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Conserved domains on  [gi|1799133847|ref|NP_001364577|]
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DNA2/NAM7 helicase-like C-terminal domain-containing protein [Caenorhabditis elegans]

Protein Classification

DEAD/DEAH box helicase( domain architecture ID 11437895)

DEAD/DEAH box containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA

CATH:  3.40.50.300
EC:  3.6.4.-
Gene Ontology:  GO:0016887|GO:0003676|GO:0004386|GO:0005524
PubMed:  20206133|20225155

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DNA2 super family cl34114
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
39-318 7.67e-33

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG1112:

Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 130.63  E-value: 7.67e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847  39 QLVIGTAAAiklaFSQAPFLEiKDRFDITFIDEASQLAL-YVLGSLAtmLPKsRMILVGDMHQLPPYMEEALPAELKRAA 117
Cdd:COG1112   536 PVVGMTPAS----VARLLPLG-EGSFDLVIIDEASQATLaEALGALA--RAK-RVVLVGDPKQLPPVVFGEEAEEVAEEG 607

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847 118 IGEPL-TLAVKGRRWPSMHLTRVHRCPKMITEVLGDLFYGNTLTSsKPGVTDIPvlkamGLPSRHPMVFVNYTSPQTAVG 196
Cdd:COG1112   608 LDESLlDRLLARLPERGVMLREHYRMHPEIIAFSNRLFYDGKLVP-LPSPKARR-----LADPDSPLVFIDVDGVYERRG 681

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847 197 KSFSNEGEARYALQLVEALtryASTANKKITAAILNFYGAQYSYV-------YSMAEDEVTVNTIDGCQGQEYDVTIVLL 269
Cdd:COG1112   682 GSRTNPEEAEAVVELVREL---LEDGPDGESIGVITPYRAQVALIrellreaLGDGLEPVFVGTVDRFQGDERDVIIFSL 758

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1799133847 270 TRSDPYERSK---FLV-NANRINVALSRPKIATVIIGQRHLTGNQPDPRQPKR 318
Cdd:COG1112   759 VYSNDEDVPRnfgFLNgGPRRLNVAVSRARRKLIVVGSRELLDSDPSTPALKR 811
 
Name Accession Description Interval E-value
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
39-318 7.67e-33

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 130.63  E-value: 7.67e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847  39 QLVIGTAAAiklaFSQAPFLEiKDRFDITFIDEASQLAL-YVLGSLAtmLPKsRMILVGDMHQLPPYMEEALPAELKRAA 117
Cdd:COG1112   536 PVVGMTPAS----VARLLPLG-EGSFDLVIIDEASQATLaEALGALA--RAK-RVVLVGDPKQLPPVVFGEEAEEVAEEG 607

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847 118 IGEPL-TLAVKGRRWPSMHLTRVHRCPKMITEVLGDLFYGNTLTSsKPGVTDIPvlkamGLPSRHPMVFVNYTSPQTAVG 196
Cdd:COG1112   608 LDESLlDRLLARLPERGVMLREHYRMHPEIIAFSNRLFYDGKLVP-LPSPKARR-----LADPDSPLVFIDVDGVYERRG 681

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847 197 KSFSNEGEARYALQLVEALtryASTANKKITAAILNFYGAQYSYV-------YSMAEDEVTVNTIDGCQGQEYDVTIVLL 269
Cdd:COG1112   682 GSRTNPEEAEAVVELVREL---LEDGPDGESIGVITPYRAQVALIrellreaLGDGLEPVFVGTVDRFQGDERDVIIFSL 758

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1799133847 270 TRSDPYERSK---FLV-NANRINVALSRPKIATVIIGQRHLTGNQPDPRQPKR 318
Cdd:COG1112   759 VYSNDEDVPRnfgFLNgGPRRLNVAVSRARRKLIVVGSRELLDSDPSTPALKR 811
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 140-302 3.79e-25

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: 101.09  E-value: 3.79e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847 140 HRCPKMITEVLGDLFYGNTLTSSkPGVTDIPVLKAMGLPSR-HPMVFVNY-TSPQTAV--GKSFSNEGEARYALQLVEAL 215
Cdd:pfam13087  24 YRMHPEIMEFPSKLFYGGKLKDG-PSVAERPLPDDFHLPDPlGPLVFIDVdGSEEEESdgGTSYSNEAEAELVVQLVEKL 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847 216 TRYASTANKKItaAILNFYGAQYSYV------YSMAEDEVTVNTIDGCQGQEYDVTIVLLTRSDPYERSKFLVNANRINV 289
Cdd:pfam13087 103 IKSGPEEPSDI--GVITPYRAQVRLIrkllkrKLGGKLEIEVNTVDGFQGREKDVIIFSCVRSNEKGGIGFLSDPRRLNV 180

                         170
                  ....*....|...
gi 1799133847 290 ALSRPKIATVIIG 302
Cdd:pfam13087 181 ALTRAKRGLIIVG 193
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 153-302 8.59e-24

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: 96.92  E-value: 8.59e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847 153 LFYGNTLTSSKPGVTDIPVLKAMGLPsrHPMVFVNYTSPQT--AVGKSFSNEGEARYALQLVEALTRyASTANKKITaaI 230
Cdd:cd18808    12 LFYEGKLKAGVSVAARLNPPPLPGPS--KPLVFVDVSGGEEreESGTSKSNEAEAELVVELVKYLLK-SGVKPSSIG--V 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1799133847 231 LNFYGAQYSYVYSM------AEDEVTVNTIDGCQGQEYDVTIVLLTRSDPYERSK-FLVNANRINVALSRPKIATVIIG 302
Cdd:cd18808    87 ITPYRAQVALIRELlrkrggLLEDVEVGTVDNFQGREKDVIILSLVRSNESGGSIgFLSDPRRLNVALTRAKRGLIIVG 165
recD_rel TIGR01448
helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the ...
 58-141 1.82e-04

helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273632 [Multi-domain]  Cd Length: 720  Bit Score: 43.62  E-value: 1.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847  58 LEIKDRFDITFIDEASQLALYVLGSLATMLP-KSRMILVGDMHQLPPymeealpaelkrAAIGEPLTLAVKGRRWPSMHL 136
Cdd:TIGR01448 411 LEDPIDCDLLIVDESSMMDTWLALSLLAALPdHARLLLVGDTDQLPS------------VGPGQVLKDLILSQAIPVTRL 478


                  ....*
gi 1799133847 137 TRVHR 141
Cdd:TIGR01448 479 TKVYR 483
 
Name Accession Description Interval E-value
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
39-318 7.67e-33

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 130.63  E-value: 7.67e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847  39 QLVIGTAAAiklaFSQAPFLEiKDRFDITFIDEASQLAL-YVLGSLAtmLPKsRMILVGDMHQLPPYMEEALPAELKRAA 117
Cdd:COG1112   536 PVVGMTPAS----VARLLPLG-EGSFDLVIIDEASQATLaEALGALA--RAK-RVVLVGDPKQLPPVVFGEEAEEVAEEG 607

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847 118 IGEPL-TLAVKGRRWPSMHLTRVHRCPKMITEVLGDLFYGNTLTSsKPGVTDIPvlkamGLPSRHPMVFVNYTSPQTAVG 196
Cdd:COG1112   608 LDESLlDRLLARLPERGVMLREHYRMHPEIIAFSNRLFYDGKLVP-LPSPKARR-----LADPDSPLVFIDVDGVYERRG 681

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847 197 KSFSNEGEARYALQLVEALtryASTANKKITAAILNFYGAQYSYV-------YSMAEDEVTVNTIDGCQGQEYDVTIVLL 269
Cdd:COG1112   682 GSRTNPEEAEAVVELVREL---LEDGPDGESIGVITPYRAQVALIrellreaLGDGLEPVFVGTVDRFQGDERDVIIFSL 758

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1799133847 270 TRSDPYERSK---FLV-NANRINVALSRPKIATVIIGQRHLTGNQPDPRQPKR 318
Cdd:COG1112   759 VYSNDEDVPRnfgFLNgGPRRLNVAVSRARRKLIVVGSRELLDSDPSTPALKR 811
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 140-302 3.79e-25

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: 101.09  E-value: 3.79e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847 140 HRCPKMITEVLGDLFYGNTLTSSkPGVTDIPVLKAMGLPSR-HPMVFVNY-TSPQTAV--GKSFSNEGEARYALQLVEAL 215
Cdd:pfam13087  24 YRMHPEIMEFPSKLFYGGKLKDG-PSVAERPLPDDFHLPDPlGPLVFIDVdGSEEEESdgGTSYSNEAEAELVVQLVEKL 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847 216 TRYASTANKKItaAILNFYGAQYSYV------YSMAEDEVTVNTIDGCQGQEYDVTIVLLTRSDPYERSKFLVNANRINV 289
Cdd:pfam13087 103 IKSGPEEPSDI--GVITPYRAQVRLIrkllkrKLGGKLEIEVNTVDGFQGREKDVIIFSCVRSNEKGGIGFLSDPRRLNV 180

                         170
                  ....*....|...
gi 1799133847 290 ALSRPKIATVIIG 302
Cdd:pfam13087 181 ALTRAKRGLIIVG 193
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 153-302 8.59e-24

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: 96.92  E-value: 8.59e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847 153 LFYGNTLTSSKPGVTDIPVLKAMGLPsrHPMVFVNYTSPQT--AVGKSFSNEGEARYALQLVEALTRyASTANKKITaaI 230
Cdd:cd18808    12 LFYEGKLKAGVSVAARLNPPPLPGPS--KPLVFVDVSGGEEreESGTSKSNEAEAELVVELVKYLLK-SGVKPSSIG--V 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1799133847 231 LNFYGAQYSYVYSM------AEDEVTVNTIDGCQGQEYDVTIVLLTRSDPYERSK-FLVNANRINVALSRPKIATVIIG 302
Cdd:cd18808    87 ITPYRAQVALIRELlrkrggLLEDVEVGTVDNFQGREKDVIILSLVRSNESGGSIgFLSDPRRLNVALTRAKRGLIIVG 165
deltaCoV_Nsp13-helicase cd21721
helicase domain of deltacoronavirus non-structural protein 13; This model represents the ...
 65-301 1.66e-13

helicase domain of deltacoronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from deltacoronavirus, including Bulbul coronavirus (CoV) HKU11 and Common moorhen CoV HKU21. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core.


Pssm-ID: 409654 [Multi-domain]  Cd Length: 342  Bit Score: 71.11  E-value: 1.66e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847  65 DITFIDEASQLALYVLGSLATMLPKSRMILVGDMHQLPPYMEEALPAELKRAAIGEPLTLAVKGRrwPSMHLTRVHRCPK 144
Cdd:cd21721   119 DIVVVDEVSMLTNYELSSVNARLVYNHIVYVGDPYQLPSPRTMLTTGQLSPADYNVVTDIMVHAG--ADVMLDMCYRCPR 196

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847 145 MITEVLGDLFYGNTLTSSKPgvtdipvlkamglPSRHPM-VFVNYTSPQTAV-GKSFSNEGEARYALQLVEALTRYASTA 222
Cdd:cd21721   197 EIVDTVSKLVYDNKLKAAKP-------------NSRQCYkTIINNGNNDIAHeGQSAYNEPQLRFALAFRQYKRWDNVTF 263

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1799133847 223 NKKITAaiLNFYGAQYSYvysmaedevTVNTIDGCQGQEYDVTIVLLTRSdpyerSKFLVNANRINVALSRPKIATVII 301
Cdd:cd21721   264 ISPYNA--MNVKAAMAGF---------STQTVDSSQGSEYDYVIFCVTTD-----SAHALNMSRLNVALTRAKIGILVV 326
CoV_Nsp13-helicase cd21718
helicase domain of coronavirus non-structural protein 13; This model represents the helicase ...
 65-301 4.23e-10

helicase domain of coronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from alpha-, beta-, gamma-, and deltacoronavirus, including pathogenic human viruses such as Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core.


Pssm-ID: 409652 [Multi-domain]  Cd Length: 341  Bit Score: 60.62  E-value: 4.23e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847  65 DITFIDEASQLALYVLGSLATMLPKSRMILVGDMHQLPPymeealPAELKRAAIGEPLTLAVKGRRW----PSMHLTRVH 140
Cdd:cd21718   119 DIVVVDEVSMCTNYDLSVVNARLKYKHIVYVGDPAQLPA------PRTLLTEGSLEPKDYNVVTRLMvgsgPDVFLSKCY 192

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847 141 RCPKMITEVLGDLFYGNTLTSSKPgvtdipvlkamglPSRHpmVF-VNYTSPQTAVGKSFSNEGEARYALQLVEALTRYA 219
Cdd:cd21718   193 RCPKEIVDTVSKLVYDNKLKAIKP-------------KSRQ--CFkTFGKGDVRHDNGSAINRPQLEFVKRFLDRNPRWR 257

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847 220 StankkitAAILNFYGAQYSYVYSMAedEVTVNTIDGCQGQEYDVTIVLLTrsdpyERSKFLVNANRINVALSRPKIATV 299
Cdd:cd21718   258 K-------AVFISPYNAMNNRASRLL--GLSTQTVDSSQGSEYDYVIFCQT-----TDTAHALNINRFNVAITRAKHGIL 323


                  ..
gi 1799133847 300 II 301
Cdd:cd21718   324 VI 325
gammaCoV_Nsp13-helicase cd21720
helicase domain of gammacoronavirus non-structural protein 13; This model represents the ...
 65-301 1.70e-09

helicase domain of gammacoronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from gammacoronavirus, including Avian infectious bronchitis virus. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. Coronavirus (CoV) Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core.


Pssm-ID: 409653 [Multi-domain]  Cd Length: 343  Bit Score: 58.78  E-value: 1.70e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847  65 DITFIDEASQLALYVLGSLATMLPKSRMILVGDMHQLP-PYMEEALPAELKRAAIGEPLTLAVKgrrwPSMHLTRVHRCP 143
Cdd:cd21720   119 DILLVDEVSMLTNYELSFINGKINYQYVVYVGDPAQLPaPRTLLNGSLSPKDYNVVTNLMVCVK----PDIFLAKCYRCP 194

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847 144 KMITEVLGDLFYGNTLTSSKPgvtdipvlkamglPSRHPM-VFVNytSPQTAVGKsfsnEGEARYALQLVEALTRYASTA 222
Cdd:cd21720   195 KEIVDTVSTLVYDGKFIANNP-------------ESRQCFkVIVN--NGNSDVGH----ESGSAYNTTQLEFVKDFVCRN 255

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1799133847 223 NKKITAAILNFYGAQYSYVYSMAEdeVTVNTIDGCQGQEYDVTIVLLTRSDPYErskflVNANRINVALSRPKIATVII 301
Cdd:cd21720   256 KEWREATFISPYNAMNQRAYRMLG--LNVQTVDSSQGSEYDYVIFCVTADSQHA-----LNINRFNVALTRAKRGILVV 327
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 62-118 1.16e-07

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: 49.93  E-value: 1.16e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1799133847  62 DRFDITFIDEASQLALYVLgsLATMLPKSRMILVGDMHQLPPYMEEALPAELKRAAI 118
Cdd:cd17934    43 DNVDVVIIDEASQITEPEL--LIALIRAKKVVLVGDPKQLPPVVQEDHAALLGLSFI 97
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
 35-103 2.20e-06

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: 48.00  E-value: 2.20e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847  35 IHDPQLVIGTAaaikLAFSQAPFleIKDRFDITFIDEASQLAL-YVLGSLatmLPKSRMILVGDMHQLPP 103
Cdd:cd18041   107 YESVSVVATTC----LGINHPIF--RRRTFDYCIVDEASQITLpICLGPL---RLAKKFVLVGDHYQLPP 167
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 69-141 7.11e-06

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: 48.05  E-value: 7.11e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1799133847  69 IDEASQLALYVLGSLATMLPKS--RMILVGDMHQLPPYmeEAlpaelkraaiGEPLTLAVKGRRWPSMHLTRVHR 141
Cdd:COG0507   224 VDEASMVDTRLMAALLEALPRAgaRLILVGDPDQLPSV--GA----------GAVLRDLIESGTVPVVELTEVYR 286
alphaCoV_Nsp13-helicase cd21723
helicase domain of alphacoronavirus non-structural protein 13; This model represents the ...
 65-295 1.22e-05

helicase domain of alphacoronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from alphacoronavirus, including Porcine epidemic diarrhea virus and Human coronavirus (CoV) NL63. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core.


Pssm-ID: 409656 [Multi-domain]  Cd Length: 340  Bit Score: 46.65  E-value: 1.22e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847  65 DITFIDEASQLALYVLGSLATMLPKSRMILVGDMHQLPPymeealPAELKRAAIGEPLTLAVKGRRW----PSMHLTRVH 140
Cdd:cd21723   119 DIVVVDEVSMCTNYDLSVINQRVSYKHIVYVGDPQQLPA------PRTMITRGVLEPKDYNVVTQRMcalgPDVFLHKCY 192

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847 141 RCPKMITEVLGDLFYGNTLTSSKPgvtdipvlkamglPSRHPMVFVNYTSPQTAVGKSFSnegeaRYALQLVEA-LTRYA 219
Cdd:cd21723   193 RCPAEIVNTVSELVYENKFKPVHP-------------ESKQCFKIFCKGNVQVDNGSSIN-----RRQLDVVKMfLAKNP 254

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1799133847 220 STANkkitAAILNFYGAQySYVYSMAEDeVTVNTIDGCQGQEYDVTIVLLTrSDpyerSKFLVNANRINVALSRPK 295
Cdd:cd21723   255 KWSK----AVFISPYNSQ-NYVASRVLG-LQIQTVDSSQGSEYDYVIYTQT-SD----TAHACNVNRFNVAITRAK 319
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 35-103 1.23e-05

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: 46.18  E-value: 1.23e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1799133847  35 IHDPQLVIGTaaaikLAFSQAPFLEIKDRFDITFIDEASQlALyvlgSLATMLP----KSRMILVGDMHQLPP 103
Cdd:pfam13086 181 LDEAQIVCST-----LSGAGSRLLSSLANFDVVIIDEAAQ-AL----EPSTLIPllrgPKKVVLVGDPKQLPP 243
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
 50-103 5.64e-05

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: 43.74  E-value: 5.64e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1799133847  50 LAFSQAPFLE-IKDRFDITFIDEASQLAlyvlgSLATMLPK----SRMILVGDMHQLPP 103
Cdd:cd18042   130 LSSSGSDLLEsLPRGFDTVIIDEAAQAV-----ELSTLIPLrlgcKRLILVGDPKQLPA 183
recD_rel TIGR01448
helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the ...
 58-141 1.82e-04

helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273632 [Multi-domain]  Cd Length: 720  Bit Score: 43.62  E-value: 1.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847  58 LEIKDRFDITFIDEASQLALYVLGSLATMLP-KSRMILVGDMHQLPPymeealpaelkrAAIGEPLTLAVKGRRWPSMHL 136
Cdd:TIGR01448 411 LEDPIDCDLLIVDESSMMDTWLALSLLAALPdHARLLLVGDTDQLPS------------VGPGQVLKDLILSQAIPVTRL 478


                  ....*
gi 1799133847 137 TRVHR 141
Cdd:TIGR01448 479 TKVYR 483
Viral_helicase1 pfam01443
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...
 60-293 8.57e-04

Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis.


Pssm-ID: 366646 [Multi-domain]  Cd Length: 227  Bit Score: 40.44  E-value: 8.57e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847  60 IKDRFDITFIDEASQLALYVLGSLATMLPKSRMILVGDMHQLPPymeEALPAELKRAAIgEPLTLAVKGRRwpsmhltRV 139
Cdd:pfam01443  55 LKPTGKILILDEYTLLPPGYILLLAAISGAKLVILFGDPLQIPY---HSRAPSFLIPHF-PSSLSHRVGRR-------TT 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1799133847 140 HRCPKMITEVLGDLFYGNTLTSSKPGVTDipvlkamglpsrhpmvfvnYTSPQTAVgksfsnegearyalqlvealtrya 219
Cdd:pfam01443 124 YLLPSLRAPILSAKGFEVVVERSGEYKVD-------------------YDPNGVLV------------------------ 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1799133847 220 sTANKKITAAILNFYGaqysyvysmaedeVTVNTIDGCQGQEYD-VTIVLLTRSD--PYERSKflvnANRInVALSR 293
Cdd:pfam01443 161 -LVYLTFTQALKESLG-------------VRVTTVHEVQGLTFDsVTLVLDTDTDllIISDSP----EHLY-VALTR 218
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 61-103 1.84e-03

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: 37.95  E-value: 1.84e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1799133847  61 KDRFDITFIDEASQlaLYVLGSLATMLPKSRMILVGDMHQLPP 103
Cdd:cd18043    78 RNLFDLVIFDEASQ--IPIEEALPALFRGKQVVVVGDDKQLPP 118
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 69-140 2.87e-03

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: 37.92  E-value: 2.87e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1799133847  69 IDEASQLALYVLGSLATMLPK-SRMILVGDMHQLPPymeealpaelkrAAIGEPLTLAVKGRRWPSMHLTRVH 140
Cdd:cd17933    95 VDEASMVDTRLMAALLSAIPAgARLILVGDPDQLPS------------VGAGNVLRDLIASKGVPTVELTEVF 155
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 62-103 3.21e-03

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: 37.08  E-value: 3.21e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1799133847  62 DRFDITFIDEASQLALYVLGSLATMLPK-SRMILVGDMHQLPP 103
Cdd:cd17914    45 AQLDNILVDEAAQILEPETSRLIDLALDqGRVILVGDHDQLGP 87
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
 58-103 4.31e-03

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: 37.97  E-value: 4.31e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1799133847  58 LEIKDRFDITFIDEASQlALYVlGSLATMLPKSRMILVGDMHQLPP 103
Cdd:cd18044   111 LLPNELFDVVVIDEAAQ-ALEA-SCWIPLLKARRCILAGDHKQLPP 154
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 247-302 5.32e-03

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: 35.88  E-value: 5.32e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1799133847 247 DEVTVNTIDGCQGQEYDVTIVLLTRSDPYERskflvnaNRINVALSRPKIATVIIG 302
Cdd:cd18786    41 QLVGAITIDSSQGLTFDVVTLYLPTANSLTP-------RRLYVALTRARKRLVIYD 89
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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