Protein 3607127 in Dinoroseobacter shibae DFL-12
Annotation: FitnessBrowser__Dino:3607127
Length: 272 amino acids
Source: Dino in FitnessBrowser
Candidate for 22 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| xylitol catabolism | Dshi_0549 | hi | ABC transporter for Xylitol, permease component 2 (characterized) | 100% | 100% | 530 | ABC transporter for D-mannitol and D-mannose, permease component 2 | 41% | 213.4 |
| D-mannitol catabolism | mtlG | med | ABC transporter for D-mannitol and D-mannose, permease component 2 (characterized) | 41% | 99% | 213.4 | ABC transporter for Xylitol, permease component 2 | 100% | 530.0 |
| D-sorbitol (glucitol) catabolism | mtlG | med | MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 42% | 93% | 210.7 | ABC transporter for Xylitol, permease component 2 | 100% | 530.0 |
| D-maltose catabolism | thuG | lo | Maltose transport system permease protein malG aka TT_C1629, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 38% | 94% | 190.7 | ABC transporter for Xylitol, permease component 2 | 100% | 530.0 |
| sucrose catabolism | thuG | lo | Maltose transport system permease protein malG aka TT_C1629, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 38% | 94% | 190.7 | ABC transporter for Xylitol, permease component 2 | 100% | 530.0 |
| trehalose catabolism | thuG | lo | Maltose transport system permease protein malG aka TT_C1629, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 38% | 94% | 190.7 | ABC transporter for Xylitol, permease component 2 | 100% | 530.0 |
| L-fucose catabolism | SM_b21105 | lo | ABC transporter for L-Fucose, permease component 2 (characterized) | 35% | 94% | 177.6 | ABC transporter for Xylitol, permease component 2 | 100% | 530.0 |
| xylitol catabolism | HSERO_RS17010 | lo | ABC-type sugar transport system, permease component protein (characterized, see rationale) | 36% | 92% | 174.5 | ABC transporter for Xylitol, permease component 2 | 100% | 530.0 |
| glycerol catabolism | glpQ | lo | GlpQ, component of Glycerol uptake porter, GlpSTPQV (characterized) | 33% | 94% | 170.2 | ABC transporter for Xylitol, permease component 2 | 100% | 530.0 |
| D-cellobiose catabolism | msdB2 | lo | Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) | 31% | 92% | 142.9 | ABC transporter for Xylitol, permease component 2 | 100% | 530.0 |
| N-acetyl-D-glucosamine catabolism | SMc02871 | lo | ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 (characterized) | 31% | 100% | 133.7 | ABC transporter for Xylitol, permease component 2 | 100% | 530.0 |
| D-glucosamine (chitosamine) catabolism | SMc02871 | lo | ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 (characterized) | 31% | 100% | 133.7 | ABC transporter for Xylitol, permease component 2 | 100% | 530.0 |
| D-cellobiose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 31% | 62% | 115.5 | ABC transporter for Xylitol, permease component 2 | 100% | 530.0 |
| D-glucose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 31% | 62% | 115.5 | ABC transporter for Xylitol, permease component 2 | 100% | 530.0 |
| lactose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 31% | 62% | 115.5 | ABC transporter for Xylitol, permease component 2 | 100% | 530.0 |
| D-maltose catabolism | aglG | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 31% | 62% | 115.5 | ABC transporter for Xylitol, permease component 2 | 100% | 530.0 |
| D-maltose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 31% | 62% | 115.5 | ABC transporter for Xylitol, permease component 2 | 100% | 530.0 |
| sucrose catabolism | aglG | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 31% | 62% | 115.5 | ABC transporter for Xylitol, permease component 2 | 100% | 530.0 |
| sucrose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 31% | 62% | 115.5 | ABC transporter for Xylitol, permease component 2 | 100% | 530.0 |
| trehalose catabolism | aglG | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 31% | 62% | 115.5 | ABC transporter for Xylitol, permease component 2 | 100% | 530.0 |
| trehalose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 31% | 62% | 115.5 | ABC transporter for Xylitol, permease component 2 | 100% | 530.0 |
| putrescine catabolism | potC | lo | spermidine/putrescine ABC transporter, permease protein PotC (characterized) | 32% | 82% | 98.2 | ABC transporter for Xylitol, permease component 2 | 100% | 530.0 |
Sequence Analysis Tools
View 3607127 at FitnessBrowser
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
MTSTRSLFSQIALLVLIITVCVFPFYWMVTTSLKTQIVALEAPPVWIFEPTLSNYREALF
EDGVLRTLINSLIIAISTTFLALVLGVPAAFALARFEFRGKKDLWFWFITNRMISPIVLA
LPFFLIARNLGLLDKHITLILIYLTFNLPIVIWIVTDQFRGIPYDLDEAARLEGASQFTI
MRKICLPLAMPGVAVSAIFSFIFSWNELMFGLILTRSEAKTAPAMAVSFMEGYNLPYGKI
MATSTLIVIPVLIFALIASKQLVRGLTMGAVK
This GapMind analysis is from Sep 17 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