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Conserved domains on  [gi|971743448|ref|YP_009197875|]
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exonuclease VIII [Klebsiella phage 1513]

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: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 ...
 180-321 3.01e-12

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 pfam12684:

Pssm-ID: 469855 [Multi-domain]  Cd Length: 231  Bit Score: 65.40  E-value: 3.01e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971743448  180 QRELSIFGEIFGVKVKVRLDhvdvvsdpeLIKEWGFnqdevfevvvITDYKTTQSSKPDEFGRLAF------NLGYYLKM 253
Cdd:pfam12684  95 EKEVIFTGELFGVPWKIKID---------SLNPEGY----------FVDLKTTRDIHKRKWNEDAGrrvtieAYGYDLQM 155

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 971743448  254 ALQRDLFVKTYNEKRPVVvrLLTQEKKSPFAPLAFTLTSQQIDIGRKQYQSVIHQYAECVKHDSWPSY 321
Cdd:pfam12684 156 AVYQEGLRQNTGKTLPPY--IIAVEKETPPDKAIITAGQSFLDEGLDEVEENLERLKKVKNGEVEPGY 221
 
Name Accession Description Interval E-value
DUF3799 pfam12684
PDDEXK-like domain of unknown function (DUF3799); This family of proteins is functionally ...
 180-321 3.01e-12

PDDEXK-like domain of unknown function (DUF3799); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 265 and 420 amino acids in length. It appears that these proteins are distantly related to the PDDEXK superfamily and so these domains are likely to be nucleases. This family has a C-terminal cysteine cluster similar to that found in pfam01930.


Pssm-ID: 432717 [Multi-domain]  Cd Length: 231  Bit Score: 65.40  E-value: 3.01e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971743448  180 QRELSIFGEIFGVKVKVRLDhvdvvsdpeLIKEWGFnqdevfevvvITDYKTTQSSKPDEFGRLAF------NLGYYLKM 253
Cdd:pfam12684  95 EKEVIFTGELFGVPWKIKID---------SLNPEGY----------FVDLKTTRDIHKRKWNEDAGrrvtieAYGYDLQM 155

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 971743448  254 ALQRDLFVKTYNEKRPVVvrLLTQEKKSPFAPLAFTLTSQQIDIGRKQYQSVIHQYAECVKHDSWPSY 321
Cdd:pfam12684 156 AVYQEGLRQNTGKTLPPY--IIAVEKETPPDKAIITAGQSFLDEGLDEVEENLERLKKVKNGEVEPGY 221
 
Name Accession Description Interval E-value
DUF3799 pfam12684
PDDEXK-like domain of unknown function (DUF3799); This family of proteins is functionally ...
 180-321 3.01e-12

PDDEXK-like domain of unknown function (DUF3799); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 265 and 420 amino acids in length. It appears that these proteins are distantly related to the PDDEXK superfamily and so these domains are likely to be nucleases. This family has a C-terminal cysteine cluster similar to that found in pfam01930.


Pssm-ID: 432717 [Multi-domain]  Cd Length: 231  Bit Score: 65.40  E-value: 3.01e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 971743448  180 QRELSIFGEIFGVKVKVRLDhvdvvsdpeLIKEWGFnqdevfevvvITDYKTTQSSKPDEFGRLAF------NLGYYLKM 253
Cdd:pfam12684  95 EKEVIFTGELFGVPWKIKID---------SLNPEGY----------FVDLKTTRDIHKRKWNEDAGrrvtieAYGYDLQM 155

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 971743448  254 ALQRDLFVKTYNEKRPVVvrLLTQEKKSPFAPLAFTLTSQQIDIGRKQYQSVIHQYAECVKHDSWPSY 321
Cdd:pfam12684 156 AVYQEGLRQNTGKTLPPY--IIAVEKETPPDKAIITAGQSFLDEGLDEVEENLERLKKVKNGEVEPGY 221
 
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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