GapMind for catabolism of small carbon sources

 

Protein 206399 in Desulfovibrio vulgaris Hildenborough

Annotation: DVU0967 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family

Length: 337 amino acids

Source: 882 in MicrobesOnline

Candidate for 28 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) 37% 90% 154.8 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
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) 35% 92% 139.8 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
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) 35% 92% 139.8 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
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) 35% 92% 139.8 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
L-asparagine catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 38% 93% 139.4 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
L-asparagine catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 34% 78% 139.4 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
L-aspartate catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 38% 93% 139.4 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
L-aspartate catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 34% 78% 139.4 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
L-glutamate catabolism gltK lo Glutamate/aspartate import permease protein GltK (characterized) 38% 93% 139.4 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
D-glucosamine (chitosamine) catabolism AO353_21715 lo ABC transporter for D-Glucosamine, permease component 2 (characterized) 35% 92% 137.9 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
L-arginine catabolism artM lo AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter (characterized) 35% 90% 133.7 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
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% 133.7 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
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% 133.7 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
L-lysine catabolism hisM lo ABC transporter for L-Lysine, permease component 2 (characterized) 35% 90% 132.1 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
D-glucosamine (chitosamine) catabolism AO353_21720 lo ABC transporter for D-Glucosamine, permease component 1 (characterized) 32% 91% 127.1 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
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) 33% 90% 123.6 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
L-citrulline catabolism AO353_03045 lo ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized) 33% 90% 122.5 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
L-histidine catabolism BPHYT_RS24005 lo Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale) 32% 83% 122.5 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
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% 54% 119 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
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% 54% 119 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
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% 54% 119 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
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% 54% 119 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
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% 54% 119 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
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% 54% 119 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
L-glutamate catabolism gluD lo GluD aka CGL1953, component of Glutamate porter (characterized) 32% 74% 113.6 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
L-glutamate catabolism gluC lo GluC aka CGL1952, component of Glutamate porter (characterized) 32% 95% 107.8 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
D-alanine catabolism Pf6N2E2_5403 lo ABC transporter for D-Alanine, permease component 2 (characterized) 31% 63% 102.1 Probable glutamine ABC transporter permease protein GlnM 45% 170.2
L-histidine catabolism aapQ lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized) 32% 51% 95.9 Probable glutamine ABC transporter permease protein GlnM 45% 170.2

Sequence Analysis Tools

View 206399 at MicrobesOnline

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

MTQYRGLDKPRGQGYFLFWKAVFVGIMLCTVAFFWYASSSVEYIWRWNRVPQYFWVAEKT
DVRAEVSGDVVSVETTAEGATRITVKGDDGSETYTVPPAGKVLISGGDYIYSGDPVGRYE
VSKPGILLEGLWITLEVSMLAIIIGIVLGVVTGLARISVNPALRWLAITYIEIIRGSPLL
VQVFLWYFVVGTLLNALFEKVGLSAIPPLWYGVMALAIFTGAYVAEIVRAGIQSVHRGQM
EAARSLGMSYAQSMRKVILPQAFRRIMPPLAGQFISLVKDSSLLGVIAVRELTKATREVV
TTSLQPFELWIVCALLYLVLTFTLSLCVQYLERRAVR

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