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1  structure 881  species 0  interactions 952  sequences 4  architectures

Family: PilM_2 (PF11104)

Summary: Type IV pilus assembly protein PilM;

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Type IV pilus assembly protein PilM; Provide feedback

The type IV pilus assembly protein PilM is required for competency and pilus biogenesis [1-2]. It binds to PilN and ATP [3].

Literature references

  1. Roine E, Nunn DN, Paulin L, Romantschuk M;, J Bacteriol. 1996;178:410-417.: Characterization of genes required for pilus expression in Pseudomonas syringae pathovar phaseolicola. PUBMED:8550460 EPMC:8550460

  2. Rumszauer J, Schwarzenlander C, Averhoff B;, FEBS J. 2006;273:3261-3272.: Identification, subcellular localization and functional interactions of PilMNOWQ and PilA4 involved in transformation competency and pilus biogenesis in the thermophilic bacterium Thermus thermophilus HB27. PUBMED:16857013 EPMC:16857013

  3. Karuppiah V, Derrick JP;, J Biol Chem. 2011;286:24434-24442.: Structure of the PilM-PilN inner membrane type IV pilus biogenesis complex from Thermus thermophilus. PUBMED:21596754 EPMC:21596754


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005883

The opportunistic pathogen Pseudomonas aeruginosa produces type 4 fimbriae which promote adhesion to epithelial cells and are associated with a form of surface translocation called twitching motility [PUBMED:7565110]. Four genes, pilM-P, encode the necessary proteins with predicted sizes of 37.9, 22.2, 22.8 and 19.0 kDa, respectively and appear to form an operon. This protein is required for the assembly of the type IV fimbria in P. aeruginosa and for a similar pilus-like structure in Synechocystis. It is also found in species such as Deinococcus described as having natural transformation (for which a type IV pilus-like structure is proposed) but not fimbria.

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 Actin_ATPase (CL0108), which has the following description:

The actin-like ATPase domain forms an alpha/beta canonical fold. The domain can be subdivided into 1A, 1B, 2A and 2B subdomains. Subdomains 1A and 1B share the same RNAseH-like fold (a five-stranded beta-sheet decorated by a number of alpha-helices). Domains 1A and 2A are conserved in all members of this superfamily, whereas domain 1B and 2B have a variable structure and are even missing from some homologues [1]. Within the actin-like ATPase domain the ATP-binding site is highly conserved. The phosphate part of the ATP is bound in a cleft between subdomains 1A and 2A, whereas the adenosine moiety is bound to residues from domains 2A and 2B[1].

The clan contains the following 29 members:

Acetate_kinase Actin BcrAD_BadFG CmcH_NodU DDR DUF1464 DUF1786 EutA FGGY_C FGGY_N FtsA Fumble GDA1_CD39 Glucokinase Hexokinase_1 Hexokinase_2 HSP70 Hydant_A_N Hydantoinase_A MreB_Mbl MutL Pan_kinase Peptidase_M22 PilM_2 Ppx-GppA ROK StbA T2SL UPF0075

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
(37)
Full
(952)
Representative proteomes NCBI
(846)
Meta
(348)
RP15
(121)
RP35
(226)
RP55
(283)
RP75
(318)
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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
(37)
Full
(952)
Representative proteomes NCBI
(846)
Meta
(348)
RP15
(121)
RP35
(226)
RP55
(283)
RP75
(318)
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
(37)
Full
(952)
Representative proteomes NCBI
(846)
Meta
(348)
RP15
(121)
RP35
(226)
RP55
(283)
RP75
(318)
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: PRODOM
Previous IDs: Competence_A;
Type: Family
Author: Pollington J, Finn RD, Eberhardt R
Number in seed: 37
Number in full: 952
Average length of the domain: 315.90 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 86.32 %

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 66.5 66.5
Trusted cut-off 66.5 67.0
Noise cut-off 66.4 65.9
Model length: 340
Family (HMM) version: 3
Download: download the raw HMM for this family

Species distribution

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the PilM_2 domain has been found. There are 1 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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