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Conserved domains on  [gi|5327|emb|CAA42380|]
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hypothetical protein [Saccharomyces cerevisiae]

Protein Classification

3'-5' exonuclease family protein( domain architecture ID 1085)

3'-5' exonuclease family protein may cleave nucleotides one at a time from the end (exo) of a polynucleotide chain

CATH:  3.30.420.10
Gene Ontology:  GO:0003676
PubMed:  11988770|11222749
SCOP:  4000547

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DnaQ super family cl34053
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 381-476 8.32e-05

DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG0847:

Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 43.24  E-value: 8.32e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5327     381 RAFVGHHVSGDLKWL----ETIGVKFPGRGYeghldhtlllaetpgdldvfiLDTEQFYRKSY-GEKGSSLGKILRLFEI 455
Cdd:COG0847  81 AVLVAHNAAFDLGFLnaelRRAGLPLPPFPV---------------------LDTLRLARRLLpGLPSYSLDALCERLGI 139

                        90       100
                ....*....|....*....|.
gi 5327     456 PHAFLHNAGNDAYYTLHLFMK 476
Cdd:COG0847 140 PFDERHRALADAEATAELFLA 160
 
Name Accession Description Interval E-value
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 381-476 8.32e-05

DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 43.24  E-value: 8.32e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5327     381 RAFVGHHVSGDLKWL----ETIGVKFPGRGYeghldhtlllaetpgdldvfiLDTEQFYRKSY-GEKGSSLGKILRLFEI 455
Cdd:COG0847  81 AVLVAHNAAFDLGFLnaelRRAGLPLPPFPV---------------------LDTLRLARRLLpGLPSYSLDALCERLGI 139

                        90       100
                ....*....|....*....|.
gi 5327     456 PHAFLHNAGNDAYYTLHLFMK 476
Cdd:COG0847 140 PFDERHRALADAEATAELFLA 160
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 380-475 5.58e-03

DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.


Pssm-ID: 176648 [Multi-domain]  Cd Length: 159  Bit Score: 37.67  E-value: 5.58e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5327     380 SRAFVGHHVSGDLKWLETIGVKFPGRgyeghldhtlllaetpgDLDVFILDTEQFYRKSYGEKGSSLGKILR--LFEIPH 457
Cdd:cd06127  79 GRVLVAHNASFDLRFLNRELRRLGGP-----------------PLPNPWIDTLRLARRLLPGLRSHRLGLLLaeRYGIPL 141

                        90
                ....*....|....*...
gi 5327     458 AFLHNAGNDAYYTLHLFM 475
Cdd:cd06127 142 EGAHRALADALATAELLL 159
 
Name Accession Description Interval E-value
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 381-476 8.32e-05

DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 43.24  E-value: 8.32e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5327     381 RAFVGHHVSGDLKWL----ETIGVKFPGRGYeghldhtlllaetpgdldvfiLDTEQFYRKSY-GEKGSSLGKILRLFEI 455
Cdd:COG0847  81 AVLVAHNAAFDLGFLnaelRRAGLPLPPFPV---------------------LDTLRLARRLLpGLPSYSLDALCERLGI 139

                        90       100
                ....*....|....*....|.
gi 5327     456 PHAFLHNAGNDAYYTLHLFMK 476
Cdd:COG0847 140 PFDERHRALADAEATAELFLA 160
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 380-475 5.58e-03

DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.


Pssm-ID: 176648 [Multi-domain]  Cd Length: 159  Bit Score: 37.67  E-value: 5.58e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5327     380 SRAFVGHHVSGDLKWLETIGVKFPGRgyeghldhtlllaetpgDLDVFILDTEQFYRKSYGEKGSSLGKILR--LFEIPH 457
Cdd:cd06127  79 GRVLVAHNASFDLRFLNRELRRLGGP-----------------PLPNPWIDTLRLARRLLPGLRSHRLGLLLaeRYGIPL 141

                        90
                ....*....|....*...
gi 5327     458 AFLHNAGNDAYYTLHLFM 475
Cdd:cd06127 142 EGAHRALADALATAELLL 159
 
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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