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

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
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
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
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
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

Internal database links

SCOOP:	Acetyltransf_6 FemAB_like
Similarity to PfamA using HHSearch:	FemAB_like Acetyltransf_6

External database links

SCOP:

1p4n

This tab holds annotation information from the InterPro database.

InterPro entry IPR003447

The entry represents the FemABX peptidyl transferase family.

FemABX peptidyl transferases catalyse the incorporation of amino acid(s) into the interchain peptide bridge of peptidoglycan using aminoacyl-tRNA as the amino acid donor, a reaction involved in the synthesis of the bacterial cell wall. The femABX enzymes catalyse the addition of amino acids to a peptidoglycan precursor, which in most cases is a lipid-linked sugar pentapeptide or, alternatively, a soluble nucleotide precursor for W. viridescens femX. The resulting branched peptide chain consists of one to five amino acids and is cross-linked to a pentapeptide of a neighbouring disaccharide chain by a transpeptidase in the final step of peptidoglycan synthesis. The interchain peptide and the femABX enzymes for their synthesis are found in several Gram-positive bacteria and in some Gram-negative, mainly pathogenic species. The femABX transferases differ by type, position and number of amino acids that are incoporated into the interchain. Some femABX proteins function as immunity factors that protect producers of interpeptide-specific endopeptidases against their own products. In addition, the interpeptide plays an important role in cell separation and virulence [ PUBMED:11083873 , PUBMED:12604510 , PUBMED:12679335 , PUBMED:14962386 ].

Some proteins known to belong to the femABX peptidyl transferase family:

Staphylococcal femA and femB, factors essential for expression of methicillin resistance. FemA adds glycines 2 and 3 of the pentaglycine interpeptide, while femB adds glycines 4 and 5.
Staphylococcal fmhB (for fem homologue) or femX, which incorporates the first glycine of the pentaglycine interchain peptide in peptidoglycan.
Weissella viridescens femX, which catalyses the transfer of an L-alanine from Ala-tRNA to the epsilon-amino group of L-lysine of UDP-MurNAc pentapeptide [ PUBMED:12679335 , PUBMED:14962386 ].
Streptococcus pneumoniae fibA/murM and fibB/murN, which synthesize branched structured cell wall muropeptides that are strain-specific.
Staphylococcus capitis epr (endopeptidase resistance), which renders the cells resistant to glycylglycine endopeptidase by increasing the serine content and decreasing the glycine content of the interpeptide chains.

Gene Ontology

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

Molecular function	transferase activity, transferring amino-acyl groups (GO:0016755)
Biological process	cell wall macromolecule biosynthetic process (GO:0044038)

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 45 members:

Acetyltransf_1 Acetyltransf_10 Acetyltransf_13 Acetyltransf_15 Acetyltransf_16 Acetyltransf_17 Acetyltransf_18 Acetyltransf_19 Acetyltransf_3 Acetyltransf_4 Acetyltransf_5 Acetyltransf_6 Acetyltransf_7 Acetyltransf_8 Acetyltransf_9 Acetyltransf_CG AstA ATE_C ATE_N Autoind_synth DUF1122 DUF1248 DUF1999 DUF5613 DUF5645 FemAB FemAB_like FR47 Gly_acyl_tr_C GNAT_acetyltr_2 GNAT_acetyltran GNAT_C HAT_KAT11 HlyC Leu_Phe_trans LPG_synthase_C MCD Mig-14 MOZ_SAS NAT NMT NMT_C NodA ODC_AZ PanZ

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
UniProt: alignment generated by searching the UniProtKB sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

jalview: a Java applet developed at the University of Dundee. You will need Java installed before running jalview
HTML: an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

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You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.

Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

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 (21)	Full (3014)	Representative proteomes				UniProt (17572)
	Seed (21)	Full (3014)	RP15 (399)	RP35 (1390)	RP55 (3099)	RP75 (5200)	UniProt (17572)
Jalview	View	View	View	View	View	View	View
HTML	View	View
PP/heatmap	₁	View

¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (21)	Full (3014)	Representative proteomes				UniProt (17572)
	Seed (21)	Full (3014)	RP15 (399)	RP35 (1390)	RP55 (3099)	RP75 (5200)	UniProt (17572)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	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 (21)	Full (3014)	Representative proteomes				UniProt (17572)
	Seed (21)	Full (3014)	RP15 (399)	RP35 (1390)	RP55 (3099)	RP75 (5200)	UniProt (17572)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download
Gzipped	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.

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

Seed source:

Pfam-B_1214 (release 5.2)

Previous IDs:

none

Type:

Family

Sequence Ontology:

SO:0100021

Author:

Bateman A

, Mian N

Number in seed:

21

Number in full:

3014

Average length of the domain:

198.30 aa

Average identity of full alignment:

17 %

Average coverage of the sequence by the domain:

90.01 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	20.9	20.9
Trusted cut-off	20.9	20.9
Noise cut-off	20.8	20.8

Model length:

408

Family (HMM) version:

18

Download:

download the raw HMM for this family

Species distribution

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

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family
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Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.

Anomalies in the taxonomy tree

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Missing taxonomic levels

Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.

Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

Too many species/sequences

For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.

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The tree shows the occurrence of this domain across different species. More...

Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

You can use the tree controls to manipulate how the interactive tree is displayed:

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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 16 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 sequence.

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Family: FemAB (PF02388)

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