GapMind for catabolism of small carbon sources

 

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

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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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:

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:

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:

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