Protein 18060 in Escherichia coli BW25113
Annotation: FitnessBrowser__Keio:18060
Length: 296 amino acids
Source: Keio in FitnessBrowser
Candidate for 27 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 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) (characterized) | 100% | 100% | 582.8 | ABC-type maltose transporter (subunit 1/2) (EC 7.5.2.1) | 45% | 199.9 |
| D-maltose catabolism | malG_Aa | lo | Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) | 35% | 91% | 174.1 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| D-maltose catabolism | malG_Bb | lo | ABC-type Maltose/ Maltodextrin permease (characterized, see rationale) | 34% | 97% | 158.3 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| D-maltose catabolism | thuG | lo | Putative maltose permease, component of MalEFG (K unknown), involved in maltose and maltodextrin uptake (characterized) | 32% | 92% | 146 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| 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) | 33% | 95% | 139 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| 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) | 33% | 95% | 139 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| L-fucose catabolism | SM_b21105 | lo | ABC transporter for L-Fucose, permease component 2 (characterized) | 33% | 98% | 136.3 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| trehalose catabolism | thuG | lo | Trehalose transport system permease protein SugB (characterized) | 31% | 96% | 128.6 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| sucrose catabolism | thuG | lo | ABC transporter for D-Trehalose, permease component 2 (characterized) | 31% | 96% | 123.6 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| D-sorbitol (glucitol) catabolism | mtlG | lo | ABC transporter for D-Sorbitol, permease component 1 (characterized) | 36% | 75% | 106.7 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| D-maltose catabolism | aglG | lo | ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) | 31% | 56% | 100.9 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| sucrose catabolism | aglG | lo | ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) | 31% | 56% | 100.9 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| trehalose catabolism | aglG | lo | ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) | 31% | 56% | 100.9 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| D-mannitol catabolism | mtlG | lo | MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 31% | 89% | 97.8 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| 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) | 30% | 97% | 95.9 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| 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) | 30% | 97% | 95.9 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| 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) | 30% | 97% | 95.9 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| 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) | 30% | 97% | 95.9 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| 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) | 30% | 97% | 95.9 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| 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) | 30% | 97% | 95.9 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| 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) | 30% | 97% | 95.9 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| D-cellobiose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 54% | 94.4 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| D-glucose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 54% | 94.4 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| lactose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 54% | 94.4 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| D-maltose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 54% | 94.4 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| sucrose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 54% | 94.4 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
| trehalose catabolism | aglG' | lo | Inner membrane ABC transporter permease protein (characterized, see rationale) | 33% | 54% | 94.4 | ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) | 100% | 582.8 |
Sequence Analysis Tools
View 18060 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
MAMVQPKSQKARLFITHLLLLLFIAAIMFPLLMVVAISLRQGNFATGSLIPEQISWDHWK
LALGFSVEQADGRITPPPFPVLLWLWNSVKVAGISAIGIVALSTTCAYAFARMRFPGKAT
LLKGMLIFQMFPAVLSLVALYALFDRLGEYIPFIGLNTHGGVIFAYLGGIALHVWTIKGY
FETIDSSLEEAAALDGATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDV
NSYTLAVGMQQYLNPQNYLWGDFAAAAVMSALPITIVFLLAQRWLVNGLTAGGVKG
This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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