Annotation: NCBI__GCF_002017945.1:WP_035717838.1
Length: 510 amino acids
Source: GCF_002017945.1 in NCBI
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|---|---|---|---|---|---|---|---|---|
| acetate catabolism | deh | med | Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized) | 57% | 71% | 396.4 | Fosfomycin resistance protein AbaF; Acinetobacter baumannii fosfomycin efflux | 41% | 238.0 |
| L-proline catabolism | proP | lo | proline porter II (characterized) | 35% | 63% | 201.4 | The acetate/monochloroacetate (haloacid) permease, Deh4p (Km = 5.5 mμM for acetate; 9 mμM for monochloroacetate) | 60% | 411.4 |
| 2-oxoglutarate (alpha-ketoglutarate) catabolism | kgtP | lo | Alpha-ketoglutarate permease, MFS superfamily (characterized) | 34% | 72% | 197.2 | The acetate/monochloroacetate (haloacid) permease, Deh4p (Km = 5.5 mμM for acetate; 9 mμM for monochloroacetate) | 60% | 411.4 |
| citrate catabolism | citA | lo | citrate transporter (characterized) | 32% | 73% | 193 | The acetate/monochloroacetate (haloacid) permease, Deh4p (Km = 5.5 mμM for acetate; 9 mμM for monochloroacetate) | 60% | 411.4 |
View WP_035717838.1 at NCBI
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...
MSNKSTKGIWKVISASSMGTMIEWYDFYIFGSLAVVISTKFFPADNPTAAFLATLATFAV GFVVRPFGALFFGRLGDIIGRKYTFMVTLLLMGGATFLIGCIPSYETIGFMAPLLVLILR MLQGLALGGEYGGAATYVAEHAPVGQRGYWTSWIQTTATVGLFISLMVILATRNVLTPEE FDNWGWRVPFWVSIVMVGISYLIRKNMDESPVFAKAKSEGKTSTNPLKESFGNRYNLKFV LLALFGATMGQGVVWYTGQFYAMSFLKTVMTIDSSQVDQLLGIALILGTPFFIFFGWLSD KLGRKYIMMGGMLIAILLYRPIYQAMFETTNIKNKTELVDQTTIVAETKTNKQALDSIYT TTKVFEDGTKWVEIKTIPLENGQAKIVDGKPKADIKTTLTINNTDMWMLVFYIFVQVLFV TMVYGPIAAFLVEMFPVKIRYTSMSLPYHVGNGIFGGLLPAISTYLVTNAKEAGDVNYYL EGLWYPIIIASVCFVIGMIYLDNSKTNKHV
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