GapMind for catabolism of small carbon sources

 

Protein 7023652 in Shewanella sp. ANA-3

Annotation: Shewana3_0881 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Length: 226 amino acids

Source: ANA3 in FitnessBrowser

Candidate for 29 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) 38% 95% 150.2 Arginine transport system permease protein ArtQ 44% 162.2
L-arginine catabolism artM lo AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter (characterized) 34% 94% 124.4 Arginine transport system permease protein ArtQ 44% 162.2
L-lysine catabolism hisQ lo ABC transporter for L-Lysine, permease component 1 (characterized) 33% 94% 123.2 Arginine transport system permease protein ArtQ 44% 162.2
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) 35% 91% 118.6 Arginine transport system permease protein ArtQ 44% 162.2
L-asparagine catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 30% 81% 116.7 Arginine transport system permease protein ArtQ 44% 162.2
L-aspartate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 30% 81% 116.7 Arginine transport system permease protein ArtQ 44% 162.2
L-glutamate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 30% 81% 116.7 Arginine transport system permease protein ArtQ 44% 162.2
L-asparagine catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 32% 92% 115.2 Arginine transport system permease protein ArtQ 44% 162.2
L-aspartate catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 32% 92% 115.2 Arginine transport system permease protein ArtQ 44% 162.2
L-glutamate catabolism gltK lo Glutamate/aspartate import permease protein GltK (characterized) 32% 92% 115.2 Arginine transport system permease protein ArtQ 44% 162.2
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% 91% 114 Arginine transport system permease protein ArtQ 44% 162.2
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) 33% 91% 114 Arginine transport system permease protein ArtQ 44% 162.2
L-asparagine catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 34% 55% 111.7 Arginine transport system permease protein ArtQ 44% 162.2
L-aspartate catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 34% 55% 111.7 Arginine transport system permease protein ArtQ 44% 162.2
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) 32% 52% 109.4 Arginine transport system permease protein ArtQ 44% 162.2
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) 32% 52% 109.4 Arginine transport system permease protein ArtQ 44% 162.2
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) 32% 52% 109.4 Arginine transport system permease protein ArtQ 44% 162.2
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) 32% 52% 109.4 Arginine transport system permease protein ArtQ 44% 162.2
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) 32% 52% 109.4 Arginine transport system permease protein ArtQ 44% 162.2
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) 32% 52% 109.4 Arginine transport system permease protein ArtQ 44% 162.2
L-glutamate catabolism gluD lo GluD aka CGL1953, component of Glutamate porter (characterized) 33% 75% 107.5 Arginine transport system permease protein ArtQ 44% 162.2
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) 30% 91% 103.2 Arginine transport system permease protein ArtQ 44% 162.2
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) 30% 91% 103.2 Arginine transport system permease protein ArtQ 44% 162.2
D-alanine catabolism Pf6N2E2_5404 lo ABC transporter for D-Alanine, permease component 1 (characterized) 30% 56% 100.1 Arginine transport system permease protein ArtQ 44% 162.2
L-citrulline catabolism AO353_03050 lo ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized) 31% 93% 95.1 Arginine transport system permease protein ArtQ 44% 162.2
L-asparagine catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 32% 84% 93.2 Arginine transport system permease protein ArtQ 44% 162.2
L-aspartate catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 32% 84% 93.2 Arginine transport system permease protein ArtQ 44% 162.2
L-glutamate catabolism gltJ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 32% 84% 93.2 Arginine transport system permease protein ArtQ 44% 162.2
L-glutamate catabolism gluC lo GluC aka CGL1952, component of Glutamate porter (characterized) 30% 90% 85.1 Arginine transport system permease protein ArtQ 44% 162.2

Sequence Analysis Tools

View 7023652 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

MLEAINTSLFSPIGDDGMIGILLILNGLKVTLIVTFFAMLLGAVLGVGTTLMKMSSKWYI
RFPAELYVGVIRGTPVVVQLVILYFIVLAAFDVDKVTAAIIAFGLNSGAYISEIIRAGIQ
AVDKGQTEAARSLGLSQAMTMKLIILPQAIKNILPALGNEFIVLLKETAVIGFIGGVDLM
RAGEIIRSRTFEDSIPLFTCALIYLFLTYSFTFMLSKFEKRLKQSD

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