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0  structures 31  species 0  interactions 1128  sequences 70  architectures

Family: 7TM_GPCR_Srd (PF10317)

Summary: Serpentine type 7TM GPCR chemoreceptor Srd

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Serpentine type 7TM GPCR chemoreceptor Srd 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]. Srd is part of the larger Str superfamily 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 IPR019421

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 the chemoreceptor Srd [ PUBMED:18050473 ].

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
(55)
Full
(1128)
Representative proteomes UniProt
(2216)
RP15
(729)
RP35
(828)
RP55
(1112)
RP75
(1129)
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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
(55)
Full
(1128)
Representative proteomes UniProt
(2216)
RP15
(729)
RP35
(828)
RP55
(1112)
RP75
(1129)
Alignment:
Format:
Order:
Sequence:
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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
(55)
Full
(1128)
Representative proteomes UniProt
(2216)
RP15
(729)
RP35
(828)
RP55
(1112)
RP75
(1129)
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: Srd;
Type: Family
Sequence Ontology: SO:0100021
Author: Thomas JH , Robertson H, Bateman A
Number in seed: 55
Number in full: 1128
Average length of the domain: 193.50 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 69.44 %

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 22.8 22.8
Trusted cut-off 22.8 22.8
Noise cut-off 22.7 22.7
Model length: 292
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
A0A2C9C349 View 3D Structure Click here
G4RX35 View 3D Structure Click here
G5EF74 View 3D Structure Click here
G5EFQ7 View 3D Structure Click here
G5EG08 View 3D Structure Click here
O01466 View 3D Structure Click here
O01468 View 3D Structure Click here
O01608 View 3D Structure Click here
O01609 View 3D Structure Click here
O17240 View 3D Structure Click here
O17800 View 3D Structure Click here
O17821 View 3D Structure Click here
O17822 View 3D Structure Click here
O17823 View 3D Structure Click here
O17956 View 3D Structure Click here
O44811 View 3D Structure Click here
O45326 View 3D Structure Click here
O45838 View 3D Structure Click here
P91209 View 3D Structure Click here
P91210 View 3D Structure Click here
P91211 View 3D Structure Click here
P92001 View 3D Structure Click here
P92002 View 3D Structure Click here
P92015 View 3D Structure Click here
Q09572 View 3D Structure Click here
Q17760 View 3D Structure Click here
Q18552 View 3D Structure Click here
Q19061 View 3D Structure Click here
Q19419 View 3D Structure Click here
Q19473 View 3D Structure Click here
Q19474 View 3D Structure Click here
Q19505 View 3D Structure Click here
Q19507 View 3D Structure Click here
Q19508 View 3D Structure Click here
Q19509 View 3D Structure Click here
Q19779 View 3D Structure Click here
Q19975 View 3D Structure Click here
Q19992 View 3D Structure Click here
Q20721 View 3D Structure Click here
Q21705 View 3D Structure Click here
Q21714 View 3D Structure Click here
Q21715 View 3D Structure Click here
Q21716 View 3D Structure Click here
Q21717 View 3D Structure Click here
Q21767 View 3D Structure Click here
Q22011 View 3D Structure Click here
Q22261 View 3D Structure Click here
Q22261 View 3D Structure Click here
Q22594 View 3D Structure Click here
Q23648 View 3D Structure Click here
Q3V5K2 View 3D Structure Click here
Q86MI7 View 3D Structure Click here
Q95QP0 View 3D Structure Click here
Q95QP1 View 3D Structure Click here
Q95ZX2 View 3D Structure Click here
Q9GS01 View 3D Structure Click here
Q9GS04 View 3D Structure Click here
Q9N519 View 3D Structure Click here
Q9N539 View 3D Structure Click here
Q9N5W4 View 3D Structure Click here
Q9N5X1 View 3D Structure Click here
Q9NAH9 View 3D Structure Click here
Q9U2P4 View 3D Structure Click here
Q9U338 View 3D Structure Click here
Q9U399 View 3D Structure Click here
Q9UAX5 View 3D Structure Click here
Q9XV08 View 3D Structure Click here
Q9XVD3 View 3D Structure Click here
Q9XWA0 View 3D Structure Click here

Family Structural Model

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;