Summary: DNA polymerase III polC-type N-terminus I
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DNA polymerase III polC-type N-terminus I Provide feedback
This is the first N-terminal domain, NI domain, of the DNA polymerase III polC subunit A that is found only in Firmicutes. DNA polymerase polC-type III enzyme functions as the 'replicase' in low G + C Gram-positive bacteria [1]. Purine asymmetry is a characteristic of organisms with a heterodimeric DNA polymerase III alpha-subunit constituted by polC which probably plays a direct role in the maintenance of strand-biased gene distribution; since, among prokaryotic genomes, the distribution of genes on the leading and lagging strands of the replication fork is known to be biased [2]. It has been predicted that the N-terminus of polC folds into two globular domains, NI and NII. A predicted patch of elecrostatic potential at the surface of this domain suggests a possible involvement in nucleic acid binding [3]. This domain is associated with DNA_pol3_alpha PF07733 and DNA_pol3_a_NI PF11490.
Literature references
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Flett F, de Mello Jungmann-Campello D, Mersinias V, Koh SL, Godden R, Smith CP; , Mol Microbiol. 1999;31:949-958.: A 'gram-negative-type' DNA polymerase III is essential for replication of the linear chromosome of Streptomyces coelicolor A3(2). PUBMED:10048037 EPMC:10048037
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Hu J, Zhao X, Yu J; , Genomics. 2007;90:186-194.: Replication-associated purine asymmetry may contribute to strand-biased gene distribution. PUBMED:17532183 EPMC:17532183
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Timinskas K, Venclovas C;, FEBS J. 2011;278:3109-3118.: The N-terminal region of the bacterial DNA polymerase PolC features a pair of domains, both distantly related to domain V of the DNA polymerase III tau subunit. PUBMED:21740522 EPMC:21740522
This tab holds annotation information from the InterPro database.
InterPro entry IPR028112
This entry represent the first N-terminal domain, NI domain, of the DNA polymerase III PolC subunit A. DNA polymerase PolC-type III enzyme functions as the 'replicase' in low G + C Gram-positive bacteria [ PUBMED:10048037 ]. It has been predicted that the N terminus of PolC folds into two globular domains, NI and NII. A predicted patch of elecrostatic potential at the surface of this domain suggests a possible involvement in nucleic acid binding [ PUBMED:21740522 ]. This domain is associated with DNA polymerase III, alpha subunit ( INTERPRO ) and DNA polymerase III PolC-like, N-terminal domain II ( INTERPRO ).
Domain organisation
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Alignments
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
Seed (117) |
Full (1170) |
Representative proteomes | UniProt (5858) |
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RP15 (120) |
RP35 (649) |
RP55 (1200) |
RP75 (1983) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (117) |
Full (1170) |
Representative proteomes | UniProt (5858) |
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RP15 (120) |
RP35 (649) |
RP55 (1200) |
RP75 (1983) |
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Raw Stockholm | |||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
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Trees
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Curation and family details
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Curation
Seed source: | Pfam-B_853 (release 23.0) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Eberhardt R |
Number in seed: | 117 |
Number in full: | 1170 |
Average length of the domain: | 71.9 aa |
Average identity of full alignment: | 21 % |
Average coverage of the sequence by the domain: | 5.1 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 72 | ||||||||||||
Family (HMM) version: | 9 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.
trRosetta Structure
The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.
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