|
Name |
Accession |
Description |
Interval |
E-value |
| DEXXQc_DNA2 |
cd18041 |
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ... |
636-836 |
7.08e-102 |
|
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: 319.18 E-value: 7.08e-102
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 636 NLNKVQQNAALRALTTSSHLLIKGLPGTGKTQTLVALVRLLHLLGKSVLITAQTHSAVDNLIMRLLPFGLPMMRLGSGSR 715
Cdd:cd18041 1 GLNKDQRQAIKKVLNAKDYALILGMPGTGKTTTIAALVRILVALGKSVLLTSYTHSAVDNILLKLKKFGVNFLRLGRLKK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 716 IHKQLEEISEERLTKDCKTVEELEKALGQPSIVGVTCLGCGHPLFQRRQFDYCIVDEATQVLQPTVLRPLIHCSKFVLVG 795
Cdd:cd18041 81 IHPDVQEFTLEAILKSCKSVEELESKYESVSVVATTCLGINHPIFRRRTFDYCIVDEASQITLPICLGPLRLAKKFVLVG 160
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 24640932 796 DPEQLPPIVRSKEARQRGADETLFQRLDSE--KATAVLSLQYR 836
Cdd:cd18041 161 DHYQLPPLVKSREARELGMDESLFKRLSEAhpDAVVQLTIQYR 203
|
|
| DNA2_N-like |
cd22318 |
Nuclease domain of the nuclease/helicase DNA2 and related nucleases; The eukaryotic nuclease ... |
153-378 |
1.62e-91 |
|
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: 292.50 E-value: 1.62e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 153 SGTTVTGSLFCKRKSVLQERFRGLDSGNSVMVIGTLVHELLQKVLRQKLFDKKHIQSALQEMLASSSLAHLLYASNLIQV 232
Cdd:cd22318 1 SGTSVAGSLFCMRKAVLSERFRGIDPGNKAMLIGTILHELFQKALKNNIFSREKLEKLAEKLLQSPKYLEDLYALGLTEE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 233 EMEDHLMKFIDPIVSFVAQYVKGEPPSVLLP----EVYRGQIHEICDIEENLWVPQLGLKGKVDVSVKVKNQRQ---REE 305
Cdd:cd22318 81 EALEELEEYIPSIQEWAEKYVRSNSPKGQVKlpsdGNSKGAISKILDIEENIWSPRFGLKGKIDATVEVKIHDKgksKTK 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24640932 306 IIPLELKTGRASFSMEHKGQLLLYQLMHSAQGR-DTQSGLLLYLKEGLLREVASGRNEQRDLLMLRNDLAYWLT 378
Cdd:cd22318 161 IMPLELKTGRASFSIEHRGQVILYTLMMSDRYDvDVDSGLLLYLKEGEMKEVPAGRNEKRGLIILRNELAHYLS 234
|
|
| Dna2 |
pfam08696 |
DNA replication factor Dna2; Dna2 is a DNA replication factor with single-stranded ... |
96-297 |
1.07e-71 |
|
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: 237.08 E-value: 1.07e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 96 SGGDPETADCQLLPPWNCMPMQVGDTVSLLGKWDPsaGCYVVDKEQGYCVSHPDFLISGTTVTGSLFCKRKSVLQERFRG 175
Cdd:pfam08696 1 SDKSGETRTVILRDDWVETPVEPGDIIHIIGEFES--GQCIIDNDSNLLILHPDILISATSVAGSFFCLRRAVLQERFKG 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 176 LDSGNSVMVIGTLVHELLQKVLRQKLFDKKHIQSALQEMLasSSLAHLLYASNLIQVEMEDHLMKFIDPIVSFVAQYVKG 255
Cdd:pfam08696 79 SGESSKPMLIGTILHELFQEALTANDWDLEFLEELLDELL--EKYLEELYALGETEEEAKEELMEYLPNIQEWAQKYVKK 156
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 24640932 256 EPPSVLLPE-----VYRGQIHEICDIEENLWVPQLGLKGKVDVSVKV 297
Cdd:pfam08696 157 SPKPNAVVEdgngkKVKLSISKLLDIEENIWSPMYGLKGKIDATVEV 203
|
|
| AAA_12 |
pfam13087 |
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
815-1055 |
2.19e-49 |
|
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: 173.50 E-value: 2.19e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 815 DETLFQRLDSEKATAV--LSLQYRMNKTITRLANELTYGGDLKCASDevsgarfevelLNEAPRWVQRALTTHLEQaVTL 892
Cdd:pfam13087 2 DRSLFERLQELGPSAVvmLDTQYRMHPEIMEFPSKLFYGGKLKDGPS-----------VAERPLPDDFHLPDPLGP-LVF 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 893 INTGDCLERcqefvyasqrlvdtcssieqsfsedkdEIRKLTSkkrvskYTNYCEAGIVMHLLRYLLKSGYEA-SRIGVI 971
Cdd:pfam13087 70 IDVDGSEEE---------------------------ESDGGTS------YSNEAEAELVVQLVEKLIKSGPEEpSDIGVI 116
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 972 APYRAQVELFKKLASKLDT---DLECNTVDQFQGRDKNLIIYSCSktggdfsdmeRSREAE---ILEDQRRLTVAITRAK 1045
Cdd:pfam13087 117 TPYRAQVRLIRKLLKRKLGgklEIEVNTVDGFQGREKDVIIFSCV----------RSNEKGgigFLSDPRRLNVALTRAK 186
|
250
....*....|
gi 24640932 1046 NKLILLGDIK 1055
Cdd:pfam13087 187 RGLIIVGNAK 196
|
|
| DNA2 |
COG1112 |
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]; |
438-1070 |
5.38e-49 |
|
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
Pssm-ID: 440729 [Multi-domain] Cd Length: 819 Bit Score: 188.03 E-value: 5.38e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 438 PQLLEHLSEADHAYVQHWCGLLALEEQHNRQSSHVRSFWTKDPAEREKEGIAIRHLKLVKGQEVILEEGRYRQTLELGEE 517
Cdd:COG1112 229 LLLLAALALLALALLLALLLLLLALLLLAALALLRAALRLDLLAALELLAALSLALLALLAALALALLLLAALALLLALA 308
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 518 ADPSRDLSLSGFDLGEYVVISSTSRLAVAAGFIVSIEARRLDLRLERDLSQRYSEETFIIDKHDSQSFATFNFTNLGMLL 597
Cdd:COG1112 309 LAALLALLALLALLAARLAAALAALLLLLLLEELALLAALLLLLELALLRLLAALLLALALLLLLALEELLLLALLRLLA 388
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 598 SEGERFQELRDIIVAKKPPEQHKVLPKIILTKGAPILLNLNKVQQNAALRALTTSSHLLIKGLPGTGKTQTLVALVRLLH 677
Cdd:COG1112 389 EGLALLLLLLLAALLRLARALLLLALLLAAAAAALAALLLLALALLAALLALLLLLAAALAALLALLLLLLLALAALLLL 468
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 678 LLGKSVLITAQTHSAVDNLIMRLLPFGLPMMR--LGSGSRIHKQLEEISEERltkdcKTVEEL--EKALGQPSIVGVTCL 753
Cdd:COG1112 469 LAAAAALLALALLESLLEELIEEHPEELEKLIaeLREAARLRRALRRELKKR-----RELRKLlwDALLELAPVVGMTPA 543
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 754 GCGHPL-FQRRQFDYCIVDEATQVLQPTVLRPLIHCSKFVLVGDPEQLPPIV---RSKEARQRGADETLFQRLDSEKATA 829
Cdd:COG1112 544 SVARLLpLGEGSFDLVIIDEASQATLAEALGALARAKRVVLVGDPKQLPPVVfgeEAEEVAEEGLDESLLDRLLARLPER 623
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 830 VLSL--QYRMNKTITRLANELTYGGDLKCAsdevsgarfevellneapRWVQRALTTHLEQAVTLINTGDCLERcqefvy 907
Cdd:COG1112 624 GVMLreHYRMHPEIIAFSNRLFYDGKLVPL------------------PSPKARRLADPDSPLVFIDVDGVYER------ 679
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 908 asqrlvdtcssieqsfsedkdeirkltskkRVSKYTNYCEAGIVMHLLRYLLKSGYEASRIGVIAPYRAQVELFKKL--- 984
Cdd:COG1112 680 ------------------------------RGGSRTNPEEAEAVVELVRELLEDGPDGESIGVITPYRAQVALIRELlre 729
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 985 -ASKLDTDLECNTVDQFQGRDKNLIIYScskTGGDFSDMERSREAEILEDQRRLTVAITRAKNKLILLGDIKCLEQ---Y 1060
Cdd:COG1112 730 aLGDGLEPVFVGTVDRFQGDERDVIIFS---LVYSNDEDVPRNFGFLNGGPRRLNVAVSRARRKLIVVGSRELLDSdpsT 806
|
650
....*....|
gi 24640932 1061 GPFRQLFKHI 1070
Cdd:COG1112 807 PALKRLLEYL 816
|
|
| SF1_C_Upf1 |
cd18808 |
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ... |
837-1070 |
2.12e-38 |
|
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: 141.60 E-value: 2.12e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 837 MNKTITRLANELTYGGDLKCASDEVSGARFEVELLNEAPrwvqraltthleqaVTLINTGDCLERCQEfvyasqrlvdtc 916
Cdd:cd18808 1 MHPEISEFPSKLFYEGKLKAGVSVAARLNPPPLPGPSKP--------------LVFVDVSGGEEREES------------ 54
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 917 ssieqSFSedkdeirkltskkrvskYTNYCEAGIVMHLLRYLLKSGYEASRIGVIAPYRAQVELFKKLASK---LDTDLE 993
Cdd:cd18808 55 -----GTS-----------------KSNEAEAELVVELVKYLLKSGVKPSSIGVITPYRAQVALIRELLRKrggLLEDVE 112
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24640932 994 CNTVDQFQGRDKNLIIYSCSKTGgdfsdmERSREAEILEDQRRLTVAITRAKNKLILLGDIKCLEQYGPFRQLFKHI 1070
Cdd:cd18808 113 VGTVDNFQGREKDVIILSLVRSN------ESGGSIGFLSDPRRLNVALTRAKRGLIIVGNPDTLSKDPLWKKLLEYL 183
|
|
| AAA_11 |
pfam13086 |
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
641-807 |
1.18e-30 |
|
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: 121.68 E-value: 1.18e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 641 QQNAALRALTTSSHLLIKGLPGTGKTQTLVALVRLLHL-------LGKSVLITAQTHSAVDNLIMRLLP----FGLPMMR 709
Cdd:pfam13086 2 QREAIRSALSSSHFTLIQGPPGTGKTTTIVELIRQLLSypatsaaAGPRILVCAPSNAAVDNILERLLRkgqkYGPKIVR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 710 LGSGSRIHKQLEEIS-------------------------------------------------------EERLTKDCKT 734
Cdd:pfam13086 82 IGHPAAISEAVLPVSldylvesklnneedaqivkdiskeleklakalrafekeiivekllksrnkdksklEQERRKLRSE 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 735 VEEL------------EKALGQPSIVGVTCLGCGHPLFQRR-QFDYCIVDEATQVLQPTVLRPLIH-CSKFVLVGDPEQL 800
Cdd:pfam13086 162 RKELrkelrrreqsleREILDEAQIVCSTLSGAGSRLLSSLaNFDVVIIDEAAQALEPSTLIPLLRgPKKVVLVGDPKQL 241
|
....*..
gi 24640932 801 PPIVRSK 807
Cdd:pfam13086 242 PPTVISK 248
|
|
| cas4 |
TIGR00372 |
CRISPR-associated protein Cas4; This model represents a family of proteins associated with ... |
283-415 |
1.74e-08 |
|
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: 55.11 E-value: 1.74e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 283 PQLGLKGKVDVSVKVknqrqREEIIPLELKTGRASFSMEHKGQLLLYQLMHSAQGRDTQSGLLLYLKEGLLREVASGRNE 362
Cdd:TIGR00372 63 KKYGLKGVIDIVLEE-----DGELVPVEVKSGKPSPREAHKYQLLAYAYLLEEMYGEIVRGYILYINAGKKLEVEISEEL 137
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|...
gi 24640932 363 QRDLLmlrnDLAYWLtrevaipaskEDPLEQLPLPEPVYHHSACGNCAYNTIC 415
Cdd:TIGR00372 138 RKKAV----KLIEKI----------RELLEGGKPPSPPKSGPKCKFCPYREIC 176
|
|
| AAA |
smart00382 |
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ... |
651-727 |
1.14e-03 |
|
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.
Pssm-ID: 214640 [Multi-domain] Cd Length: 148 Bit Score: 40.82 E-value: 1.14e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24640932 651 TSSHLLIKGLPGTGKTQTLVALVRLLHLLGKSVL-ITAQTHSAVDNLIMRLLPFGLPMMRLGSGSRIHKQLEEISEER 727
Cdd:smart00382 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIyIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLK 78
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| DEXXQc_DNA2 |
cd18041 |
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ... |
636-836 |
7.08e-102 |
|
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: 319.18 E-value: 7.08e-102
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 636 NLNKVQQNAALRALTTSSHLLIKGLPGTGKTQTLVALVRLLHLLGKSVLITAQTHSAVDNLIMRLLPFGLPMMRLGSGSR 715
Cdd:cd18041 1 GLNKDQRQAIKKVLNAKDYALILGMPGTGKTTTIAALVRILVALGKSVLLTSYTHSAVDNILLKLKKFGVNFLRLGRLKK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 716 IHKQLEEISEERLTKDCKTVEELEKALGQPSIVGVTCLGCGHPLFQRRQFDYCIVDEATQVLQPTVLRPLIHCSKFVLVG 795
Cdd:cd18041 81 IHPDVQEFTLEAILKSCKSVEELESKYESVSVVATTCLGINHPIFRRRTFDYCIVDEASQITLPICLGPLRLAKKFVLVG 160
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 24640932 796 DPEQLPPIVRSKEARQRGADETLFQRLDSE--KATAVLSLQYR 836
Cdd:cd18041 161 DHYQLPPLVKSREARELGMDESLFKRLSEAhpDAVVQLTIQYR 203
|
|
| DNA2_N-like |
cd22318 |
Nuclease domain of the nuclease/helicase DNA2 and related nucleases; The eukaryotic nuclease ... |
153-378 |
1.62e-91 |
|
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: 292.50 E-value: 1.62e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 153 SGTTVTGSLFCKRKSVLQERFRGLDSGNSVMVIGTLVHELLQKVLRQKLFDKKHIQSALQEMLASSSLAHLLYASNLIQV 232
Cdd:cd22318 1 SGTSVAGSLFCMRKAVLSERFRGIDPGNKAMLIGTILHELFQKALKNNIFSREKLEKLAEKLLQSPKYLEDLYALGLTEE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 233 EMEDHLMKFIDPIVSFVAQYVKGEPPSVLLP----EVYRGQIHEICDIEENLWVPQLGLKGKVDVSVKVKNQRQ---REE 305
Cdd:cd22318 81 EALEELEEYIPSIQEWAEKYVRSNSPKGQVKlpsdGNSKGAISKILDIEENIWSPRFGLKGKIDATVEVKIHDKgksKTK 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24640932 306 IIPLELKTGRASFSMEHKGQLLLYQLMHSAQGR-DTQSGLLLYLKEGLLREVASGRNEQRDLLMLRNDLAYWLT 378
Cdd:cd22318 161 IMPLELKTGRASFSIEHRGQVILYTLMMSDRYDvDVDSGLLLYLKEGEMKEVPAGRNEKRGLIILRNELAHYLS 234
|
|
| Dna2 |
pfam08696 |
DNA replication factor Dna2; Dna2 is a DNA replication factor with single-stranded ... |
96-297 |
1.07e-71 |
|
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: 237.08 E-value: 1.07e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 96 SGGDPETADCQLLPPWNCMPMQVGDTVSLLGKWDPsaGCYVVDKEQGYCVSHPDFLISGTTVTGSLFCKRKSVLQERFRG 175
Cdd:pfam08696 1 SDKSGETRTVILRDDWVETPVEPGDIIHIIGEFES--GQCIIDNDSNLLILHPDILISATSVAGSFFCLRRAVLQERFKG 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 176 LDSGNSVMVIGTLVHELLQKVLRQKLFDKKHIQSALQEMLasSSLAHLLYASNLIQVEMEDHLMKFIDPIVSFVAQYVKG 255
Cdd:pfam08696 79 SGESSKPMLIGTILHELFQEALTANDWDLEFLEELLDELL--EKYLEELYALGETEEEAKEELMEYLPNIQEWAQKYVKK 156
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 24640932 256 EPPSVLLPE-----VYRGQIHEICDIEENLWVPQLGLKGKVDVSVKV 297
Cdd:pfam08696 157 SPKPNAVVEdgngkKVKLSISKLLDIEENIWSPMYGLKGKIDATVEV 203
|
|
| AAA_12 |
pfam13087 |
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
815-1055 |
2.19e-49 |
|
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: 173.50 E-value: 2.19e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 815 DETLFQRLDSEKATAV--LSLQYRMNKTITRLANELTYGGDLKCASDevsgarfevelLNEAPRWVQRALTTHLEQaVTL 892
Cdd:pfam13087 2 DRSLFERLQELGPSAVvmLDTQYRMHPEIMEFPSKLFYGGKLKDGPS-----------VAERPLPDDFHLPDPLGP-LVF 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 893 INTGDCLERcqefvyasqrlvdtcssieqsfsedkdEIRKLTSkkrvskYTNYCEAGIVMHLLRYLLKSGYEA-SRIGVI 971
Cdd:pfam13087 70 IDVDGSEEE---------------------------ESDGGTS------YSNEAEAELVVQLVEKLIKSGPEEpSDIGVI 116
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 972 APYRAQVELFKKLASKLDT---DLECNTVDQFQGRDKNLIIYSCSktggdfsdmeRSREAE---ILEDQRRLTVAITRAK 1045
Cdd:pfam13087 117 TPYRAQVRLIRKLLKRKLGgklEIEVNTVDGFQGREKDVIIFSCV----------RSNEKGgigFLSDPRRLNVALTRAK 186
|
250
....*....|
gi 24640932 1046 NKLILLGDIK 1055
Cdd:pfam13087 187 RGLIIVGNAK 196
|
|
| DNA2 |
COG1112 |
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]; |
438-1070 |
5.38e-49 |
|
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
Pssm-ID: 440729 [Multi-domain] Cd Length: 819 Bit Score: 188.03 E-value: 5.38e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 438 PQLLEHLSEADHAYVQHWCGLLALEEQHNRQSSHVRSFWTKDPAEREKEGIAIRHLKLVKGQEVILEEGRYRQTLELGEE 517
Cdd:COG1112 229 LLLLAALALLALALLLALLLLLLALLLLAALALLRAALRLDLLAALELLAALSLALLALLAALALALLLLAALALLLALA 308
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 518 ADPSRDLSLSGFDLGEYVVISSTSRLAVAAGFIVSIEARRLDLRLERDLSQRYSEETFIIDKHDSQSFATFNFTNLGMLL 597
Cdd:COG1112 309 LAALLALLALLALLAARLAAALAALLLLLLLEELALLAALLLLLELALLRLLAALLLALALLLLLALEELLLLALLRLLA 388
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 598 SEGERFQELRDIIVAKKPPEQHKVLPKIILTKGAPILLNLNKVQQNAALRALTTSSHLLIKGLPGTGKTQTLVALVRLLH 677
Cdd:COG1112 389 EGLALLLLLLLAALLRLARALLLLALLLAAAAAALAALLLLALALLAALLALLLLLAAALAALLALLLLLLLALAALLLL 468
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 678 LLGKSVLITAQTHSAVDNLIMRLLPFGLPMMR--LGSGSRIHKQLEEISEERltkdcKTVEEL--EKALGQPSIVGVTCL 753
Cdd:COG1112 469 LAAAAALLALALLESLLEELIEEHPEELEKLIaeLREAARLRRALRRELKKR-----RELRKLlwDALLELAPVVGMTPA 543
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 754 GCGHPL-FQRRQFDYCIVDEATQVLQPTVLRPLIHCSKFVLVGDPEQLPPIV---RSKEARQRGADETLFQRLDSEKATA 829
Cdd:COG1112 544 SVARLLpLGEGSFDLVIIDEASQATLAEALGALARAKRVVLVGDPKQLPPVVfgeEAEEVAEEGLDESLLDRLLARLPER 623
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 830 VLSL--QYRMNKTITRLANELTYGGDLKCAsdevsgarfevellneapRWVQRALTTHLEQAVTLINTGDCLERcqefvy 907
Cdd:COG1112 624 GVMLreHYRMHPEIIAFSNRLFYDGKLVPL------------------PSPKARRLADPDSPLVFIDVDGVYER------ 679
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 908 asqrlvdtcssieqsfsedkdeirkltskkRVSKYTNYCEAGIVMHLLRYLLKSGYEASRIGVIAPYRAQVELFKKL--- 984
Cdd:COG1112 680 ------------------------------RGGSRTNPEEAEAVVELVRELLEDGPDGESIGVITPYRAQVALIRELlre 729
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 985 -ASKLDTDLECNTVDQFQGRDKNLIIYScskTGGDFSDMERSREAEILEDQRRLTVAITRAKNKLILLGDIKCLEQ---Y 1060
Cdd:COG1112 730 aLGDGLEPVFVGTVDRFQGDERDVIIFS---LVYSNDEDVPRNFGFLNGGPRRLNVAVSRARRKLIVVGSRELLDSdpsT 806
|
650
....*....|
gi 24640932 1061 GPFRQLFKHI 1070
Cdd:COG1112 807 PALKRLLEYL 816
|
|
| DEXXQc_SMUBP2 |
cd18044 |
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ... |
636-836 |
1.96e-40 |
|
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: 147.76 E-value: 1.96e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 636 NLNKVQQNAALRALTTSSHLLIKGLPGTGKTQTLVALVRLLHLLGKSVLITAQTHSAVDNLIMRLLPFGLPMMRLGSGSR 715
Cdd:cd18044 1 NLNDSQKEAVKFALSQKDVALIHGPPGTGKTTTVVEIILQAVKRGEKVLACAPSNIAVDNLVERLVALKVKVVRIGHPAR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 716 IHKQLEEISEERLTkdcktveelekalgQPSIVGVTCLGCGHPLFQR-RQFDYCIVDEATQVLQPTVLRPLIHCSKFVLV 794
Cdd:cd18044 81 LLESVLDHSLDALV--------------AAQVVLATNTGAGSRQLLPnELFDVVVIDEAAQALEASCWIPLLKARRCILA 146
|
170 180 190 200
....*....|....*....|....*....|....*....|....*
gi 24640932 795 GDPEQLPPIVRSKEARQRGADETLFQRLDS---EKATAVLSLQYR 836
Cdd:cd18044 147 GDHKQLPPTILSDKAARGGLGVTLFERLVNlygESVVRMLTVQYR 191
|
|
| SF1_C_Upf1 |
cd18808 |
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ... |
837-1070 |
2.12e-38 |
|
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: 141.60 E-value: 2.12e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 837 MNKTITRLANELTYGGDLKCASDEVSGARFEVELLNEAPrwvqraltthleqaVTLINTGDCLERCQEfvyasqrlvdtc 916
Cdd:cd18808 1 MHPEISEFPSKLFYEGKLKAGVSVAARLNPPPLPGPSKP--------------LVFVDVSGGEEREES------------ 54
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 917 ssieqSFSedkdeirkltskkrvskYTNYCEAGIVMHLLRYLLKSGYEASRIGVIAPYRAQVELFKKLASK---LDTDLE 993
Cdd:cd18808 55 -----GTS-----------------KSNEAEAELVVELVKYLLKSGVKPSSIGVITPYRAQVALIRELLRKrggLLEDVE 112
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24640932 994 CNTVDQFQGRDKNLIIYSCSKTGgdfsdmERSREAEILEDQRRLTVAITRAKNKLILLGDIKCLEQYGPFRQLFKHI 1070
Cdd:cd18808 113 VGTVDNFQGREKDVIILSLVRSN------ESGGSIGFLSDPRRLNVALTRAKRGLIIVGNPDTLSKDPLWKKLLEYL 183
|
|
| DEXXQc_SETX |
cd18042 |
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ... |
637-836 |
1.40e-34 |
|
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: 131.95 E-value: 1.40e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 637 LNKVQQNAALRALTTSSHL-LIKGLPGTGKTQTLVALVRLLHLL-------------------------GKSVLITAQTH 690
Cdd:cd18042 1 LNESQLEAIASALQNSPGItLIQGPPGTGKTKTIVGILSVLLAGkyrkyyekvkkklrklqrnlnnkkkKNRILVCAPSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 691 SAVDNLIMRLLPFGLP----------MMRLGSgsrihkqleeiseerltkdcktvEELEKA-LGQPSIVGVTCLGCGHPL 759
Cdd:cd18042 81 AAVDEIVLRLLSEGFLdgdgrsykpnVVRVGR-----------------------QELRASiLNEADIVCTTLSSSGSDL 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 760 FQR--RQFDYCIVDEATQVLQPTVLRPLIH-CSKFVLVGDPEQLPPIVRSKEARQRGADETLFQRL-DSEKATAVLSLQY 835
Cdd:cd18042 138 LESlpRGFDTVIIDEAAQAVELSTLIPLRLgCKRLILVGDPKQLPATVFSKVAQKLGYDRSLFERLqLAGYPVLMLTTQY 217
|
.
gi 24640932 836 R 836
Cdd:cd18042 218 R 218
|
|
| AAA_11 |
pfam13086 |
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
641-807 |
1.18e-30 |
|
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: 121.68 E-value: 1.18e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 641 QQNAALRALTTSSHLLIKGLPGTGKTQTLVALVRLLHL-------LGKSVLITAQTHSAVDNLIMRLLP----FGLPMMR 709
Cdd:pfam13086 2 QREAIRSALSSSHFTLIQGPPGTGKTTTIVELIRQLLSypatsaaAGPRILVCAPSNAAVDNILERLLRkgqkYGPKIVR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 710 LGSGSRIHKQLEEIS-------------------------------------------------------EERLTKDCKT 734
Cdd:pfam13086 82 IGHPAAISEAVLPVSldylvesklnneedaqivkdiskeleklakalrafekeiivekllksrnkdksklEQERRKLRSE 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 735 VEEL------------EKALGQPSIVGVTCLGCGHPLFQRR-QFDYCIVDEATQVLQPTVLRPLIH-CSKFVLVGDPEQL 800
Cdd:pfam13086 162 RKELrkelrrreqsleREILDEAQIVCSTLSGAGSRLLSSLaNFDVVIIDEAAQALEPSTLIPLLRgPKKVVLVGDPKQL 241
|
....*..
gi 24640932 801 PPIVRSK 807
Cdd:pfam13086 242 PPTVISK 248
|
|
| DEXXQc_UPF1 |
cd18039 |
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ... |
636-836 |
2.79e-30 |
|
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: 120.04 E-value: 2.79e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 636 NLNKVQQNAALRALttSSHL-LIKGLPGTGKTQTLVALVRLLHLLGKS-VLITAQTHSAVDNLIMRLLPFGLPMMRLGSG 713
Cdd:cd18039 1 ELNHSQVDAVKTAL--QRPLsLIQGPPGTGKTVTSATIVYHLVKQGNGpVLVCAPSNVAVDQLTEKIHQTGLKVVRLCAK 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 714 SR-----------IHKQLEE----ISEERLTKDCKTVEELEKA----------------LGQPSIVGVTCLGCGHPLFQR 762
Cdd:cd18039 79 SReavespvsflaLHNQVRNldsaEKLELLKLLKLETGELSSAdekryrklkrkaerelLRNADVICCTCVGAGDPRLSK 158
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24640932 763 RQFDYCIVDEATQVLQPTVLRPLIH-CSKFVLVGDPEQLPPIVRSKEARQRGADETLFQRL-DSEKATAVLSLQYR 836
Cdd:cd18039 159 MKFRTVLIDEATQATEPECLIPLVHgAKQVILVGDHCQLGPVVMCKKAAKAGLSQSLFERLvQLGIRPIRLQVQYR 234
|
|
| DEXXQc_Helz-like |
cd18038 |
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ... |
637-822 |
1.39e-28 |
|
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: 115.02 E-value: 1.39e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 637 LNKVQQNAALRALTTSSHL---LIKGLPGTGKTQTLV-ALVRLLHLLGKS-VLITAQTHSAVDNLIMRLLPFGLP---MM 708
Cdd:cd18038 2 LNDEQKLAVRNIVTGTSRPppyIIFGPPGTGKTVTLVeAILQVLRQPPEArILVCAPSNSAADLLAERLLNALVTkreIL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 709 RLGSGSRIHKQLEE-------ISEERlTKDCKTVEELEKAlgqpSIVGVTCLGCGHPL---FQRRQFDYCIVDEATQVLQ 778
Cdd:cd18038 82 RLNAPSRDRASVPPellpycnSKAEG-TFRLPSLEELKKY----RIVVCTLMTAGRLVqagVPNGHFTHIFIDEAGQATE 156
|
170 180 190 200
....*....|....*....|....*....|....*....|....*...
gi 24640932 779 PTVLRPLIHCSKF----VLVGDPEQLPPIVRSKEARQRGADETLFQRL 822
Cdd:cd18038 157 PEALIPLSELASKntqiVLAGDPKQLGPVVRSPLARKYGLGKSLLERL 204
|
|
| DEXXQc_Upf1-like |
cd17934 |
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ... |
655-836 |
8.94e-26 |
|
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: 103.08 E-value: 8.94e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 655 LLIKGLPGTGKTQTLVALVRLLH--LLGKSVLITAQTHSAVDNLimrllpfglpmmrlgsgsrihkqleeiseerltkdc 732
Cdd:cd17934 2 SLIQGPPGTGKTTTIAAIVLQLLkgLRGKRVLVTAQSNVAVDNV------------------------------------ 45
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 733 ktveelekalgqpsivgvtclgcghplfqrrqfDYCIVDEATQVLQPTVLRPLIHCSKFVLVGDPEQLPPIVRSKEARQR 812
Cdd:cd17934 46 ---------------------------------DVVIIDEASQITEPELLIALIRAKKVVLVGDPKQLPPVVQEDHAALL 92
|
170 180
....*....|....*....|....*....
gi 24640932 813 GADETLFQRLDSEKATAV-----LSLQYR 836
Cdd:cd17934 93 GLSFILSLLLLFRLLLPGspkvmLDTQYR 121
|
|
| DEXXQc_Mov10L1 |
cd18078 |
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ... |
637-822 |
1.67e-22 |
|
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: 97.44 E-value: 1.67e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 637 LNKVQQNAALRALTTSSHLL---IKGLPGTGKTQTLV-ALVRLLHLLGKS-VLITAQTHSAVDNLIMRLLPFGLP----M 707
Cdd:cd18078 2 LNELQKEAVKRILGGECRPLpyiLFGPPGTGKTVTIIeAILQVVYNLPRSrILVCAPSNSAADLVTSRLHESKVLkpgdM 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 708 MRLGSgsriHKQLEEISEERLTKDCKTVEELEKALGQPSIVGvTCLGCGHPL---FQRRQFDYCIVDEATQVLQPTVLRP 784
Cdd:cd18078 82 VRLNA----VNRFESTVIDARKLYCRLGEDLSKASRHRIVIS-TCSTAGLLYqmgLPVGHFTHVFVDEAGQATEPESLIP 156
|
170 180 190 200
....*....|....*....|....*....|....*....|..
gi 24640932 785 LIHCSK----FVLVGDPEQLPPIVRSKEARQRGADETLFQRL 822
Cdd:cd18078 157 LGLISSrdgqIILAGDPMQLGPVIKSRLASAYGLGVSFLERL 198
|
|
| DEXXc_HELZ2-C |
cd18040 |
C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ... |
636-836 |
3.16e-19 |
|
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: 89.12 E-value: 3.16e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 636 NLNKVQQNAALRALTtSSHLLIKGLPGTGKTQTLVALVRLLH-------------LLGKSVLITAQTHSAVD---NLIMR 699
Cdd:cd18040 1 KLNPSQNHAVRTALT-KPFTLIQGPPGTGKTVTGVHIAYWFAkqnreiqsvsgegDGGPCVLYCGPSNKSVDvvaELLLK 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 700 LLpfGLPMMRLGS------------------------------------------------------GSRIHKQLEEISE 725
Cdd:cd18040 80 VP--GLKILRVYSeqietteypipneprhpnkksereskpnselssitlhhrirqpsnphsqqikafEARFERTQEKITE 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 726 ERLTKDCKTVEELEKALG-QPSIVGVTCLGCGHPLFQR----RQfdyCIVDEATQVLQPTVLRPLI---HCSKFVLVGDP 797
Cdd:cd18040 158 EDIKTYKILIWEARFEELeTVDVILCTCSEAASQKMRThanvKQ---CIVDECGMCTEPESLIPIVsapRAEQVVLIGDH 234
|
250 260 270
....*....|....*....|....*....|....*....
gi 24640932 798 EQLPPIVRSKEARQRGADETLFQRLdSEKATaVLSLQYR 836
Cdd:cd18040 235 KQLRPVVQNKEAQKLGLGRSLFERY-AEKAC-MLDTQYR 271
|
|
| EEXXEc_NFX1 |
cd17936 |
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ... |
642-822 |
6.28e-19 |
|
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: 85.67 E-value: 6.28e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 642 QNAALRALTTSSHLLIKGLPGTGKTQTLVALVRLLH-----LLGKSVLITAQTHSAVDNLIMRLLPFGLP-MMRLGSgsr 715
Cdd:cd17936 6 QLEALKHALTSELALIQGPPGTGKTFLGVKLVRALLqnqdlSITGPILVVCYTNHALDQFLEGLLDFGPTkIVRLGA--- 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 716 ihkqleeiseerltkdcktveelekalgqpSIVGVTCLGCG--HPLFQRRQFDYCIVDEATQVLQPTVLRPLI-HCSKFV 792
Cdd:cd17936 83 ------------------------------RVIGMTTTGAAkyRELLQALGPKVVIVEEAAEVLEAHILAALTpSTEHLI 132
|
170 180 190
....*....|....*....|....*....|..
gi 24640932 793 LVGDPEQLPPIVRSKEARQRG--ADETLFQRL 822
Cdd:cd17936 133 LIGDHKQLRPKVNVYELTAKKynLDVSLFERL 164
|
|
| DEXXQc_SF1 |
cd18043 |
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ... |
641-808 |
4.42e-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: 72.62 E-value: 4.42e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 641 QQNAALRALTTSSHLLIKGLPGTGKTQTLVALVRLLHLLGKSVLITAQTHSAVDnlimrLLPFGLPMMRLGSGSRihkql 720
Cdd:cd18043 3 SQEAAIISARNGKNVVIQGPPGTGKSQTIANIIANALARGKRVLFVSEKKAALD-----VVRFPCWIMSPLSVSQ----- 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 721 eeiseerltkdcktveelekalgqpsivgvtCLGCGHPLfqrrqFDYCIVDEATQVLQPTVLRPLIHCSKFVLVGDPEQL 800
Cdd:cd18043 73 -------------------------------YLPLNRNL-----FDLVIFDEASQIPIEEALPALFRGKQVVVVGDDKQL 116
|
....*...
gi 24640932 801 PPIVRSKE 808
Cdd:cd18043 117 PPSILLRE 124
|
|
| RecD |
COG0507 |
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
606-848 |
1.88e-13 |
|
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: 74.24 E-value: 1.88e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 606 LRDIIVAKKPPEQHKVLPKIILTKGAPILLNLNKVQQNAALRALTTSSHLLIKGLPGTGKTQTLVALVRLLHLLGKSVLI 685
Cdd:COG0507 94 ARRLRRLARPALDEADVEAALAALEPRAGITLSDEQREAVALALTTRRVSVLTGGAGTGKTTTLRALLAALEALGLRVAL 173
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 686 TAQTHSAVDNLimrllpfglpMMRLGSGSR-IHKQLEEI-SEERLTKDCktveelEKALGQPSIVgvtclgcghplfqrr 763
Cdd:COG0507 174 AAPTGKAAKRL----------SESTGIEARtIHRLLGLRpDSGRFRHNR------DNPLTPADLL--------------- 222
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 764 qfdycIVDEATQVLQPT---VLR--PLIHCsKFVLVGDPEQLPPIvrskearqrGADETLFQRLDSEK-ATAVLSLQYRM 837
Cdd:COG0507 223 -----VVDEASMVDTRLmaaLLEalPRAGA-RLILVGDPDQLPSV---------GAGAVLRDLIESGTvPVVELTEVYRQ 287
|
250
....*....|...
gi 24640932 838 NK--TITRLANEL 848
Cdd:COG0507 288 ADdsRIIELAHAI 300
|
|
| DEXSc_RecD-like |
cd17933 |
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ... |
641-803 |
1.54e-12 |
|
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: 66.42 E-value: 1.54e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 641 QQNAALRALTTSSHLLIKGLPGTGKTQTLVALVRLLHLLGKSVLITAQTHSAVDNLimrllpfglpMMRLGSGSR-IHKQ 719
Cdd:cd17933 1 EQKAAVRLVLRNRVSVLTGGAGTGKTTTLKALLAALEAEGKRVVLAAPTGKAAKRL----------SESTGIEAStIHRL 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 720 LEEISEErltkdcktveelekalGQPSIVGVTCLGCghplfqrrqfDYCIVDEATQV---LQPTVLRPLIHCSKFVLVGD 796
Cdd:cd17933 71 LGINPGG----------------GGFYYNEENPLDA----------DLLIVDEASMVdtrLMAALLSAIPAGARLILVGD 124
|
....*..
gi 24640932 797 PEQLPPI 803
Cdd:cd17933 125 PDQLPSV 131
|
|
| AAA_30 |
pfam13604 |
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
637-805 |
8.34e-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: 59.50 E-value: 8.34e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 637 LNkVQQNAALRALTTSSHLL--IKGLPGTGKTQTLVALVRLLHLLGKSVLITAQTHSAVDnlimrllpfglpmmRLGSGS 714
Cdd:pfam13604 2 LN-AEQAAAVRALLTSGDRVavLVGPAGTGKTTALKALREAWEAAGYRVIGLAPTGRAAK--------------VLGEEL 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 715 RIhkqleeiseerltkDCKTVEELEKAL-GQPSIVGVTCLgcghplfqrrqfdycIVDEATQVLQPTVLRPLIHCSKF-- 791
Cdd:pfam13604 67 GI--------------PADTIAKLLHRLgGRAGLDPGTLL---------------IVDEAGMVGTRQMARLLKLAEDAga 117
|
170
....*....|....*.
gi 24640932 792 --VLVGDPEQLPPIVR 805
Cdd:pfam13604 118 rvILVGDPRQLPSVEA 133
|
|
| AAA_19 |
pfam13245 |
AAA domain; |
642-803 |
8.60e-10 |
|
AAA domain;
Pssm-ID: 433059 [Multi-domain] Cd Length: 136 Bit Score: 58.00 E-value: 8.60e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 642 QNAALRALTTSSHLLIKGLPGTGKTQTLVALVRLL---HLLGKSVLITAQTHSAVDNLIMRLlpfGLPmmrlgsGSRIHK 718
Cdd:pfam13245 1 QREAVRTALPSKVVLLTGGPGTGKTTTIRHIVALLvalGGVSFPILLAAPTGRAAKRLSERT---GLP------ASTIHR 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 719 QLEeiseerlTKDCKTVEELEkalgqpsivgvtclGCGHPLFQrrqfDYCIVDEATQV---LQPTVLRPLIHCSKFVLVG 795
Cdd:pfam13245 72 LLG-------FDDLEAGGFLR--------------DEEEPLDG----DLLIVDEFSMVdlpLAYRLLKALPDGAQLLLVG 126
|
....*...
gi 24640932 796 DPEQLPPI 803
Cdd:pfam13245 127 DPDQLPSV 134
|
|
| EEXXQc_AQR |
cd17935 |
EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds ... |
656-846 |
6.76e-09 |
|
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: 57.05 E-value: 6.76e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 656 LIKGLPGTGKTQTLVALVRLL---HLLGKSVLITAQTHSAVD--NLIMRLLPFGLPMMRLGSGSRIhkqleeiseerltk 730
Cdd:cd17935 24 MVVGPPGTGKTDVAVQIISNLyhnFPNQRTLIVTHSNQALNQlfEKIMALDIDERHLLRLGHGAKI-------------- 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 731 dcktveelekalgqpsiVGVTCLgcgHPLFQRR-------QFDYCIVDEATQVLQPTVLRPLIHCS---------KFVLV 794
Cdd:cd17935 90 -----------------IAMTCT---HAALKRGelvelgfKYDNILMEEAAQILEIETFIPLLLQNpedgpnrlkRLIMI 149
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 24640932 795 GDPEQLPPIVRSKEARQRG-ADETLFQRLDSEKA-TAVLSLQYRMNKTITRLAN 846
Cdd:cd17935 150 GDHHQLPPVIKNMAFQKYSnMEQSLFTRLVRLGVpTVDLDAQGRARASISSLYN 203
|
|
| cas4 |
TIGR00372 |
CRISPR-associated protein Cas4; This model represents a family of proteins associated with ... |
283-415 |
1.74e-08 |
|
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: 55.11 E-value: 1.74e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 283 PQLGLKGKVDVSVKVknqrqREEIIPLELKTGRASFSMEHKGQLLLYQLMHSAQGRDTQSGLLLYLKEGLLREVASGRNE 362
Cdd:TIGR00372 63 KKYGLKGVIDIVLEE-----DGELVPVEVKSGKPSPREAHKYQLLAYAYLLEEMYGEIVRGYILYINAGKKLEVEISEEL 137
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|...
gi 24640932 363 QRDLLmlrnDLAYWLtrevaipaskEDPLEQLPLPEPVYHHSACGNCAYNTIC 415
Cdd:TIGR00372 138 RKKAV----KLIEKI----------RELLEGGKPPSPPKSGPKCKFCPYREIC 176
|
|
| DEXXQc_HELZ |
cd18077 |
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that ... |
637-822 |
7.08e-07 |
|
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: 51.33 E-value: 7.08e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 637 LNKVQQNAALrALTTSSH-----LLIKGLPGTGKTQTLVALVR-LLHLLGKSVLITAQTHSAVDNLIMRLL-PFGLPMMR 709
Cdd:cd18077 2 LNAKQKEAVL-AITTPLSiqlppVLLIGPFGTGKTFTLAQAVKhILQQPETRILICTHSNSAADLYIKEYLhPYVETGNP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 710 LGSGSRIHKQLEEIS--EERLTKDC----------KTVEELEKAlgqpSIVGVT-------CLGCGHPLFqrrqFDYCIV 770
Cdd:cd18077 81 RARPLRVYYRNRWVKtvHPVVQKYClidehgtfrmPTREDVMRH----RVVVVTlstsqylCQLDLEPGF----FTHILL 152
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*
gi 24640932 771 DEATQVLQPTVLRPLIHCSK---FVLVGDPEQLPPIVRSKEARQRGADETLFQRL 822
Cdd:cd18077 153 DEAAQAMECEAIMPLALATKstrIVLAGDHMQLSPEVYSEFARERNLHISLLERL 207
|
|
| Cas4_I-A_I-B_I-C_I-D_II-B |
cd09637 |
CRISPR/Cas system-associated protein Cas4; CRISPR (Clustered Regularly Interspaced Short ... |
283-415 |
7.39e-07 |
|
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: 50.51 E-value: 7.39e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 283 PQLGLKGKVDVSVKVknqrqREEIIPLELKTGRASFSME-HKGQLLLYQLMHSAQGrdtqsglllylkeglLREVASGR- 360
Cdd:cd09637 63 KKYGLKGVIDIVLKE-----DGELVPVEVKSGRAGSPREaHKLQLVAYAYLLEEMY---------------GKRVARGYi 122
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*..
gi 24640932 361 --NEQRDLLMLRNDLAywLTREVAIPASKEDPLEQLPLPEPVYHHSACGNCAYNTIC 415
Cdd:cd09637 123 vyLEGGKRLEVEISEE--LRKKAEKLLEEIRKLLEGELPPPVKSSPKCKFCPYREIC 177
|
|
| SF1_C |
cd18786 |
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ... |
967-1052 |
2.52e-06 |
|
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: 46.66 E-value: 2.52e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 967 RIGVIAPY---RAQVELFKKLASKLDTDL---ECNTVDQFQGRDKNLIIYSCSKTGgdfsdmersreaeiLEDQRRLTVA 1040
Cdd:cd18786 12 KGVVLTPYhrdRAYLNQYLQGLSLDEFDLqlvGAITIDSSQGLTFDVVTLYLPTAN--------------SLTPRRLYVA 77
|
90
....*....|..
gi 24640932 1041 ITRAKNKLILLG 1052
Cdd:cd18786 78 LTRARKRLVIYD 89
|
|
| DEXXQc_HELZ2-N |
cd18076 |
N-terminal DEXXQ-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ... |
655-822 |
2.58e-06 |
|
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: 49.89 E-value: 2.58e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 655 LLIKGLPGTGKTQTL-VALVRLLHLLGKSVLITAQTHSAVDNLIMRLL--------PFGLPMmRLGSGSRIHKQLE--EI 723
Cdd:cd18076 26 LLIYGPFGTGKTFTLaMAALEVIREPGTKVLICTHTNSAADIYIREYFhpyvdkghPEARPL-RIKATDRPNAITDpdTI 104
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 724 SEERLTKDCK-----TVEELEKalgQPSIVGVTCLGcghplFQRRQ----FDYCIVDEATQVLQPTVLRPLI---HCSKF 791
Cdd:cd18076 105 TYCCLTKDRQcfrlpTRDELDF---HNIVITTTAMA-----FNLHVlsgfFTHIFIDEAAQMLECEALIPLSyagPKTRV 176
|
170 180 190
....*....|....*....|....*....|.
gi 24640932 792 VLVGDPEQLPPIVRSKeARQRGADETLFQRL 822
Cdd:cd18076 177 VLAGDHMQMTPKLFSV-ADYNRANHTLLNRL 206
|
|
| DExxQc_SF1-N |
cd17914 |
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ... |
655-835 |
3.28e-06 |
|
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: 47.10 E-value: 3.28e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 655 LLIKGLPGTGKTQTLV----ALVRLLHLLGKSVLITAQTHSAVDnlimrllpfglpmmrlgsgsrihkqleeiseerltk 730
Cdd:cd17914 2 SLIQGPPGTGKTRVLVkivaALMQNKNGEPGRILLVTPTNKAAA------------------------------------ 45
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 731 dcktveelekalgqpsivgvtclgcghplfqrrQFDYCIVDEATQVLQP--TVLRPLI-HCSKFVLVGDPEQLPPIVRSK 807
Cdd:cd17914 46 ---------------------------------QLDNILVDEAAQILEPetSRLIDLAlDQGRVILVGDHDQLGPVWRGA 92
|
170 180
....*....|....*....|....*...
gi 24640932 808 EARQRGADETLFQRLDSEKATAVLsLQY 835
Cdd:cd17914 93 VLAKICNEQSLFTRLVRLGVSLIR-LQV 119
|
|
| DEXQc_UvrD |
cd17932 |
DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch ... |
638-825 |
1.01e-04 |
|
DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. UvrD 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: 350690 [Multi-domain] Cd Length: 189 Bit Score: 44.43 E-value: 1.01e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 638 NKVQQNAALralTTSSHLLIKGLPGTGKTQTLVAlvRLLHLLGK------SVLITAQTHSAVDNLIMRLLP-FGLPMMRL 710
Cdd:cd17932 1 NPEQREAVT---HPDGPLLVLAGAGSGKTRVLTH--RIAYLILEggvppeRILAVTFTNKAAKEMRERLRKlLGEQLASG 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 711 GSGSRIHKQLEEISEERLTKDC---KTVEELEKALGQPSIVgvtclgcghplfqRRQFDYCIVDEA--TQVLQPTVLRPL 785
Cdd:cd17932 76 VWIGTFHSFALRILRRYGDFDDlllYALELLEENPDVREKL-------------QSRFRYILVDEYqdTNPLQYELLKLL 142
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 24640932 786 IHCSK-FVLVGDPEQlppivrskeA--RQRGADETLFQRLDSE 825
Cdd:cd17932 143 AGDGKnLFVVGDDDQ---------SiyGFRGADPENILDFEKD 176
|
|
| DEXSc_Pif1_like |
cd18037 |
DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like ... |
641-808 |
1.29e-04 |
|
DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like helicases involved in maintaining genome stability through unwinding double-stranded DNAs (dsDNAs), DNA/RNA hybrids, and G quadruplex (G4) structures. The members of Pif1 helicase subfamily studied so far all appear to contribute to telomere maintenance. Pif1 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: 350795 [Multi-domain] Cd Length: 183 Bit Score: 44.16 E-value: 1.29e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 641 QQNAALRALTTSSHLLIKGLPGTGKTQTLVALVRLLHLLGKSVLITAQTHSAVDNLimrllpfglpmmrlgSGSRIHK-- 718
Cdd:cd18037 1 EQRRVLDLVLDGKNVFFTGSAGTGKSYLLRRIIRALPSRPKRVAVTASTGIAACNI---------------GGTTLHSfa 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24640932 719 --QLEEISEERLTKDCKTVEELEKALgqpsivgvtclgcghplfqrRQFDYCIVDEATqVLQPT-------VLRPLIHCS 789
Cdd:cd18037 66 giGLGSEPAEDLLERVKRSPYLVQRW--------------------RKCDVLIIDEIS-MLDADlfdkldrVAREVRGSD 124
|
170 180
....*....|....*....|....*
gi 24640932 790 KF------VLVGDPEQLPPIVRSKE 808
Cdd:cd18037 125 KPfggiqlILCGDFLQLPPVTKNSE 149
|
|
| AAA |
smart00382 |
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ... |
651-727 |
1.14e-03 |
|
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.
Pssm-ID: 214640 [Multi-domain] Cd Length: 148 Bit Score: 40.82 E-value: 1.14e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24640932 651 TSSHLLIKGLPGTGKTQTLVALVRLLHLLGKSVL-ITAQTHSAVDNLIMRLLPFGLPMMRLGSGSRIHKQLEEISEER 727
Cdd:smart00382 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIyIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLK 78
|
|
| |
