Protein WP_085638931.1 in Marivita geojedonensis DPG-138
Annotation: NCBI__GCF_002115805.1:WP_085638931.1
Length: 282 amino acids
Source: GCF_002115805.1 in NCBI
Candidate for 17 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-cellobiose catabolism | gtsC | med | GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) | 34% | 98% | 170.6 | NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) | 32% | 157.1 |
| D-glucose catabolism | gtsC | med | GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) | 34% | 98% | 170.6 | NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) | 32% | 157.1 |
| lactose catabolism | gtsC | med | GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) | 34% | 98% | 170.6 | NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) | 32% | 157.1 |
| D-maltose catabolism | gtsC | med | GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) | 34% | 98% | 170.6 | NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) | 32% | 157.1 |
| sucrose catabolism | gtsC | med | GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) | 34% | 98% | 170.6 | NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) | 32% | 157.1 |
| trehalose catabolism | gtsC | med | GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) | 34% | 98% | 170.6 | NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) | 32% | 157.1 |
| D-xylose catabolism | gtsC | med | ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized) | 34% | 98% | 168.7 | ABC transporter for D-Galactose and D-Glucose, permease component 2 | 35% | 164.1 |
| D-galactose catabolism | PfGW456L13_1896 | med | ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized) | 35% | 94% | 164.1 | NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) | 32% | 157.1 |
| N-acetyl-D-glucosamine catabolism | ngcG | lo | NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) | 32% | 92% | 157.1 | GtsC (GLcG), component of Glucose porter, GtsABCD | 34% | 170.6 |
| D-glucosamine (chitosamine) catabolism | ngcG | lo | NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) | 32% | 92% | 157.1 | GtsC (GLcG), component of Glucose porter, GtsABCD | 34% | 170.6 |
| D-cellobiose catabolism | SMc04257 | lo | ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized) | 32% | 93% | 156 | GtsC (GLcG), component of Glucose porter, GtsABCD | 34% | 170.6 |
| D-mannose catabolism | TT_C0326 | lo | Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) | 32% | 94% | 155.2 | GtsC (GLcG), component of Glucose porter, GtsABCD | 34% | 170.6 |
| D-cellobiose catabolism | msdB2 | lo | Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) | 30% | 94% | 136.7 | GtsC (GLcG), component of Glucose porter, GtsABCD | 34% | 170.6 |
| N-acetyl-D-glucosamine catabolism | SMc02871 | lo | N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized) | 30% | 95% | 132.1 | GtsC (GLcG), component of Glucose porter, GtsABCD | 34% | 170.6 |
| D-glucosamine (chitosamine) catabolism | SMc02871 | lo | N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized) | 30% | 95% | 132.1 | GtsC (GLcG), component of Glucose porter, GtsABCD | 34% | 170.6 |
| sucrose catabolism | thuG | lo | Sugar ABC transporter permease (characterized, see rationale) | 30% | 94% | 127.9 | GtsC (GLcG), component of Glucose porter, GtsABCD | 34% | 170.6 |
| D-cellobiose catabolism | cebG | lo | CBP protein aka CebG, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) | 31% | 95% | 125.2 | GtsC (GLcG), component of Glucose porter, GtsABCD | 34% | 170.6 |
Sequence Analysis Tools
View WP_085638931.1 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...
Sequence
MFPRPIQQASAPAQTAYKTLLPISLILWLLPLIAVAVFSIKPASDFTQGNYWGMPGSFEL
FNNYGQVFFNSDMPRYMLNSVLITVPTVIGAVALSAMAGFALGIYKFRSNIWVFFMFVAG
NFVPFQILMVPVRDLTLDMGLYNTKTGLVLFHIAFQTGFCTLFMRNFIRALPFPLIEAAR
VEGVAEWRIFWFVVLPLMKPALAALAVLIFTFIWNDYFWAIVLTQGPDAQPVTAGITSFN
AQYRAAYHLMSAGSIVAALPPVLMFFLMQKHFIAGLTLGAVK
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Links
Downloads
Related tools
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