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0  structures 1157  species 0  interactions 1162  sequences 24  architectures

Family: DNA_pol3_a_NII (PF11490)

Summary: DNA polymerase III polC-type N-terminus II

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DNA polymerase III polC-type N-terminus II Provide feedback

This is the second N-terminal domain, NII 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 hydrophobic surface patch suggests this domain may be involved in protein binding [3]. This domain is associated with DNA_pol3_alpha PF07733 and DNA_pol3_a_NI PF14480.

Literature references

  1. 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

  2. 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

  3. 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


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR024754

This domain is found in the N-terminal region of 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]. The domain is also found in chromosomal replication initiator protein DnaA.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan DnaA_N (CL0494), which has the following description:

This superfamily includes the N-terminal domain from DnaA and the N-terminal domain from DNA polymerase III alpha subunit.

The clan contains the following 2 members:

DNA_pol3_a_NII DnaA_N

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

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
(63)
Full
(1162)
Representative proteomes NCBI
(793)
Meta
(71)
RP15
(44)
RP35
(85)
RP55
(113)
RP75
(139)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(63)
Full
(1162)
Representative proteomes NCBI
(793)
Meta
(71)
RP15
(44)
RP35
(85)
RP55
(113)
RP75
(139)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(63)
Full
(1162)
Representative proteomes NCBI
(793)
Meta
(71)
RP15
(44)
RP35
(85)
RP55
(113)
RP75
(139)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_853 (release 23.0)
Previous IDs: DNA_pol3_alph_N;
Type: Domain
Author: Finn R, Coggill P
Number in seed: 63
Number in full: 1162
Average length of the domain: 115.20 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 8.07 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.1 22.1
Trusted cut-off 22.1 22.1
Noise cut-off 21.9 22.0
Model length: 117
Family (HMM) version: 3
Download: download the raw HMM for this family

Species distribution

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