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Conserved domains on  [gi|461693623|gb|AGH19786|]
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DNA polymerase beta, partial [Xiphophorus continens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DNA_pol_B_palm pfam14792
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three ...
 15-95 3.36e-38

DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the palm domain.


:

Pssm-ID: 464318  Cd Length: 110  Bit Score: 123.44  E-value: 3.36e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 461693623   15 RIPRVEMEKMEVLILGELKKIDPEYIGTICGSYRRGAASSGDIDILLTHPNYTSQTEkQPKLLHAVVDHLESVGFVTDTL 94
Cdd:pfam14792   1 RIPREEVEALEAIVRKAAKTLDPDVEVIVCGSYRRGAESSGDVDILITHPDGTSESE-LKGLLDRLVARLKKSGFLTDDL 79


                  .
gi 461693623   95 S 95
Cdd:pfam14792  80 A 80
 
Name Accession Description Interval E-value
DNA_pol_B_palm pfam14792
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three ...
 15-95 3.36e-38

DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the palm domain.


Pssm-ID: 464318  Cd Length: 110  Bit Score: 123.44  E-value: 3.36e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 461693623   15 RIPRVEMEKMEVLILGELKKIDPEYIGTICGSYRRGAASSGDIDILLTHPNYTSQTEkQPKLLHAVVDHLESVGFVTDTL 94
Cdd:pfam14792   1 RIPREEVEALEAIVRKAAKTLDPDVEVIVCGSYRRGAESSGDVDILITHPDGTSESE-LKGLLDRLVARLKKSGFLTDDL 79


                  .
gi 461693623   95 S 95
Cdd:pfam14792  80 A 80
NT_POLXc cd00141
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
 1-96 2.36e-34

Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this family.


Pssm-ID: 143386 [Multi-domain]  Cd Length: 307  Bit Score: 119.22  E-value: 2.36e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 461693623   1 HQKIGLKYFEEFEKRIPRVEMEKMEVLILGELKKIDPEYIGTICGSYRRGAASSGDIDILLTHPNYTSQtekqpKLLHAV 80
Cdd:cd00141  123 NILIGLEYYEDFQQRIPREEALAIAEIIKEALREVDPVLQVEIAGSYRRGKETVGDIDILVTHPDATSR-----GLLEKV 197

                         90
                 ....*....|....*.
gi 461693623  81 VDHLESVGFVTDTLSK 96
Cdd:cd00141  198 VDALVELGFVTEVLSK 213
POLXc smart00483
DNA polymerase X family; includes vertebrate polymerase beta and terminal ...
 1-96 2.07e-25

DNA polymerase X family; includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases


Pssm-ID: 214688  Cd Length: 334  Bit Score: 96.28  E-value: 2.07e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 461693623     1 HQKIGLKYFEEFEKRIPRVEMEKMEVLILGELKKIDPEYIGTICGSYRRGAASSGDIDILLTHPNYTSQTE---KQPKLL 77
Cdd:smart00483 127 QQKAGLKYYEDILKKVSRAEAFAVEYIVKRAVRKILPDAIVTLTGSFRRGKETGHDVDFLITSPHPAKEKElevLDLLLL 206

                           90
                   ....*....|....*....
gi 461693623    78 HAVVDHLESVGFVTDTLSK 96
Cdd:smart00483 207 ESTFEELQLPSIRVATLDH 225
PolX COG1796
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];
2-96 4.11e-09

DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];


Pssm-ID: 441401 [Multi-domain]  Cd Length: 567  Bit Score: 51.73  E-value: 4.11e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 461693623   2 QKI--GLKYFEEFEKRIPRVEMEKMEVLILGELKKIDPEYIGTICGSYRRGAASSGDIDILLTHpnytsqteKQPKllhA 79
Cdd:COG1796  140 ENIlkGIELLRKRGGRFLLGEALPLAEEILAYLRALPGVERVEVAGSLRRRKETVGDIDILVAS--------DDPE---A 208

                         90
                 ....*....|....*..
gi 461693623  80 VVDHLESVGFVTDTLSK 96
Cdd:COG1796  209 VMDAFVKLPEVKEVLAK 225
 
Name Accession Description Interval E-value
DNA_pol_B_palm pfam14792
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three ...
 15-95 3.36e-38

DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the palm domain.


Pssm-ID: 464318  Cd Length: 110  Bit Score: 123.44  E-value: 3.36e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 461693623   15 RIPRVEMEKMEVLILGELKKIDPEYIGTICGSYRRGAASSGDIDILLTHPNYTSQTEkQPKLLHAVVDHLESVGFVTDTL 94
Cdd:pfam14792   1 RIPREEVEALEAIVRKAAKTLDPDVEVIVCGSYRRGAESSGDVDILITHPDGTSESE-LKGLLDRLVARLKKSGFLTDDL 79


                  .
gi 461693623   95 S 95
Cdd:pfam14792  80 A 80
NT_POLXc cd00141
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
 1-96 2.36e-34

Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this family.


Pssm-ID: 143386 [Multi-domain]  Cd Length: 307  Bit Score: 119.22  E-value: 2.36e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 461693623   1 HQKIGLKYFEEFEKRIPRVEMEKMEVLILGELKKIDPEYIGTICGSYRRGAASSGDIDILLTHPNYTSQtekqpKLLHAV 80
Cdd:cd00141  123 NILIGLEYYEDFQQRIPREEALAIAEIIKEALREVDPVLQVEIAGSYRRGKETVGDIDILVTHPDATSR-----GLLEKV 197

                         90
                 ....*....|....*.
gi 461693623  81 VDHLESVGFVTDTLSK 96
Cdd:cd00141  198 VDALVELGFVTEVLSK 213
POLXc smart00483
DNA polymerase X family; includes vertebrate polymerase beta and terminal ...
 1-96 2.07e-25

DNA polymerase X family; includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases


Pssm-ID: 214688  Cd Length: 334  Bit Score: 96.28  E-value: 2.07e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 461693623     1 HQKIGLKYFEEFEKRIPRVEMEKMEVLILGELKKIDPEYIGTICGSYRRGAASSGDIDILLTHPNYTSQTE---KQPKLL 77
Cdd:smart00483 127 QQKAGLKYYEDILKKVSRAEAFAVEYIVKRAVRKILPDAIVTLTGSFRRGKETGHDVDFLITSPHPAKEKElevLDLLLL 206

                           90
                   ....*....|....*....
gi 461693623    78 HAVVDHLESVGFVTDTLSK 96
Cdd:smart00483 207 ESTFEELQLPSIRVATLDH 225
PolX COG1796
DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];
2-96 4.11e-09

DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair];


Pssm-ID: 441401 [Multi-domain]  Cd Length: 567  Bit Score: 51.73  E-value: 4.11e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 461693623   2 QKI--GLKYFEEFEKRIPRVEMEKMEVLILGELKKIDPEYIGTICGSYRRGAASSGDIDILLTHpnytsqteKQPKllhA 79
Cdd:COG1796  140 ENIlkGIELLRKRGGRFLLGEALPLAEEILAYLRALPGVERVEVAGSLRRRKETVGDIDILVAS--------DDPE---A 208

                         90
                 ....*....|....*..
gi 461693623  80 VVDHLESVGFVTDTLSK 96
Cdd:COG1796  209 VMDAFVKLPEVKEVLAK 225
NT_Pol-beta-like cd05397
Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins; This ...
 22-62 1.75e-04

Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins; This superfamily includes the NT domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, and Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. The Escherichia coli CCA-adding enzyme belongs to this superfamily but is not included as this enzyme lacks the N-terminal helix conserved in the remainder of the superfamily. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate coordinate two divalent metal cations that are essential for catalysis. These divalent metal ions are involved in a two-metal ion mechanism of nucleotide addition. Two of the three catalytic carboxylates are found in Rel-Spo enzymes, with the second carboxylate of the DXD motif missing. Evidence supports a single-cation synthetase mechanism for Rel-Spo enzymes.


Pssm-ID: 143387 [Multi-domain]  Cd Length: 49  Bit Score: 36.15  E-value: 1.75e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 461693623 22 EKMEVLILGELKKIDPEYIGTICGSYRRGAA-SSGDIDILLT 62
Cdd:cd05397   1 EELLDIIKERLKKLVPGYEIVVYGSLVRGLLkKSSDIDLACV 42
 
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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