Protein BPHYT_RS35660 in Burkholderia phytofirmans PsJN
Annotation: FitnessBrowser__BFirm:BPHYT_RS35660
Length: 283 amino acids
Source: BFirm in FitnessBrowser
Candidate for 15 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-maltose catabolism | malG_Bb | med | ABC-type Maltose/ Maltodextrin permease (characterized, see rationale) | 31% | 100% | 176 | Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV | 32% | 158.3 |
| D-cellobiose catabolism | msdB2 | med | Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) | 31% | 97% | 161.8 | Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV | 32% | 158.3 |
| sucrose catabolism | thuG | med | Sugar ABC transporter permease (characterized, see rationale) | 33% | 96% | 161.4 | Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV | 32% | 158.3 |
| L-fucose catabolism | SM_b21105 | lo | ABC transporter for L-Fucose, permease component 2 (characterized) | 31% | 91% | 157.1 | Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV | 32% | 158.3 |
| 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) | 32% | 100% | 156.4 | Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV | 32% | 158.3 |
| 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) | 32% | 100% | 156.4 | Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV | 32% | 158.3 |
| D-glucosamine (chitosamine) catabolism | SM_b21219 | lo | ABC transporter for D-Glucosamine, permease component 1 (characterized) | 32% | 93% | 138.7 | Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV | 32% | 158.3 |
| D-cellobiose catabolism | gtsC | 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% | 93% | 137.9 | Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV | 32% | 158.3 |
| D-glucose catabolism | gtsC | 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% | 93% | 137.9 | Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV | 32% | 158.3 |
| lactose catabolism | gtsC | 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% | 93% | 137.9 | Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV | 32% | 158.3 |
| D-maltose catabolism | gtsC | 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% | 93% | 137.9 | Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV | 32% | 158.3 |
| 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% | 93% | 137.9 | Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV | 32% | 158.3 |
| sucrose catabolism | gtsC | 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% | 93% | 137.9 | Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV | 32% | 158.3 |
| trehalose catabolism | gtsC | 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% | 93% | 137.9 | Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV | 32% | 158.3 |
| D-maltose catabolism | malG | lo | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) (characterized) | 31% | 94% | 112.8 | Inner membrane ABC transporter permease protein YcjP, component of Probable glucoside uptake porter, YcjNOPV | 32% | 158.3 |
Sequence Analysis Tools
View BPHYT_RS35660 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
MSLSVKMKRSLWCWLALSPLVVVVLFPFAVMLFTALKPASEIFVYPARWLPVHWQWSNFS
DMWVAANFGVALRNSTVISLLSTALALAVSLPAAYALARFPFRGRGLYRQFLLVTQMLSP
ILLVVGLFRLAAMIPYGDGNLVDSKIGVIVSYAAFNIAFAVWMLSSYFQTVPRDLEESAW
LEGCGRTKAVFKVFLPLAVPAIVVTAIFTFINAWNEFAVVYTLIRSPENKTLTVQVTDMV
AGKYVVQWHLVMAATLCATLPVSVVFAWLQRYLVKGLALGAVK
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