Summary: 7 transmembrane receptor (rhodopsin family)
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This is the Wikipedia entry entitled "Rhodopsin-like receptors". More...
Rhodopsin-like receptors Edit Wikipedia article
Rhodopsin-like receptors | |||||||||||
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![]() Structure of rhodopsin: A G protein-coupled receptor.[1] | |||||||||||
Identifiers | |||||||||||
Symbol | 7tm_1 | ||||||||||
Pfam | PF00001 | ||||||||||
Pfam clan | GPCR_A | ||||||||||
InterPro | IPR000276 | ||||||||||
PROSITE | PDOC00211 | ||||||||||
SCOPe | 1f88 / SUPFAM | ||||||||||
OPM superfamily | 6 | ||||||||||
OPM protein | 1gzm | ||||||||||
CDD | cd00637 | ||||||||||
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Rhodopsin-like receptors are a family of proteins that comprise the largest group of G protein-coupled receptors.[2]
Contents
- 1 Scope
- 2 Function
- 3 Classes
- 3.1 Subfamily A1
- 3.2 Subfamily A2
- 3.3 Subfamily A3
- 3.4 Subfamily A4
- 3.5 Subfamily A5
- 3.6 Subfamily A6
- 3.7 Subfamily A7
- 3.8 Subfamily A8
- 3.9 Subfamily A9
- 3.10 Subfamily A10
- 3.11 Subfamily A11
- 3.12 Subfamily A12
- 3.13 Subfamily A13
- 3.14 Subfamily A14
- 3.15 Subfamily A15
- 3.16 Subfamily A16
- 3.17 Subfamily A17
- 3.18 Subfamily A18
- 3.19 Subfamily A19
- 3.20 Unclassified
- 4 References
- 5 External links
Scope
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. GPCRs are usually described as "superfamily" because 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.[2] The currently known superfamily members include the rhodopsin-like GPCRs (this family), 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.[3]
Function
The rhodopsin-like GPCRs themselves represent a widespread protein family that includes hormones, neurotransmitters, and light receptors, all of which transduce extracellular signals through interaction with guanine nucleotide-binding (G) proteins. Although their activating ligands vary widely in structure and character, the amino acid sequences of the receptors are very similar and are believed to adopt a common structural framework comprising 7 transmembrane (TM) helices.[4][5][6]
Classes
Rhodopsin-like GPCRs have been classified into the following 19 subgroups (A1-A19) based on a phylogenetic analysis.[7]
Subfamily A1
- Chemokine receptor InterPro: IPR000355
- Chemokine (C-C motif) receptor 1 (CCR1, CKR1)
- Chemokine (C-C motif) receptor 2 (CCR2, CKR2)
- Chemokine (C-C motif) receptor 3 (CCR3, CKR3)
- Chemokine (C-C motif) receptor 4 (CCR4, CKR4)
- Chemokine (C-C motif) receptor 5 (CCR5, CKR5)
- Chemokine (C-C motif) receptor 8 (CCR8, CKR8)
- Chemokine (C-C motif) receptor-like 2 (CCRL2, CKRX)
- chemokine (C motif) receptor 1 (XCR1, CXC1) InterPro: IPR005393
- chemokine (C-X3-C motif) receptor 1 (CX3CR1, C3X1) InterPro: IPR005387
- GPR137B (GPR137B, TM7SF1)
Subfamily A2
- Chemokine receptor InterPro: IPR000355
- Chemokine (C-C motif) receptor-like 1 (CCRL1 CCRL1, CCR11)
- Chemokine (C-C motif) receptor 6 (CCR6, CKR6)
- Chemokine (C-C motif) receptor 7 (CCR7, CKR7)
- Chemokine (C-C motif) receptor 9 (CCR9, CKR9)
- Chemokine (C-C motif) receptor 10 (CCR10, CKRA)
- CXC chemokine receptors InterPro: IPR001053
- Interleukin-8 InterPro: IPR000174 (IL8R)
- Adrenomedullin receptor (GPR182)
- Duffy blood group, chemokine receptor (DARC, DUFF)
- G Protein-coupled Receptor 30 (GPER, CML2, GPCR estrogen receptor)
Subfamily A3
- Angiotensin II receptor InterPro: IPR000248
- Angiotensin II receptor, type 1 (AGTR1, AG2S)
- Angiotensin II receptor, type 2 (AGTR2, AG22)
- Apelin receptor (AGTRL1, APJ) InterPro: IPR003904
- Bradykinin receptor InterPro: IPR000496
- Bradykinin receptor B1 (BDKRB1, BRB1)
- Bradykinin receptor B2 (BDKRB2, BRB2)
- GPR15 (GPR15, GPRF)
- GPR25 (GPR25)
Subfamily A4
- Opioid receptor InterPro: IPR001418
- delta Opioid receptor (OPRD1, OPRD)
- kappa Opioid receptor (OPRK1, OPRK)
- mu Opioid receptor (OPRM1, OPRM)
- Nociceptin receptor (OPRL1, OPRX)
- Somatostatin receptor InterPro: IPR000586
- Somatostatin receptor 1 (SSTR1, SSR1)
- Somatostatin receptor 2 (SSTR2, SSR2)
- Somatostatin receptor 3 (SSTR3, SSR3)
- Somatostatin receptor 4 (SSTR4, SSR4)
- Somatostatin receptor 5 (SSTR5, SSR5)
- GPCR neuropeptide receptor InterPro: IPR009150
- Neuropeptides B/W receptor 1 (NPBWR1, GPR7)
- Neuropeptides B/W receptor 2 (NPBWR2, GPR8)
- GPR1 orphan receptor (GPR1) InterPro: IPR002275
Subfamily A5
- Galanin receptor InterPro: IPR000405
- Galanin receptor 1 (GALR1, GALR)
- Galanin receptor 2 (GALR2, GALS)
- Galanin receptor 3 (GALR3, GALT)
- Cysteinyl leukotriene receptor InterPro: IPR004071
- Leukotriene B4 receptor InterPro: IPR003981
- Relaxin receptor InterPro: IPR008112
- Relaxin/insulin-like family peptide receptor 1 (RXFP1, LGR7)
- Relaxin/insulin-like family peptide receptor 2 (RXFP2, GPR106)
- Relaxin/insulin-like family peptide receptor 3 (RXFP3, SALPR)
- Relaxin/insulin-like family peptide receptor 4 (RXFP4, GPR100/GPR142)
- KiSS1-derived peptide receptor (GPR54) (KISS1R) InterPro: IPR008103
- Melanin-concentrating hormone receptor 1 (MCHR1, GPRO) InterPro: IPR008361
- Urotensin-II receptor (UTS2R, UR2R) InterPro: IPR000670
Subfamily A6
- Cholecystokinin receptor InterPro: IPR009126
- Cholecystokinin A receptor (CCKAR, CCKR)
- Cholecystokinin B receptor (CCKBR, GASR)
- Neuropeptide FF receptor InterPro: IPR005395
- Neuropeptide FF receptor 1 (NPFFR1, FF1R)
- Neuropeptide FF receptor 2 (NPFFR2, FF2R)
- Orexin receptor InterPro: IPR000204
- Hypocretin (orexin) receptor 1 (HCRTR1, OX1R)
- Hypocretin (orexin) receptor 2 (HCRTR2, OX2R)
- Vasopressin receptor InterPro: IPR001817
- Gonadotrophin releasing hormone receptor (GNRHR, GRHR) InterPro: IPR001658
- Pyroglutamylated RFamide peptide receptor (QRFPR, GPR103)
- GPR22 (GPR22, GPRM)
- GPR176 (GPR176, GPR)
Subfamily A7
- Bombesin receptor InterPro: IPR001556
- Endothelin receptor InterPro: IPR000499
- Endothelin receptor type A (EDNRA, ET1R)
- Endothelin receptor type B (EDNRB, ETBR)
- GPR37 (GPR37, ETBR-LP2) InterPro: IPR003909
- Neuromedin U receptor InterPro: IPR005390
- Neurotensin receptor InterPro: IPR003984
- Neurotensin receptor 1 (NTSR1, NTR1)
- Neurotensin receptor 2 (NTSR2, NTR2)
- Thyrotropin-releasing hormone receptor (TRHR, TRFR) InterPro: IPR009144
- Growth hormone secretagogue receptor (GHSR) InterPro: IPR003905
- GPR39 (GPR39)
- Motilin receptor (MLNR, GPR38)
Subfamily A8
- Anaphylatoxin receptors InterPro: IPR002234
- C3a receptor (C3AR1, C3AR)
- C5a receptor (C5AR1, C5AR)
- Chemokine-like receptor 1 (CMKLR1, CML1) InterPro: IPR002258
- Formyl peptide receptor InterPro: IPR000826
- Formyl peptide receptor 1 (FPR1, FMLR)
- Formyl peptide receptor-like 1 (FPRL1, FML2)
- Formyl peptide receptor-like 2 (FPRL2, FML1)
- MAS1 oncogene InterPro: IPR000820
- GPR1 (GPR1)
- GPR32 (GPR32, GPRW)
- GPR44 (GPR44)
- GPR77 (GPR77, C5L2)
Subfamily A9
- Melatonin receptor InterPro: IPR000025
- Melatonin receptor 1A (MTNR1A, ML1A)
- Melatonin receptor 1B (MTNR1B, ML1B)
- Neurokinin receptor InterPro: IPR001681
- Tachykinin receptor 1 (TACR1, NK1R)
- Tachykinin receptor 2 (TACR2, NK2R)
- Tachykinin receptor 3 (TACR3, NK3R)
- Neuropeptide Y receptor InterPro: IPR000611
- Neuropeptide Y receptor Y1 (NPY1R, NY1R)
- Neuropeptide Y receptor Y2 (NPY2R, NY2R)
- Pancreatic polypeptide receptor 1 (PPYR1, NY4R)
- Neuropeptide Y receptor Y5 (NPY5R, NY5R)
- Prolactin-releasing peptide receptor (PRLHR, GPRA) InterPro: IPR001402
- Prokineticin receptor 1 (PROKR1, GPR73)
- Prokineticin receptor 2 (PROKR2, PKR2)
- GPR19 (GPR19, GPRJ)
- GPR50 (GPR50, ML1X)
- GPR75 (GPR75)
- GPR83 (GPR83, GPR72)
Subfamily A10
- Glycoprotein hormone receptor InterPro: IPR002131
- Leucine-rich repeat-containing G protein-coupled receptor 4 (LGR4, GPR48)
- Leucine-rich repeat-containing G protein-coupled receptor 5 (LGR5, GPR49)
- Leucine-rich repeat-containing G protein-coupled receptor 6 (LGR6)
Subfamily A11
- GPR40-related receptor InterPro: IPR013312
- Free fatty acid receptor 1 (FFAR1, GPR40)
- Free fatty acid receptor 2 (FFAR2, GPR43)
- Free fatty acid receptor 3 (FFAR3, GPR41)
- GPR42 (GPR42, FFAR1L)
- P2 purinoceptor InterPro: IPR002286
- Hydroxycarboxylic acid receptor 1 (HCAR1, GPR81)
- Hydroxycarboxylic acid receptor 2, Niacin receptor 1 (HCAR2, GPR109A)
- Hydroxycarboxylic acid receptor 3, Niacin receptor 2 (HCAR3, GPR109B, HM74)
- GPR31 (GPR31, GPRV)
- GPR82 (GPR82)
- Oxoglutarate (alpha-ketoglutarate) receptor 1 (OXGR1, GPR80)
- Succinate receptor 1 (SUCNR1, GPR91)
Subfamily A12
- P2 purinoceptor InterPro: IPR002286
- Purinergic receptor P2Y12 (P2RY12)
- Purinergic receptor P2Y13 (P2RY13, GPR86) InterPro: IPR008109
- Purinergic receptor P2Y14 (P2RY14, UDP-glucose receptor, KI01) InterPro: IPR005466
- GPR34 (GPR34)
- GPR87 (GPR87)
- GPR171 (GPR171, H963)
- Platelet-activating factor receptor (PTAFR, PAFR) InterPro: IPR002282
Subfamily A13
- Cannabinoid receptor InterPro: IPR002230
- Cannabinoid receptor 1 (brain) (CNR1, CB1R)
- Cannabinoid receptor 2 (macrophage) (CNR2, CB2R)
- Lysophosphatidic acid receptor InterPro: IPR004065
- Sphingosine 1-phosphate receptor InterPro: IPR004061
- Melanocortin/ACTH receptor InterPro: IPR001671
- Melanocortin 1 receptor (MC1R, MSHR)
- Melanocortin 3 receptor (MC3R)
- Melanocortin 4 receptor (MC4R)
- Melanocortin 5 receptor (MC5R)
- ACTH receptor (MC2R), ACTR)
- GPR3 (GPR3)
- GPR6 (GPR6)
- GPR12 (GPR12, GPRC)
Subfamily A14
- Eicosanoid receptor InterPro: IPR008365
- Prostaglandin D2 receptor (PTGDR, PD2R)
- Prostaglandin E1 receptor (PTGER1, PE21)
- Prostaglandin E2 receptor (PTGER2, PE22)
- Prostaglandin E3 receptor (PTGER3, PE23)
- Prostaglandin E4 receptor (PTGER4, PE24)
- Prostaglandin F receptor (PTGFR, PF2R)
- Prostaglandin I2 (prostacyclin) receptor (PTGIR, PI2R)
- Thromboxane A2 receptor (TBXA2R, TA2R)
Subfamily A15
- Lysophosphatidic acid receptor InterPro: IPR004065
- P2 purinoceptor InterPro: IPR002286
- Purinergic receptor P2Y10 (P2RY10, P2Y10)
- Protease-activated receptor InterPro: IPR003912
- Epstein-Barr virus induced gene 2 (lymphocyte-specific G protein-coupled receptor) (GPR183)
- Proton-sensing G protein-coupled receptors
- GPR17 (GPR17, GPRH)
- GPR18 (GPR18, GPRI)
- GPR20 (GPR20, GPRK)
- GPR35 (GPR35)
- GPR55 (GPR55)
- Coagulation factor II receptor (F2R, THRR)
Subfamily A16
- Opsins InterPro: IPR001760[8]
- Rhodopsin (RHO, OPSD)
- Opsin 1 (cone pigments), short-wave-sensitive (color blindness, tritan) (OPN1SW, OPSB) (blue-sensitive opsin)
- Opsin 1 (cone pigments), medium-wave-sensitive (color blindness, deutan) (OPN1MW, OPSG) (green-sensitive opsin)
- Opsin 1 (cone pigments), long-wave-sensitive (color blindness, protan) (OPN1LW, OPSR) (red-sensitive opsin)
- Opsin 3, Panopsin (OPN3)
- Opsin 4, Melanopsin (OPN4)
- Opsin 5 (OPN5, GPR136)
- Retinal G protein coupled receptor (RGR)
- Retinal pigment epithelium-derived rhodopsin homolog (RRH, OPSX) (visual pigment-like receptor opsin) InterPro: IPR001793
Subfamily A17
- 5-Hydroxytryptamine (5-HT) receptor InterPro: IPR002231
- Adrenergic receptor InterPro: IPR002233
- Dopamine receptor InterPro: IPR000929
- Trace amine receptor InterPro: IPR009132
- Histamine H2 receptor (HRH2, HH2R) InterPro: IPR000503
Subfamily A18
- Histamine H1 receptor (HRH1, HH1R) InterPro: IPR000921
- Histamine H3 receptor (HRH3) InterPro: IPR003980
- Histamine H4 receptor (HRH4) InterPro: IPR008102
- Adenosine receptor InterPro: IPR001634
- Muscarinic acetylcholine receptor InterPro: IPR000995
- GPR21 (GPR21, GPRL)
- GPR27 (GPR27)
- GPR45 (GPR45, PSP24)
- GPR52 (GPR52)
- GPR61 (GPR61)
- GPR62 (GPR62)
- GPR63 (GPR63)
- GPR78 (GPR78)
- GPR84 (GPR84)
- GPR85 (GPR85)
- GPR88 (GPR88)
- GPR101 (GPR101)
- GPR161 (GPR161, RE2)
- GPR173 (GPR173, SREB3)
Subfamily A19
Unclassified
- Olfactory receptor InterPro: IPR000725
- Nematode chemoreceptor[9] (multiple, including InterPro: IPR000344InterPro: IPR019424)
- Taste receptor type 2[9] InterPro: IPR007960
- Vomeronasal receptor type 1 InterPro: IPR004072
References
- ^ Palczewski K, Kumasaka T, Hori T, et al. (August 2000). "Crystal structure of rhodopsin: A G protein-coupled receptor". Science. 289 (5480): 739–45. doi:10.1126/science.289.5480.739. PMID 10926528.
- ^ a b Attwood TK, Findlay JB (1994). "Fingerprinting G-protein-coupled receptors". Protein Eng. 7 (2): 195–203. doi:10.1093/protein/7.2.195. PMID 8170923.
- ^ "Information system for G protein-coupled receptors". GPCRDB. www.gpcr.org. Archived from the original on 2009-04-22. Retrieved 2008-12-05.
- ^ Birnbaumer L (1990). "G proteins in signal transduction". Annu. Rev. Pharmacol. Toxicol. 30: 675–705. doi:10.1146/annurev.pa.30.040190.003331. PMID 2111655.
- ^ Gilman AG, Casey PJ (1988). "G protein involvement in receptor-effector coupling". J. Biol. Chem. 263 (6): 2577–2580. PMID 2830256.
- ^ Attwood TK, Findlay JB (1993). "Design of a discriminating fingerprint for G-protein-coupled receptors". Protein Eng. 6 (2): 167–176. doi:10.1093/protein/6.2.167. PMID 8386361.
- ^ Joost P, Methner A (2002). "Phylogenetic analysis of 277 human G-protein-coupled receptors as a tool for the prediction of orphan receptor ligands". Genome Biol. 3 (11): research0063.1–0063.16. doi:10.1186/gb-2002-3-11-research0063. PMC 133447. PMID 12429062.
- ^ Terakita A (2005). "The opsins". Genome Biol. 6 (3): 213. doi:10.1186/gb-2005-6-3-213. PMC 1088937. PMID 15774036.
- ^ a b Nordström KJ, Sällman Almén M, Edstam MM, Fredriksson R, Schiöth HB (September 2011). "Independent HHsearch, Needleman—Wunsch-based, and motif analyses reveal the overall hierarchy for most of the G protein-coupled receptor families". Molecular Biology and Evolution. 28 (9): 2471–80. doi:10.1093/molbev/msr061. PMID 21402729.
External links
- Vriend G, Horn F, Oliveira L, Bywater RP, Cohen FE. "GPCRDB (G Protein-Coupled Receptor Data Base): sequence-derived data". Archived from the original on 2007-11-14. Retrieved 2007-12-10.
- Horn F, Bettler E, Oliveira L, Campagne F, Cohen FE, Vriend G (2003). "GPCRDB information system for G protein-coupled receptors". Nucleic Acids Res. 31 (1): 294–7. doi:10.1093/nar/gkg103. PMC 165550. PMID 12520006. This database includes multiple sequence alignments of all GPCR families and sub-families.
This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.
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.
7 transmembrane receptor (rhodopsin family) Provide feedback
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].
Literature references
-
Terakita A; , Genome Biol 2005;6:213.: The opsins. PUBMED:15774036 EPMC:15774036
Internal database links
External database links
PRINTS: | PR00237 PR00652 PR00425 PR00527 PR00857 PR00245 |
PROSITE: | PDOC00210 PDOC00211 |
SCOP: | 1f88 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR000276
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].
The rhodopsin-like GPCRs (GPCRA) represent a widespread protein family that includes hormone, neurotransmitter and light receptors, all of which transduce extracellular signals through interaction with guanine nucleotide-binding (G) proteins. Although their activating ligands vary widely in structure and character, the amino acid sequences of the receptors are very similar and are believed to adopt a common structural framework comprising 7 transmembrane (TM) helices [PUBMED:2111655, PUBMED:2830256, PUBMED:8386361].
This entry represents the G protein-coupled receptor, rhodopsin-like family.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | integral component of membrane (GO:0016021) |
Molecular function | G protein-coupled receptor activity (GO:0004930) |
Biological process | G protein-coupled receptor signaling pathway (GO:0007186) |
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 V1RAlignments
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, the UniProtKB sequence database, 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 (64) |
Full (84481) |
Representative proteomes | UniProt (164979) |
NCBI (393720) |
Meta (9) |
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RP15 (16511) |
RP35 (30525) |
RP55 (60383) |
RP75 (86847) |
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HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (64) |
Full (84481) |
Representative proteomes | UniProt (164979) |
NCBI (393720) |
Meta (9) |
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RP15 (16511) |
RP35 (30525) |
RP55 (60383) |
RP75 (86847) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Prosite |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Sonnhammer ELL |
Number in seed: | 64 |
Number in full: | 84481 |
Average length of the domain: | 255.60 aa |
Average identity of full alignment: | 19 % |
Average coverage of the sequence by the domain: | 66.73 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 263 | ||||||||||||
Family (HMM) version: | 22 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There are 12 interactions for this family. More...
Cytochrom_B562 SRP_SPB 7tm_1 Rhodopsin_N WD40 Phage_lysozyme CXCR4_N Phage_lysozyme SRP_SPB SRP19 Rhodopsin_N G-alphaStructures
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the 7tm_1 domain has been found. There are 465 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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