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Conserved domains on  [gi|767981205|ref|XP_011535339|]
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Fanconi anemia group M protein isoform X8 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XPF_nuclease_FANCM cd20077
XPF-like nuclease domain of Fanconi anemia group M protein (FANCM); FANCM (EC 3.6.4.13), also ...
 1161-1299 5.25e-74

XPF-like nuclease domain of Fanconi anemia group M protein (FANCM); FANCM (EC 3.6.4.13), also called Fanconi anemia-associated polypeptide of 250 kDa (FAAP250), or protein Hef ortholog, or ATP-dependent RNA helicase FANCM, is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. In complex with CENPS and CENPX, it binds double-stranded DNA (dsDNA), fork-structured DNA (fsDNA) and Holliday junction substrates. In complex with FAAP24, it efficiently binds to single-strand DNA (ssDNA), splayed-arm DNA, and 3'-flap substrates. In vitro, on its own, FANCM strongly binds ssDNA oligomers and weakly fsDNA, but does not bind to dsDNA.


:

Pssm-ID: 410853 [Multi-domain]  Cd Length: 139  Bit Score: 242.17  E-value: 5.25e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205 1161 TCILVGGHEITSGLEVISSLRAIHGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVI 1240
Cdd:cd20077     1 LVILVDSREISSGQEVISSLRIKHGIKVEVCQLGGCDYIVSNRMGVERKSLSEFANGSNRSKLVERIQHLCDLYDRPCLI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 767981205 1241 VEKDREKTGDTSRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKN 1299
Cdd:cd20077    81 IEKDRVKPGETSRIFHRTKYYDSTLAALAQAGVRVLFSDSQEETARLLADLAQLEQRKN 139
FANCM-MHF_bd pfam16783
FANCM to MHF binding domain; FANCM-MHF_bd is a structured region on Fanconi anaemia ...
 13-128 9.87e-62

FANCM to MHF binding domain; FANCM-MHF_bd is a structured region on Fanconi anaemia complementation group protein M that binds to a two-histone-fold-containing protein complex MHF. MHF binds double-strand DNA, stimulates the DNA-binding activity of FANCM, and contributes to the targeting of FANCM to chromatin.


:

Pssm-ID: 465270  Cd Length: 116  Bit Score: 206.05  E-value: 9.87e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205    13 KKDWFLSEEEFKLWNRLYRLRDSDEIKEITLPQVQFSSLQNEENKPAQESTTGIHQLSLSEWRLWQDHPLPTHQVDHSDR 92
Cdd:pfam16783    1 KSDGFLSEEEFELWNRLYRLEEDDIKKEPTLPRSQFTTLPNEETPPKPEPGAARRELSLSEWRHWQNRPLPTHVVDHSDR 80

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 767981205    93 CRHFIGLMQMIEGMRHEEGECSYELEVESYLQMEDV 128
Cdd:pfam16783   81 CLHFIAVMEMIELMRQEEDECSYELELKPYLQMEDV 116
MRC1 super family cl09684
MRC1-like domain; This putative domain is found to be the most conserved region in mediator of ...
 848-931 8.50e-04

MRC1-like domain; This putative domain is found to be the most conserved region in mediator of replication checkpoint protein 1.


The actual alignment was detected with superfamily member pfam09444:

Pssm-ID: 430616  Cd Length: 141  Bit Score: 41.01  E-value: 8.50e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205   848 KHVARKFLDDEAELSEEDAEYVSSDENDESENEQDSSLLDFLNDETqlSQAINDSEMRAIYMKSLRspmmNNKYKMIHKT 927
Cdd:pfam09444    2 KSGASEFVEEEAEESEDEYAGLGGADDEDSDDEEDSELEEMIDDES--DEDVDEDELAALKAKEER----EEDEKEVEKL 75


                   ....
gi 767981205   928 HKNI 931
Cdd:pfam09444   76 LKDI 79
 
Name Accession Description Interval E-value
XPF_nuclease_FANCM cd20077
XPF-like nuclease domain of Fanconi anemia group M protein (FANCM); FANCM (EC 3.6.4.13), also ...
 1161-1299 5.25e-74

XPF-like nuclease domain of Fanconi anemia group M protein (FANCM); FANCM (EC 3.6.4.13), also called Fanconi anemia-associated polypeptide of 250 kDa (FAAP250), or protein Hef ortholog, or ATP-dependent RNA helicase FANCM, is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. In complex with CENPS and CENPX, it binds double-stranded DNA (dsDNA), fork-structured DNA (fsDNA) and Holliday junction substrates. In complex with FAAP24, it efficiently binds to single-strand DNA (ssDNA), splayed-arm DNA, and 3'-flap substrates. In vitro, on its own, FANCM strongly binds ssDNA oligomers and weakly fsDNA, but does not bind to dsDNA.


Pssm-ID: 410853 [Multi-domain]  Cd Length: 139  Bit Score: 242.17  E-value: 5.25e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205 1161 TCILVGGHEITSGLEVISSLRAIHGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVI 1240
Cdd:cd20077     1 LVILVDSREISSGQEVISSLRIKHGIKVEVCQLGGCDYIVSNRMGVERKSLSEFANGSNRSKLVERIQHLCDLYDRPCLI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 767981205 1241 VEKDREKTGDTSRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKN 1299
Cdd:cd20077    81 IEKDRVKPGETSRIFHRTKYYDSTLAALAQAGVRVLFSDSQEETARLLADLAQLEQRKN 139
FANCM-MHF_bd pfam16783
FANCM to MHF binding domain; FANCM-MHF_bd is a structured region on Fanconi anaemia ...
 13-128 9.87e-62

FANCM to MHF binding domain; FANCM-MHF_bd is a structured region on Fanconi anaemia complementation group protein M that binds to a two-histone-fold-containing protein complex MHF. MHF binds double-strand DNA, stimulates the DNA-binding activity of FANCM, and contributes to the targeting of FANCM to chromatin.


Pssm-ID: 465270  Cd Length: 116  Bit Score: 206.05  E-value: 9.87e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205    13 KKDWFLSEEEFKLWNRLYRLRDSDEIKEITLPQVQFSSLQNEENKPAQESTTGIHQLSLSEWRLWQDHPLPTHQVDHSDR 92
Cdd:pfam16783    1 KSDGFLSEEEFELWNRLYRLEEDDIKKEPTLPRSQFTTLPNEETPPKPEPGAARRELSLSEWRHWQNRPLPTHVVDHSDR 80

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 767981205    93 CRHFIGLMQMIEGMRHEEGECSYELEVESYLQMEDV 128
Cdd:pfam16783   81 CLHFIAVMEMIELMRQEEDECSYELELKPYLQMEDV 116
MUS81 COG1948
ERCC4-type crossover junction endonuclease [Replication, recombination and repair];
1185-1370 8.34e-19

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


Pssm-ID: 441551 [Multi-domain]  Cd Length: 214  Bit Score: 86.38  E-value: 8.34e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205 1185 GLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVEkdrektGD---TSRMFRRTKSY 1261
Cdd:COG1948    23 GVEVRVKTLEVGDYVVSDRVAVERKTVRDFVNSLIDGRLFEQASRLAEAYERPVLIIE------GDllyEERNIHPNAIR 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205 1262 DSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKNV-GIHVPTVVNSNKSEALQFYL--SIPNISYITALNMCHQFS 1338
Cdd:COG1948    97 GALASLALDFGIPVLPTRDAEDTAELLVTLARREQEEEKrEVSLHGKKKPKTLREQQLYVveSLPGIGPKLARRLLEHFG 176

                         170       180       190
                  ....*....|....*....|....*....|..
gi 767981205 1339 SVKRMANSSLQEISMYAQVTHQKAEEIYRYIH 1370
Cdd:COG1948   177 SVEAVFNASEEELMKVEGIGEKTAERIREVLD 208
PRK13766 PRK13766
Hef nuclease; Provisional
 1157-1369 1.38e-15

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 82.23  E-value: 1.38e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205 1157 EGKGTCILVGGHEITSGleVISSLRAIhGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNS-VNKNKFiEQIQHLQSMFE 1235
Cdd:PRK13766  559 EPEGPKIIVDSRELRSN--VARHLKRL-GAEVELKTLEVGDYVVSDRVAVERKTAEDFVDSiIDRRLF-EQVKDLKRAYE 634

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205 1236 RICVIVEkdrektGD--TSRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKN---VGIHvptvvnS 1310
Cdd:PRK13766  635 RPVLIIE------GDlyTIRNIHPNAIRGALASIAVDFGIPILFTRDEEETADLLKVIAKREQEEEkreVSVH------G 702

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767981205 1311 NKS----EALQFYL--SIPNISYITALNMCHQFSSVKRMANSSLQEISMYAQVTHQKAEEIYRYI 1369
Cdd:PRK13766  703 EKKamtlKEQQEYIveSLPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKRIREVV 767
ERCC4 pfam02732
ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an ...
 1184-1291 2.97e-12

ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an essential component of a Holliday junction resolvase. EME1 interacts with MUS81 to form a DNA structure-specific endonuclease.


Pssm-ID: 426945 [Multi-domain]  Cd Length: 139  Bit Score: 65.53  E-value: 2.97e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205  1184 HGLQVEVCPLNGCDYIVSNR-----------MVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVE---KDREKTG 1249
Cdd:pfam02732   18 LGVEVVVETLPVGDYLWVPReydlelevvldVIVERKSLDDLVSSIIDGRLFEQKSRLKRGYKKPILLVEgldLFSRKLK 97

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 767981205  1250 DTSRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKEL 1291
Cdd:pfam02732   98 NKRRDINPNAIEGALASLQVDYGVRIIRTRSAEETAEWLASL 139
ERCC4 smart00891
ERCC4 domain; This entry represents a structural motif found in several DNA repair nucleases, ...
 1162-1242 3.52e-12

ERCC4 domain; This entry represents a structural motif found in several DNA repair nucleases, such as Rad1/Mus81/XPF endonucleases, and in ATP-dependent helicases. The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases.


Pssm-ID: 214888 [Multi-domain]  Cd Length: 98  Bit Score: 63.91  E-value: 3.52e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205   1162 CILVGGHEITSGLE--VISSLRAIHGLQVEVCPLNGCDYIVSNR-------------MVVERRSQSEMLNSVNKNKFIEQ 1226
Cdd:smart00891    1 EIIVDSRELRSALEapIPRSLRWKRGVKVEYDRLEAGDFVLVARdkqsllphvnslnELVERKSLTDLVASIPDGRLFEQ 80

                            90
                    ....*....|....*..
gi 767981205   1227 IQHL-QSMFERICVIVE 1242
Cdd:smart00891   81 VRRLqQIAYPSPQLLVE 97
rad1 TIGR00596
DNA repair protein (rad1); All proteins in this family for which functions are known are ...
 1175-1370 6.03e-10

DNA repair protein (rad1); All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombinational repair in some species. Most Archaeal species also have homologs of these genes, but the function of these Archaeal genes is not known, so we have set our cutoff to only pick up the eukaryotic genes.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273163 [Multi-domain]  Cd Length: 814  Bit Score: 64.06  E-value: 6.03e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205  1175 EVISSLRAI---HGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVEKDREK---- 1247
Cdd:TIGR00596  595 EFRSSLPSLlhrRGIRVIPCMLTVGDYILTPDICVERKSISDLIGSLNNGRLYNQCEKMLRYYAYPVLLIEFDQNKsfsl 674

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205  1248 ------TGDTSRMFRRTKSYDSLLtTLIGAGIRILFSSCQEETADLLKELSLVEQRKN------VGIHVPTVVNSNK--S 1313
Cdd:TIGR00596  675 eprndlSQEISSVNNDIQQKLALL-TLHFPKLRIIWSSSPYATAEIFEELKLGKEEPDpataaaLGSDENTTAEGLKfnD 753

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 767981205  1314 EALQFYLSIPNISYITALNMCHQFSSVKRMANSSLQEISMYAQvTHQKAEEIYRYIH 1370
Cdd:TIGR00596  754 GPQDFLLKLPGVTKKNYRNLRKKVKSIRELAKLSQNELNELIG-DEEAAKRLYDFLR 809
MRC1 pfam09444
MRC1-like domain; This putative domain is found to be the most conserved region in mediator of ...
 848-931 8.50e-04

MRC1-like domain; This putative domain is found to be the most conserved region in mediator of replication checkpoint protein 1.


Pssm-ID: 430616  Cd Length: 141  Bit Score: 41.01  E-value: 8.50e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205   848 KHVARKFLDDEAELSEEDAEYVSSDENDESENEQDSSLLDFLNDETqlSQAINDSEMRAIYMKSLRspmmNNKYKMIHKT 927
Cdd:pfam09444    2 KSGASEFVEEEAEESEDEYAGLGGADDEDSDDEEDSELEEMIDDES--DEDVDEDELAALKAKEER----EEDEKEVEKL 75


                   ....
gi 767981205   928 HKNI 931
Cdd:pfam09444   76 LKDI 79
 
Name Accession Description Interval E-value
XPF_nuclease_FANCM cd20077
XPF-like nuclease domain of Fanconi anemia group M protein (FANCM); FANCM (EC 3.6.4.13), also ...
 1161-1299 5.25e-74

XPF-like nuclease domain of Fanconi anemia group M protein (FANCM); FANCM (EC 3.6.4.13), also called Fanconi anemia-associated polypeptide of 250 kDa (FAAP250), or protein Hef ortholog, or ATP-dependent RNA helicase FANCM, is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. In complex with CENPS and CENPX, it binds double-stranded DNA (dsDNA), fork-structured DNA (fsDNA) and Holliday junction substrates. In complex with FAAP24, it efficiently binds to single-strand DNA (ssDNA), splayed-arm DNA, and 3'-flap substrates. In vitro, on its own, FANCM strongly binds ssDNA oligomers and weakly fsDNA, but does not bind to dsDNA.


Pssm-ID: 410853 [Multi-domain]  Cd Length: 139  Bit Score: 242.17  E-value: 5.25e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205 1161 TCILVGGHEITSGLEVISSLRAIHGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVI 1240
Cdd:cd20077     1 LVILVDSREISSGQEVISSLRIKHGIKVEVCQLGGCDYIVSNRMGVERKSLSEFANGSNRSKLVERIQHLCDLYDRPCLI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 767981205 1241 VEKDREKTGDTSRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKN 1299
Cdd:cd20077    81 IEKDRVKPGETSRIFHRTKYYDSTLAALAQAGVRVLFSDSQEETARLLADLAQLEQRKN 139
FANCM-MHF_bd pfam16783
FANCM to MHF binding domain; FANCM-MHF_bd is a structured region on Fanconi anaemia ...
 13-128 9.87e-62

FANCM to MHF binding domain; FANCM-MHF_bd is a structured region on Fanconi anaemia complementation group protein M that binds to a two-histone-fold-containing protein complex MHF. MHF binds double-strand DNA, stimulates the DNA-binding activity of FANCM, and contributes to the targeting of FANCM to chromatin.


Pssm-ID: 465270  Cd Length: 116  Bit Score: 206.05  E-value: 9.87e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205    13 KKDWFLSEEEFKLWNRLYRLRDSDEIKEITLPQVQFSSLQNEENKPAQESTTGIHQLSLSEWRLWQDHPLPTHQVDHSDR 92
Cdd:pfam16783    1 KSDGFLSEEEFELWNRLYRLEEDDIKKEPTLPRSQFTTLPNEETPPKPEPGAARRELSLSEWRHWQNRPLPTHVVDHSDR 80

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 767981205    93 CRHFIGLMQMIEGMRHEEGECSYELEVESYLQMEDV 128
Cdd:pfam16783   81 CLHFIAVMEMIELMRQEEDECSYELELKPYLQMEDV 116
XPF_nuclease-like cd19940
nuclease domain of XPF/MUS81 family proteins; The XPF/MUS81 family belongs to 3'-flap ...
 1162-1293 1.69e-40

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: 145.60  E-value: 1.69e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205 1162 CILVGGHEITSglEVISSLRAIhGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIV 1241
Cdd:cd19940     1 SIVVDPRERRS--ELLSELQRL-GVQVEFEDLAVGDYVLSNRTCVERKSLSDLVSSINKGRLREQLQRLTRKFERRVLLV 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 767981205 1242 EKDREKTgdtsRMFRRTKSYDSLLTTLIG-AGIRILFSSCQEETADLLKELSL 1293
Cdd:cd19940    78 EKDRSKF----RSMVSSVQALSALTKLQLlTGIRLLIVASPKETADLLEELTQ 126
XPF_ERCC4_MUS81-like cd22367
XPF family DNA repair endonuclease; (Xeroderma Pigmentosum group F) DNA repair gene homologs ...
 1163-1292 2.08e-22

XPF family DNA repair endonuclease; (Xeroderma Pigmentosum group F) DNA repair gene homologs are members of the XPF/Rad1/Mus81-dependent nuclease family which specifically cleave branched structures generated during DNA repair, replication, and recombination, and they are essential for maintaining genome stability. They belong to a wider superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


Pssm-ID: 411771 [Multi-domain]  Cd Length: 123  Bit Score: 93.86  E-value: 2.08e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205 1163 ILVGGHEITSGLEVISSLraiHGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVE 1242
Cdd:cd22367     1 IVVDSRERRSGLPELLRK---LGVRVEVRTLEVGDYILSADIIVERKTVSDLISSIIDGRLFEQAERLKRSYERPILLIE 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 767981205 1243 KDREKTgdtsRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKELS 1292
Cdd:cd22367    78 GDPDKA----RRLVRPAALGAAISSLLVIGGLLVLRTPNFETTALLLSLL 123
MUS81 COG1948
ERCC4-type crossover junction endonuclease [Replication, recombination and repair];
1185-1370 8.34e-19

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


Pssm-ID: 441551 [Multi-domain]  Cd Length: 214  Bit Score: 86.38  E-value: 8.34e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205 1185 GLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVEkdrektGD---TSRMFRRTKSY 1261
Cdd:COG1948    23 GVEVRVKTLEVGDYVVSDRVAVERKTVRDFVNSLIDGRLFEQASRLAEAYERPVLIIE------GDllyEERNIHPNAIR 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205 1262 DSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKNV-GIHVPTVVNSNKSEALQFYL--SIPNISYITALNMCHQFS 1338
Cdd:COG1948    97 GALASLALDFGIPVLPTRDAEDTAELLVTLARREQEEEKrEVSLHGKKKPKTLREQQLYVveSLPGIGPKLARRLLEHFG 176

                         170       180       190
                  ....*....|....*....|....*....|..
gi 767981205 1339 SVKRMANSSLQEISMYAQVTHQKAEEIYRYIH 1370
Cdd:COG1948   177 SVEAVFNASEEELMKVEGIGEKTAERIREVLD 208
PRK13766 PRK13766
Hef nuclease; Provisional
 1157-1369 1.38e-15

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 82.23  E-value: 1.38e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205 1157 EGKGTCILVGGHEITSGleVISSLRAIhGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNS-VNKNKFiEQIQHLQSMFE 1235
Cdd:PRK13766  559 EPEGPKIIVDSRELRSN--VARHLKRL-GAEVELKTLEVGDYVVSDRVAVERKTAEDFVDSiIDRRLF-EQVKDLKRAYE 634

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205 1236 RICVIVEkdrektGD--TSRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKN---VGIHvptvvnS 1310
Cdd:PRK13766  635 RPVLIIE------GDlyTIRNIHPNAIRGALASIAVDFGIPILFTRDEEETADLLKVIAKREQEEEkreVSVH------G 702

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767981205 1311 NKS----EALQFYL--SIPNISYITALNMCHQFSSVKRMANSSLQEISMYAQVTHQKAEEIYRYI 1369
Cdd:PRK13766  703 EKKamtlKEQQEYIveSLPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKRIREVV 767
XPF_nuclease_XPF_arch cd20075
nuclease domain of XPF found in archaea; XPF, also called DNA excision repair protein ERCC-4, ...
 1175-1291 2.80e-15

nuclease domain of XPF found in archaea; XPF, also called DNA excision repair protein ERCC-4, or DNA repair protein complementing XP-F cells, or Xeroderma pigmentosum group F-complementing protein, is a 3'-flap repair endonuclease that cleaves 5' of ds/ssDNA interfaces in 3' flap structures, although it also cuts bubble, Y-DNA structures and mobile and immobile Holliday junctions. XPF cuts preferentially after pyrimidines, may continue to progressively cleave substrate upstream of the initial cleavage, at least in vitro. It may be involved in nucleotide excision repair. The nuclease domains of the catalytic subunits XPF have the GDX(n)ERKX(3)D motif which is required for metal-dependent endonuclease activity but not for DNA junction binding. XPF-ERRC1 and its yeast homolog Rad1-Rad10 play key roles in the excision of DNA lesions and are required for certain types of homologous recombination events and for the repair of DNA cross-links.


Pssm-ID: 410851 [Multi-domain]  Cd Length: 127  Bit Score: 73.57  E-value: 2.80e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205 1175 EVISSLRAiHGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVEkdrektGDTSRM 1254
Cdd:cd20075    12 GVVRELKE-LGVEVEFKQLEVGDYIVSDRVAIERKTVDDFVSSIIDGRLFDQAKRLKEAYEKPILIIE------GDLLYL 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 767981205 1255 FRRTKS---YDSLLTTLIGAGIRILFSSCQEETADLLKEL 1291
Cdd:cd20075    85 KRRIHPnaiRGALASIALDFGIPIIFTKDPEETAELLYSL 124
ERCC4 pfam02732
ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an ...
 1184-1291 2.97e-12

ERCC4 domain; This domain is a family of nucleases. The family includes EME1 which is an essential component of a Holliday junction resolvase. EME1 interacts with MUS81 to form a DNA structure-specific endonuclease.


Pssm-ID: 426945 [Multi-domain]  Cd Length: 139  Bit Score: 65.53  E-value: 2.97e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205  1184 HGLQVEVCPLNGCDYIVSNR-----------MVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVE---KDREKTG 1249
Cdd:pfam02732   18 LGVEVVVETLPVGDYLWVPReydlelevvldVIVERKSLDDLVSSIIDGRLFEQKSRLKRGYKKPILLVEgldLFSRKLK 97

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 767981205  1250 DTSRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKEL 1291
Cdd:pfam02732   98 NKRRDINPNAIEGALASLQVDYGVRIIRTRSAEETAEWLASL 139
ERCC4 smart00891
ERCC4 domain; This entry represents a structural motif found in several DNA repair nucleases, ...
 1162-1242 3.52e-12

ERCC4 domain; This entry represents a structural motif found in several DNA repair nucleases, such as Rad1/Mus81/XPF endonucleases, and in ATP-dependent helicases. The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases.


Pssm-ID: 214888 [Multi-domain]  Cd Length: 98  Bit Score: 63.91  E-value: 3.52e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205   1162 CILVGGHEITSGLE--VISSLRAIHGLQVEVCPLNGCDYIVSNR-------------MVVERRSQSEMLNSVNKNKFIEQ 1226
Cdd:smart00891    1 EIIVDSRELRSALEapIPRSLRWKRGVKVEYDRLEAGDFVLVARdkqsllphvnslnELVERKSLTDLVASIPDGRLFEQ 80

                            90
                    ....*....|....*..
gi 767981205   1227 IQHL-QSMFERICVIVE 1242
Cdd:smart00891   81 VRRLqQIAYPSPQLLVE 97
rad1 TIGR00596
DNA repair protein (rad1); All proteins in this family for which functions are known are ...
 1175-1370 6.03e-10

DNA repair protein (rad1); All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombinational repair in some species. Most Archaeal species also have homologs of these genes, but the function of these Archaeal genes is not known, so we have set our cutoff to only pick up the eukaryotic genes.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273163 [Multi-domain]  Cd Length: 814  Bit Score: 64.06  E-value: 6.03e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205  1175 EVISSLRAI---HGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVEKDREK---- 1247
Cdd:TIGR00596  595 EFRSSLPSLlhrRGIRVIPCMLTVGDYILTPDICVERKSISDLIGSLNNGRLYNQCEKMLRYYAYPVLLIEFDQNKsfsl 674

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205  1248 ------TGDTSRMFRRTKSYDSLLtTLIGAGIRILFSSCQEETADLLKELSLVEQRKN------VGIHVPTVVNSNK--S 1313
Cdd:TIGR00596  675 eprndlSQEISSVNNDIQQKLALL-TLHFPKLRIIWSSSPYATAEIFEELKLGKEEPDpataaaLGSDENTTAEGLKfnD 753

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 767981205  1314 EALQFYLSIPNISYITALNMCHQFSSVKRMANSSLQEISMYAQvTHQKAEEIYRYIH 1370
Cdd:TIGR00596  754 GPQDFLLKLPGVTKKNYRNLRKKVKSIRELAKLSQNELNELIG-DEEAAKRLYDFLR 809
XPF_nuclease_XPF_euk cd20078
nuclease domain of XPF found in eukaryotes; XPF, also called DNA excision repair protein ...
 1184-1291 3.77e-04

nuclease domain of XPF found in eukaryotes; XPF, also called DNA excision repair protein ERCC-4, or DNA repair protein complementing XP-F cells, or Xeroderma pigmentosum group F-complementing protein, is a DNA repair endonuclease that is a catalytic component of a structure-specific DNA repair endonuclease responsible for the 5-prime incision during DNA repair. It is involved in homologous recombination that assists in removing interstrand cross-link. The nuclease domains of the catalytic subunits XPF have the GDX(n)ERKX(3)D motif which is required for metal-dependent endonuclease activity but not for DNA junction binding. XPF-ERRC1 and its yeast homolog Rad1-Rad10 play key roles in the excision of DNA lesions and are required for certain types of homologous recombination events and for the repair of DNA cross-links.


Pssm-ID: 410854 [Multi-domain]  Cd Length: 136  Bit Score: 42.09  E-value: 3.77e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205 1184 HGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVEKDREKTGDTSRM--FRRTKSY 1261
Cdd:cd20078    20 AGIDLIPVTLEVGDYILSPDICVERKSISDLISSLNSGRLYTQLEAMCRYYKHPILLIEFDENKPFSLQSKssLSSEISS 99

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 767981205 1262 DSL---LTTLIGA--GIRILFSSCQEETADLLKEL 1291
Cdd:cd20078   100 NSLiskLVLLLLHfpKLRIIWSRSPHFTAELFREL 134
MRC1 pfam09444
MRC1-like domain; This putative domain is found to be the most conserved region in mediator of ...
 848-931 8.50e-04

MRC1-like domain; This putative domain is found to be the most conserved region in mediator of replication checkpoint protein 1.


Pssm-ID: 430616  Cd Length: 141  Bit Score: 41.01  E-value: 8.50e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767981205   848 KHVARKFLDDEAELSEEDAEYVSSDENDESENEQDSSLLDFLNDETqlSQAINDSEMRAIYMKSLRspmmNNKYKMIHKT 927
Cdd:pfam09444    2 KSGASEFVEEEAEESEDEYAGLGGADDEDSDDEEDSELEEMIDDES--DEDVDEDELAALKAKEER----EEDEKEVEKL 75


                   ....
gi 767981205   928 HKNI 931
Cdd:pfam09444   76 LKDI 79
 
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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