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Conserved domains on  [gi|530426033|ref|XP_005260924|]
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mitochondrial genome maintenance exonuclease 1 isoform X1 [Homo sapiens]

Protein Classification

PD-(D/E)XK nuclease family protein( domain architecture ID 1193)

PD-(D/E)XK nuclease family protein similar to CRISPR-associated exonuclease Cas4

EC:  3.1.-.-
Gene Ontology:  GO:0000738|GO:0004527
PubMed:  15972856

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Cas4_I-A_I-B_I-C_I-D_II-B super family cl00641
CRISPR/Cas system-associated protein Cas4; CRISPR (Clustered Regularly Interspaced Short ...
 191-300 1.72e-03

CRISPR/Cas system-associated protein Cas4; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas4 is RecB-like nuclease with three-cysteine C-terminal cluster


The actual alignment was detected with superfamily member pfam12705:

Pssm-ID: 469855 [Multi-domain]  Cd Length: 250  Bit Score: 39.44  E-value: 1.72e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530426033  191 GKRFHEALESILSPQETLKERDENLLK-------------------------------SGYIESVQHILKDVSGVR--AL 237
Cdd:pfam12705  37 GTLVHAALERFYRWGRLPEEDLEELLQalleelwpelglqseilprlpwlagrlrrrlERMLRRLAEWLRARRGFRpvAV 116

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 530426033  238 ESAVQHETLNYIGLLDCV-AEYQGKLCVIDWKTSEKPKPFIQSTFDNPLQVVAYMGAMNHDTNY 300
Cdd:pfam12705 117 ELGFGGTTVRLVGRIDRVdLDGEGYLRIIDYKTGSAPPQSEDLDLYEGLQLLLYLLALAAGEKA 180
 
Name Accession Description Interval E-value
PDDEXK_1 pfam12705
PD-(D/E)XK nuclease superfamily; Members of this family belong to the PD-(D/E)XK nuclease ...
 191-300 1.72e-03

PD-(D/E)XK nuclease superfamily; Members of this family belong to the PD-(D/E)XK nuclease superfamily


Pssm-ID: 432731 [Multi-domain]  Cd Length: 250  Bit Score: 39.44  E-value: 1.72e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530426033  191 GKRFHEALESILSPQETLKERDENLLK-------------------------------SGYIESVQHILKDVSGVR--AL 237
Cdd:pfam12705  37 GTLVHAALERFYRWGRLPEEDLEELLQalleelwpelglqseilprlpwlagrlrrrlERMLRRLAEWLRARRGFRpvAV 116

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 530426033  238 ESAVQHETLNYIGLLDCV-AEYQGKLCVIDWKTSEKPKPFIQSTFDNPLQVVAYMGAMNHDTNY 300
Cdd:pfam12705 117 ELGFGGTTVRLVGRIDRVdLDGEGYLRIIDYKTGSAPPQSEDLDLYEGLQLLLYLLALAAGEKA 180
RecB_C-like cd22352
C-terminal nuclease domain of exodeoxyribonuclease V subunit RecB and similar proteins; ...
 194-269 2.14e-03

C-terminal nuclease domain of exodeoxyribonuclease V subunit RecB and similar proteins; Exodeoxyribonuclease V subunit beta (RecB) is a helicase/nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair; it binds to DSBs and unwinds DNA via a rapid and highly processive ATP-dependent bidirectional helicase. The C-terminal PDDEXK nuclease domain belongs to a 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: 411756 [Multi-domain]  Cd Length: 215  Bit Score: 38.80  E-value: 2.14e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530426033 194 FHEALESIlspqETLKERDENL-LKSGY-IESVQHILKDVSGVRALESAvQHETLN-YI-GLLDCVAEYQGKLCVIDWKT 269
Cdd:cd22352   55 LHEILENI----DRLSEMEFYLpLSDKLdAEALNELLRQHGPPGALPPL-SFETLRgFLkGFIDLVFEHEGRYYILDYKS 129
RecB COG1074
3#-5# helicase subunit RecB of the DNA repair enzyme RecBCD (exonuclease V) [Replication, ...
 250-309 4.38e-03

3#-5# helicase subunit RecB of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440692 [Multi-domain]  Cd Length: 866  Bit Score: 39.18  E-value: 4.38e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 530426033 250 GLLDCVAEYQGKLCVIDWKTSEKPKPFIQSTFDN-PLQVVAYMGAMnHDTNYSFQVQCGLI 309
Cdd:COG1074  797 GRIDLVFEDDGRVYIVDYKTNRLGPDDEEYLPERyRLQLALYALAL-ERLLPGRPVRAGLY 856
 
Name Accession Description Interval E-value
PDDEXK_1 pfam12705
PD-(D/E)XK nuclease superfamily; Members of this family belong to the PD-(D/E)XK nuclease ...
 191-300 1.72e-03

PD-(D/E)XK nuclease superfamily; Members of this family belong to the PD-(D/E)XK nuclease superfamily


Pssm-ID: 432731 [Multi-domain]  Cd Length: 250  Bit Score: 39.44  E-value: 1.72e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530426033  191 GKRFHEALESILSPQETLKERDENLLK-------------------------------SGYIESVQHILKDVSGVR--AL 237
Cdd:pfam12705  37 GTLVHAALERFYRWGRLPEEDLEELLQalleelwpelglqseilprlpwlagrlrrrlERMLRRLAEWLRARRGFRpvAV 116

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 530426033  238 ESAVQHETLNYIGLLDCV-AEYQGKLCVIDWKTSEKPKPFIQSTFDNPLQVVAYMGAMNHDTNY 300
Cdd:pfam12705 117 ELGFGGTTVRLVGRIDRVdLDGEGYLRIIDYKTGSAPPQSEDLDLYEGLQLLLYLLALAAGEKA 180
RecB_C-like cd22352
C-terminal nuclease domain of exodeoxyribonuclease V subunit RecB and similar proteins; ...
 194-269 2.14e-03

C-terminal nuclease domain of exodeoxyribonuclease V subunit RecB and similar proteins; Exodeoxyribonuclease V subunit beta (RecB) is a helicase/nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair; it binds to DSBs and unwinds DNA via a rapid and highly processive ATP-dependent bidirectional helicase. The C-terminal PDDEXK nuclease domain belongs to a 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: 411756 [Multi-domain]  Cd Length: 215  Bit Score: 38.80  E-value: 2.14e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530426033 194 FHEALESIlspqETLKERDENL-LKSGY-IESVQHILKDVSGVRALESAvQHETLN-YI-GLLDCVAEYQGKLCVIDWKT 269
Cdd:cd22352   55 LHEILENI----DRLSEMEFYLpLSDKLdAEALNELLRQHGPPGALPPL-SFETLRgFLkGFIDLVFEHEGRYYILDYKS 129
RecB COG1074
3#-5# helicase subunit RecB of the DNA repair enzyme RecBCD (exonuclease V) [Replication, ...
 250-309 4.38e-03

3#-5# helicase subunit RecB of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440692 [Multi-domain]  Cd Length: 866  Bit Score: 39.18  E-value: 4.38e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 530426033 250 GLLDCVAEYQGKLCVIDWKTSEKPKPFIQSTFDN-PLQVVAYMGAMnHDTNYSFQVQCGLI 309
Cdd:COG1074  797 GRIDLVFEDDGRVYIVDYKTNRLGPDDEEYLPERyRLQLALYALAL-ERLLPGRPVRAGLY 856
 
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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