Annotation: NCBI__GCF_000785105.2:WP_035166778.1
Length: 238 amino acids
Source: GCF_000785105.2 in NCBI
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|---|---|---|---|---|---|---|---|---|
| citrate catabolism | fecE | lo | iron(III) dicitrate transport ATP-binding protein FecE (characterized) | 35% | 87% | 132.5 | Manganese import ATP-binding protein ScaC; ORF1; EC 7.2.2.5 | 48% | 231.9 |
| L-proline catabolism | HSERO_RS00895 | lo | ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) | 31% | 91% | 101.7 | Manganese import ATP-binding protein ScaC; ORF1; EC 7.2.2.5 | 48% | 231.9 |
| D-alanine catabolism | AZOBR_RS08245 | lo | Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 32% | 74% | 95.5 | Manganese import ATP-binding protein ScaC; ORF1; EC 7.2.2.5 | 48% | 231.9 |
| L-proline catabolism | AZOBR_RS08245 | lo | Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 32% | 74% | 95.5 | Manganese import ATP-binding protein ScaC; ORF1; EC 7.2.2.5 | 48% | 231.9 |
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
Find the best match in UniProt
Compare to protein structures
Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
Fitness BLAST: loading...
MLIVNGVSVVYQNRKKVLSDVSFSVPTGTITGIIGPNGAGKSTLLNSILGVIPHEGGATF DGVSLPQMAKKIGYVQQKSKVDLNFPITVAETIGLGILPRLRLFQRLSKKKYRHEIESVM DRIEMTEFADRQIGQLSGGQLQRVMIGRCIIQQPELILLDEPFAGIDAHSEATIMKILRE LKAEGKTILMVHHDLNKVSEYFDNTVIIKKNLIAAGKTDDTFNSKNMSAAYGLPMLEV
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory