Each row of the table corresponds to a single hit to an annotation source for a given protein.
If a protein has multiple domains or multiple weak hits (or redundant strong hits) for a given
domain that protein will have multiple rows in the table. Each column is described below, columns
are occupied only when applicable.
| Column Name |
Definition |
| Biosequence Set Name |
name of organism or sequence set |
| Biosequence Name |
gene/sequence name |
| Accession |
gene/sequence accession |
| Gene Symbol |
|
| Full gene name |
|
| Protein EC number |
EC number corresponding to |
| TMR Class |
Results of TMHMM. 0 == soluble protein, TM == transmembrane protein |
| Number of TMRs |
number of TM regions |
| pI |
isoelectric point |
| Match Source |
program used to derive/detect match. Pfam indicates that HMMER was used to find the match to Pfam. pdbblast indicates that PSI-BLAST was used to detect a match to a given PDB sequence. mamSum indicates that the match is the result of a Rosetta prediction. |
| Domain Index |
If protein is a multi-domain protein, as detected by ginzu, domains are labeled as domain 0-domainN. |
| Overall-P |
Probability that one of the top five rosetta predictions is the correct fold |
| BH |
Best Hit, Y if this is the Rosetta model for this protein with the highest Z-score to match to the PDB. |
| Cluster |
Rosetta model number. Cluster00 is the center of the largest cluster and thus the top Rosetta model prior to considering the Z-score of each models best match to the PDB. |
| Query start (stop) |
Start and stop of hit with reference to the query protein(domain) |
| Query length |
length of protein in case of single protein, length of domain if query is a single domain from Ginzu. |
| Match start(end) |
start and stop of match with reference to domain matched in external database (eg. PDB, Pfam, etc.) |
| Match length |
|
| Match Type |
possible types are pdbblast, pfam and PDB |
| Match name |
ID in external database (PDB id, Pfam domain) |
| Domain EC numbers |
EC number if hit/match has a corresponding EC number. |
| Prob |
Probability of individual Rosetta prediction being correct. |
| E value |
confidence of corresponding method |
| Score |
confidence of corresponding method |
| Z-score |
strength of match between Rosetta predicted structure and the PDB, expressed as a Z-score. |
| Second Reference |
CATH id of matched PDB. |
| Match Annotation |
Additional annotation information associated with this match in the match source |