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0  structures 994  species 0  interactions 1793  sequences 7  architectures

Family: MobC (PF05713)

Summary: Bacterial mobilisation protein (MobC)

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Bacterial mobilisation protein (MobC) Provide feedback

This family consists of several bacterial MobC-like, mobilisation proteins. MobC proteins belong to the group of relaxases. Together with MobA and MobB they bind to a single cis-active site of a mobilising plasmid, the origin of transfer (oriT) region [1]. The absence of MobC has several different effects on oriT DNA. Site- and strand-specific nicking by MobA protein is severely reduced, accounting for the lower frequency of mobilisation. The localised DNA strand separation required for this nicking is less affected, but becomes more sensitive to the level of active DNA gyrase in the cell. In addition, strand separation is not efficiently extended through the region containing the nick site. These effects suggest a model in which MobC acts as a molecular wedge for the relaxosome-induced melting of oriT DNA. The effect of MobC on strand separation may be partially complemented by the helical distortion induced by supercoiling. However, MobC extends the melted region through the nick site, thus providing the single-stranded substrate required for cleavage by MobA [2].

Literature references

  1. Hofreuter D, Haas R; , J Bacteriol 2002;184:2755-2766.: Characterization of two cryptic Helicobacter pylori plasmids: a putative source for horizontal gene transfer and gene shuffling. PUBMED:11976306 EPMC:11976306

  2. Zhang S, Meyer R; , Mol Microbiol 1997;25:509-516.: The relaxosome protein MobC promotes conjugal plasmid mobilization by extending DNA strand separation to the nick site at the origin of transfer. PUBMED:9302013 EPMC:9302013


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008687

This family consists of several bacterial MobC-like, mobilisation proteins. MobC proteins belong to the group of relaxases. Together with MobA and MobB they bind to a single cis-active site of a mobilising plasmid, the origin of transfer (oriT) region [PUBMED:11976306]. The absence of MobC has several different effects on oriT DNA. Site- and strand-specific nicking by MobA protein is severely reduced, accounting for the lower frequency of mobilisation. The localised DNA strand separation required for this nicking is less affected, but becomes more sensitive to the level of active DNA gyrase in the cell. In addition, strand separation is not efficiently extended through the region containing the nick site. These effects suggest a model in which MobC acts as a molecular wedge for the relaxosome-induced melting of oriT DNA. The effect of MobC on strand separation may be partially complemented by the helical distortion induced by supercoiling. However, MobC extends the melted region through the nick site, thus providing the single-stranded substrate required for cleavage by MobA [PUBMED:9302013].

Domain organisation

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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...

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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
(27)
Full
(1793)
Representative proteomes NCBI
(1402)
Meta
(105)
RP15
(71)
RP35
(131)
RP55
(175)
RP75
(198)
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Format an alignment

  Seed
(27)
Full
(1793)
Representative proteomes NCBI
(1402)
Meta
(105)
RP15
(71)
RP35
(131)
RP55
(175)
RP75
(198)
Alignment:
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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
(27)
Full
(1793)
Representative proteomes NCBI
(1402)
Meta
(105)
RP15
(71)
RP35
(131)
RP55
(175)
RP75
(198)
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

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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_2832 (release 8.0)
Previous IDs: none
Type: Family
Author: Moxon SJ
Number in seed: 27
Number in full: 1793
Average length of the domain: 47.80 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 39.04 %

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 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 48
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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