Output files
In this section, the various final and intermediate output files of gapseq are going to be described.
gapseq find
*-Pathways.tbl
This file contains detailed information for all pathways that were considered by the gapseq find command.
It is a tab-separated text file with the following columns:
| ID | Name | Prediction | Completeness | VagueReactions | KeyReactions | KeyReactionsFound | ReactionsFound |
|---|---|---|---|---|---|---|---|
| Pathway ID | Pathway Name | Inferred presence true/false | Ratio of found/total reactions (%) | Number of reactions without available sequences | Total number of important key reactions | Number of found key reactions | Names of found reactions |
*-Reactions.tbl
This tab-separated text file contains detailed information about all checked reactions.
| rxn | name | ec | bihit | qseqid | pident | evalue | bitscore | qcovs | stitle | sstart | send | pathway | status | pathway.status | dbhit | complex | exception | complex.status |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Reaction ID | Reaction name | EC number | Bidirectional hit | Query Seq-id | Percentage of identical matches | Expect value | Bit score | Query Coverage Per Subject | Subject Title | Start of alignment | End of alignment | Associated pathway | Blast status of reaction* | Status of associated pathway** | Mapped model reactions | Detected protein complex | Higher identity cutoff used*** | Status of protein complex |
*The blast status of a reaction informs about the result of the homology search. It is defined to be:
bad_blast(blast hit with lower quality, i.e. lower bitscore, coverage, or identity than needed for cutoffs),good_blast(all cutoffs satisfying blast hit),no_blast(no blast hit found),no_seq_data(no sequence data available),spontaneous(no enzyme needed).**The status of the associated pathway provides background to the criteria by which a pathway was predicted. The following values are possible:
full(All reactions were found),keyenzyme(Found key reactions indicate pathway presence (at least 66% of the pathway reactions are present)),NA(The pathway is not predicted to be present),threshold(Pathway is present because at least 80% of its reactions are present)***For enzymes which have a high similar sequence to other enzymes with different function a higher identity cutoff is used for the blast search (this exceptions are defined in
gapseq/dat/exceptions.tbl)
gapseq find-transport
*-Transporter.tbl
Data about found transporter is listed in this tab-separated text file.
| id | tc | sub | exid | rea | qseqid | pident | evalue | bitscore | qcovs | stitle | sstart | send |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Transporter ID | TC number | Transported substance | Exchange ID | Associated model reaction | Query Seq-id | Percentage of identical matches | E value | Bit score | Query Coverage | Subject Title | Start of alignment | End of alignment |
gapseq draft
*-rxnWeights.RDS
Reaction weights table (temporary file needed for gapseq fill).
*-rxnXgenes.RDS
Table with gene-X-reaction association (temporary file needed for gapseq fill).
*-draft.RDS
Model draft file as R object.
*-draft.xml
Draft model in SBML format (only created if sybilSBML is installed).
gapseq fill
*.RDS
Final model saved as R object.
*.xml
Final model in SBML format (only created if sybilSBML is installed).