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Conserved domains on  [gi|2524725000|ref|WP_286746188|]
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endonuclease domain-containing protein [Roseivirga sp. UBA1976]

Protein Classification

endonuclease domain-containing protein( domain architecture ID 10789861)

endonuclease domain-containing protein belonging to the PDDEXK superfamily; similar to Enterobacter cloacae YcjD

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YcjD COG2852
Very-short-patch-repair endonuclease [Replication, recombination and repair];
15-94 3.97e-31

Very-short-patch-repair endonuclease [Replication, recombination and repair];


:

Pssm-ID: 442100  Cd Length: 104  Bit Score: 105.33  E-value: 3.97e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524725000  15 LRNESTPGEAILWKYvLRGKGFYGLQFNRQFIIENYIVDFICRELKLIIELDGKYHDQITR--EDEIRDNRLKELGYRVI 92
Cdd:COG2852     1 LRRNDTPAERRLWQR-LRNRQLRGLKFRRQVPIGGYIVDFYCPEARLAIEVDGGYHGSPEQreRDRRRDAYLERLGWRVL 79


                  ..
gi 2524725000  93 RI 94
Cdd:COG2852    80 RF 81
 
Name Accession Description Interval E-value
YcjD COG2852
Very-short-patch-repair endonuclease [Replication, recombination and repair];
15-94 3.97e-31

Very-short-patch-repair endonuclease [Replication, recombination and repair];


Pssm-ID: 442100  Cd Length: 104  Bit Score: 105.33  E-value: 3.97e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524725000  15 LRNESTPGEAILWKYvLRGKGFYGLQFNRQFIIENYIVDFICRELKLIIELDGKYHDQITR--EDEIRDNRLKELGYRVI 92
Cdd:COG2852     1 LRRNDTPAERRLWQR-LRNRQLRGLKFRRQVPIGGYIVDFYCPEARLAIEVDGGYHGSPEQreRDRRRDAYLERLGWRVL 79


                  ..
gi 2524725000  93 RI 94
Cdd:COG2852    80 RF 81
Endonuclease_DUF559 cd01038
Putative endonuclease; Domain of unknown function 559 (DUF559) is a putative endonuclease of ...
 19-95 5.78e-24

Putative endonuclease; Domain of unknown function 559 (DUF559) is a putative endonuclease of unknown function, 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: 411708  Cd Length: 97  Bit Score: 86.87  E-value: 5.78e-24
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2524725000 19 STPGEAILWkYVLRGKGFYGLQFNRQFIIENYIVDFICRELKLIIELDGKYHDQI--TREDEIRDNRLKELGYRVIRIP 95
Cdd:cd01038    1 QTEAERKLW-QHLRNRQFLGLKFRRQKPIGFYIVDFYCAEKKLVIEIDGGQHHEKkaEEYDARRDKYLESLGYTVLRFW 78
DUF559 pfam04480
Protein of unknown function (DUF559);
20-93 1.30e-20

Protein of unknown function (DUF559);


Pssm-ID: 398268  Cd Length: 95  Bit Score: 78.18  E-value: 1.30e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2524725000 20 TPGEAILWKYvLRGKGFYGLQFNRQFIIENYIVDFICRELKLIIELDGKYHDQITREDEIRDNRLKELGYRVIR 93
Cdd:pfam04480  1 TDAERKLWQL-LRNRRLGGFKFRRQKPIGSYIVDFVCEKAKLIVELDGSQHDEQEEYDARRTAFLESQGFTVLR 73
PRK09767 PRK09767
DUF559 domain-containing protein;
8-93 1.35e-12

DUF559 domain-containing protein;


Pssm-ID: 182067  Cd Length: 117  Bit Score: 58.50  E-value: 1.35e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524725000   8 LKHNARKLRNESTPGEAILWKYvLRGKGFYGLQFNRQFIIENYIVDFICRELKLIIELDGKYHDQITREDEIRDNRLKEL 87
Cdd:PRK09767    5 IKSNARDLRRNLTLQERKLWRY-LRSRRFGDFKFRRQHPVGSYILDFACCSARVVVELDGGQHDLAVAYDTRRTSWLESQ 83


                  ....*.
gi 2524725000  88 GYRVIR 93
Cdd:PRK09767   84 GWTVLR 89
 
Name Accession Description Interval E-value
YcjD COG2852
Very-short-patch-repair endonuclease [Replication, recombination and repair];
15-94 3.97e-31

Very-short-patch-repair endonuclease [Replication, recombination and repair];


Pssm-ID: 442100  Cd Length: 104  Bit Score: 105.33  E-value: 3.97e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524725000  15 LRNESTPGEAILWKYvLRGKGFYGLQFNRQFIIENYIVDFICRELKLIIELDGKYHDQITR--EDEIRDNRLKELGYRVI 92
Cdd:COG2852     1 LRRNDTPAERRLWQR-LRNRQLRGLKFRRQVPIGGYIVDFYCPEARLAIEVDGGYHGSPEQreRDRRRDAYLERLGWRVL 79


                  ..
gi 2524725000  93 RI 94
Cdd:COG2852    80 RF 81
Endonuclease_DUF559 cd01038
Putative endonuclease; Domain of unknown function 559 (DUF559) is a putative endonuclease of ...
 19-95 5.78e-24

Putative endonuclease; Domain of unknown function 559 (DUF559) is a putative endonuclease of unknown function, 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: 411708  Cd Length: 97  Bit Score: 86.87  E-value: 5.78e-24
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2524725000 19 STPGEAILWkYVLRGKGFYGLQFNRQFIIENYIVDFICRELKLIIELDGKYHDQI--TREDEIRDNRLKELGYRVIRIP 95
Cdd:cd01038    1 QTEAERKLW-QHLRNRQFLGLKFRRQKPIGFYIVDFYCAEKKLVIEIDGGQHHEKkaEEYDARRDKYLESLGYTVLRFW 78
DUF559 pfam04480
Protein of unknown function (DUF559);
20-93 1.30e-20

Protein of unknown function (DUF559);


Pssm-ID: 398268  Cd Length: 95  Bit Score: 78.18  E-value: 1.30e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2524725000 20 TPGEAILWKYvLRGKGFYGLQFNRQFIIENYIVDFICRELKLIIELDGKYHDQITREDEIRDNRLKELGYRVIR 93
Cdd:pfam04480  1 TDAERKLWQL-LRNRRLGGFKFRRQKPIGSYIVDFVCEKAKLIVELDGSQHDEQEEYDARRTAFLESQGFTVLR 73
PRK09767 PRK09767
DUF559 domain-containing protein;
8-93 1.35e-12

DUF559 domain-containing protein;


Pssm-ID: 182067  Cd Length: 117  Bit Score: 58.50  E-value: 1.35e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524725000   8 LKHNARKLRNESTPGEAILWKYvLRGKGFYGLQFNRQFIIENYIVDFICRELKLIIELDGKYHDQITREDEIRDNRLKEL 87
Cdd:PRK09767    5 IKSNARDLRRNLTLQERKLWRY-LRSRRFGDFKFRRQHPVGSYILDFACCSARVVVELDGGQHDLAVAYDTRRTSWLESQ 83


                  ....*.
gi 2524725000  88 GYRVIR 93
Cdd:PRK09767   84 GWTVLR 89
 
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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