|
Name |
Accession |
Description |
Interval |
E-value |
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
24-1172 |
0e+00 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 1782.31 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 24 GLKEQLLAGLSGSARSVFTSALANETNKPIFLITHNLYQAQKVTDDLTSLLEDRSVLLYPVNELISSEIAVASPELRAQR 103
Cdd:COG1197 1 GGGRLTLSGLPGSARALLLAALARALGRPLLVVTADEREAERLAEDLRFFLPDLPVLLFPAWETLPYDRFSPSPDIVSER 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 104 LDVINRLTNGEAPIVVAPVAAIRRMLPPVEVWKSSQMLIQVGHDIEPDQLASRLVEVGYERSDMVSAPGEFSIRGGIIDI 183
Cdd:COG1197 81 LATLRRLASGKPGIVVTPVRALLQRLPPPELLAAASLSLKVGDELDLEELRERLVAAGYERVDQVEEPGEFAVRGGILDI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 184 YPLTSENPVRIELFDTEVDSIRSFNSDDQRSIETLTSINIGPAKELIIRPEEKARAMEKIdsglaaslkklkadKQKEIL 263
Cdd:COG1197 161 FPPGSEHPVRIEFFGDEIESIRTFDPETQRSLEKVDEVELLPAREFPLDEEAIERFRERL--------------RELFGL 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 264 HANISHDKERLSEGQTDQELVKYLSYFYEKPASLLDYTPDNTLLILDEVSRIHEMEEQLQKEEAEFITNLL-EEGKILHD 342
Cdd:COG1197 227 DPKLDELYEALSEGIAFAGIEYYLPLFYEELATLFDYLPEDALVVLDEPERIEEAAEEFWEEIEERYEARRhDRGRPLLP 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 343 -IRLSFSFQKIVAE-QKRPLLYYSLFLrhvHHTSPQNIVNVSGRQMQSFHGQMNVLAGEMERFKKSNFTVVFLGANKERT 420
Cdd:COG1197 307 pEELFLDPEELFAAlKRRPRVTLSPFA---ALPEGAGVVNLGARPLPSFAGQLEALLEELKRLLKDGGRVLLAAESEGRR 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 421 QKLSSVLADYDIEAAVTDSKKALVQGQVYIMEGELQSGFELPLMKLAVITEEELFKNRVKKKPRKQKLTNAERIKSYSEL 500
Cdd:COG1197 384 ERLLELLRDHGIPARLVESLAELSPGGVAITVGPLEHGFELPDAKLAVITESELFGERVKRRRRKKKRSADAFIRDLSEL 463
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 501 QIGDYVVHINHGIGKYLGIETLEINGIHKDYLNIHYQGSDKLYVPVEQIDQVQKYVGSEGKEPKLYKLGGSEWKRVKKKV 580
Cdd:COG1197 464 KPGDYVVHVDHGIGRYLGLETLEVGGAERDYLVLEYAGGDKLYVPVDQLDLISRYVGSEGEAPKLDKLGGSDWQKAKAKA 543
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 581 ETSVQDIADDLIKLYAEREASKGYAFSPDHEMQREFESAFPYQETEDQLRSIHEIKKDMERERPMDRLLCGDVGYGKTEV 660
Cdd:COG1197 544 KKAVRDIAAELLKLYAERAARKGFAFSPDTPWQREFEAAFPYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKTEV 623
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 661 AIRAAFKAIGDGKQVALLVPTTILAQQHYETIKERFQDYPINIGLLSRFRTRKEANETIKGLKNGTVDIVIGTHRLLSKD 740
Cdd:COG1197 624 ALRAAFKAVMDGKQVAVLVPTTLLAQQHYETFKERFAGFPVRVEVLSRFRTAKEQKETLEGLADGKVDIVIGTHRLLSKD 703
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 741 VVYKDLGLLIIDEEQRFGVTHKEKIKQIKANVDVLTLTATPIPRTLHMSMLGVRDLSVIETPPENRFPVQTYVVEYNGAL 820
Cdd:COG1197 704 VKFKDLGLLIIDEEQRFGVRHKEKLKALRANVDVLTLTATPIPRTLQMSLSGIRDLSIIATPPEDRLPVKTFVGEYDDAL 783
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 821 VREAIERELARGGQVYFLYNRVEDIERKADEISMLVPDAKVAYAHGKMTENELETVMLSFLEGESDVLVSTTIIETGVDI 900
Cdd:COG1197 784 IREAILRELLRGGQVFYVHNRVEDIEKVAARLQELVPEARIAVAHGQMSERELERVMLDFYEGEFDVLVCTTIIETGIDI 863
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 901 PNVNTLIVFDADKMGLSQLYQLRGRVGRSNRVAYAYFTYRRDKVLTEVAEKRLQAIKEFTELGSGFKIAMRDLTIRGAGN 980
Cdd:COG1197 864 PNANTIIIERADRFGLAQLYQLRGRVGRSHRRAYAYLLYPPDKVLTEDAEKRLEAIQEFTELGAGFKLAMHDLEIRGAGN 943
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 981 LLGAQQHGFIDSVGFDLYSQMLKEAIEERKGDTAKTEQFETEIDVELDAYIPETYIQDGKQKIDMYKRFRSVATIEEKNE 1060
Cdd:COG1197 944 LLGEEQSGHIAEVGFDLYLQMLEEAVAALKGGKEPEEEWEPEINLGVPALIPEDYIPDVRQRLELYKRIASAESEEELDE 1023
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 1061 LQDEMIDRFGNYPKEVEYLFTVAEMKVYARQERVELIKQDKDAVRLTISEEASaeIDGQKLFELGNKYGRQIGLGMEgKK 1140
Cdd:COG1197 1024 LQEELIDRFGPLPEEVENLLAVARLKLLARRLGIEKIDAGGKGIRIEFSPNTP--LDPEKLIRLIQKQPGRYKLDGD-DK 1100
|
1130 1140 1150
....*....|....*....|....*....|..
gi 754290790 1141 LKISIQTkgRSADEWLDTVLGMLKGLKDVKKQ 1172
Cdd:COG1197 1101 LVITLDL--EDPEERLEALEELLEALAKLAKE 1130
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
157-1098 |
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: 1418.66 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 157 LVEVGYERSDMVSAPGEFSIRGGIIDIYPLTSENPVRIELFDTEVDSIRSFNSDDQRSIETLTSINIGPAKELIIrPEEK 236
Cdd:TIGR00580 1 LVELGYERVDLVEEEGEFSVRGEILDIFPPGSELPVRIEFFGDEIESIREFDVDSQRSLEELLEITILPAKEFIL-LEEE 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 237 ARAMEKIDSGLAASLKKLkadkqkeilhanisHDKERLSEGQTDQELVKYLSYFYEKPASLLDYTPDNTLLILDEVSRIH 316
Cdd:TIGR00580 80 TIARLKDNAARVEDAKHL--------------ETIEALSEGTLPAGEEMFLPLFFEDLSSLFDYLPDNTPILLDDPERFH 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 317 EMEEQLQKEEAEFITNLLEEGKILHDIRLSFSFQKIVAEQKrpllYYSLFLRHV--HHTSPQNIVNVSGRQMQSFHGQMN 394
Cdd:TIGR00580 146 SAARFLQRELEEFYNALEEAKKLINPPRLDLDPSELAFEAS----AISLSRVQLenEHLSLKASEAIEGAQKHSRLEFGE 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 395 VLAGEME--RFKKSNFTVVFLGANKERTQKLSSVLADYDIEAAVTDSKKALVQGQVYIMEGELQSGFELPLMKLAVITEE 472
Cdd:TIGR00580 222 ILAFKEElfRWLKAGFKITVAAESESQAERLKSLLAEHDIAAQVIDESCIIIPAVRYVMIGALSSGFILPTAGLAVITES 301
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 473 ELFKNRVKKKPRKQKLTNAeRIKSYSELQIGDYVVHINHGIGKYLGIETLEINGIHKDYLNIHYQGSDKLYVPVEQIDQV 552
Cdd:TIGR00580 302 ELFGSRVLRRPKKSRLKSK-PIESLNELNPGDYVVHLDHGIGRFLGLETLEVGGIERDYLVLEYAGEDKLYVPVEQLHLI 380
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 553 QKYVGSEGKEPKLYKLGGSEWKRVKKKVETSVQDIADDLIKLYAEREASKGYAFSPDHEMQREFESAFPYQETEDQLRSI 632
Cdd:TIGR00580 381 SRYVGGSGKNPALDKLGGKSWEKTKAKVKKSVREIAAKLIELYAKRKAIKGHAFPPDLEWQQEFEDSFPFEETPDQLKAI 460
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 633 HEIKKDMERERPMDRLLCGDVGYGKTEVAIRAAFKAIGDGKQVALLVPTTILAQQHYETIKERFQDYPINIGLLSRFRTR 712
Cdd:TIGR00580 461 EEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSA 540
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 713 KEANETIKGLKNGTVDIVIGTHRLLSKDVVYKDLGLLIIDEEQRFGVTHKEKIKQIKANVDVLTLTATPIPRTLHMSMLG 792
Cdd:TIGR00580 541 KEQNEILKELASGKIDILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSG 620
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 793 VRDLSVIETPPENRFPVQTYVVEYNGALVREAIERELARGGQVYFLYNRVEDIERKADEISMLVPDAKVAYAHGKMTENE 872
Cdd:TIGR00580 621 IRDLSIIATPPEDRLPVRTFVMEYDPELVREAIRRELLRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENE 700
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 873 LETVMLSFLEGESDVLVSTTIIETGVDIPNVNTLIVFDADKMGLSQLYQLRGRVGRSNRVAYAYFTYRRDKVLTEVAEKR 952
Cdd:TIGR00580 701 LEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDAQKR 780
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 953 LQAIKEFTELGSGFKIAMRDLTIRGAGNLLGAQQHGFIDSVGFDLYSQMLKEAIEERKGDTAKTEQFETEIDVELDAYIP 1032
Cdd:TIGR00580 781 LEAIQEFSELGAGFKIALHDLEIRGAGNLLGEEQSGHIESIGFDLYMELLEEAIEELKGGKPPKLEEETDIELPYSAFIP 860
|
890 900 910 920 930 940
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 754290790 1033 ETYIQDGKQKIDMYKRFRSVATIEEKNELQDEMIDRFGNYPKEVEYLFTVAEMKVYARQERVELIK 1098
Cdd:TIGR00580 861 DDYIADDSLRLEFYKRIASAETEEELEKIRDELIDRFGPLPEEARTLLDVARLKLLARKLGIRKLK 926
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
26-1090 |
0e+00 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 759.28 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 26 KEQLLAGLSGSARSVFTSALANETNKPIFLITHNLYQA-------QKVTDDLTSLLEDRSVLLY----PVNELISSeiav 94
Cdd:PRK10689 15 DQRQLGELTGAACATEVAEIAERHAGPVVLIAPDMQNAlrlhdeiQQFTDQMVMNLADWETLPYdsfsPHQDIISS---- 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 95 aspelraqRLDVINRLTNGEAPIVVAPVAAIRRMLPPVEVWKSSQMLIQVGHDIEPDQLASRLVEVGYERSDMVSAPGEF 174
Cdd:PRK10689 91 --------RLSTLYQLPTMQRGVLILPVNTLMQRVCPHSFLHGHALVMKKGQRLSRDALRAQLEQAGYRHVDQVMEHGEY 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 175 SIRGGIIDIYPLTSENPVRIELFDTEVDSIRSFNSDDQRSIETLTSINIGPAKELiirPEEKAramekidsglAASLKKL 254
Cdd:PRK10689 163 ATRGALLDLFPMGSEEPYRIDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEF---PTDKA----------AIELFRS 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 255 KADKQKEIlHANISHDKERLSEGQTDQELVKYLSYFYEKP-ASLLDYTPDNTLLIldevsrihemeeqlqkeeaefITNL 333
Cdd:PRK10689 230 QWRDTFEV-KRDAEHIYQQVSKGTLPAGIEYWQPLFFSEPlPPLFSYFPANTLLV---------------------NTGD 287
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 334 LEEG--KILHDIRLSFSFQKIvaEQKRPLLY-YSLFLRH---------------VHHTSPQNIVNVS-GRQMQ---SFHG 391
Cdd:PRK10689 288 LETSaeRFWADTLARFENRGV--DPMRPLLPpESLWLRVdelfselknwprvqlKTEHLPTKAANTNlGYQKLpdlAVQA 365
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 392 QMNVLAGEMERFKKS-NFTVVFLGANKERTQKLSSVLADYDIEAAVTDSKKALVQGQVYIMEGELQSGFELPLMKLAVIT 470
Cdd:PRK10689 366 QQKAPLDALRRFLESfDGPVVFSVESEGRREALGELLARIKIAPKRIMRLDEASDRGRYLMIGAAEHGFIDTVRNLALIC 445
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 471 EEELFKNRVKKKPRKQKLT-NAER-IKSYSELQIGDYVVHINHGIGKYLGIETLEINGIHKDYLNIHYQGSDKLYVPVEQ 548
Cdd:PRK10689 446 ESDLLGERVARRRQDSRRTiNPDTlIRNLAELHPGQPVVHLEHGVGRYAGMTTLEAGGIKGEYLMLTYANDAKLYVPVSS 525
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 549 IDQVQKYVGSEGKEPKLYKLGGSEWKRVKKKVETSVQDIADDLIKLYAEREASKGYAFSPDHEMQREFESAFPYQETEDQ 628
Cdd:PRK10689 526 LHLISRYAGGAEENAPLHKLGGDAWSRARQKAAEKVRDVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQ 605
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 629 LRSIHEIKKDMERERPMDRLLCGDVGYGKTEVAIRAAFKAIGDGKQVALLVPTTILAQQHYETIKERFQDYPINIGLLSR 708
Cdd:PRK10689 606 AQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSR 685
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 709 FRTRKEANETIKGLKNGTVDIVIGTHRLLSKDVVYKDLGLLIIDEEQRFGVTHKEKIKQIKANVDVLTLTATPIPRTLHM 788
Cdd:PRK10689 686 FRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEHRFGVRHKERIKAMRADVDILTLTATPIPRTLNM 765
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 789 SMLGVRDLSVIETPPENRFPVQTYVVEYNGALVREAIERELARGGQVYFLYNRVEDIERKADEISMLVPDAKVAYAHGKM 868
Cdd:PRK10689 766 AMSGMRDLSIIATPPARRLAVKTFVREYDSLVVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQM 845
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 869 TENELETVMLSFLEGESDVLVSTTIIETGVDIPNVNTLIVFDADKMGLSQLYQLRGRVGRSNRVAYAYFTYRRDKVLTEV 948
Cdd:PRK10689 846 RERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTD 925
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 949 AEKRLQAIKEFTELGSGFKIAMRDLTIRGAGNLLGAQQHGFIDSVGFDLYSQMLKEAIEERK-GDTAKTEQF---ETEID 1024
Cdd:PRK10689 926 AQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGEEQSGQMETIGFSLYMELLENAVDALKaGREPSLEDLtsqQTEVE 1005
|
1050 1060 1070 1080 1090 1100
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 754290790 1025 VELDAYIPETYIQDGKQKIDMYKRFRSVATIEEKNELQDEMIDRFGNYPKEVEYLFTVAEMKVYAR 1090
Cdd:PRK10689 1006 LRMPSLLPDDFIPDVNTRLSFYKRIASAKNENELEEIKVELIDRFGLLPDPARNLLDIARLRQQAQ 1071
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
591-991 |
1.97e-132 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 419.45 E-value: 1.97e-132
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 591 LIKLYAEREASKGYAFSPDHEMQREFESAFPYQETEDQLRSIHEIKKDMERERPMDRLLCGDVGYGKTEVAIRAAFKAIG 670
Cdd:COG1200 227 LLLRRARRRKRKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVE 306
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 671 DGKQVALLVPTTILAQQHYETIKERFQDYPINIGLLSRFRTRKEANETIKGLKNGTVDIVIGTHRLLSKDVVYKDLGLLI 750
Cdd:COG1200 307 AGYQAALMAPTEILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVV 386
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 751 IDEEQRFGVTHKEKIKQIKANVDVLTLTATPIPRTLHMSMLGVRDLSVI-ETPPeNRFPVQTYVV-EYNGALVREAIERE 828
Cdd:COG1200 387 IDEQHRFGVEQRLALREKGEAPHVLVMTATPIPRTLAMTLYGDLDVSVIdELPP-GRKPIKTRVVpEERRDEVYERIREE 465
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 829 LARGGQVYFLYNRVED---------IERkADEISMLVPDAKVAYAHGKMTENELETVMLSFLEGESDVLVSTTIIETGVD 899
Cdd:COG1200 466 IAKGRQAYVVCPLIEEsekldlqaaEET-YEELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGVD 544
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 900 IPNVNTLIVFDADKMGLSQLYQLRGRVGRSNRVAYAYFTYrrDKVLTEVAEKRLQAIKEFTelgSGFKIAMRDLTIRGAG 979
Cdd:COG1200 545 VPNATVMVIENAERFGLSQLHQLRGRVGRGSAQSYCLLLY--DAPLSETARERLEVMRETN---DGFEIAEEDLELRGPG 619
|
410
....*....|..
gi 754290790 980 NLLGAQQHGFID 991
Cdd:COG1200 620 EFLGTRQSGLPD 631
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
609-801 |
3.85e-128 |
|
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: 389.62 E-value: 3.85e-128
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 609 DHEMQREFESAFPYQETEDQLRSIHEIKKDMERERPMDRLLCGDVGYGKTEVAIRAAFKAIGDGKQVALLVPTTILAQQH 688
Cdd:cd17991 1 DGEEQEEFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 689 YETIKERFQDYPINIGLLSRFRTRKEANETIKGLKNGTVDIVIGTHRLLSKDVVYKDLGLLIIDEEQRFGVTHKEKIKQI 768
Cdd:cd17991 81 YETFKERFANFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQKEKLKEL 160
|
170 180 190
....*....|....*....|....*....|...
gi 754290790 769 KANVDVLTLTATPIPRTLHMSMLGVRDLSVIET 801
Cdd:cd17991 161 RPNVDVLTLSATPIPRTLHMALSGIRDLSVIAT 193
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
591-991 |
6.53e-127 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 404.92 E-value: 6.53e-127
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 591 LIKLYAEREASKGYAFSPDHEMQREFESAFPYQETEDQLRSIHEIKKDMERERPMDRLLCGDVGYGKTEVAIRAAFKAIG 670
Cdd:PRK10917 229 LLLLRAGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIE 308
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 671 DGKQVALLVPTTILAQQHYETIKERFQDYPINIGLLSRFRTRKEANETIKGLKNGTVDIVIGTHRLLSKDVVYKDLGLLI 750
Cdd:PRK10917 309 AGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVI 388
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 751 IDEEQRFGVTHKEKIKQIKANVDVLTLTATPIPRTLHMSMLGVRDLSVI-ETPPEnRFPVQTYVV---EYNGALvrEAIE 826
Cdd:PRK10917 389 IDEQHRFGVEQRLALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIdELPPG-RKPITTVVIpdsRRDEVY--ERIR 465
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 827 RELARGGQVYFLYNRVEDIERK--------ADEISMLVPDAKVAYAHGKMTENELETVMLSFLEGESDVLVSTTIIETGV 898
Cdd:PRK10917 466 EEIAKGRQAYVVCPLIEESEKLdlqsaeetYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGV 545
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 899 DIPNVNTLIVFDADKMGLSQLYQLRGRVGRSNRVAYAYFTYrrDKVLTEVAEKRLQAIKEFTelgSGFKIAMRDLTIRGA 978
Cdd:PRK10917 546 DVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLY--KDPLSETARERLKIMRETN---DGFVIAEKDLELRGP 620
|
410
....*....|...
gi 754290790 979 GNLLGAQQHGFID 991
Cdd:PRK10917 621 GELLGTRQSGLPE 633
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
595-991 |
4.80e-115 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 371.67 E-value: 4.80e-115
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 595 YAEREASKGYAFSPDHEMQREFESAFPYQETEDQLRSIHEIKKDMERERPMDRLLCGDVGYGKTEVAIRAAFKAIGDGKQ 674
Cdd:TIGR00643 207 LGEKQQFSAPPANPSEELLTKFLASLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQ 286
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 675 VALLVPTTILAQQHYETIKERFQDYPINIGLLSRFRTRKEANETIKGLKNGTVDIVIGTHRLLSKDVVYKDLGLLIIDEE 754
Cdd:TIGR00643 287 VALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQ 366
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 755 QRFGVTHKEKIK---QIKANVDVLTLTATPIPRTLHMSMLGVRDLSVIETPPENRFPVQTYVVEYNGA-LVREAIERELA 830
Cdd:TIGR00643 367 HRFGVEQRKKLRekgQGGFTPHVLVMSATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLIKHDEKdIVYEFIEEEIA 446
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 831 RGGQVYFLYNRVEDIE----RKADEISMLV----PDAKVAYAHGKMTENELETVMLSFLEGESDVLVSTTIIETGVDIPN 902
Cdd:TIGR00643 447 KGRQAYVVYPLIEESEkldlKAAEALYERLkkafPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPN 526
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 903 VNTLIVFDADKMGLSQLYQLRGRVGRSNRVAYAYFTYRRDKvlTEVAEKRLQAIKEFTElgsGFKIAMRDLTIRGAGNLL 982
Cdd:TIGR00643 527 ATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKNPK--SESAKKRLRVMADTLD---GFVIAEEDLELRGPGDLL 601
|
....*....
gi 754290790 983 GAQQHGFID 991
Cdd:TIGR00643 602 GTKQSGYPE 610
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
808-958 |
5.20e-81 |
|
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: 261.12 E-value: 5.20e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 808 PVQTYVVEYNGALVREAIERELARGGQVYFLYNRVEDIERKADEISMLVPDAKVAYAHGKMTENELETVMLSFLEGESDV 887
Cdd:cd18810 1 PVRTYVMPYDDELIREAIERELLRGGQVFYVHNRIESIEKLATQLRQLVPEARIAIAHGQMTENELEEVMLEFAKGEYDI 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 754290790 888 LVSTTIIETGVDIPNVNTLIVFDADKMGLSQLYQLRGRVGRSNRVAYAYFTYRRDKVLTEVAEKRLQAIKE 958
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 ... |
591-803 |
2.10e-74 |
|
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: 245.91 E-value: 2.10e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 591 LIKLYAEREASKGYAFSPDHEMQREFESAFPYQETEDQLRSIHEIKKDMERERPMDRLLCGDVGYGKTEVAIRAAFKAIG 670
Cdd:cd17992 13 LLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKTVVAALAMLAAVE 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 671 DGKQVALLVPTTILAQQHYETIKERFQDYPINIGLLSRFRTRKEANETIKGLKNGTVDIVIGTHRLLSKDVVYKDLGLLI 750
Cdd:cd17992 93 NGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQEDVEFHNLGLVI 172
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 754290790 751 IDEEQRFGVTHKEKIKQIKANVDVLTLTATPIPRTLHMSMLGVRDLSVIETPP 803
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 ... |
808-958 |
2.91e-69 |
|
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: 228.69 E-value: 2.91e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 808 PVQTYVVEYNGA-LVREAIERELARGGQVYFLYNRVE--------DIERKADEISMLVPDAKVAYAHGKMTENELETVML 878
Cdd:cd18792 1 PIRTYVIPHDDLdLVYEAIERELARGGQVYYVYPRIEesekldlkSIEALAEELKELVPEARVALLHGKMTEDEKEAVML 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 879 SFLEGESDVLVSTTIIETGVDIPNVNTLIVFDADKMGLSQLYQLRGRVGRSNRVAYAYFTYRRDKVLTEVAEKRLQAIKE 958
Cdd:cd18792 81 EFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYPDPKKLTETAKKRLRAIAE 160
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
609-799 |
1.37e-60 |
|
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: 204.96 E-value: 1.37e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 609 DHEMQREFESAFPYQETEDQLRSIHEIKKDMERERPMDRLLCGDVGYGKTEVAIRAAFKAIGDGKQVALLVPTTILAQQH 688
Cdd:cd17918 1 DRALIQELCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 689 YETIKERFQdyPINIGLLSRFRTRKEANEtikglkngtVDIVIGTHRLLSKDVVYKDLGLLIIDEEQRFGVTHKEKIKQi 768
Cdd:cd17918 81 YEEARKFLP--FINVELVTGGTKAQILSG---------ISLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYN- 148
|
170 180 190
....*....|....*....|....*....|.
gi 754290790 769 KANVDVLTLTATPIPRTLHMSMLGVRDLSVI 799
Cdd:cd17918 149 LGATHFLEATATPIPRTLALALSGLLDLSVI 179
|
|
| CarD_TRCF |
smart01058 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
499-596 |
9.02e-45 |
|
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of light- and starvation-inducible genes. This family includes the presumed N-terminal domain. CarD interacts with the zinc-binding protein CarG, to form a complex that regulates multiple processes in Myxococcus xanthus. This family also includes a domain to the N-terminal side of the DEAD helicase of TRCF proteins. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription. This domain is involved in binding to the stalled RNA polymerase.
Pssm-ID: 215001 [Multi-domain] Cd Length: 99 Bit Score: 156.46 E-value: 9.02e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 499 ELQIGDYVVHINHGIGKYLGIETLEINGIHKDYLNIHYQGSDKLYVPVEQIDQVQKYVGSEGK-EPKLYKLGGSEWKRVK 577
Cdd:smart01058 1 ELKIGDYVVHPDHGVGRYEGIETIEVGGEKREYLVLEYAGGDKLYVPVDNLDLGSRYVGSEGEvEPVLDKLGGGSWSKRK 80
|
90
....*....|....*....
gi 754290790 578 KKVETSVQDIADDLIKLYA 596
Cdd:smart01058 81 RKAKSGIRDIAAELLRLYA 99
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
808-958 |
2.42e-40 |
|
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: 146.34 E-value: 2.42e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 808 PVQTYVV-EYNGALVREAIERELARGGQVYFLYNRVEDIE----RKADEISM-----LVPDAKVAYAHGKMTENELETVM 877
Cdd:cd18811 1 PITTYLIfHTRLDKVYEFVREEIAKGRQAYVIYPLIEESEkldlKAAVAMYEylkerFRPELNVGLLHGRLKSDEKDAVM 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 878 LSFLEGESDVLVSTTIIETGVDIPNVNTLIVFDADKMGLSQLYQLRGRVGRSNRVAYAYFTYrrDKVLTEVAEKRLQAIK 957
Cdd:cd18811 81 AEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVY--KDPLTETAKQRLRVMT 158
|
.
gi 754290790 958 E 958
Cdd:cd18811 159 E 159
|
|
| UvrB_inter |
pfam17757 |
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ... |
142-228 |
1.40e-34 |
|
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: 127.13 E-value: 1.40e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 142 IQVGHDIEPDQLASRLVEVGYERSDMVSAPGEFSIRGGIIDIYPLTSE-NPVRIELFDTEVDSIRSFNSDDQRSIETLTS 220
Cdd:pfam17757 3 LKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYSEdEAIRIEFFGDEIESIREFDPLTGRSLEKLDE 82
|
....*...
gi 754290790 221 INIGPAKE 228
Cdd:pfam17757 83 VTIYPASH 90
|
|
| TRCF |
smart00982 |
This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in ... |
1024-1122 |
1.82e-32 |
|
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: 121.42 E-value: 1.82e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 1024 DVELDAYIPETYIQDGKQKIDMYKRFRSVATIEEKNELQDEMIDRFGNYPKEVEYLFTVAEMKVYARQERVELIKQDKDA 1103
Cdd:smart00982 1 DLPVPALIPEDYIPDVRQRLELYKRIASAETEEELDEIQEELIDRFGPLPEEVKNLLEVARLKLLAKKLGIEKIDAGGKG 80
|
90
....*....|....*....
gi 754290790 1104 VRLTISEEASAEIDGQKLF 1122
Cdd:smart00982 81 IVIEFSPDTPIDPEKLILL 99
|
|
| CarD_CdnL_TRCF |
pfam02559 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
500-595 |
2.13e-31 |
|
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: 117.93 E-value: 2.13e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 500 LQIGDYVVHINHGIGKYLGIETLEingiHKDYLNIHYQGSDKLYVPVEQIDQVQKYVGSEgkepKLYKLG-GSEWKRVKK 578
Cdd:pfam02559 1 LKVGDYVVHPDHGIGRIEGIEKLE----TKDYYVLEYAGGDKLYVPVDNLDLIRKYISKG----ELDKLGdGRRWRKYKE 72
|
90
....*....|....*..
gi 754290790 579 KVETSVQDIADDLIKLY 595
Cdd:pfam02559 73 KLKSGDIEEAAELIKLY 89
|
|
| TRCF |
pfam03461 |
TRCF domain; |
1025-1118 |
1.17e-30 |
|
TRCF domain;
Pssm-ID: 460928 [Multi-domain] Cd Length: 95 Bit Score: 116.37 E-value: 1.17e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 1025 VELDAYIPETYIQDGKQKIDMYKRFRSVATIEEKNELQDEMIDRFGNYPKEVEYLFTVAEMKVYARQERVELIKQDKDAV 1104
Cdd:pfam03461 1 LDVDAYIPDDYIPDESQRLELYKRLASIETEEELDDLQEELIDRFGPLPEEVENLLEIARLKLLAKKLGIEKIDLKGGGI 80
|
90
....*....|....
gi 754290790 1105 RLTISEEASAEIDG 1118
Cdd:pfam03461 81 RITFSEDAKIDPEK 94
|
|
| PRK05298 |
PRK05298 |
excinuclease ABC subunit UvrB; |
117-318 |
1.30e-29 |
|
excinuclease ABC subunit UvrB;
Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 126.32 E-value: 1.30e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 117 IVVAPVAAIRRMLPPVEvWKSSQMLIQVGHDIEPDQLASRLVEVGYERSDMVSAPGEFSIRGGIIDIYP-LTSENPVRIE 195
Cdd:PRK05298 137 IVVASVSCIYGLGSPEE-YLKMVLSLRVGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPaYYEERAIRIE 215
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 196 LFDTEVDSIRSFNSDDQRSIETLTSINIGPAKELIIRPEEKARAMEKIDSGLAASLKKLKadKQKEILHAnishdkERLS 275
Cdd:PRK05298 216 FFGDEIERISEFDPLTGEVLGELDRVTIYPASHYVTPRERLERAIESIKEELEERLKELE--KEGKLLEA------QRLE 287
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 754290790 276 EgQT--DQELVK----------YLSYFY-----EKPASLLDYTPDNTLLILDE----VSRIHEM 318
Cdd:PRK05298 288 Q-RTryDLEMLRelgycsgienYSRHLDgrkpgEPPYTLLDYFPDDFLLFIDEshvtVPQIGGM 350
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
616-806 |
1.04e-26 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 108.73 E-value: 1.04e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 616 FESAFPYQETEDQLRSIHEIkkdmeRERPMDRLLCGDVGYGKTEVAIRAAFKAI--GDGKQVALLVPTTILAQQHYETIK 693
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEAL-----LSGLRDVILAAPTGSGKTLAALLPALEALkrGKGGRVLVLVPTRELAEQWAEELK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 694 ERFQDYPINIGLLsrfRTRKEANETIKGLKNGTVDIVIGT-----HRLLSKDVVYKDLGLLIIDEEQR-----FGVTHKE 763
Cdd:smart00487 76 KLGPSLGLKVVGL---YGGDSKREQLRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRlldggFGDQLEK 152
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 754290790 764 KIKQIKANVDVLTLTATP---IPRTLHMSMLGVRDLSVIETPPENR 806
Cdd:smart00487 153 LLKLLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPLEPI 198
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
625-788 |
2.18e-26 |
|
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: 106.56 E-value: 2.18e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 625 TEDQLRSIHEI--KKDMererpmdrLLCGDVGYGKTEVAIRAAFKAIG---DGKQVALLVPTTILAQQHYETIKERFQDY 699
Cdd:pfam00270 1 TPIQAEAIPAIleGRDV--------LVQAPTGSGKTLAFLLPALEALDkldNGPQALVLAPTRELAEQIYEELKKLGKGL 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 700 PINIgllSRFRTRKEANETIKGLKNgtVDIVIGTH-RLLS---KDVVYKDLGLLIIDEEQR-----FGVTHKEKIKQIKA 770
Cdd:pfam00270 73 GLKV---ASLLGGDSRKEQLEKLKG--PDILVGTPgRLLDllqERKLLKNLKLLVLDEAHRlldmgFGPDLEEILRRLPK 147
|
170
....*....|....*...
gi 754290790 771 NVDVLTLTATPiPRTLHM 788
Cdd:pfam00270 148 KRQILLLSATL-PRNLED 164
|
|
| UvrB |
COG0556 |
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; |
117-311 |
6.67e-25 |
|
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
Pssm-ID: 440322 [Multi-domain] Cd Length: 657 Bit Score: 111.64 E-value: 6.67e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 117 IVVAPVAAIRRMLPPVEvWKSSQMLIQVGHDIEPDQLASRLVEVGYERSDMVSAPGEFSIRGGIIDIYPL-TSENPVRIE 195
Cdd:COG0556 134 IVVASVSCIYGLGSPEE-YLKMVLSLRVGEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAySEERAIRIE 212
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 196 LFDTEVDSIRSFNSDDQRSIETLTSINIGPAKELIIRPEEKARAMEKIDSGLAASLKKLKadKQKEILHAnishdkERLS 275
Cdd:COG0556 213 FFGDEIERISEFDPLTGEVLGELDRVTIYPASHYVTPRERLERAIESIKEELEERLAEFE--SEGKLLEA------QRLE 284
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 754290790 276 EgQT--DQELVK----------YLSYFY-----EKPASLLDYTPDNTLLILDE 311
Cdd:COG0556 285 Q-RTryDLEMLRelgycsgienYSRHLDgrkpgEPPPTLLDYFPDDFLLFIDE 336
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
648-931 |
3.86e-20 |
|
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: 95.53 E-value: 3.86e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 648 LLCGDVGYGKTEVAIRAAFKAIGDGKQVALLVPTTILAQQHYETIKERFQDypiNIGLLSRFRTRKEANETIKGLKNGTV 727
Cdd:TIGR00595 1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGS---QVAVLHSGLSDSEKLQAWRKVKNGEI 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 728 DIVIGTHRLLSkdVVYKDLGLLIIDEEQ----------RFGVTHKEKIKQIKANVDVLTLTATPIPRTLHMSMLGVRDLS 797
Cdd:TIGR00595 78 LVVIGTRSALF--LPFKNLGLIIVDEEHdssykqeegpRYHARDVAVYRAKKFNCPVVLGSATPSLESYHNAKQKAYRLL 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 798 VIETPPENRFPVQTYVVEYNGALVR--------EAIERELARGGQVYFLYNR---------------------------- 841
Cdd:TIGR00595 156 VLTRRVSGRKPPEVKLIDMRKEPRQsflspeliTAIEQTLAAGEQSILFLNRrgysknllcrscgyilccpncdvsltyh 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 842 -------------------------VEDI-------ERKADEISMLVPDAKVAYAHGKMT--ENELETVMLSFLEGESDV 887
Cdd:TIGR00595 236 kkegklrchycgyqepipktcpqcgSEDLvykgygtEQVEEELAKLFPGARIARIDSDTTsrKGAHEALLNQFANGKADI 315
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*
gi 754290790 888 LVSTTIIETGVDIPNVNTLIVFDAD-----------KMGLSQLYQLRGRVGRSNR 931
Cdd:TIGR00595 316 LIGTQMIAKGHHFPNVTLVGVLDADsglhspdfraaERGFQLLTQVAGRAGRAED 370
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
823-930 |
5.40e-20 |
|
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: 86.11 E-value: 5.40e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 823 EAIEREL--ARGGQVYFLYNRVEDIERkadEISMLVPDAKVAYAHGKMTENELETVMLSFLEGESDVLVSTTIIETGVDI 900
Cdd:pfam00271 4 EALLELLkkERGGKVLIFSQTKKTLEA---ELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDL 80
|
90 100 110
....*....|....*....|....*....|
gi 754290790 901 PNVNTLIVFDADKmGLSQLYQLRGRVGRSN 930
Cdd:pfam00271 81 PDVDLVINYDLPW-NPASYIQRIGRAGRAG 109
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
645-780 |
2.61e-18 |
|
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: 82.84 E-value: 2.61e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 645 MDRLLCGDVGYGKTEVAIRAAFKAIGD-GKQVALLVPTTILAQQHYETIKERFqDYPINIGLLSRFRTRKEAnetiKGLK 723
Cdd:cd00046 2 ENVLITAPTGSGKTLAALLAALLLLLKkGKKVLVLVPTKALALQTAERLRELF-GPGIRVAVLVGGSSAEER----EKNK 76
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 724 NGTVDIVIGTHRLLSKDV------VYKDLGLLIIDEEQRFGVTHKEK-------IKQIKANVDVLTLTAT 780
Cdd:cd00046 77 LGDADIIIATPDMLLNLLlredrlFLKDLKLIIVDEAHALLIDSRGAlildlavRKAGLKNAQVILLSAT 146
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
860-928 |
6.31e-17 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 76.48 E-value: 6.31e-17
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 754290790 860 KVAYAHGKMTENELETVMLSFLEGESDVLVSTTIIETGVDIPNVNTLIVFDADKmGLSQLYQLRGRVGR 928
Cdd:smart00490 13 KVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPW-SPASYIQRIGRAGR 80
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
620-1071 |
7.93e-16 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 82.38 E-value: 7.93e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 620 FPYQEtedqlRSIHEIKKDMERERpmDR-LLCGDVGYGKTEVAIRAAfKAIGDGKQVALLVPTTILAQQHYETIKERFQD 698
Cdd:COG1061 82 RPYQQ-----EALEALLAALERGG--GRgLVVAPTGTGKTVLALALA-AELLRGKRVLVLVPRRELLEQWAEELRRFLGD 153
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 699 yPINIGllsrfrtrkeanetikGLKNGTVDIVIGTHRLLSKDVVYKDL----GLLIIDEEQRFG-VTHKEKIKQIKANVd 773
Cdd:COG1061 154 -PLAGG----------------GKKDSDAPITVATYQSLARRAHLDELgdrfGLVIIDEAHHAGaPSYRRILEAFPAAY- 215
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 774 VLTLTATPIpRTLHMSMLGVRDLSVI-ETPP----ENRFPVQTYVVEYNGAL---------VREAIERELARGGQVyfLY 839
Cdd:COG1061 216 RLGLTATPF-RSDGREILLFLFDGIVyEYSLkeaiEDGYLAPPEYYGIRVDLtderaeydaLSERLREALAADAER--KD 292
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 840 NRVEDIERK----------------ADEISMLVPDA--KVAYAHGKMTENELETVMLSFLEGESDVLVSTTIIETGVDIP 901
Cdd:COG1061 293 KILRELLREhpddrktlvfcssvdhAEALAELLNEAgiRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVP 372
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 902 NVNTLIVFDADKmGLSQLYQLRGR----------------VGRSNRVAYAYFTYRRDKVLTEVAEKRLQAIKEFTELGSG 965
Cdd:COG1061 373 RLDVAILLRPTG-SPREFIQRLGRglrpapgkedalvydfVGNDVPVLEELAKDLRDLAGYRVEFLDEEESEELALLIAV 451
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 966 FKIAMRDLTIRGAGNLLGAQ-QHGFIDSVGFDLYSQMLKEAIEERKGDTAKTEQFETEIDVELDAYIPETYIQDGKQKID 1044
Cdd:COG1061 452 KPALEVKGELEEELLEELELlEDALLLVLAELLLLELLALALELLELAKAEGKAEEEEEEKELLLLLALAKLLKLLLLLL 531
|
490 500
....*....|....*....|....*..
gi 754290790 1045 MYKRFRSVATIEEKNELQDEMIDRFGN 1071
Cdd:COG1061 532 LLLLLELLELLAALLRLEELAALLLKE 558
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
628-754 |
1.68e-15 |
|
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: 75.71 E-value: 1.68e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 628 QLRSIHEIKKDMERERPMdrLLCGDVGYGKTEVAIRAAFKAIGDGKQVALLVPTTILAQQHYETIKERFQDypiNIGLLS 707
Cdd:cd17929 1 QRKAYEAIVSSLGGFKTF--LLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRFGD---KVAVLH 75
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 754290790 708 RFRTRKEANETIKGLKNGTVDIVIGTHRLLSkdVVYKDLGLLIIDEE 754
Cdd:cd17929 76 SKLSDKERADEWRKIKRGEAKVVIGARSALF--APFKNLGLIIVDEE 120
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
654-929 |
1.34e-13 |
|
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: 74.53 E-value: 1.34e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 654 GYGKTEVAIRAAFKAIGDGKQVALLVPTTILAQQHYETIKERFQDYPInIGLlsrfrtRKEANETIKGlkngtVDIVIGT 733
Cdd:COG4098 139 GAGKTEMLFPAIAEALKQGGRVCIATPRVDVVLELAPRLQQAFPGVDI-AAL------YGGSEEKYRY-----AQLVIAT 206
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 734 -HRLLSkdvVYKDLGLLIIDE---------EQ-RFGVthkEKIKqiKANVDVLTLTATPiPRTLhMSMLGVRDLSVIETP 802
Cdd:COG4098 207 tHQLLR---FYQAFDLLIIDEvdafpysgdPMlQYAV---KRAR--KPDGKLIYLTATP-SKAL-QRQVKRGKLKVVKLP 276
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 803 peNRF-----PVQTYVVEYN-------GAL---VREAIERELARGGQVYFLYNRVEDIERKADEISMLVPDAKVAYAHGK 867
Cdd:COG4098 277 --ARYhghplPVPKFKWLGNwkkrlrrGKLprkLLKWLKKRLKEGRQLLIFVPTIELLEQLVALLQKLFPEERIAGVHAE 354
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 754290790 868 mTENELETVMlSFLEGESDVLVSTTIIETGVDIPNVNTLI------VFDAdkmglSQLYQLRGRVGRS 929
Cdd:COG4098 355 -DPERKEKVQ-AFRDGEIPILVTTTILERGVTFPNVDVAVlgadhpVFTE-----AALVQIAGRVGRS 415
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
648-931 |
9.15e-13 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 72.50 E-value: 9.15e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 648 LLCGDVGYGKTEVAIRAAFKAIGDGKQVALLVPTTILAQQHYETIKERFQDypiNIGLL-SRFrTRKEANETIKGLKNGT 726
Cdd:PRK05580 166 LLDGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQMLARFRARFGA---PVAVLhSGL-SDGERLDEWRKAKRGE 241
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 727 VDIVIGThR---LLSkdvvYKDLGLLIIDEE------QRFGVT-----------HKEKIKqikanvdVLTLTATPIPRTL 786
Cdd:PRK05580 242 AKVVIGA-RsalFLP----FKNLGLIIVDEEhdssykQQEGPRyhardlavvraKLENIP-------VVLGSATPSLESL 309
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 787 HMSMLGVRDLSVIETPPENRFPVQTYVVEYNGAL-----------VREAIERELARGGQV-YFLyNR------------- 841
Cdd:PRK05580 310 ANAQQGRYRLLRLTKRAGGARLPEVEIIDMRELLrgengsflsppLLEAIKQRLERGEQVlLFL-NRrgyapfllcrdcg 388
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 842 ----------------------------------------VEDI-------ERKADEISMLVPDAKVAyahgKM------ 868
Cdd:PRK05580 389 wvaecphcdasltlhrfqrrlrchhcgyqepipkacpecgSTDLvpvgpgtERLEEELAELFPEARIL----RIdrdttr 464
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 754290790 869 TENELETVMLSFLEGESDVLVSTTIIETGVDIPNVNTLIVFDADkMGL------------SQLYQLRGRVGRSNR 931
Cdd:PRK05580 465 RKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDAD-LGLfspdfrasertfQLLTQVAGRAGRAEK 538
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
613-931 |
9.30e-12 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 69.38 E-value: 9.30e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 613 QREFESAFPYQETEDQLRSIHEIKKDMERERPMdrLLCGDVGYGKTEVAIRAAFKAIGDGKQVALLVPTTILAQQHYETI 692
Cdd:COG1198 185 APDVPAEPPPTLNEEQQAAVEAIRAAAGGFSVF--LLHGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQTVERF 262
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 693 KERFQDypiNIGLL-S------RFRTRKEAnetikglKNGTVDIVIGThR---LLSkdvvYKDLGLLIIDEEqrfgvtHK 762
Cdd:COG1198 263 RARFGA---RVAVLhSglsdgeRLDEWRRA-------RRGEARIVIGT-RsalFAP----FPNLGLIIVDEE------HD 321
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 763 EKIKQI----------------KANVDVLTLTATPIPRTLHMSMLGVRDLSVIETPPENRFPVQTYVV-------EYNGA 819
Cdd:COG1198 322 SSYKQEdgpryhardvavvrakLEGAPVVLGSATPSLESLYNAQKGRYRLLELPERAGGAPLPEVELVdmreeplEGGRI 401
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 820 L---VREAIERELARGGQV-YFLyNR---------------VE----DI------------------------------- 845
Cdd:COG1198 402 LsppLLEAIEETLERGEQVlLFL-NRrgyapfllcrdcgwvAKcpncDVsltyhrsrrrlrchycgyeepvpkqcpecgs 480
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 846 ----------ERKADEISMLVPDAKVAyahgKM------TENELETVMLSFLEGESDVLVSTTIIETGVDIPNVNTLIVF 909
Cdd:COG1198 481 dslrpfgpgtERVEEELAELFPDARVL----RMdrdttrRKGALEKLLEAFARGEADILVGTQMLAKGHDFPNVTLVGVL 556
|
410 420 430
....*....|....*....|....*....|....
gi 754290790 910 DADkMGLS-----------QLY-QLRGRVGRSNR 931
Cdd:COG1198 557 DAD-LGLNspdfraaertfQLLtQVAGRAGRAEK 589
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
656-928 |
6.94e-09 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 59.91 E-value: 6.94e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 656 GKTEVAIRAAFKAIGDGKQVALLVPTTILAQQHYETIKERFQDYPINIGLLSRFRTRKEAnetikglKNGTVDIVIGT-- 733
Cdd:COG1204 50 GKTLIAELAILKALLNGGKALYIVPLRALASEKYREFKRDFEELGIKVGVSTGDYDSDDE-------WLGRYDILVATpe 122
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 734 --HRLLSKDV-VYKDLGLLIIDE------EQRfGVTHK---EKIKQIKANVDVLTLTAT--------------------- 780
Cdd:COG1204 123 klDSLLRNGPsWLRDVDLVVVDEahliddESR-GPTLEvllARLRRLNPEAQIVALSATignaeeiaewldaelvksdwr 201
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 781 PIPRtlhmsMLGVRDLSVIETPPENRFPVQTYVveyngALVREAIErelaRGGQVYFLYNRVEDIERKADEIS-----ML 855
Cdd:COG1204 202 PVPL-----NEGVLYDGVLRFDDGSRRSKDPTL-----ALALDLLE----EGGQVLVFVSSRRDAESLAKKLAdelkrRL 267
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 856 VPDAK------------------------------VAYAHGKMTENELETVMLSFLEGESDVLVSTTIIETGVDIPnVNT 905
Cdd:COG1204 268 TPEEReeleelaeellevseethtnekladclekgVAFHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLP-ARR 346
|
330 340
....*....|....*....|....*...
gi 754290790 906 LIVFDADKMGLSQL-----YQLRGRVGR 928
Cdd:COG1204 347 VIIRDTKRGGMVPIpvlefKQMAGRAGR 374
|
|
| CdnL |
COG1329 |
RNA polymerase-interacting regulator, CarD/CdnL/TRCF family [Transcription]; |
501-552 |
4.48e-08 |
|
RNA polymerase-interacting regulator, CarD/CdnL/TRCF family [Transcription];
Pssm-ID: 440940 [Multi-domain] Cd Length: 155 Bit Score: 53.60 E-value: 4.48e-08
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 754290790 501 QIGDYVVHINHGIGKYLGIETLEINGIHKDYLNIHYQGSD-KLYVPVEQIDQV 552
Cdd:COG1329 2 KVGDKVVYPMHGVGVIEAIEEKEIAGEKKEYYVLRFPYDDmTIMVPVDKAESV 54
|
|
| Cas3 |
COG1203 |
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
654-931 |
7.02e-08 |
|
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system
Pssm-ID: 440816 [Multi-domain] Cd Length: 535 Bit Score: 56.63 E-value: 7.02e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 654 GYGKTEVAIRAAFKAIGDGKQ----VALlvPTTILAQQHYETIKERFQDypiNIGL------LSRFRTRKEANETIKGLK 723
Cdd:COG1203 157 GGGKTEAALLFALRLAAKHGGrriiYAL--PFTSIINQTYDRLRDLFGE---DVLLhhsladLDLLEEEEEYESEARWLK 231
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 724 NGT----VDIVIGT-------------------HRLLSKDVV--------YKDLGLLI--IDEEQRFGVThkekikqika 770
Cdd:COG1203 232 LLKelwdAPVVVTTidqlfeslfsnrkgqerrlHNLANSVIIldevqaypPYMLALLLrlLEWLKNLGGS---------- 301
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 771 nvdVLTLTATpIPRTLHMSMLGVRDLSVIETPPENRFP-------VQTYVVEYNGALVREAIERELARGGQVYFLYNRVE 843
Cdd:COG1203 302 ---VILMTAT-LPPLLREELLEAYELIPDEPEELPEYFrafvrkrVELKEGPLSDEELAELILEALHKGKSVLVIVNTVK 377
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 844 DIERKADEISMLVPDAKVAYAHGKMTENE----LETVMLSFLEGESDVLVSTTIIETGVDIpnvntlivfDADKM----- 914
Cdd:COG1203 378 DAQELYEALKEKLPDEEVYLLHSRFCPADrseiEKEIKERLERGKPCILVSTQVVEAGVDI---------DFDVVirdla 448
|
330
....*....|....*..
gi 754290790 915 GLSQLYQLRGRVGRSNR 931
Cdd:COG1203 449 PLDSLIQRAGRCNRHGR 465
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
845-930 |
7.54e-08 |
|
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: 54.56 E-value: 7.54e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 845 IERKADEISMLVPDAKVAyahgKM------TENELETVMLSFLEGESDVLVSTTIIETGVDIPNVNTLIVFDADKM---- 914
Cdd:cd18804 103 TERVEEELKTLFPEARIA----RIdrdttrKKGALEKLLDQFERGEIDILIGTQMIAKGLDFPNVTLVGILNADSGlnsp 178
|
90 100
....*....|....*....|...
gi 754290790 915 -------GLSQLYQLRGRVGRSN 930
Cdd:cd18804 179 dfraserAFQLLTQVSGRAGRGD 201
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
869-939 |
1.36e-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: 50.01 E-value: 1.36e-07
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 754290790 869 TENELETVMLSFLegesdVLVSTTIIETGVDIPNVNTLIVFDADKmGLSQLYQLRGRVGRSNRVAYAYFTY 939
Cdd:cd18785 12 SIEHAEEIASSLE-----ILVATNVLGEGIDVPSLDTVIFFDPPS-SAASYIQRVGRAGRGGKDEGEVILF 76
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
620-781 |
1.54e-07 |
|
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: 51.92 E-value: 1.54e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 620 FPYQETedqlrSIHEIKKDMERERpmdRLLCGDVGYGKTEVAIRAAFKAigdGKQVAL-LVPTTILAQQhyetIKERFQD 698
Cdd:cd17926 2 RPYQEE-----ALEAWLAHKNNRR---GILVLPTGSGKTLTALALIAYL---KELRTLiVVPTDALLDQ----WKERFED 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 699 Y--PINIGLLSrfRTRKEANETIkglkngtvDIVIGTHRLLSKDV-----VYKDLGLLIIDEEQRFG-VTHKEKIKQIKA 770
Cdd:cd17926 67 FlgDSSIGLIG--GGKKKDFDDA--------NVVVATYQSLSNLAeeekdLFDQFGLLIVDEAHHLPaKTFSEILKELNA 136
|
170
....*....|.
gi 754290790 771 NVdVLTLTATP 781
Cdd:cd17926 137 KY-RLGLTATP 146
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
628-780 |
4.22e-07 |
|
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: 51.49 E-value: 4.22e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 628 QLRSIHEIkkdMERERPMdrLLCGDVGYGKTEVAIRAAFKAIGDGKQVAL-LVPTTILAQQHYETIKERFQDYPINIGLL 706
Cdd:cd17921 6 QREALRAL---YLSGDSV--LVSAPTSSGKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFGPLGKNVGLL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 707 SRfrtrkeaNETIKGLKNGTVDIVIGT----HRLLSK--DVVYKDLGLLIIDE------EQRfGVTHKE---KIKQIKAN 771
Cdd:cd17921 81 TG-------DPSVNKLLLAEADILVATpeklDLLLRNggERLIQDVRLVVVDEahligdGER-GVVLELllsRLLRINKN 152
|
....*....
gi 754290790 772 VDVLTLTAT 780
Cdd:cd17921 153 ARFVGLSAT 161
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
648-782 |
4.86e-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: 51.91 E-value: 4.86e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 648 LLCGDVGYGKTEVAIRAA--FKAIGDGKQVALLVPTTILAQQHYEtIKERFQdypINIGLLSRFRTRKEanETIKGLKNG 725
Cdd:cd18011 21 LLADEVGLGKTIEAGLIIkeLLLRGDAKRVLILCPASLVEQWQDE-LQDKFG---LPFLILDRETAAQL--RRLIGNPFE 94
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 754290790 726 TVDIVIGTHRLL------SKDVVYKDLGLLIIDEEQRFGVTHKEK-------IKQIKANVD-VLTLTATPI 782
Cdd:cd18011 95 EFPIVIVSLDLLkrseerRGLLLSEEWDLVVVDEAHKLRNSGGGKetkryklGRLLAKRARhVLLLTATPH 165
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
654-782 |
1.10e-06 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 49.59 E-value: 1.10e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 654 GYGKTEVAIRAA--FKAIGDGKQVALLVPTTILAQQHYETIKERFQDYpinigllsrfrtrKEANETIKGLKN----GTV 727
Cdd:pfam04851 33 GSGKTLTAAKLIarLFKKGPIKKVLFLVPRKDLLEQALEEFKKFLPNY-------------VEIGEIISGDKKdesvDDN 99
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 754290790 728 DIVIGTHRLLSKDVVYKDL-------GLLIIDEEQRFGVTHKEKIKQ-IKANVdVLTLTATPI 782
Cdd:pfam04851 100 KIVVTTIQSLYKALELASLellpdffDVIIIDEAHRSGASSYRNILEyFKPAF-LLGLTATPE 161
|
|
| DDXDc_reverse_gyrase |
cd17924 |
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
654-752 |
1.86e-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: 49.63 E-value: 1.86e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 654 GYGKTEVAIRAAFKAIGDGKQVALLVPTTILAQQHYETIKERFQDYPINIGLL---SRFRTrKEANETIKGLKNGTVDIV 730
Cdd:cd17924 42 GVGKTTFGLATSLYLASKGKRSYLIFPTKSLVKQAYERLSKYAEKAGVEVKILvyhSRLKK-KEKEELLEKIEKGDFDIL 120
|
90 100
....*....|....*....|....*
gi 754290790 731 IGTHRLLSKDV---VYKDLGLLIID 752
Cdd:cd17924 121 VTTNQFLSKNFdllSNKKFDFVFVD 145
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
654-931 |
2.34e-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: 51.28 E-value: 2.34e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 654 GYGKTEVAIRAAFKAIGDGK--QVALLVPTTILAQQHYETIKERFQDyPINIGLLSRFRTRKE----------------- 714
Cdd:cd09639 9 GYGKTEAALLWALHSLKSQKadRVIIALPTRATINAMYRRAKEAFGE-TGLYHSSILSSRIKEmgdseefehlfplyihs 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 715 -ANETIKGLKNGTVDIVIGT------HRLLSKDVVykDLGLLIIDEEQRFGVTHKEKI----KQIKAN-VDVLTLTATpI 782
Cdd:cd09639 88 nDTLFLDPITVCTIDQVLKSvfgefgHYEFTLASI--ANSLLIFDEVHFYDEYTLALIlavlEVLKDNdVPILLMSAT-L 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 783 P---RTLHMSMLGVRDLSVIETPPENRFPVQTYVVEYNGAL-VREAIERELARGGQVYFLYNRVEDIERKADEISMLVPD 858
Cdd:cd09639 165 PkflKEYAEKIGYVEENEPLDLKPNERAPFIKIESDKVGEIsSLERLLEFIKKGGSVAIIVNTVDRAQEFYQQLKEKGPE 244
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 754290790 859 AKVAYAHGKMTENE----LETVMLSFLEGESDVLVSTTIIETGVDIpNVNTLIvfdADKMGLSQLYQLRGRVGRSNR 931
Cdd:cd09639 245 EEIMLIHSRFTEKDrakkEAELLLEFKKSEKFVIVATQVIEASLDI-SVDVMI---TELAPIDSLIQRLGRLHRYGE 317
|
|
| SF2_C_FANCM_Hef |
cd18801 |
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
859-930 |
2.93e-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: 2.93e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 754290790 859 AKVAYAHGkMTENELETVMLSFLEGESDVLVSTTIIETGVDIPNVNTLIVFDADKMGLsQLYQLRGRVGRSN 930
Cdd:cd18801 66 ASGKSSKG-MSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPI-RMIQRMGRTGRKR 135
|
|
| PTZ00424 |
PTZ00424 |
helicase 45; Provisional |
654-931 |
3.83e-06 |
|
helicase 45; Provisional
Pssm-ID: 185609 [Multi-domain] Cd Length: 401 Bit Score: 50.60 E-value: 3.83e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 654 GYGKTEVAIRAAFKAIG---DGKQVALLVPTTILAQQhyetikerFQDYPINIGLLSRFRTR-----KEANETIKGLKNG 725
Cdd:PTZ00424 75 GTGKTATFVIAALQLIDydlNACQALILAPTRELAQQ--------IQKVVLALGDYLKVRCHacvggTVVRDDINKLKAG 146
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 726 tVDIVIGT----HRLLSKDVVYKD-LGLLIIDEEQR-----FGVTHKEKIKQIKANVDVLTLTATPIPRTLHMSMLGVRD 795
Cdd:PTZ00424 147 -VHMVVGTpgrvYDMIDKRHLRVDdLKLFILDEADEmlsrgFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRD 225
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 796 lsvietppENRFPVQTYVVEYNGalVRE---AIERELARGGQVYFLYNRVE--------DIERKADEIS--MLVPDAKVA 862
Cdd:PTZ00424 226 --------PKRILVKKDELTLEG--IRQfyvAVEKEEWKFDTLCDLYETLTitqaiiycNTRRKVDYLTkkMHERDFTVS 295
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 754290790 863 YAHGKMTENELETVMLSFLEGESDVLVSTTIIETGVDIPNVNTLIVFDADKMGLSQLYqlrgRVGRSNR 931
Cdd:PTZ00424 296 CMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIH----RIGRSGR 360
|
|
| RecQ |
COG0514 |
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
711-961 |
3.01e-05 |
|
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 47.83 E-value: 3.01e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 711 TRKEANETIKGLKNGTVDIV-IGTHRLLSKDVVYK----DLGLLIIDE-------------EQRfgvthkeKIKQIKA-- 770
Cdd:COG0514 92 SAEERREVLRALRAGELKLLyVAPERLLNPRFLELlrrlKISLFAIDEahcisqwghdfrpDYR-------RLGELRErl 164
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 771 -NVDVLTLTATPIPRTLH--MSMLGVRD--------------LSVIETPPENRFpvqtyvveyngALVREAIERELARGG 833
Cdd:COG0514 165 pNVPVLALTATATPRVRAdiAEQLGLEDprvfvgsfdrpnlrLEVVPKPPDDKL-----------AQLLDFLKEHPGGSG 233
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 834 QVYFLyNRvedieRKADEIS-MLVPDA-KVAYAHGKMTENELETVMLSFLEGESDVLVSTTIIETGVDIPNVNTLIVFDA 911
Cdd:COG0514 234 IVYCL-SR-----KKVEELAeWLREAGiRAAAYHAGLDAEEREANQDRFLRDEVDVIVATIAFGMGIDKPDVRFVIHYDL 307
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 754290790 912 DKmGLSQLYQLRGRVGRSNRVAYAYFTYRR-DKVL--------------TEVAEKRLQAIKEFTE 961
Cdd:COG0514 308 PK-SIEAYYQEIGRAGRDGLPAEALLLYGPeDVAIqrffieqsppdeerKRVERAKLDAMLAYAE 371
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
847-931 |
3.95e-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: 44.42 E-value: 3.95e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 847 RKADEISMLVPDA--KVAYAHGKMTENELETVMLSFLEGESDVLVSTTIIETGVDIPNVNTLIVFDA--DkmglSQLYQL 922
Cdd:cd18787 38 KRVDRLAELLEELgiKVAALHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGVDHVINYDLprD----AEDYVH 113
|
90
....*....|
gi 754290790 923 R-GRVGRSNR 931
Cdd:cd18787 114 RiGRTGRAGR 123
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
868-1071 |
6.65e-05 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 47.03 E-value: 6.65e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 868 MTENELETVMLSFLEGESDVLVSTTIIETGVDIPNVNTLIVFDAdkmGLSQL--YQLRGRVGRSN--RV----------- 932
Cdd:COG1111 395 LTQKEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVIFYEP---VPSEIrsIQRKGRTGRKRegRVvvliakgtrde 471
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 933 AYAYFTYRRDKvlteVAEKRLQAIK-EFTELGSGFKIAMRDLTIRGAGNLLGAQQHGFIDSVGFDLYSQMLKEAIEERK- 1010
Cdd:COG1111 472 AYYWSSRRKEK----KMKSILKKLKkLLDKQEKEKLKESAQATLDEFESIKELAEDEINEKDLDEIESSENGAHVDWREp 547
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 754290790 1011 --GDTAKTEQFETEIDVELDAYIPETYIQDGKQKIDMYKRFRSVATIEEKNELQDEMIDRFGN 1071
Cdd:COG1111 548 vlLQVIVSTLAESLELRELGEKVDDEVNLILEIDRVDVVDDGSVLRVSRLLVEIGELDGKTRV 610
|
|
| PLN00206 |
PLN00206 |
DEAD-box ATP-dependent RNA helicase; Provisional |
722-910 |
1.30e-04 |
|
DEAD-box ATP-dependent RNA helicase; Provisional
Pssm-ID: 215103 [Multi-domain] Cd Length: 518 Bit Score: 45.93 E-value: 1.30e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 722 LKNGtVDIVIGTH----RLLSK-DVVYKDLGLLIIDE-----EQRFgvthKEKIKQI---KANVDVLTLTATPIPRTLHM 788
Cdd:PLN00206 243 IQQG-VELIVGTPgrliDLLSKhDIELDNVSVLVLDEvdcmlERGF----RDQVMQIfqaLSQPQVLLFSATVSPEVEKF 317
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 789 SMLGVRDLSVIETPPENRfPvqtyvveyNGALVREAIERELARGGQ----------------VYFLYNRVeDIERKADEI 852
Cdd:PLN00206 318 ASSLAKDIILISIGNPNR-P--------NKAVKQLAIWVETKQKKQklfdilkskqhfkppaVVFVSSRL-GADLLANAI 387
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*...
gi 754290790 853 SMlVPDAKVAYAHGKMTENELETVMLSFLEGESDVLVSTTIIETGVDIPNVNTLIVFD 910
Cdd:PLN00206 388 TV-VTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFD 444
|
|
| DEADc_DDX18 |
cd17942 |
DEAD-box helicase domain of DEAD box protein 18; This DDX18 gene encodes a DEAD box protein ... |
648-768 |
3.22e-04 |
|
DEAD-box helicase domain of DEAD box protein 18; This DDX18 gene encodes a DEAD box protein and is activated by Myc protein. DDX18 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350700 [Multi-domain] Cd Length: 198 Bit Score: 43.12 E-value: 3.22e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 648 LLCG-DV------GYGKT--------EVAIRAAFKAiGDGKQVALLVPTTILAQQHYETIKERF----QDYPINIGLLSR 708
Cdd:cd17942 24 LLEGrDVlgaaktGSGKTlaflipaiELLYKLKFKP-RNGTGVIIISPTRELALQIYGVAKELLkyhsQTFGIVIGGANR 102
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 754290790 709 frtRKEANETIKGlkngtVDIVIGT-HRLL-----SKDVVYKDLGLLIIDEEQR-FGVTHKEKIKQI 768
Cdd:cd17942 103 ---KAEAEKLGKG-----VNILVATpGRLLdhlqnTKGFLYKNLQCLIIDEADRiLEIGFEEEMRQI 161
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
648-780 |
1.94e-03 |
|
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: 40.40 E-value: 1.94e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 648 LLCGDVGYGKTEVAIRAAFKAIGDGKQVALLVPTTILAQQHYETIKeRFQDYPINIGLlsrfrTRKEANETIKGLKNgtV 727
Cdd:cd18028 21 LISIPTASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEEFK-KLEEIGLKVGI-----STGDYDEDDEWLGD--Y 92
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 754290790 728 DIVIGTHR-----LLSKDVVYKDLGLLIIDE------EQRFGVTHK--EKIKQIKANVDVLTLTAT 780
Cdd:cd18028 93 DIIVATYEkfdslLRHSPSWLRDVGVVVVDEihlisdEERGPTLESivARLRRLNPNTQIIGLSAT 158
|
|
| SF2_C_EcoAI-like |
cd18799 |
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ... |
857-925 |
1.98e-03 |
|
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family is composed of helicase restriction enzymes, including the HsdR subunit of restriction-modification enzymes such as Escherichia coli type I restriction enzyme EcoAI R protein (R.EcoAI). The EcoAI enzyme recognizes 5'-GAGN(7)GTCA-3'. The HsdR or R subunit is required for both nuclease and ATPase activities, but not for modification. These proteins are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350186 [Multi-domain] Cd Length: 116 Bit Score: 39.08 E-value: 1.98e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 857 PDAKVAYAHGKMTENELETVMLSFL-EGESDVLVSTTIIETGVDIPNVNTlIVFDADKMGLSQLYQLRGR 925
Cdd:cd18799 31 IDAVALNSDYSDRERGDEALILLFFgELKPPILVTVDLLTTGVDIPEVDN-VVFLRPTESRTLFLQMLGR 99
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
648-781 |
2.52e-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: 40.49 E-value: 2.52e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 648 LLCGDVGYGKTEVAI-----RAAFKAIGDGKQVALLVPTTILAQQHYETIKERFQDYPINIGLLSRFRTRKEANETIKgl 722
Cdd:cd17927 21 IICLPTGSGKTFVAVlicehHLKKFPAGRKGKVVFLANKVPLVEQQKEVFRKHFERPGYKVTGLSGDTSENVSVEQIV-- 98
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 754290790 723 knGTVDIVIGTHRLLSKD------VVYKDLGLLIIDEEQRFGVTH----------KEKIKQIKANVDVLTLTATP 781
Cdd:cd17927 99 --ESSDVIIVTPQILVNDlksgtiVSLSDFSLLVFDECHNTTKNHpyneimfrylDQKLGSSGPLPQILGLTASP 171
|
|
| SF2_C_Ski2 |
cd18795 |
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ... |
825-928 |
3.86e-03 |
|
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. This family includes spliceosomal Brr2 RNA helicase, ASCC3 (involved in the repair of N-alkylated nucleotides), Mtr4 (involved in processing of structured RNAs), DDX60 (involved in viral RNA degradation), and other proteins. Ski2-like RNA 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: 350182 [Multi-domain] Cd Length: 154 Bit Score: 39.07 E-value: 3.86e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 825 IERELARGGQV-YFLYNRVEDiERKADEIsmlvpdAKVAYAHGKMTENELETVMLSFLEGESDVLVSTTIIETGVDIPN- 902
Cdd:cd18795 36 KIETVSEGKPVlVFCSSRKEC-EKTAKDL------AGIAFHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLPAr 108
|
90 100 110
....*....|....*....|....*....|..
gi 754290790 903 ---VNTLIVFDADKM---GLSQLYQLRGRVGR 928
Cdd:cd18795 109 tviIKGTQRYDGKGYrelSPLEYLQMIGRAGR 140
|
|
| DEXHc_Hef |
cd18035 |
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
654-781 |
5.15e-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: 39.42 E-value: 5.15e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 754290790 654 GYGKTEVAIR-AAFKAIGDGKQVALLVPTTILAQQHYETIKeRFQDYPINIGLLSRFRTRKEANETIKGLKngtvdIVIG 732
Cdd:cd18035 26 GLGKTIIAILvAADRLTKKGGKVLILAPSRPLVEQHAENLK-RVLNIPDKITSLTGEVKPEERAERWDASK-----IIVA 99
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 754290790 733 THRLLSKDVV-----YKDLGLLIIDEEQRFGVTHK-----EKIKQIKANVDVLTLTATP 781
Cdd:cd18035 100 TPQVIENDLLagritLDDVSLLIFDEAHHAVGNYAyvyiaHRYKREANNPLILGLTASP 158
|
|
| UB2H |
pfam14814 |
Bifunctional transglycosylase second domain; UB2H is the second domain of the ... |
142-184 |
9.04e-03 |
|
Bifunctional transglycosylase second domain; UB2H is the second domain of the transglycosylases, or penicillin-binding proteins PBP1bs)), the multi-domain membrane proteins essential for cell wall synthesis that are targeted by penicillin antibiotics. The exact function of the UB2H domain is uncertain, but it may act as the binding component of PBP1b with different binding partners, or it may participate in the regulation between DNA repair and/or synthesis and cell wall formation during the bacterial cell cycle.
Pssm-ID: 434234 [Multi-domain] Cd Length: 85 Bit Score: 36.38 E-value: 9.04e-03
10 20 30 40
....*....|....*....|....*....|....*....|...
gi 754290790 142 IQVGHDIEPDQLASRLVEVGYERSDMVSAPGEFSIRGGIIDIY 184
Cdd:pfam14814 1 LYPGQALSAAQLEQELKLLGYRKVSNPTRPGEYSVSGNRIELY 43
|
|
| |
