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13  structures 1044  species 0  interactions 2929  sequences 8  architectures

Family: FemAB (PF02388)

Summary: FemAB family

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FemAB family Provide feedback

The femAB operon codes for two nearly identical approximately 50-kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan [1]. These proteins are also considered as a factor influencing the level of methicillin resistance [2].

Literature references

  1. Ehlert K, Schroder W, Labischinski H; , J Bacteriol 1997;179:7573-7576.: Specificities of FemA and FemB for different glycine residues: FemB cannot substitute for FemA in staphylococcal peptidoglycan pentaglycine side chain formation. PUBMED:9393725 EPMC:9393725

  2. Vannuffel P, Heusterspreute M, Bouyer M, Vandercam B, Philippe M, Gala JL; , Res Microbiol 1999;150:129-141.: Molecular characterization of femA from Staphylococcus hominis and Staphylococcus saprophyticus, and femA-based discrimination of staphylococcal species. PUBMED:10209768 EPMC:10209768

  3. Berger-Bachi B, Barberis-Maino L, Strassle A, Kayser FH; , Mol Gen Genet 1989;219:263-269.: FemA, a host-mediated factor essential for methicillin resistance in Staphylococcus aureus: molecular cloning and characterization. PUBMED:2559314 EPMC:2559314

  4. Stranden AM, Ehlert K, Labischinski H, Berger-Bachi B; , J Bacteriol 1997;179:9-16.: Cell wall monoglycine cross-bridges and methicillin hypersusceptibility in a femAB null mutant of methicillin-resistant Staphylococcus aureus. PUBMED:8981974 EPMC:8981974

  5. Henze U, Sidow T, Wecke J, Labischinski H, Berger-Bachi B; , J Bacteriol 1993;175:1612-1620.: Influence of femB on methicillin resistance and peptidoglycan metabolism in Staphylococcus aureus. PUBMED:8383661 EPMC:8383661


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003447

The femAB operon codes for two nearly identical approximately 50kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan [PUBMED:9393725]. These proteins are also considered as a factor influencing the level of methicillin resistance [PUBMED:10209768].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 Acetyltrans (CL0257), which has the following description:

This clan contains families related to N-acetyltransferases. N-acetyltransferases catalyse the transfer of acetyl groups from acetyl-CoA to arylamines.

The clan contains the following 31 members:

Acetyltransf_1 Acetyltransf_10 Acetyltransf_13 Acetyltransf_3 Acetyltransf_4 Acetyltransf_5 Acetyltransf_6 Acetyltransf_7 Acetyltransf_8 Acetyltransf_9 Acetyltransf_CG ATE_C ATE_N Autoind_synth DUF1248 DUF1999 DUF2156 DUF3749 DUF482 DUF619 FemAB FR47 Gly_acyl_tr_C GNAT_acetyltr_2 GNAT_acetyltran Leu_Phe_trans Mec-17 Mig-14 MOZ_SAS NMT NodA

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
(46)
Full
(2929)
Representative proteomes NCBI
(2189)
Meta
(375)
RP15
(151)
RP35
(260)
RP55
(364)
RP75
(402)
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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
(46)
Full
(2929)
Representative proteomes NCBI
(2189)
Meta
(375)
RP15
(151)
RP35
(260)
RP55
(364)
RP75
(402)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(46)
Full
(2929)
Representative proteomes NCBI
(2189)
Meta
(375)
RP15
(151)
RP35
(260)
RP55
(364)
RP75
(402)
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_1214 (release 5.2)
Previous IDs: none
Type: Family
Author: Bateman A, Mian N
Number in seed: 46
Number in full: 2929
Average length of the domain: 322.00 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 95.28 %

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 20.6 20.6
Trusted cut-off 20.6 20.6
Noise cut-off 20.5 20.5
Model length: 406
Family (HMM) version: 11
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 FemAB domain has been found. There are 13 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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