GapMind for catabolism of small carbon sources

 

Protein GFF136 in Pseudomonas stutzeri RCH2

Annotation: Psest_0136 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Length: 229 amino acids

Source: psRCH2 in FitnessBrowser

Candidate for 25 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-lysine catabolism hisM hi ABC transporter for L-Lysine, permease component 2 (characterized) 78% 100% 364 AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter 50% 223.8
L-arginine catabolism artM hi 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) 70% 99% 330.1
L-histidine catabolism hisM hi 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) 70% 99% 330.1 AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter 50% 223.8
L-citrulline catabolism AO353_03045 med ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized) 47% 97% 211.5 ABC transporter for L-Lysine, permease component 2 78% 364.0
L-histidine catabolism BPHYT_RS24010 med Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale) 46% 81% 179.1 ABC transporter for L-Lysine, permease component 2 78% 364.0
L-citrulline catabolism PS417_17600 med ABC transporter permease; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine ABC transporter permease HisM; SubName: Full=Histidine transport system permease protein; SubName: Full=Histidine/lysine/arginine/ornithine ABC transporter permease HisM (characterized, see rationale) 43% 92% 168.3 ABC transporter for L-Lysine, permease component 2 78% 364.0
L-lysine catabolism hisQ lo ABC transporter for L-Lysine, permease component 1 (characterized) 32% 87% 114 ABC transporter for L-Lysine, permease component 2 78% 364.0
L-asparagine catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 36% 54% 110.5 ABC transporter for L-Lysine, permease component 2 78% 364.0
L-aspartate catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 36% 54% 110.5 ABC transporter for L-Lysine, permease component 2 78% 364.0
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) 31% 91% 108.6 ABC transporter for L-Lysine, permease component 2 78% 364.0
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) 31% 91% 108.6 ABC transporter for L-Lysine, permease component 2 78% 364.0
L-glutamate catabolism gltJ 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) 31% 94% 106.3 ABC transporter for L-Lysine, permease component 2 78% 364.0
L-asparagine catabolism aatQ lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 2 (characterized) 31% 94% 105.1 ABC transporter for L-Lysine, permease component 2 78% 364.0
L-aspartate catabolism aatQ lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 2 (characterized) 31% 94% 105.1 ABC transporter for L-Lysine, permease component 2 78% 364.0
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) 32% 91% 104.8 ABC transporter for L-Lysine, permease component 2 78% 364.0
D-glucosamine (chitosamine) catabolism AO353_21720 lo ABC transporter for D-glucosamine, permease component 2 (characterized) 32% 95% 104.8 ABC transporter for L-Lysine, permease component 2 78% 364.0
L-glutamate catabolism gluD lo GluD aka CGL1953, component of Glutamate porter (characterized) 33% 80% 104.8 ABC transporter for L-Lysine, permease component 2 78% 364.0
L-citrulline catabolism AO353_03050 lo ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized) 30% 92% 99 ABC transporter for L-Lysine, permease component 2 78% 364.0
L-histidine catabolism BPHYT_RS24005 lo Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale) 30% 85% 87.4 ABC transporter for L-Lysine, permease component 2 78% 364.0
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) 31% 53% 85.5 ABC transporter for L-Lysine, permease component 2 78% 364.0
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) 31% 53% 85.5 ABC transporter for L-Lysine, permease component 2 78% 364.0
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) 31% 53% 85.5 ABC transporter for L-Lysine, permease component 2 78% 364.0
L-histidine 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) 31% 53% 85.5 ABC transporter for L-Lysine, permease component 2 78% 364.0
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) 31% 53% 85.5 ABC transporter for L-Lysine, permease component 2 78% 364.0
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) 31% 53% 85.5 ABC transporter for L-Lysine, permease component 2 78% 364.0

Sequence Analysis Tools

View GFF136 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

MTWEIFIKWLPSFIDGAWLTLQLVGVSVIAGLIVAVPLGIARSSRHLAVRALPYGYIFFF
RGTPLLVQLFLVYYGMAQFDVVRQSALWPYLRDPYWCAIITMTLHTAAYIAEIIRGAIQN
VPHGEIEAARALGMSRSQALLHIILPRATRIGLPAYSNEVILMLKASALASTITLLELTG
MARKIAARTYLHEEMFLTAGLIYLLIAFILMQGFKLLERWLRVDACQGR

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