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Conserved domains on  [gi|568924115|ref|XP_006502172|]
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5'-3' DNA helicase ZGRF1 isoform X2 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
1651-1976 1.13e-70

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


:

Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 255.82  E-value: 1.13e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1651 YSLHAGSDNESEQLKELNALLKEELTPIERVY--VRKSIEQHKLGTNRvLLKQVRVVGVTCAACA-FPCLNDLKFPVVVL 1727
Cdd:COG1112   483 SLLEELIEEHPEELEKLIAELREAARLRRALRreLKKRRELRKLLWDA-LLELAPVVGMTPASVArLLPLGEGSFDLVII 561

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1728 DECSQMTEPASLLPIARfqCEKLILVGDPKQLPPTIQGSDAA--HENGLEQTLFDRLC-LMGHKPVLLRTQYRCHPAISA 1804
Cdd:COG1112   562 DEASQATLAEALGALAR--AKRVVLVGDPKQLPPVVFGEEAEevAEEGLDESLLDRLLaRLPERGVMLREHYRMHPEIIA 639

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1805 IANDLFYEGSLVNGISERERSPVLEWLPtLCFYNVTGAEQvERENSFVNVAEATFTLKLIQSLMASGVESCMIGVITLYK 1884
Cdd:COG1112   640 FSNRLFYDGKLVPLPSPKARRLADPDSP-LVFIDVDGVYE-RRGGSRTNPEEAEAVVELVRELLEDGPDGESIGVITPYR 717

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1885 SQMYKICNLLSAVDVGHPDvkAVQVSTVDAFQGAEKEITILSCVRT------RQVGFI-DSEKRMNVALTRGRRHLLIVG 1957
Cdd:COG1112   718 AQVALIRELLREALGDGLE--PVFVGTVDRFQGDERDVIIFSLVYSndedvpRNFGFLnGGPRRLNVAVSRARRKLIVVG 795

                         330       340
                  ....*....|....*....|..
gi 568924115 1958 SLSCL---RKNRLWGRVIQHCE 1976
Cdd:COG1112   796 SRELLdsdPSTPALKRLLEYLE 817
DUF2439 pfam10382
Protein of unknown function (DUF2439); This domain can be found in proteins that have been ...
 3-75 8.37e-24

Protein of unknown function (DUF2439); This domain can be found in proteins that have been implicated in telomere maintenance in Saccharomyces cerevisiae and in meiotic chromosome segregation in Schizosaccharomyces pombe. It can also be found in Mte1 (Mph1-associated telomere maintenance protein 1), human zinc finger protein ZGRF1 (C4ORF21) and fission yeast Dbl2. Mte1 is a D-loop-binding protein that interacts and stimulates the helicase and fork regression activities of Mph1 while inhibiting the ability of Mph1 to dissociate recombination intermediates. Mph1 and Mte1 interdependently colocalize at DNA damage-induced foci and dysfunctional telomeres. Mte1 is indicated to play a role in regulation of crossover recombination, response to replication stress, and telomere maintenance. The fission yeast, Dbl2 is needed for cellular resistance to the topoisomerase I poison camptothecin, forms DNA damage-induced foci, and is needed for the optimal recruitment of Fml1 to DNA damage, while the human ZGRF1 protein has been linked to DNA cross-link repair and mutations of it have been found in a variety of human tumors. ZGRF1 is a 5'-to-3'helicase that interacts with RAD51 and stimulates homologous recombination and, thus, promotes the repair of replication-blocking DNA lesions. Having said that, there is no evidence to suggest that this domain is implicated in DNA damage resistance or for nuclear focus formation.


:

Pssm-ID: 463065  Cd Length: 74  Bit Score: 96.42  E-value: 8.37e-24
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568924115     3 CQEFIVLYTHQKMKKSKVWQDGVLKITHLGNKAILYDDKGACLESLFLK-CLEVKPGDDLESERYLITVEEAKA 75
Cdd:pfam10382    1 VHEYRCLYTHDVRKKHKRWHDGKLKYHTFNKRVMLYDEDGNLIGSDFWTsSEDLEEGEELELDRYLVQIEELLG 74
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 1267-1311 2.74e-13

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


:

Pssm-ID: 462017  Cd Length: 45  Bit Score: 65.89  E-value: 2.74e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 568924115  1267 PSCHHNQPAKLVMVKKEGPNKGRLFYTCDKSKDNQCKFFKWLEEV 1311
Cdd:pfam06839    1 PLCPCGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWADEV 45
 
Name Accession Description Interval E-value
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
1651-1976 1.13e-70

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 255.82  E-value: 1.13e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1651 YSLHAGSDNESEQLKELNALLKEELTPIERVY--VRKSIEQHKLGTNRvLLKQVRVVGVTCAACA-FPCLNDLKFPVVVL 1727
Cdd:COG1112   483 SLLEELIEEHPEELEKLIAELREAARLRRALRreLKKRRELRKLLWDA-LLELAPVVGMTPASVArLLPLGEGSFDLVII 561

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1728 DECSQMTEPASLLPIARfqCEKLILVGDPKQLPPTIQGSDAA--HENGLEQTLFDRLC-LMGHKPVLLRTQYRCHPAISA 1804
Cdd:COG1112   562 DEASQATLAEALGALAR--AKRVVLVGDPKQLPPVVFGEEAEevAEEGLDESLLDRLLaRLPERGVMLREHYRMHPEIIA 639

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1805 IANDLFYEGSLVNGISERERSPVLEWLPtLCFYNVTGAEQvERENSFVNVAEATFTLKLIQSLMASGVESCMIGVITLYK 1884
Cdd:COG1112   640 FSNRLFYDGKLVPLPSPKARRLADPDSP-LVFIDVDGVYE-RRGGSRTNPEEAEAVVELVRELLEDGPDGESIGVITPYR 717

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1885 SQMYKICNLLSAVDVGHPDvkAVQVSTVDAFQGAEKEITILSCVRT------RQVGFI-DSEKRMNVALTRGRRHLLIVG 1957
Cdd:COG1112   718 AQVALIRELLREALGDGLE--PVFVGTVDRFQGDERDVIIFSLVYSndedvpRNFGFLnGGPRRLNVAVSRARRKLIVVG 795

                         330       340
                  ....*....|....*....|..
gi 568924115 1958 SLSCL---RKNRLWGRVIQHCE 1976
Cdd:COG1112   796 SRELLdsdPSTPALKRLLEYLE 817
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 1774-1958 9.06e-65

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: 218.57  E-value: 9.06e-65
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115  1774 LEQTLFDRLCLMG-HKPVLLRTQYRCHPAISAIANDLFYEGSLVNGISERERS-PVLEWLPT----LCFYNVTGAEQ--V 1845
Cdd:pfam13087    1 LDRSLFERLQELGpSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPlPDDFHLPDplgpLVFIDVDGSEEeeS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115  1846 ERENSFVNVAEATFTLKLIQSLMASGV-ESCMIGVITLYKSQMYKICNLLSAVDVGHPDVKavqVSTVDAFQGAEKEITI 1924
Cdd:pfam13087   81 DGGTSYSNEAEAELVVQLVEKLIKSGPeEPSDIGVITPYRAQVRLIRKLLKRKLGGKLEIE---VNTVDGFQGREKDVII 157

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 568924115  1925 LSCVRTRQ---VGFIDSEKRMNVALTRGRRHLLIVGS 1958
Cdd:pfam13087  158 FSCVRSNEkggIGFLSDPRRLNVALTRAKRGLIIVGN 194
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 1798-1976 9.40e-57

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: 195.15  E-value: 9.40e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1798 CHPAISAIANDLFYEGSLVNGISERERSPVLEWLPT---LCFYNVTGAEQVERE-NSFVNVAEATFTLKLIQSLMASGVE 1873
Cdd:cd18808     1 MHPEISEFPSKLFYEGKLKAGVSVAARLNPPPLPGPskpLVFVDVSGGEEREESgTSKSNEAEAELVVELVKYLLKSGVK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1874 SCMIGVITLYKSQMYKICNLLSAVDVGHPDVKavqVSTVDAFQGAEKEITILSCVRTRQ----VGFIDSEKRMNVALTRG 1949
Cdd:cd18808    81 PSSIGVITPYRAQVALIRELLRKRGGLLEDVE---VGTVDNFQGREKDVIILSLVRSNEsggsIGFLSDPRRLNVALTRA 157

                         170       180
                  ....*....|....*....|....*..
gi 568924115 1950 RRHLLIVGSLSCLRKNRLWGRVIQHCE 1976
Cdd:cd18808   158 KRGLIIVGNPDTLSKDPLWKKLLEYLE 184
DUF2439 pfam10382
Protein of unknown function (DUF2439); This domain can be found in proteins that have been ...
 3-75 8.37e-24

Protein of unknown function (DUF2439); This domain can be found in proteins that have been implicated in telomere maintenance in Saccharomyces cerevisiae and in meiotic chromosome segregation in Schizosaccharomyces pombe. It can also be found in Mte1 (Mph1-associated telomere maintenance protein 1), human zinc finger protein ZGRF1 (C4ORF21) and fission yeast Dbl2. Mte1 is a D-loop-binding protein that interacts and stimulates the helicase and fork regression activities of Mph1 while inhibiting the ability of Mph1 to dissociate recombination intermediates. Mph1 and Mte1 interdependently colocalize at DNA damage-induced foci and dysfunctional telomeres. Mte1 is indicated to play a role in regulation of crossover recombination, response to replication stress, and telomere maintenance. The fission yeast, Dbl2 is needed for cellular resistance to the topoisomerase I poison camptothecin, forms DNA damage-induced foci, and is needed for the optimal recruitment of Fml1 to DNA damage, while the human ZGRF1 protein has been linked to DNA cross-link repair and mutations of it have been found in a variety of human tumors. ZGRF1 is a 5'-to-3'helicase that interacts with RAD51 and stimulates homologous recombination and, thus, promotes the repair of replication-blocking DNA lesions. Having said that, there is no evidence to suggest that this domain is implicated in DNA damage resistance or for nuclear focus formation.


Pssm-ID: 463065  Cd Length: 74  Bit Score: 96.42  E-value: 8.37e-24
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568924115     3 CQEFIVLYTHQKMKKSKVWQDGVLKITHLGNKAILYDDKGACLESLFLK-CLEVKPGDDLESERYLITVEEAKA 75
Cdd:pfam10382    1 VHEYRCLYTHDVRKKHKRWHDGKLKYHTFNKRVMLYDEDGNLIGSDFWTsSEDLEEGEELELDRYLVQIEELLG 74
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 1267-1311 2.74e-13

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


Pssm-ID: 462017  Cd Length: 45  Bit Score: 65.89  E-value: 2.74e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 568924115  1267 PSCHHNQPAKLVMVKKEGPNKGRLFYTCDKSKDNQCKFFKWLEEV 1311
Cdd:pfam06839    1 PLCPCGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWADEV 45
 
Name Accession Description Interval E-value
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
1651-1976 1.13e-70

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 255.82  E-value: 1.13e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1651 YSLHAGSDNESEQLKELNALLKEELTPIERVY--VRKSIEQHKLGTNRvLLKQVRVVGVTCAACA-FPCLNDLKFPVVVL 1727
Cdd:COG1112   483 SLLEELIEEHPEELEKLIAELREAARLRRALRreLKKRRELRKLLWDA-LLELAPVVGMTPASVArLLPLGEGSFDLVII 561

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1728 DECSQMTEPASLLPIARfqCEKLILVGDPKQLPPTIQGSDAA--HENGLEQTLFDRLC-LMGHKPVLLRTQYRCHPAISA 1804
Cdd:COG1112   562 DEASQATLAEALGALAR--AKRVVLVGDPKQLPPVVFGEEAEevAEEGLDESLLDRLLaRLPERGVMLREHYRMHPEIIA 639

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1805 IANDLFYEGSLVNGISERERSPVLEWLPtLCFYNVTGAEQvERENSFVNVAEATFTLKLIQSLMASGVESCMIGVITLYK 1884
Cdd:COG1112   640 FSNRLFYDGKLVPLPSPKARRLADPDSP-LVFIDVDGVYE-RRGGSRTNPEEAEAVVELVRELLEDGPDGESIGVITPYR 717

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1885 SQMYKICNLLSAVDVGHPDvkAVQVSTVDAFQGAEKEITILSCVRT------RQVGFI-DSEKRMNVALTRGRRHLLIVG 1957
Cdd:COG1112   718 AQVALIRELLREALGDGLE--PVFVGTVDRFQGDERDVIIFSLVYSndedvpRNFGFLnGGPRRLNVAVSRARRKLIVVG 795

                         330       340
                  ....*....|....*....|..
gi 568924115 1958 SLSCL---RKNRLWGRVIQHCE 1976
Cdd:COG1112   796 SRELLdsdPSTPALKRLLEYLE 817
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 1774-1958 9.06e-65

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: 218.57  E-value: 9.06e-65
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115  1774 LEQTLFDRLCLMG-HKPVLLRTQYRCHPAISAIANDLFYEGSLVNGISERERS-PVLEWLPT----LCFYNVTGAEQ--V 1845
Cdd:pfam13087    1 LDRSLFERLQELGpSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPlPDDFHLPDplgpLVFIDVDGSEEeeS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115  1846 ERENSFVNVAEATFTLKLIQSLMASGV-ESCMIGVITLYKSQMYKICNLLSAVDVGHPDVKavqVSTVDAFQGAEKEITI 1924
Cdd:pfam13087   81 DGGTSYSNEAEAELVVQLVEKLIKSGPeEPSDIGVITPYRAQVRLIRKLLKRKLGGKLEIE---VNTVDGFQGREKDVII 157

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 568924115  1925 LSCVRTRQ---VGFIDSEKRMNVALTRGRRHLLIVGS 1958
Cdd:pfam13087  158 FSCVRSNEkggIGFLSDPRRLNVALTRAKRGLIIVGN 194
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 1798-1976 9.40e-57

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: 195.15  E-value: 9.40e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1798 CHPAISAIANDLFYEGSLVNGISERERSPVLEWLPT---LCFYNVTGAEQVERE-NSFVNVAEATFTLKLIQSLMASGVE 1873
Cdd:cd18808     1 MHPEISEFPSKLFYEGKLKAGVSVAARLNPPPLPGPskpLVFVDVSGGEEREESgTSKSNEAEAELVVELVKYLLKSGVK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1874 SCMIGVITLYKSQMYKICNLLSAVDVGHPDVKavqVSTVDAFQGAEKEITILSCVRTRQ----VGFIDSEKRMNVALTRG 1949
Cdd:cd18808    81 PSSIGVITPYRAQVALIRELLRKRGGLLEDVE---VGTVDNFQGREKDVIILSLVRSNEsggsIGFLSDPRRLNVALTRA 157

                         170       180
                  ....*....|....*....|....*..
gi 568924115 1950 RRHLLIVGSLSCLRKNRLWGRVIQHCE 1976
Cdd:cd18808   158 KRGLIIVGNPDTLSKDPLWKKLLEYLE 184
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
 1533-1797 4.96e-33

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: 127.74  E-value: 4.96e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1533 RLNKDQATALIQIaqMMAsqgsdEDalepfghslpITVIHGVFGAGKSYLLAVvilfLVELFEKCdsgtvGNarpwKVLV 1612
Cdd:cd18041     1 GLNKDQRQAIKKV--LNA-----KD----------YALILGMPGTGKTTTIAA----LVRILVAL-----GK----SVLL 50

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1613 SSSTNVAVDRVLLGLLSLGFEkFIRVGSVRKIAKPVLPYSLHAGSDNEseqlkelnallkeeltpiervyvrKSIEQHKL 1692
Cdd:cd18041    51 TSYTHSAVDNILLKLKKFGVN-FLRLGRLKKIHPDVQEFTLEAILKSC------------------------KSVEELES 105

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1693 gtnrvLLKQVRVVGVTCAACAFPCLNDLKFPVVVLDECSQMTEPASLLPIARfqCEKLILVGDPKQLPPTIQgSDAAHEN 1772
Cdd:cd18041   106 -----KYESVSVVATTCLGINHPIFRRRTFDYCIVDEASQITLPICLGPLRL--AKKFVLVGDHYQLPPLVK-SREAREL 177

                         250       260
                  ....*....|....*....|....*.
gi 568924115 1773 GLEQTLFDRLCLMGHKPVL-LRTQYR 1797
Cdd:cd18041   178 GMDESLFKRLSEAHPDAVVqLTIQYR 203
DEXXQc_UPF1 cd18039
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ...
 1567-1797 1.57e-32

DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of Nonsense Transcripts, or ATP-Dependent Helicase RENT1) is an RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. It is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. It is recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) located downstream from the termination codon through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Diseases associated with UPF1 include juvenile amyotrophic lateral sclerosis and epidermolysis bullosa, junctional, non-Herlitz type. UPF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350797 [Multi-domain]  Cd Length: 234  Bit Score: 127.36  E-value: 1.57e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1567 PITVIHGVFGAGKSyllaVVILFLVELFEKCDSGtvgnarpwKVLVSSSTNVAVDRVLLGLLSLGFeKFIRVGSVRK--I 1644
Cdd:cd18039    17 PLSLIQGPPGTGKT----VTSATIVYHLVKQGNG--------PVLVCAPSNVAVDQLTEKIHQTGL-KVVRLCAKSReaV 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1645 AKPVLPYSLHAGSDNESE-QLKELNALLKEELTPIERVYVRKSIEQhKLGTNRVLLKQVRVVGVTCAACAFPCLNDLKFP 1723
Cdd:cd18039    84 ESPVSFLALHNQVRNLDSaEKLELLKLLKLETGELSSADEKRYRKL-KRKAERELLRNADVICCTCVGAGDPRLSKMKFR 162

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568924115 1724 VVVLDECSQMTEPASLLPIARfQCEKLILVGDPKQLPPTIQGSDAAhENGLEQTLFDRLCLMGHKPVLLRTQYR 1797
Cdd:cd18039   163 TVLIDEATQATEPECLIPLVH-GAKQVILVGDHCQLGPVVMCKKAA-KAGLSQSLFERLVQLGIRPIRLQVQYR 234
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
 1534-1797 4.32e-29

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: 116.93  E-value: 4.32e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1534 LNKDQATALIQIAQMMAsqgsdedalepfghslPITVIHGVFGAGKSY-LLAVVILFLVELFEK------------CDSG 1600
Cdd:cd18042     1 LNESQLEAIASALQNSP----------------GITLIQGPPGTGKTKtIVGILSVLLAGKYRKyyekvkkklrklQRNL 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1601 TVGNARPwKVLVSSSTNVAVDRVLLGLLSLGFEKFIRVGSVRKIAkpvlpyslhagsdneseqlkelnallkeeltpieR 1680
Cdd:cd18042    65 NNKKKKN-RILVCAPSNAAVDEIVLRLLSEGFLDGDGRSYKPNVV----------------------------------R 109

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1681 VyVRKSIEQHklgtnrvLLKQVRVVGVTCAACAFPCLN--DLKFPVVVLDECSQMTEPASLLPIaRFQCEKLILVGDPKQ 1758
Cdd:cd18042   110 V-GRQELRAS-------ILNEADIVCTTLSSSGSDLLEslPRGFDTVIIDEAAQAVELSTLIPL-RLGCKRLILVGDPKQ 180

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 568924115 1759 LPPTIQGSDAAhENGLEQTLFDRLCLMGHKPVLLRTQYR 1797
Cdd:cd18042   181 LPATVFSKVAQ-KLGYDRSLFERLQLAGYPVLMLTTQYR 218
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
 1567-1797 2.74e-28

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: 113.86  E-value: 2.74e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1567 PITVIHGVFGAGKSYLLAVVILFLVElfekcdsgtvgnaRPWKVLVSSSTNVAVDRVLLGLLSLGfEKFIRVGSVRKIAK 1646
Cdd:cd18044    18 DVALIHGPPGTGKTTTVVEIILQAVK-------------RGEKVLACAPSNIAVDNLVERLVALK-VKVVRIGHPARLLE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1647 PVLPYSLHAgsdneseqlkelnallkeeltpiervyvrksieqhklgtnrvlLKQVRVVGVTC-AACAFPCLNDLKFPVV 1725
Cdd:cd18044    84 SVLDHSLDA-------------------------------------------LVAAQVVLATNtGAGSRQLLPNELFDVV 120

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568924115 1726 VLDECSQMTEPASLLPIARFQceKLILVGDPKQLPPTIQgSDAAHENGLEQTLFDRLC-LMGHKPV-LLRTQYR 1797
Cdd:cd18044   121 VIDEAAQALEASCWIPLLKAR--RCILAGDHKQLPPTIL-SDKAARGGLGVTLFERLVnLYGESVVrMLTVQYR 191
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 1568-1797 1.40e-25

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: 103.47  E-value: 1.40e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1568 ITVIHGVFGAGKSYLLAVVILFLVElfekcdsgtvgNARPWKVLVSSSTNVAVDRVllgllslgfekfirvgsvrkiakp 1647
Cdd:cd17934     1 ISLIQGPPGTGKTTTIAAIVLQLLK-----------GLRGKRVLVTAQSNVAVDNV------------------------ 45

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1648 vlpyslhagsdneseqlkelnallkeeltpiervyvrksieqhklgtnrvllkqvrvvgvtcaacafpclndlkfPVVVL 1727
Cdd:cd17934    46 ---------------------------------------------------------------------------DVVII 50

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 568924115 1728 DECSQMTEPASLLPIARfqCEKLILVGDPKQLPPTIQGSDAAH---ENGLEQTLFDRLCLMGHKPVLLRTQYR 1797
Cdd:cd17934    51 DEASQITEPELLIALIR--AKKVVLVGDPKQLPPVVQEDHAALlglSFILSLLLLFRLLLPGSPKVMLDTQYR 121
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 1567-1763 2.28e-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: 404072 [Multi-domain]  Cd Length: 248  Bit Score: 107.04  E-value: 2.28e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115  1567 PITVIHGVFGAGKSYLLAVVILFLVElfekcDSGTVGNARPwKVLVSSSTNVAVDRVLLGLLSLGFE---KFIRVGSVRK 1643
Cdd:pfam13086   14 HFTLIQGPPGTGKTTTIVELIRQLLS-----YPATSAAAGP-RILVCAPSNAAVDNILERLLRKGQKygpKIVRIGHPAA 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115  1644 IAKPVLPYSL-----------------HAGSDNESEQLKELNALLKEELTPIERVYV---------------------RK 1685
Cdd:pfam13086   88 ISEAVLPVSLdylvesklnneedaqivKDISKELEKLAKALRAFEKEIIVEKLLKSRnkdkskleqerrklrserkelRK 167

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 568924115  1686 SIEQHKLGTNRVLLKQVRVVGVTCAACAFPCLNDL-KFPVVVLDECSQMTEPASLLPIaRFQCEKLILVGDPKQLPPTI 1763
Cdd:pfam13086  168 ELRRREQSLEREILDEAQIVCSTLSGAGSRLLSSLaNFDVVIIDEAAQALEPSTLIPL-LRGPKKVVLVGDPKQLPPTV 245
DUF2439 pfam10382
Protein of unknown function (DUF2439); This domain can be found in proteins that have been ...
 3-75 8.37e-24

Protein of unknown function (DUF2439); This domain can be found in proteins that have been implicated in telomere maintenance in Saccharomyces cerevisiae and in meiotic chromosome segregation in Schizosaccharomyces pombe. It can also be found in Mte1 (Mph1-associated telomere maintenance protein 1), human zinc finger protein ZGRF1 (C4ORF21) and fission yeast Dbl2. Mte1 is a D-loop-binding protein that interacts and stimulates the helicase and fork regression activities of Mph1 while inhibiting the ability of Mph1 to dissociate recombination intermediates. Mph1 and Mte1 interdependently colocalize at DNA damage-induced foci and dysfunctional telomeres. Mte1 is indicated to play a role in regulation of crossover recombination, response to replication stress, and telomere maintenance. The fission yeast, Dbl2 is needed for cellular resistance to the topoisomerase I poison camptothecin, forms DNA damage-induced foci, and is needed for the optimal recruitment of Fml1 to DNA damage, while the human ZGRF1 protein has been linked to DNA cross-link repair and mutations of it have been found in a variety of human tumors. ZGRF1 is a 5'-to-3'helicase that interacts with RAD51 and stimulates homologous recombination and, thus, promotes the repair of replication-blocking DNA lesions. Having said that, there is no evidence to suggest that this domain is implicated in DNA damage resistance or for nuclear focus formation.


Pssm-ID: 463065  Cd Length: 74  Bit Score: 96.42  E-value: 8.37e-24
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568924115     3 CQEFIVLYTHQKMKKSKVWQDGVLKITHLGNKAILYDDKGACLESLFLK-CLEVKPGDDLESERYLITVEEAKA 75
Cdd:pfam10382    1 VHEYRCLYTHDVRKKHKRWHDGKLKYHTFNKRVMLYDEDGNLIGSDFWTsSEDLEEGEELELDRYLVQIEELLG 74
DEXXc_HELZ2-C cd18040
C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 1534-1797 2.82e-18

C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known as PPAR-alpha-interacting complex protein 285 or PRIC285 and PPAR-gamma DBD-interacting protein 1 or PDIP1) acts as a transcriptional coactivator for a number of nuclear receptors including PPARA, PPARG, THRA, THRB and RXRA. It belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350798 [Multi-domain]  Cd Length: 271  Bit Score: 87.20  E-value: 2.82e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1534 LNKDQATALIQiaqmmasqgsdedALEPfghslPITVIHGVFGAGKSYLLAVVILFLVELFEKCDSGTVGNARPWKVLVS 1613
Cdd:cd18040     2 LNPSQNHAVRT-------------ALTK-----PFTLIQGPPGTGKTVTGVHIAYWFAKQNREIQSVSGEGDGGPCVLYC 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1614 SSTNVAVDRVLLGLLSLGFEKFIRVGSvRKIAKPVLPY------------------------SLH----AGSDNESEQLK 1665
Cdd:cd18040    64 GPSNKSVDVVAELLLKVPGLKILRVYS-EQIETTEYPIpneprhpnkksereskpnselssiTLHhrirQPSNPHSQQIK 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1666 ELNALLKEELTPIERvyvrKSIEQHK---LGTNRVLLKQVRVVGVTCAACAFPCLNdLKFPV--VVLDECSQMTEPASLL 1740
Cdd:cd18040   143 AFEARFERTQEKITE----EDIKTYKiliWEARFEELETVDVILCTCSEAASQKMR-THANVkqCIVDECGMCTEPESLI 217

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 568924115 1741 PI-ARFQCEKLILVGDPKQLPPTIQgSDAAHENGLEQTLFDRLclmGHKPVLLRTQYR 1797
Cdd:cd18040   218 PIvSAPRAEQVVLIGDHKQLRPVVQ-NKEAQKLGLGRSLFERY---AEKACMLDTQYR 271
EEXXEc_NFX1 cd17936
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ...
 1555-1796 1.23e-15

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: 76.81  E-value: 1.23e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1555 DEDALEPFGHSL--PITVIHGVFGAGKSYLlAVVILFLveLFEKCDSGTVGnarpwKVLVSSSTNVAVDRVLLGLLSLGF 1632
Cdd:cd17936     3 DPSQLEALKHALtsELALIQGPPGTGKTFL-GVKLVRA--LLQNQDLSITG-----PILVVCYTNHALDQFLEGLLDFGP 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1633 EKFIRVGsvrkiakpvlpyslhagsdneseqlkelnallkeeltpiervyvrksieqhklgtnrvllkqVRVVGVTCAAC 1712
Cdd:cd17936    75 TKIVRLG--------------------------------------------------------------ARVIGMTTTGA 92

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1713 A--FPCLNDLKFPVVVLDECSQMTEP---ASLLPiarfQCEKLILVGDPKQLPPTIQG-SDAAHENGLEQTLFDRLCLMG 1786
Cdd:cd17936    93 AkyRELLQALGPKVVIVEEAAEVLEAhilAALTP----STEHLILIGDHKQLRPKVNVyELTAKKYNLDVSLFERLVKNG 168

                         250
                  ....*....|
gi 568924115 1787 HKPVLLRTQY 1796
Cdd:cd17936   169 LPFVTLNVQR 178
DEXXQc_Helz-like cd18038
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ...
 1533-1784 3.25e-15

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: 76.89  E-value: 3.25e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1533 RLNKDQATALIQIAQMMASQGsdedalePFghslpitVIHGVFGAGKSYLLAVVILFLVELFEKCdsgtvgnarpwKVLV 1612
Cdd:cd18038     1 ELNDEQKLAVRNIVTGTSRPP-------PY-------IIFGPPGTGKTVTLVEAILQVLRQPPEA-----------RILV 55

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1613 SSSTNVAVDRVLLGLLslgfekfirvgsvRKIAKPVLPYSLHAGSDNESEQLKELNALLKEELtpiERVYVRKSIEQhkl 1692
Cdd:cd18038    56 CAPSNSAADLLAERLL-------------NALVTKREILRLNAPSRDRASVPPELLPYCNSKA---EGTFRLPSLEE--- 116

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1693 gtnrvlLKQVRVVGVTCAACAFpcLNDLKFPV-----VVLDECSQMTEPASLLPIARFQCEK--LILVGDPKQLPPTIQg 1765
Cdd:cd18038   117 ------LKKYRIVVCTLMTAGR--LVQAGVPNghfthIFIDEAGQATEPEALIPLSELASKNtqIVLAGDPKQLGPVVR- 187

                         250
                  ....*....|....*....
gi 568924115 1766 SDAAHENGLEQTLFDRLCL 1784
Cdd:cd18038   188 SPLARKYGLGKSLLERLME 206
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 1267-1311 2.74e-13

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


Pssm-ID: 462017  Cd Length: 45  Bit Score: 65.89  E-value: 2.74e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 568924115  1267 PSCHHNQPAKLVMVKKEGPNKGRLFYTCDKSKDNQCKFFKWLEEV 1311
Cdd:pfam06839    1 PLCPCGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWADEV 45
EEXXQc_AQR cd17935
EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds ...
 1703-1807 2.37e-11

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: 65.14  E-value: 2.37e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1703 RVVGVTCAACAFPcLNDL-----KFPVVVLDECSQMTEPASLLPIA--RFQCE-----KLILVGDPKQLPPTIQGSDAAH 1770
Cdd:cd17935    88 KIIAMTCTHAALK-RGELvelgfKYDNILMEEAAQILEIETFIPLLlqNPEDGpnrlkRLIMIGDHHQLPPVIKNMAFQK 166

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 568924115 1771 ENGLEQTLFDRLCLMGHKPVLLRTQYRCHPAISAIAN 1807
Cdd:cd17935   167 YSNMEQSLFTRLVRLGVPTVDLDAQGRARASISSLYN 203
DEXXQc_Mov10L1 cd18078
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ...
 1534-1782 2.55e-10

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: 62.77  E-value: 2.55e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1534 LNKDQATALIQIaqmmasqgsdedaLEPFGHSLPItVIHGVFGAGKSYLLAVVILFLVELFEKCdsgtvgnarpwKVLVS 1613
Cdd:cd18078     2 LNELQKEAVKRI-------------LGGECRPLPY-ILFGPPGTGKTVTIIEAILQVVYNLPRS-----------RILVC 56

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1614 SSTNVAVDRVLLGLLSlgfEKFIRVGsvrkiakpvlpyslhagsdneseQLKELNALLKEELT--PIERVYVRKSIEQHK 1691
Cdd:cd18078    57 APSNSAADLVTSRLHE---SKVLKPG-----------------------DMVRLNAVNRFESTviDARKLYCRLGEDLSK 110

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1692 LGTNRVLLKQVRVVGVtcaacafpcLNDLKFPV-----VVLDECSQMTEPASLLPIARFQCE--KLILVGDPKQLPPTIQ 1764
Cdd:cd18078   111 ASRHRIVISTCSTAGL---------LYQMGLPVghfthVFVDEAGQATEPESLIPLGLISSRdgQIILAGDPMQLGPVIK 181

                         250
                  ....*....|....*...
gi 568924115 1765 gSDAAHENGLEQTLFDRL 1782
Cdd:cd18078   182 -SRLASAYGLGVSFLERL 198
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 1720-1796 9.07e-09

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: 55.57  E-value: 9.07e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 568924115 1720 LKFPVVVLDECSQMTEPASLLPIARF-QCEKLILVGDPKQLPPTIQGSDAAhENGLEQTLFDRLCLMGHKPVLLRTQY 1796
Cdd:cd17914    45 AQLDNILVDEAAQILEPETSRLIDLAlDQGRVILVGDHDQLGPVWRGAVLA-KICNEQSLFTRLVRLGVSLIRLQVQY 121
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 1877-1957 1.87e-08

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: 53.60  E-value: 1.87e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1877 IGVITLYKSQMYKICNLLSAVDVGHPDVKAVQVSTVDAFQGAEKEITILSCVRTrqvgFIDSEKRMNVALTRGRRHLLIV 1956
Cdd:cd18786    13 GVVLTPYHRDRAYLNQYLQGLSLDEFDLQLVGAITIDSSQGLTFDVVTLYLPTA----NSLTPRRLYVALTRARKRLVIY 88


                  .
gi 568924115 1957 G 1957
Cdd:cd18786    89 D 89
CoV_Nsp13-helicase cd21718
helicase domain of coronavirus non-structural protein 13; This model represents the helicase ...
 1717-1956 1.29e-07

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: 56.00  E-value: 1.29e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1717 LNDLKFPVVVLDECSQMTEPASLLPIARFQCEKLILVGDPKQLP-PTIQGSdaahENGLEQTLFDRLC-LMGH-KP-VLL 1792
Cdd:cd21718   113 LPECSADIVVVDEVSMCTNYDLSVVNARLKYKHIVYVGDPAQLPaPRTLLT----EGSLEPKDYNVVTrLMVGsGPdVFL 188

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1793 RTQYRCHPAISAIANDLFYEGSL--VNGISErerspvlewlptlCFYNVTGAEQVEREN-SFVNVAEatftLKLIQSLMA 1869
Cdd:cd21718   189 SKCYRCPKEIVDTVSKLVYDNKLkaIKPKSR-------------QCFKTFGKGDVRHDNgSAINRPQ----LEFVKRFLD 251

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1870 SGVESCMIGVITLYKSQMYKICNLLsavdvghpdvkAVQVSTVDAFQGAEKEITILsCVrTRQVGFIDSEKRMNVALTRG 1949
Cdd:cd21718   252 RNPRWRKAVFISPYNAMNNRASRLL-----------GLSTQTVDSSQGSEYDYVIF-CQ-TTDTAHALNINRFNVAITRA 318


                  ....*..
gi 568924115 1950 RRHLLIV 1956
Cdd:cd21718   319 KHGILVI 325
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 1717-1763 8.69e-07

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: 49.89  E-value: 8.69e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 568924115 1717 LNDLKFPVVVLDECSQMTEPASLLPIARfqCEKLILVGDPKQLPPTI 1763
Cdd:cd18043    76 LNRNLFDLVIFDEASQIPIEEALPALFR--GKQVVVVGDDKQLPPSI 120
alphaCoV_Nsp13-helicase cd21723
helicase domain of alphacoronavirus non-structural protein 13; This model represents the ...
 1724-1956 2.25e-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: 48.96  E-value: 2.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1724 VVVLDECSQMTEPASLLPIARFQCEKLILVGDPKQLP-PTIQGSDAAHENGLEQTLFDRLCLMGhKPVLLRTQYRCHPAI 1802
Cdd:cd21723   120 IVVVDEVSMCTNYDLSVINQRVSYKHIVYVGDPQQLPaPRTMITRGVLEPKDYNVVTQRMCALG-PDVFLHKCYRCPAEI 198

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1803 SAIANDLFYEGSL--VNGISERerspvlewlptlCF-YNVTGAEQVErENSFVNVAEatftLKLIQSLMASGVESCMIGV 1879
Cdd:cd21723   199 VNTVSELVYENKFkpVHPESKQ------------CFkIFCKGNVQVD-NGSSINRRQ----LDVVKMFLAKNPKWSKAVF 261

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568924115 1880 ITLYKSQMYKICNLLsavdvghpdvkAVQVSTVDAFQGAEKEITILScvRTRQVGFIDSEKRMNVALTRGRRHLLIV 1956
Cdd:cd21723   262 ISPYNSQNYVASRVL-----------GLQIQTVDSSQGSEYDYVIYT--QTSDTAHACNVNRFNVAITRAKKGILCV 325
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 1718-1761 6.91e-05

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: 45.24  E-value: 6.91e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 568924115 1718 NDLKFPVVVLDECSQMTEP--ASLLPIARFQCeKLILVGDPKQLPP 1761
Cdd:cd17933    86 NPLDADLLIVDEASMVDTRlmAALLSAIPAGA-RLILVGDPDQLPS 130
gammaCoV_Nsp13-helicase cd21720
helicase domain of gammacoronavirus non-structural protein 13; This model represents the ...
 1724-1956 7.45e-05

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: 47.22  E-value: 7.45e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1724 VVVLDECSQMTEPASLLPIARFQCEKLILVGDPKQLPPT---IQGSDAAHENGLEQTLFdrLCLmghKP-VLLRTQYRCH 1799
Cdd:cd21720   120 ILLVDEVSMLTNYELSFINGKINYQYVVYVGDPAQLPAPrtlLNGSLSPKDYNVVTNLM--VCV---KPdIFLAKCYRCP 194

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1800 PAISAIANDLFYEGSLVNGISERERspvlewlptlCFYNV--TGAEQVEREN-SFVNVAEATFTLKLIQSLMaSGVESCM 1876
Cdd:cd21720   195 KEIVDTVSTLVYDGKFIANNPESRQ----------CFKVIvnNGNSDVGHESgSAYNTTQLEFVKDFVCRNK-EWREATF 263

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1877 IGVITLYKSQMYKICNLlsavdvghpdvkavQVSTVDAFQGAEKEITILsCVRTrqvgfiDSE-----KRMNVALTRGRR 1951
Cdd:cd21720   264 ISPYNAMNQRAYRMLGL--------------NVQTVDSSQGSEYDYVIF-CVTA------DSQhalniNRFNVALTRAKR 322


                  ....*
gi 568924115 1952 HLLIV 1956
Cdd:cd21720   323 GILVV 327
DEXXQc_HELZ cd18077
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that ...
 1533-1782 2.45e-04

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: 44.78  E-value: 2.45e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1533 RLNKDQATALIQIAQmmasqgsdedalePFGHSLPITVIHGVFGAGKSYLLAVVILFLVElfekcDSGTvgnarpwKVLV 1612
Cdd:cd18077     1 RLNAKQKEAVLAITT-------------PLSIQLPPVLLIGPFGTGKTFTLAQAVKHILQ-----QPET-------RILI 55

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1613 SSSTNVAVDRVLLGLLslgfEKFIRVGSVRkiAKPVLPYsLHAGSDNESEQLKELNALLKEELTpiERVYVRKSIEQHkl 1692
Cdd:cd18077    56 CTHSNSAADLYIKEYL----HPYVETGNPR--ARPLRVY-YRNRWVKTVHPVVQKYCLIDEHGT--FRMPTREDVMRH-- 124

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568924115 1693 gtnrvllkqvRVVGVTCAACAFPCLNDLK---FPVVVLDECSQMTEPASLLPIA-RFQCEKLILVGDPKQLPPTIQgSDA 1768
Cdd:cd18077   125 ----------RVVVVTLSTSQYLCQLDLEpgfFTHILLDEAAQAMECEAIMPLAlATKSTRIVLAGDHMQLSPEVY-SEF 193

                         250
                  ....*....|....
gi 568924115 1769 AHENGLEQTLFDRL 1782
Cdd:cd18077   194 ARERNLHISLLERL 207
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 1724-1761 1.96e-03

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: 43.04  E-value: 1.96e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 568924115 1724 VVVLDECSQMTEP--ASLLPIARFQCEKLILVGDPKQLPP 1761
Cdd:COG0507   221 LLVVDEASMVDTRlmAALLEALPRAGARLILVGDPDQLPS 260
 
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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