cPSORTdb Fields

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cPSORTdb general fields

The following table lists the general cPSORTdb fields which identify the protein and its source genome/organism. Default fields displayed in results pages are in bold. Numerical fields are followed by a #.

Field name Description
GI # NCBI GI number of the protein (primary identification key, unique to each protein)
RefSeq Accession ID RefSeq accession identifier of the protein
Protein name The name of the protein
Gene name The name of the gene
Alternate gene name The alternative name of the gene
Chromosome Acc ID NCBI chromosome accession identifier associated with the protein (NC_00XXXX)
Taxonomy ID # NCBI taxonomy identifier of the source organism
Organism Genus and species of the source organism
Phylum Phylum of the source organism
Class Class of the source organism
Gram stain Gram classification of the source organism
Amino acid sequence Amino acid sequence of the protein
Sequence length # Number of amino acids in the protein sequence
ePSORTdb GI Link # GI of the protein in the current ePSORTdb dataset*

*: If the protein in cPSORTdb is identical at the sequence level and the species level to a protein in ePSORTdb, a link to the ePSORTdb record will appear here.
#: numerical field

PSORTb v.2.0 & v.3.0 prediction fields

The following table lists the cPSORTdb fields which contain information regarding computationally predicted SCLs. Default fields displayed in results pages are in bold.

Field name Description
PSORTb version Version of PSORTb used to generate prediction
SCL-BLAST localization Predicted localization site (all possible SCL*)
SCL-BLAST details Protein GI of ePSORTdb dataset
Motif localization Predicted localization site (all possible SCL*)
Motif details Motif accession number from PROSITE (list Gram neg. & pos.)
OMPmotif localization (N) Predicted localization site (either outer membrane or unknown)
OMPmotif details (N) OMPmotif accession number (list)
ModHMM localization (#) Predicted localization site (either cytoplasmic membrane or unknown)
ModHMM helices count Number of predicted transmembrane alpha helices
Signal localization Predicted localization site (Non-cytoplasmic or unknown)
Signal details Presence or absence of a predicted signal peptide
Profile localization Predicted localization site (all possible SCL*)
Profile details Profile accession number from PROSITE (list Gram neg. & pos.)
SCL-BLASTe localization Predicted localization site (all possible SCL*)
SCL-BLASTe details Protein GI of ePSORTdb dataset


CytoSVM localization Predicted localization site (either cytoplasmic or unknown)
CMSVM localization Predicted localization site (either cytoplasmic membrane or unknown)
PPSVM localization (N) Predicted localization site (either periplasmic or unknown)
CWSVM localization (P) Predicted localization site (either cell wall or unknown)
OMSVM localization (N) Predicted localization site (either outer membrane or unknown)
ECSVM localization (§) Predicted localization site (either extracellular or unknown)


Cytoplasmic score (#) Probability of cytoplasmic localization returned by PSORTb
Cytoplasmic membrane score (#) Probability of cytoplasmic membrane localization returned by PSORTb
Periplasmic score (#,N) Probability of periplasmic localization returned by PSORTb
Cell wall score (#,P) Probability of cell wall localization returned by PSORTb
Outer membrane score (#,N) Probability of outer membrane localization returned by PSORTb
Extracellular score (#) Probability of extracellular localization returned by PSORTb
Predicted Localization ** Localization site returned by PSORTb
Secondary Localization *** (§) Localization site returned by PSORTb
GO Accession ID Gene Ontology (GO) accession identifier
GO Accession Definition Gene Ontology (GO) accession definition
Predicted Localization Score (#) Probability of PSORTb predicted localization

*: for Gram-negative; : cytoplasmic, cytoplasmic membrane, periplasmic, outer membrane, extracellular and for Gram-positive cytoplasmic, cytoplasmic membrane, cell wall, extracellular
**: Localization site returns by PSORTb specific to Archaea, Gram-negative, Gram-positive, Advanced: Gram-negative without outer membrane, or Advanced: Gram-postive with outer membrane.
***: Main secondary localizations: flagellar, fimbrial, host-associated, type III secretion apparatus (T3SS), spore, with others to be added later on
N: available only for Gram-negative and Advanced: Gram-positive with an outer membrane
P: available only for Gram-positive
#: numerical field
§: only available in PSORTb versin 3.0

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