Protein WP_004119214.1 in Rhizobium freirei PRF 81
Annotation: NCBI__GCF_000359745.1:WP_004119214.1
Length: 295 amino acids
Source: GCF_000359745.1 in NCBI
Candidate for 18 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| trehalose catabolism | thuG | lo | Trehalose transport system permease protein SugB (characterized) | 37% | 97% | 174.9 | Diacetylchitobiose uptake system permease protein NgcG | 34% | 189.5 |
| N-acetyl-D-glucosamine catabolism | ngcG | lo | NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) | 34% | 95% | 174.1 | Diacetylchitobiose uptake system permease protein NgcG | 34% | 189.5 |
| D-glucosamine (chitosamine) catabolism | ngcG | lo | NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) | 34% | 95% | 174.1 | Diacetylchitobiose uptake system permease protein NgcG | 34% | 189.5 |
| D-maltose catabolism | thuG | lo | ABC transporter for D-Trehalose, permease component 2 (characterized) | 35% | 95% | 174.1 | Diacetylchitobiose uptake system permease protein NgcG | 34% | 189.5 |
| sucrose catabolism | thuG | lo | ABC transporter for D-Trehalose, permease component 2 (characterized) | 35% | 95% | 174.1 | Diacetylchitobiose uptake system permease protein NgcG | 34% | 189.5 |
| N-acetyl-D-glucosamine catabolism | SMc02871 | lo | N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized) | 35% | 94% | 167.2 | Diacetylchitobiose uptake system permease protein NgcG | 34% | 189.5 |
| D-glucosamine (chitosamine) catabolism | SMc02871 | lo | N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized) | 35% | 94% | 167.2 | Diacetylchitobiose uptake system permease protein NgcG | 34% | 189.5 |
| D-cellobiose catabolism | glcU | lo | GlcU, component of Glucose, mannose, galactose porter (characterized) | 31% | 95% | 136.3 | Diacetylchitobiose uptake system permease protein NgcG | 34% | 189.5 |
| D-galactose catabolism | glcU | lo | GlcU, component of Glucose, mannose, galactose porter (characterized) | 31% | 95% | 136.3 | Diacetylchitobiose uptake system permease protein NgcG | 34% | 189.5 |
| D-glucose catabolism | glcU | lo | GlcU, component of Glucose, mannose, galactose porter (characterized) | 31% | 95% | 136.3 | Diacetylchitobiose uptake system permease protein NgcG | 34% | 189.5 |
| lactose catabolism | glcU | lo | GlcU, component of Glucose, mannose, galactose porter (characterized) | 31% | 95% | 136.3 | Diacetylchitobiose uptake system permease protein NgcG | 34% | 189.5 |
| D-maltose catabolism | glcU | lo | GlcU, component of Glucose, mannose, galactose porter (characterized) | 31% | 95% | 136.3 | Diacetylchitobiose uptake system permease protein NgcG | 34% | 189.5 |
| D-mannose catabolism | glcU | lo | GlcU, component of Glucose, mannose, galactose porter (characterized) | 31% | 95% | 136.3 | Diacetylchitobiose uptake system permease protein NgcG | 34% | 189.5 |
| sucrose catabolism | glcU | lo | GlcU, component of Glucose, mannose, galactose porter (characterized) | 31% | 95% | 136.3 | Diacetylchitobiose uptake system permease protein NgcG | 34% | 189.5 |
| trehalose catabolism | glcU | lo | GlcU, component of Glucose, mannose, galactose porter (characterized) | 31% | 95% | 136.3 | Diacetylchitobiose uptake system permease protein NgcG | 34% | 189.5 |
| D-maltose catabolism | malG_Sm | lo | MalG, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 30% | 99% | 133.7 | Diacetylchitobiose uptake system permease protein NgcG | 34% | 189.5 |
| trehalose catabolism | malG | lo | MalG, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 30% | 99% | 133.7 | Diacetylchitobiose uptake system permease protein NgcG | 34% | 189.5 |
| glycerol catabolism | glpQ | lo | GlpQ, component of Glycerol uptake porter, GlpSTPQV (characterized) | 30% | 96% | 125.2 | Diacetylchitobiose uptake system permease protein NgcG | 34% | 189.5 |
Sequence Analysis Tools
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Find functional residues: SitesBLAST
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
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Sequence
MTAVSATSMPDDFETIAPAKHRRDPVLIGLWIALLLVAAIWLAPFVFIVFTSLKTQADVT
STGAFMPPFDPAFENYSNAWGRGNFASAFLNSAIITVIKVPLGLILSAMAAYALAKIRMR
FSKIMLLAIVFGTMIPFQVMLAPLFTLVNSLGLIDTYPGVILPYIAFGVPYQVFILHGFF
KGIPKELSEAALIDGASHFTIFRRIFLPVCLPVLAALLILDFVSTWNEFAMALVLLQDQH
MWTLPLGLMSFQGQFSNDYGQLNAAIVMTVLPATIVYLIFQRYFVSGLTSGAVKG
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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About GapMind
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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").
Otherwise, a candidate is "medium confidence" if either:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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