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Conserved domains on  [gi|149056194|gb|EDM07625|]
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similar to RIKEN cDNA C230052I12 (predicted) [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XPF_nuclease_FAAP24 cd20076
XPF-like nuclease domain of Fanconi anemia associated protein 24 kDa (FAAP24); FAAP24, also ...
 17-139 3.96e-71

XPF-like nuclease domain of Fanconi anemia associated protein 24 kDa (FAAP24); FAAP24, also called Fanconi anemia core complex-associated protein 24, plays a role in DNA repair through recruitment of the Fanconi anemia (FA) core complex to damaged DNA. It regulates FANCD2 monoubiquitination upon DNA damage and induces chromosomal instability as well as hypersensitivity to DNA cross-linking agents, when repressed. FAAP24 may possess a high affinity toward single-stranded DNA (ssDNA). The nuclease domain of FAAP24 lacks the catalytic motif. The FANCM/FAAP24 complex is related to XPF/MUS81 endonucleases but lacks endonucleolytic activity. It binds branched DNA structures containing ssDNA regions, such as splayed-arm and 3'-flap DNA structures, and anchors the FA core complex to chromatin in repairing DNA interstrand crosslinks.


:

Pssm-ID: 410852  Cd Length: 123  Bit Score: 212.45  E-value: 3.96e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149056194  17 GHIVANEKWRGSQLAQELQGKVRLIFEEGLASTDFYLSSKSCILYITEADLVAGHGYKKRLARFRNSAHLQGIVIVEKTQ 96
Cdd:cd20076    1 GHILVNEKWRGSELVKSLQGKVKVIFEDGLGVVDFYPSNDCAVIYISEADLVAGNGYKRKLVKLRKANYLRGIVIAEKTP 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 149056194  97 MSEQYFPAAQKFTVLDLGMVLLPVASQSEASCLIFQLVQEQTR 139
Cdd:cd20076   81 MSEQYFPALQKFVVLELGLVLLPVTSQSEAAQLLIQMVNEETK 123
HHH_2 pfam12826
Helix-hairpin-helix motif; The HhH domain of DisA, a bacterial checkpoint control protein, is ...
 166-218 2.10e-12

Helix-hairpin-helix motif; The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain.


:

Pssm-ID: 432812 [Multi-domain]  Cd Length: 64  Bit Score: 60.23  E-value: 2.10e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 149056194  166 IPGVGKVKAPLLLQKFPSIQQLSNASTQELEEV--VGRTVAQQIHTFFTQPKRQQ 218
Cdd:pfam12826   8 IRHVGETTAKLLARRFGSLDALAEASLEELLEVddIGPEIAQSIVEFFADPANRE 62
 
Name Accession Description Interval E-value
XPF_nuclease_FAAP24 cd20076
XPF-like nuclease domain of Fanconi anemia associated protein 24 kDa (FAAP24); FAAP24, also ...
 17-139 3.96e-71

XPF-like nuclease domain of Fanconi anemia associated protein 24 kDa (FAAP24); FAAP24, also called Fanconi anemia core complex-associated protein 24, plays a role in DNA repair through recruitment of the Fanconi anemia (FA) core complex to damaged DNA. It regulates FANCD2 monoubiquitination upon DNA damage and induces chromosomal instability as well as hypersensitivity to DNA cross-linking agents, when repressed. FAAP24 may possess a high affinity toward single-stranded DNA (ssDNA). The nuclease domain of FAAP24 lacks the catalytic motif. The FANCM/FAAP24 complex is related to XPF/MUS81 endonucleases but lacks endonucleolytic activity. It binds branched DNA structures containing ssDNA regions, such as splayed-arm and 3'-flap DNA structures, and anchors the FA core complex to chromatin in repairing DNA interstrand crosslinks.


Pssm-ID: 410852  Cd Length: 123  Bit Score: 212.45  E-value: 3.96e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149056194  17 GHIVANEKWRGSQLAQELQGKVRLIFEEGLASTDFYLSSKSCILYITEADLVAGHGYKKRLARFRNSAHLQGIVIVEKTQ 96
Cdd:cd20076    1 GHILVNEKWRGSELVKSLQGKVKVIFEDGLGVVDFYPSNDCAVIYISEADLVAGNGYKRKLVKLRKANYLRGIVIAEKTP 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 149056194  97 MSEQYFPAAQKFTVLDLGMVLLPVASQSEASCLIFQLVQEQTR 139
Cdd:cd20076   81 MSEQYFPALQKFVVLELGLVLLPVTSQSEAAQLLIQMVNEETK 123
PND pfam17949
FANCM pseudonuclease domain; This entry represents the pseudonuclease domain (PND) from the ...
 11-135 3.22e-63

FANCM pseudonuclease domain; This entry represents the pseudonuclease domain (PND) from the FANCM protein. This domain is part of the PD(D/E)XK superfamily but does not appear to have a full set of catalytic residues.


Pssm-ID: 375443  Cd Length: 125  Bit Score: 192.67  E-value: 3.22e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149056194   11 PVHVPLGHIVANEKWRGSQLAQELQGKVRLIFEEGLASTDFYLSSKSCILYITEADLVAGHGYKKRLARFRNSAHLQGIV 90
Cdd:pfam17949   1 NVSVPLGHILCSEKWRNSSLVQILKDKIKIIFEDRLGVVDFHPSNDTAIIYISEADIIAGNGYKRRLVKLRNANVFQGIV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 149056194   91 IVEKTQMSEQYFPAAQKFTVLDLGMVLLPVASQSEASCLIFQLVQ 135
Cdd:pfam17949  81 LAEKTTLSEQYFSALQKFAVLELGLVLLPVLNQTEAADLIIQLVS 125
HHH_2 pfam12826
Helix-hairpin-helix motif; The HhH domain of DisA, a bacterial checkpoint control protein, is ...
 166-218 2.10e-12

Helix-hairpin-helix motif; The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain.


Pssm-ID: 432812 [Multi-domain]  Cd Length: 64  Bit Score: 60.23  E-value: 2.10e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 149056194  166 IPGVGKVKAPLLLQKFPSIQQLSNASTQELEEV--VGRTVAQQIHTFFTQPKRQQ 218
Cdd:pfam12826   8 IRHVGETTAKLLARRFGSLDALAEASLEELLEVddIGPEIAQSIVEFFADPANRE 62
MUS81 COG1948
ERCC4-type crossover junction endonuclease [Replication, recombination and repair];
19-208 4.47e-12

ERCC4-type crossover junction endonuclease [Replication, recombination and repair];


Pssm-ID: 441551 [Multi-domain]  Cd Length: 214  Bit Score: 62.89  E-value: 4.47e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149056194  19 IVANEKWRGSQLAQELQGK-VRLIFEEgLASTDFYLSSKSCILYITEADLVA----GHGYK--KRLARfrnsAHLQGIVI 91
Cdd:COG1948    4 IVVDSREKNSGVPRLLSRLgVEVRVKT-LEVGDYVVSDRVAVERKTVRDFVNslidGRLFEqaSRLAE----AYERPVLI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149056194  92 VE------KTQMSEQYFPAAQKFTVLDLGMVLLPVASQSEASCLIFQLVQEQTREPSKNPFLRKKRSmlSESSLVQT--- 162
Cdd:COG1948   79 IEgdllyeERNIHPNAIRGALASLALDFGIPVLPTRDAEDTAELLVTLARREQEEEKREVSLHGKKK--PKTLREQQlyv 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 149056194 163 VQQIPGVGKVKAPLLLQKFPSIQQLSNASTQELEEV--VGRTVAQQIH 208
Cdd:COG1948  157 VESLPGIGPKLARRLLEHFGSVEAVFNASEEELMKVegIGEKTAERIR 204
uvrC PRK00558
excinuclease ABC subunit UvrC;
146-211 4.01e-10

excinuclease ABC subunit UvrC;


Pssm-ID: 234792 [Multi-domain]  Cd Length: 598  Bit Score: 58.59  E-value: 4.01e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 149056194 146 FLRKKRSM-LSESSLvqtvQQIPGVGKVKAPLLLQKFPSIQQLSNASTQELEEV--VGRTVAQQIHTFF 211
Cdd:PRK00558 531 FHRKKRSKaRLTSAL----DDIPGIGPKRRKALLKHFGSLKAIKEASVEELAKVpgISKKLAEAIYEAL 595
Lig COG0272
NAD-dependent DNA ligase [Replication, recombination and repair];
166-218 1.58e-09

NAD-dependent DNA ligase [Replication, recombination and repair];


Pssm-ID: 440042 [Multi-domain]  Cd Length: 668  Bit Score: 56.96  E-value: 1.58e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 149056194 166 IPGVGKVKAPLLLQKFPSIQQLSNASTQELEEV--VGRTVAQQIHTFFTQPKRQQ 218
Cdd:COG0272  517 IRHVGETTAKLLARHFGSLDALMAASEEELAAVdgIGPVVAESIVEFFAEPHNRE 571
PRK13766 PRK13766
Hef nuclease; Provisional
 111-207 1.54e-04

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 42.17  E-value: 1.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149056194 111 LDLGMVLLPVASQSEASCLIFQLVQ-EQ-TREPSKNPFLRKKRSMLSEsslvqtvQQ------IPGVGKVKAPLLLQKFP 182
Cdd:PRK13766 664 VDFGIPILFTRDEEETADLLKVIAKrEQeEEKREVSVHGEKKAMTLKE-------QQeyivesLPDVGPVLARNLLEHFG 736

                         90       100
                 ....*....|....*....|....*..
gi 149056194 183 SIQQLSNASTQELEEV--VGRTVAQQI 207
Cdd:PRK13766 737 SVEAVMTASEEELMEVegIGEKTAKRI 763
 
Name Accession Description Interval E-value
XPF_nuclease_FAAP24 cd20076
XPF-like nuclease domain of Fanconi anemia associated protein 24 kDa (FAAP24); FAAP24, also ...
 17-139 3.96e-71

XPF-like nuclease domain of Fanconi anemia associated protein 24 kDa (FAAP24); FAAP24, also called Fanconi anemia core complex-associated protein 24, plays a role in DNA repair through recruitment of the Fanconi anemia (FA) core complex to damaged DNA. It regulates FANCD2 monoubiquitination upon DNA damage and induces chromosomal instability as well as hypersensitivity to DNA cross-linking agents, when repressed. FAAP24 may possess a high affinity toward single-stranded DNA (ssDNA). The nuclease domain of FAAP24 lacks the catalytic motif. The FANCM/FAAP24 complex is related to XPF/MUS81 endonucleases but lacks endonucleolytic activity. It binds branched DNA structures containing ssDNA regions, such as splayed-arm and 3'-flap DNA structures, and anchors the FA core complex to chromatin in repairing DNA interstrand crosslinks.


Pssm-ID: 410852  Cd Length: 123  Bit Score: 212.45  E-value: 3.96e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149056194  17 GHIVANEKWRGSQLAQELQGKVRLIFEEGLASTDFYLSSKSCILYITEADLVAGHGYKKRLARFRNSAHLQGIVIVEKTQ 96
Cdd:cd20076    1 GHILVNEKWRGSELVKSLQGKVKVIFEDGLGVVDFYPSNDCAVIYISEADLVAGNGYKRKLVKLRKANYLRGIVIAEKTP 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 149056194  97 MSEQYFPAAQKFTVLDLGMVLLPVASQSEASCLIFQLVQEQTR 139
Cdd:cd20076   81 MSEQYFPALQKFVVLELGLVLLPVTSQSEAAQLLIQMVNEETK 123
PND pfam17949
FANCM pseudonuclease domain; This entry represents the pseudonuclease domain (PND) from the ...
 11-135 3.22e-63

FANCM pseudonuclease domain; This entry represents the pseudonuclease domain (PND) from the FANCM protein. This domain is part of the PD(D/E)XK superfamily but does not appear to have a full set of catalytic residues.


Pssm-ID: 375443  Cd Length: 125  Bit Score: 192.67  E-value: 3.22e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149056194   11 PVHVPLGHIVANEKWRGSQLAQELQGKVRLIFEEGLASTDFYLSSKSCILYITEADLVAGHGYKKRLARFRNSAHLQGIV 90
Cdd:pfam17949   1 NVSVPLGHILCSEKWRNSSLVQILKDKIKIIFEDRLGVVDFHPSNDTAIIYISEADIIAGNGYKRRLVKLRNANVFQGIV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 149056194   91 IVEKTQMSEQYFPAAQKFTVLDLGMVLLPVASQSEASCLIFQLVQ 135
Cdd:pfam17949  81 LAEKTTLSEQYFSALQKFAVLELGLVLLPVLNQTEAADLIIQLVS 125
XPF_nuclease-like cd19940
nuclease domain of XPF/MUS81 family proteins; The XPF/MUS81 family belongs to 3'-flap ...
 18-135 3.30e-20

nuclease domain of XPF/MUS81 family proteins; The XPF/MUS81 family belongs to 3'-flap endonuclease that act upon 3'-flap structures and involved in DNA repair pathways that are necessary for the removal of UV-light-induced DNA lesions and cross-links between DNA strands. Family members exist either as heterodimers or as homodimers in their functionally competent states which consist of a catalytic and a noncatalytic subunit. The catalytic subunits have a DX(n)RKX(3)D motif. This motif is required for metal-dependent endonuclease activity but not for DNA junction binding. The equivalent regions of the noncatalytic subunits (ERCC1, EME1, and FAAP24) have diverged. The noncatalytic subunits have roles such as binding ssDNA or an ability to target the endonuclease to defined DNA structures or sites of DNA damage.


Pssm-ID: 410849 [Multi-domain]  Cd Length: 126  Bit Score: 82.43  E-value: 3.30e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149056194  18 HIVANEKWRGSQLAQELQG-KVRLIFEEgLASTDFYLSSKSCILYITEADLVAG---HGYKKRLARFRNSaHLQGIVIVE 93
Cdd:cd19940    1 SIVVDPRERRSELLSELQRlGVQVEFED-LAVGDYVLSNRTCVERKSLSDLVSSinkGRLREQLQRLTRK-FERRVLLVE 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 149056194  94 KTQ-------MSEQYFPAAQKFTVLDlGMVLLPVASQSEASCLIFQLVQ 135
Cdd:cd19940   79 KDRskfrsmvSSVQALSALTKLQLLT-GIRLLIVASPKETADLLEELTQ 126
HHH_2 pfam12826
Helix-hairpin-helix motif; The HhH domain of DisA, a bacterial checkpoint control protein, is ...
 166-218 2.10e-12

Helix-hairpin-helix motif; The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain.


Pssm-ID: 432812 [Multi-domain]  Cd Length: 64  Bit Score: 60.23  E-value: 2.10e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 149056194  166 IPGVGKVKAPLLLQKFPSIQQLSNASTQELEEV--VGRTVAQQIHTFFTQPKRQQ 218
Cdd:pfam12826   8 IRHVGETTAKLLARRFGSLDALAEASLEELLEVddIGPEIAQSIVEFFADPANRE 62
MUS81 COG1948
ERCC4-type crossover junction endonuclease [Replication, recombination and repair];
19-208 4.47e-12

ERCC4-type crossover junction endonuclease [Replication, recombination and repair];


Pssm-ID: 441551 [Multi-domain]  Cd Length: 214  Bit Score: 62.89  E-value: 4.47e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149056194  19 IVANEKWRGSQLAQELQGK-VRLIFEEgLASTDFYLSSKSCILYITEADLVA----GHGYK--KRLARfrnsAHLQGIVI 91
Cdd:COG1948    4 IVVDSREKNSGVPRLLSRLgVEVRVKT-LEVGDYVVSDRVAVERKTVRDFVNslidGRLFEqaSRLAE----AYERPVLI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149056194  92 VE------KTQMSEQYFPAAQKFTVLDLGMVLLPVASQSEASCLIFQLVQEQTREPSKNPFLRKKRSmlSESSLVQT--- 162
Cdd:COG1948   79 IEgdllyeERNIHPNAIRGALASLALDFGIPVLPTRDAEDTAELLVTLARREQEEEKREVSLHGKKK--PKTLREQQlyv 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 149056194 163 VQQIPGVGKVKAPLLLQKFPSIQQLSNASTQELEEV--VGRTVAQQIH 208
Cdd:COG1948  157 VESLPGIGPKLARRLLEHFGSVEAVFNASEEELMKVegIGEKTAERIR 204
uvrC PRK00558
excinuclease ABC subunit UvrC;
146-211 4.01e-10

excinuclease ABC subunit UvrC;


Pssm-ID: 234792 [Multi-domain]  Cd Length: 598  Bit Score: 58.59  E-value: 4.01e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 149056194 146 FLRKKRSM-LSESSLvqtvQQIPGVGKVKAPLLLQKFPSIQQLSNASTQELEEV--VGRTVAQQIHTFF 211
Cdd:PRK00558 531 FHRKKRSKaRLTSAL----DDIPGIGPKRRKALLKHFGSLKAIKEASVEELAKVpgISKKLAEAIYEAL 595
Lig COG0272
NAD-dependent DNA ligase [Replication, recombination and repair];
166-218 1.58e-09

NAD-dependent DNA ligase [Replication, recombination and repair];


Pssm-ID: 440042 [Multi-domain]  Cd Length: 668  Bit Score: 56.96  E-value: 1.58e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 149056194 166 IPGVGKVKAPLLLQKFPSIQQLSNASTQELEEV--VGRTVAQQIHTFFTQPKRQQ 218
Cdd:COG0272  517 IRHVGETTAKLLARHFGSLDALMAASEEELAAVdgIGPVVAESIVEFFAEPHNRE 571
ligA PRK14351
NAD-dependent DNA ligase LigA; Provisional
 136-212 1.90e-06

NAD-dependent DNA ligase LigA; Provisional


Pssm-ID: 184640 [Multi-domain]  Cd Length: 689  Bit Score: 47.83  E-value: 1.90e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 149056194 136 EQTREPSKNPFLrkkrSMLSesslvqtvqqIPGVGKVKAPLLLQKFPSIQQLSNASTQELEEV--VGRTVAQQIHTFFT 212
Cdd:PRK14351 517 EASREPPLADFL----VALG----------IPEVGPTTARNLAREFGTFEAIMDADEEALRAVddVGPTVAEEIREFFD 581
PRK13766 PRK13766
Hef nuclease; Provisional
 111-207 1.54e-04

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 42.17  E-value: 1.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 149056194 111 LDLGMVLLPVASQSEASCLIFQLVQ-EQ-TREPSKNPFLRKKRSMLSEsslvqtvQQ------IPGVGKVKAPLLLQKFP 182
Cdd:PRK13766 664 VDFGIPILFTRDEEETADLLKVIAKrEQeEEKREVSVHGEKKAMTLKE-------QQeyivesLPDVGPVLARNLLEHFG 736

                         90       100
                 ....*....|....*....|....*..
gi 149056194 183 SIQQLSNASTQELEEV--VGRTVAQQI 207
Cdd:PRK13766 737 SVEAVMTASEEELMEVegIGEKTAKRI 763
 
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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