GapMind for catabolism of small carbon sources

 

Protein BWI76_RS18355 in Klebsiella michiganensis M5al

Annotation: BWI76_RS18355 amino acid ABC transporter permease

Length: 222 amino acids

Source: Koxy in FitnessBrowser

Candidate for 24 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 36% 96% 141.4 L-cystine transport system permease protein YecS 93% 409.1
L-aspartate catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 36% 96% 141.4 L-cystine transport system permease protein YecS 93% 409.1
L-glutamate catabolism gltK lo Glutamate/aspartate import permease protein GltK (characterized) 36% 96% 141.4 L-cystine transport system permease protein YecS 93% 409.1
L-histidine catabolism BPHYT_RS24010 lo Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale) 35% 91% 132.5 L-cystine transport system permease protein YecS 93% 409.1
L-histidine catabolism aapM lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized) 38% 55% 130.6 L-cystine transport system permease protein YecS 93% 409.1
L-asparagine catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 31% 84% 129 L-cystine transport system permease protein YecS 93% 409.1
L-aspartate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 31% 84% 129 L-cystine transport system permease protein YecS 93% 409.1
L-glutamate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 31% 84% 129 L-cystine transport system permease protein YecS 93% 409.1
L-asparagine catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 31% 75% 122.9 L-cystine transport system permease protein YecS 93% 409.1
L-aspartate catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 31% 75% 122.9 L-cystine transport system permease protein YecS 93% 409.1
D-alanine catabolism Pf6N2E2_5404 lo ABC transporter for D-Alanine, permease component 1 (characterized) 36% 56% 120.9 L-cystine transport system permease protein YecS 93% 409.1
L-arginine catabolism artQ lo ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized) 32% 93% 119.8 L-cystine transport system permease protein YecS 93% 409.1
L-asparagine catabolism aapM lo AapM, 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) 36% 54% 119.8 L-cystine transport system permease protein YecS 93% 409.1
L-aspartate catabolism aapM lo AapM, 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) 36% 54% 119.8 L-cystine transport system permease protein YecS 93% 409.1
L-citrulline catabolism AO353_03050 lo ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized) 32% 93% 119.8 L-cystine transport system permease protein YecS 93% 409.1
L-glutamate catabolism aapM lo AapM, 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) 36% 54% 119.8 L-cystine transport system permease protein YecS 93% 409.1
L-leucine catabolism aapM lo AapM, 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) 36% 54% 119.8 L-cystine transport system permease protein YecS 93% 409.1
L-proline catabolism aapM lo AapM, 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) 36% 54% 119.8 L-cystine transport system permease protein YecS 93% 409.1
L-asparagine catabolism natH lo Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) 34% 53% 117.9 L-cystine transport system permease protein YecS 93% 409.1
L-aspartate catabolism natH lo Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) 34% 53% 117.9 L-cystine transport system permease protein YecS 93% 409.1
L-asparagine catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 32% 52% 111.3 L-cystine transport system permease protein YecS 93% 409.1
L-aspartate catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 32% 52% 111.3 L-cystine transport system permease protein YecS 93% 409.1
L-glutamate catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 32% 52% 111.3 L-cystine transport system permease protein YecS 93% 409.1
L-glutamate catabolism gluC lo GluC aka CGL1952, component of Glutamate porter (characterized) 33% 91% 98.2 L-cystine transport system permease protein YecS 93% 409.1

Sequence Analysis Tools

View BWI76_RS18355 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

MQESIQLVIDSAPFLLKGAVFTLQLSIGGMFFGLVLGFILALMRMSPVWPIKWLARMYIS
IFRGTPLIAQLFMIYYGLPQFGIELDPIPAAMIGLSLNTAAYAAETLRAAIASIDKGQWE
AAASIGMTRWQAMRRAILPQAARVALPPLSNSFISLVKDTSLAATIQVPELFRQAQLITS
RTLEVFTMYLAASLIYWVMATVLSTLQNYFENQLNRQERDPK

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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