GapMind for catabolism of small carbon sources

 

Protein GFF18 in Pseudomonas stutzeri RCH2

Annotation: Psest_0018 ectoine/hydroxyectoine ABC transporter, permease protein EhuC

Length: 219 amino acids

Source: psRCH2 in FitnessBrowser

Candidate for 26 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism Ac3H11_2554 lo ABC transporter for L-Histidine, permease component 1 (characterized) 40% 94% 152.1 L-cystine transport system permease protein YecS 43% 162.5
L-arginine catabolism artQ lo Probable permease of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 36% 95% 125.2 L-cystine transport system permease protein YecS 43% 162.5
L-histidine catabolism hisQ lo Probable permease of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 36% 95% 125.2 L-cystine transport system permease protein YecS 43% 162.5
L-lysine catabolism hisQ lo Probable permease of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 36% 95% 125.2 L-cystine transport system permease protein YecS 43% 162.5
L-lysine catabolism hisM lo Amino acid ABC transporter, membrane protein (characterized, see rationale) 36% 90% 116.7 L-cystine transport system permease protein YecS 43% 162.5
L-citrulline catabolism AO353_03050 lo ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized) 32% 94% 115.5 L-cystine transport system permease protein YecS 43% 162.5
L-citrulline catabolism PS417_17595 lo ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale) 36% 93% 111.7 L-cystine transport system permease protein YecS 43% 162.5
L-glutamate catabolism gluC lo GluC aka CGL1952, component of Glutamate porter (characterized) 35% 96% 104.4 L-cystine transport system permease protein YecS 43% 162.5
L-arginine catabolism artM lo Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 34% 97% 102.8 L-cystine transport system permease protein YecS 43% 162.5
D-glucosamine (chitosamine) catabolism AO353_21720 lo ABC transporter for D-Glucosamine, permease component 1 (characterized) 31% 84% 102.8 L-cystine transport system permease protein YecS 43% 162.5
L-histidine catabolism hisM lo Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 34% 97% 102.8 L-cystine transport system permease protein YecS 43% 162.5
L-glutamate catabolism gltK lo Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized) 32% 97% 101.7 L-cystine transport system permease protein YecS 43% 162.5
L-asparagine catabolism aatQ lo ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 1 (characterized) 33% 84% 100.5 L-cystine transport system permease protein YecS 43% 162.5
L-aspartate catabolism aatQ lo ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 1 (characterized) 33% 84% 100.5 L-cystine transport system permease protein YecS 43% 162.5
L-glutamate catabolism gltJ lo ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized) 32% 86% 100.1 L-cystine transport system permease protein YecS 43% 162.5
L-citrulline catabolism AO353_03045 lo ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized) 35% 86% 99.8 L-cystine transport system permease protein YecS 43% 162.5
L-histidine catabolism aapM lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized) 33% 55% 99.8 L-cystine transport system permease protein YecS 43% 162.5
D-alanine catabolism Pf6N2E2_5404 lo ABC transporter for D-Alanine, permease component 1 (characterized) 33% 57% 99.4 L-cystine transport system permease protein YecS 43% 162.5
L-histidine catabolism BPHYT_RS24010 lo Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale) 32% 87% 98.6 L-cystine transport system permease protein YecS 43% 162.5
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) 32% 56% 96.3 L-cystine transport system permease protein YecS 43% 162.5
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) 32% 56% 96.3 L-cystine transport system permease protein YecS 43% 162.5
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) 32% 56% 96.3 L-cystine transport system permease protein YecS 43% 162.5
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) 32% 56% 96.3 L-cystine transport system permease protein YecS 43% 162.5
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) 32% 56% 96.3 L-cystine transport system permease protein YecS 43% 162.5
L-asparagine catabolism aatM lo ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 (characterized) 32% 95% 89.4 L-cystine transport system permease protein YecS 43% 162.5
L-aspartate catabolism aatM lo ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 (characterized) 32% 95% 89.4 L-cystine transport system permease protein YecS 43% 162.5

Sequence Analysis Tools

View GFF18 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MIELLPLLLQGAWVTVKVTFFGSLLAIACALIAALARLSPVAPLRWLAITYIEVFRGSSL
LVQLFWLYFVLPMPPFNIEMSAFAVAVVGLGLNIGAYGAEVLRGAIRSVHRGQHEACQAL
NMTPLTRMRRIILPQALLAAIPPGTNLLIELLKNTSLVSLITLSDLAFRARQLDQATLMT
MEIFGLALVIYFVLAQTINFGMRQLERRLARGRMRGGLS

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, 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