GapMind for catabolism of small carbon sources

 

Protein AZOBR_RS15675 in Azospirillum brasilense Sp245

Annotation: AZOBR_RS15675 ABC transporter permease

Length: 224 amino acids

Source: azobra in FitnessBrowser

Candidate for 14 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-glucosamine (chitosamine) catabolism AO353_21715 lo ABC transporter for D-glucosamine, permease component 1 (characterized) 38% 96% 147.9 L-cystine transport system permease protein YecS 39% 155.6
L-lysine catabolism hisQ lo ABC transporter for L-Lysine, permease component 1 (characterized) 36% 95% 117.5 L-cystine transport system permease protein YecS 39% 155.6
L-histidine catabolism BPHYT_RS24010 lo Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale) 32% 86% 111.7 L-cystine transport system permease protein YecS 39% 155.6
L-asparagine catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 32% 69% 109.4 L-cystine transport system permease protein YecS 39% 155.6
L-aspartate catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 32% 69% 109.4 L-cystine transport system permease protein YecS 39% 155.6
L-arginine catabolism artQ lo arginine/ornithine transport protein (characterized) 31% 87% 104 L-cystine transport system permease protein YecS 39% 155.6
L-asparagine catabolism bgtB' lo ABC-type permease for basic amino acids and glutamine (characterized, see rationale) 34% 51% 90.1 L-cystine transport system permease protein YecS 39% 155.6
L-aspartate catabolism bgtB' lo ABC-type permease for basic amino acids and glutamine (characterized, see rationale) 34% 51% 90.1 L-cystine transport system permease protein YecS 39% 155.6
L-asparagine catabolism aapQ lo AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 31% 52% 89.4 L-cystine transport system permease protein YecS 39% 155.6
L-aspartate catabolism aapQ lo AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 31% 52% 89.4 L-cystine transport system permease protein YecS 39% 155.6
L-glutamate catabolism aapQ lo AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 31% 52% 89.4 L-cystine transport system permease protein YecS 39% 155.6
L-histidine catabolism aapQ lo AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 31% 52% 89.4 L-cystine transport system permease protein YecS 39% 155.6
L-leucine catabolism aapQ lo AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 31% 52% 89.4 L-cystine transport system permease protein YecS 39% 155.6
L-proline catabolism aapQ lo AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 31% 52% 89.4 L-cystine transport system permease protein YecS 39% 155.6

Sequence Analysis Tools

View AZOBR_RS15675 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

VNYTFDFKAVVDSWDYLLQGAWLTVQLSIGAMVLGLIVAILCALGKTSGPKPVRWVINAY
IEVVRNTPFLVQIFLIFFGLPTMGVRLSPDLAALIAMVVNVGAYATEIIRAGIESIQKGQ
IEAGLALGLKPLQVFRYIVIKPALRTVYPALTSQFILLMLSSSVVSAISADELTSVANNI
QSQTFRSFEIYIVVTGIYLMLAMMFSALFAGIYKLAFAYDTDRR

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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