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Conserved domains on  [gi|502840999|ref|WP_013075975|]
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3'-5' exonuclease KapD [Kyrpidia tusciae]

Protein Classification

3'-5' exonuclease family protein; 3'-5' exonuclease( domain architecture ID 10792978)

3'-5' exonuclease family protein may cleave nucleotides one at a time from the end (exo) of a polynucleotide chain| 3'-5' exonuclease has a fundamental role in reducing polymerase errors and is involved in proofreading activity

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK07748 PRK07748
3'-5' exonuclease KapD;
1-206 2.71e-133

3'-5' exonuclease KapD;


:

Pssm-ID: 236087  Cd Length: 207  Bit Score: 372.48  E-value: 2.71e-133
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999   1 MSEQLLFLDFEFTMPEDRSTPEQFRPEIIELGLVSVIDGEIFDRLSTFVRPMRFPTLTERCKNFLQIRQEDVDAGISFRE 80
Cdd:PRK07748   2 DEQQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGCEVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFEE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999  81 LVETLQTYVELCPTTPVTWGNADLQVLRENCGHAGLPFPFDRRERDLSLEYKRFFGNRQQTGLWKAIEEYGRTGVGRHHR 160
Cdd:PRK07748  82 LVEKLAEYDKRCKPTIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERNQTGLWKAIEEYGKEGTGKHHC 161

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 502840999 161 ALDDALTTVEIFRMIEKDKEYLNRRERMTLGDRVDLEDVWKKLNDW 206
Cdd:PRK07748 162 ALDDAMTTYNIFKLVEKDKEYLVKPEPPTIGERVDFSKVLKKVSTQ 207
 
Name Accession Description Interval E-value
PRK07748 PRK07748
3'-5' exonuclease KapD;
1-206 2.71e-133

3'-5' exonuclease KapD;


Pssm-ID: 236087  Cd Length: 207  Bit Score: 372.48  E-value: 2.71e-133
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999   1 MSEQLLFLDFEFTMPEDRSTPEQFRPEIIELGLVSVIDGEIFDRLSTFVRPMRFPTLTERCKNFLQIRQEDVDAGISFRE 80
Cdd:PRK07748   2 DEQQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGCEVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFEE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999  81 LVETLQTYVELCPTTPVTWGNADLQVLRENCGHAGLPFPFDRRERDLSLEYKRFFGNRQQTGLWKAIEEYGRTGVGRHHR 160
Cdd:PRK07748  82 LVEKLAEYDKRCKPTIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERNQTGLWKAIEEYGKEGTGKHHC 161

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 502840999 161 ALDDALTTVEIFRMIEKDKEYLNRRERMTLGDRVDLEDVWKKLNDW 206
Cdd:PRK07748 162 ALDDAMTTYNIFKLVEKDKEYLVKPEPPTIGERVDFSKVLKKVSTQ 207
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 4-181 4.55e-73

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 218.96  E-value: 4.55e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999   4 QLLFLDFEFTMPEDRsTPEQFRPEIIELGLVSV-IDGEIFDRLSTFVRPMRFPTLTERCKNFLQIRQEDVDAGISFRELV 82
Cdd:COG5018    3 KYLVIDLEATCWDGK-PPPGFPMEIIEIGAVKVdENGEIIDEFSSFVKPVRRPKLSPFCTELTGITQEDVDSAPSFAEAI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999  83 ETLQTYVELCPTTPVTWGNADLQVLRENCGHAGLPFPFDRRERDLSLEYKRFFGNRQQTGLWKAIEEYGRTGVGRHHRAL 162
Cdd:COG5018   82 EDFKKWIGSEDYILCSWGDYDRKQLERNCRFHGVPYPFGDRHINLKKLFALYFGLKKRIGLKKALELLGLEFEGTHHRAL 161

                        170
                 ....*....|....*....
gi 502840999 163 DDALTTVEIFRMIEKDKEY 181
Cdd:COG5018  162 DDARNTAKLFKKILGDKRL 180
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 5-173 4.97e-51

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: 162.77  E-value: 4.97e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999   5 LLFLDFEFTMPEDRSTPEqFRPEIIELGLVsVID---GEIFDRLSTFVRPMRFPTLTERCKNFLQIRQEDVDAGISFREL 81
Cdd:cd06133    1 YLVIDFEATCWEGNSKPD-YPNEIIEIGAV-LVDvktKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999  82 VETLQTYV-ELCPTTPVTWGNADLQVLRENCGHAGL--PFPFDRRERDLSLEYKRFFGNRQQTGLWKAIEEYGRTGVGRH 158
Cdd:cd06133   79 LKEFLEWLgKNGKYAFVTWGDWDLKDLLQNQCKYKIinLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEGRH 158

                        170
                 ....*....|....*
gi 502840999 159 HRALDDALTTVEIFR 173
Cdd:cd06133  159 HRGLDDARNIARILK 173
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 5-180 1.43e-29

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 107.77  E-value: 1.43e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999     5 LLFLDFEFTMPEDRstpeqfRPEIIELGLVSVIDGEIFDRLSTFVRPmrFPTLTERCKNFLQIRQEDVDAGISFRELVET 84
Cdd:smart00479   2 LVVIDCETTGLDPG------KDEIIEIAAVDVDGGEIIEVFDTYVKP--DRPITDYATEIHGITPEMLDDAPTFEEVLEE 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999    85 LQTYVELCPTTPVTWGNADLQVLRENCGHAGLPFPFDRRERDLSLEYKRFFGNRQQTGLWKAIEEYGRTGVGRHHRALDD 164
Cdd:smart00479  74 LLEFLRGRILVAGNSAHFDLRFLKLEHPRLGIKQPPKLPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIQRAHRALDD 153

                          170
                   ....*....|....*.
gi 502840999   165 ALTTVEIFRMIEKDKE 180
Cdd:smart00479 154 ARATAKLFKKLLERLE 169
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 6-172 8.92e-18

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: 77.01  E-value: 8.92e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999    6 LFLDFEFTMPEdrstpeQFRPEIIELGLVSVIDGE--IFDRLSTFVRPMRFPTLTERCKNFLQIRQEDVDAGISFRELVE 83
Cdd:pfam00929   1 VVIDLETTGLD------PEKDEIIEIAAVVIDGGEneIGETFHTYVKPTRLPKLTDECTKFTGITQAMLDNKPSFEEVLE 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999   84 TLQTYVEL------CPTTP-VTWGNADL-QVLRENCghagLPFPFDRRERDLSleyKRFFGNRQQTGLWKAIEEYGRTGV 155
Cdd:pfam00929  75 EFLEFLRKgnllvaHNASFdVGFLRYDDkRFLKKPM----PKLNPVIDTLILD---KATYKELPGRSLDALAEKLGLEHI 147

                         170
                  ....*....|....*..
gi 502840999  156 GRHHRALDDALTTVEIF 172
Cdd:pfam00929 148 GRAHRALDDARATAKLF 164
 
Name Accession Description Interval E-value
PRK07748 PRK07748
3'-5' exonuclease KapD;
1-206 2.71e-133

3'-5' exonuclease KapD;


Pssm-ID: 236087  Cd Length: 207  Bit Score: 372.48  E-value: 2.71e-133
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999   1 MSEQLLFLDFEFTMPEDRSTPEQFRPEIIELGLVSVIDGEIFDRLSTFVRPMRFPTLTERCKNFLQIRQEDVDAGISFRE 80
Cdd:PRK07748   2 DEQQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGCEVEDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFEE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999  81 LVETLQTYVELCPTTPVTWGNADLQVLRENCGHAGLPFPFDRRERDLSLEYKRFFGNRQQTGLWKAIEEYGRTGVGRHHR 160
Cdd:PRK07748  82 LVEKLAEYDKRCKPTIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERNQTGLWKAIEEYGKEGTGKHHC 161

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 502840999 161 ALDDALTTVEIFRMIEKDKEYLNRRERMTLGDRVDLEDVWKKLNDW 206
Cdd:PRK07748 162 ALDDAMTTYNIFKLVEKDKEYLVKPEPPTIGERVDFSKVLKKVSTQ 207
KapD COG5018
3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction ...
 4-181 4.55e-73

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


Pssm-ID: 444042 [Multi-domain]  Cd Length: 181  Bit Score: 218.96  E-value: 4.55e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999   4 QLLFLDFEFTMPEDRsTPEQFRPEIIELGLVSV-IDGEIFDRLSTFVRPMRFPTLTERCKNFLQIRQEDVDAGISFRELV 82
Cdd:COG5018    3 KYLVIDLEATCWDGK-PPPGFPMEIIEIGAVKVdENGEIIDEFSSFVKPVRRPKLSPFCTELTGITQEDVDSAPSFAEAI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999  83 ETLQTYVELCPTTPVTWGNADLQVLRENCGHAGLPFPFDRRERDLSLEYKRFFGNRQQTGLWKAIEEYGRTGVGRHHRAL 162
Cdd:COG5018   82 EDFKKWIGSEDYILCSWGDYDRKQLERNCRFHGVPYPFGDRHINLKKLFALYFGLKKRIGLKKALELLGLEFEGTHHRAL 161

                        170
                 ....*....|....*....
gi 502840999 163 DDALTTVEIFRMIEKDKEY 181
Cdd:COG5018  162 DDARNTAKLFKKILGDKRL 180
ERI-1_3'hExo_like cd06133
DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and ...
 5-173 4.97e-51

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: 162.77  E-value: 4.97e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999   5 LLFLDFEFTMPEDRSTPEqFRPEIIELGLVsVID---GEIFDRLSTFVRPMRFPTLTERCKNFLQIRQEDVDAGISFREL 81
Cdd:cd06133    1 YLVIDFEATCWEGNSKPD-YPNEIIEIGAV-LVDvktKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999  82 VETLQTYV-ELCPTTPVTWGNADLQVLRENCGHAGL--PFPFDRRERDLSLEYKRFFGNRQQTGLWKAIEEYGRTGVGRH 158
Cdd:cd06133   79 LKEFLEWLgKNGKYAFVTWGDWDLKDLLQNQCKYKIinLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEGRH 158

                        170
                 ....*....|....*
gi 502840999 159 HRALDDALTTVEIFR 173
Cdd:cd06133  159 HRGLDDARNIARILK 173
EXOIII smart00479
exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other ...
 5-180 1.43e-29

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


Pssm-ID: 214685 [Multi-domain]  Cd Length: 169  Bit Score: 107.77  E-value: 1.43e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999     5 LLFLDFEFTMPEDRstpeqfRPEIIELGLVSVIDGEIFDRLSTFVRPmrFPTLTERCKNFLQIRQEDVDAGISFRELVET 84
Cdd:smart00479   2 LVVIDCETTGLDPG------KDEIIEIAAVDVDGGEIIEVFDTYVKP--DRPITDYATEIHGITPEMLDDAPTFEEVLEE 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999    85 LQTYVELCPTTPVTWGNADLQVLRENCGHAGLPFPFDRRERDLSLEYKRFFGNRQQTGLWKAIEEYGRTGVGRHHRALDD 164
Cdd:smart00479  74 LLEFLRGRILVAGNSAHFDLRFLKLEHPRLGIKQPPKLPVIDTLKLARATNPGLPKYSLKKLAKRLLLEVIQRAHRALDD 153

                          170
                   ....*....|....*.
gi 502840999   165 ALTTVEIFRMIEKDKE 180
Cdd:smart00479 154 ARATAKLFKKLLERLE 169
RNase_T pfam00929
Exonuclease; This family includes a variety of exonuclease proteins, such as ribonuclease T ...
 6-172 8.92e-18

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: 77.01  E-value: 8.92e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999    6 LFLDFEFTMPEdrstpeQFRPEIIELGLVSVIDGE--IFDRLSTFVRPMRFPTLTERCKNFLQIRQEDVDAGISFRELVE 83
Cdd:pfam00929   1 VVIDLETTGLD------PEKDEIIEIAAVVIDGGEneIGETFHTYVKPTRLPKLTDECTKFTGITQAMLDNKPSFEEVLE 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999   84 TLQTYVEL------CPTTP-VTWGNADL-QVLRENCghagLPFPFDRRERDLSleyKRFFGNRQQTGLWKAIEEYGRTGV 155
Cdd:pfam00929  75 EFLEFLRKgnllvaHNASFdVGFLRYDDkRFLKKPM----PKLNPVIDTLILD---KATYKELPGRSLDALAEKLGLEHI 147

                         170
                  ....*....|....*..
gi 502840999  156 GRHHRALDDALTTVEIF 172
Cdd:pfam00929 148 GRAHRALDDARATAKLF 164
DEDDh cd06127
DEDDh 3'-5' exonuclease domain family; DEDDh exonucleases, part of the DnaQ-like (or DEDD) ...
 25-173 1.47e-17

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: 76.19  E-value: 1.47e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999  25 RPEIIELGLVSVIDG-EIFDRLSTFVRPMRFptLTERCKNFLQIRQEDVDAGISFRELVETLQTYVELCPttPVTWgNA- 102
Cdd:cd06127   14 KDRIIEIGAVKVDGGiEIVERFETLVNPGRP--IPPEATAIHGITDEMLADAPPFEEVLPEFLEFLGGRV--LVAH-NAs 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 502840999 103 -DLQVLRENCGHAGLPfPFDRRERDLSLEYKRFFGNRQQTGLWKAIEEYGRTGVGRHHRALDDALTTVEIFR 173
Cdd:cd06127   89 fDLRFLNRELRRLGGP-PLPNPWIDTLRLARRLLPGLRSHRLGLLLAERYGIPLEGAHRALADALATAELLL 159
PolC COG2176
DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]; ...
 27-180 3.74e-17

DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair];


Pssm-ID: 441779 [Multi-domain]  Cd Length: 181  Bit Score: 75.57  E-value: 3.74e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999  27 EIIELGLVSVIDGEIFDRLSTFVRP-MRFPTLTERCKNflqIRQEDVDAGISFRELVETLQTYVELCPttPVTWgNA--D 103
Cdd:COG2176   26 EIIEIGAVKVENGEIVDRFSTLVNPgRPIPPFITELTG---ITDEMVADAPPFEEVLPEFLEFLGDAV--LVAH-NAsfD 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999 104 LQVLRENCGHAGLPFPF---DrrerdlSLE-YKRFFGNRQQTGLWKAIEEYGrTGVGRHHRALDDALTTVEIF-RMIEKD 178
Cdd:COG2176  100 LGFLNAALKRLGLPFDNpvlD------TLElARRLLPELKSYKLDTLAERLG-IPLEDRHRALGDAEATAELFlKLLEKL 172


                 ..
gi 502840999 179 KE 180
Cdd:COG2176  173 EE 174
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 5-175 4.10e-17

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


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 75.21  E-value: 4.10e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999   5 LLFLDFEFT--MPEdrstpeqfRPEIIELGLVSVIDGEIFDRLSTFVRP-MRFPTLTERcknFLQIRQEDVDAGISFREL 81
Cdd:COG0847    2 FVVLDTETTglDPA--------KDRIIEIGAVKVDDGRIVETFHTLVNPeRPIPPEATA---IHGITDEDVADAPPFAEV 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999  82 VETLQTYVElcpttpvtwG------NA--DLQVLRENCGHAGLPFPFDRReRDLSLEYKRFFGNRQQTGLWKAIEEYGRT 153
Cdd:COG0847   71 LPELLEFLG---------GavlvahNAafDLGFLNAELRRAGLPLPPFPV-LDTLRLARRLLPGLPSYSLDALCERLGIP 140

                        170       180
                 ....*....|....*....|..
gi 502840999 154 gVGRHHRALDDALTTVEIFRMI 175
Cdd:COG0847  141 -FDERHRALADAEATAELFLAL 161
PRK06722 PRK06722
exonuclease; Provisional
 24-212 1.76e-09

exonuclease; Provisional


Pssm-ID: 180670 [Multi-domain]  Cd Length: 281  Bit Score: 56.21  E-value: 1.76e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999  24 FRP-------EIIELGLVSVIDG--EIFDRLSTFVRPMrfPTLTERCKNFLQIRQEDVDAGISFRELVETLQTYVELcPT 94
Cdd:PRK06722  16 FRPyksedpsEIVDIGAVKIEAStmKVIGEFSELVKPG--ARLTRHTTKLTGITKKDLIGVEKFPQIIEKFIQFIGE-DS 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999  95 TPVTWGNADLQVLRENCGHAGLPFPFDRRERDLSLE------YKRFFgnRQQTGLWKAIEEYGRTGVGRHHRALDDALTT 168
Cdd:PRK06722  93 IFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQkfvfqaYEELF--EHTPSLQSAVEQLGLIWEGKQHRALADAENT 170

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 502840999 169 VEIFRMIEKDKEYLNRRERMTLGDRVD----LEDVWKKLNDWQVKTAK 212
Cdd:PRK06722 171 ANILLKAYSERDITKRYKRHGELELVKngklTEKAKKKMRKWVFKEMR 218
polC PRK00448
DNA polymerase III PolC; Validated
 27-180 5.09e-09

DNA polymerase III PolC; Validated


Pssm-ID: 234767 [Multi-domain]  Cd Length: 1437  Bit Score: 55.61  E-value: 5.09e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999   27 EIIELGLVSVIDGEIFDRLSTFVRPmRFPtLTERCKNFLQIRQEDVDAGISfreLVETLQTYVELCPTTPVTWGNA--DL 104
Cdd:PRK00448  437 EIIEIGAVKIKNGEIIDKFEFFIKP-GHP-LSAFTTELTGITDDMVKDAPS---IEEVLPKFKEFCGDSILVAHNAsfDV 511

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999  105 QVLRENCGHAGLPFP----FDRRE--RDLSLEYKRFfgnrqqtGLWKAIEEYgrtGVG--RHHRALDDALTTVEIF-RMI 175
Cdd:PRK00448  512 GFINTNYEKLGLEKIknpvIDTLElsRFLYPELKSH-------RLNTLAKKF---GVEleHHHRADYDAEATAYLLiKFL 581


                  ....*
gi 502840999  176 EKDKE 180
Cdd:PRK00448  582 KDLKE 586
DNA_pol_III_epsilon_like cd06130
an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with ...
 8-172 1.24e-06

an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III; This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains 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. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex.


Pssm-ID: 99834 [Multi-domain]  Cd Length: 156  Bit Score: 46.35  E-value: 1.24e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999   8 LDFEftmpedrsTPEQFRPEIIELGLVSVIDGEIFDRLSTFVRP-MRFptlterckNFLQ-----IRQEDV-DAGiSFRE 80
Cdd:cd06130    4 IDFE--------TANADRASACSIGLVKVRDGQIVDTFYTLIRPpTRF--------DPFNiaihgITPEDVaDAP-TFPE 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999  81 LVETLQTYVElcpTTPVTWGNA--DLQVLRENCGHAGLPFP----FD-----RRERDLSLEYK-----RFFGnrqqtglw 144
Cdd:cd06130   67 VWPEIKPFLG---GSLVVAHNAsfDRSVLRAALEAYGLPPPpyqyLCtvrlaRRVWPLLPNHKlntvaEHLG-------- 135

                        170       180
                 ....*....|....*....|....*...
gi 502840999 145 kaIEEygrtgvgRHHRALDDALTTVEIF 172
Cdd:cd06130  136 --IEL-------NHHDALEDARACAEIL 154
PTZ00315 PTZ00315
2'-phosphotransferase; Provisional
 8-164 3.00e-06

2'-phosphotransferase; Provisional


Pssm-ID: 240356 [Multi-domain]  Cd Length: 582  Bit Score: 47.20  E-value: 3.00e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999   8 LDFEFTMPEDRSTPEqfrPEIIELGLVsVIDGEIFDRLSTF---VRPMRFPTLTERCKNFLQIRQEDVDAGISFREL-VE 83
Cdd:PTZ00315  61 LDFEATCEADRRIED---AEVIEFPMV-LVDARTATPVAEFqryVRPVKNPVLSRFCTELTGITQSMVSRADPFPVVyCE 136

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999  84 TLQTYVE--------LCPTTPVTWGNADLQVL----RENCGHAGLPFPFdRRERDLSLEYKRF-FGNRQQTGLWKAiEEY 150
Cdd:PTZ00315 137 ALQFLAEaglgdappLRSYCVVTCGDWDLKTMlpsqMRVSGQQGTPLSF-QRWCNLKKYMSQLgFGNGSGCGGGAT-PPL 214

                        170       180
                 ....*....|....*....|....*.
gi 502840999 151 GRTGV------------GRHHRALDD 164
Cdd:PTZ00315 215 GPSDMpdmlqmlglplqGRHHSGIDD 240
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 8-178 3.51e-06

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 46.70  E-value: 3.51e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999   8 LDFEfTMPEDRSTPEQfrpeiieLGLVSVIDGEIFDRLSTFVRP--MRFPTLTERCKNflqIRQEDVDAGISFRELVETL 85
Cdd:PRK06195   6 IDFE-TANEKRNSPCS-------IGIVVVKDGEIVEKVHYLIKPkeMRFMPINIGIHG---IRPHMVEDELEFDKIWEKI 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999  86 QTYVElcpTTPVTWGNA--DLQVLRENCGHAGLPFPfdrrerdlSLEY-------KRFFGNRQQTGL-----WKAIEeyg 151
Cdd:PRK06195  75 KHYFN---NNLVIAHNAsfDISVLRKTLELYNIPMP--------SFEYictmklaKNFYSNIDNARLntvnnFLGYE--- 140

                        170       180
                 ....*....|....*....|....*..
gi 502840999 152 rtgvGRHHRALDDALTTVEIFRMIEKD 178
Cdd:PRK06195 141 ----FKHHDALADAMACSNILLNISKE 163
PRK08074 PRK08074
bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
 27-201 3.21e-04

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


Pssm-ID: 236148 [Multi-domain]  Cd Length: 928  Bit Score: 41.09  E-value: 3.21e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999  27 EIIELGLVSVIDGEIFDRLSTFVRPMR-FPTLTERCKNflqIRQEDVDAGISFRELVETLqtyVELCPTTPVTWGNA--D 103
Cdd:PRK08074  22 KIIQIAAVVVEDGEILERFSSFVNPERpIPPFITELTG---ISEEMVKQAPLFEDVAPEI---VELLEGAYFVAHNVhfD 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502840999 104 LQVLRENCGHAGLPfPFDRRERDlSLEYKRFfgnrqqtgLWKAIEEYGRTGVGRH--------HRALDDALTTVEIF-RM 174
Cdd:PRK08074  96 LNFLNEELERAGYT-EIHCPKLD-TVELARI--------LLPTAESYKLRDLSEElglehdqpHRADSDAEVTAELFlQL 165

                        170       180
                 ....*....|....*....|....*..
gi 502840999 175 IEKdkeyLNRRERMTLGDRVDLEDVWK 201
Cdd:PRK08074 166 LNK----LERLPLVTLQQLRRLSDHLK 188
 
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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