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Conserved domains on  [gi|2462598042|ref|XP_054206398|]
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protein ZGRF1 isoform X7 [Homo sapiens]

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];
1608-1979 9.73e-69

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


:

Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 249.66  E-value: 9.73e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1608 ARPWKLLISSSTNVAVDRVLLGLLSLGFENFIRVGSVRKIAKPILPYSLHAGSENESEQLKELHALMKEDLTPTERVY-- 1685
Cdd:COG1112    437 LLALLLLLAAALAALLALLLLLLLALAALLLLLAAAAALLALALLESLLEELIEEHPEELEKLIAELREAARLRRALRre 516

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1686 VRKSIEQHKLGTNRtLLKQVRVVGVTCAACP-FPCMNDLKFPVVVLDECSQITEPASLLPIARfeCEKLILVGDPKQLPP 1764
Cdd:COG1112    517 LKKRRELRKLLWDA-LLELAPVVGMTPASVArLLPLGEGSFDLVIIDEASQATLAEALGALAR--AKRVVLVGDPKQLPP 593

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1765 TIQGSDAA--HENGLEQTLFDRLC-LMGHKPILLRTQYRCHPAISAIANDLFYKGALMNGVTEIERSPLLEWLPtLCFYN 1841
Cdd:COG1112    594 VVFGEEAEevAEEGLDESLLDRLLaRLPERGVMLREHYRMHPEIIAFSNRLFYDGKLVPLPSPKARRLADPDSP-LVFID 672

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1842 VKGLEQiERDNSFHNVAEATFTLKLIQSLIASGIAGSMIGVITLYKSQMYKLCHLLSAVDFHHPDikTVQVSTVDAFQGA 1921
Cdd:COG1112    673 VDGVYE-RRGGSRTNPEEAEAVVELVRELLEDGPDGESIGVITPYRAQVALIRELLREALGDGLE--PVFVGTVDRFQGD 749

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462598042 1922 EKEIIILSCVRT------RQVGFI-DSEKRMNVALTRGKRHLLIVGNLACL---RKNQLWGRVIQHCE 1979
Cdd:COG1112    750 ERDVIIFSLVYSndedvpRNFGFLnGGPRRLNVAVSRARRKLIVVGSRELLdsdPSTPALKRLLEYLE 817
DUF2439 pfam10382
Protein of unknown function (DUF2439); This domain can be found in proteins that have been ...
 4-54 6.09e-14

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: 68.69  E-value: 6.09e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462598042    4 QEFIVLYTHQKMKKSKVWQDGILKITHLGNKV---------------------KPGDDLESDRYLITVEEVK 54
Cdd:pfam10382    2 HEYRCLYTHDVRKKHKRWHDGKLKYHTFNKRVmlydedgnligsdfwtssedlEEGEELELDRYLVQIEELL 73
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 1269-1313 2.33e-12

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: 63.19  E-value: 2.33e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2462598042 1269 PSCHHSQPAKLVMVKKEGPNKGRLFYTCDGPKADRCKFFKWLEDV 1313
Cdd:pfam06839    1 PLCPCGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWADEV 45
 
Name Accession Description Interval E-value
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
1608-1979 9.73e-69

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 249.66  E-value: 9.73e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1608 ARPWKLLISSSTNVAVDRVLLGLLSLGFENFIRVGSVRKIAKPILPYSLHAGSENESEQLKELHALMKEDLTPTERVY-- 1685
Cdd:COG1112    437 LLALLLLLAAALAALLALLLLLLLALAALLLLLAAAAALLALALLESLLEELIEEHPEELEKLIAELREAARLRRALRre 516

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1686 VRKSIEQHKLGTNRtLLKQVRVVGVTCAACP-FPCMNDLKFPVVVLDECSQITEPASLLPIARfeCEKLILVGDPKQLPP 1764
Cdd:COG1112    517 LKKRRELRKLLWDA-LLELAPVVGMTPASVArLLPLGEGSFDLVIIDEASQATLAEALGALAR--AKRVVLVGDPKQLPP 593

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1765 TIQGSDAA--HENGLEQTLFDRLC-LMGHKPILLRTQYRCHPAISAIANDLFYKGALMNGVTEIERSPLLEWLPtLCFYN 1841
Cdd:COG1112    594 VVFGEEAEevAEEGLDESLLDRLLaRLPERGVMLREHYRMHPEIIAFSNRLFYDGKLVPLPSPKARRLADPDSP-LVFID 672

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1842 VKGLEQiERDNSFHNVAEATFTLKLIQSLIASGIAGSMIGVITLYKSQMYKLCHLLSAVDFHHPDikTVQVSTVDAFQGA 1921
Cdd:COG1112    673 VDGVYE-RRGGSRTNPEEAEAVVELVRELLEDGPDGESIGVITPYRAQVALIRELLREALGDGLE--PVFVGTVDRFQGD 749

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462598042 1922 EKEIIILSCVRT------RQVGFI-DSEKRMNVALTRGKRHLLIVGNLACL---RKNQLWGRVIQHCE 1979
Cdd:COG1112    750 ERDVIIFSLVYSndedvpRNFGFLnGGPRRLNVAVSRARRKLIVVGSRELLdsdPSTPALKRLLEYLE 817
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 1777-1961 2.09e-67

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: 225.89  E-value: 2.09e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1777 LEQTLFDRLCLMG-HKPILLRTQYRCHPAISAIANDLFYKGALMNGVTEIERSPL-LEWLPT----LCFYNVKGLEQIER 1850
Cdd:pfam13087    1 LDRSLFERLQELGpSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPdDFHLPDplgpLVFIDVDGSEEEES 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1851 D--NSFHNVAEATFTLKLIQSLIASGI-AGSMIGVITLYKSQMYKLCHLLSAVDFHHPDIKtvqVSTVDAFQGAEKEIII 1927
Cdd:pfam13087   81 DggTSYSNEAEAELVVQLVEKLIKSGPeEPSDIGVITPYRAQVRLIRKLLKRKLGGKLEIE---VNTVDGFQGREKDVII 157

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 2462598042 1928 LSCVRTRQ---VGFIDSEKRMNVALTRGKRHLLIVGN 1961
Cdd:pfam13087  158 FSCVRSNEkggIGFLSDPRRLNVALTRAKRGLIIVGN 194
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 1801-1979 2.71e-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: 196.69  E-value: 2.71e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1801 CHPAISAIANDLFYKGALMNGVTEIERSPLLEWLPT---LCFYNVKGLEQIERD-NSFHNVAEATFTLKLIQSLIASGIA 1876
Cdd:cd18808      1 MHPEISEFPSKLFYEGKLKAGVSVAARLNPPPLPGPskpLVFVDVSGGEEREESgTSKSNEAEAELVVELVKYLLKSGVK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1877 GSMIGVITLYKSQMYKLCHLLSAvdfHHPDIKTVQVSTVDAFQGAEKEIIILSCVRTRQ----VGFIDSEKRMNVALTRG 1952
Cdd:cd18808     81 PSSIGVITPYRAQVALIRELLRK---RGGLLEDVEVGTVDNFQGREKDVIILSLVRSNEsggsIGFLSDPRRLNVALTRA 157

                          170       180
                   ....*....|....*....|....*..
gi 2462598042 1953 KRHLLIVGNLACLRKNQLWGRVIQHCE 1979
Cdd:cd18808    158 KRGLIIVGNPDTLSKDPLWKKLLEYLE 184
DUF2439 pfam10382
Protein of unknown function (DUF2439); This domain can be found in proteins that have been ...
 4-54 6.09e-14

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: 68.69  E-value: 6.09e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462598042    4 QEFIVLYTHQKMKKSKVWQDGILKITHLGNKV---------------------KPGDDLESDRYLITVEEVK 54
Cdd:pfam10382    2 HEYRCLYTHDVRKKHKRWHDGKLKYHTFNKRVmlydedgnligsdfwtssedlEEGEELELDRYLVQIEELL 73
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 1269-1313 2.33e-12

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: 63.19  E-value: 2.33e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2462598042 1269 PSCHHSQPAKLVMVKKEGPNKGRLFYTCDGPKADRCKFFKWLEDV 1313
Cdd:pfam06839    1 PLCPCGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWADEV 45
 
Name Accession Description Interval E-value
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
1608-1979 9.73e-69

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 249.66  E-value: 9.73e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1608 ARPWKLLISSSTNVAVDRVLLGLLSLGFENFIRVGSVRKIAKPILPYSLHAGSENESEQLKELHALMKEDLTPTERVY-- 1685
Cdd:COG1112    437 LLALLLLLAAALAALLALLLLLLLALAALLLLLAAAAALLALALLESLLEELIEEHPEELEKLIAELREAARLRRALRre 516

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1686 VRKSIEQHKLGTNRtLLKQVRVVGVTCAACP-FPCMNDLKFPVVVLDECSQITEPASLLPIARfeCEKLILVGDPKQLPP 1764
Cdd:COG1112    517 LKKRRELRKLLWDA-LLELAPVVGMTPASVArLLPLGEGSFDLVIIDEASQATLAEALGALAR--AKRVVLVGDPKQLPP 593

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1765 TIQGSDAA--HENGLEQTLFDRLC-LMGHKPILLRTQYRCHPAISAIANDLFYKGALMNGVTEIERSPLLEWLPtLCFYN 1841
Cdd:COG1112    594 VVFGEEAEevAEEGLDESLLDRLLaRLPERGVMLREHYRMHPEIIAFSNRLFYDGKLVPLPSPKARRLADPDSP-LVFID 672

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1842 VKGLEQiERDNSFHNVAEATFTLKLIQSLIASGIAGSMIGVITLYKSQMYKLCHLLSAVDFHHPDikTVQVSTVDAFQGA 1921
Cdd:COG1112    673 VDGVYE-RRGGSRTNPEEAEAVVELVRELLEDGPDGESIGVITPYRAQVALIRELLREALGDGLE--PVFVGTVDRFQGD 749

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462598042 1922 EKEIIILSCVRT------RQVGFI-DSEKRMNVALTRGKRHLLIVGNLACL---RKNQLWGRVIQHCE 1979
Cdd:COG1112    750 ERDVIIFSLVYSndedvpRNFGFLnGGPRRLNVAVSRARRKLIVVGSRELLdsdPSTPALKRLLEYLE 817
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 1777-1961 2.09e-67

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: 225.89  E-value: 2.09e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1777 LEQTLFDRLCLMG-HKPILLRTQYRCHPAISAIANDLFYKGALMNGVTEIERSPL-LEWLPT----LCFYNVKGLEQIER 1850
Cdd:pfam13087    1 LDRSLFERLQELGpSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPdDFHLPDplgpLVFIDVDGSEEEES 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1851 D--NSFHNVAEATFTLKLIQSLIASGI-AGSMIGVITLYKSQMYKLCHLLSAVDFHHPDIKtvqVSTVDAFQGAEKEIII 1927
Cdd:pfam13087   81 DggTSYSNEAEAELVVQLVEKLIKSGPeEPSDIGVITPYRAQVRLIRKLLKRKLGGKLEIE---VNTVDGFQGREKDVII 157

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 2462598042 1928 LSCVRTRQ---VGFIDSEKRMNVALTRGKRHLLIVGN 1961
Cdd:pfam13087  158 FSCVRSNEkggIGFLSDPRRLNVALTRAKRGLIIVGN 194
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 1801-1979 2.71e-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: 196.69  E-value: 2.71e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1801 CHPAISAIANDLFYKGALMNGVTEIERSPLLEWLPT---LCFYNVKGLEQIERD-NSFHNVAEATFTLKLIQSLIASGIA 1876
Cdd:cd18808      1 MHPEISEFPSKLFYEGKLKAGVSVAARLNPPPLPGPskpLVFVDVSGGEEREESgTSKSNEAEAELVVELVKYLLKSGVK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1877 GSMIGVITLYKSQMYKLCHLLSAvdfHHPDIKTVQVSTVDAFQGAEKEIIILSCVRTRQ----VGFIDSEKRMNVALTRG 1952
Cdd:cd18808     81 PSSIGVITPYRAQVALIRELLRK---RGGLLEDVEVGTVDNFQGREKDVIILSLVRSNEsggsIGFLSDPRRLNVALTRA 157

                          170       180
                   ....*....|....*....|....*..
gi 2462598042 1953 KRHLLIVGNLACLRKNQLWGRVIQHCE 1979
Cdd:cd18808    158 KRGLIIVGNPDTLSKDPLWKKLLEYLE 184
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
 1536-1800 6.96e-34

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: 130.05  E-value: 6.96e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1536 KLNKDQATALIQIaqMMASHesieevkelqthtfpITIIHGVFGAGKSYLLAVVILFFVQLfekseaptiGNarpwKLLI 1615
Cdd:cd18041      1 GLNKDQRQAIKKV--LNAKD---------------YALILGMPGTGKTTTIAALVRILVAL---------GK----SVLL 50

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1616 SSSTNVAVDRVLLGLLSLGFeNFIRVGSVRKIAKPILPYSLHAGSENESEqLKELHalmkedltptervyvrksieqhkl 1695
Cdd:cd18041     51 TSYTHSAVDNILLKLKKFGV-NFLRLGRLKKIHPDVQEFTLEAILKSCKS-VEELE------------------------ 104

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1696 gtnrTLLKQVRVVGVTCAACPFPCMNDLKFPVVVLDECSQITEPASLLPIARfeCEKLILVGDPKQLPPTIQgSDAAHEN 1775
Cdd:cd18041    105 ----SKYESVSVVATTCLGINHPIFRRRTFDYCIVDEASQITLPICLGPLRL--AKKFVLVGDHYQLPPLVK-SREAREL 177

                          250       260
                   ....*....|....*....|....*.
gi 2462598042 1776 GLEQTLFDRLCLMGHKPIL-LRTQYR 1800
Cdd:cd18041    178 GMDESLFKRLSEAHPDAVVqLTIQYR 203
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
 1537-1800 1.98e-28

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: 115.00  E-value: 1.98e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1537 LNKDQATALIQIAQMMashesieevkelqthtFPITIIHGVFGAGK--------SYLLAVVILFFVQLFEKSEAPTIGNA 1608
Cdd:cd18042      1 LNESQLEAIASALQNS----------------PGITLIQGPPGTGKtktivgilSVLLAGKYRKYYEKVKKKLRKLQRNL 64

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1609 RPW----KLLISSSTNVAVDRVLLGLLSLGFENFIRVGSVRKIAkpilpyslhagseneseqlkelhalmkedltpteRV 1684
Cdd:cd18042     65 NNKkkknRILVCAPSNAAVDEIVLRLLSEGFLDGDGRSYKPNVV----------------------------------RV 110

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1685 yVRKSIEQHklgtnrtLLKQVRVVGVT--CAACPFPCMNDLKFPVVVLDECSQITEPASLLPIaRFECEKLILVGDPKQL 1762
Cdd:cd18042    111 -GRQELRAS-------ILNEADIVCTTlsSSGSDLLESLPRGFDTVIIDEAAQAVELSTLIPL-RLGCKRLILVGDPKQL 181

                          250       260       270
                   ....*....|....*....|....*....|....*...
gi 2462598042 1763 PPTIQGSDAAhENGLEQTLFDRLCLMGHKPILLRTQYR 1800
Cdd:cd18042    182 PATVFSKVAQ-KLGYDRSLFERLQLAGYPVLMLTTQYR 218
DEXXQc_UPF1 cd18039
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ...
 1570-1800 3.24e-28

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: 115.04  E-value: 3.24e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1570 PITIIHGVFGAGKSYLLAVVILFFVQLfekseapTIGnarpwKLLISSSTNVAVDRVLLGLLSLGFeNFIRVGSVRK--I 1647
Cdd:cd18039     17 PLSLIQGPPGTGKTVTSATIVYHLVKQ-------GNG-----PVLVCAPSNVAVDQLTEKIHQTGL-KVVRLCAKSReaV 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1648 AKPILPYSLH----AGSENESEQLKELHALMKEDLTPTERVYVRKSIEQhklgTNRTLLKQVRVVGVTCAACPFPCMNDL 1723
Cdd:cd18039     84 ESPVSFLALHnqvrNLDSAEKLELLKLLKLETGELSSADEKRYRKLKRK----AERELLRNADVICCTCVGAGDPRLSKM 159

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462598042 1724 KFPVVVLDECSQITEPASLLPIARfECEKLILVGDPKQLPPTIQGSDAAhENGLEQTLFDRLCLMGHKPILLRTQYR 1800
Cdd:cd18039    160 KFRTVLIDEATQATEPECLIPLVH-GAKQVILVGDHCQLGPVVMCKKAA-KAGLSQSLFERLVQLGIRPIRLQVQYR 234
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
 1570-1800 2.50e-26

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: 108.08  E-value: 2.50e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1570 PITIIHGVFGAGKSYLLAVVILFFVQlfekseaptignaRPWKLLISSSTNVAVDRVLLGLLSLGfENFIRVGSVRKIAK 1649
Cdd:cd18044     18 DVALIHGPPGTGKTTTVVEIILQAVK-------------RGEKVLACAPSNIAVDNLVERLVALK-VKVVRIGHPARLLE 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1650 PILPYSLHAgseneseqlkelhalmkedltptervyvrksieqhklgtnrtlLKQVRVVGVTC-AACPFPCMNDLKFPVV 1728
Cdd:cd18044     84 SVLDHSLDA-------------------------------------------LVAAQVVLATNtGAGSRQLLPNELFDVV 120

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462598042 1729 VLDECSQITEPASLLPIARFEceKLILVGDPKQLPPTIQgSDAAHENGLEQTLFDRLcLMGHKP---ILLRTQYR 1800
Cdd:cd18044    121 VIDEAAQALEASCWIPLLKAR--RCILAGDHKQLPPTIL-SDKAARGGLGVTLFERL-VNLYGEsvvRMLTVQYR 191
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 1571-1800 1.49e-24

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: 100.39  E-value: 1.49e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1571 ITIIHGVFGAGKSYLLAVVILFFVQlfekseaptigNARPWKLLISSSTNVAVDRVllgllslgfenfirvgsvrkiakp 1650
Cdd:cd17934      1 ISLIQGPPGTGKTTTIAAIVLQLLK-----------GLRGKRVLVTAQSNVAVDNV------------------------ 45

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1651 ilpyslhagseneseqlkelhalmkedltptervyvrksieqhklgtnrtllkqvrvvgvtcaacpfpcmndlkfPVVVL 1730
Cdd:cd17934     46 ---------------------------------------------------------------------------DVVII 50

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462598042 1731 DECSQITEPASLLPIARfeCEKLILVGDPKQLPPTIQGSDAAH---ENGLEQTLFDRLCLMGHKPILLRTQYR 1800
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 ...
 1570-1766 1.29e-23

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: 102.04  E-value: 1.29e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1570 PITIIHGVFGAGKSyllaVVIL-FFVQLFekSEAPTIGNARPwKLLISSSTNVAVDRVLLGLLSLGFE---NFIRVGSVR 1645
Cdd:pfam13086   14 HFTLIQGPPGTGKT----TTIVeLIRQLL--SYPATSAAAGP-RILVCAPSNAAVDNILERLLRKGQKygpKIVRIGHPA 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1646 KIAKPILPYSL----------------------------HAGSENESEQLKELHALMKEDLTPTERVY----------VR 1687
Cdd:pfam13086   87 AISEAVLPVSLdylvesklnneedaqivkdiskeleklaKALRAFEKEIIVEKLLKSRNKDKSKLEQErrklrserkeLR 166

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1688 KSIEQHKLGTNRTLLKQVRVVGVTCAACPFPCMNDL-KFPVVVLDECSQITEPASLLPIaRFECEKLILVGDPKQLPPTI 1766
Cdd:pfam13086  167 KELRRREQSLEREILDEAQIVCSTLSGAGSRLLSSLaNFDVVIIDEAAQALEPSTLIPL-LRGPKKVVLVGDPKQLPPTV 245
DEXXc_HELZ2-C cd18040
C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 1536-1800 1.13e-17

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


Pssm-ID: 350798 [Multi-domain]  Cd Length: 271  Bit Score: 85.27  E-value: 1.13e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1536 KLNKDQATAliqiaqmmashesieeVKELQTHtfPITIIHGVFGAGKSYLLAVVILFFVQLFEKSEAPTIGNARPWKLLI 1615
Cdd:cd18040      1 KLNPSQNHA----------------VRTALTK--PFTLIQGPPGTGKTVTGVHIAYWFAKQNREIQSVSGEGDGGPCVLY 62

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1616 SSSTNVAVDRVLLGLLSLGFENFIRVGSVR----KIAKPILPYSLHAGSENESEQLKE-----LHALMKEDLTPT----- 1681
Cdd:cd18040     63 CGPSNKSVDVVAELLLKVPGLKILRVYSEQiettEYPIPNEPRHPNKKSERESKPNSElssitLHHRIRQPSNPHsqqik 142

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1682 --ERVYVRksiEQHKLGTNRT-------------LLKQVRVVGVTCAACPFPCMNdLKFPV--VVLDECSQITEPASLLP 1744
Cdd:cd18040    143 afEARFER---TQEKITEEDIktykiliwearfeELETVDVILCTCSEAASQKMR-THANVkqCIVDECGMCTEPESLIP 218

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462598042 1745 I-ARFECEKLILVGDPKQLPPTIQgSDAAHENGLEQTLFDRLclmGHKPILLRTQYR 1800
Cdd:cd18040    219 IvSAPRAEQVVLIGDHKQLRPVVQ-NKEAQKLGLGRSLFERY---AEKACMLDTQYR 271
DUF2439 pfam10382
Protein of unknown function (DUF2439); This domain can be found in proteins that have been ...
 4-54 6.09e-14

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: 68.69  E-value: 6.09e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462598042    4 QEFIVLYTHQKMKKSKVWQDGILKITHLGNKV---------------------KPGDDLESDRYLITVEEVK 54
Cdd:pfam10382    2 HEYRCLYTHDVRKKHKRWHDGKLKYHTFNKRVmlydedgnligsdfwtssedlEEGEELELDRYLVQIEELL 73
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 1269-1313 2.33e-12

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: 63.19  E-value: 2.33e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2462598042 1269 PSCHHSQPAKLVMVKKEGPNKGRLFYTCDGPKADRCKFFKWLEDV 1313
Cdd:pfam06839    1 PLCPCGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWADEV 45
EEXXEc_NFX1 cd17936
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ...
 1537-1799 2.89e-12

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: 67.18  E-value: 2.89e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1537 LNKDQATALiqiaQMMASHEsieevkelqthtfpITIIHGVFGAGKSYLLAVVILFFVQLFEKSEAPTIgnarpwklLIS 1616
Cdd:cd17936      2 LDPSQLEAL----KHALTSE--------------LALIQGPPGTGKTFLGVKLVRALLQNQDLSITGPI--------LVV 55

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1617 SSTNVAVDRVLLGLLSLGFENFIRVGsvrkiakpilpyslhagseneseqlkelhalmkedltptervyvrksieqhklg 1696
Cdd:cd17936     56 CYTNHALDQFLEGLLDFGPTKIVRLG------------------------------------------------------ 81

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1697 tnrtllkqVRVVGVT--CAACPFPCMNDLKFPVVVLDECSQITEP---ASLLPiarfECEKLILVGDPKQLPPTIQG-SD 1770
Cdd:cd17936     82 --------ARVIGMTttGAAKYRELLQALGPKVVIVEEAAEVLEAhilAALTP----STEHLILIGDHKQLRPKVNVyEL 149

                          250       260
                   ....*....|....*....|....*....
gi 2462598042 1771 AAHENGLEQTLFDRLCLMGHKPILLRTQY 1799
Cdd:cd17936    150 TAKKYNLDVSLFERLVKNGLPFVTLNVQR 178
DEXXQc_Helz-like cd18038
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ...
 1537-1787 7.37e-12

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: 67.26  E-value: 7.37e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1537 LNKDQATALIQIAQmmashesieevkelQTHTFPITIIHGVFGAGKSYLLAVVILFFVQLFEKSeaptignarpwKLLIS 1616
Cdd:cd18038      2 LNDEQKLAVRNIVT--------------GTSRPPPYIIFGPPGTGKTVTLVEAILQVLRQPPEA-----------RILVC 56

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1617 SSTNVAVDRVLLGLLslgfenfirvgsvRKIAKPILPYSLHAGSENESEQLKELHALMKEDLtptERVYVRKSIEQhklg 1696
Cdd:cd18038     57 APSNSAADLLAERLL-------------NALVTKREILRLNAPSRDRASVPPELLPYCNSKA---EGTFRLPSLEE---- 116

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1697 tnrtlLKQVRVVGVTC--------AACPFPcmndlKFPVVVLDECSQITEPASLLPIAR---FECEkLILVGDPKQLPPT 1765
Cdd:cd18038    117 -----LKKYRIVVCTLmtagrlvqAGVPNG-----HFTHIFIDEAGQATEPEALIPLSElasKNTQ-IVLAGDPKQLGPV 185

                          250       260
                   ....*....|....*....|..
gi 2462598042 1766 IQgSDAAHENGLEQTLFDRLCL 1787
Cdd:cd18038    186 VR-SPLARKYGLGKSLLERLME 206
EEXXQc_AQR cd17935
EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds ...
 1706-1810 9.82e-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: 63.21  E-value: 9.82e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1706 RVVGVTCAACPFP----CMNDLKFPVVVLDECSQITEPASLLPIA--RFECE-----KLILVGDPKQLPPTIQGSDAAHE 1774
Cdd:cd17935     88 KIIAMTCTHAALKrgelVELGFKYDNILMEEAAQILEIETFIPLLlqNPEDGpnrlkRLIMIGDHHQLPPVIKNMAFQKY 167

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 2462598042 1775 NGLEQTLFDRLCLMGHKPILLRTQYRCHPAISAIAN 1810
Cdd:cd17935    168 SNMEQSLFTRLVRLGVPTVDLDAQGRARASISSLYN 203
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 1723-1799 5.74e-10

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: 58.65  E-value: 5.74e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462598042 1723 LKFPVVVLDECSQITEPASLLPIARFE-CEKLILVGDPKQLPPTIQGSDAAhENGLEQTLFDRLCLMGHKPILLRTQY 1799
Cdd:cd17914     45 AQLDNILVDEAAQILEPETSRLIDLALdQGRVILVGDHDQLGPVWRGAVLA-KICNEQSLFTRLVRLGVSLIRLQVQY 121
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 1880-1960 1.80e-09

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: 56.29  E-value: 1.80e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1880 IGVITLYKSQMYKLCHLLSAVDFHHPDIKTVQVSTVDAFQGAEKEIIILSCVRTrqvgFIDSEKRMNVALTRGKRHLLIV 1959
Cdd:cd18786     13 GVVLTPYHRDRAYLNQYLQGLSLDEFDLQLVGAITIDSSQGLTFDVVTLYLPTA----NSLTPRRLYVALTRARKRLVIY 88


                   .
gi 2462598042 1960 G 1960
Cdd:cd18786     89 D 89
DEXXQc_Mov10L1 cd18078
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ...
 1573-1785 3.73e-09

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: 59.30  E-value: 3.73e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1573 IIHGVFGAGKSYLLAVVILFFVQLFEKSeaptignarpwKLLISSSTNVAVDRVLLGLLSlgfENFIRVGSVRKIAKpil 1652
Cdd:cd18078     24 ILFGPPGTGKTVTIIEAILQVVYNLPRS-----------RILVCAPSNSAADLVTSRLHE---SKVLKPGDMVRLNA--- 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1653 pyslhagseneseqlkelHALMKEDLTPTERVYVRKSIEQHKLGTNRTLLKQVRVVGVtcaacpfpcMNDLKFPV----- 1727
Cdd:cd18078     87 ------------------VNRFESTVIDARKLYCRLGEDLSKASRHRIVISTCSTAGL---------LYQMGLPVghfth 139

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1728 VVLDECSQITEPASLLPIARFECE--KLILVGDPKQLPPTIQgSDAAHENGLEQTLFDRL 1785
Cdd:cd18078    140 VFVDEAGQATEPESLIPLGLISSRdgQIILAGDPMQLGPVIK-SRLASAYGLGVSFLERL 198
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 1724-1766 1.32e-06

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: 49.50  E-value: 1.32e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 2462598042 1724 KFPVVVLDECSQITEPASLLPIARfeCEKLILVGDPKQLPPTI 1766
Cdd:cd18043     80 LFDLVIFDEASQIPIEEALPALFR--GKQVVVVGDDKQLPPSI 120
DEXXQc_HELZ cd18077
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that ...
 1570-1800 1.61e-06

DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. HELZ is a member of the family I class of RNA helicases of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350835 [Multi-domain]  Cd Length: 226  Bit Score: 51.33  E-value: 1.61e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1570 PITIIhGVFGAGKSYLLAVVIlffVQLFEKSEAptignarpwKLLISSSTNVAVDrvllgllsLGFENFIR--VGSVRKI 1647
Cdd:cd18077     23 PVLLI-GPFGTGKTFTLAQAV---KHILQQPET---------RILICTHSNSAAD--------LYIKEYLHpyVETGNPR 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1648 AKPILPYsLHAGSENESEQLKELHALMKEDltPTERVYVRKSIEQHklgtnrtllkqvRVVGVTCAACPFPCMNDLK--- 1724
Cdd:cd18077     82 ARPLRVY-YRNRWVKTVHPVVQKYCLIDEH--GTFRMPTREDVMRH------------RVVVVTLSTSQYLCQLDLEpgf 146

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1725 FPVVVLDECSQITEPASLLPIARFECE-KLILVGDPKQLPPTIQgSDAAHENGLEQTLFDRlcLMGHKP------ILLRT 1797
Cdd:cd18077    147 FTHILLDEAAQAMECEAIMPLALATKStRIVLAGDHMQLSPEVY-SEFARERNLHISLLER--LYEHYPsehpcrILLCE 223


                   ...
gi 2462598042 1798 QYR 1800
Cdd:cd18077    224 NYR 226
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 1721-1764 5.02e-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: 45.62  E-value: 5.02e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 2462598042 1721 NDLKFPVVVLDECSQITEP--ASLLPIARFECeKLILVGDPKQLPP 1764
Cdd:cd17933     86 NPLDADLLIVDEASMVDTRlmAALLSAIPAGA-RLILVGDPDQLPS 130
alphaCoV_Nsp13-helicase cd21723
helicase domain of alphacoronavirus non-structural protein 13; This model represents the ...
 1727-1959 6.63e-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: 47.42  E-value: 6.63e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1727 VVVLDECSQITEPASLLPIARFECEKLILVGDPKQLP-PTIQGSDAAHENGLEQTLFDRLCLMGhKPILLRTQYRCHPAI 1805
Cdd:cd21723    120 IVVVDEVSMCTNYDLSVINQRVSYKHIVYVGDPQQLPaPRTMITRGVLEPKDYNVVTQRMCALG-PDVFLHKCYRCPAEI 198

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462598042 1806 SAIANDLFYKGALMnGVTEIERSpllewlptlCF-YNVKGLEQIERDNSFHNVaeatfTLKLIQSLIASGIAGSMIGVIT 1884
Cdd:cd21723    199 VNTVSELVYENKFK-PVHPESKQ---------CFkIFCKGNVQVDNGSSINRR-----QLDVVKMFLAKNPKWSKAVFIS 263

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462598042 1885 LYKSQMYKLCHLLSavdfhhpdiktVQVSTVDAFQGAEKEIIILScvRTRQVGFIDSEKRMNVALTRGKRHLLIV 1959
Cdd:cd21723    264 PYNSQNYVASRVLG-----------LQIQTVDSSQGSEYDYVIYT--QTSDTAHACNVNRFNVAITRAKKGILCV 325
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 1727-1764 3.15e-04

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: 45.74  E-value: 3.15e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 2462598042 1727 VVVLDECSQITEP--ASLLPIARFECEKLILVGDPKQLPP 1764
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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