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Conserved domains on  [gi|2225520570|ref|WP_245538473|]
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Uma2 family endonuclease [Thauera phenylacetica]

Protein Classification

Uma2 family endonuclease( domain architecture ID 10008647)

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

Gene Ontology:  GO:0003676|GO:0004519
PubMed:  17584917|16011798
SCOP:  3000104

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Uma2 COG4636
Endonuclease, Uma2 family (restriction endonuclease fold) [General function prediction only];
23-116 2.42e-15

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


:

Pssm-ID: 443674  Cd Length: 187  Bit Score: 68.47  E-value: 2.42e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2225520570  23 RRSRAELAIEHPRLVVEVLSGSTAACDRSIEFVAYRKlADLRECLLVDVDQRRLELHRREAGHWILLESEGDGPALRLES 102
Cdd:COG4636    94 REERESYLEGAPDLVVEVLSPSTARYDRGEKLALYAR-AGVPEYWLVDPEQRTVEVYRLPEGEYELLTYEGGDTLSSLPV 172

                          90
                  ....*....|....*
gi 2225520570 103 V-DMTLSPAEAFEDL 116
Cdd:COG4636   173 LpGLELDLEELFEAV 187
 
Name Accession Description Interval E-value
Uma2 COG4636
Endonuclease, Uma2 family (restriction endonuclease fold) [General function prediction only];
23-116 2.42e-15

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


Pssm-ID: 443674  Cd Length: 187  Bit Score: 68.47  E-value: 2.42e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2225520570  23 RRSRAELAIEHPRLVVEVLSGSTAACDRSIEFVAYRKlADLRECLLVDVDQRRLELHRREAGHWILLESEGDGPALRLES 102
Cdd:COG4636    94 REERESYLEGAPDLVVEVLSPSTARYDRGEKLALYAR-AGVPEYWLVDPEQRTVEVYRLPEGEYELLTYEGGDTLSSLPV 172

                          90
                  ....*....|....*
gi 2225520570 103 V-DMTLSPAEAFEDL 116
Cdd:COG4636   173 LpGLELDLEELFEAV 187
Uma2 pfam05685
Putative restriction endonuclease; This entry includes a group of putative nuclease, including ...
 20-103 8.98e-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: 55.88  E-value: 8.98e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2225520570  20 GRARRSRAELAIEHPRLVVEVLSGSTAAcDRSIEFVAYRKlADLRECLLVDVDQRRLELHRREAGHWILLESEGDGPALR 99
Cdd:pfam05685  81 ERLPRRSRLFLPIAPDLVVEVLSPSTSY-DLGDKRRLYAA-AGVPEYWLVDPKERRVEVFRLEDGEYQLVEVLEGGETLS 158


                  ....
gi 2225520570 100 LESV 103
Cdd:pfam05685 159 LEEA 162
DUF820-like cd06260
Uncharacterized PDDEXK family nuclease; The Domain of unknown function 820 (DUF820) family is ...
 21-106 2.87e-10

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: 54.36  E-value: 2.87e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2225520570  21 RARRSRAELAIEHPRLVVEVLSGSTAACDRSIEFVAYRKlADLRECLLVDVDQRRLELHRREAG-HWILLESEGDGPALR 99
Cdd:cd06260    70 LPDLGIDKFFPGAPDLVVEVLSPSTRYRDLGDKLELYAR-AGVPEYWLVDPEERTVEVYRLEDGeAYVLVGGETLSGESV 148


                  ....*..
gi 2225520570 100 LESVDMT 106
Cdd:cd06260   149 LPGLELR 155
 
Name Accession Description Interval E-value
Uma2 COG4636
Endonuclease, Uma2 family (restriction endonuclease fold) [General function prediction only];
23-116 2.42e-15

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


Pssm-ID: 443674  Cd Length: 187  Bit Score: 68.47  E-value: 2.42e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2225520570  23 RRSRAELAIEHPRLVVEVLSGSTAACDRSIEFVAYRKlADLRECLLVDVDQRRLELHRREAGHWILLESEGDGPALRLES 102
Cdd:COG4636    94 REERESYLEGAPDLVVEVLSPSTARYDRGEKLALYAR-AGVPEYWLVDPEQRTVEVYRLPEGEYELLTYEGGDTLSSLPV 172

                          90
                  ....*....|....*
gi 2225520570 103 V-DMTLSPAEAFEDL 116
Cdd:COG4636   173 LpGLELDLEELFEAV 187
Uma2 pfam05685
Putative restriction endonuclease; This entry includes a group of putative nuclease, including ...
 20-103 8.98e-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: 55.88  E-value: 8.98e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2225520570  20 GRARRSRAELAIEHPRLVVEVLSGSTAAcDRSIEFVAYRKlADLRECLLVDVDQRRLELHRREAGHWILLESEGDGPALR 99
Cdd:pfam05685  81 ERLPRRSRLFLPIAPDLVVEVLSPSTSY-DLGDKRRLYAA-AGVPEYWLVDPKERRVEVFRLEDGEYQLVEVLEGGETLS 158


                  ....
gi 2225520570 100 LESV 103
Cdd:pfam05685 159 LEEA 162
DUF820-like cd06260
Uncharacterized PDDEXK family nuclease; The Domain of unknown function 820 (DUF820) family is ...
 21-106 2.87e-10

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: 54.36  E-value: 2.87e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2225520570  21 RARRSRAELAIEHPRLVVEVLSGSTAACDRSIEFVAYRKlADLRECLLVDVDQRRLELHRREAG-HWILLESEGDGPALR 99
Cdd:cd06260    70 LPDLGIDKFFPGAPDLVVEVLSPSTRYRDLGDKLELYAR-AGVPEYWLVDPEERTVEVYRLEDGeAYVLVGGETLSGESV 148


                  ....*..
gi 2225520570 100 LESVDMT 106
Cdd:cd06260   149 LPGLELR 155
 
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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