Protein BWI76_RS01820 in Klebsiella michiganensis M5al
Annotation: FitnessBrowser__Koxy:BWI76_RS01820
Length: 296 amino acids
Source: Koxy in FitnessBrowser
Candidate for 18 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 | hi | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 100% | 100% | 584.7 | ABC-type maltose transporter (subunit 1/2) (EC 7.5.2.1) | 44% | 198.7 |
| D-maltose catabolism | thuG | lo | Putative maltose permease, component of MalEFG (K unknown), involved in maltose and maltodextrin uptake (characterized) | 40% | 69% | 147.5 | Maltose-transporting ATPase (EC 3.6.3.19) | 100% | 584.7 |
| 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) | 32% | 99% | 144.4 | Maltose-transporting ATPase (EC 3.6.3.19) | 100% | 584.7 |
| 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) | 32% | 99% | 144.4 | Maltose-transporting ATPase (EC 3.6.3.19) | 100% | 584.7 |
| trehalose catabolism | thuG | lo | Trehalose/maltose transport system permease protein MalG (characterized) | 31% | 97% | 132.5 | Maltose-transporting ATPase (EC 3.6.3.19) | 100% | 584.7 |
| sucrose catabolism | thuG | lo | ABC transporter for D-Trehalose, permease component 2 (characterized) | 32% | 96% | 125.9 | Maltose-transporting ATPase (EC 3.6.3.19) | 100% | 584.7 |
| D-glucosamine (chitosamine) catabolism | SM_b21219 | lo | ABC transporter for D-Glucosamine, permease component 1 (characterized) | 31% | 94% | 111.3 | Maltose-transporting ATPase (EC 3.6.3.19) | 100% | 584.7 |
| D-sorbitol (glucitol) catabolism | mtlG | lo | ABC transporter for D-Sorbitol, permease component 1 (characterized) | 34% | 71% | 105.5 | Maltose-transporting ATPase (EC 3.6.3.19) | 100% | 584.7 |
| D-mannitol catabolism | mtlG | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, permease component 1 (characterized) | 30% | 96% | 94.4 | Maltose-transporting ATPase (EC 3.6.3.19) | 100% | 584.7 |
| D-cellobiose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 32% | 54% | 94 | Maltose-transporting ATPase (EC 3.6.3.19) | 100% | 584.7 |
| D-glucose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 32% | 54% | 94 | Maltose-transporting ATPase (EC 3.6.3.19) | 100% | 584.7 |
| lactose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 32% | 54% | 94 | Maltose-transporting ATPase (EC 3.6.3.19) | 100% | 584.7 |
| D-maltose catabolism | aglG | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 32% | 54% | 94 | Maltose-transporting ATPase (EC 3.6.3.19) | 100% | 584.7 |
| D-maltose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 32% | 54% | 94 | Maltose-transporting ATPase (EC 3.6.3.19) | 100% | 584.7 |
| sucrose catabolism | aglG | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 32% | 54% | 94 | Maltose-transporting ATPase (EC 3.6.3.19) | 100% | 584.7 |
| sucrose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 32% | 54% | 94 | Maltose-transporting ATPase (EC 3.6.3.19) | 100% | 584.7 |
| trehalose catabolism | aglG | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 32% | 54% | 94 | Maltose-transporting ATPase (EC 3.6.3.19) | 100% | 584.7 |
| trehalose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 32% | 54% | 94 | Maltose-transporting ATPase (EC 3.6.3.19) | 100% | 584.7 |
Sequence Analysis Tools
View BWI76_RS01820 at FitnessBrowser
Find papers: PaperBLAST
Find functional residues: SitesBLAST
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Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
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Sequence
MAMVQPKSQKLRLFTTHLLLLVFIAAIMFPLLMVIAISLREGNFATGSLIPESISWEHWR
LALGFSVEHADGRVTPPPFPVLLWLWNSIKVAGITAIGIVALSTTCAYAFARMRFPGKAT
LLKGMLIFQMFPAVLSLVALYALFDRLGQYVPFVGLNTHGGVIFAYMGGIALHVWTIKGY
FETIDGSLEEAAALDGATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDV
NSYTLAVGMQQYLNPQNYLWGDFAAAAVLSAIPITVVFLLAQRWLVNGLTAGGVKG
This GapMind analysis is from Apr 09 2024. 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