6. cPSORTdb Fields
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 |
| RefSeq Accession ID | RefSeq accession identifier of the protein |
| Protein name | The name of the protein |
| Gene name | The 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 |
*: 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 v3.0 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-positive 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
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