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0  structures 42  species 0  interactions 529  sequences 14  architectures

Family: 7TM_GPCR_Srbc (PF10316)

Summary: Serpentine type 7TM GPCR chemoreceptor Srbc

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Serpentine type 7TM GPCR chemoreceptor Srbc 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]. Srbc is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf' [2].

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


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR019420

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.

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 [ PUBMED:12679517 ]. The term clan can be used 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 rhodopsin-like GPCRs (Class A, GPCRA), secretin-like GPCRs (Class B, GPCRB), metabotropic glutamate receptor family (Class C, GPCRC), fungal mating pheromone receptors (Class D, GPCRD), cAMP receptors (Class E, GPCRE) and frizzled/smoothened (Class F, GPCRF) [ PUBMED:8170923 , PUBMED:8081729 , PUBMED:15914470 , PUBMED:18948278 , PUBMED:16753280 ]. GPCRs are major drug targets, and are consequently the subject of considerable research interest. It has been reported that the repertoire of GPCRs for endogenous ligands consists of approximately 400 receptors in humans and mice [ PUBMED:12679517 ]. Most GPCRs are identified on the basis of their DNA sequences, rather than the ligand they bind, those that are unmatched to known natural ligands are designated by as orphan GPCRs, or unclassified GPCRs [ PUBMED:23020293 ].

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.

Srbc is a solo family amongst the superfamilies of chemoreceptors.

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 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 45 members:

7TM-7TMR_HD 7tm_1 7tm_2 7tm_3 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 7TMR-DISM_7TM Bac_rhodopsin Ceramidase Dicty_CAR DUF1182 DUF3522 DUF621 Frizzled Git3 GpcrRhopsn4 GPR_Gpa2_C Heliorhodopsin HisKA_7TM HlyIII Lung_7-TM_R Ocular_alb Per1 Pombe_5TM Serpentine_r_xa SID-1_RNA_chan 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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(59)
Full
(529)
Representative proteomes UniProt
(780)
RP15
(238)
RP35
(289)
RP55
(530)
RP75
(532)
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PP/heatmap 1 View           

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

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(59)
Full
(529)
Representative proteomes UniProt
(780)
RP15
(238)
RP35
(289)
RP55
(530)
RP75
(532)
Alignment:
Format:
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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
(59)
Full
(529)
Representative proteomes UniProt
(780)
RP15
(238)
RP35
(289)
RP55
(530)
RP75
(532)
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 View help on the curation process

Seed source: Thomas JH, Robertson H
Previous IDs: Srbc;
Type: Family
Sequence Ontology: SO:0100021
Author: Thomas JH , Robertson H, Bateman A
Number in seed: 59
Number in full: 529
Average length of the domain: 206.10 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 82.16 %

HMM information View help on HMM parameters

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 21.3 21.3
Trusted cut-off 21.3 21.3
Noise cut-off 21.2 21.2
Model length: 275
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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Selections

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
F0IWT0 View 3D Structure Click here
G5ECV4 View 3D Structure Click here
G5EFL6 View 3D Structure Click here
G5EGF9 View 3D Structure Click here
O16260 View 3D Structure Click here
O16345 View 3D Structure Click here
O16411 View 3D Structure Click here
O16942 View 3D Structure Click here
O16943 View 3D Structure Click here
O17016 View 3D Structure Click here
O17957 View 3D Structure Click here
O17958 View 3D Structure Click here
O44636 View 3D Structure Click here
O44692 View 3D Structure Click here
O44694 View 3D Structure Click here
O44695 View 3D Structure Click here
O44696 View 3D Structure Click here
O44697 View 3D Structure Click here
O44700 View 3D Structure Click here
O44705 View 3D Structure Click here
O45280 View 3D Structure Click here
O45281 View 3D Structure Click here
O45557 View 3D Structure Click here
O45559 View 3D Structure Click here
O45564 View 3D Structure Click here
O45565 View 3D Structure Click here
O45567 View 3D Structure Click here
O45752 View 3D Structure Click here
O45789 View 3D Structure Click here
O61938 View 3D Structure Click here
O61941 View 3D Structure Click here
O61944 View 3D Structure Click here
O62362 View 3D Structure Click here
O62491 View 3D Structure Click here
O62492 View 3D Structure Click here
O62494 View 3D Structure Click here
O76412 View 3D Structure Click here
O76681 View 3D Structure Click here
P91075 View 3D Structure Click here
P91076 View 3D Structure Click here
P91077 View 3D Structure Click here
P91513 View 3D Structure Click here
Q19912 View 3D Structure Click here
Q1XFZ2 View 3D Structure Click here
Q23331 View 3D Structure Click here
Q23339 View 3D Structure Click here
Q23340 View 3D Structure Click here
Q564Y1 View 3D Structure Click here
Q5CZ33 View 3D Structure Click here
Q5CZ34 View 3D Structure Click here
Q5CZ36 View 3D Structure Click here
Q5DX29 View 3D Structure Click here
Q5DX30 View 3D Structure Click here
Q5DX38 View 3D Structure Click here
Q5F4U4 View 3D Structure Click here
Q5F4U8 View 3D Structure Click here
Q5F4U9 View 3D Structure Click here
Q5F4V0 View 3D Structure Click here
Q5F4V2 View 3D Structure Click here
Q5F4V3 View 3D Structure Click here
Q5F4V5 View 3D Structure Click here
Q5F4V6 View 3D Structure Click here
Q5F4V7 View 3D Structure Click here
Q5FAM6 View 3D Structure Click here
Q5FAM7 View 3D Structure Click here
Q6BER8 View 3D Structure Click here
Q965T8 View 3D Structure Click here
Q966H6 View 3D Structure Click here
Q9GYT6 View 3D Structure Click here
Q9GYT8 View 3D Structure Click here
Q9N4Q8 View 3D Structure Click here
Q9N5K7 View 3D Structure Click here
Q9U2X4 View 3D Structure Click here
Q9UAQ0 View 3D Structure Click here
Q9UAQ1 View 3D Structure Click here
Q9XTV7 View 3D Structure Click here
Q9XV28 View 3D Structure Click here
Q9XV31 View 3D Structure Click here
Q9XVF5 View 3D Structure Click here
Q9XVG1 View 3D Structure Click here
Q9XX34 View 3D Structure Click here
Q9XXK0 View 3D Structure Click here
Q9XXP2 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;