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Conserved domains on  [gi|497070524|ref|WP_009457171|]
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Uma2 family endonuclease [Fischerella thermalis]

Protein Classification

Uma2 family endonuclease( domain architecture ID 10156002)

Uma2 family endonuclease belongs to the PDDEXK nuclease superfamily and may act as a restriction endonuclease

CATH:  3.40.960.10
Gene Ontology:  GO:0004519|GO:0003677
PubMed:  15972856|16011798
SCOP:  3000104

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DUF820-like cd06260
Uncharacterized PDDEXK family nuclease; The Domain of unknown function 820 (DUF820) family is ...
 70-162 2.72e-13

Uncharacterized PDDEXK family nuclease; The Domain of unknown function 820 (DUF820) family is composed of hypothetical proteins that are greatly expanded in cyanobacteria. The proteins are found sporadically in other bacteria. They have been predicted to belong to the PD-(D/E)xK superfamily of nucleases, which includes 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: 411709  Cd Length: 155  Bit Score: 65.15  E-value: 2.72e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497070524  70 APDVMVVFGRPKADRGSYLQWKEnniAPQVVFEILSPSNTTKEMTNKLLFYQRYGVEEYYIYNPDTLELTGL-LRSGDDL 148
Cdd:cd06260   59 EPDVAVVCGERLPDLGIDKFFPG---APDLVVEVLSPSTRYRDLGDKLELYARAGVPEYWLVDPEERTVEVYrLEDGEAY 135

                         90
                 ....*....|....
gi 497070524 149 EIIEEMNGWVSPRL 162
Cdd:cd06260  136 VLVGGETLSGESVL 149
 
Name Accession Description Interval E-value
DUF820-like cd06260
Uncharacterized PDDEXK family nuclease; The Domain of unknown function 820 (DUF820) family is ...
 70-162 2.72e-13

Uncharacterized PDDEXK family nuclease; The Domain of unknown function 820 (DUF820) family is composed of hypothetical proteins that are greatly expanded in cyanobacteria. The proteins are found sporadically in other bacteria. They have been predicted to belong to the PD-(D/E)xK superfamily of nucleases, which includes 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: 411709  Cd Length: 155  Bit Score: 65.15  E-value: 2.72e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497070524  70 APDVMVVFGRPKADRGSYLQWKEnniAPQVVFEILSPSNTTKEMTNKLLFYQRYGVEEYYIYNPDTLELTGL-LRSGDDL 148
Cdd:cd06260   59 EPDVAVVCGERLPDLGIDKFFPG---APDLVVEVLSPSTRYRDLGDKLELYARAGVPEYWLVDPEERTVEVYrLEDGEAY 135

                         90
                 ....*....|....
gi 497070524 149 EIIEEMNGWVSPRL 162
Cdd:cd06260  136 VLVGGETLSGESVL 149
Uma2 pfam05685
Putative restriction endonuclease; This entry includes a group of putative nuclease, including ...
 43-152 1.67e-11

Putative restriction endonuclease; This entry includes a group of putative nuclease, including hypothetical protein TT1808 (also known as Uma2 or TTHA1514), an AT-rich DNA-binding protein from Thermus thermophilus. This domain has a 3-layer alpha/beta/alpha topology similar to that found in restriction endonucleases. The nuclease domain is ubiquitously found in enzymes involved in metabolism of nucleic acids, mostly in nucleases with diverse biological functions.


Pssm-ID: 428585  Cd Length: 169  Bit Score: 60.88  E-value: 1.67e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497070524   43 LFASQSDVFIAGDLLWYPVEGNNKlcqAPDVMVVFGRPkaDRGSYLQWKENNIAPQVVFEILSPSnTTKEMTNKLLFYQR 122
Cdd:pfam05685  46 LRERGLGRVFDSDLGVRLPEGSEP---EPDVAVVRGEW--ERLPRRSRLFLPIAPDLVVEVLSPS-TSYDLGDKRRLYAA 119

                          90       100       110
                  ....*....|....*....|....*....|
gi 497070524  123 YGVEEYYIYNPDTLELTGLLRSGDDLEIIE 152
Cdd:pfam05685 120 AGVPEYWLVDPKERRVEVFRLEDGEYQLVE 149
Uma2 COG4636
Endonuclease, Uma2 family (restriction endonuclease fold) [General function prediction only];
71-158 8.67e-11

Endonuclease, Uma2 family (restriction endonuclease fold) [General function prediction only];


Pssm-ID: 443674  Cd Length: 187  Bit Score: 59.22  E-value: 8.67e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497070524  71 PDVMVVFGR--PKADRGSYLQwkennIAPQVVFEILSPSNTTKEMTNKLLFYQRYGVEEYYIYNPDTLELTGLLRSGDDL 148
Cdd:COG4636   82 PDVAVVCGErlDREERESYLE-----GAPDLVVEVLSPSTARYDRGEKLALYARAGVPEYWLVDPEQRTVEVYRLPEGEY 156

                         90
                 ....*....|
gi 497070524 149 EIIEEMNGWV 158
Cdd:COG4636  157 ELLTYEGGDT 166
 
Name Accession Description Interval E-value
DUF820-like cd06260
Uncharacterized PDDEXK family nuclease; The Domain of unknown function 820 (DUF820) family is ...
 70-162 2.72e-13

Uncharacterized PDDEXK family nuclease; The Domain of unknown function 820 (DUF820) family is composed of hypothetical proteins that are greatly expanded in cyanobacteria. The proteins are found sporadically in other bacteria. They have been predicted to belong to the PD-(D/E)xK superfamily of nucleases, which includes 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: 411709  Cd Length: 155  Bit Score: 65.15  E-value: 2.72e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497070524  70 APDVMVVFGRPKADRGSYLQWKEnniAPQVVFEILSPSNTTKEMTNKLLFYQRYGVEEYYIYNPDTLELTGL-LRSGDDL 148
Cdd:cd06260   59 EPDVAVVCGERLPDLGIDKFFPG---APDLVVEVLSPSTRYRDLGDKLELYARAGVPEYWLVDPEERTVEVYrLEDGEAY 135

                         90
                 ....*....|....
gi 497070524 149 EIIEEMNGWVSPRL 162
Cdd:cd06260  136 VLVGGETLSGESVL 149
Uma2 pfam05685
Putative restriction endonuclease; This entry includes a group of putative nuclease, including ...
 43-152 1.67e-11

Putative restriction endonuclease; This entry includes a group of putative nuclease, including hypothetical protein TT1808 (also known as Uma2 or TTHA1514), an AT-rich DNA-binding protein from Thermus thermophilus. This domain has a 3-layer alpha/beta/alpha topology similar to that found in restriction endonucleases. The nuclease domain is ubiquitously found in enzymes involved in metabolism of nucleic acids, mostly in nucleases with diverse biological functions.


Pssm-ID: 428585  Cd Length: 169  Bit Score: 60.88  E-value: 1.67e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497070524   43 LFASQSDVFIAGDLLWYPVEGNNKlcqAPDVMVVFGRPkaDRGSYLQWKENNIAPQVVFEILSPSnTTKEMTNKLLFYQR 122
Cdd:pfam05685  46 LRERGLGRVFDSDLGVRLPEGSEP---EPDVAVVRGEW--ERLPRRSRLFLPIAPDLVVEVLSPS-TSYDLGDKRRLYAA 119

                          90       100       110
                  ....*....|....*....|....*....|
gi 497070524  123 YGVEEYYIYNPDTLELTGLLRSGDDLEIIE 152
Cdd:pfam05685 120 AGVPEYWLVDPKERRVEVFRLEDGEYQLVE 149
Uma2 COG4636
Endonuclease, Uma2 family (restriction endonuclease fold) [General function prediction only];
71-158 8.67e-11

Endonuclease, Uma2 family (restriction endonuclease fold) [General function prediction only];


Pssm-ID: 443674  Cd Length: 187  Bit Score: 59.22  E-value: 8.67e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497070524  71 PDVMVVFGR--PKADRGSYLQwkennIAPQVVFEILSPSNTTKEMTNKLLFYQRYGVEEYYIYNPDTLELTGLLRSGDDL 148
Cdd:COG4636   82 PDVAVVCGErlDREERESYLE-----GAPDLVVEVLSPSTARYDRGEKLALYARAGVPEYWLVDPEQRTVEVYRLPEGEY 156

                         90
                 ....*....|
gi 497070524 149 EIIEEMNGWV 158
Cdd:COG4636  157 ELLTYEGGDT 166
 
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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