Support Vector Machine GPCR Subfamily Classification Results for gi|16179332|ref|XP_051505.2|

>gi|16179332|ref|XP_051505.2| opioid receptor, kappa 1 [Homo sapiens] MDSPIQIFRGEPGPTCAPSACLPPNSSAWFPGWAEPDSNGSAGSEDAQLEPAHISPAIPVIITAVYSVVF VVGLVGNSLVMFVIIRYTKMKTATNIYIFNLALVYALVTTTMPFQSTVYLMNSWPFGDVLCKIVISIDYY NMFTSIFTLTMMSVDRYIAVCHPVKALDFRTPLKAKIINICIWLLSSSVGISAIVLGGTKVREDVDVIEC SLQFPDDDYSWWDLFMKICVFIFAFVIPVLIIIVCYTLMILRLKSVRLLSGSREKDRNLRRITRLVLVVV AVFVVCWTPIHIFILVEALGSTSHSTAALSSYYFCIALGYTNSSLNPILYAFLDENFKRCFRDFCFPLKM RMERQSTSRVRNTVQDPAYLRDIDGMNKPV


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.

1.0246717 Peptide GPCRDB Peptide
  0.9660245 Opioid GPCRDB Opioid
   0.9587259 Opioid type K GPCRDB Opioid type K
  -0.60618526 Opioid type X
  -0.7962416 Opioid type M
  -1.0573119 Opioid type D
 -0.5325415Chemokine
 -0.88766855Galanin
 -0.93468213Tachykinin
 -0.9528468Angiotensin
 -1.0207865Endothelin
 -1.0268909Neuromedin U
 -1.052253Thrombin
 -1.0706737C5a anaphylatoxin
 -1.0780597Somatostatin
 -1.0818862Fmet-leu-phe
 -1.0931294CCK
 -1.0961038Urotensin II
 -1.119261Bombesin
 -1.1348237Melanocortin
 -1.1432248APJ like
 -1.1612097GPR37 / endothelin B-like
 -1.1690226Chemokine receptor-like
 -1.1695236Interleukin-8
 -1.1851552Adrenomedullin (G10D)
 -1.2023363Orexin & neuropeptide FF
 -1.2170492Neurotensin
 -1.2413824Bradykinin
 -1.2434995Proteinase activated
 -1.2549651Vasopressin-like
 -1.3088734Neuropeptide Y
-0.27502745Class A Orphan/other
-0.2818352Amine
-0.29808524Nucleotide-like
-0.94059354Thyrotropin-releasing hormone & Secretagogue
-0.9714322Gonadotropin-releasing hormone
-1.0723647Melatonin
-1.0737618Prostanoid
-1.07718Hormone protein
-1.0875425Cannabis
-1.0890067Viral
-1.1118345Platelet activating factor
-1.123518Olfactory
-1.1309427(Rhod)opsin
-1.3177954Lysosphingolipid & LPA (EDG)




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]