GapMind for catabolism of small carbon sources

 

Protein GFF966 in Pseudomonas simiae WCS417

Annotation: PS417_04900 amino acid ABC transporter substrate-binding protein

Length: 343 amino acids

Source: WCS417 in FitnessBrowser

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-alanine catabolism Pf6N2E2_5402 hi ABC transporter for D-Alanine, periplasmic substrate-binding component (characterized) 93% 100% 644.8 AapJ, 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) 58% 401.7
L-asparagine catabolism aapJ med AapJ, 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) 58% 99% 401.7 ABC transporter for D-Alanine, periplasmic substrate-binding component 93% 644.8
L-aspartate catabolism aapJ med AapJ, 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) 58% 99% 401.7 ABC transporter for D-Alanine, periplasmic substrate-binding component 93% 644.8
L-glutamate catabolism aapJ med AapJ, 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) 58% 99% 401.7 ABC transporter for D-Alanine, periplasmic substrate-binding component 93% 644.8
L-histidine catabolism aapJ med AapJ, 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) 58% 99% 401.7 ABC transporter for D-Alanine, periplasmic substrate-binding component 93% 644.8
L-leucine catabolism aapJ med AapJ, 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) 58% 99% 401.7 ABC transporter for D-Alanine, periplasmic substrate-binding component 93% 644.8
L-proline catabolism aapJ med AapJ, 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) 58% 99% 401.7 ABC transporter for D-Alanine, periplasmic substrate-binding component 93% 644.8
L-asparagine catabolism bztA med BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 52% 100% 344 ABC transporter for D-Alanine, periplasmic substrate-binding component 93% 644.8
L-aspartate catabolism bztA med BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 52% 100% 344 ABC transporter for D-Alanine, periplasmic substrate-binding component 93% 644.8
L-glutamate catabolism bztA med BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 52% 100% 344 ABC transporter for D-Alanine, periplasmic substrate-binding component 93% 644.8
L-asparagine catabolism natF med Extracellular solute-binding protein, family 3 (characterized, see rationale) 43% 96% 297.4 ABC transporter for D-Alanine, periplasmic substrate-binding component 93% 644.8
L-aspartate catabolism natF med Extracellular solute-binding protein, family 3 (characterized, see rationale) 43% 96% 297.4 ABC transporter for D-Alanine, periplasmic substrate-binding component 93% 644.8

Sequence Analysis Tools

View GFF966 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

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

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MKVLKSTLAIVSAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDASGKILG
IDADVCRAVAAAVFGDATKVKFSQLNAKERFTALQSGEVDILSRNTTMTSSRDAGMGLKF
PGFITYYDGIGFLVNNKLGVKSAKELDGATICIQAGTTTELNVSDYFRGNNLKYTPITFD
TSDESAKSLESGRCDVLTSDKSQLFAQRSKLAAPKDYVVLPETISKEPLGPVVRNGDDEW
LAIVRWVGYAMLNAEEAGITSKNVEAEAKSTKNPDVARLLGADGEYGKDLKVKKDWVVQI
VKQVGNYGEVFERNLGKSTPLEIDRGLNALWNNGGIQYAPPVR

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 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