GapMind for catabolism of small carbon sources

 

Protein WP_040537128.1 in Lactobacillus shenzhenensis LY-73

Annotation: NCBI__GCF_000469325.1:WP_040537128.1

Length: 276 amino acids

Source: GCF_000469325.1 in NCBI

Candidate for 6 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_Sm hi 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) 66% 95% 355.5 CymG, component of Cyclodextrin porter 41% 206.8
trehalose catabolism malG hi 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) 66% 95% 355.5 CymG, component of Cyclodextrin porter 41% 206.8
D-maltose catabolism malG_Bb lo ABC-type Maltose/ Maltodextrin permease (characterized, see rationale) 37% 100% 187.2 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) 66% 355.5
D-maltose catabolism malG_Aa lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 32% 90% 164.5 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) 66% 355.5
D-maltose catabolism malG lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 32% 96% 149.4 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) 66% 355.5
D-maltose catabolism thuG lo Putative maltose permease, component of MalEFG (K unknown), involved in maltose and maltodextrin uptake (characterized) 30% 86% 144.1 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) 66% 355.5

Sequence Analysis Tools

View WP_040537128.1 at NCBI

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

MKKKALWPRITLVILGIVWMFPIFWTVLTAFRGESGQFVSYIFPKHYSLNNFRNLFSNNP
NFPFLLWLKNTLIVSIFSCLLSTFITVSMAYVLSRLRFKFRNTILKVALVLNMFPAFMAM
IAVYYILKAFDLTQTLLALVLVYSSTAALTFYVAKGFFDTIPMSLDESAMIDGATKFQIF
TKITLPMSQPIIVYTALMAFMQPWMDFIFAKIIMGDNVPKYTVSIGLYAMLNQTTANTLY
TTFAAGCLVIALPITVLFIYLQKYYVAGITSGAVKG

This GapMind analysis is from Sep 24 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