PANDIT+

KeywordFamilyClanGene   

Entry: 7tm_1 (PF00001)

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(e.g. CL0192) or by clan name (e.g. GPCR_A).
Display a clan
Very fast search for clan entries. The
search can be done either by clan ID
(e.g. CL0192) or by clan name (e.g. GPCR_A).

Pfam summary

Description

7 transmembrane receptor (rhodopsin family)

This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins [1].
 
Literature1. Terakita A; Genome Biol 2005;6:213.The opsins. PUBMED:15774036
 
Clan

CL0192 (GPCR_A)

The clan contains the following members: PF01534(Frizzled); PF03125(Sre); PF00001(7tm_1); PF00002(7tm_2); PF01036(Bac_rhodopsin); PF03383(DUF286); PF02117(Sra); PF02118(Srg); PF03402(V1R); PF05296(TAS2R); PF05462(Dicty_CAR); PF06681(DUF1182); PF06814(Lung_7-TM_R); PF07698(7TM-7TMR_HD);
 
InterPro entry IPR000276
 

Alignment

New Hampshire tree

The seed alignment for this family in the PANDIT database contains 64 aligned sequences:

  5HT1A_HUMAN/53-400   5HT1B_HUMAN/66-369   5HT1R_DROME/179-507   5HT2A_CRIGR/91-380   5HT5A_MOUSE/57-338   5HT6R_RAT/43-320   5HT7R_HUMAN/98-384   AA1R_BOVIN/26-288   ACM1_HUMAN/42-418   ADA1D_HUMAN/113-402   ADMR_RAT/66-316   ADRB1_HUMAN/75-377   AG22_MOUSE/61-318   AG2R_BOVIN/45-302   APJ_HUMAN/45-309   BKRB2_HUMAN/74-332   BRS3_CAVPO/64-330   C5AR_CANFA/55-302   CCKAR_HUMAN/58-370   CCR1_HUMAN/51-301   CCR7_HUMAN/75-326   CCRL1_BOVIN/58-303   CNR1_HUMAN/133-397   CNR2_HUMAN/50-299   CX3C1_RAT/49-294   CXCR1_HUMAN/56-305   CXCR4_BOVIN/56-303   CXCR5_HUMAN/68-322   DRD1_HUMAN/40-331   DRD2_BOVIN/51-427   EBI2_HUMAN/48-308   EDG1_HUMAN/62-310   FSHR_BOVIN/379-626   GPR83_MOUSE/88-345   GU27_RAT/22-271   HRH2_CANFA/35-288   MC3R_MOUSE/55-299   MRGRF_RAT/61-291   NK1R_CAVPO/49-305   NPY1R_HUMAN/57-320   NPYR_DROME/122-383   NTR1_HUMAN/80-364   O10J1_HUMAN/52-300   OLF15_MOUSE/41-290   OLF1_CHICK/41-290   OLF6_RAT/44-293   OPRD_MOUSE/66-318   OPS1_DROME/67-329   OPS3_DROME/75-338   OPSB_HUMAN/51-303   OPSD_LOLFO/51-315   More...

The full alignment for this family in the Pfam database contains 23760 aligned sequences

Species in the seed alignment

List of species covered in the seed alignment. The number in brackets denotes the number of sequences taken from each organism.

  Homo sapiens (27);   Rattus norvegicus (6);   Bos taurus (6);   Mus musculus (6);   Drosophila melanogaster (5);   Cavia porcellus (3);   Human herpesvirus 5 strain AD169 (3);   Canis lupus familiaris (3);   Gallus gallus (2);   Cricetulus longicaudatus (1);   Cricetulus griseus (1);   Loligo forbesi (1);  

The full alignment covers 4483 species.

Pre-computed estimates from Markov codon substitution models (explanation)

Following are maximum-likelihood estimates and log-likelihood scores from codon models M0, M1, M2, M7 and M8, implemented in PAML v.4.1

Model name  

Model M0

Model M1

Model M2

Model M7

Model M8

Log-likelihood score  

-40822.53-40686.391083-40686.391083-39823.267637-39822.745353

Tree Length  

1697.941697.944821697.944821697.944821697.94482

κ  

1.561.5618451.5618591.6219851.61531

ω-ratio  

ω=0.00995p0=0.911091 ~ ω0=0.011868
p1=0.088909 ~ ω1=1
p0=0.911086 ~ ω0=0.011868
p1=0.000376 ~ ω1=1
p2=0.088538 ~ ω2=1
ω~Β(1.252194,99)p0=0.999891 ~ ω~Β(1.33421,99)
p1=0.000109 ~ ω=315.903671

P-value for testing  
positive selection  

M1 vs M2: P-value=1
family classification: conserved
M7 vs M8: P-value=0.593164
family classification: conserved

Maximum-likelihood estimates and log-likelihood scores from codon models Nonsynonymous and Dual implemented in HYPHY

Model name  

Model Nonsynonymous

Model Dual

Log-likelihood score  

-53351.12965-53235.0691

Mean ω-ratio  

ω = 0.26507ω = 0.52002

Coeff. of variation  
of ω-ratio  

CVω = 1.71931CVω = 3.72562
 

Annotations

InteractionsThis family has 2 known interactions:
PF07686; PF10413;

StructuresThis family has 62 structures:
Notation: PDB_ID (PDB chain, PDB residues)
More...

Gene Ontologies
Cellular component
 integral to membrane[GO:0016021]
Biological Process
 G-protein coupled receptor protein signaling pathway[GO:0007186]

KEGG Pathways - for genes coding for sequences from full alignment
Metabolism
Carbohydrate Metabolism
Glycolysis / Gluconeogenesis [KEGG]
Fructose and mannose metabolism [KEGG]
Starch and sucrose metabolism [KEGG]
Aminosugars metabolism [KEGG]
Inositol phosphate metabolism [KEGG]
Pyruvate metabolism [KEGG]
Propanoate metabolism [KEGG]
Butanoate metabolism [KEGG]
Energy Metabolism
Oxidative phosphorylation [KEGG]
Nitrogen metabolism [KEGG]
Lipid Metabolism
Fatty acid elongation in mitochondria [KEGG]
Fatty acid metabolism [KEGG]
Glycerophospholipid metabolism [KEGG]
Nucleotide Metabolism
Purine metabolism [KEGG]
Amino Acid Metabolism
Urea cycle and metabolism of amino groups [KEGG]
Glycine, serine and threonine metabolism [KEGG]
Methionine metabolism [KEGG]
Valine, leucine and isoleucine degradation [KEGG]
Lysine degradation [KEGG]
Arginine and proline metabolism [KEGG]
Tryptophan metabolism [KEGG]
Metabolism of Other Amino Acids
beta-Alanine metabolism [KEGG]
Glutathione metabolism [KEGG]
Glycan Biosynthesis and Metabolism
N-Glycan biosynthesis [KEGG]
Peptidoglycan biosynthesis [KEGG]
Glycosylphosphatidylinositol(GPI)-anchor biosynthesis [KEGG]
Metabolism of Cofactors and Vitamins
Ubiquinone and menaquinone biosynthesis [KEGG]
Nicotinate and nicotinamide metabolism [KEGG]
Porphyrin and chlorophyll metabolism [KEGG]
Biosynthesis of Secondary Metabolites
Limonene and pinene degradation [KEGG]
Xenobiotics Biodegradation and Metabolism
Benzoate degradation via CoA ligation [KEGG]
Caprolactam degradation [KEGG]
Genetic Information Processing
Folding, Sorting and Degradation
Protein export [KEGG]
Type III secretion system [KEGG]
Type IV secretion system [KEGG]
Type II secretion system [KEGG]
Ubiquitin mediated proteolysis [KEGG]
Environmental Information Processing
Membrane Transport
ABC transporters [KEGG]
Phosphotransferase system (PTS) [KEGG]
Signal Transduction
Two-component system [KEGG]
MAPK signaling pathway [KEGG]
MAPK signaling pathway - yeast [KEGG]
Calcium signaling pathway [KEGG]
Phosphatidylinositol signaling system [KEGG]
Wnt signaling pathway [KEGG]
Signaling Molecules and Interaction
Cytokine-cytokine receptor interaction [KEGG]
Neuroactive ligand-receptor interaction [KEGG]
Cellular Processes
Cell Motility
Flagellar assembly [KEGG]
Regulation of actin cytoskeleton [KEGG]
Cell Growth and Death
p53 signaling pathway [KEGG]
Cell Communication
Gap junction [KEGG]
Endocrine System
Renin - angiotensin system [KEGG]
GnRH signaling pathway [KEGG]
Melanogenesis [KEGG]
Immune System
Complement and coagulation cascades [KEGG]
Leukocyte transendothelial migration [KEGG]
Nervous System
Long-term potentiation [KEGG]
Sensory System
Olfactory transduction [KEGG]
Taste transduction [KEGG]
Development
Axon guidance [KEGG]
Human Diseases
Cancers
Pathways in cancer [KEGG]
Colorectal cancer [KEGG]
Basal cell carcinoma [KEGG]
Immune Disorders
Autoimmune thyroid disease [KEGG]
Neurodegenerative Diseases
Alzheimer's disease [KEGG]
Parkinson's disease [KEGG]
Huntington's disease [KEGG]
Metabolic Disorders
Type II diabetes mellitus [KEGG]
Infectious Diseases
Vibrio cholerae infection [KEGG]
Epithelial cell signaling in Helicobacter pylori infection [KEGG]

DisProt- disorder annotation inferred from homologous DisProt sequences
DP00271
Intrinsically disordered region starting at position 80 with length 5
Intrinsically disordered region starting at position 183 with length 4
DP00272
Intrinsically disordered region starting at position 42 with length 16
 

Expression data (explanation)

 
Bgee expression data - for genes coding for sequences from seed alignment     Click here for overview of Bgee data

The numbers in brackets correspond to the number of genes that are associated with the selected family and are expressed in the corresponding tissue. Click on the tissue to see all the families that possibly have function in that tissue and click on the genes to see the corresponding genes.

Homo sapiens
Mus musculus
Xenopus (Silurana) tropicalis

HumanProteinpedia expression data - for human genes coding for sequences from full alignment     Click here for overview of Human Proteinpedia data

The numbers in brackets correspond to the number of human genes that are associated with the selected family and are expressed in the corresponding tissue. Click on the tissue to see all the families that possibly have function in that tissue and click on the genes to see the corresponding genes.

Healthy tissues
Disease tissues

Human disease association

 
Genetic Association Database - data for human genes coding for sequences from full alignment

The numbers in brackets correspond to the number of genes that are associated with the selected family and are associated with the corresponding disease. Click on the disease name to see all the families possibly associated with that disease and click on the genes to see the corresponding genes.

Associated diseases and disorders
More...

Links to OMIM - for human genes coding for sequences from full alignment
 
607449 (1) 607235 (1) 601834 (1) 600445 (1) 612303 (1) 604265 (1) 110700 (1) 138850 (1) 602927 (1) 602885 (1) 182132 (1) 146928 (1) 602001 (1) 604796 (1) 605062 (1) 612243 (1) 606653 (1) 182455 (1) 601723 (1) 612307 (1) 604106 (1) 608496 (1) 118495 (1) 601373 (1) 600446 (1) 109690 (1) 131243 (1) 606695 (1) 609949 (1) 601166 (1) 300241 (1) 109760 (1) 609046 (1) 162341 (1) 602697 (1) 607468 (1) 605666 (1) 602684 (1) 182452 (1) 609521 (1) 604161 (1) 300207 (1) 604153 (1) 118493 (1) 601267 (1) 608282 (1) 104250 (1) 601974 (1) 136537 (1) 606923 (1) 600895 (1) 602043 (1) 608923 (1) 609044 (1) 611677 (1) 600041 (1) 606380 (1) 606381 (1) 601469 (1) 607970 (1) 192321 (1) 612302 (1) 608379 (1) 604837 (1) 608494 (1) 605051 (1) 104210 (1) 300034 (1) 612250 (1) 601898 (1) 600730 (1) More...