GapMind for catabolism of small carbon sources

 

Protein 200226 in Shewanella oneidensis MR-1

Annotation: FitnessBrowser__MR1:200226

Length: 226 amino acids

Source: MR1 in FitnessBrowser

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% 95% 148.3 Arginine transport system permease protein ArtQ 43% 160.6
L-lysine catabolism hisQ lo ABC transporter for L-Lysine, permease component 1 (characterized) 33% 94% 124.4 Arginine transport system permease protein ArtQ 43% 160.6
L-arginine catabolism artM lo AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter (characterized) 33% 94% 122.1 Arginine transport system permease protein ArtQ 43% 160.6
L-asparagine catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 30% 81% 118.2 Arginine transport system permease protein ArtQ 43% 160.6
L-aspartate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 30% 81% 118.2 Arginine transport system permease protein ArtQ 43% 160.6
L-glutamate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 30% 81% 118.2 Arginine transport system permease protein ArtQ 43% 160.6
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) 33% 91% 117.5 Arginine transport system permease protein ArtQ 43% 160.6
L-asparagine catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 33% 92% 116.3 Arginine transport system permease protein ArtQ 43% 160.6
L-aspartate catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 33% 92% 116.3 Arginine transport system permease protein ArtQ 43% 160.6
L-glutamate catabolism gltK lo Glutamate/aspartate import permease protein GltK (characterized) 33% 92% 116.3 Arginine transport system permease protein ArtQ 43% 160.6
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% 112.8 Arginine transport system permease protein ArtQ 43% 160.6
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% 112.8 Arginine transport system permease protein ArtQ 43% 160.6
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% 112.5 Arginine transport system permease protein ArtQ 43% 160.6
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% 112.5 Arginine transport system permease protein ArtQ 43% 160.6
L-histidine catabolism aapM lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized) 33% 55% 110.5 Arginine transport system permease protein ArtQ 43% 160.6
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 Arginine transport system permease protein ArtQ 43% 160.6
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 Arginine transport system permease protein ArtQ 43% 160.6
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 Arginine transport system permease protein ArtQ 43% 160.6
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 Arginine transport system permease protein ArtQ 43% 160.6
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 Arginine transport system permease protein ArtQ 43% 160.6
L-glutamate catabolism gluD lo GluD aka CGL1953, component of Glutamate porter (characterized) 33% 75% 107.8 Arginine transport system permease protein ArtQ 43% 160.6
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% 105.5 Arginine transport system permease protein ArtQ 43% 160.6
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% 105.5 Arginine transport system permease protein ArtQ 43% 160.6
D-alanine catabolism Pf6N2E2_5404 lo ABC transporter for D-Alanine, permease component 1 (characterized) 30% 56% 100.9 Arginine transport system permease protein ArtQ 43% 160.6
L-citrulline catabolism AO353_03050 lo ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized) 31% 93% 95.9 Arginine transport system permease protein ArtQ 43% 160.6
L-asparagine catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 32% 84% 94.7 Arginine transport system permease protein ArtQ 43% 160.6
L-aspartate catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 32% 84% 94.7 Arginine transport system permease protein ArtQ 43% 160.6
L-glutamate catabolism gltJ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 32% 84% 94.7 Arginine transport system permease protein ArtQ 43% 160.6

Sequence Analysis Tools

View 200226 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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Sequence

MLEAINTSLFSPIGDDGMIGILLILNGLKVTLIVTFFAMLLGAVLGVGTTLMKMSSKWYI
RFPAELYVGVIRGTPVVVQLVILYFIVLAALDVDKITAAIIAFGLNSGAYISEIIRAGIQ
AVDKGQTEAARSLGLSQAMTMKLIILPQAIKNILPALGNEFIVLLKETAVIGFIGGVDLM
RAGEIIRSRTFEDSVPLFTCALIYLFLTYSFTFMLSKFEKRLKQSD

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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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