|
Name |
Accession |
Description |
Interval |
E-value |
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
41-1199 |
0e+00 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 1488.01 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 41 GEDELALTGA-DAVRSHLIYAM--STKVPVLVITATGREAEDLTAEVKSMIGD-RVAMFPSWETLPHEKLSPAVDTVAQR 116
Cdd:COG1197 1 GGGRLTLSGLpGSARALLLAALarALGRPLLVVTADEREAERLAEDLRFFLPDlPVLLFPAWETLPYDRFSPSPDIVSER 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 117 RKALYDVRRGKVDVLIAAVRSLVQPIVD-DLEAEASAPIHV--QLDRDceNLVERLVHHGYSHVDMVGRRGQFAVRGGIV 193
Cdd:COG1197 81 LATLRRLASGKPGIVVTPVRALLQRLPPpELLAAASLSLKVgdELDLE--ELRERLVAAGYERVDQVEEPGEFAVRGGIL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 194 DVFPATEELPVRIELWGDEVTDLRAFSVADQRTISEVevDQLDIFPCRALLIDDDVKAAAEKLATTRSG---QVQEMLTR 270
Cdd:COG1197 159 DIFPPGSEHPVRIEFFGDEIESIRTFDPETQRSLEKV--DEVELLPAREFPLDEEAIERFRERLRELFGldpKLDELYEA 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 271 IGDGQWVEGMESLIPLISQHpMKMLTEVMPEKTHVLMCGPERIRSRAQDLISAGEEFmaaaWETAAMGGSAPIatdgLEP 350
Cdd:COG1197 237 LSEGIAFAGIEYYLPLFYEE-LATLFDYLPEDALVVLDEPERIEEAAEEFWEEIEER----YEARRHDRGRPL----LPP 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 351 SA--------YRSLASIPMPTswhISPpgmLEAGVTEDDVLPLTFEPGPAPRGDLKEIGHLMKQLRDAtvaGERVAYVAA 422
Cdd:COG1197 308 EElfldpeelFAALKRRPRVT---LSP---FAALPEGAGVVNLGARPLPSFAGQLEALLEELKRLLKD---GGRVLLAAE 378
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 423 TPAGARRQAEKFREAGIATRMAAGPEYPESGRITVYQGVLHGGLVFPripGGALTLITEQDITGNRIAegALGGRRKPAK 502
Cdd:COG1197 379 SEGRRERLLELLRDHGIPARLVESLAELSPGGVAITVGPLEHGFELP---DAKLAVITESELFGERVK--RRRRKKKRSA 453
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 503 RRGRVDPLALKAGDYVVHDTHGIGRFVKLTERTIGtgedQARREYVVLEYAPSkrggpsDQLYVPMESLDLLSRYVG--G 580
Cdd:COG1197 454 DAFIRDLSELKPGDYVVHVDHGIGRYLGLETLEVG----GAERDYLVLEYAGG------DKLYVPVDQLDLISRYVGseG 523
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 581 EKPTLSKMGGSDWKSTKRKARGAVREIAEELVKLYAERQAAPGHAFAPDTPWQQEMEDNFPFTETEDQLQAIDEIKSDME 660
Cdd:COG1197 524 EAPKLDKLGGSDWQKAKAKAKKAVRDIAAELLKLYAERAARKGFAFSPDTPWQREFEAAFPYEETPDQLRAIEEVKADME 603
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 661 KPVPMDRVLIGDVGYGKTEVALRAAFKAVQDGRQVAVLVPTTLLAQQHLTTFTQRMEGFPVTIRGLSRFTSPKDSKEVLE 740
Cdd:COG1197 604 SPRPMDRLVCGDVGFGKTEVALRAAFKAVMDGKQVAVLVPTTLLAQQHYETFKERFAGFPVRVEVLSRFRTAKEQKETLE 683
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 741 GLKNGTVDIVIGTHRLLQTGVQWKELGLVIVDEEQRFGVEHKEHIKALRHHVDVLTMSATPIPRTLEMSIAGIREMSQIL 820
Cdd:COG1197 684 GLADGKVDIVIGTHRLLSKDVKFKDLGLLIIDEEQRFGVRHKEKLKALRANVDVLTLTATPIPRTLQMSLSGIRDLSIIA 763
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 821 TPPQDRHPVLTYVGAQSDKQVAAAIRRELLRDGQVFYLHNKVETIDKVAQTIRNLVPEARVVVAHGQMGEEQLERTVDGF 900
Cdd:COG1197 764 TPPEDRLPVKTFVGEYDDALIREAILRELLRGGQVFYVHNRVEDIEKVAARLQELVPEARIAVAHGQMSERELERVMLDF 843
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 901 WQREYDVLVCTTIVETGLDIANANTLIVENAHHMGLSQLHQLRGRVGRSRERAYAYFLYPENQTLTETSYDRLSTIAQNN 980
Cdd:COG1197 844 YEGEFDVLVCTTIIETGIDIPNANTIIIERADRFGLAQLYQLRGRVGRSHRRAYAYLLYPPDKVLTEDAEKRLEAIQEFT 923
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 981 DLGAGMAVAMKDLEMRGAGNILGAEQSGHIAGVGFDMYVRLVGEAVAALKAvadGETPDasdnEPKEVRIDLPVDANIPA 1060
Cdd:COG1197 924 ELGAGFKLAMHDLEIRGAGNLLGEEQSGHIAEVGFDLYLQMLEEAVAALKG---GKEPE----EEWEPEINLGVPALIPE 996
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 1061 EYVSSERLRLEAYRKFAAASALDDIDVVLEELVDRYGTPPIEVERLAVISRLRIICREFGVHEVQAMGAHIRITPMELAD 1140
Cdd:COG1197 997 DYIPDVRQRLELYKRIASAESEEELDELQEELIDRFGPLPEEVENLLAVARLKLLARRLGIEKIDAGGKGIRIEFSPNTP 1076
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|....*....
gi 1948637819 1141 SKQVRLKRLypqatYRAATRTVSVGMPKEGRgLRAKPVRDIALVQWVADFLTSMAGIPR 1199
Cdd:COG1197 1077 LDPEKLIRL-----IQKQPGRYKLDGDDKLV-ITLDLEDPEERLEALEELLEALAKLAK 1129
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
169-1121 |
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: 1096.25 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 169 LVHHGYSHVDMVGRRGQFAVRGGIVDVFPATEELPVRIELWGDEVTDLRAFSVADQRTISEVevDQLDIFPCRA-LLIDD 247
Cdd:TIGR00580 1 LVELGYERVDLVEEEGEFSVRGEILDIFPPGSELPVRIEFFGDEIESIREFDVDSQRSLEEL--LEITILPAKEfILLEE 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 248 DVKAAAEKLATTRSG-QVQEMLTRIGDGQWVEGMESLIPL-ISQHPMkmLTEVMPEKTHVLMCGPERIRSRAQDLISAGE 325
Cdd:TIGR00580 79 ETIARLKDNAARVEDaKHLETIEALSEGTLPAGEEMFLPLfFEDLSS--LFDYLPDNTPILLDDPERFHSAARFLQRELE 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 326 EFMAAAWETAAMGgSAPIATdgLEPSA------YRSLASIPMPtSWHISPPGMleagvteddVLPLTFepGPAPRGDLKE 399
Cdd:TIGR00580 157 EFYNALEEAKKLI-NPPRLD--LDPSElafeasAISLSRVQLE-NEHLSLKAS---------EAIEGA--QKHSRLEFGE 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 400 IGHLMKQLRDATVAGERVAYVAATPAGARRQAEKFREAGIATRMAAGPEYPESGRITVYQGVLHGGLVFPripGGALTLI 479
Cdd:TIGR00580 222 ILAFKEELFRWLKAGFKITVAAESESQAERLKSLLAEHDIAAQVIDESCIIIPAVRYVMIGALSSGFILP---TAGLAVI 298
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 480 TEQDITGNRIaegalggRRKPAKRRGR----VDPLALKAGDYVVHDTHGIGRFVKLTERTIGtgedQARREYVVLEYAPS 555
Cdd:TIGR00580 299 TESELFGSRV-------LRRPKKSRLKskpiESLNELNPGDYVVHLDHGIGRFLGLETLEVG----GIERDYLVLEYAGE 367
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 556 KRggpsdqLYVPMESLDLLSRYVGGE--KPTLSKMGGSDWKSTKRKARGAVREIAEELVKLYAERQAAPGHAFAPDTPWQ 633
Cdd:TIGR00580 368 DK------LYVPVEQLHLISRYVGGSgkNPALDKLGGKSWEKTKAKVKKSVREIAAKLIELYAKRKAIKGHAFPPDLEWQ 441
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 634 QEMEDNFPFTETEDQLQAIDEIKSDMEKPVPMDRVLIGDVGYGKTEVALRAAFKAVQDGRQVAVLVPTTLLAQQHLTTFT 713
Cdd:TIGR00580 442 QEFEDSFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFK 521
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 714 QRMEGFPVTIRGLSRFTSPKDSKEVLEGLKNGTVDIVIGTHRLLQTGVQWKELGLVIVDEEQRFGVEHKEHIKALRHHVD 793
Cdd:TIGR00580 522 ERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELRTSVD 601
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 794 VLTMSATPIPRTLEMSIAGIREMSQILTPPQDRHPVLTYVGAQSDKQVAAAIRRELLRDGQVFYLHNKVETIDKVAQTIR 873
Cdd:TIGR00580 602 VLTLSATPIPRTLHMSMSGIRDLSIIATPPEDRLPVRTFVMEYDPELVREAIRRELLRGGQVFYVHNRIESIEKLATQLR 681
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 874 NLVPEARVVVAHGQMGEEQLERTVDGFWQREYDVLVCTTIVETGLDIANANTLIVENAHHMGLSQLHQLRGRVGRSRERA 953
Cdd:TIGR00580 682 ELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKA 761
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 954 YAYFLYPENQTLTETSYDRLSTIAQNNDLGAGMAVAMKDLEMRGAGNILGAEQSGHIAGVGFDMYVRLVGEAVAALKava 1033
Cdd:TIGR00580 762 YAYLLYPHQKALTEDAQKRLEAIQEFSELGAGFKIALHDLEIRGAGNLLGEEQSGHIESIGFDLYMELLEEAIEELK--- 838
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 1034 DGETPDASDnepkEVRIDLPVDANIPAEYVSSERLRLEAYRKFAAASALDDIDVVLEELVDRYGTPPIEVERLAVISRLR 1113
Cdd:TIGR00580 839 GGKPPKLEE----ETDIELPYSAFIPDDYIADDSLRLEFYKRIASAETEEELEKIRDELIDRFGPLPEEARTLLDVARLK 914
|
....*...
gi 1948637819 1114 IICREFGV 1121
Cdd:TIGR00580 915 LLARKLGI 922
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
66-1126 |
0e+00 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 711.52 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 66 PVLVITATGREAEDLTAEVKSMIGDRVAMFPSWETLPHEKLSPAVDTVAQRRKALYDVRRGKVDVLIAAVRSLVQPIVDD 145
Cdd:PRK10689 41 PVVLIAPDMQNALRLHDEIQQFTDQMVMNLADWETLPYDSFSPHQDIISSRLSTLYQLPTMQRGVLILPVNTLMQRVCPH 120
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 146 LEAEASAPIHV---QLDRDceNLVERLVHHGYSHVDMVGRRGQFAVRGGIVDVFPATEELPVRIELWGDEVTDLRAFSVA 222
Cdd:PRK10689 121 SFLHGHALVMKkgqRLSRD--ALRAQLEQAGYRHVDQVMEHGEYATRGALLDLFPMGSEEPYRIDFFDDEIDSLRVFDVD 198
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 223 DQRTISEVEvdQLDIFPCRALLIDddvKAAAEKLATTRSGQ------VQEMLTRIGDGQWVEGMESLIPLISQHPMKMLT 296
Cdd:PRK10689 199 SQRTLEEVE--AINLLPAHEFPTD---KAAIELFRSQWRDTfevkrdAEHIYQQVSKGTLPAGIEYWQPLFFSEPLPPLF 273
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 297 EVMPEKTHVLMCGperirsraqDLISAGEEFmaaaWETAAmggsapiatdglepSAYRSLASIPMPTswhISPPGMLEAG 376
Cdd:PRK10689 274 SYFPANTLLVNTG---------DLETSAERF----WADTL--------------ARFENRGVDPMRP---LLPPESLWLR 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 377 VTEddvlpLTFEPGPAPRGDLK------EIGHL---MKQLRDATVAGERVAYVAATpagaRRQAEKF------------- 434
Cdd:PRK10689 324 VDE-----LFSELKNWPRVQLKtehlptKAANTnlgYQKLPDLAVQAQQKAPLDAL----RRFLESFdgpvvfsvesegr 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 435 REA--GIATRMAAGP-------EYPESGRITVYQGVLHGGLVFPRipggALTLITEQDITGNRIAEgalggRRKPAKRRG 505
Cdd:PRK10689 395 REAlgELLARIKIAPkrimrldEASDRGRYLMIGAAEHGFIDTVR----NLALICESDLLGERVAR-----RRQDSRRTI 465
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 506 RVDPL-----ALKAGDYVVHDTHGIGRFVKLTerTIGTGEDQArrEYVVLEYAPSkrggpsDQLYVPMESLDLLSRYVGG 580
Cdd:PRK10689 466 NPDTLirnlaELHPGQPVVHLEHGVGRYAGMT--TLEAGGIKG--EYLMLTYAND------AKLYVPVSSLHLISRYAGG 535
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 581 --EKPTLSKMGGSDWKSTKRKARGAVREIAEELVKLYAERQAAPGHAFAPDTPWQQEMEDNFPFTETEDQLQAIDEIKSD 658
Cdd:PRK10689 536 aeENAPLHKLGGDAWSRARQKAAEKVRDVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSD 615
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 659 MEKPVPMDRVLIGDVGYGKTEVALRAAFKAVQDGRQVAVLVPTTLLAQQHLTTFTQRMEGFPVTIRGLSRFTSPKDSKEV 738
Cdd:PRK10689 616 MCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQI 695
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 739 LEGLKNGTVDIVIGTHRLLQTGVQWKELGLVIVDEEQRFGVEHKEHIKALRHHVDVLTMSATPIPRTLEMSIAGIREMSQ 818
Cdd:PRK10689 696 LAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEHRFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSI 775
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 819 ILTPPQDRHPVLTYVGAQSDKQVAAAIRRELLRDGQVFYLHNKVETIDKVAQTIRNLVPEARVVVAHGQMGEEQLERTVD 898
Cdd:PRK10689 776 IATPPARRLAVKTFVREYDSLVVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMN 855
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 899 GFWQREYDVLVCTTIVETGLDIANANTLIVENAHHMGLSQLHQLRGRVGRSRERAYAYFLYPENQTLTETSYDRLSTIAQ 978
Cdd:PRK10689 856 DFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIAS 935
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 979 NNDLGAGMAVAMKDLEMRGAGNILGAEQSGHIAGVGFDMYVRLVGEAVAALKAvadGETPDASDNEPKEVRIDLPVDANI 1058
Cdd:PRK10689 936 LEDLGAGFALATHDLEIRGAGELLGEEQSGQMETIGFSLYMELLENAVDALKA---GREPSLEDLTSQQTEVELRMPSLL 1012
|
1050 1060 1070 1080 1090 1100
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1948637819 1059 PAEYVSSERLRLEAYRKFAAASALDDIDVVLEELVDRYGTPPIEVERLAVISRLRIICREFGVHEVQA 1126
Cdd:PRK10689 1013 PDDFIPDVNTRLSFYKRIASAKNENELEEIKVELIDRFGLLPDPARNLLDIARLRQQAQKLGIRKLEG 1080
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
611-1008 |
7.22e-118 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 381.32 E-value: 7.22e-118
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 611 LVKLYAERQAAPGHAFAPDTPWQQEMEDNFPFTETEDQLQAIDEIKSDMEKPVPMDRVLIGDVGYGKTEVALRAAFKAVQ 690
Cdd:COG1200 227 LLLRRARRRKRKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVE 306
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 691 DGRQVAVLVPTTLLAQQHLTTFTQRMEGFPVTIRGLSRFTSPKDSKEVLEGLKNGTVDIVIGTHRLLQTGVQWKELGLVI 770
Cdd:COG1200 307 AGYQAALMAPTEILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVV 386
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 771 VDEEQRFGVEHKEhikALR---HHVDVLTMSATPIPRTLEMSIAG------IREMsqiltpPQDRHPVLTYVGAQSD-KQ 840
Cdd:COG1200 387 IDEQHRFGVEQRL---ALRekgEAPHVLVMTATPIPRTLAMTLYGdldvsvIDEL------PPGRKPIKTRVVPEERrDE 457
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 841 VAAAIRRELLRDGQVFYlhnkV-------ETID-----KVAQTIRNLVPEARVVVAHGQMGEEQLERTVDGFWQREYDVL 908
Cdd:COG1200 458 VYERIREEIAKGRQAYV----VcplieesEKLDlqaaeETYEELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVL 533
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 909 VCTTIVETGLDIANANTLIVENAHHMGLSQLHQLRGRVGRSRERAYAYFLYpeNQTLTETSYDRLSTIAQNNDlgaGMAV 988
Cdd:COG1200 534 VATTVIEVGVDVPNATVMVIENAERFGLSQLHQLRGRVGRGSAQSYCLLLY--DAPLSETARERLEVMRETND---GFEI 608
|
410 420
....*....|....*....|
gi 1948637819 989 AMKDLEMRGAGNILGAEQSG 1008
Cdd:COG1200 609 AEEDLELRGPGEFLGTRQSG 628
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
629-821 |
2.75e-117 |
|
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: 361.50 E-value: 2.75e-117
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 629 DTPWQQEMEDNFPFTETEDQLQAIDEIKSDMEKPVPMDRVLIGDVGYGKTEVALRAAFKAVQDGRQVAVLVPTTLLAQQH 708
Cdd:cd17991 1 DGEEQEEFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 709 LTTFTQRMEGFPVTIRGLSRFTSPKDSKEVLEGLKNGTVDIVIGTHRLLQTGVQWKELGLVIVDEEQRFGVEHKEHIKAL 788
Cdd:cd17991 81 YETFKERFANFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQKEKLKEL 160
|
170 180 190
....*....|....*....|....*....|...
gi 1948637819 789 RHHVDVLTMSATPIPRTLEMSIAGIREMSQILT 821
Cdd:cd17991 161 RPNVDVLTLSATPIPRTLHMALSGIRDLSVIAT 193
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
611-1008 |
1.93e-115 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 374.87 E-value: 1.93e-115
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 611 LVKLYAERQAAPGHAFAPDTPWQQEMEDNFPFTETEDQLQAIDEIKSDMEKPVPMDRVLIGDVGYGKTEVALRAAFKAVQ 690
Cdd:PRK10917 229 LLLLRAGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIE 308
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 691 DGRQVAVLVPTTLLAQQHLTTFTQRMEGFPVTIRGLSRFTSPKDSKEVLEGLKNGTVDIVIGTHRLLQTGVQWKELGLVI 770
Cdd:PRK10917 309 AGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVI 388
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 771 VDEEQRFGVEHKEHIKALRHHVDVLTMSATPIPRTLEMSIAG------IREMsqiltPPQdRHPVLTYVGAQSDK-QVAA 843
Cdd:PRK10917 389 IDEQHRFGVEQRLALREKGENPHVLVMTATPIPRTLAMTAYGdldvsvIDEL-----PPG-RKPITTVVIPDSRRdEVYE 462
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 844 AIRRELLRDGQVFylhnkV--------ETID-----KVAQTIRNLVPEARVVVAHGQMGEEQLERTVDGFWQREYDVLVC 910
Cdd:PRK10917 463 RIREEIAKGRQAY-----VvcplieesEKLDlqsaeETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVA 537
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 911 TTIVETGLDIANANTLIVENAHHMGLSQLHQLRGRVGRSRERAYAYFLYpeNQTLTETSYDRLSTIAQNNDlgaGMAVAM 990
Cdd:PRK10917 538 TTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLY--KDPLSETARERLKIMRETND---GFVIAE 612
|
410
....*....|....*...
gi 1948637819 991 KDLEMRGAGNILGAEQSG 1008
Cdd:PRK10917 613 KDLELRGPGELLGTRQSG 630
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
594-1008 |
1.15e-105 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 347.02 E-value: 1.15e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 594 KSTKRKARGAVREIAEELVKL--------YAERQAAPGHAFAPDTPWQQEMEDNFPFTETEDQLQAIDEIKSDMEKPVPM 665
Cdd:TIGR00643 178 KTLSLLELARRRLIFDEFFYLqlamlarrLGEKQQFSAPPANPSEELLTKFLASLPFKLTRAQKRVVKEILQDLKSDVPM 257
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 666 DRVLIGDVGYGKTEVALRAAFKAVQDGRQVAVLVPTTLLAQQHLTTFTQRMEGFPVTIRGLSRFTSPKDSKEVLEGLKNG 745
Cdd:TIGR00643 258 NRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASG 337
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 746 TVDIVIGTHRLLQTGVQWKELGLVIVDEEQRFGVEHKEHIKA---LRHHVDVLTMSATPIPRTLEMSIAGIREMSQILTP 822
Cdd:TIGR00643 338 QIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLREkgqGGFTPHVLVMSATPIPRTLALTVYGDLDTSIIDEL 417
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 823 PQDRHPVLTYVGAQSDK-QVAAAIRRELLRDGQVFYLHNKVETIDKV-AQT-------IRNLVPEARVVVAHGQMGEEQL 893
Cdd:TIGR00643 418 PPGRKPITTVLIKHDEKdIVYEFIEEEIAKGRQAYVVYPLIEESEKLdLKAaealyerLKKAFPKYNVGLLHGRMKSDEK 497
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 894 ERTVDGFWQREYDVLVCTTIVETGLDIANANTLIVENAHHMGLSQLHQLRGRVGRSRERAYAYFLYPEnqTLTETSYDRL 973
Cdd:TIGR00643 498 EAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKN--PKSESAKKRL 575
|
410 420 430
....*....|....*....|....*....|....*
gi 1948637819 974 STIAQNNDlgaGMAVAMKDLEMRGAGNILGAEQSG 1008
Cdd:TIGR00643 576 RVMADTLD---GFVIAEEDLELRGPGDLLGTKQSG 607
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
828-978 |
8.85e-74 |
|
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: 241.48 E-value: 8.85e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 828 PVLTYVGAQSDKQVAAAIRRELLRDGQVFYLHNKVETIDKVAQTIRNLVPEARVVVAHGQMGEEQLERTVDGFWQREYDV 907
Cdd:cd18810 1 PVRTYVMPYDDELIREAIERELLRGGQVFYVHNRIESIEKLATQLRQLVPEARIAIAHGQMTENELEEVMLEFAKGEYDI 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1948637819 908 LVCTTIVETGLDIANANTLIVENAHHMGLSQLHQLRGRVGRSRERAYAYFLYPENQTLTETSYDRLSTIAQ 978
Cdd:cd18810 81 LVCTTIIESGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAYFLYPDQKKLTEDALKRLEAIQE 151
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
611-823 |
1.28e-66 |
|
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: 223.95 E-value: 1.28e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 611 LVKLYAERQAAPGHAFAPDTPWQQEMEDNFPFTETEDQLQAIDEIKSDMEKPVPMDRVLIGDVGYGKTEVALRAAFKAVQ 690
Cdd:cd17992 13 LLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKTVVAALAMLAAVE 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 691 DGRQVAVLVPTTLLAQQHLTTFTQRMEGFPVTIRGLSRFTSPKDSKEVLEGLKNGTVDIVIGTHRLLQTGVQWKELGLVI 770
Cdd:cd17992 93 NGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQEDVEFHNLGLVI 172
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 1948637819 771 VDEEQRFGVEHKEHIKALRHHVDVLTMSATPIPRTLEMSIAGIREMSQILTPP 823
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 ... |
828-978 |
1.72e-60 |
|
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: 204.04 E-value: 1.72e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 828 PVLTYVGAQSDK-QVAAAIRRELLRDGQVFYLHNKVETIDK--------VAQTIRNLVPEARVVVAHGQMGEEQLERTVD 898
Cdd:cd18792 1 PIRTYVIPHDDLdLVYEAIERELARGGQVYYVYPRIEESEKldlksieaLAEELKELVPEARVALLHGKMTEDEKEAVML 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 899 GFWQREYDVLVCTTIVETGLDIANANTLIVENAHHMGLSQLHQLRGRVGRSRERAYAYFLYPENQTLTETSYDRLSTIAQ 978
Cdd:cd18792 81 EFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYPDPKKLTETAKKRLRAIAE 160
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
634-819 |
7.78e-55 |
|
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: 188.78 E-value: 7.78e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 634 QEMEDNFPFTETEDQLQAIDEIKSDMEKPVPMDRVLIGDVGYGKTEVALRAAFKAVQDGRQVAVLVPTTLLAQQHLTTFT 713
Cdd:cd17918 6 QELCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEEAR 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 714 QRMEGFPVTIrgLSRFTSPKDSKEvleglkngtVDIVIGTHRLLQTGVQWKELGLVIVDEEQRFGVEHKEHIKALRhHVD 793
Cdd:cd17918 86 KFLPFINVEL--VTGGTKAQILSG---------ISLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNLG-ATH 153
|
170 180
....*....|....*....|....*.
gi 1948637819 794 VLTMSATPIPRTLEMSIAGIREMSQI 819
Cdd:cd17918 154 FLEATATPIPRTLALALSGLLDLSVI 179
|
|
| CarD_TRCF |
smart01058 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
512-616 |
1.17e-35 |
|
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: 130.65 E-value: 1.17e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 512 LKAGDYVVHDTHGIGRFVKLTERTIGtGEDqarREYVVLEYAPSkrggpsDQLYVPMESLDLLSRYVGGE---KPTLSKM 588
Cdd:smart01058 2 LKIGDYVVHPDHGVGRYEGIETIEVG-GEK---REYLVLEYAGG------DKLYVPVDNLDLGSRYVGSEgevEPVLDKL 71
|
90 100
....*....|....*....|....*...
gi 1948637819 589 GGSDWKSTKRKARGAVREIAEELVKLYA 616
Cdd:smart01058 72 GGGSWSKRKRKAKSGIRDIAAELLRLYA 99
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
828-978 |
1.14e-31 |
|
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: 121.68 E-value: 1.14e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 828 PVLTYVGAQSDK-QVAAAIRRELLRDGQVFYLHNKVETIDKV----AQTIRN-----LVPEARVVVAHGQMGEEQLERTV 897
Cdd:cd18811 1 PITTYLIFHTRLdKVYEFVREEIAKGRQAYVIYPLIEESEKLdlkaAVAMYEylkerFRPELNVGLLHGRLKSDEKDAVM 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 898 DGFWQREYDVLVCTTIVETGLDIANANTLIVENAHHMGLSQLHQLRGRVGRSRERAYAYFLYPEnqTLTETSYDRLSTIA 977
Cdd:cd18811 81 AEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKD--PLTETAKQRLRVMT 158
|
.
gi 1948637819 978 Q 978
Cdd:cd18811 159 E 159
|
|
| TRCF |
smart00982 |
This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in ... |
1051-1148 |
5.12e-28 |
|
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: 108.71 E-value: 5.12e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 1051 DLPVDANIPAEYVSSERLRLEAYRKFAAASALDDIDVVLEELVDRYGTPPIEVERLAVISRLRIICREFGVHEVQAMGAH 1130
Cdd:smart00982 1 DLPVPALIPEDYIPDVRQRLELYKRIASAETEEELDEIQEELIDRFGPLPEEVKNLLEVARLKLLAKKLGIEKIDAGGKG 80
|
90 100
....*....|....*....|
gi 1948637819 1131 IRIT--PMELADSKQVRLKR 1148
Cdd:smart00982 81 IVIEfsPDTPIDPEKLILLI 100
|
|
| CarD_CdnL_TRCF |
pfam02559 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
512-615 |
4.20e-27 |
|
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of light- and starvation-inducible genes. This family includes the presumed N-terminal domain, CdnL. CarD interacts with the zinc-binding protein CarG to form a complex that regulates multiple processes in Myxococcus xanthus. This family also includes a domain to the N-terminal side of the DEAD helicase of TRCF (transcription-repair-coupling factor) proteins. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription. This domain is involved in binding to the stalled RNA polymerase. The family includes members otherwise referred to as CdnL, for CarD N-terminal like, which differ functionally from CarD. The TRCF domain mentioned above is the RNA polymerase-interacting domain or RID.
Pssm-ID: 460590 [Multi-domain] Cd Length: 89 Bit Score: 105.99 E-value: 4.20e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 512 LKAGDYVVHDTHGIGRFVKLtertigtgEDQARREYVVLEYApskrggPSDQLYVPMESLDLLSRYVGGEKptLSKMG-G 590
Cdd:pfam02559 1 LKVGDYVVHPDHGIGRIEGI--------EKLETKDYYVLEYA------GGDKLYVPVDNLDLIRKYISKGE--LDKLGdG 64
|
90 100
....*....|....*....|....*
gi 1948637819 591 SDWKSTKRKARGAVREIAEELVKLY 615
Cdd:pfam02559 65 RRWRKYKEKLKSGDIEEAAELIKLY 89
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
645-808 |
7.88e-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: 107.71 E-value: 7.88e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 645 TEDQLQAIDEIKSDMekpvpmDRVLIGDVGYGKTEVALRAAFKAV---QDGRQVAVLVPTTLLAQQHLTTFTQRMEGFPV 721
Cdd:pfam00270 1 TPIQAEAIPAILEGR------DVLVQAPTGSGKTLAFLLPALEALdklDNGPQALVLAPTRELAEQIYEELKKLGKGLGL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 722 TIrglSRFTSPKDSKEVLEGLKNgtVDIVIGTH----RLLQTGVQWKELGLVIVDEEQR-----FGVEHKEHIKALRHHV 792
Cdd:pfam00270 75 KV---ASLLGGDSRKEQLEKLKG--PDILVGTPgrllDLLQERKLLKNLKLLVLDEAHRlldmgFGPDLEEILRRLPKKR 149
|
170
....*....|....*.
gi 1948637819 793 DVLTMSATPiPRTLEM 808
Cdd:pfam00270 150 QILLLSATL-PRNLED 164
|
|
| UvrB_inter |
pfam17757 |
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ... |
157-239 |
2.48e-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: 100.93 E-value: 2.48e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 157 QLDRDceNLVERLVHHGYSHVDMVGRRGQFAVRGGIVDVFPAT-EELPVRIELWGDEVTDLRAFSVADQRTISevEVDQL 235
Cdd:pfam17757 8 EIDRD--ELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYsEDEAIRIEFFGDEIESIREFDPLTGRSLE--KLDEV 83
|
....
gi 1948637819 236 DIFP 239
Cdd:pfam17757 84 TIYP 87
|
|
| TRCF |
pfam03461 |
TRCF domain; |
1052-1134 |
1.58e-24 |
|
TRCF domain;
Pssm-ID: 460928 [Multi-domain] Cd Length: 95 Bit Score: 98.65 E-value: 1.58e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 1052 LPVDANIPAEYVSSERLRLEAYRKFAAASALDDIDVVLEELVDRYGTPPIEVERLAVISRLRIICREFGVHEVQAMGAHI 1131
Cdd:pfam03461 1 LDVDAYIPDDYIPDESQRLELYKRLASIETEEELDDLQEELIDRFGPLPEEVENLLEIARLKLLAKKLGIEKIDLKGGGI 80
|
...
gi 1948637819 1132 RIT 1134
Cdd:pfam03461 81 RIT 83
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
637-827 |
4.22e-24 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 101.41 E-value: 4.22e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 637 EDNFPFTETEDQLQAIDEIKSDMekpvpMDRVLIGDVGYGKTEVALRAAFKAVQ--DGRQVAVLVPTTLLAQQHLTTFTQ 714
Cdd:smart00487 2 EKFGFEPLRPYQKEAIEALLSGL-----RDVILAAPTGSGKTLAALLPALEALKrgKGGRVLVLVPTRELAEQWAEELKK 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 715 RMEGFPVTIrglSRFTSPKDSKEVLEGLKNGTVDIVIGT-----HRLLQTGVQWKELGLVIVDEEQR-----FGVEHKEH 784
Cdd:smart00487 77 LGPSLGLKV---VGLYGGDSKREQLRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRlldggFGDQLEKL 153
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 1948637819 785 IKALRHHVDVLTMSATP---IPRTLEMSIAGIREMSQILTPPQDRH 827
Cdd:smart00487 154 LKLLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPLEPIE 199
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
648-801 |
3.14e-16 |
|
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' superfamily 2 DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350687 [Multi-domain] Cd Length: 178 Bit Score: 78.02 E-value: 3.14e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 648 QLQAIDEIKS--DMEKPVpmdrVLIGDVGYGKTEVALRAAFKAVQDGRQVAVLVPTTLLAQQHLTTFTQRMeGFPVTIrg 725
Cdd:cd17929 1 QRKAYEAIVSslGGFKTF----LLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRF-GDKVAV-- 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 726 LSRFTSPKDSKEVLEGLKNGTVDIVIGTHRLLQTGVqwKELGLVIVDEEQ----------RFGVEHKEHIKALRHHVDVL 795
Cdd:cd17929 74 LHSKLSDKERADEWRKIKRGEAKVVIGARSALFAPF--KNLGLIIVDEEHdssykqdsgpRYHARDVAIYRAKLENAPVV 151
|
....*.
gi 1948637819 796 TMSATP 801
Cdd:cd17929 152 LGSATP 157
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
665-800 |
5.17e-15 |
|
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: 73.21 E-value: 5.17e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 665 MDRVLIGDVGYGKTEVALRAAF-KAVQDGRQVAVLVPTTLLAQQHLTTFtQRMEGFPVTIRGLSRFTSPKDskevLEGLK 743
Cdd:cd00046 2 ENVLITAPTGSGKTLAALLAALlLLLKKGKKVLVLVPTKALALQTAERL-RELFGPGIRVAVLVGGSSAEE----REKNK 76
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 744 NGTVDIVIGTHRLLQTGVQW------KELGLVIVDEEQRFGVEHKE-------HIKALRHHVDVLTMSAT 800
Cdd:cd00046 77 LGDADIIIATPDMLLNLLLRedrlflKDLKLIIVDEAHALLIDSRGalildlaVRKAGLKNAQVILLSAT 146
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
848-948 |
1.14e-14 |
|
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: 71.09 E-value: 1.14e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 848 ELLRDGQVFYLHNKVETIDkvAQTIRNLvPEARVVVAHGQMGEEQLERTVDGFWQREYDVLVCTTIVETGLDIANANTLI 927
Cdd:pfam00271 11 KKERGGKVLIFSQTKKTLE--AELLLEK-EGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVI 87
|
90 100
....*....|....*....|.
gi 1948637819 928 VENAHHmGLSQLHQLRGRVGR 948
Cdd:pfam00271 88 NYDLPW-NPASYIQRIGRAGR 107
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
648-1114 |
1.72e-14 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 78.14 E-value: 1.72e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 648 QLQAIDEIKSDMEKPvPMDRVLIGDVGYGKTEVALRAAfKAVQDGRQVAVLVPTTLLAQQhlttftqrmegfpvTIRGLS 727
Cdd:COG1061 85 QQEALEALLAALERG-GGRGLVVAPTGTGKTVLALALA-AELLRGKRVLVLVPRRELLEQ--------------WAEELR 148
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 728 RFTspkDSKEVLEGLKNGTVDIVIGTHRLLQTGVQWKEL----GLVIVDEEQRFGVEHKEHIKALRHHVDVLTMSATPIP 803
Cdd:COG1061 149 RFL---GDPLAGGGKKDSDAPITVATYQSLARRAHLDELgdrfGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLTATPFR 225
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 804 R-----------------TLEMSIAG-------IREMSQILTPPQDRHPVLTYV-------GAQSDKQVAAAIRRELLRD 852
Cdd:COG1061 226 SdgreillflfdgivyeySLKEAIEDgylappeYYGIRVDLTDERAEYDALSERlrealaaDAERKDKILRELLREHPDD 305
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 853 GQVFYLHNKVETIDKVAQTIRNLVPEARVVvaHGQMGEEQLERTVDGFWQREYDVLVCTTIVETGLDIANANTLIVeNAH 932
Cdd:COG1061 306 RKTLVFCSSVDHAEALAELLNEAGIRAAVV--TGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAIL-LRP 382
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 933 HMGLSQLHQLRGRVGRSRER-AYAYFLypenqTLTETSYDRLSTIAQNNDLGAGMAVAMKDLEMRGAGNILGAEQsghIA 1011
Cdd:COG1061 383 TGSPREFIQRLGRGLRPAPGkEDALVY-----DFVGNDVPVLEELAKDLRDLAGYRVEFLDEEESEELALLIAVK---PA 454
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 1012 GVGFDMYVRLVGEAVAALKAVADGETPDASDNEPKEVRIDLPVDANIPAEYVSSERLRLEAYRKFAAASALDDIDVVLEE 1091
Cdd:COG1061 455 LEVKGELEEELLEELELLEDALLLVLAELLLLELLALALELLELAKAEGKAEEEEEEKELLLLLALAKLLKLLLLLLLLL 534
|
490 500
....*....|....*....|...
gi 1948637819 1092 LVDRYGTPPIEVERLAVISRLRI 1114
Cdd:COG1061 535 LLELLELLAALLRLEELAALLLK 557
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
866-948 |
2.37e-12 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 63.77 E-value: 2.37e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 866 DKVAQTIRNLvpEARVVVAHGQMGEEQLERTVDGFWQREYDVLVCTTIVETGLDIANANTLIVENAhHMGLSQLHQLRGR 945
Cdd:smart00490 1 EELAELLKEL--GIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL-PWSPASYIQRIGR 77
|
...
gi 1948637819 946 VGR 948
Cdd:smart00490 78 AGR 80
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
607-774 |
2.81e-12 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 70.96 E-value: 2.81e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 607 IAEELVKLYAERQAAPGHAFAPDTPwqqemednfPFTETEDQLQAIDEIKSDMEKPVpmdrVLI-GDVGYGKTEVALRAA 685
Cdd:PRK05580 117 VKKGLIELEEVEVLRLRPPPDPAFE---------PPTLNPEQAAAVEAIRAAAGFSP----FLLdGVTGSGKTEVYLQAI 183
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 686 FKAVQDGRQVAVLVPTTLLAQQHLTTFTQRMeGFPVTI--RGLsrftSPKDSKEVLEGLKNGTVDIVIGTHRLLQTgvQW 763
Cdd:PRK05580 184 AEVLAQGKQALVLVPEIALTPQMLARFRARF-GAPVAVlhSGL----SDGERLDEWRKAKRGEAKVVIGARSALFL--PF 256
|
170
....*....|.
gi 1948637819 764 KELGLVIVDEE 774
Cdd:PRK05580 257 KNLGLIIVDEE 267
|
|
| PRK05298 |
PRK05298 |
excinuclease ABC subunit UvrB; |
157-239 |
4.70e-12 |
|
excinuclease ABC subunit UvrB;
Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 70.46 E-value: 4.70e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 157 QLDRDceNLVERLVHHGYSHVDMVGRRGQFAVRGGIVDVFPA-TEELPVRIELWGDEVTDLRAFSVADQRTISevEVDQL 235
Cdd:PRK05298 166 EIDRR--ELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPAyYEERAIRIEFFGDEIERISEFDPLTGEVLG--ELDRV 241
|
....
gi 1948637819 236 DIFP 239
Cdd:PRK05298 242 TIYP 245
|
|
| UvrB |
COG0556 |
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; |
157-239 |
5.47e-12 |
|
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
Pssm-ID: 440322 [Multi-domain] Cd Length: 657 Bit Score: 70.04 E-value: 5.47e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 157 QLDRDceNLVERLVHHGYSHVDMVGRRGQFAVRGGIVDVFPA-TEELPVRIELWGDEVTDLRAFSVADQRTISevEVDQL 235
Cdd:COG0556 163 EIDRD--ELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAySEERAIRIEFFGDEIERISEFDPLTGEVLG--ELDRV 238
|
....
gi 1948637819 236 DIFP 239
Cdd:COG0556 239 TIYP 242
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
585-774 |
6.96e-12 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 69.76 E-value: 6.96e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 585 LSKMGGSDWKSTKRKARGAVREIAEELVKL-YAERQAAPghafAPDTPWQQEMEDNFPFTETEDQLQAIDEIKSDMEKPV 663
Cdd:COG1198 140 LREHGGPLTLSELAKEAGVSRSVLKALVKKgLLEIEERE----VDRDPFAPDVPAEPPPTLNEEQQAAVEAIRAAAGGFS 215
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 664 PmdrVLI-GDVGYGKTEVALRAAFKAVQDGRQVAVLVPTTLLAQQHLTTFTQRmegFPVTIR----GLS---RFtspkds 735
Cdd:COG1198 216 V---FLLhGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQTVERFRAR---FGARVAvlhsGLSdgeRL------ 283
|
170 180 190 200
....*....|....*....|....*....|....*....|....
gi 1948637819 736 kEVLEGLKNGTVDIVIGThRL-----LqtgvqwKELGLVIVDEE 774
Cdd:COG1198 284 -DEWRRARRGEARIVIGT-RSalfapF------PNLGLIIVDEE 319
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
669-807 |
5.65e-10 |
|
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: 63.17 E-value: 5.65e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 669 LIGDVGYGKTEVALRAAFKAVQDGRQVAVLVPTTLLAQQHLTTFTQRMeGFPVTI--RGLSrfTSPKdsKEVLEGLKNGT 746
Cdd:TIGR00595 2 LFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRF-GSQVAVlhSGLS--DSEK--LQAWRKVKNGE 76
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1948637819 747 VDIVIGTHRLLQTgvQWKELGLVIVDEEQRFGVE-------HKEHIKALRHH---VDVLTMSATPiprTLE 807
Cdd:TIGR00595 77 ILVVIGTRSALFL--PFKNLGLIIVDEEHDSSYKqeegpryHARDVAVYRAKkfnCPVVLGSATP---SLE 142
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
641-952 |
4.94e-09 |
|
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: 60.27 E-value: 4.94e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 641 PFTETEDQLQAIDEIKSDMEKPVPMdrvLIGDV-GYGKTEVALRAAFKAVQDGRQVAVLVPTT-----LLaqqhlttftQ 714
Cdd:COG4098 108 EGTLTPAQQKASDELLEAIKKKEEH---LVWAVcGAGKTEMLFPAIAEALKQGGRVCIATPRVdvvleLA---------P 175
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 715 RM-EGFP-VTIRGLSrftspKDSKEVLEGlkngtVDIVIGT-HRLLQtgvqWKE-LGLVIVDE---------EQ-RFGVE 780
Cdd:COG4098 176 RLqQAFPgVDIAALY-----GGSEEKYRY-----AQLVIATtHQLLR----FYQaFDLLIIDEvdafpysgdPMlQYAVK 241
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 781 hkehiKALRHHVDVLTMSATPiPRTLEMSIA-GIREMSQILTppqdRH-------PVLTYVGAQSDK--------QVAAA 844
Cdd:COG4098 242 -----RARKPDGKLIYLTATP-SKALQRQVKrGKLKVVKLPA----RYhghplpvPKFKWLGNWKKRlrrgklprKLLKW 311
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 845 IRRELLRDGQVFYLHNKVETIDKVAQTIRNLVPEARVVVAHGQmgEEQLERTVDGFWQREYDVLVCTTIVETGLDIANAN 924
Cdd:COG4098 312 LKKRLKEGRQLLIFVPTIELLEQLVALLQKLFPEERIAGVHAE--DPERKEKVQAFRDGEIPILVTTTILERGVTFPNVD 389
|
330 340 350
....*....|....*....|....*....|
gi 1948637819 925 TLIVeNAHH--MGLSQLHQLRGRVGRSRER 952
Cdd:COG4098 390 VAVL-GADHpvFTEAALVQIAGRVGRSADY 418
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
674-961 |
7.93e-09 |
|
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: 58.98 E-value: 7.93e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 674 GYGKTEVALRAAFKAVQDGR--QVAVLVPTTLLAQQHLTTFTQRM--EGFPVTIRGLSRFTSPKDSKEVLE--------- 740
Cdd:cd09639 9 GYGKTEAALLWALHSLKSQKadRVIIALPTRATINAMYRRAKEAFgeTGLYHSSILSSRIKEMGDSEEFEHlfplyihsn 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 741 ------GLKNGTVDIVI-------GTHRLLQTGVQwkeLGLVIVDEEQRFGVEHKEHI-KALRHHVD----VLTMSATpI 802
Cdd:cd09639 89 dtlfldPITVCTIDQVLksvfgefGHYEFTLASIA---NSLLIFDEVHFYDEYTLALIlAVLEVLKDndvpILLMSAT-L 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 803 PRTLEMSIAGIrEM--SQILTPPQDRHPVLTYVGAQ---SDKQVAAAIRRELLRDGQVFYLHNKVETIDKVAQTIRNLVP 877
Cdd:cd09639 165 PKFLKEYAEKI-GYveENEPLDLKPNERAPFIKIESdkvGEISSLERLLEFIKKGGSVAIIVNTVDRAQEFYQQLKEKGP 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 878 EARVVVAHGQMGE---EQLERTVDGFWQR-EYDVLVCTTIVETGLDIaNANTLIVEnahHMGLSQLHQLRGRVGR--SRE 951
Cdd:cd09639 244 EEEIMLIHSRFTEkdrAKKEAELLLEFKKsEKFVIVATQVIEASLDI-SVDVMITE---LAPIDSLIQRLGRLHRygEKN 319
|
330
....*....|
gi 1948637819 952 RAYAYFLYPE 961
Cdd:cd09639 320 GEEVYIITDA 329
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
659-802 |
1.07e-07 |
|
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: 53.83 E-value: 1.07e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 659 MEKPVPmdRVLIGD-VGYGKT--------EVALRAafkavqDGRQVAVLVPTTLLAQQHLTTFTQRMEGFPVtirgLSRF 729
Cdd:cd18011 13 LRKPPV--RLLLADeVGLGKTieagliikELLLRG------DAKRVLILCPASLVEQWQDELQDKFGLPFLI----LDRE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 730 TspKDSKEVLEGLKNGTVDIVIGTHRLL------QTGVQWKELGLVIVDEEQRFGVEHKEH-------IKALRHHVD-VL 795
Cdd:cd18011 81 T--AAQLRRLIGNPFEEFPIVIVSLDLLkrseerRGLLLSEEWDLVVVDEAHKLRNSGGGKetkryklGRLLAKRARhVL 158
|
....*..
gi 1948637819 796 TMSATPI 802
Cdd:cd18011 159 LLTATPH 165
|
|
| Cas3 |
COG1203 |
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
591-952 |
1.40e-06 |
|
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: 52.39 E-value: 1.40e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 591 SDWKST--KRKARGAVREIAEELVKLYAERQAAPGhafAPDTPWQQEMEDNfpftetedQLQAIDEIKSDMekpvpmdrV 668
Cdd:COG1203 91 ADWLDSanFDMARQALDHLLAERLERLLPKKSKPR---TPINPLQNEALEL--------ALEAAEEEPGLF--------I 151
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 669 LIGDVGYGKTEVALRAAFK--AVQDGRQVAVLVPTTLLAQQHLTTFtQRMEGFPVTI----RGLSRFTSPKDSKEVLEGL 742
Cdd:COG1203 152 LTAPTGGGKTEAALLFALRlaAKHGGRRIIYALPFTSIINQTYDRL-RDLFGEDVLLhhslADLDLLEEEEEYESEARWL 230
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 743 KNGT----VDIVIGTHrllqtgVQW-------------KELGL----VIVDEEQRFGVE-HKEHIKALRHH----VDVLT 796
Cdd:COG1203 231 KLLKelwdAPVVVTTI------DQLfeslfsnrkgqerRLHNLansvIILDEVQAYPPYmLALLLRLLEWLknlgGSVIL 304
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 797 MSATpIPRTLEMSIAGIREM-------SQILTPPQDRHPVLTYVGAQSDKQVAAAIRRELLRDGQVFYLhnkVETID--- 866
Cdd:COG1203 305 MTAT-LPPLLREELLEAYELipdepeeLPEYFRAFVRKRVELKEGPLSDEELAELILEALHKGKSVLVI---VNTVKdaq 380
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 867 KVAQTIRNLVPEARVVVAHGQMG----EEQLERTVDGFWQREYDVLVCTTIVETGLDIaNANTLIVENAhhmGLSQLHQL 942
Cdd:COG1203 381 ELYEALKEKLPDEEVYLLHSRFCpadrSEIEKEIKERLERGKPCILVSTQVVEAGVDI-DFDVVIRDLA---PLDSLIQR 456
|
410
....*....|
gi 1948637819 943 RGRVGRSRER 952
Cdd:COG1203 457 AGRCNRHGRK 466
|
|
| cas3_core |
TIGR01587 |
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ... |
668-952 |
1.62e-06 |
|
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.
Pssm-ID: 273707 [Multi-domain] Cd Length: 359 Bit Score: 51.69 E-value: 1.62e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 668 VLIGDVGYGKTEVALRAAFKAVQDGRQVAVLV--PTTLLAQQHLTTFTqrmEGFPVTIRGL------SRFTSPKDSKEVL 739
Cdd:TIGR01587 3 VIEAPTGYGKTEAALLWALHSIKSQKADRVIIalPTRATINAMYRRAK---ELFGSELVGLhhsssfSRIKEMGDSEEFE 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 740 E---------------GLKNGTVDIVI-------GTHRLLQTGVQwkeLGLVIVDEEQRFGVEHKEHI-KALRHHVD--- 793
Cdd:TIGR01587 80 HlfplyihsndklfldPITVCTIDQVLksvfgefGHYEFTLASIA---NSLLIFDEVHFYDEYTLALIlAVLEVLKDndv 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 794 -VLTMSATpIPRTLEMSIAGIREMSQILTPPQD------RHPVLTYVGAQ-SDKQVAAAIRRELLRDGQVFYLHNKVETI 865
Cdd:TIGR01587 157 pILLMSAT-LPKFLKEYAEKIGYVEFNEPLDLKeerrfeNHRFILIESDKvGEISSLERLLEFIKKGGSIAIIVNTVDRA 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 866 DKVAQTIRNLVPEARVVVAHGQMGE---EQLERTVDGFWQREYD--VLVCTTIVETGLDIaNANTLIVEnahHMGLSQLH 940
Cdd:TIGR01587 236 QEFYQQLKEKAPEEEIILYHSRFTEkdrAKKEAELLREMKKSNEkfVIVATQVIEASLDI-SADVMITE---LAPIDSLI 311
|
330
....*....|..
gi 1948637819 941 QLRGRVGRSRER 952
Cdd:TIGR01587 312 QRLGRLHRYGRK 323
|
|
| SF2_C_FANCM_Hef |
cd18801 |
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
862-950 |
3.04e-06 |
|
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: 48.12 E-value: 3.04e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 862 VETIDKVAQTIR--NLVPEARVVVAHGQMGEEQLErTVDGFWQREYDVLVCTTIVETGLDIANANTLIVENAHHMGLSQL 939
Cdd:cd18801 47 VNFLSKIRPGIRatRFIGQASGKSSKGMSQKEQKE-VIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMI 125
|
90
....*....|.
gi 1948637819 940 hQLRGRVGRSR 950
Cdd:cd18801 126 -QRMGRTGRKR 135
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
676-948 |
2.01e-05 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 48.74 E-value: 2.01e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 676 GKTEVALRAAFKAVQDGRQVAVLVPTTLLAQQHLTTFTQRME--GFPVTIRglsrfTSPKDSkevlEGLKNGTVDIVIGT 753
Cdd:COG1204 50 GKTLIAELAILKALLNGGKALYIVPLRALASEKYREFKRDFEelGIKVGVS-----TGDYDS----DDEWLGRYDILVAT 120
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 754 ----HRLLQTGVQW-KELGLVIVDE------EQR-FGVEHK-EHIKALRHHVDVLTMSATpiprtlemsIAGIREMSQIL 820
Cdd:COG1204 121 peklDSLLRNGPSWlRDVDLVVVDEahliddESRgPTLEVLlARLRRLNPEAQIVALSAT---------IGNAEEIAEWL 191
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 821 ----------TPPQDR----HPVLTYV--GAQSDKQVAAAIRRELLRDGQ--VF------------YLHNKV-------- 862
Cdd:COG1204 192 daelvksdwrPVPLNEgvlyDGVLRFDdgSRRSKDPTLALALDLLEEGGQvlVFvssrrdaeslakKLADELkrrltpee 271
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 863 -ETIDKVAQTIRNLV-------PEARVV---VA--HGQMGEEQLERTVDGFWQREYDVLVCTTIVETGLdiaN--ANTLI 927
Cdd:COG1204 272 rEELEELAEELLEVSeethtneKLADCLekgVAfhHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGV---NlpARRVI 348
|
330 340
....*....|....*....|....*.
gi 1948637819 928 VENAHHMGLSQL-----HQLRGRVGR 948
Cdd:COG1204 349 IRDTKRGGMVPIpvlefKQMAGRAGR 374
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
903-960 |
3.50e-05 |
|
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: 43.08 E-value: 3.50e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 1948637819 903 REYDVLVCTTIVETGLDIANANTLIVENAHHmGLSQLHQLRGRVGRSRERAYAYFLYP 960
Cdd:cd18785 21 SSLEILVATNVLGEGIDVPSLDTVIFFDPPS-SAASYIQRVGRAGRGGKDEGEVILFV 77
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
676-800 |
6.27e-05 |
|
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: 44.95 E-value: 6.27e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 676 GKTEVALRAAFKAVQDGRQVAV-LVPTTLLAQQHLTTFTQRMEGFPVTIRGLSRFTSPKDSKEvleglknGTVDIVIGTH 754
Cdd:cd17921 29 GKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFGPLGKNVGLLTGDPSVNKLLL-------AEADILVATP 101
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 755 -----RLLQTGVQW-KELGLVIVDEEQRFGVEHK--------EHIKALRHHVDVLTMSAT 800
Cdd:cd17921 102 ekldlLLRNGGERLiQDVRLVVVDEAHLIGDGERgvvlelllSRLLRINKNARFVGLSAT 161
|
|
| DDXDc_reverse_gyrase |
cd17924 |
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
668-772 |
9.35e-05 |
|
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350682 [Multi-domain] Cd Length: 189 Bit Score: 44.63 E-value: 9.35e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 668 VLIGDVGYGKTEVALRAAFKAVQDGRQVAVLVPTTLLAQQ---HLTTFTQRMEGfPVTIRGLSRFTSPKDSKEVLEGLKN 744
Cdd:cd17924 36 AIIAPTGVGKTTFGLATSLYLASKGKRSYLIFPTKSLVKQayeRLSKYAEKAGV-EVKILVYHSRLKKKEKEELLEKIEK 114
|
90 100 110
....*....|....*....|....*....|.
gi 1948637819 745 GTVDIVIGTHRLLQTGVQ---WKELGLVIVD 772
Cdd:cd17924 115 GDFDILVTTNQFLSKNFDllsNKKFDFVFVD 145
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
674-800 |
1.26e-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: 44.25 E-value: 1.26e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 674 GYGKTEVALRAAFKAVQDGRQVAVLVPTTLLAQQHLTTFTQRMEgfpvtiRGLSRFTSPKDSKEVLEGLKNgtVDIVIGT 753
Cdd:cd18028 27 ASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEEFKKLEE------IGLKVGISTGDYDEDDEWLGD--YDIIVAT 98
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 754 HR----LLQTGVQW-KELGLVIVDEEQRFGVEHK--------EHIKALRHHVDVLTMSAT 800
Cdd:cd18028 99 YEkfdsLLRHSPSWlRDVGVVVVDEIHLISDEERgptlesivARLRRLNPNTQIIGLSAT 158
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
891-951 |
1.34e-03 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 42.79 E-value: 1.34e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1948637819 891 EQLErTVDGFWQREYDVLVCTTIVETGLDIANANTLI----VENAHHMglsqlHQLRGRVGRSRE 951
Cdd:COG1111 399 EQIE-ILERFRAGEFNVLVATSVAEEGLDIPEVDLVIfyepVPSEIRS-----IQRKGRTGRKRE 457
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
674-806 |
1.40e-03 |
|
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: 41.26 E-value: 1.40e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 674 GYGKTEVALRAA------FKAVQDGRqVAVLVPTTLLAQQHLTTFTQRMEGFPVTIRGLSRFTSPKDS-KEVLEglkngT 746
Cdd:cd17927 27 GSGKTFVAVLICehhlkkFPAGRKGK-VVFLANKVPLVEQQKEVFRKHFERPGYKVTGLSGDTSENVSvEQIVE-----S 100
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1948637819 747 VDIVIGTHRLLQ------TGVQWKELGLVIVDEEQRFGVEHKeHIKALRHHVDVLTMSATPIPRTL 806
Cdd:cd17927 101 SDVIIVTPQILVndlksgTIVSLSDFSLLVFDECHNTTKNHP-YNEIMFRYLDQKLGSSGPLPQIL 165
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
674-801 |
1.52e-03 |
|
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: 40.37 E-value: 1.52e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 674 GYGKTEVALRAAFKAVQDGrqVAVLVPTTLLAQQ---HLTTFTQRMEgfpvtirgLSRFTSPKDSKEVLEGLKNGTVDIV 750
Cdd:cd17926 28 GSGKTLTALALIAYLKELR--TLIVVPTDALLDQwkeRFEDFLGDSS--------IGLIGGGKKKDFDDANVVVATYQSL 97
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 1948637819 751 IGTHRLLQTGVQwkELGLVIVDEEQRFGVEHKEHIKALRHHVDVLTMSATP 801
Cdd:cd17926 98 SNLAEEEKDLFD--QFGLLIVDEAHHLPAKTFSEILKELNAKYRLGLTATP 146
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
865-972 |
3.79e-03 |
|
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350191 [Multi-domain] Cd Length: 238 Bit Score: 40.31 E-value: 3.79e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 865 IDKVAQTIRNLVPEARVV------VAHGQMGEEQLERTVDGfwqrEYDVLVCTTIVETGLDIANANTLIVENAHHM---- 934
Cdd:cd18804 103 TERVEEELKTLFPEARIAridrdtTRKKGALEKLLDQFERG----EIDILIGTQMIAKGLDFPNVTLVGILNADSGlnsp 178
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|
gi 1948637819 935 -------GLSQLHQLRGRVGRSRERAYAYF--LYPEN---QTLTETSYDR 972
Cdd:cd18804 179 dfraserAFQLLTQVSGRAGRGDKPGKVIIqtYNPEHpliQAAKEEDYEA 228
|
|
| CdnL |
COG1329 |
RNA polymerase-interacting regulator, CarD/CdnL/TRCF family [Transcription]; |
513-572 |
4.36e-03 |
|
RNA polymerase-interacting regulator, CarD/CdnL/TRCF family [Transcription];
Pssm-ID: 440940 [Multi-domain] Cd Length: 155 Bit Score: 38.96 E-value: 4.36e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 513 KAGDYVVHDTHGIGRFVKLTERTIGtGEdqaRREYVVLEyaPSKRGGpsdQLYVPMESLD 572
Cdd:COG1329 2 KVGDKVVYPMHGVGVIEAIEEKEIA-GE---KKEYYVLR--FPYDDM---TIMVPVDKAE 52
|
|
| DEXHc_RLR-3 |
cd18075 |
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ... |
674-820 |
6.04e-03 |
|
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of genetics and physiology 2 or LGP2 and DHX58) appears to positively and negatively regulate MDA5 and RIG-I signaling, respectively. RLR-3 resembles a chimera combining a MDA5-like helicase domain and RIG-I like CTD supporting both stem and end binding. RNA binding is required for RLR-3-mediated enhancement of MDA5 activation. RLR-3 end-binding may promote nucleation of MDA5 oligomerization on dsRNA. RLR-3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350833 [Multi-domain] Cd Length: 200 Bit Score: 39.46 E-value: 6.04e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 674 GYGKTEVALRAAFKAVQ--DGRQVAVLVPTTLLAQQHLTTFTQRMEGfPVTIRGLSRFTSPKDskevLEGLKNGTVDIVI 751
Cdd:cd18075 27 GAGKTRAAVYVARRHLEtkRGAKVAVLVNKVHLVDQHLEKEFHVLLD-KYTVTAISGDSSHKC----FFGQLARGSDVVI 101
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1948637819 752 GTHRLLQTG---------VQWKELGLVIVDEeqrfgvehkehikalRHHVDVLTMSATPIPRTLEMSIAGIREMSQIL 820
Cdd:cd18075 102 CTAQILQNAllsgeeeahVELTDFSLLVIDE---------------CHHTHKEAVYNKIMLSYLEKKLSRQGDLPQIL 164
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
860-922 |
7.11e-03 |
|
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: 37.87 E-value: 7.11e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1948637819 860 NKVETIDKVAQTIRNLvpEARVVVAHGQMGEEQLERTVDGFWQREYDVLVCTTIVETGLDIAN 922
Cdd:cd18787 35 NTKKRVDRLAELLEEL--GIKVAALHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPG 95
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
839-933 |
7.84e-03 |
|
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350792 [Multi-domain] Cd Length: 200 Bit Score: 39.17 E-value: 7.84e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 839 KQVAAAIRRELLRDGQVFYLHNKVETIDKVAQTIRNLVPeARVVVAHGQMGEEQLErtvDGFWQRE---YDVLVCT---- 911
Cdd:cd18034 38 KEMGELNRKEKNPKKRAVFLVPTVPLVAQQAEAIRSHTD-LKVGEYSGEMGVDKWT---KERWKEElekYDVLVMTaqil 113
|
90 100
....*....|....*....|....
gi 1948637819 912 -TIVETG-LDIANANTLIVENAHH 933
Cdd:cd18034 114 lDALRHGfLSLSDINLLIFDECHH 137
|
|
| DEXHc_RLR |
cd18036 |
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
674-754 |
8.29e-03 |
|
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: 39.00 E-value: 8.29e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948637819 674 GYGKTEVALRAAFKAVQDGRQ------VAVLVPTTLLAQQHLTTFTQRME-GFPVTirGLSRFTSpkdskevlegLKNGT 746
Cdd:cd18036 27 GSGKTRVAVYICRHHLEKRRSagekgrVVVLVNKVPLVEQQLEKFFKYFRkGYKVT--GLSGDSS----------HKVSF 94
|
....*...
gi 1948637819 747 VDIVIGTH 754
Cdd:cd18036 95 GQIVKASD 102
|
|
| |
