GapMind for catabolism of small carbon sources

 

Protein BPHYT_RS21915 in Burkholderia phytofirmans PsJN

Annotation: BPHYT_RS21915 ABC transporter permease

Length: 222 amino acids

Source: BFirm in FitnessBrowser

Candidate for 23 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 hi ABC transporter for L-Histidine, permease component 1 (characterized) 80% 100% 357.1 Basic amino acid uptake transporter, BgtAB 44% 185.3
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) 37% 97% 144.1 ABC transporter for L-Histidine, permease component 1 80% 357.1
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) 37% 97% 144.1 ABC transporter for L-Histidine, permease component 1 80% 357.1
L-lysine 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) 37% 97% 144.1 ABC transporter for L-Histidine, permease component 1 80% 357.1
L-histidine catabolism BPHYT_RS24010 lo Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale) 35% 92% 138.7 ABC transporter for L-Histidine, permease component 1 80% 357.1
L-asparagine catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 33% 83% 130.6 ABC transporter for L-Histidine, permease component 1 80% 357.1
L-aspartate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 33% 83% 130.6 ABC transporter for L-Histidine, permease component 1 80% 357.1
L-glutamate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 33% 83% 130.6 ABC transporter for L-Histidine, permease component 1 80% 357.1
L-asparagine catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 36% 55% 122.1 ABC transporter for L-Histidine, permease component 1 80% 357.1
L-aspartate catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 36% 55% 122.1 ABC transporter for L-Histidine, permease component 1 80% 357.1
L-asparagine catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 34% 88% 121.3 ABC transporter for L-Histidine, permease component 1 80% 357.1
L-aspartate catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 34% 88% 121.3 ABC transporter for L-Histidine, permease component 1 80% 357.1
L-glutamate catabolism gltJ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 34% 88% 121.3 ABC transporter for L-Histidine, permease component 1 80% 357.1
L-asparagine catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 31% 98% 115.9 ABC transporter for L-Histidine, permease component 1 80% 357.1
L-aspartate catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 31% 98% 115.9 ABC transporter for L-Histidine, permease component 1 80% 357.1
L-glutamate catabolism gltK lo Glutamate/aspartate import permease protein GltK (characterized) 31% 98% 115.9 ABC transporter for L-Histidine, permease component 1 80% 357.1
L-glutamate catabolism gluD lo GluD aka CGL1953, component of Glutamate porter (characterized) 33% 75% 115.5 ABC transporter for L-Histidine, permease component 1 80% 357.1
L-asparagine catabolism aapQ lo AapQ, 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% 50% 96.7 ABC transporter for L-Histidine, permease component 1 80% 357.1
L-aspartate catabolism aapQ lo AapQ, 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% 50% 96.7 ABC transporter for L-Histidine, permease component 1 80% 357.1
L-glutamate catabolism aapQ lo AapQ, 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% 50% 96.7 ABC transporter for L-Histidine, permease component 1 80% 357.1
L-histidine catabolism aapQ lo AapQ, 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% 50% 96.7 ABC transporter for L-Histidine, permease component 1 80% 357.1
L-leucine catabolism aapQ lo AapQ, 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% 50% 96.7 ABC transporter for L-Histidine, permease component 1 80% 357.1
L-proline catabolism aapQ lo AapQ, 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% 50% 96.7 ABC transporter for L-Histidine, permease component 1 80% 357.1

Sequence Analysis Tools

View BPHYT_RS21915 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

MELDFSPVIAGLPDILHGAVVTVEVTAASLALSCVLGLLIGIGRLTPKRRIVYGFCTAYL
TFFRGTPLLVQLFLLFFGLPQFGILLPAFVCGMLGLGLYSAAYVSEIVRGAIQSVDRGQM
EAARSIGMSSGQAMRAIILPQAIVRMIPPLGNEFIALIKNSALVSLLTIDDLMHEGQKII
SVSYRSLEVYLAIALVYLVLTQATNYALHRVERHLRAGGMVQ

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