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Conserved domains on  [gi|1084058677|gb|OGK63631|]
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hypothetical protein A3K27_02445 [Candidatus Roizmanbacteria bacterium RIFOXYA1_FULL_37_12]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HolA super family cl34275
DNA polymerase III, delta subunit [Replication, recombination and repair];
99-210 4.24e-06

DNA polymerase III, delta subunit [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG1466:

Pssm-ID: 441075 [Multi-domain]  Cd Length: 305  Bit Score: 46.40  E-value: 4.24e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084058677  99 GRDIKLKDIAQIKEFKPHDSIFKLLESCYPGNRNVFVQLLQTICDS-HDATFIFIMIYRHIRSLI---LAYERIFSPRQ- 173
Cdd:COG1466   179 GGTITLEDVEALVGDSAEFNVFDLADALLAGDAARALRILRRLLAEgEEPVLILAALARQFRLLLqvkALLAQGKSLAEi 258

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1084058677 174 ------QSWQQHKLHSQAARWSQNILVKFYEGLYRIESSTKSG 210
Cdd:COG1466   259 akelgvPPFRVKLALRALRRWSLERLARALQLLAEADLALKGG 301
 
Name Accession Description Interval E-value
HolA COG1466
DNA polymerase III, delta subunit [Replication, recombination and repair];
99-210 4.24e-06

DNA polymerase III, delta subunit [Replication, recombination and repair];


Pssm-ID: 441075 [Multi-domain]  Cd Length: 305  Bit Score: 46.40  E-value: 4.24e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084058677  99 GRDIKLKDIAQIKEFKPHDSIFKLLESCYPGNRNVFVQLLQTICDS-HDATFIFIMIYRHIRSLI---LAYERIFSPRQ- 173
Cdd:COG1466   179 GGTITLEDVEALVGDSAEFNVFDLADALLAGDAARALRILRRLLAEgEEPVLILAALARQFRLLLqvkALLAQGKSLAEi 258

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1084058677 174 ------QSWQQHKLHSQAARWSQNILVKFYEGLYRIESSTKSG 210
Cdd:COG1466   259 akelgvPPFRVKLALRALRRWSLERLARALQLLAEADLALKGG 301
holA TIGR01128
DNA polymerase III, delta subunit; DNA polymerase III delta (holA) and delta prime (holB) ...
 99-223 8.09e-04

DNA polymerase III, delta subunit; DNA polymerase III delta (holA) and delta prime (holB) subunits are distinct proteins encoded by separate genes. The delta prime subunit (holB) exhibits sequence homology to the tau and gamma subunits (dnaX), but the delta subunit (holA) does not demonstrate this same homology with dnaX. The delta, delta prime, gamma, chi and psi subunits form the gamma complex subassembly of DNA polymerase III holoenzyme, which couples ATP to assemble the ring-shaped beta subunit around DNA forming a DNA sliding clamp. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273455 [Multi-domain]  Cd Length: 302  Bit Score: 39.55  E-value: 8.09e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084058677  99 GRDIKLKDIAQIKEFKPHDSIFKLLESCYPGNRNVFVQLLQTICDS-HDATFIFIMIYRHIRSLILAYE--RIFSPRQQS 175
Cdd:TIGR01128 163 DGKITLEDVEEAVSDSARFNVFDLTDALLEGKAARALRILKGLLGEgEEPLILLALLQRQLRLLLQLKRlaQQGGPLAQL 242

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1084058677 176 WQQHKLH--------SQAARWSQNILVKFYEGLYRIESSTKsGNNPYGVKKSLEIL 223
Cdd:TIGR01128 243 ASKLGIWpyrrklalKALRRLSLAKLEQALQELAEADLQLK-GTGGGDPWLALERL 297
 
Name Accession Description Interval E-value
HolA COG1466
DNA polymerase III, delta subunit [Replication, recombination and repair];
99-210 4.24e-06

DNA polymerase III, delta subunit [Replication, recombination and repair];


Pssm-ID: 441075 [Multi-domain]  Cd Length: 305  Bit Score: 46.40  E-value: 4.24e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084058677  99 GRDIKLKDIAQIKEFKPHDSIFKLLESCYPGNRNVFVQLLQTICDS-HDATFIFIMIYRHIRSLI---LAYERIFSPRQ- 173
Cdd:COG1466   179 GGTITLEDVEALVGDSAEFNVFDLADALLAGDAARALRILRRLLAEgEEPVLILAALARQFRLLLqvkALLAQGKSLAEi 258

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1084058677 174 ------QSWQQHKLHSQAARWSQNILVKFYEGLYRIESSTKSG 210
Cdd:COG1466   259 akelgvPPFRVKLALRALRRWSLERLARALQLLAEADLALKGG 301
holA TIGR01128
DNA polymerase III, delta subunit; DNA polymerase III delta (holA) and delta prime (holB) ...
 99-223 8.09e-04

DNA polymerase III, delta subunit; DNA polymerase III delta (holA) and delta prime (holB) subunits are distinct proteins encoded by separate genes. The delta prime subunit (holB) exhibits sequence homology to the tau and gamma subunits (dnaX), but the delta subunit (holA) does not demonstrate this same homology with dnaX. The delta, delta prime, gamma, chi and psi subunits form the gamma complex subassembly of DNA polymerase III holoenzyme, which couples ATP to assemble the ring-shaped beta subunit around DNA forming a DNA sliding clamp. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273455 [Multi-domain]  Cd Length: 302  Bit Score: 39.55  E-value: 8.09e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084058677  99 GRDIKLKDIAQIKEFKPHDSIFKLLESCYPGNRNVFVQLLQTICDS-HDATFIFIMIYRHIRSLILAYE--RIFSPRQQS 175
Cdd:TIGR01128 163 DGKITLEDVEEAVSDSARFNVFDLTDALLEGKAARALRILKGLLGEgEEPLILLALLQRQLRLLLQLKRlaQQGGPLAQL 242

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1084058677 176 WQQHKLH--------SQAARWSQNILVKFYEGLYRIESSTKsGNNPYGVKKSLEIL 223
Cdd:TIGR01128 243 ASKLGIWpyrrklalKALRRLSLAKLEQALQELAEADLQLK-GTGGGDPWLALERL 297
 
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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