GapMind for catabolism of small carbon sources

 

Protein 5210737 in Shewanella loihica PV-4

Annotation: FitnessBrowser__PV4:5210737

Length: 226 amino acids

Source: PV4 in FitnessBrowser

Candidate for 21 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) 36% 95% 143.3 Arginine transport system permease protein ArtQ 45% 167.9
L-lysine catabolism hisQ lo ABC transporter for L-Lysine, permease component 1 (characterized) 34% 87% 123.6 Arginine transport system permease protein ArtQ 45% 167.9
L-arginine catabolism artM lo AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter (characterized) 32% 90% 119.8 Arginine transport system permease protein ArtQ 45% 167.9
L-asparagine catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 32% 92% 117.5 Arginine transport system permease protein ArtQ 45% 167.9
L-aspartate catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 32% 92% 117.5 Arginine transport system permease protein ArtQ 45% 167.9
L-glutamate catabolism gltK lo Glutamate/aspartate import permease protein GltK (characterized) 32% 92% 117.5 Arginine transport system permease protein ArtQ 45% 167.9
L-glutamate catabolism gluD lo GluD aka CGL1953, component of Glutamate porter (characterized) 33% 81% 115.9 Arginine transport system permease protein ArtQ 45% 167.9
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% 114 Arginine transport system permease protein ArtQ 45% 167.9
D-glucosamine (chitosamine) catabolism AO353_21715 lo ABC transporter for D-Glucosamine Hydrochloride, permease component 2 (characterized) 32% 91% 114 Arginine transport system permease protein ArtQ 45% 167.9
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 45% 167.9
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 45% 167.9
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% 111.3 Arginine transport system permease protein ArtQ 45% 167.9
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% 111.3 Arginine transport system permease protein ArtQ 45% 167.9
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% 106.3 Arginine transport system permease protein ArtQ 45% 167.9
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% 106.3 Arginine transport system permease protein ArtQ 45% 167.9
L-histidine catabolism aapM lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized) 32% 60% 103.6 Arginine transport system permease protein ArtQ 45% 167.9
L-citrulline catabolism AO353_03050 lo ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized) 31% 93% 102.8 Arginine transport system permease protein ArtQ 45% 167.9
L-asparagine catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 31% 90% 102.4 Arginine transport system permease protein ArtQ 45% 167.9
L-aspartate catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 31% 90% 102.4 Arginine transport system permease protein ArtQ 45% 167.9
L-glutamate catabolism gltJ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 31% 90% 102.4 Arginine transport system permease protein ArtQ 45% 167.9
D-alanine catabolism Pf6N2E2_5404 lo ABC transporter for D-Alanine, permease component 1 (characterized) 31% 59% 99 Arginine transport system permease protein ArtQ 45% 167.9

Sequence Analysis Tools

View 5210737 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

Fitness BLAST: loading...

Sequence

MLDAINSSLFTPIGEDGLIGIYLILNGLKVTLIVTLFAMILGAILGVATTLMKMSSRWYL
RWPANLYVGVIRGTPVVVQLVILYFIVLATWDVDKVSAAIIAFGLNSGAYISEIIRAGIQ
AVDKGQTEAARSLGLSQAVTMKEVILPQAIKNILPALGNEFIVLLKETAVIGFIGGVDLM
RSGEIIRSRTFEDSVPLFTCALIYLALTYSFTFMLSKFEKRLKQSD

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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