GapMind for catabolism of small carbon sources

 

Protein WP_012278550.1 in Shewanella halifaxensis HAW-EB4

Annotation: NCBI__GCF_000019185.1:WP_012278550.1

Length: 226 amino acids

Source: GCF_000019185.1 in NCBI

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% 149.1 Arginine transport system permease protein ArtQ 47% 174.9
L-lysine catabolism hisQ lo ABC transporter for L-Lysine, permease component 1 (characterized) 34% 87% 121.7 Arginine transport system permease protein ArtQ 47% 174.9
L-arginine catabolism artM lo AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter (characterized) 32% 90% 120.6 Arginine transport system permease protein ArtQ 47% 174.9
L-asparagine catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 30% 84% 119 Arginine transport system permease protein ArtQ 47% 174.9
L-aspartate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 30% 84% 119 Arginine transport system permease protein ArtQ 47% 174.9
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) 34% 91% 119 Arginine transport system permease protein ArtQ 47% 174.9
L-glutamate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 30% 84% 119 Arginine transport system permease protein ArtQ 47% 174.9
L-asparagine catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 32% 92% 114 Arginine transport system permease protein ArtQ 47% 174.9
L-aspartate catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 32% 92% 114 Arginine transport system permease protein ArtQ 47% 174.9
D-glucosamine (chitosamine) catabolism AO353_21715 lo ABC transporter for D-Glucosamine, permease component 2 (characterized) 31% 91% 114 Arginine transport system permease protein ArtQ 47% 174.9
L-glutamate catabolism gltK lo Glutamate/aspartate import permease protein GltK (characterized) 32% 92% 114 Arginine transport system permease protein ArtQ 47% 174.9
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 47% 174.9
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 47% 174.9
L-glutamate catabolism gluD lo GluD aka CGL1953, component of Glutamate porter (characterized) 33% 75% 110.5 Arginine transport system permease protein ArtQ 47% 174.9
L-histidine catabolism aapM lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized) 32% 58% 110.5 Arginine transport system permease protein ArtQ 47% 174.9
L-asparagine catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 32% 55% 109.8 Arginine transport system permease protein ArtQ 47% 174.9
L-aspartate catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 32% 55% 109.8 Arginine transport system permease protein ArtQ 47% 174.9
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% 109.4 Arginine transport system permease protein ArtQ 47% 174.9
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% 109.4 Arginine transport system permease protein ArtQ 47% 174.9
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% 52% 107.1 Arginine transport system permease protein ArtQ 47% 174.9
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% 52% 107.1 Arginine transport system permease protein ArtQ 47% 174.9
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% 52% 107.1 Arginine transport system permease protein ArtQ 47% 174.9
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% 52% 107.1 Arginine transport system permease protein ArtQ 47% 174.9
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% 52% 107.1 Arginine transport system permease protein ArtQ 47% 174.9
D-alanine catabolism Pf6N2E2_5404 lo ABC transporter for D-Alanine, permease component 1 (characterized) 31% 59% 102.1 Arginine transport system permease protein ArtQ 47% 174.9
L-asparagine catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 31% 90% 97.1 Arginine transport system permease protein ArtQ 47% 174.9
L-aspartate catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 31% 90% 97.1 Arginine transport system permease protein ArtQ 47% 174.9
L-glutamate catabolism gltJ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 31% 90% 97.1 Arginine transport system permease protein ArtQ 47% 174.9

Sequence Analysis Tools

View WP_012278550.1 at NCBI

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

Fitness BLAST: loading...

Sequence

MIDAINTSLFTPIGEDGLIGIYLILNGLKVTLIVTFFAMIIGSILGVATTLMKMSSKWYL
RWPANFYVSVIRGTPVVVQLVILYFIVLAALDVDKITAAVIAFGLNSGAYISEIIRAGIQ
AVDKGQMEAARSLGLSQAATMKEVILPQAIKNILPSLGNEFIVLLKETAVIGFIGGVDLM
RAGEIIRSRTFEDSVPLFTCALIYLLLTYIFTFILSRFETRLKQSD

This GapMind analysis is from Sep 24 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