Support Vector Machine GPCR Subfamily Classification Results for gi|4505515|ref|NP_000905.1|

>gi|4505515|ref|NP_000905.1| opioid receptor, mu 1 [Homo sapiens] MDSSAAPTNASNCTDALAYSSCSPAPSPGSWVNLSHLDGNLSDPCGPNRTNLGGRDSLCPPTGSPSMITA ITIMALYSIVCVVGLFGNFLVMYVIVRYTKMKTATNIYIFNLALADALATSTLPFQSVNYLMGTWPFGTI LCKIVISIDYYNMFTSIFTLCTMSVDRYIAVCHPVKALDFRTPRNAKIINVCNWILSSAIGLPVMFMATT KYRQGSIDCTLTFSHPTWYWENLVKICVFIFAFIMPVLIITVCYGLMILRLKSVRMLSGSKEKDRNLRRI TRMVLVVVAVFIVCWTPIHIYVIIKALVTIPETTFQTVSWHFCIALGYTNSCLNPVLYAFLDENFKRCFR EFCIPTSSNIEQQNSTRIRQNTRDHPSTANTVDRTNHQLENLEAETAPLP


Here is a list of Class A Rhodopsin like subfamilies with support vector machine models and the score this sequence received with respect to each model.

1.3446275 Peptide GPCRDB Peptide
  1.2377506 Opioid GPCRDB Opioid
   1.0311645 Opioid type M GPCRDB Opioid type M
  -0.5832562 Opioid type X
  -0.70533824 Opioid type D
  -1.0030781 Opioid type K
 -0.8521475Galanin
 -0.93431586Tachykinin
 -0.9376428Chemokine
 -0.9650875Angiotensin
 -0.98231125C5a anaphylatoxin
 -0.99709034Endothelin
 -1.000973Neuromedin U
 -1.0048866Fmet-leu-phe
 -1.0351874Somatostatin
 -1.0430443CCK
 -1.0586357Thrombin
 -1.0747364Urotensin II
 -1.1027112Melanocortin
 -1.1278298Interleukin-8
 -1.1283611Bombesin
 -1.145193GPR37 / endothelin B-like
 -1.1472176APJ like
 -1.1509702Chemokine receptor-like
 -1.1954819Neuropeptide Y
 -1.2031422Adrenomedullin (G10D)
 -1.2124717Bradykinin
 -1.2156773Vasopressin-like
 -1.2293574Orexin & neuropeptide FF
 -1.2468486Neurotensin
 -1.2614067Proteinase activated
-0.8971546Thyrotropin-releasing hormone & Secretagogue
-0.931972Gonadotropin-releasing hormone
-0.9360765Nucleotide-like
-0.9545168Hormone protein
-1.0002252Melatonin
-1.0072482Class A Orphan/other
-1.0687249Prostanoid
-1.0852542Cannabis
-1.0876456Viral
-1.095867Olfactory
-1.102872Platelet activating factor
-1.2537601(Rhod)opsin
-1.299741Lysosphingolipid & LPA (EDG)
-1.7097061Amine




HOW TO INTERPRET THE SCORES:

Subfamily Scoring:

The support vector machine for each subfamily is trained to score positive examples (members of the subfamily) as 1.0 and negative examples (non-members) as -1.0

If this sequence receives a negative score with respect to a subfamily, it is probably not a member of the subfamily.

If this sequence receives a positive score with respect to a subfamily, it is probably in the subfamily.

In general, the score's distance from zero gives you the confidence level of the prediction. Positive scores greater than +1.0 mean a classifier has strongly accepted your sequence. Negative scores less than -1.0 mean a classifier has strongly rejected your sequence. For a more detailed evaluation of scores and confidence levels, take a look at Classification Statistics.
SOME ADDITIONAL INFORMATION:

There were 19 Class B Secretin like and 11 Class C Metabotropic glutamate / pheromone and 2 Class D Fungal pheromone and 5 Frizzled/Smoothened family and 4 Nematode chemoreceptors and 4 Vomeronasal receptors (V1R & V3R) and 84 Class A Rhodopsin like subfamilies whose classifiers were not run, because the families or subfamilies that contain them were rejected by classifiers higher in the hierarchy. For example, if the Amine receptor classifier scores this sequence negatively, it will not be checked with respect to the subfamilies of Amine receptors (Histamine, Serotonin, Dopamine, Octopamine and Acetylcholine (muscarinic) receptors).

Not all subfamilies have models yet. This sequence may be in a subfamily that has not yet been modeled.

Please cite: R. Karchin, K. Karplus and D. Haussler "Classifying G-Protein Coupled Receptors with Support Vector Machines" Bioinformatics 2002 in press [postscript, pdf]