....|....*....|....*....
gi 499229419 758 VDVLTLTATPIPRTLGMSLEGIRDFSVIA 786
Cdd:cd17918 152 THFLEATATPIPRTLALALSGLLDLSVID 180
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
799-942 |
2.21e-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: 143.64 E-value: 2.21e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 799 VRREDGSTIREALLRELKRGGQVYF---LHNEVETIHNRRA-----RL-EELVPEARIAVAHGQMPERELEQVMKGFYQQ 869
Cdd:cd18811 7 IFHTRLDKVYEFVREEIAKGRQAYViypLIEESEKLDLKAAvamyeYLkERFRPELNVGLLHGRLKSDEKDAVMAEFREG 86
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499229419 870 RHNVLLCTTIIETGIDIPTANTIVIHRADRFGLAQLHQLRGRVGRSHHQAYAYLLTPgeDAITNNAKKRLEAI 942
Cdd:cd18811 87 EVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYK--DPLTETAKQRLRVM 157
|
|
| CarD_TRCF |
smart01058 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
485-582 |
1.55e-38 |
|
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: 138.74 E-value: 1.55e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 485 ELRAGDPVVHAQHGIGRYHGLVNMDMGEGEMEFLHLEYASGSTLYVPVSQLHVIARYSGADPDA-APLHQLGSGQWDKAR 563
Cdd:smart01058 1 ELKIGDYVVHPDHGVGRYEGIETIEVGGEKREYLVLEYAGGDKLYVPVDNLDLGSRYVGSEGEVePVLDKLGGGSWSKRK 80
|
90
....*....|....*....
gi 499229419 564 RKAARQVRDTAAELLALYA 582
Cdd:smart01058 81 RKAKSGIRDIAAELLRLYA 99
|
|
| TRCF |
smart00982 |
This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in ... |
1014-1113 |
6.00e-38 |
|
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: 137.21 E-value: 6.00e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 1014 NLHAPALLPSDYCPDVHGRLAIYKRLSHADGEDDLIRIQEELIDRFGKLPEAAQTLLATHRLRLAAQPLGIVKIDASETQ 1093
Cdd:smart00982 1 DLPVPALIPEDYIPDVRQRLELYKRIASAETEEELDEIQEELIDRFGPLPEEVKNLLEVARLKLLAKKLGIEKIDAGGKG 80
|
90 100
....*....|....*....|
gi 499229419 1094 ALLQFGAKTTVDPLRIIELV 1113
Cdd:smart00982 81 IVIEFSPDTPIDPEKLILLI 100
|
|
| TRCF |
pfam03461 |
TRCF domain; |
1015-1109 |
2.56e-33 |
|
TRCF domain;
Pssm-ID: 460928 [Multi-domain] Cd Length: 95 Bit Score: 123.69 E-value: 2.56e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 1015 LHAPALLPSDYCPDVHGRLAIYKRLSHADGEDDLIRIQEELIDRFGKLPEAAQTLLATHRLRLAAQPLGIVKIDASETQA 1094
Cdd:pfam03461 1 LDVDAYIPDDYIPDESQRLELYKRLASIETEEELDDLQEELIDRFGPLPEEVENLLEIARLKLLAKKLGIEKIDLKGGGI 80
|
90
....*....|....*
gi 499229419 1095 LLQFGAKTTVDPLRI 1109
Cdd:pfam03461 81 RITFSEDAKIDPEKL 95
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
611-772 |
6.74e-28 |
|
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 110.80 E-value: 6.74e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 611 TPDQAAAIQAVImdmtSGRPMdrLVCGDVGFGKTEVALRAAFLAVA---NGKQVALLCPTTLLAEQHAQTFSDRFADWPV 687
Cdd:pfam00270 1 TPIQAEAIPAIL----EGRDV--LVQAPTGSGKTLAFLLPALEALDkldNGPQALVLAPTRELAEQIYEELKKLGKGLGL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 688 RVvelSRFRSAKEVAAAVEGINdgRVDIVIGTH----KILSKDVRFKRLGLVIIDEEHR-----FGVRQKETLKALRAEV 758
Cdd:pfam00270 75 KV---ASLLGGDSRKEQLEKLK--GPDILVGTPgrllDLLQERKLLKNLKLLVLDEAHRlldmgFGPDLEEILRRLPKKR 149
|
170
....*....|....
gi 499229419 759 DVLTLTATPiPRTL 772
Cdd:pfam00270 150 QILLLSATL-PRNL 162
|
|
| CarD_CdnL_TRCF |
pfam02559 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
486-581 |
4.28e-26 |
|
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: 102.91 E-value: 4.28e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 486 LRAGDPVVHAQHGIGRYHGLVNMDmgegEMEFLHLEYASGSTLYVPVSQLHVIARYSGADpdaaPLHQLGSGQ-WDKARR 564
Cdd:pfam02559 1 LKVGDYVVHPDHGIGRIEGIEKLE----TKDYYVLEYAGGDKLYVPVDNLDLIRKYISKG----ELDKLGDGRrWRKYKE 72
|
90
....*....|....*..
gi 499229419 565 KAARQVRDTAAELLALY 581
Cdd:pfam02559 73 KLKSGDIEEAAELIKLY 89
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
602-789 |
5.07e-26 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 106.81 E-value: 5.07e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 602 FAEGFGFEETPDQAAAIQAVIMDMtsgrpMDRLVCGDVGFGKTEVALRAAFLAVANG--KQVALLCPTTLLAEQHAQTFS 679
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALLSGL-----RDVILAAPTGSGKTLAALLPALEALKRGkgGRVLVLVPTRELAEQWAEELK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 680 DRFADWPVRVVELsrfRSAKEVAAAVEGINDGRVDIVIGT-----HKILSKDVRFKRLGLVIIDEEHRFGVRQ-----KE 749
Cdd:smart00487 76 KLGPSLGLKVVGL---YGGDSKREQLRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRLLDGGfgdqlEK 152
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 499229419 750 TLKALRAEVDVLTLTATP---IPRTLGMSLEGIRDFSVIATAP 789
Cdd:smart00487 153 LLKLLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPL 195
|
|
| UvrB_inter |
pfam17757 |
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ... |
140-228 |
6.62e-25 |
|
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: 99.78 E-value: 6.62e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 140 SFKQKDRLDEAALRAQLTLANYSHVTQVTAPGEFCLRGGLIDLFPMGSV-VPYRLDLFDDEIESIRSFDVDTQRSLYPVG 218
Cdd:pfam17757 2 SLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYSEdEAIRIEFFGDEIESIREFDPLTGRSLEKLD 81
|
90
....*....|
gi 499229419 219 EVQLLPGREF 228
Cdd:pfam17757 82 EVTIYPASHY 91
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
631-766 |
1.71e-22 |
|
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: 94.78 E-value: 1.71e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 631 MDRLVCGDVGFGKTEVALRAAF-LAVANGKQVALLCPTTLLAEQHAQTFSDRFaDWPVRVVELSRFRSAKEVAAAVEgin 709
Cdd:cd00046 2 ENVLITAPTGSGKTLAALLAALlLLLKKGKKVLVLVPTKALALQTAERLRELF-GPGIRVAVLVGGSSAEEREKNKL--- 77
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 710 dGRVDIVIGTHKILSKDV------RFKRLGLVIIDEEHRFGVRQKETL-------KALRAEVDVLTLTAT 766
Cdd:cd00046 78 -GDADIIIATPDMLLNLLlredrlFLKDLKLIIVDEAHALLIDSRGALildlavrKAGLKNAQVILLSAT 146
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
603-916 |
1.15e-20 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 97.40 E-value: 1.15e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 603 AEGFGFEETPDQAAAIQAVIMDMTSGRpmDR-LVCGDVGFGKTEVALRAAfLAVANGKQVALLCPTTLLAEQHAQTFSDR 681
Cdd:COG1061 74 ASGTSFELRPYQQEALEALLAALERGG--GRgLVVAPTGTGKTVLALALA-AELLRGKRVLVLVPRRELLEQWAEELRRF 150
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 682 FADwpvrvvelsrfrsakevAAAVEGINDGRVDIVIGTHKILSKDVRFKRL----GLVIIDEEHRFGVRQ-KETLKALRA 756
Cdd:COG1061 151 LGD-----------------PLAGGGKKDSDAPITVATYQSLARRAHLDELgdrfGLVIIDEAHHAGAPSyRRILEAFPA 213
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 757 EVdVLTLTATPIpRTLGMSLEGIRDFSVIATAPQKRLAIKTFVR--------------REDGSTIREALLRELKRGGQ-- 820
Cdd:COG1061 214 AY-RLGLTATPF-RSDGREILLFLFDGIVYEYSLKEAIEDGYLAppeyygirvdltdeRAEYDALSERLREALAADAErk 291
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 821 VYFLHNEVETIHNRRA------------RLEELVPEA--RIAVAHGQMPERELEQVMKGFYQQRHNVLLCTTIIETGIDI 886
Cdd:COG1061 292 DKILRELLREHPDDRKtlvfcssvdhaeALAELLNEAgiRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDV 371
|
330 340 350
....*....|....*....|....*....|
gi 499229419 887 PTANTIVIHRADRFgLAQLHQLRGRVGRSH 916
Cdd:COG1061 372 PRLDVAILLRPTGS-PREFIQRLGRGLRPA 400
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
809-914 |
1.90e-19 |
|
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: 84.57 E-value: 1.90e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 809 EALLRELK--RGGQVYFLHNEVETIHNRRARLEElvpEARIAVAHGQMPERELEQVMKGFYQQRHNVLLCTTIIETGIDI 886
Cdd:pfam00271 4 EALLELLKkeRGGKVLIFSQTKKTLEAELLLEKE---GIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDL 80
|
90 100
....*....|....*....|....*...
gi 499229419 887 PTANTIVIHRADrFGLAQLHQLRGRVGR 914
Cdd:pfam00271 81 PDVDLVINYDLP-WNPASYIQRIGRAGR 107
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
611-950 |
8.26e-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: 81.46 E-value: 8.26e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 611 TPDQAAAIQAVIMDMTSGRPMdrL---VCGDvgfGKTEVALRAAFLAVANGKQVALLCPTTllaeqhaqtfsdrfaDwpV 687
Cdd:COG4098 112 TPAQQKASDELLEAIKKKEEH--LvwaVCGA---GKTEMLFPAIAEALKQGGRVCIATPRV---------------D--V 169
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 688 rVVELS-RFRSA-KEVA-AAVEGIND---GRVDIVIGT-HKILskdvRFKR-LGLVIIDEEHRFGVRQKETL-----KAL 754
Cdd:COG4098 170 -VLELApRLQQAfPGVDiAALYGGSEekyRYAQLVIATtHQLL----RFYQaFDLLIIDEVDAFPYSGDPMLqyavkRAR 244
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 755 RAEVDVLTLTATPiPRTLGMSL-EGIRDFSVIAT------APQKRLAI-----KTFVRREDGSTIREALLRELKRGGQVY 822
Cdd:COG4098 245 KPDGKLIYLTATP-SKALQRQVkRGKLKVVKLPAryhghpLPVPKFKWlgnwkKRLRRGKLPRKLLKWLKKRLKEGRQLL 323
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 823 -FLHnEVETIHNRRARLEELVPEARIAVAHGQMPERElEQVMKgFYQQRHNVLLCTTIIETGIDIPTANTIVIHRADR-F 900
Cdd:COG4098 324 iFVP-TIELLEQLVALLQKLFPEERIAGVHAEDPERK-EKVQA-FRDGEIPILVTTTILERGVTFPNVDVAVLGADHPvF 400
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*
gi 499229419 901 GLAQLHQLRGRVGRSHHQAYaylltpGE-----DAITNNAKKRLEAIQAMEELGS 950
Cdd:COG4098 401 TEAALVQIAGRVGRSADYPT------GEviffhHGKTRAMKRAIREIKRMNREAK 449
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
614-741 |
2.53e-14 |
|
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: 72.24 E-value: 2.53e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 614 QAAAIQAVIMDMTSGRPMdrLVCGDVGFGKTEVALRAAFLAVANGKQVALLCPTTLLAEQHAQTFSDRFADwpvRVVELS 693
Cdd:cd17929 1 QRKAYEAIVSSLGGFKTF--LLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRFGD---KVAVLH 75
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 499229419 694 RFRSAKEVAAAVEGINDGRVDIVIGTHKILSkdVRFKRLGLVIIDEEH 741
Cdd:cd17929 76 SKLSDKERADEWRKIKRGEAKVVIGARSALF--APFKNLGLIIVDEEH 121
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
846-914 |
2.62e-14 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 69.16 E-value: 2.62e-14
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499229419 846 RIAVAHGQMPERELEQVMKGFYQQRHNVLLCTTIIETGIDIPTANTIVIHRADrFGLAQLHQLRGRVGR 914
Cdd:smart00490 13 KVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-WSPASYIQRIGRAGR 80
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
611-741 |
1.12e-12 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 72.46 E-value: 1.12e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 611 TPDQAAAIQAVIMDMTSGRPMdrLVCGDVGFGKTEVALRAAFLAVANGKQVALLCPTTLLAEQHAQTFSDRFADwpvRVV 690
Cdd:COG1198 197 NEEQQAAVEAIRAAAGGFSVF--LLHGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQTVERFRARFGA---RVA 271
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 499229419 691 EL-SRFrSAKEVAAAVEGINDGRVDIVIGThkilskdvR------FKRLGLVIIDEEH 741
Cdd:COG1198 272 VLhSGL-SDGERLDEWRRARRGEARIVIGT--------RsalfapFPNLGLIIVDEEH 320
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
611-836 |
3.18e-10 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 64.41 E-value: 3.18e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 611 TPDQAAAIQAvIMDMTSGRPMdrLVCGDVGFGKTEVALRAAFLAVANGKQVALLCPTTLLAEQHAQTFSDRFAdwpVRVV 690
Cdd:PRK05580 146 NPEQAAAVEA-IRAAAGFSPF--LLDGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQMLARFRARFG---APVA 219
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 691 EL-SRFrSAKEVAAAVEGINDGRVDIVIGThkilskdvR------FKRLGLVIIDEEHRFGVRQKETLK------AL-RA 756
Cdd:PRK05580 220 VLhSGL-SDGERLDEWRKAKRGEAKVVIGA--------RsalflpFKNLGLIIVDEEHDSSYKQQEGPRyhardlAVvRA 290
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 757 EVD----VLTlTATPiprtlgmSLEGI--------------RDFSVIATAPQKRLAIKTFVRREDGSTIREALLRE---- 814
Cdd:PRK05580 291 KLEnipvVLG-SATP-------SLESLanaqqgryrllrltKRAGGARLPEVEIIDMRELLRGENGSFLSPPLLEAikqr 362
|
250 260
....*....|....*....|...
gi 499229419 815 LKRGGQV-YFLhnevetihNRRA 836
Cdd:PRK05580 363 LERGEQVlLFL--------NRRG 377
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
611-775 |
4.73e-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: 59.97 E-value: 4.73e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 611 TPDQAAAIQAVimdMTSGRPMdrLVCGDVGFGKTEVALRAAFLAVANGKQVAL-LCPTTLLAEQHAQTFSDRFADWPVRV 689
Cdd:cd17921 3 NPIQREALRAL---YLSGDSV--LVSAPTSSGKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFGPLGKNV 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 690 VELSRFRSakevaaaVEGINDGRVDIVIGTHKIL------SKDVRFKRLGLVIIDEEHRFGVRQketlKALRAEVDVLTL 763
Cdd:cd17921 78 GLLTGDPS-------VNKLLLAEADILVATPEKLdlllrnGGERLIQDVRLVVVDEAHLIGDGE----RGVVLELLLSRL 146
|
170
....*....|...
gi 499229419 764 -TATPIPRTLGMS 775
Cdd:cd17921 147 lRINKNARFVGLS 159
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
640-767 |
1.83e-09 |
|
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350684 [Multi-domain] Cd Length: 146 Bit Score: 57.32 E-value: 1.83e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 640 GFGKTEVALrAAFLAVANGKqVALLCPTTLLAEQhaqtFSDRFADWpVRVVELSRFRSakEVAAAVEGINdgrvdIVIGT 719
Cdd:cd17926 28 GSGKTLTAL-ALIAYLKELR-TLIVVPTDALLDQ----WKERFEDF-LGDSSIGLIGG--GKKKDFDDAN-----VVVAT 93
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....
gi 499229419 720 HKILSKDVR-----FKRLGLVIIDEEHRFGVRQ-KETLKALRAEVdVLTLTATP 767
Cdd:cd17926 94 YQSLSNLAEeekdlFDQFGLLIVDEAHHLPAKTfSEILKELNAKY-RLGLTATP 146
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
634-742 |
2.95e-07 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 54.74 E-value: 2.95e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 634 LVCGDVGFGKTEVALR--AAFLAVANGKqVALLCPTTLLAEQHAQTFSDRFADWPVRVVELSRFRSAKEVAAAVEgindg 711
Cdd:COG1111 21 LVVLPTGLGKTAVALLviAERLHKKGGK-VLFLAPTKPLVEQHAEFFKEALNIPEDEIVVFTGEVSPEKRKELWE----- 94
|
90 100 110
....*....|....*....|....*....|....*.
gi 499229419 712 RVDIVIGTHKILSKDVRFKRL-----GLVIIDEEHR 742
Cdd:COG1111 95 KARIIVATPQVIENDLIAGRIdlddvSLLIFDEAHR 130
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
634-767 |
6.30e-07 |
|
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350685 [Multi-domain] Cd Length: 201 Bit Score: 51.28 E-value: 6.30e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 634 LVCGDVGFGKTEVAL-----RAAFLAVANGKQVALLCPTTLLAEQHAQTFSDRFADWPVRVVELSRFRSAKE-VAAAVEg 707
Cdd:cd17927 21 IICLPTGSGKTFVAVlicehHLKKFPAGRKGKVVFLANKVPLVEQQKEVFRKHFERPGYKVTGLSGDTSENVsVEQIVE- 99
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499229419 708 indgRVDIVIGTHKILSKD------VRFKRLGLVIIDEEHR--------FGVRQ--KETLKALRAEVDVLTLTATP 767
Cdd:cd17927 100 ----SSDVIIVTPQILVNDlksgtiVSLSDFSLLVFDECHNttknhpynEIMFRylDQKLGSSGPLPQILGLTASP 171
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
872-924 |
7.60e-07 |
|
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350172 [Multi-domain] Cd Length: 77 Bit Score: 47.70 E-value: 7.60e-07
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 499229419 872 NVLLCTTIIETGIDIPTANTIVIHRADRFgLAQLHQLRGRVGRSHHQAYAYLL 924
Cdd:cd18785 24 EILVATNVLGEGIDVPSLDTVIFFDPPSS-AASYIQRVGRAGRGGKDEGEVIL 75
|
|
| PRK05298 |
PRK05298 |
excinuclease ABC subunit UvrB; |
102-233 |
7.97e-07 |
|
excinuclease ABC subunit UvrB;
Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 53.13 E-value: 7.97e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 102 RLRTLHALMNQGvDILTVPVTTALYRLAPPAFLAAYTFSFKQKDRLDEAALRAQLTLANYSHVTQVTAPGEFCLRGGLID 181
Cdd:PRK05298 123 RHSATKSLLERR-DVIVVASVSCIYGLGSPEEYLKMVLSLRVGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIE 201
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|...
gi 499229419 182 LFPMGSV-VPYRLDLFDDEIESIRSFDVDTQRSLYPVGEVQLLPGREFPMDEE 233
Cdd:PRK05298 202 IFPAYYEeRAIRIEFFGDEIERISEFDPLTGEVLGELDRVTIYPASHYVTPRE 254
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
618-768 |
1.39e-06 |
|
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350769 [Multi-domain] Cd Length: 207 Bit Score: 50.37 E-value: 1.39e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 618 IQAVIMDMTSGRPmdRLVCGD-VGFGKTEVALRAA--FLAVANGKQVALLCPTTLlAEQHAQTFSDRFADWPVRVVELSR 694
Cdd:cd18011 6 IDAVLRALRKPPV--RLLLADeVGLGKTIEAGLIIkeLLLRGDAKRVLILCPASL-VEQWQDELQDKFGLPFLILDRETA 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 695 FRSAKEvaaavEGINDGRVDIVIGTH------KILSKDVRFKRLGLVIIDEEHRFGVRQK-------ETLKALRAEVD-V 760
Cdd:cd18011 83 AQLRRL-----IGNPFEEFPIVIVSLdllkrsEERRGLLLSEEWDLVVVDEAHKLRNSGGgketkryKLGRLLAKRARhV 157
|
....*...
gi 499229419 761 LTLTATPI 768
Cdd:cd18011 158 LLLTATPH 165
|
|
| DDXDc_reverse_gyrase |
cd17924 |
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
640-738 |
3.26e-06 |
|
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: 48.86 E-value: 3.26e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 640 GFGKTEVALRAAFLAVANGKQVALLCPTTLLAEQHAQTFSD--RFADWPVRVVELSRFRSAKEVAAAVEGINDGRVDIVI 717
Cdd:cd17924 42 GVGKTTFGLATSLYLASKGKRSYLIFPTKSLVKQAYERLSKyaEKAGVEVKILVYHSRLKKKEKEELLEKIEKGDFDILV 121
|
90 100
....*....|....*....|....
gi 499229419 718 GTHKILSKDVRF---KRLGLVIID 738
Cdd:cd17924 122 TTNQFLSKNFDLlsnKKFDFVFVD 145
|
|
| SrmB |
COG0513 |
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
607-943 |
4.63e-06 |
|
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 50.53 E-value: 4.63e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 607 GFEE-TPDQAAAIQAVImdmtSGRpmDRLVCGDVGFGKTevalrAAF-------LAVANGKQV-AL-LCPTTLLAEQHAQ 676
Cdd:COG0513 21 GYTTpTPIQAQAIPLIL----AGR--DVLGQAQTGTGKT-----AAFllpllqrLDPSRPRAPqALiLAPTRELALQVAE 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 677 TFSDrfadwpvrvveLSRFRSAKeVAAAVEGINDGR--------VDIVIGT------HkILSKDVRFKRLGLVIIDEEHR 742
Cdd:COG0513 90 ELRK-----------LAKYLGLR-VATVYGGVSIGRqiralkrgVDIVVATpgrlldL-IERGALDLSGVETLVLDEADR 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 743 ---FGVRQ--KETLKALRAEVDVLTLTATpiprtlgMSlEGIRDFS--------VIATAPQKRLA--IKTFVRREDGSTI 807
Cdd:COG0513 157 mldMGFIEdiERILKLLPKERQTLLFSAT-------MP-PEIRKLAkrylknpvRIEVAPENATAetIEQRYYLVDKRDK 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 808 REALLRELKRggqvyflHNEVETI--HNRRARLEELV---PEARIAVA--HGQMPERELEQVMKGFYQQRHNVLLCTTII 880
Cdd:COG0513 229 LELLRRLLRD-------EDPERAIvfCNTKRGADRLAeklQKRGISAAalHGDLSQGQRERALDAFRNGKIRVLVATDVA 301
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499229419 881 ETGIDIPTAnTIVIHradrFGLAQ-----LHqlR-GRVGRSHHQAYAYLLTPGEDaitnnaKKRLEAIQ 943
Cdd:COG0513 302 ARGIDIDDV-SHVIN----YDLPEdpedyVH--RiGRTGRAGAEGTAISLVTPDE------RRLLRAIE 357
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
640-948 |
4.97e-06 |
|
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I
Pssm-ID: 187770 [Multi-domain] Cd Length: 353 Bit Score: 50.12 E-value: 4.97e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 640 GFGKTEVALRAAFLAVANGK--QVALLCPTTLLAEQHAQTFSDRFADwPVRVVELSRFRSAKEVAAAVE--------GIN 709
Cdd:cd09639 9 GYGKTEAALLWALHSLKSQKadRVIIALPTRATINAMYRRAKEAFGE-TGLYHSSILSSRIKEMGDSEEfehlfplyIHS 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 710 DGRV---DIVIGTHKILSKDV------RFKRLG-----LVIIDEEHrfgVRQKET----LKALR--AEVDV--LTLTATp 767
Cdd:cd09639 88 NDTLfldPITVCTIDQVLKSVfgefghYEFTLAsiansLLIFDEVH---FYDEYTlaliLAVLEvlKDNDVpiLLMSAT- 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 768 IP---RTLGMSLEGIRDFSVIATAPQKRLAIKTFVRREDGS-TIREALLRELKRGGQVYFLHNEVETIHNRRARLEELVP 843
Cdd:cd09639 164 LPkflKEYAEKIGYVEENEPLDLKPNERAPFIKIESDKVGEiSSLERLLEFIKKGGSVAIIVNTVDRAQEFYQQLKEKGP 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 844 EARIAVAHGQMPE----RELEQVMKGFYQQRHNVLLCTTIIETGIDIpTANTIV--IHRADRfglaqLHQLRGRVGRsHH 917
Cdd:cd09639 244 EEEIMLIHSRFTEkdraKKEAELLLEFKKSEKFVIVATQVIEASLDI-SVDVMIteLAPIDS-----LIQRLGRLHR-YG 316
|
330 340 350
....*....|....*....|....*....|....*..
gi 499229419 918 QAYA------YLLTPGEDAITNNAKKRLEAIQAMEEL 948
Cdd:cd09639 317 EKNGeevyiiTDAPDGKGQKPYPYDLVERTIELLEEG 353
|
|
| DEXHc_Snf |
cd17919 |
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
638-769 |
6.51e-06 |
|
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350677 [Multi-domain] Cd Length: 182 Bit Score: 47.95 E-value: 6.51e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 638 DVGFGKTEVALraAFLAV-----ANGKQVALLCPTTLLaeqhaQTFSDRFADW--PVRVVELsrFRSAKEVAAAVEGIND 710
Cdd:cd17919 27 EMGLGKTLQAI--AFLAYllkegKERGPVLVVCPLSVL-----ENWEREFEKWtpDLRVVVY--HGSQRERAQIRAKEKL 97
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 499229419 711 GRVDIVIGTHKILSKDV-RFKRL--GLVIIDEEHRF---GVRQKETLKALRAEVDVLtLTATPIP 769
Cdd:cd17919 98 DKFDVVLTTYETLRRDKaSLRKFrwDLVVVDEAHRLknpKSQLSKALKALRAKRRLL-LTGTPLQ 161
|
|
| UvrB |
COG0556 |
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; |
124-233 |
3.31e-05 |
|
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
Pssm-ID: 440322 [Multi-domain] Cd Length: 657 Bit Score: 48.08 E-value: 3.31e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 124 ALYRLAPPAFLAAYTFSFKQKDRLDEAALRAQLTLANYSHVTQVTAPGEFCLRGGLIDLFPMGSV-VPYRLDLFDDEIES 202
Cdd:COG0556 141 CIYGLGSPEEYLKMVLSLRVGEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAYSEeRAIRIEFFGDEIER 220
|
90 100 110
....*....|....*....|....*....|.
gi 499229419 203 IRSFDVDTQRSLYPVGEVQLLPGREFPMDEE 233
Cdd:COG0556 221 ISEFDPLTGEVLGELDRVTIYPASHYVTPRE 251
|
|
| SF2_C_dicer |
cd18802 |
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
853-911 |
3.76e-05 |
|
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350189 [Multi-domain] Cd Length: 142 Bit Score: 44.89 E-value: 3.76e-05
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499229419 853 QMPERELEQVMKGFYQQRHNVLLCTTIIETGIDIPTANTIVihradRFGLA----QLHQLRGR 911
Cdd:cd18802 73 LMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVI-----RFDLPktlrSYIQSRGR 130
|
|
| DEXHc_RLR |
cd18036 |
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
634-767 |
5.02e-05 |
|
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprise RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). RIG-I-like receptors (RLRs) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350794 [Multi-domain] Cd Length: 204 Bit Score: 45.54 E-value: 5.02e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 634 LVCGDVGFGKTEVALRAA------FLAVANGKQVALLCPTTLLAEQHAQTFSDRFADWpVRVVELSRFRSAKE-VAAAVE 706
Cdd:cd18036 21 IICAPTGSGKTRVAVYICrhhlekRRSAGEKGRVVVLVNKVPLVEQQLEKFFKYFRKG-YKVTGLSGDSSHKVsFGQIVK 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 707 GindgrVDIVIGTHKIL---------SKDVRFKRLGLVIIDE------EHRFGV----RQKETLKALRAEVDVLTLTATP 767
Cdd:cd18036 100 A-----SDVIICTPQILinnllsgreEERVYLSDFSLLIFDEchhtqkEHPYNKimrmYLDKKLSSQGPLPQILGLTASP 174
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
837-924 |
5.35e-05 |
|
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: 44.04 E-value: 5.35e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 837 RLEELVPEARIAVA--HGQMPERELEQVMKGFYQQRHNVLLCTTIIETGIDIPTANTIV-----------IHRAdrfgla 903
Cdd:cd18787 42 RLAELLEELGIKVAalHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGVDHVInydlprdaedyVHRI------ 115
|
90 100
....*....|....*....|.
gi 499229419 904 qlhqlrGRVGRSHHQAYAYLL 924
Cdd:cd18787 116 ------GRTGRAGRKGTAITF 130
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
640-768 |
6.40e-05 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 44.59 E-value: 6.40e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 640 GFGKTEVALRAAFLAVANG--KQVALLCPTTLLAEQHAQTFSDRFADwpvrVVELSRFRSAKEVAAAVEGIndgrvDIVI 717
Cdd:pfam04851 33 GSGKTLTAAKLIARLFKKGpiKKVLFLVPRKDLLEQALEEFKKFLPN----YVEIGEIISGDKKDESVDDN-----KIVV 103
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 499229419 718 GTHKILSKDVRFKRL-------GLVIIDEEHRFGV-RQKETLKALRAEVdVLTLTATPI 768
Cdd:pfam04851 104 TTIQSLYKALELASLellpdffDVIIIDEAHRSGAsSYRNILEYFKPAF-LLGLTATPE 161
|
|
| SF2_C_FANCM_Hef |
cd18801 |
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
854-924 |
7.94e-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: 43.88 E-value: 7.94e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 499229419 854 MPERELEQVMKGFYQQRHNVLLCTTIIETGIDIPTANTIVIHRADRFGLAQLhQLRGRVGRsHHQAYAYLL 924
Cdd:cd18801 74 MSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMI-QRMGRTGR-KRQGRVVVL 142
|
|
| SNF2-rel_dom |
pfam00176 |
SNF2-related domain; This domain is found in proteins involved in a variety of processes ... |
634-772 |
9.21e-05 |
|
SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.
Pssm-ID: 425504 [Multi-domain] Cd Length: 289 Bit Score: 45.75 E-value: 9.21e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 634 LVCGDVGFGKT--EVALRAAFLAVAN--GKQVALLCPTTLLaEQHAQTFsDRFADWP-VRVVELSRFRSAKEvaaavEGI 708
Cdd:pfam00176 21 ILADEMGLGKTlqTISLLLYLKHVDKnwGGPTLIVVPLSLL-HNWMNEF-ERWVSPPaLRVVVLHGNKRPQE-----RWK 93
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 499229419 709 NDGRV----DIVIGTHKILSKD-VRFKRLG--LVIIDEEHRF-GVRQK--ETLKALRAEVDVLtLTATPIPRTL 772
Cdd:pfam00176 94 NDPNFladfDVVITTYETLRKHkELLKKVHwhRIVLDEGHRLkNSKSKlsKALKSLKTRNRWI-LTGTPLQNNL 166
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
612-766 |
1.68e-04 |
|
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play an important role in RNA degradation, processing and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350786 [Multi-domain] Cd Length: 177 Bit Score: 43.48 E-value: 1.68e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 612 PDQAAAIQAVIMDmtsGRPMdrLVCGDVGFGKTEVALRAAFLAVANGKQVALLCPTTLLAEQHAQTFSDrFADWPVRV-V 690
Cdd:cd18028 4 PPQAEAVRAGLLK---GENL--LISIPTASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEEFKK-LEEIGLKVgI 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 691 ELSRFRSAKEvaaavegiNDGRVDIVIGTHKILSKDVRFK-----RLGLVIIDEEH-----RFGVRQKETLKALRA---E 757
Cdd:cd18028 78 STGDYDEDDE--------WLGDYDIIVATYEKFDSLLRHSpswlrDVGVVVVDEIHlisdeERGPTLESIVARLRRlnpN 149
|
....*....
gi 499229419 758 VDVLTLTAT 766
Cdd:cd18028 150 TQIIGLSAT 158
|
|
| HepA |
COG0553 |
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
367-769 |
3.38e-04 |
|
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];
Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 44.83 E-value: 3.38e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 367 ARRADDPVARLRALLAQTGDRVLLCADSAGRRETLAQMLGEHGLAPEAQADSIQAFLDDGARFGLAVAPLSAGFCVPGGA 446
Cdd:COG0553 1 LLLLLLLLALGALGLLLTELLLLLRLGALLLELVLARELLLLLLAADALLLLALLLLLELLLLLAALLLLALLLLALSAL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 447 LLFLTENDLYPGHAGVTRRGKRTQERTSNVEAMVRDLAELRAGDPVVHAQHGIGRYHGLVnmDMGEGEMEFLHLEYASGS 526
Cdd:COG0553 81 ALLLLRLLLALLLLALLLLLAGLLALALLLLALLGLLLSLALLLLLLLLLLLLLLALLLV--LLAALLLLLLLLLLLALL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 527 TLYVPVSQLHVIARYSGADPDAAPLHQLGSGQWDKARRKAARQVRDTAAELLALYAQRAAREGYAFKLPMSDYEAFAEGF 606
Cdd:COG0553 159 LGRLLLLALLLLALEALLLLGLLLALALLALLELALLAAEAELLLLLELLLELELLAEAAVDAFRLRRLREALESLPAGL 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 607 GFEETPDQAAAIQAVIMdmtsgrpMDRLVCG-----DVGFGKT-EVALRAAFLAVANGKQVAL-LCPTTLLaEQHAQTFs 679
Cdd:COG0553 239 KATLRPYQLEGAAWLLF-------LRRLGLGglladDMGLGKTiQALALLLELKERGLARPVLiVAPTSLV-GNWQREL- 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 680 DRFA-DWPVRVVELSRFRSAKEVAAAvegindgRVDIVIGTHKILSKDVRF---KRLGLVIIDEEHRF---GVRQKETLK 752
Cdd:COG0553 310 AKFApGLRVLVLDGTRERAKGANPFE-------DADLVITSYGLLRRDIELlaaVDWDLVILDEAQHIknpATKRAKAVR 382
|
410
....*....|....*..
gi 499229419 753 ALRAEVdVLTLTATPIP 769
Cdd:COG0553 383 ALKARH-RLALTGTPVE 398
|
|
| DEXHc_RecQ |
cd17920 |
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ... |
599-772 |
1.28e-03 |
|
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: 41.37 E-value: 1.28e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 599 YEAFAEGFGFEE-TPDQAAAIQAVImdmtSGRpmDRLVCGDVGFGKTEVAlraaflavangkQV-ALLCP-TT-----LL 670
Cdd:cd17920 1 EQILKEVFGYDEfRPGQLEAINAVL----AGR--DVLVVMPTGGGKSLCY------------QLpALLLDgVTlvvspLI 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 671 AEQHAQTfsDRFADWPVRVVELSRFRSAKEVAAAVEGINDGRVDIVI---------GTHKILSKDVRFKRLGLVIIDEEH 741
Cdd:cd17920 63 SLMQDQV--DRLQQLGIRAAALNSTLSPEEKREVLLRIKNGQYKLLYvtperllspDFLELLQRLPERKRLALIVVDEAH 140
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 499229419 742 ---------RFGVRQketLKALRAE---VDVLTLTATPIPRTL 772
Cdd:cd17920 141 cvsqwghdfRPDYLR---LGRLRRAlpgVPILALTATATPEVR 180
|
|
| PRK13766 |
PRK13766 |
Hef nuclease; Provisional |
634-742 |
1.49e-03 |
|
Hef nuclease; Provisional
Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 42.94 E-value: 1.49e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 634 LVCGDVGFGKTEVAL--RAAFLAVANGKqVALLCPTTLLAEQHAQTFSDRFADWPVRVVELS-RFRSAKEVAAAVEGind 710
Cdd:PRK13766 33 LVVLPTGLGKTAIALlvIAERLHKKGGK-VLILAPTKPLVEQHAEFFRKFLNIPEEKIVVFTgEVSPEKRAELWEKA--- 108
|
90 100 110
....*....|....*....|....*....|....*..
gi 499229419 711 grvDIVIGTHKILSKDVRFKRLGL-----VIIDEEHR 742
Cdd:PRK13766 109 ---KVIVATPQVIENDLIAGRISLedvslLIFDEAHR 142
|
|
| SF2_C_LHR |
cd18796 |
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ... |
831-918 |
1.92e-03 |
|
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases. LHR family helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350183 [Multi-domain] Cd Length: 150 Bit Score: 39.94 E-value: 1.92e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 831 IHNRRARLEELVPEARIAVAHGQMPERELEQVMKGFYQQRHNVLLCTTIIETGIDIPTANTiVIHRADRFGLAQLHQlrg 910
Cdd:cd18796 55 AQRLRELCPDRVPPDFIALHHGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIGDVDL-VIQIGSPKSVARLLQ--- 130
|
....*...
gi 499229419 911 RVGRSHHQ 918
Cdd:cd18796 131 RLGRSGHR 138
|
|
| DEADc |
cd00268 |
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ... |
604-739 |
2.57e-03 |
|
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: 40.50 E-value: 2.57e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 604 EGFGFEE-TPDQAAAIQAVImdmtSGRpmDRLVCGDVGFGKTevalrAAFL------------AVANGKQVALLCPTTLL 670
Cdd:cd00268 6 KKLGFEKpTPIQAQAIPLIL----SGR--DVIGQAQTGSGKT-----LAFLlpilekllpepkKKGRGPQALVLAPTREL 74
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90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 671 AEQHAQTFSdrfadwpvrvvELSRFRSAKeVAAAVEGIN--------DGRVDIVIGT------HkILSKDVRFKRLGLVI 736
Cdd:cd00268 75 AMQIAEVAR-----------KLGKGTGLK-VAAIYGGAPikkqiealKKGPDIVVGTpgrlldL-IERGKLDLSNVKYLV 141
|
...
gi 499229419 737 IDE 739
Cdd:cd00268 142 LDE 144
|
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| DEXHc_Hef |
cd18035 |
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
634-742 |
2.57e-03 |
|
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: 40.19 E-value: 2.57e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 634 LVCGDVGFGKTEVA-LRAAFLAVANGKQVALLCPTTLLAEQHAQTFSdRFADWPVRVVELSRFRSAKEVAAAVEgindgR 712
Cdd:cd18035 20 LIVLPTGLGKTIIAiLVAADRLTKKGGKVLILAPSRPLVEQHAENLK-RVLNIPDKITSLTGEVKPEERAERWD-----A 93
|
90 100 110
....*....|....*....|....*....|....*
gi 499229419 713 VDIVIGTHKILSKDVRFKRL-----GLVIIDEEHR 742
Cdd:cd18035 94 SKIIVATPQVIENDLLAGRItlddvSLLIFDEAHH 128
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| UB2H |
pfam14814 |
Bifunctional transglycosylase second domain; UB2H is the second domain of the ... |
146-214 |
5.01e-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: 37.15 E-value: 5.01e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 499229419 146 RLDEAALRAQLTLANYSHVTQVTAPGEFCLRGGLIDL------FPMGSV--VPYRLDLFDDEIESIRsfDVDTQRSL 214
Cdd:pfam14814 6 ALSAAQLEQELKLLGYRKVSNPTRPGEYSVSGNRIELyrrgfdFPDGAEpaRRVRLRFAGGRVARLQ--DLDTGRDL 80
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| YprA |
COG1205 |
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ... |
729-931 |
8.89e-03 |
|
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, recombination and repair];
Pssm-ID: 440818 [Multi-domain] Cd Length: 758 Bit Score: 40.20 E-value: 8.89e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 729 FKRLGLVIIDEEHRF-GV----------RQKETLKALRAEVDVLTLTATpI--PRTLGMSLEGiRDFSVI--ATAPQkrl 793
Cdd:COG1205 178 FRNLRYVVIDEAHTYrGVfgshvanvlrRLRRICRHYGSDPQFILASAT-IgnPAEHAERLTG-RPVTVVdeDGSPR--- 252
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 794 AIKTFV--------RREDGSTIREA--LLREL-KRGGQvyFL-----HNEVETIHNR-RARLEELVPEARIAVAHGQ-MP 855
Cdd:COG1205 253 GERTFVlwnpplvdDGIRRSALAEAarLLADLvREGLR--TLvftrsRRGAELLARYaRRALREPDLADRVAAYRAGyLP 330
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499229419 856 E--RELEqvmKGFYQQRHNVLLCTTIIETGIDIPTANTIVIHradrfG----LAQLHQLRGRVGRSHHQAYAYLLtPGED 929
Cdd:COG1205 331 EerREIE---RGLRSGELLGVVSTNALELGIDIGGLDAVVLA-----GypgtRASFWQQAGRAGRRGQDSLVVLV-AGDD 401
|
..
gi 499229419 930 AI 931
Cdd:COG1205 402 PL 403
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