|
Name |
Accession |
Description |
Interval |
E-value |
| DEXXQc_DNA2 |
cd18041 |
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ... |
626-829 |
1.81e-123 |
|
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses different enzymatic activities, such as single-stranded DNA (ssDNA)-dependent ATPase, 5-3 helicase, and endonuclease activities, and is involved in DNA replication and DNA repair in the nucleus and mitochondrion. It is involved in Okazaki fragment processing by cleaving long flaps that escape FEN1: flaps that are longer than 27 nucleotides are coated by replication protein A complex (RPA), leading to recruit DNA2 which cleaves the flap until it is too short to bind RPA and becomes a substrate for FEN1. It is also involved in 5-end resection of DNA during double-strand break (DSB) repair; it is recruited by BLM and mediates the cleavage of 5-ssDNA, while the 3-ssDNA cleavage is prevented by the presence of RPA. DNA2 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: 350799 [Multi-domain] Cd Length: 203 Bit Score: 375.42 E-value: 1.81e-123
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 626 GLNKPQRQAMKRVLLSKDYTLIVGMPGTGKTTTICALVRILSACGFSVLLTSYTHSAVDNILLKLAKFKVGFLRLGQSHK 705
Cdd:cd18041 1 GLNKDQRQAIKKVLNAKDYALILGMPGTGKTTTIAALVRILVALGKSVLLTSYTHSAVDNILLKLKKFGVNFLRLGRLKK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 706 VHPDIQKFTEEEIcrSRSIASLAHLEELYNSHPIVATTCMGINHPIFSRKTFDFCIVDEASQISQPVCLGPLFFSRRFVL 785
Cdd:cd18041 81 IHPDVQEFTLEAI--LKSCKSVEELESKYESVSVVATTCLGINHPIFRRRTFDYCIVDEASQITLPICLGPLRLAKKFVL 158
|
170 180 190 200
....*....|....*....|....*....|....*....|....*
gi 283837769 786 VGDHQQLPPLVVNREARALGMSESLFKRLERNE-SAVVQLTVQYR 829
Cdd:cd18041 159 VGDHYQLPPLVKSREARELGMDESLFKRLSEAHpDAVVQLTIQYR 203
|
|
| DNA2_N-like |
cd22318 |
Nuclease domain of the nuclease/helicase DNA2 and related nucleases; The eukaryotic nuclease ... |
127-366 |
1.39e-111 |
|
Nuclease domain of the nuclease/helicase DNA2 and related nucleases; The eukaryotic nuclease/helicase DNA2 processes double-strand breaks in DNA that have single-stranded ends/overhangs, as well as Okazaki fragments and stalled replication forks; it is therefore crucial for maintaining the integrity of the genome. The nuclease domain modeled here belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.
Pssm-ID: 411722 [Multi-domain] Cd Length: 234 Bit Score: 345.27 E-value: 1.39e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 127 SGTSVASSIRCLRRAVLSETFRGSDPATRQMLIGTILHEVFQKAISE-SFAPERLQELALQTLREVRHLKEMYRLNLSQD 205
Cdd:cd22318 1 SGTSVAGSLFCMRKAVLSERFRGIDPGNKAMLIGTILHELFQKALKNnIFSREKLEKLAEKLLQSPKYLEDLYALGLTEE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 206 EILCEVEEYLPSFSKWAEDFMRkgpsSEFPQMQLSLPSDGSnrsspCNIEVVKSLDIEESIWSPRFGLKGKIDVTVGVKI 285
Cdd:cd22318 81 EALEELEEYIPSIQEWAEKYVR----SNSPKGQVKLPSDGN-----SKGAISKILDIEENIWSPRFGLKGKIDATVEVKI 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 286 HRDCKMKYKVMPLELKTGKESNSIEHRSQVVLYTLLSQERRE-DPEAGWLLYLKTGQMYPVPANHLDKRELLKLRNWLAA 364
Cdd:cd22318 152 HDKGKSKTKIMPLELKTGRASFSIEHRGQVILYTLMMSDRYDvDVDSGLLLYLKEGEMKEVPAGRNEKRGLIILRNELAH 231
|
..
gi 283837769 365 SL 366
Cdd:cd22318 232 YL 233
|
|
| Dna2 |
pfam08696 |
DNA replication factor Dna2; Dna2 is a DNA replication factor with single-stranded ... |
72-283 |
3.21e-86 |
|
DNA replication factor Dna2; Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, ( 5'-flap endonuclease) and helicase activities. It is required for Okazaki fragment processing and is involved in DNA repair pathways.
Pssm-ID: 462565 Cd Length: 203 Bit Score: 276.37 E-value: 3.21e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 72 SQDREHEVLCILRNGWSSVPVEPGDIVHLEGDCTSEPWIIDDDFGYFILYPDMMISGTSVASSIRCLRRAVLSETFRGSD 151
Cdd:pfam08696 1 SDKSGETRTVILRDDWVETPVEPGDIIHIIGEFESGQCIIDNDSNLLILHPDILISATSVAGSFFCLRRAVLQERFKGSG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 152 PATRQMLIGTILHEVFQKAISE-SFAPERLQELALQTLRevRHLKEMYRLNLSQDEILCEVEEYLPSFSKWAEDFMRKGP 230
Cdd:pfam08696 81 ESSKPMLIGTILHELFQEALTAnDWDLEFLEELLDELLE--KYLEELYALGETEEEAKEELMEYLPNIQEWAQKYVKKSP 158
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 283837769 231 SSEFPQMqlslpsdgSNRSSPCNIEVVKSLDIEESIWSPRFGLKGKIDVTVGV 283
Cdd:pfam08696 159 KPNAVVE--------DGNGKKVKLSISKLLDIEENIWSPMYGLKGKIDATVEV 203
|
|
| AAA_12 |
pfam13087 |
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
806-1020 |
5.39e-71 |
|
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Pssm-ID: 463780 [Multi-domain] Cd Length: 196 Bit Score: 234.36 E-value: 5.39e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 806 MSESLFKRL-ERNESAVVQLTVQYRMNRKIMSLSNKLTYAGKLECGsdrvanavlalPNLKDARLslqlyadysdsPWLA 884
Cdd:pfam13087 1 LDRSLFERLqELGPSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKDG-----------PSVAERPL-----------PDDF 58
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 885 GVLEPDNPVCFLNTDKVPAPEQVENGGVSNVTEARLIVFLTSTFIKAGCSP-SDIGVIAPYRQQLRIISDLLARSSVG-- 961
Cdd:pfam13087 59 HLPDPLGPLVFIDVDGSEEEESDGGTSYSNEAEAELVVQLVEKLIKSGPEEpSDIGVITPYRAQVRLIRKLLKRKLGGkl 138
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*....
gi 283837769 962 MVEVNTVDKYQGRDKSLILVSFVRSNEDGTLGeLLKDWRRLNVALTRAKHKLILLGSVS 1020
Cdd:pfam13087 139 EIEVNTVDGFQGREKDVIIFSCVRSNEKGGIG-FLSDPRRLNVALTRAKRGLIIVGNAK 196
|
|
| TIGR00376 |
TIGR00376 |
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ... |
472-1034 |
1.52e-70 |
|
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273041 [Multi-domain] Cd Length: 636 Bit Score: 247.81 E-value: 1.52e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 472 ELEESGNCVGNL---VRTEPVsrvcdGQYLHNFQRKNGPmpATNLMAGDrIILSGEERKLFALSKGYVKKMNKAAVTCLL 548
Cdd:TIGR00376 21 QRERRGRAILNLqgkIRGGLL-----GFLLVRFGRRKAI--ATEISVGD-IVLVSRGNPLQSDLTGVVTRVGKRFITVAL 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 549 DRNLSTLPATTVfRLDREERHGDISTPLGNLSKLMEStdpSKRLRELIIDFREPQFIAYLSSVLPHDakdtvanilKGLN 628
Cdd:TIGR00376 93 EESVPQWSLKRV-RIDLYANDVTFKRMKEALRALTEN---HSRLLEFLLGREAPSKASEIHDFQFFD---------PNLN 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 629 KPQRQAMKRVLLSKDYTLIVGMPGTGKTTTICALVRILSACGFSVLLTSYTHSAVDNILLKLAKFKVGFLRLGQSHKV-- 706
Cdd:TIGR00376 160 ESQKEAVLFALSSKDLFLIHGPPGTGKTRTVVELIRQLVKRGLRVLVTAPSNIAVDNLLERLALCDQKIVRLGHPARLlk 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 707 -------------HPDIQK----------------------------FTEEEICR------------SRSIASLAH---- 729
Cdd:TIGR00376 240 snkqhsldylienHPKYQIvadirekidelieernkktkpspqkrrgLSDIKILRkalkkreargieSLKIASMAEwiet 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 730 -------LEELYNSHPIVATTCMGINHPIFSRKT--------FDFCIVDEASQISQPVCLGPLFFSRRFVLVGDHQQLPP 794
Cdd:TIGR00376 320 nksidrlLKLLPESEERIMNEILAESDATNSMAGseilngqyFDVAVIDEASQAMEPSCLIPLLKARKLILAGDHKQLPP 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 795 LVVNREARalGMSESLFKRL-ERNESAVVQLTVQYRMNRKIMSLSNKLTYAGKLecgsdrVANAVLAlpnlkdARLSLQL 873
Cdd:TIGR00376 400 TILSHDAE--ELSLTLFERLiKEYPERSRTLNVQYRMNQKIMEFPSREFYNGKL------TAHESVA------NILLRDL 465
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 874 YADYSDSpwLAGVLEPDNPVCFLNTDKVPAPEQVENGGVS--NVTEARLIVFLTSTFIKAGCSPSDIGVIAPYRQQLRII 951
Cdd:TIGR00376 466 PKVEATE--SEDDLETGIPLLFIDTSGCELFELKEADSTSkyNPGEAELVSEIIQALVKMGVPANDIGVITPYDAQVDLL 543
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 952 SDLLARSSVGmVEVNTVDKYQGRDKSLILVSFVRSNEDGTLGeLLKDWRRLNVALTRAKHKLILLGSVSSLKRFPPLGTL 1031
Cdd:TIGR00376 544 RQLLEHRHID-IEVSSVDGFQGREKEVIIISFVRSNRKGEVG-FLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKRL 621
|
...
gi 283837769 1032 FDH 1034
Cdd:TIGR00376 622 IEW 624
|
|
| DNA2 |
COG1112 |
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]; |
299-1035 |
2.00e-65 |
|
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
Pssm-ID: 440729 [Multi-domain] Cd Length: 819 Bit Score: 237.33 E-value: 2.00e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 299 ELKTGKESNSIEHRSQVVLYTLLSQERREDPEAGWLLYLKTGQMYPVPANHLDKRELLKLRNWLAASLLHRVSRAAPGEE 378
Cdd:COG1112 98 LLLLLLLLLLLAALLLALAALLLALALLLLALALLALLALLLAELLDLLAALAALAALLAALLLLLLLLAALLLLDLRLL 177
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 379 ARLSALPQIIEEEKTCKYCSQIGNCALYSRAVEEQGDDASIPEAMLSKIQEETRHLQLAHLKYFSLWCLMLTLESQSKDN 458
Cdd:COG1112 178 ALLELLLAAALALALLALLALALEDELALLLLLLLLALLLLLALLLLLDALLLLLAALALLALALLLALLLLLLALLLLA 257
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 459 RKTHQSIWLTPASELEESGNcvGNLVRTEPVSRVCDGQYLHNFQRKNGPMPATNLMAGDRIILSGEERKLFALSKGYVKK 538
Cdd:COG1112 258 ALALLRAALRLDLLAALELL--AALSLALLALLAALALALLLLAALALLLALALAALLALLALLALLAARLAAALAALLL 335
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 539 MNKAAVTCLLDRNLSTLPATTVFRLDREERHGDISTPLGNLSKLMESTDPSKRLRELIIDFREPQFIAYLSSVLPHDAKD 618
Cdd:COG1112 336 LLLLEELALLAALLLLLELALLRLLAALLLALALLLLLALEELLLLALLRLLAEGLALLLLLLLAALLRLARALLLLALL 415
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 619 TVANILKGLNKPQRQAMKRVLLSKDYTLIVGMPGTGKTTTICALVRILSACGFSVLLTSYTHSAVDNILL--KLAKFKVG 696
Cdd:COG1112 416 LAAAAAALAALLLLALALLAALLALLLLLAAALAALLALLLLLLLALAALLLLLAAAAALLALALLESLLeeLIEEHPEE 495
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 697 FLRLGQSHKVHPDIQKFTEEEICRSRSIASLAhLEELYNSHPIVATTCMGI-NHPIFSRKTFDFCIVDEASQISQPVCLG 775
Cdd:COG1112 496 LEKLIAELREAARLRRALRRELKKRRELRKLL-WDALLELAPVVGMTPASVaRLLPLGEGSFDLVIIDEASQATLAEALG 574
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 776 PLFFSRRFVLVGDHQQLPPLVVNREA---RALGMSESLFKRL-ERNESAVVQLTVQYRMNRKIMSLSNKLTYAGKLEcgs 851
Cdd:COG1112 575 ALARAKRVVLVGDPKQLPPVVFGEEAeevAEEGLDESLLDRLlARLPERGVMLREHYRMHPEIIAFSNRLFYDGKLV--- 651
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 852 drvanavlALPNLKDARLSlqlyadysdspwlagvlEPDNPVCFLNTDKVPAPeqvENGGVSNVTEARLIVFLTSTFIKA 931
Cdd:COG1112 652 --------PLPSPKARRLA-----------------DPDSPLVFIDVDGVYER---RGGSRTNPEEAEAVVELVRELLED 703
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 932 GCSPSDIGVIAPYRQQLRIISDLLARSSVGM---VEVNTVDKYQGRDKSLILVSFVRSNEDGTLGE---LLKDWRRLNVA 1005
Cdd:COG1112 704 GPDGESIGVITPYRAQVALIRELLREALGDGlepVFVGTVDRFQGDERDVIIFSLVYSNDEDVPRNfgfLNGGPRRLNVA 783
|
730 740 750
....*....|....*....|....*....|...
gi 283837769 1006 LTRAKHKLILLGSVSSLKRFP---PLGTLFDHL 1035
Cdd:COG1112 784 VSRARRKLIVVGSRELLDSDPstpALKRLLEYL 816
|
|
| SF1_C_Upf1 |
cd18808 |
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ... |
830-1035 |
4.58e-54 |
|
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), and similar proteins. They are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 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: 350195 [Multi-domain] Cd Length: 184 Bit Score: 186.29 E-value: 4.58e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 830 MNRKIMSLSNKLTYAGKLECGSDRVANavlalpnlkdarlslqlyadysdsPWLAGVLEPDNPVCFLNTDKvpaPEQVEN 909
Cdd:cd18808 1 MHPEISEFPSKLFYEGKLKAGVSVAAR------------------------LNPPPLPGPSKPLVFVDVSG---GEEREE 53
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 910 GGVS--NVTEARLIVFLTSTFIKAGCSPSDIGVIAPYRQQLRIISDLLARSSVGM--VEVNTVDKYQGRDKSLILVSFVR 985
Cdd:cd18808 54 SGTSksNEAEAELVVELVKYLLKSGVKPSSIGVITPYRAQVALIRELLRKRGGLLedVEVGTVDNFQGREKDVIILSLVR 133
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 283837769 986 SNEDGTLGELLKDWRRLNVALTRAKHKLILLGSVSSLKRFPPLGTLFDHL 1035
Cdd:cd18808 134 SNESGGSIGFLSDPRRLNVALTRAKRGLIIVGNPDTLSKDPLWKKLLEYL 183
|
|
| AAA_11 |
pfam13086 |
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
630-796 |
5.60e-28 |
|
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Pssm-ID: 404072 [Multi-domain] Cd Length: 248 Bit Score: 113.59 E-value: 5.60e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 630 PQRQAMKRVLLSKDYTLIVGMPGTGKTTTICALVRILSACGFS-------VLLTSYTHSAVDNILLKLA----KFKVGFL 698
Cdd:pfam13086 1 SQREAIRSALSSSHFTLIQGPPGTGKTTTIVELIRQLLSYPATsaaagprILVCAPSNAAVDNILERLLrkgqKYGPKIV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 699 RLGQSHKVHPDIQKFTEEEI---------------CRSRSIASLAHL--------------------------------- 730
Cdd:pfam13086 81 RIGHPAAISEAVLPVSLDYLvesklnneedaqivkDISKELEKLAKAlrafekeiivekllksrnkdkskleqerrklrs 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 731 -----------------EELYNSHPIVATTCMGINHPIFSRKT-FDFCIVDEASQISQPVCLGPLFF-SRRFVLVGDHQQ 791
Cdd:pfam13086 161 erkelrkelrrreqsleREILDEAQIVCSTLSGAGSRLLSSLAnFDVVIIDEAAQALEPSTLIPLLRgPKKVVLVGDPKQ 240
|
....*
gi 283837769 792 LPPLV 796
Cdd:pfam13086 241 LPPTV 245
|
|
| Cas4 |
COG1468 |
CRISPR/Cas system-associated exonuclease Cas4, RecB family [Defense mechanisms]; CRISPR/Cas ... |
255-398 |
1.36e-08 |
|
CRISPR/Cas system-associated exonuclease Cas4, RecB family [Defense mechanisms]; CRISPR/Cas system-associated exonuclease Cas4, RecB family is part of the Pathway/BioSystem: CRISPR-Cas system
Pssm-ID: 441077 [Multi-domain] Cd Length: 184 Bit Score: 55.74 E-value: 1.36e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 255 EVVKSLDIEESIWSPRFGLKGKIDVtvgVKIHRDckmkyKVMPLELKTGKESNSIEHRSQVVLYTLLSQERREDPEA-GW 333
Cdd:COG1468 50 KRLERLRREVPLDSERLGLTGKIDL---VEFEDG-----ELVPVEYKKSKPKPWEADRMQLCAYALLLEEMLGIPVPkGY 121
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 283837769 334 LLYLKTGQMYPVPanhLDKRELLKLRNWLAAslLHRVsraapgeeARLSALPQIIEEEKTCKYCS 398
Cdd:COG1468 122 LYYPEERKREEVE---LTEELREEVEEAIEE--IREI--------LESEKPPPPTKSKKKCKKCS 173
|
|
| cas4 |
TIGR00372 |
CRISPR-associated protein Cas4; This model represents a family of proteins associated with ... |
256-398 |
2.89e-07 |
|
CRISPR-associated protein Cas4; This model represents a family of proteins associated with CRISPR repeats in a wide set of prokaryotic genomes. This scope of this model has been broadened since it was first built to describe an archaeal subset only. The function of the protein is undefined. Distantly related proteins, excluded from this model, include ORFs from Mycobacteriophage D29 and Sulfolobus islandicus filamentous virus and a region of the Schizosaccharomyces pombe DNA replication helicase Dna2p.
Pssm-ID: 273040 [Multi-domain] Cd Length: 178 Bit Score: 51.64 E-value: 2.89e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 256 VVKSLD---IEESIW--SPRFGLKGKIDVtvgVKIHRDckmkyKVMPLELKTGKESNSIEHRSQVVLYTLLSQERREDPE 330
Cdd:TIGR00372 45 FLKSLGevrEEKEVPlkSKKYGLKGVIDI---VLEEDG-----ELVPVEVKSGKPSPREAHKYQLLAYAYLLEEMYGEIV 116
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 283837769 331 AGWLLYLKTGQMYPVPANHLDKRELLKLRNWLAASLLHRVsraapgeearlsaLPQIIEEEKTCKYCS 398
Cdd:TIGR00372 117 RGYILYINAGKKLEVEISEELRKKAVKLIEKIRELLEGGK-------------PPSPPKSGPKCKFCP 171
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
627-765 |
1.91e-05 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 46.72 E-value: 1.91e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 627 LNKPQRQAMKRVLLSKDYTLIVGMPGTGKTTTIC--ALVRILSACGFSVLLTSYTHSAVDNILLKLAKFkvgflrlgqsh 704
Cdd:smart00487 9 LRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALlpALEALKRGKGGRVLVLVPTRELAEQWAEELKKL----------- 77
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 283837769 705 kvhpdIQKFTEEEICRSRSIASLAHLEELYNSHP--IVATTCMGINHPI---FSRKTFDFCIVDEA 765
Cdd:smart00487 78 -----GPSLGLKVVGLYGGDSKREQLRKLESGKTdiLVTTPGRLLDLLEndkLSLSNVDLVILDEA 138
|
|
| ftsY |
TIGR00064 |
signal recognition particle-docking protein FtsY; There is a weak division between FtsY and ... |
572-675 |
1.04e-04 |
|
signal recognition particle-docking protein FtsY; There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein. [Protein fate, Protein and peptide secretion and trafficking]
Pssm-ID: 272883 [Multi-domain] Cd Length: 277 Bit Score: 45.33 E-value: 1.04e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 572 ISTPLGNLSKLMESTDPSKrLRELIIDfrepqfiAYLSSVLPHDAKDTVANILKGLNKPQrqamkrVLLskdytlIVGMP 651
Cdd:TIGR00064 27 IIEALKKELKGKKVKDAEK-LKEILKE-------YLKEILKEDLLKNTDLELIVEENKPN------VIL------FVGVN 86
|
90 100
....*....|....*....|....
gi 283837769 652 GTGKTTTICALVRILSACGFSVLL 675
Cdd:TIGR00064 87 GVGKTTTIAKLANKLKKQGKSVLL 110
|
|
| PRK14489 |
PRK14489 |
putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobA/MobB; ... |
596-684 |
2.29e-03 |
|
putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobA/MobB; Provisional
Pssm-ID: 237727 [Multi-domain] Cd Length: 366 Bit Score: 41.66 E-value: 2.29e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 596 IIDFREPQFIAYLSSVLPHDAkdtvaniLKGLNKPQRQAMKRVLLSKDYTL------IVGMPGTGKTTTICALVRILSAC 669
Cdd:PRK14489 160 LFDFFQRQRVRYVDLSTQKDA-------FFNVNTPEDLEQLRAIPDGTTTGappllgVVGYSGTGKTTLLEKLIPELIAR 232
|
90
....*....|....*
gi 283837769 670 GFSVLLTSYTHSAVD 684
Cdd:PRK14489 233 GYRIGLIKHSHHRVD 247
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| DEXXQc_DNA2 |
cd18041 |
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ... |
626-829 |
1.81e-123 |
|
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses different enzymatic activities, such as single-stranded DNA (ssDNA)-dependent ATPase, 5-3 helicase, and endonuclease activities, and is involved in DNA replication and DNA repair in the nucleus and mitochondrion. It is involved in Okazaki fragment processing by cleaving long flaps that escape FEN1: flaps that are longer than 27 nucleotides are coated by replication protein A complex (RPA), leading to recruit DNA2 which cleaves the flap until it is too short to bind RPA and becomes a substrate for FEN1. It is also involved in 5-end resection of DNA during double-strand break (DSB) repair; it is recruited by BLM and mediates the cleavage of 5-ssDNA, while the 3-ssDNA cleavage is prevented by the presence of RPA. DNA2 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: 350799 [Multi-domain] Cd Length: 203 Bit Score: 375.42 E-value: 1.81e-123
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 626 GLNKPQRQAMKRVLLSKDYTLIVGMPGTGKTTTICALVRILSACGFSVLLTSYTHSAVDNILLKLAKFKVGFLRLGQSHK 705
Cdd:cd18041 1 GLNKDQRQAIKKVLNAKDYALILGMPGTGKTTTIAALVRILVALGKSVLLTSYTHSAVDNILLKLKKFGVNFLRLGRLKK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 706 VHPDIQKFTEEEIcrSRSIASLAHLEELYNSHPIVATTCMGINHPIFSRKTFDFCIVDEASQISQPVCLGPLFFSRRFVL 785
Cdd:cd18041 81 IHPDVQEFTLEAI--LKSCKSVEELESKYESVSVVATTCLGINHPIFRRRTFDYCIVDEASQITLPICLGPLRLAKKFVL 158
|
170 180 190 200
....*....|....*....|....*....|....*....|....*
gi 283837769 786 VGDHQQLPPLVVNREARALGMSESLFKRLERNE-SAVVQLTVQYR 829
Cdd:cd18041 159 VGDHYQLPPLVKSREARELGMDESLFKRLSEAHpDAVVQLTIQYR 203
|
|
| DNA2_N-like |
cd22318 |
Nuclease domain of the nuclease/helicase DNA2 and related nucleases; The eukaryotic nuclease ... |
127-366 |
1.39e-111 |
|
Nuclease domain of the nuclease/helicase DNA2 and related nucleases; The eukaryotic nuclease/helicase DNA2 processes double-strand breaks in DNA that have single-stranded ends/overhangs, as well as Okazaki fragments and stalled replication forks; it is therefore crucial for maintaining the integrity of the genome. The nuclease domain modeled here belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.
Pssm-ID: 411722 [Multi-domain] Cd Length: 234 Bit Score: 345.27 E-value: 1.39e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 127 SGTSVASSIRCLRRAVLSETFRGSDPATRQMLIGTILHEVFQKAISE-SFAPERLQELALQTLREVRHLKEMYRLNLSQD 205
Cdd:cd22318 1 SGTSVAGSLFCMRKAVLSERFRGIDPGNKAMLIGTILHELFQKALKNnIFSREKLEKLAEKLLQSPKYLEDLYALGLTEE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 206 EILCEVEEYLPSFSKWAEDFMRkgpsSEFPQMQLSLPSDGSnrsspCNIEVVKSLDIEESIWSPRFGLKGKIDVTVGVKI 285
Cdd:cd22318 81 EALEELEEYIPSIQEWAEKYVR----SNSPKGQVKLPSDGN-----SKGAISKILDIEENIWSPRFGLKGKIDATVEVKI 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 286 HRDCKMKYKVMPLELKTGKESNSIEHRSQVVLYTLLSQERRE-DPEAGWLLYLKTGQMYPVPANHLDKRELLKLRNWLAA 364
Cdd:cd22318 152 HDKGKSKTKIMPLELKTGRASFSIEHRGQVILYTLMMSDRYDvDVDSGLLLYLKEGEMKEVPAGRNEKRGLIILRNELAH 231
|
..
gi 283837769 365 SL 366
Cdd:cd22318 232 YL 233
|
|
| Dna2 |
pfam08696 |
DNA replication factor Dna2; Dna2 is a DNA replication factor with single-stranded ... |
72-283 |
3.21e-86 |
|
DNA replication factor Dna2; Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, ( 5'-flap endonuclease) and helicase activities. It is required for Okazaki fragment processing and is involved in DNA repair pathways.
Pssm-ID: 462565 Cd Length: 203 Bit Score: 276.37 E-value: 3.21e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 72 SQDREHEVLCILRNGWSSVPVEPGDIVHLEGDCTSEPWIIDDDFGYFILYPDMMISGTSVASSIRCLRRAVLSETFRGSD 151
Cdd:pfam08696 1 SDKSGETRTVILRDDWVETPVEPGDIIHIIGEFESGQCIIDNDSNLLILHPDILISATSVAGSFFCLRRAVLQERFKGSG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 152 PATRQMLIGTILHEVFQKAISE-SFAPERLQELALQTLRevRHLKEMYRLNLSQDEILCEVEEYLPSFSKWAEDFMRKGP 230
Cdd:pfam08696 81 ESSKPMLIGTILHELFQEALTAnDWDLEFLEELLDELLE--KYLEELYALGETEEEAKEELMEYLPNIQEWAQKYVKKSP 158
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 283837769 231 SSEFPQMqlslpsdgSNRSSPCNIEVVKSLDIEESIWSPRFGLKGKIDVTVGV 283
Cdd:pfam08696 159 KPNAVVE--------DGNGKKVKLSISKLLDIEENIWSPMYGLKGKIDATVEV 203
|
|
| AAA_12 |
pfam13087 |
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
806-1020 |
5.39e-71 |
|
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Pssm-ID: 463780 [Multi-domain] Cd Length: 196 Bit Score: 234.36 E-value: 5.39e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 806 MSESLFKRL-ERNESAVVQLTVQYRMNRKIMSLSNKLTYAGKLECGsdrvanavlalPNLKDARLslqlyadysdsPWLA 884
Cdd:pfam13087 1 LDRSLFERLqELGPSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKDG-----------PSVAERPL-----------PDDF 58
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 885 GVLEPDNPVCFLNTDKVPAPEQVENGGVSNVTEARLIVFLTSTFIKAGCSP-SDIGVIAPYRQQLRIISDLLARSSVG-- 961
Cdd:pfam13087 59 HLPDPLGPLVFIDVDGSEEEESDGGTSYSNEAEAELVVQLVEKLIKSGPEEpSDIGVITPYRAQVRLIRKLLKRKLGGkl 138
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*....
gi 283837769 962 MVEVNTVDKYQGRDKSLILVSFVRSNEDGTLGeLLKDWRRLNVALTRAKHKLILLGSVS 1020
Cdd:pfam13087 139 EIEVNTVDGFQGREKDVIIFSCVRSNEKGGIG-FLSDPRRLNVALTRAKRGLIIVGNAK 196
|
|
| TIGR00376 |
TIGR00376 |
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ... |
472-1034 |
1.52e-70 |
|
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273041 [Multi-domain] Cd Length: 636 Bit Score: 247.81 E-value: 1.52e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 472 ELEESGNCVGNL---VRTEPVsrvcdGQYLHNFQRKNGPmpATNLMAGDrIILSGEERKLFALSKGYVKKMNKAAVTCLL 548
Cdd:TIGR00376 21 QRERRGRAILNLqgkIRGGLL-----GFLLVRFGRRKAI--ATEISVGD-IVLVSRGNPLQSDLTGVVTRVGKRFITVAL 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 549 DRNLSTLPATTVfRLDREERHGDISTPLGNLSKLMEStdpSKRLRELIIDFREPQFIAYLSSVLPHDakdtvanilKGLN 628
Cdd:TIGR00376 93 EESVPQWSLKRV-RIDLYANDVTFKRMKEALRALTEN---HSRLLEFLLGREAPSKASEIHDFQFFD---------PNLN 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 629 KPQRQAMKRVLLSKDYTLIVGMPGTGKTTTICALVRILSACGFSVLLTSYTHSAVDNILLKLAKFKVGFLRLGQSHKV-- 706
Cdd:TIGR00376 160 ESQKEAVLFALSSKDLFLIHGPPGTGKTRTVVELIRQLVKRGLRVLVTAPSNIAVDNLLERLALCDQKIVRLGHPARLlk 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 707 -------------HPDIQK----------------------------FTEEEICR------------SRSIASLAH---- 729
Cdd:TIGR00376 240 snkqhsldylienHPKYQIvadirekidelieernkktkpspqkrrgLSDIKILRkalkkreargieSLKIASMAEwiet 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 730 -------LEELYNSHPIVATTCMGINHPIFSRKT--------FDFCIVDEASQISQPVCLGPLFFSRRFVLVGDHQQLPP 794
Cdd:TIGR00376 320 nksidrlLKLLPESEERIMNEILAESDATNSMAGseilngqyFDVAVIDEASQAMEPSCLIPLLKARKLILAGDHKQLPP 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 795 LVVNREARalGMSESLFKRL-ERNESAVVQLTVQYRMNRKIMSLSNKLTYAGKLecgsdrVANAVLAlpnlkdARLSLQL 873
Cdd:TIGR00376 400 TILSHDAE--ELSLTLFERLiKEYPERSRTLNVQYRMNQKIMEFPSREFYNGKL------TAHESVA------NILLRDL 465
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 874 YADYSDSpwLAGVLEPDNPVCFLNTDKVPAPEQVENGGVS--NVTEARLIVFLTSTFIKAGCSPSDIGVIAPYRQQLRII 951
Cdd:TIGR00376 466 PKVEATE--SEDDLETGIPLLFIDTSGCELFELKEADSTSkyNPGEAELVSEIIQALVKMGVPANDIGVITPYDAQVDLL 543
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 952 SDLLARSSVGmVEVNTVDKYQGRDKSLILVSFVRSNEDGTLGeLLKDWRRLNVALTRAKHKLILLGSVSSLKRFPPLGTL 1031
Cdd:TIGR00376 544 RQLLEHRHID-IEVSSVDGFQGREKEVIIISFVRSNRKGEVG-FLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKRL 621
|
...
gi 283837769 1032 FDH 1034
Cdd:TIGR00376 622 IEW 624
|
|
| DNA2 |
COG1112 |
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]; |
299-1035 |
2.00e-65 |
|
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
Pssm-ID: 440729 [Multi-domain] Cd Length: 819 Bit Score: 237.33 E-value: 2.00e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 299 ELKTGKESNSIEHRSQVVLYTLLSQERREDPEAGWLLYLKTGQMYPVPANHLDKRELLKLRNWLAASLLHRVSRAAPGEE 378
Cdd:COG1112 98 LLLLLLLLLLLAALLLALAALLLALALLLLALALLALLALLLAELLDLLAALAALAALLAALLLLLLLLAALLLLDLRLL 177
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 379 ARLSALPQIIEEEKTCKYCSQIGNCALYSRAVEEQGDDASIPEAMLSKIQEETRHLQLAHLKYFSLWCLMLTLESQSKDN 458
Cdd:COG1112 178 ALLELLLAAALALALLALLALALEDELALLLLLLLLALLLLLALLLLLDALLLLLAALALLALALLLALLLLLLALLLLA 257
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 459 RKTHQSIWLTPASELEESGNcvGNLVRTEPVSRVCDGQYLHNFQRKNGPMPATNLMAGDRIILSGEERKLFALSKGYVKK 538
Cdd:COG1112 258 ALALLRAALRLDLLAALELL--AALSLALLALLAALALALLLLAALALLLALALAALLALLALLALLAARLAAALAALLL 335
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 539 MNKAAVTCLLDRNLSTLPATTVFRLDREERHGDISTPLGNLSKLMESTDPSKRLRELIIDFREPQFIAYLSSVLPHDAKD 618
Cdd:COG1112 336 LLLLEELALLAALLLLLELALLRLLAALLLALALLLLLALEELLLLALLRLLAEGLALLLLLLLAALLRLARALLLLALL 415
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 619 TVANILKGLNKPQRQAMKRVLLSKDYTLIVGMPGTGKTTTICALVRILSACGFSVLLTSYTHSAVDNILL--KLAKFKVG 696
Cdd:COG1112 416 LAAAAAALAALLLLALALLAALLALLLLLAAALAALLALLLLLLLALAALLLLLAAAAALLALALLESLLeeLIEEHPEE 495
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 697 FLRLGQSHKVHPDIQKFTEEEICRSRSIASLAhLEELYNSHPIVATTCMGI-NHPIFSRKTFDFCIVDEASQISQPVCLG 775
Cdd:COG1112 496 LEKLIAELREAARLRRALRRELKKRRELRKLL-WDALLELAPVVGMTPASVaRLLPLGEGSFDLVIIDEASQATLAEALG 574
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 776 PLFFSRRFVLVGDHQQLPPLVVNREA---RALGMSESLFKRL-ERNESAVVQLTVQYRMNRKIMSLSNKLTYAGKLEcgs 851
Cdd:COG1112 575 ALARAKRVVLVGDPKQLPPVVFGEEAeevAEEGLDESLLDRLlARLPERGVMLREHYRMHPEIIAFSNRLFYDGKLV--- 651
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 852 drvanavlALPNLKDARLSlqlyadysdspwlagvlEPDNPVCFLNTDKVPAPeqvENGGVSNVTEARLIVFLTSTFIKA 931
Cdd:COG1112 652 --------PLPSPKARRLA-----------------DPDSPLVFIDVDGVYER---RGGSRTNPEEAEAVVELVRELLED 703
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 932 GCSPSDIGVIAPYRQQLRIISDLLARSSVGM---VEVNTVDKYQGRDKSLILVSFVRSNEDGTLGE---LLKDWRRLNVA 1005
Cdd:COG1112 704 GPDGESIGVITPYRAQVALIRELLREALGDGlepVFVGTVDRFQGDERDVIIFSLVYSNDEDVPRNfgfLNGGPRRLNVA 783
|
730 740 750
....*....|....*....|....*....|...
gi 283837769 1006 LTRAKHKLILLGSVSSLKRFP---PLGTLFDHL 1035
Cdd:COG1112 784 VSRARRKLIVVGSRELLDSDPstpALKRLLEYL 816
|
|
| SF1_C_Upf1 |
cd18808 |
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ... |
830-1035 |
4.58e-54 |
|
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), and similar proteins. They are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 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: 350195 [Multi-domain] Cd Length: 184 Bit Score: 186.29 E-value: 4.58e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 830 MNRKIMSLSNKLTYAGKLECGSDRVANavlalpnlkdarlslqlyadysdsPWLAGVLEPDNPVCFLNTDKvpaPEQVEN 909
Cdd:cd18808 1 MHPEISEFPSKLFYEGKLKAGVSVAAR------------------------LNPPPLPGPSKPLVFVDVSG---GEEREE 53
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 910 GGVS--NVTEARLIVFLTSTFIKAGCSPSDIGVIAPYRQQLRIISDLLARSSVGM--VEVNTVDKYQGRDKSLILVSFVR 985
Cdd:cd18808 54 SGTSksNEAEAELVVELVKYLLKSGVKPSSIGVITPYRAQVALIRELLRKRGGLLedVEVGTVDNFQGREKDVIILSLVR 133
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 283837769 986 SNEDGTLGELLKDWRRLNVALTRAKHKLILLGSVSSLKRFPPLGTLFDHL 1035
Cdd:cd18808 134 SNESGGSIGFLSDPRRLNVALTRAKRGLIIVGNPDTLSKDPLWKKLLEYL 183
|
|
| DEXXQc_SMUBP2 |
cd18044 |
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ... |
627-829 |
4.07e-43 |
|
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, or IGHMBP2) is a 5' to 3' helicase that unwinds RNA and DNA duplexes in an ATP-dependent reaction. It is a DNA-binding protein specific to 5'-phosphorylated single-stranded guanine-rich sequence (5'-GGGCT-3') related to the immunoglobulin mu chain switch region. The IGHMBP2 gene is responsible for Charcot-Marie-Tooth disease (CMT) type 2S and spinal muscular atrophy with respiratory distress type 1 (SMARD1). It is also thought to play a role in frontotemporal dementia (FTD) with amyotrophic lateral sclerosis (ALS) and major depressive disorder (MDD). SMUBP2 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: 350802 [Multi-domain] Cd Length: 191 Bit Score: 155.46 E-value: 4.07e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 627 LNKPQRQAMKRVLLSKDYTLIVGMPGTGKTTTICALVRILSACGFSVLLTSYTHSAVDNILLKLAKFKVGFLRLGQSHKV 706
Cdd:cd18044 2 LNDSQKEAVKFALSQKDVALIHGPPGTGKTTTVVEIILQAVKRGEKVLACAPSNIAVDNLVERLVALKVKVVRIGHPARL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 707 HPDIQKFTEEEICRSRsiaslahleelynshpIVATTCMGINHPIFSRK-TFDFCIVDEASQISQPVCLGPLFFSRRFVL 785
Cdd:cd18044 82 LESVLDHSLDALVAAQ----------------VVLATNTGAGSRQLLPNeLFDVVVIDEAAQALEASCWIPLLKARRCIL 145
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 283837769 786 VGDHQQLPPLVVNREARALGMSESLFKRLER--NESAVVQLTVQYR 829
Cdd:cd18044 146 AGDHKQLPPTILSDKAARGGLGVTLFERLVNlyGESVVRMLTVQYR 191
|
|
| DEXXQc_SETX |
cd18042 |
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ... |
627-829 |
2.31e-36 |
|
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in transcription, neurogenesis, and antiviral response. SEXT is an R-loop-associated protein that is thought to function as an RNA/DNA helicase. R-loops consist of RNA/DNA hybrids, formed during transcription when nascent RNA hybridizes to the DNA template strand, displacing the non-template DNA strand. Mutations in SETX are linked to two neurodegenerative disorders: ataxia with oculomotor apraxia type 2 (AOA2) and amyotrophic lateral sclerosis type 4 (ALS4). S. cerevisiae homolog splicing endonuclease 1 (Sen1) is an exclusively nuclear protein, important for nucleolar organization. S. cerevisiae Sen1 and its ortholog, the Schizosaccharomyces pombe Sen1, share conserved domains and belong to the family I class of helicases. Both proteins translocate 5' to 3' and unwind both DNA and RNA duplexes and also RNA/DNA hybrids in vitro. SETX 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: 438712 [Multi-domain] Cd Length: 218 Bit Score: 136.96 E-value: 2.31e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 627 LNKPQRQAMKRVLL-SKDYTLIVGMPGTGKTTTICALV-RILSACGFS------------------------VLLTSYTH 680
Cdd:cd18042 1 LNESQLEAIASALQnSPGITLIQGPPGTGKTKTIVGILsVLLAGKYRKyyekvkkklrklqrnlnnkkkknrILVCAPSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 681 SAVDNILLKLAKfkvGFLRLGQSHKVHPDIQKFTEEEICRSrsIASLAHleelynshpIVATTCMGINHPIFSRKT--FD 758
Cdd:cd18042 81 AAVDEIVLRLLS---EGFLDGDGRSYKPNVVRVGRQELRAS--ILNEAD---------IVCTTLSSSGSDLLESLPrgFD 146
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 283837769 759 FCIVDEASQISQPVCLGPL-FFSRRFVLVGDHQQLPPLVVNREARALGMSESLFKRLERNESAVVQLTVQYR 829
Cdd:cd18042 147 TVIIDEAAQAVELSTLIPLrLGCKRLILVGDPKQLPATVFSKVAQKLGYDRSLFERLQLAGYPVLMLTTQYR 218
|
|
| DEXXQc_Upf1-like |
cd17934 |
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ... |
644-829 |
1.57e-34 |
|
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), coronavirus Nsp13, and similar proteins. They belong to 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: 438708 [Multi-domain] Cd Length: 121 Bit Score: 128.12 E-value: 1.57e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 644 YTLIVGMPGTGKTTTICALVRILSA--CGFSVLLTSYTHSAVDNIllklakfkvgflrlgqshkvhpdiqkfteeeicrs 721
Cdd:cd17934 1 ISLIQGPPGTGKTTTIAAIVLQLLKglRGKRVLVTAQSNVAVDNV----------------------------------- 45
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 722 rsiaslahleelynshpivattcmginhpifsrktfDFCIVDEASQISQPVCLGPLFFSRRFVLVGDHQQLPPLVVNREA 801
Cdd:cd17934 46 ------------------------------------DVVIIDEASQITEPELLIALIRAKKVVLVGDPKQLPPVVQEDHA 89
|
170 180 190
....*....|....*....|....*....|..
gi 283837769 802 RALG----MSESLFKRLERNESAVVQLTVQYR 829
Cdd:cd17934 90 ALLGlsfiLSLLLLFRLLLPGSPKVMLDTQYR 121
|
|
| DEXXQc_UPF1 |
cd18039 |
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ... |
627-829 |
3.26e-32 |
|
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of Nonsense Transcripts, or ATP-Dependent Helicase RENT1) is an RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. It is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. It is recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) located downstream from the termination codon through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Diseases associated with UPF1 include juvenile amyotrophic lateral sclerosis and epidermolysis bullosa, junctional, non-Herlitz type. UPF1 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: 350797 [Multi-domain] Cd Length: 234 Bit Score: 125.44 E-value: 3.26e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 627 LNKPQRQAMKRVLlSKDYTLIVGMPGTGKTTTICALVRILS-ACGFSVLLTSYTHSAVDNILLKLAKFKVGFLRL----- 700
Cdd:cd18039 2 LNHSQVDAVKTAL-QRPLSLIQGPPGTGKTVTSATIVYHLVkQGNGPVLVCAPSNVAVDQLTEKIHQTGLKVVRLcaksr 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 701 --------------------GQSHKVHPDIQKFTEEEICRS---RSIASLAHLE-ELYNSHPIVATTCMGINHPIFSRKT 756
Cdd:cd18039 81 eavespvsflalhnqvrnldSAEKLELLKLLKLETGELSSAdekRYRKLKRKAErELLRNADVICCTCVGAGDPRLSKMK 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 283837769 757 FDFCIVDEASQISQPVCLGPLFF-SRRFVLVGDHQQLPPLVVNREARALGMSESLFKRLERNESAVVQLTVQYR 829
Cdd:cd18039 161 FRTVLIDEATQATEPECLIPLVHgAKQVILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVQLGIRPIRLQVQYR 234
|
|
| AAA_11 |
pfam13086 |
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
630-796 |
5.60e-28 |
|
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Pssm-ID: 404072 [Multi-domain] Cd Length: 248 Bit Score: 113.59 E-value: 5.60e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 630 PQRQAMKRVLLSKDYTLIVGMPGTGKTTTICALVRILSACGFS-------VLLTSYTHSAVDNILLKLA----KFKVGFL 698
Cdd:pfam13086 1 SQREAIRSALSSSHFTLIQGPPGTGKTTTIVELIRQLLSYPATsaaagprILVCAPSNAAVDNILERLLrkgqKYGPKIV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 699 RLGQSHKVHPDIQKFTEEEI---------------CRSRSIASLAHL--------------------------------- 730
Cdd:pfam13086 81 RIGHPAAISEAVLPVSLDYLvesklnneedaqivkDISKELEKLAKAlrafekeiivekllksrnkdkskleqerrklrs 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 731 -----------------EELYNSHPIVATTCMGINHPIFSRKT-FDFCIVDEASQISQPVCLGPLFF-SRRFVLVGDHQQ 791
Cdd:pfam13086 161 erkelrkelrrreqsleREILDEAQIVCSTLSGAGSRLLSSLAnFDVVIIDEAAQALEPSTLIPLLRgPKKVVLVGDPKQ 240
|
....*
gi 283837769 792 LPPLV 796
Cdd:pfam13086 241 LPPTV 245
|
|
| DEXXQc_Helz-like |
cd18038 |
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ... |
627-829 |
3.76e-27 |
|
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and similar proteins. Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. All 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: 350796 [Multi-domain] Cd Length: 229 Bit Score: 110.79 E-value: 3.76e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 627 LNKPQRQAMKRVLLSKD----YtLIVGMPGTGKTTT----ICALVRILsaCGFSVLLTSYTHSAVDNILLKLAKFKVG-- 696
Cdd:cd18038 2 LNDEQKLAVRNIVTGTSrpppY-IIFGPPGTGKTVTlveaILQVLRQP--PEARILVCAPSNSAADLLAERLLNALVTkr 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 697 -FLRLG----QSHKVHPDIQKFTeeeICRSRSIASLAHLEELYnSHPIVATTCMGINHPI---FSRKTFDFCIVDEASQI 768
Cdd:cd18038 79 eILRLNapsrDRASVPPELLPYC---NSKAEGTFRLPSLEELK-KYRIVVCTLMTAGRLVqagVPNGHFTHIFIDEAGQA 154
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 283837769 769 SQPVCLGPLFFSR----RFVLVGDHQQLPPLVVNREARALGMSESLFKRL----------ERNESAVVQLTVQYR 829
Cdd:cd18038 155 TEPEALIPLSELAskntQIVLAGDPKQLGPVVRSPLARKYGLGKSLLERLmerplyykdgEYNPSYITKLLKNYR 229
|
|
| DEXXc_HELZ2-C |
cd18040 |
C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ... |
626-829 |
5.20e-18 |
|
C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known as PPAR-alpha-interacting complex protein 285 or PRIC285 and PPAR-gamma DBD-interacting protein 1 or PDIP1) acts as a transcriptional coactivator for a number of nuclear receptors including PPARA, PPARG, THRA, THRB and RXRA. It belongs to 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: 350798 [Multi-domain] Cd Length: 271 Bit Score: 85.27 E-value: 5.20e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 626 GLNKPQRQAMKRVLlSKDYTLIVGMPGTGKTTTICALV--------RILSACGFS-----VLLTSYTHSAVD---NILLK 689
Cdd:cd18040 1 KLNPSQNHAVRTAL-TKPFTLIQGPPGTGKTVTGVHIAywfakqnrEIQSVSGEGdggpcVLYCGPSNKSVDvvaELLLK 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 690 LAKFKV------------------------GFLRLGQSHKVHPDI----------------------------QKFTEEE 717
Cdd:cd18040 80 VPGLKIlrvyseqietteypipneprhpnkKSERESKPNSELSSItlhhrirqpsnphsqqikafearfertqEKITEED 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 718 ICRSRSIASLAHLEELyNSHPIVATTCMGINHPIFSRKT-FDFCIVDEASQISQPVCLGPL---FFSRRFVLVGDHQQLP 793
Cdd:cd18040 160 IKTYKILIWEARFEEL-ETVDVILCTCSEAASQKMRTHAnVKQCIVDECGMCTEPESLIPIvsaPRAEQVVLIGDHKQLR 238
|
250 260 270
....*....|....*....|....*....|....*.
gi 283837769 794 PLVVNREARALGMSESLFkrlERNESAVVQLTVQYR 829
Cdd:cd18040 239 PVVQNKEAQKLGLGRSLF---ERYAEKACMLDTQYR 271
|
|
| DEXXQc_Mov10L1 |
cd18078 |
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ... |
627-814 |
7.80e-18 |
|
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. Mov10L1 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: 350836 [Multi-domain] Cd Length: 230 Bit Score: 83.96 E-value: 7.80e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 627 LNKPQRQAMKRVLLSKDYTL---IVGMPGTGKTTTIC-ALVRILSACGFS-VLLTSYTHSAVDNILLKLAKFKVgfLRLG 701
Cdd:cd18078 2 LNELQKEAVKRILGGECRPLpyiLFGPPGTGKTVTIIeAILQVVYNLPRSrILVCAPSNSAADLVTSRLHESKV--LKPG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 702 QSHKVHPDIQkfTEEEICRSRsIASLAHLEELYNS--HPIVATTC--MGINHPI-FSRKTFDFCIVDEASQISQPVCLGP 776
Cdd:cd18078 80 DMVRLNAVNR--FESTVIDAR-KLYCRLGEDLSKAsrHRIVISTCstAGLLYQMgLPVGHFTHVFVDEAGQATEPESLIP 156
|
170 180 190 200
....*....|....*....|....*....|....*....|..
gi 283837769 777 L-FFSRR---FVLVGDHQQLPPLVVNREARALGMSESLFKRL 814
Cdd:cd18078 157 LgLISSRdgqIILAGDPMQLGPVIKSRLASAYGLGVSFLERL 198
|
|
| EEXXQc_AQR |
cd17935 |
EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds ... |
645-839 |
1.11e-17 |
|
EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds precursor-mRNA introns at a defined position and is part of a pentameric intron-binding complex (IBC). It 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: 350693 [Multi-domain] Cd Length: 207 Bit Score: 82.86 E-value: 1.11e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 645 TLIVGMPGTGKTTTICALVRIL--SACGFSVLLTSYTHSAVDNILLKLAK---FKVGFLRLGQSHKvhpdiqkfteeeic 719
Cdd:cd17935 23 TMVVGPPGTGKTDVAVQIISNLyhNFPNQRTLIVTHSNQALNQLFEKIMAldiDERHLLRLGHGAK-------------- 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 720 rsrsiaslahleelynshpIVATTCmgiNHPIFSRKTF---DFC----IVDEASQISQPVCLGPLFFSR---------RF 783
Cdd:cd17935 89 -------------------IIAMTC---THAALKRGELvelGFKydniLMEEAAQILEIETFIPLLLQNpedgpnrlkRL 146
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*..
gi 283837769 784 VLVGDHQQLPPLVVNREARALG-MSESLFKRLERNESAVVQLTVQYRMNRKIMSLSN 839
Cdd:cd17935 147 IMIGDHHQLPPVIKNMAFQKYSnMEQSLFTRLVRLGVPTVDLDAQGRARASISSLYN 203
|
|
| EEXXEc_NFX1 |
cd17936 |
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ... |
626-828 |
5.09e-17 |
|
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that represses class II MHC (major histocompatibility complex) gene expression. NFX1 binds a conserved cis-acting element, termed the X-box, in promoters of human class II MHC genes. The Cys-rich region contains several NFX1-type zinc finger domains. Frequently, a R3H domain is present in the C-terminus, and a RING finger domain and a PAM2 motif are present in the N-terminus. The lack of R3H and PAM2 motifs in the plant proteins indicates functional differences. Plant NFX1-like proteins are proposed to modulate growth and survival by coordinating reactive oxygen species, salicylic acid, further biotic stress and abscisic acid responses. A common feature of all members may be E3 ubiquitin ligase, due to the presence of a RING finger domain, as well as DNA binding. NFX1 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: 350694 [Multi-domain] Cd Length: 178 Bit Score: 79.90 E-value: 5.09e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 626 GLNKPQRQAMKRVLlSKDYTLIVGMPGTGKTTTICALVRIL-----SACGFSVLLTSYTHSAVDNILLKLAKFKVG-FLR 699
Cdd:cd17936 1 TLDPSQLEALKHAL-TSELALIQGPPGTGKTFLGVKLVRALlqnqdLSITGPILVVCYTNHALDQFLEGLLDFGPTkIVR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 700 LGqsHKVhpdiqkfteeeicrsrsIAslahleelynshpiVATTCMGINHPIFSRKTFDFCIVDEASQISQP---VCLGP 776
Cdd:cd17936 80 LG--ARV-----------------IG--------------MTTTGAAKYRELLQALGPKVVIVEEAAEVLEAhilAALTP 126
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 283837769 777 LFfsRRFVLVGDHQQLPPLVVNRE--ARALGMSESLFKRLERNESAVVQLTVQY 828
Cdd:cd17936 127 ST--EHLILIGDHKQLRPKVNVYEltAKKYNLDVSLFERLVKNGLPFVTLNVQR 178
|
|
| DEXXQc_SF1 |
cd18043 |
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ... |
628-800 |
1.18e-15 |
|
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. This is central to many aspects of cellular DNA and RNA metabolism and accordingly, they are implicated in a wide range of nucleic acid processing events including DNA replication, recombination, and repair as well as many aspects of RNA metabolism. Superfamily 1 helicases 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: 350801 [Multi-domain] Cd Length: 127 Bit Score: 74.54 E-value: 1.18e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 628 NKPQRQAMKRVLLSKDyTLIVGMPGTGKTTTICALVRILSACGFSVLLTSYTHSAVDNILLKlakfkvgflrlgqshkvh 707
Cdd:cd18043 1 DSSQEAAIISARNGKN-VVIQGPPGTGKSQTIANIIANALARGKRVLFVSEKKAALDVVRFP------------------ 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 708 pdiqkfteeeiCRSRSIASLAHLEELynshpivattcmginhpifSRKTFDFCIVDEASQISQPVCLGPLFFSRRFVLVG 787
Cdd:cd18043 62 -----------CWIMSPLSVSQYLPL-------------------NRNLFDLVIFDEASQIPIEEALPALFRGKQVVVVG 111
|
170
....*....|...
gi 283837769 788 DHQQLPPLVVNRE 800
Cdd:cd18043 112 DDKQLPPSILLRE 124
|
|
| RecD |
COG0507 |
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
627-1024 |
4.12e-15 |
|
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];
Pssm-ID: 440273 [Multi-domain] Cd Length: 514 Bit Score: 79.64 E-value: 4.12e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 627 LNKPQRQAMKRVLLSKDYTLIVGMPGTGKTTTICALVRILSACGFSVLLTSYTHSAVDNIllklakfkvgflrlgqshkv 706
Cdd:COG0507 125 LSDEQREAVALALTTRRVSVLTGGAGTGKTTTLRALLAALEALGLRVALAAPTGKAAKRL-------------------- 184
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 707 hpdiqkftEEEICR-SRSIASLahLEELYNSHPIVAttcmGINHPIFSRKTFdfcIVDEASQISQPVclgplfFSR---- 781
Cdd:COG0507 185 --------SESTGIeARTIHRL--LGLRPDSGRFRH----NRDNPLTPADLL---VVDEASMVDTRL------MAAllea 241
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 782 ------RFVLVGDHQQLPPlvVNREArALGMseslfkRLERNESAVVQLTVQYRM--NRKIMSLSNKLTyAGKLECGSDR 853
Cdd:COG0507 242 lpragaRLILVGDPDQLPS--VGAGA-VLRD------LIESGTVPVVELTEVYRQadDSRIIELAHAIR-EGDAPEALNA 311
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 854 VANAVLALPNLKDARLSLQLYADYSDSPWLAG---VLEPDNP-VCFLNT---DKVPAPEQVENGGVSNVTEA----RLIV 922
Cdd:COG0507 312 RYADVVFVEAEDAEEAAEAIVELYADRPAGGEdiqVLAPTNAgVDALNQairEALNPAGELERELAEDGELElyvgDRVM 391
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 923 FLT---STFIKAGcspsDIGV---IAPYRQQLRIISDLLARSSVGMVEVN--------TVDKYQGR--DKSLILVSfvrS 986
Cdd:COG0507 392 FTRndyDLGVFNG----DIGTvlsIDEDEGRLTVRFDGREIVTYDPSELDqlelayaiTVHKSQGStfDRVILVLP---S 464
|
410 420 430
....*....|....*....|....*....|....*...
gi 283837769 987 NEDGTLgellkDWRRLNVALTRAKHKLILLGSVSSLKR 1024
Cdd:COG0507 465 EHSPLL-----SRELLYTALTRARELLTLVGDRDALAR 497
|
|
| DEXSc_RecD-like |
cd17933 |
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ... |
631-794 |
5.91e-14 |
|
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD 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: 350691 [Multi-domain] Cd Length: 155 Bit Score: 70.28 E-value: 5.91e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 631 QRQAMKRVLLSKdYTLIVGMPGTGKTTTICALVRILSACGFSVLLTSYTHSAvdnillklAKfkvgflRLGQSHKVHpdi 710
Cdd:cd17933 2 QKAAVRLVLRNR-VSVLTGGAGTGKTTTLKALLAALEAEGKRVVLAAPTGKA--------AK------RLSESTGIE--- 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 711 qkfteeeicrSRSIASLAHLEELYNSHPIVATTCMginhpifsrkTFDFCIVDEASQISQPVclgplfFSR--------- 781
Cdd:cd17933 64 ----------ASTIHRLLGINPGGGGFYYNEENPL----------DADLLIVDEASMVDTRL------MAAllsaipaga 117
|
170
....*....|...
gi 283837769 782 RFVLVGDHQQLPP 794
Cdd:cd17933 118 RLILVGDPDQLPS 130
|
|
| SF1_C |
cd18786 |
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ... |
937-1017 |
1.43e-11 |
|
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Similar to SF2 helicases, they do not form toroidal, predominantly hexameric structures like SF3-6. SF1 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: 350173 [Multi-domain] Cd Length: 89 Bit Score: 61.68 E-value: 1.43e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 937 DIGVIAPYRQQLRIISDLLARSSV-----GMVEVNTVDKYQGRDKSLILVSFVRSNEDgtlgellkDWRRLNVALTRAKH 1011
Cdd:cd18786 12 KGVVLTPYHRDRAYLNQYLQGLSLdefdlQLVGAITIDSSQGLTFDVVTLYLPTANSL--------TPRRLYVALTRARK 83
|
....*.
gi 283837769 1012 KLILLG 1017
Cdd:cd18786 84 RLVIYD 89
|
|
| DEXXQc_HELZ |
cd18077 |
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that ... |
627-814 |
4.68e-11 |
|
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. HELZ is a member of the family I class of RNA helicases 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: 350835 [Multi-domain] Cd Length: 226 Bit Score: 63.66 E-value: 4.68e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 627 LNKPQRQAMKRVLLSKDYT----LIVGMPGTGKTTTICALVR-ILSACGFSVLLTSYTHSAVD-----------NILLKL 690
Cdd:cd18077 2 LNAKQKEAVLAITTPLSIQlppvLLIGPFGTGKTFTLAQAVKhILQQPETRILICTHSNSAADlyikeylhpyvETGNPR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 691 AKFKVGFLRLGQSHKVHPDIQKFTeeeICRSRSIASLAHLEELYNSHPIVAT--TCMGINHPIFSRKTFDFCIVDEASQI 768
Cdd:cd18077 82 ARPLRVYYRNRWVKTVHPVVQKYC---LIDEHGTFRMPTREDVMRHRVVVVTlsTSQYLCQLDLEPGFFTHILLDEAAQA 158
|
170 180 190 200
....*....|....*....|....*....|....*....|....*....
gi 283837769 769 SQPVCLGPLFF---SRRFVLVGDHQQLPPLVVNREARALGMSESLFKRL 814
Cdd:cd18077 159 MECEAIMPLALatkSTRIVLAGDHMQLSPEVYSEFARERNLHISLLERL 207
|
|
| AAA_30 |
pfam13604 |
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
626-794 |
2.36e-10 |
|
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
Pssm-ID: 433343 [Multi-domain] Cd Length: 191 Bit Score: 61.04 E-value: 2.36e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 626 GLNKPQRQAMKRVLLSKD-YTLIVGMPGTGKTTTICALVRILSACGFSVLLTSYTHSAVDnillklakfkvgflRLGQsh 704
Cdd:pfam13604 1 TLNAEQAAAVRALLTSGDrVAVLVGPAGTGKTTALKALREAWEAAGYRVIGLAPTGRAAK--------------VLGE-- 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 705 kvhpdiqkftEEEIcRSRSIASLAHLeelynshpivATTCMGINHPifsrktfDFCIVDEASQISQPVCLGplFFSR--- 781
Cdd:pfam13604 65 ----------ELGI-PADTIAKLLHR----------LGGRAGLDPG-------TLLIVDEAGMVGTRQMAR--LLKLaed 114
|
170
....*....|....*.
gi 283837769 782 ---RFVLVGDHQQLPP 794
Cdd:pfam13604 115 agaRVILVGDPRQLPS 130
|
|
| Cas4 |
COG1468 |
CRISPR/Cas system-associated exonuclease Cas4, RecB family [Defense mechanisms]; CRISPR/Cas ... |
255-398 |
1.36e-08 |
|
CRISPR/Cas system-associated exonuclease Cas4, RecB family [Defense mechanisms]; CRISPR/Cas system-associated exonuclease Cas4, RecB family is part of the Pathway/BioSystem: CRISPR-Cas system
Pssm-ID: 441077 [Multi-domain] Cd Length: 184 Bit Score: 55.74 E-value: 1.36e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 255 EVVKSLDIEESIWSPRFGLKGKIDVtvgVKIHRDckmkyKVMPLELKTGKESNSIEHRSQVVLYTLLSQERREDPEA-GW 333
Cdd:COG1468 50 KRLERLRREVPLDSERLGLTGKIDL---VEFEDG-----ELVPVEYKKSKPKPWEADRMQLCAYALLLEEMLGIPVPkGY 121
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 283837769 334 LLYLKTGQMYPVPanhLDKRELLKLRNWLAAslLHRVsraapgeeARLSALPQIIEEEKTCKYCS 398
Cdd:COG1468 122 LYYPEERKREEVE---LTEELREEVEEAIEE--IREI--------LESEKPPPPTKSKKKCKKCS 173
|
|
| AAA_19 |
pfam13245 |
AAA domain; |
631-794 |
9.64e-08 |
|
AAA domain;
Pssm-ID: 433059 [Multi-domain] Cd Length: 136 Bit Score: 51.84 E-value: 9.64e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 631 QRQAMKRVLLSKdYTLIVGMPGTGKTTTICALVRILSACG---FSVLLTSYTHSAVDNillkLAKfkvgflRLGQshkvh 707
Cdd:pfam13245 1 QREAVRTALPSK-VVLLTGGPGTGKTTTIRHIVALLVALGgvsFPILLAAPTGRAAKR----LSE------RTGL----- 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 708 pdiqkfteeeicRSRSIASLAHLeelynsHPIVATTCMGINHPIFSRKTFdfcIVDEASQISQPVC---LGPLFFSRRFV 784
Cdd:pfam13245 65 ------------PASTIHRLLGF------DDLEAGGFLRDEEEPLDGDLL---IVDEFSMVDLPLAyrlLKALPDGAQLL 123
|
170
....*....|
gi 283837769 785 LVGDHQQLPP 794
Cdd:pfam13245 124 LVGDPDQLPS 133
|
|
| DExxQc_SF1-N |
cd17914 |
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ... |
645-828 |
2.63e-07 |
|
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. 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. SF1 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: 438706 [Multi-domain] Cd Length: 121 Bit Score: 50.56 E-value: 2.63e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 645 TLIVGMPGTGKTTT----ICALVRILSACGFSVLLTSYTHSAVDNillklakfkvgflrlgqshkvhpdiqkfteeeicr 720
Cdd:cd17914 2 SLIQGPPGTGKTRVlvkiVAALMQNKNGEPGRILLVTPTNKAAAQ----------------------------------- 46
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 721 srsiaslahleelynshpivattcmginhpifsrktFDFCIVDEASQISQPVCLGP-LFFSR--RFVLVGDHQQLPPLVV 797
Cdd:cd17914 47 ------------------------------------LDNILVDEAAQILEPETSRLiDLALDqgRVILVGDHDQLGPVWR 90
|
170 180 190
....*....|....*....|....*....|.
gi 283837769 798 NREARALGMSESLFKRLERNESAVVQLTVQY 828
Cdd:cd17914 91 GAVLAKICNEQSLFTRLVRLGVSLIRLQVQY 121
|
|
| cas4 |
TIGR00372 |
CRISPR-associated protein Cas4; This model represents a family of proteins associated with ... |
256-398 |
2.89e-07 |
|
CRISPR-associated protein Cas4; This model represents a family of proteins associated with CRISPR repeats in a wide set of prokaryotic genomes. This scope of this model has been broadened since it was first built to describe an archaeal subset only. The function of the protein is undefined. Distantly related proteins, excluded from this model, include ORFs from Mycobacteriophage D29 and Sulfolobus islandicus filamentous virus and a region of the Schizosaccharomyces pombe DNA replication helicase Dna2p.
Pssm-ID: 273040 [Multi-domain] Cd Length: 178 Bit Score: 51.64 E-value: 2.89e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 256 VVKSLD---IEESIW--SPRFGLKGKIDVtvgVKIHRDckmkyKVMPLELKTGKESNSIEHRSQVVLYTLLSQERREDPE 330
Cdd:TIGR00372 45 FLKSLGevrEEKEVPlkSKKYGLKGVIDI---VLEEDG-----ELVPVEVKSGKPSPREAHKYQLLAYAYLLEEMYGEIV 116
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 283837769 331 AGWLLYLKTGQMYPVPANHLDKRELLKLRNWLAASLLHRVsraapgeearlsaLPQIIEEEKTCKYCS 398
Cdd:TIGR00372 117 RGYILYINAGKKLEVEISEELRKKAVKLIEKIRELLEGGK-------------PPSPPKSGPKCKFCP 171
|
|
| Cas4_I-A_I-B_I-C_I-D_II-B |
cd09637 |
CRISPR/Cas system-associated protein Cas4; CRISPR (Clustered Regularly Interspaced Short ... |
262-358 |
9.19e-06 |
|
CRISPR/Cas system-associated protein Cas4; 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; Cas4 is RecB-like nuclease with three-cysteine C-terminal cluster
Pssm-ID: 187768 [Multi-domain] Cd Length: 178 Bit Score: 47.43 E-value: 9.19e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 262 IEESIW--SPRFGLKGKIDVTVGVKihrdckmKYKVmPLELKTGKESNSIE-HRSQVVLYTLLSQERREDPEA-GWLLYL 337
Cdd:cd09637 54 EEKEVPlkSKKYGLKGVIDIVLKED-------GELV-PVEVKSGRAGSPREaHKLQLVAYAYLLEEMYGKRVArGYIVYL 125
|
90 100
....*....|....*....|.
gi 283837769 338 KTGQMYPVPANHLDKRELLKL 358
Cdd:cd09637 126 EGGKRLEVEISEELRKKAEKL 146
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
627-765 |
1.91e-05 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 46.72 E-value: 1.91e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 627 LNKPQRQAMKRVLLSKDYTLIVGMPGTGKTTTIC--ALVRILSACGFSVLLTSYTHSAVDNILLKLAKFkvgflrlgqsh 704
Cdd:smart00487 9 LRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALlpALEALKRGKGGRVLVLVPTRELAEQWAEELKKL----------- 77
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 283837769 705 kvhpdIQKFTEEEICRSRSIASLAHLEELYNSHP--IVATTCMGINHPI---FSRKTFDFCIVDEA 765
Cdd:smart00487 78 -----GPSLGLKVVGLYGGDSKREQLRKLESGKTdiLVTTPGRLLDLLEndkLSLSNVDLVILDEA 138
|
|
| DEXXQc_HELZ2-N |
cd18076 |
N-terminal DEXXQ-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ... |
646-794 |
4.46e-05 |
|
N-terminal DEXXQ-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known as PPAR-alpha-interacting complex protein 285 or PRIC285 and PPAR-gamma DBD-interacting protein 1 or PDIP1) acts as a transcriptional coactivator for a number of nuclear receptors including PPARA, PPARG, THRA, THRB, and RXRA. It belongs to 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: 350834 [Multi-domain] Cd Length: 230 Bit Score: 46.04 E-value: 4.46e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 646 LIVGMPGTGKTTTIC-ALVRILSACGFSVLLTSYTHSAVDnilLKLAKFKVGFLRLGQSHKV--------HPDIQKFTEE 716
Cdd:cd18076 27 LIYGPFGTGKTFTLAmAALEVIREPGTKVLICTHTNSAAD---IYIREYFHPYVDKGHPEARplrikatdRPNAITDPDT 103
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 717 EI--CRSRSIASLAH-LEELYNSHPIVATTCMGINHPIFSRKTFDFCIVDEASQISQPVCLGPLF---FSRRFVLVGDHQ 790
Cdd:cd18076 104 ITycCLTKDRQCFRLpTRDELDFHNIVITTTAMAFNLHVLSGFFTHIFIDEAAQMLECEALIPLSyagPKTRVVLAGDHM 183
|
....
gi 283837769 791 QLPP 794
Cdd:cd18076 184 QMTP 187
|
|
| ftsY |
TIGR00064 |
signal recognition particle-docking protein FtsY; There is a weak division between FtsY and ... |
572-675 |
1.04e-04 |
|
signal recognition particle-docking protein FtsY; There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein. [Protein fate, Protein and peptide secretion and trafficking]
Pssm-ID: 272883 [Multi-domain] Cd Length: 277 Bit Score: 45.33 E-value: 1.04e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 572 ISTPLGNLSKLMESTDPSKrLRELIIDfrepqfiAYLSSVLPHDAKDTVANILKGLNKPQrqamkrVLLskdytlIVGMP 651
Cdd:TIGR00064 27 IIEALKKELKGKKVKDAEK-LKEILKE-------YLKEILKEDLLKNTDLELIVEENKPN------VIL------FVGVN 86
|
90 100
....*....|....*....|....
gi 283837769 652 GTGKTTTICALVRILSACGFSVLL 675
Cdd:TIGR00064 87 GVGKTTTIAKLANKLKKQGKSVLL 110
|
|
| MobB |
COG1763 |
Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme transport and metabolism]; ... |
647-673 |
1.13e-03 |
|
Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme transport and metabolism]; Molybdopterin-guanine dinucleotide biosynthesis protein is part of the Pathway/BioSystem: Molybdopterin biosynthesis
Pssm-ID: 441369 [Multi-domain] Cd Length: 162 Bit Score: 40.93 E-value: 1.13e-03
10 20
....*....|....*....|....*..
gi 283837769 647 IVGMPGTGKTTTICALVRILSACGFSV 673
Cdd:COG1763 6 IVGYSGSGKTTLLEKLIPELKARGLRV 32
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
590-765 |
2.27e-03 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 41.93 E-value: 2.27e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 590 KRLRELIIDFREPQFIAYLSSVLPHDAKDTVANILKGLNKPQRQAMKRVLL----SKDYTLIVGMPGTGKTTTICALVRI 665
Cdd:COG1061 44 EGTREDGRRLPEEDTERELAEAEALEAGDEASGTSFELRPYQQEALEALLAalerGGGRGLVVAPTGTGKTVLALALAAE 123
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 666 LSACGfSVLLTSYTHSAVDNILLKLAKFKVGFLRLGQSHKVHPDIQkfteeeICRSRSIASLAHLEELynshpivattcm 745
Cdd:COG1061 124 LLRGK-RVLVLVPRRELLEQWAEELRRFLGDPLAGGGKKDSDAPIT------VATYQSLARRAHLDEL------------ 184
|
170 180
....*....|....*....|
gi 283837769 746 ginhpifsRKTFDFCIVDEA 765
Cdd:COG1061 185 --------GDRFGLVIIDEA 196
|
|
| PRK14489 |
PRK14489 |
putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobA/MobB; ... |
596-684 |
2.29e-03 |
|
putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobA/MobB; Provisional
Pssm-ID: 237727 [Multi-domain] Cd Length: 366 Bit Score: 41.66 E-value: 2.29e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 596 IIDFREPQFIAYLSSVLPHDAkdtvaniLKGLNKPQRQAMKRVLLSKDYTL------IVGMPGTGKTTTICALVRILSAC 669
Cdd:PRK14489 160 LFDFFQRQRVRYVDLSTQKDA-------FFNVNTPEDLEQLRAIPDGTTTGappllgVVGYSGTGKTTLLEKLIPELIAR 232
|
90
....*....|....*
gi 283837769 670 GFSVLLTSYTHSAVD 684
Cdd:PRK14489 233 GYRIGLIKHSHHRVD 247
|
|
| AAA |
cd00009 |
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ... |
646-710 |
2.88e-03 |
|
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
Pssm-ID: 99707 [Multi-domain] Cd Length: 151 Bit Score: 39.44 E-value: 2.88e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 283837769 646 LIVGMPGTGKTTTICALVRILSACGFSVLLTSYTHSAVDNILLKLAKFKVGFLRLGQSHKVHPDI 710
Cdd:cd00009 23 LLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKPGV 87
|
|
| FtsY |
cd17874 |
signal recognition particle receptor FtsY; FtsY, the bacterial signal-recognition particle ... |
646-675 |
6.57e-03 |
|
signal recognition particle receptor FtsY; FtsY, the bacterial signal-recognition particle (SRP) receptor (SR), is homologous to the SRP receptor alpha-subunit (SRalpha) of the eukaryotic SR. It interacts with the signal-recognition particle (SRP) and is required for the co-translational membrane targeting of proteins.
Pssm-ID: 349783 Cd Length: 199 Bit Score: 39.09 E-value: 6.57e-03
10 20 30
....*....|....*....|....*....|
gi 283837769 646 LIVGMPGTGKTTTICALVRILSACGFSVLL 675
Cdd:cd17874 4 LFVGVNGVGKTTTIGKLAHYLKNQGKKVVL 33
|
|
| DEXHc_RE_I_III_res |
cd18032 |
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
627-765 |
8.43e-03 |
|
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs 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: 350790 [Multi-domain] Cd Length: 163 Bit Score: 38.31 E-value: 8.43e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 283837769 627 LNKPQRQAMKRVLLS----KDYTLIVgMP-GTGKTTTICALV-RILSACGFS-VLLTsyTHSavdNILLKLAK--FKvGF 697
Cdd:cd18032 1 PRYYQQEAIEALEEArekgQRRALLV-MAtGTGKTYTAAFLIkRLLEANRKKrILFL--AHR---EELLEQAErsFK-EV 73
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 283837769 698 LRLGQSHKVHPDIQKFTEEEICRSrSIASLAHLEELYnshpivattcmginhpIFSRKTFDFCIVDEA 765
Cdd:cd18032 74 LPDGSFGNLKGGKKKPDDARVVFA-TVQTLNKRKRLE----------------KFPPDYFDLIIIDEA 124
|
|
| TrwB_TraG_TraD_VirD4 |
cd01127 |
TrwB/TraG/TraD/VirD4 family of bacterial conjugation proteins; The TraG/TraD/VirD4 family are ... |
645-677 |
9.11e-03 |
|
TrwB/TraG/TraD/VirD4 family of bacterial conjugation proteins; The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion (T4S) systems, versatile bacterial secretion systems mediating transport of protein and/or DNA. They are present in gram-negative and gram-positive bacteria, as well as archaea. They form hexameric rings and belong to the RecA-like NTPases superfamily, which also includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases.
Pssm-ID: 410871 [Multi-domain] Cd Length: 144 Bit Score: 37.97 E-value: 9.11e-03
10 20 30
....*....|....*....|....*....|...
gi 283837769 645 TLIVGMPGTGKTTTICALVRILSACGFSVLLTS 677
Cdd:cd01127 2 TLVLGTTGSGKTTSIVIPLLDQAARGGSVIITD 34
|
|
| UvrD |
COG0210 |
Superfamily I DNA or RNA helicase [Replication, recombination and repair]; |
622-682 |
9.97e-03 |
|
Superfamily I DNA or RNA helicase [Replication, recombination and repair];
Pssm-ID: 439980 [Multi-domain] Cd Length: 721 Bit Score: 39.92 E-value: 9.97e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 283837769 622 NILKGLNKPQRQAmkrVLLSKDYTLIVGMPGTGKTTTI-CALVRILSACG---FSVLLTSYTHSA 682
Cdd:COG0210 2 DLLAGLNPEQRAA---VEHPEGPLLVLAGAGSGKTRVLtHRIAYLIAEGGvdpEQILAVTFTNKA 63
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|
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