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0  structures 2849  species 0  interactions 6186  sequences 36  architectures

Family: Bac_surface_Ag (PF01103)

Summary: Surface antigen

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Surface antigen Provide feedback

This entry includes the following surface antigens; D15 antigen from H.influenzae, OMA87 from P.multocida, OMP85 from N.meningitidis and N.gonorrhoeae. The family also includes a number of eukaryotic proteins that are members of the UPF0140 family. There also appears to be a relationship to PF03865 (personal obs: C Yeats). In eukaryotes, it appears that these proteins are not surface antigens; S. cerevisiae YNL026W (SAM50, P53969) is an essential component of the Sorting and Assembly Machinery (SAM) of the mitochondrial outer membrane. The protein was localised to the mitochondria [3].

Literature references

  1. Flack FS, Loosmore S, Chong P, Thomas WR; , Gene 1995;156:97-99.: The sequencing of the 80-kDa D15 protective surface antigen of Haemophilus influenzae. PUBMED:7737523 EPMC:7737523

  2. Ruffolo CG, Adler B; , Infect Immun 1996;64:3161-3167.: Cloning, sequencing, expression, and protective capacity of the oma87 gene encoding the Pasteurella multocida 87-kilodalton outer membrane antigen. PUBMED:8757848 EPMC:8757848

  3. Kozjak V, Wiedemann N, Milenkovic D, Lohaus C, Meyer HE, Guiard B, Meisinger C, Pfanner N; , J Biol Chem 2003;278:48520-48523.: An essential role of Sam50 in the protein sorting and assembly machinery of the mitochondrial outer membrane. PUBMED:14570913 EPMC:14570913


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000184

The protein sequences of d15 from various strains of Haemophilus influenzae are highly conserved, with only a small variable region identified near the carboxyl terminus of the protein [PUBMED:7737523]. D15 is a highly conserved antigen that is protective in animal models and it may be a useful component of a universal subunit vaccine against Haemophilus infection and disease [PUBMED:9284140]. Membrane proteins from other bacteria have been shown to elicit protective immunity. Oma87 is a protective outer membrane antigen of Pasteurella multocida [PUBMED:8757848].

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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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
(70)
Full
(6186)
Representative proteomes NCBI
(5261)
Meta
(3202)
RP15
(578)
RP35
(1140)
RP55
(1548)
RP75
(1843)
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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
(70)
Full
(6186)
Representative proteomes NCBI
(5261)
Meta
(3202)
RP15
(578)
RP35
(1140)
RP55
(1548)
RP75
(1843)
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
(70)
Full
(6186)
Representative proteomes NCBI
(5261)
Meta
(3202)
RP15
(578)
RP35
(1140)
RP55
(1548)
RP75
(1843)
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_1201 (release 3.0)
Previous IDs: Bac_suface_Ag;
Type: Family
Author: Finn RD, Bateman A
Number in seed: 70
Number in full: 6186
Average length of the domain: 320.30 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 47.88 %

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 20.5 20.5
Trusted cut-off 20.5 20.5
Noise cut-off 20.4 20.4
Model length: 323
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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