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Conserved domains on  [gi|30697546|ref|NP_176934|]
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Restriction endonuclease, type II-like superfamily protein [Arabidopsis thaliana]

Protein Classification

lambda exonuclease family protein( domain architecture ID 16909715)

lambda exonuclease family protein similar to Escherichia phage Lambda exonuclease, which facilitates phage DNA recombination through the double-strand break repair (DSBR) and single-strand annealing pathways; also important for the late, rolling-circle mode of lambda DNA replication

CATH:  3.90.320.10
EC:  3.1.11.3
Gene Ontology:  GO:0046872|GO:0004527
PubMed:  22638584

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PDDEXK_lambda_exonuclease-like cd22343
Uncharacterized nucleases similar to lambda phage exonuclease; This model characterizes a ...
 116-295 2.04e-59

Uncharacterized nucleases similar to lambda phage exonuclease; This model characterizes a diverse set of nucleases such as alkaline exonuclease from Laribacter hongkongensis, lambda phage exonuclease, or a Cas4-like protein from the Mimivirus virophage resistance element system. They belong 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: 411747 [Multi-domain]  Cd Length: 182  Bit Score: 189.47  E-value: 2.04e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30697546 116 QKSEEWFALRKDKLTTSTFSTALGFW--KGNRRAELWHEKVYDSDARVVEesarfAMNWGVQMESSAIERYKRIMGCEVG 193
Cdd:cd22343   2 QRSPEWFEARKGRITASNFGRVLTTVenKKAPPASLLKRILGPRPFKSTA-----ATRWGIENEPEAREAYEELTGVKVK 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30697546 194 TMGFAIHsnEEFHWLGASPDGILDC----FGILEVKCPYNKG--KTETVLPWKKVPYYYMPQLQGQMEIMDREWVNLYCW 267
Cdd:cd22343  77 ECGLVIH--PEHPWLGASPDGLVTCdccgKGLLEIKCPYSKDrkLKENFKLDKLETHPYYYQVQGQMAVTGREWCDFVVY 154

                       170       180
                ....*....|....*....|....*...
gi 30697546 268 TRNGSTVFRVMRDRSYWRIIHDVLREFW 295
Cdd:cd22343 155 TPKGSHIERIKRDEEFWAEILPKLEEFY 182
 
Name Accession Description Interval E-value
PDDEXK_lambda_exonuclease-like cd22343
Uncharacterized nucleases similar to lambda phage exonuclease; This model characterizes a ...
 116-295 2.04e-59

Uncharacterized nucleases similar to lambda phage exonuclease; This model characterizes a diverse set of nucleases such as alkaline exonuclease from Laribacter hongkongensis, lambda phage exonuclease, or a Cas4-like protein from the Mimivirus virophage resistance element system. They belong 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: 411747 [Multi-domain]  Cd Length: 182  Bit Score: 189.47  E-value: 2.04e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30697546 116 QKSEEWFALRKDKLTTSTFSTALGFW--KGNRRAELWHEKVYDSDARVVEesarfAMNWGVQMESSAIERYKRIMGCEVG 193
Cdd:cd22343   2 QRSPEWFEARKGRITASNFGRVLTTVenKKAPPASLLKRILGPRPFKSTA-----ATRWGIENEPEAREAYEELTGVKVK 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30697546 194 TMGFAIHsnEEFHWLGASPDGILDC----FGILEVKCPYNKG--KTETVLPWKKVPYYYMPQLQGQMEIMDREWVNLYCW 267
Cdd:cd22343  77 ECGLVIH--PEHPWLGASPDGLVTCdccgKGLLEIKCPYSKDrkLKENFKLDKLETHPYYYQVQGQMAVTGREWCDFVVY 154

                       170       180
                ....*....|....*....|....*...
gi 30697546 268 TRNGSTVFRVMRDRSYWRIIHDVLREFW 295
Cdd:cd22343 155 TPKGSHIERIKRDEEFWAEILPKLEEFY 182
YqaJ pfam09588
YqaJ-like viral recombinase domain; This protein family is found in many different bacterial ...
 120-260 5.16e-23

YqaJ-like viral recombinase domain; This protein family is found in many different bacterial species but is of viral origin. The protein forms an oligomer and functions as a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, It has a preference for 5'-phosphorylated DNA ends. It thus forms part of the two-component SynExo viral recombinase functional unit.


Pssm-ID: 430702 [Multi-domain]  Cd Length: 142  Bit Score: 93.20  E-value: 5.16e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30697546   120 EWFALRKDKLTTSTFSTALGFWKGNRRAELWHEKVYdsdaRVVEESARFAMNWGVQMESSAIERYKRIMGCEVGTMGFAI 199
Cdd:pfam09588   1 EWLEARRGGITASDAAAALGTNPYKSSVSLWLEKTG----QVEPFKDKKAMAWGTELEPIARAEYEFRTGVKVRRVNGLL 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 30697546   200 HsNEEFHWLGASPDGILDCF-----GILEVKCPYNKGKTETV-LPWKKVPYYYMPQLQGQMEIMDRE 260
Cdd:pfam09588  77 Q-HPEDPFLLASPDGIVVGArdgdrGILEIKCPFSATFGASLwGGADGIPEEYMLQVQHQLAVTGAE 142
phage_rel_nuc TIGR03033
putative phage-type endonuclease; Members of this protein family are found often in phage ...
 113-256 1.50e-17

putative phage-type endonuclease; Members of this protein family are found often in phage genomes and in prokaryotic genomes in uncharacterized regions that resemble integrated prophage regions.


Pssm-ID: 200235 [Multi-domain]  Cd Length: 153  Bit Score: 78.62  E-value: 1.50e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30697546   113 DIPQKSEEWFALRKDKLTTSTFSTALGFWKGNRRAELWHEKVydsdARVVEESARFAMNWGVQMESSAIErYKRIMGCEV 192
Cdd:TIGR03033   1 DLVQRTEEWHAWRKGGITASDIAAIMGLNPYKTPEELWKEKT----GFVEPEDMNEAMYHGVKLEPEARE-AFRDKYGIM 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30697546   193 GTMGFAIHsnEEFHWLGASPDGI-LDCFGILEVKCPYNKG-KTETVLPWKKVPYYYMPQLQGQMEI 256
Cdd:TIGR03033  76 AEPFCLEH--DEYPWMAASLDGLvADDKQILEIKCPSERVsKLWVSELSGEVPAYYQAQVQWQLYV 139
 
Name Accession Description Interval E-value
PDDEXK_lambda_exonuclease-like cd22343
Uncharacterized nucleases similar to lambda phage exonuclease; This model characterizes a ...
 116-295 2.04e-59

Uncharacterized nucleases similar to lambda phage exonuclease; This model characterizes a diverse set of nucleases such as alkaline exonuclease from Laribacter hongkongensis, lambda phage exonuclease, or a Cas4-like protein from the Mimivirus virophage resistance element system. They belong 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: 411747 [Multi-domain]  Cd Length: 182  Bit Score: 189.47  E-value: 2.04e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30697546 116 QKSEEWFALRKDKLTTSTFSTALGFW--KGNRRAELWHEKVYDSDARVVEesarfAMNWGVQMESSAIERYKRIMGCEVG 193
Cdd:cd22343   2 QRSPEWFEARKGRITASNFGRVLTTVenKKAPPASLLKRILGPRPFKSTA-----ATRWGIENEPEAREAYEELTGVKVK 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30697546 194 TMGFAIHsnEEFHWLGASPDGILDC----FGILEVKCPYNKG--KTETVLPWKKVPYYYMPQLQGQMEIMDREWVNLYCW 267
Cdd:cd22343  77 ECGLVIH--PEHPWLGASPDGLVTCdccgKGLLEIKCPYSKDrkLKENFKLDKLETHPYYYQVQGQMAVTGREWCDFVVY 154

                       170       180
                ....*....|....*....|....*...
gi 30697546 268 TRNGSTVFRVMRDRSYWRIIHDVLREFW 295
Cdd:cd22343 155 TPKGSHIERIKRDEEFWAEILPKLEEFY 182
YqaJ pfam09588
YqaJ-like viral recombinase domain; This protein family is found in many different bacterial ...
 120-260 5.16e-23

YqaJ-like viral recombinase domain; This protein family is found in many different bacterial species but is of viral origin. The protein forms an oligomer and functions as a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, It has a preference for 5'-phosphorylated DNA ends. It thus forms part of the two-component SynExo viral recombinase functional unit.


Pssm-ID: 430702 [Multi-domain]  Cd Length: 142  Bit Score: 93.20  E-value: 5.16e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30697546   120 EWFALRKDKLTTSTFSTALGFWKGNRRAELWHEKVYdsdaRVVEESARFAMNWGVQMESSAIERYKRIMGCEVGTMGFAI 199
Cdd:pfam09588   1 EWLEARRGGITASDAAAALGTNPYKSSVSLWLEKTG----QVEPFKDKKAMAWGTELEPIARAEYEFRTGVKVRRVNGLL 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 30697546   200 HsNEEFHWLGASPDGILDCF-----GILEVKCPYNKGKTETV-LPWKKVPYYYMPQLQGQMEIMDRE 260
Cdd:pfam09588  77 Q-HPEDPFLLASPDGIVVGArdgdrGILEIKCPFSATFGASLwGGADGIPEEYMLQVQHQLAVTGAE 142
phage_rel_nuc TIGR03033
putative phage-type endonuclease; Members of this protein family are found often in phage ...
 113-256 1.50e-17

putative phage-type endonuclease; Members of this protein family are found often in phage genomes and in prokaryotic genomes in uncharacterized regions that resemble integrated prophage regions.


Pssm-ID: 200235 [Multi-domain]  Cd Length: 153  Bit Score: 78.62  E-value: 1.50e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30697546   113 DIPQKSEEWFALRKDKLTTSTFSTALGFWKGNRRAELWHEKVydsdARVVEESARFAMNWGVQMESSAIErYKRIMGCEV 192
Cdd:TIGR03033   1 DLVQRTEEWHAWRKGGITASDIAAIMGLNPYKTPEELWKEKT----GFVEPEDMNEAMYHGVKLEPEARE-AFRDKYGIM 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30697546   193 GTMGFAIHsnEEFHWLGASPDGI-LDCFGILEVKCPYNKG-KTETVLPWKKVPYYYMPQLQGQMEI 256
Cdd:TIGR03033  76 AEPFCLEH--DEYPWMAASLDGLvADDKQILEIKCPSERVsKLWVSELSGEVPAYYQAQVQWQLYV 139
 
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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