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Conserved domains on  [gi|1141158198|ref|WP_076923190|]
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MULTISPECIES: 3'-5' exonuclease [Pseudoalteromonas]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
KapD super family cl42586
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
3-68 3.29e-28

3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];


The actual alignment was detected with superfamily member COG5018:

Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 99.16  E-value: 3.29e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1141158198   3 LDEFSTFIQPQRHPKLTDFCTNLTSITQHNVDHAPYYPEAINTFQNWLGnYHNYLFCSWGEYGKQQ 68
Cdd:COG5018    41 IDEFSSFVKPVRRPKLSPFCTELTGITQEDVDSAPSFAEAIEDFKKWIG-SEDYILCSWGDYDRKQ 105
 
Name Accession Description Interval E-value
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
3-68 3.29e-28

3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 99.16  E-value: 3.29e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1141158198   3 LDEFSTFIQPQRHPKLTDFCTNLTSITQHNVDHAPYYPEAINTFQNWLGnYHNYLFCSWGEYGKQQ 68
Cdd:COG5018    41 IDEFSSFVKPVRRPKLSPFCTELTGITQEDVDSAPSFAEAIEDFKKWIG-SEDYILCSWGDYDRKQ 105
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
3-65 6.86e-27

DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo.


Pssm-ID: 99836 [Multi-domain]  Cd Length: 176  Bit Score: 95.36  E-value: 6.86e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1141158198   3 LDEFSTFIQPQRHPKLTDFCTNLTSITQHNVDHAPYYPEAINTFQNWLGNYHNYLFCSWGEYG 65
Cdd:cd06133    39 IDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLKEFLEWLGKNGKYAFVTWGDWD 101
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
4-57 3.89e-10

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 52.30  E-value: 3.89e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1141158198    4 DEFSTFIQPqrHPKLTDFCTNLTSITQHNVDHAPYYPEAINTFQNWLGNY----HNYL 57
Cdd:smart00479  34 EVFDTYVKP--DRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGRilvaGNSA 89
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
4-51 1.38e-08

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 48.12  E-value: 1.38e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1141158198   4 DEFSTFIQPQRHPKLTDFCTNLTSITQHNVDHAPYYPEAINTFQNWLG 51
Cdd:pfam00929  34 ETFHTYVKPTRLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFLR 81
PRK07748 PRK07748
3'-5' exonuclease KapD;
4-62 2.27e-08

3'-5' exonuclease KapD;


Pssm-ID: 236087  Cd Length: 207  Bit Score: 47.76  E-value: 2.27e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1141158198   4 DEFSTFIQPQRHPKLTDFCTNLTSITQHNVDHAPYYPEAINTFQNWLGNYHNYLFcSWG 62
Cdd:PRK07748   44 DTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFEELVEKLAEYDKRCKPTIV-TWG 101
 
Name Accession Description Interval E-value
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
3-68 3.29e-28

3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms];


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 99.16  E-value: 3.29e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1141158198   3 LDEFSTFIQPQRHPKLTDFCTNLTSITQHNVDHAPYYPEAINTFQNWLGnYHNYLFCSWGEYGKQQ 68
Cdd:COG5018    41 IDEFSSFVKPVRRPKLSPFCTELTGITQEDVDSAPSFAEAIEDFKKWIG-SEDYILCSWGDYDRKQ 105
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
3-65 6.86e-27

DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins; This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo.


Pssm-ID: 99836 [Multi-domain]  Cd Length: 176  Bit Score: 95.36  E-value: 6.86e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1141158198   3 LDEFSTFIQPQRHPKLTDFCTNLTSITQHNVDHAPYYPEAINTFQNWLGNYHNYLFCSWGEYG 65
Cdd:cd06133    39 IDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLKEFLEWLGKNGKYAFVTWGDWD 101
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
4-57 3.89e-10

exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases;


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 52.30  E-value: 3.89e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1141158198    4 DEFSTFIQPqrHPKLTDFCTNLTSITQHNVDHAPYYPEAINTFQNWLGNY----HNYL 57
Cdd:smart00479  34 EVFDTYVKP--DRPITDYATEIHGITPEMLDDAPTFEEVLEELLEFLRGRilvaGNSA 89
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
4-51 1.38e-08

Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;


Pssm-ID: 395743 [Multi-domain]  Cd Length: 164  Bit Score: 48.12  E-value: 1.38e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1141158198   4 DEFSTFIQPQRHPKLTDFCTNLTSITQHNVDHAPYYPEAINTFQNWLG 51
Cdd:pfam00929  34 ETFHTYVKPTRLPKLTDECTKFTGITQAMLDNKPSFEEVLEEFLEFLR 81
PRK07748 PRK07748
3'-5' exonuclease KapD;
4-62 2.27e-08

3'-5' exonuclease KapD;


Pssm-ID: 236087  Cd Length: 207  Bit Score: 47.76  E-value: 2.27e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1141158198   4 DEFSTFIQPQRHPKLTDFCTNLTSITQHNVDHAPYYPEAINTFQNWLGNYHNYLFcSWG 62
Cdd:PRK07748   44 DTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFEELVEKLAEYDKRCKPTIV-TWG 101
PTZ00315 PTZ00315
2'-phosphotransferase; Provisional
3-64 2.90e-08

2'-phosphotransferase; Provisional


Pssm-ID: 240356 [Multi-domain]  Cd Length: 582  Bit Score: 47.97  E-value: 2.90e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1141158198   3 LDEFSTFIQPQRHPKLTDFCTNLTSITQHNVDHAPYYP----EAINTF-QNWLGN---YHNYLFCSWGEY 64
Cdd:PTZ00315   94 VAEFQRYVRPVKNPVLSRFCTELTGITQSMVSRADPFPvvycEALQFLaEAGLGDappLRSYCVVTCGDW 163
polC PRK00448
DNA polymerase III PolC; Validated
4-55 4.66e-08

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 47.53  E-value: 4.66e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1141158198    4 DEFSTFIQPQRhpKLTDFCTNLTSITQHNVDHAPYYPEAINTFQNWLGNY----HN 55
Cdd:PRK00448   453 DKFEFFIKPGH--PLSAFTTELTGITDDMVKDAPSIEEVLPKFKEFCGDSilvaHN 506
PRK06722 PRK06722
exonuclease; Provisional
1-63 1.79e-04

exonuclease; Provisional


Pssm-ID: 180670 [Multi-domain]  Cd Length: 281  Bit Score: 37.34  E-value: 1.79e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1141158198   1 MK-LDEFSTFIQPQrhPKLTDFCTNLTSITQHNVDHAPYYPEAINTFQNWLGnyHNYLFCSWGE 63
Cdd:PRK06722   40 MKvIGEFSELVKPG--ARLTRHTTKLTGITKKDLIGVEKFPQIIEKFIQFIG--EDSIFVTWGK 99
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
3-58 2.52e-04

bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 36.85  E-value: 2.52e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1141158198   3 LDEFSTFIQPQRhpKLTDFCTNLTSITQHNVDHAPYYPE-AINTFQNWLGNY---HNYLF 58
Cdd:PRK08074   37 LERFSSFVNPER--PIPPFITELTGISEEMVKQAPLFEDvAPEIVELLEGAYfvaHNVHF 94
 
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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