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0  structures 5  species 0  interactions 69  sequences 4  architectures

Family: 7TM_GPCR_Srb (PF02175)

Summary: Serpentine type 7TM GPCR chemoreceptor Srb

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Serpentine type 7TM GPCR chemoreceptor Srb Provide feedback

Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type [1]. Srb is part of the Sra superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf' [3].

Literature references

  1. Troemel ER, Chou JH, Dwyer ND, Colbert HA, Bargmann CI; , Cell 1995;83:207-218.: Divergent seven transmembrane receptors are candidate chemosensory receptors in C. elegans. PUBMED:7585938 EPMC:7585938

  2. Troemel ER; , Bioessays 1999;21:1011-1020.: Chemosensory signaling in C. elegans. PUBMED:10580986 EPMC:10580986

  3. Robertson HM, Thomas JH; , WormBook. 2006; [Epub ahead of print]: The putative chemoreceptor families of C. elegans. PUBMED:18050473 EPMC:18050473

  4. Chen N, Pai S, Zhao Z, Mah A, Newbury R, Johnsen RC, Altun Z, Moerman DG, Baillie DL, Stein LD; , Proc Natl Acad Sci U S A. 2005;102:146-151.: Identification of a nematode chemosensory gene family. PUBMED:15618405 EPMC:15618405


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002184

G-protein-coupled receptors, GPCRs, constitute a vast protein family that encompasses a wide range of functions (including various autocrine, paracrine and endocrine processes). They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups. We use the term clan to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence [PUBMED:8170923]. The currently known clan members include the rhodopsin-like GPCRs, the secretin-like GPCRs, the cAMP receptors, the fungal mating pheromone receptors, and the metabotropic glutamate receptor family. There is a specialised database for GPCRs (http://www.gpcr.org/7tm/).

The nematode Caenorhabditis elegans has only 14 types of chemosensory neuron, yet is able to sense and respond to several hundred different chemicals because each neuron detects several stimuli [PUBMED:10580986]. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf' [PUBMED:18050473]. Chemoreception in C. elegans is mediated by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs). More than 1300 potential chemoreceptor genes have been identified in C. elegans, which are generally prefixed sr for serpentine receptor. The receptor superfamilies include Sra (Sra, Srb, Srab, Sre), Str (Srh, Str, Sri, Srd, Srj, Srm, Srn) and Srg (Srx, Srt, Srg, Sru, Srv, Srxa), as well as the families Srw, Srz, Srbc, Srsx and Srr [PUBMED:7585938, PUBMED:18050473, PUBMED:15618405]. Many of these proteins have homologues in Caenorhabditis briggsae.

This entry represents serpentine receptor class b (Srb) from the Sra superfamily [PUBMED:15618405]. Srb receptors contain 6-8 hydrophobic, putative transmembrane, regions and can be distinguished from other 7TM GPCR receptors by their own characteristic TM signatures.

Gene Ontology

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Domain organisation

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Pfam Clan

This family is a member of clan GPCR_A (CL0192), which has the following description:

This clan contains various seven-transmembrane receptors and related proteins. A major member is Pfam:PF00001, members of which have been considered to be typical members of the rhodopsin superfamily. Many members of this clan are Caenorhabditis proteins, suggesting great expansion of the relevant families in these nematode worms.

The clan contains the following 35 members:

7TM-7TMR_HD 7tm_1 7tm_2 7tm_4 7TM_GPCR_Sra 7TM_GPCR_Srab 7TM_GPCR_Srb 7TM_GPCR_Srbc 7TM_GPCR_Srd 7TM_GPCR_Srh 7TM_GPCR_Sri 7TM_GPCR_Srj 7TM_GPCR_Srsx 7TM_GPCR_Srt 7TM_GPCR_Sru 7TM_GPCR_Srv 7TM_GPCR_Srw 7TM_GPCR_Srx 7TM_GPCR_Srz 7TM_GPCR_Str Bac_rhodopsin Dicty_CAR DUF1182 DUF621 Frizzled Git3 Git3_C GpcrRhopsn4 Lung_7-TM_R Ocular_alb Serpentine_r_xa Sre Srg TAS2R V1R

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
(3)
Full
(69)
Representative proteomes NCBI
(166)
Meta
(0)
RP15
(13)
RP35
(20)
RP55
(68)
RP75
(68)
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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
(3)
Full
(69)
Representative proteomes NCBI
(166)
Meta
(0)
RP15
(13)
RP35
(20)
RP55
(68)
RP75
(68)
Alignment:
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Sequence:
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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
(3)
Full
(69)
Representative proteomes NCBI
(166)
Meta
(0)
RP15
(13)
RP35
(20)
RP55
(68)
RP75
(68)
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.

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: IPR002184
Previous IDs: Srb;
Type: Family
Author: Mian N, Bateman A
Number in seed: 3
Number in full: 69
Average length of the domain: 199.20 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 65.84 %

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 21.7 21.7
Trusted cut-off 21.9 21.8
Noise cut-off 21.6 21.6
Model length: 236
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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