GapMind for catabolism of small carbon sources

 

Protein GFF3090 in Marinobacter adhaerens HP15

Annotation: HP15_3033 amino acid ABC transporter, inner membrane subunit

Length: 240 amino acids

Source: Marino in FitnessBrowser

Candidate for 11 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism artM hi AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter (characterized) 53% 93% 237.7 NocM aka ATU6025 aka AGR_PTI_65, component of Nopaline porter 46% 192.2
L-citrulline catabolism AO353_03045 hi ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized) 49% 98% 232.3 ABC transporter for L-Arginine, permease component 1 49% 204.1
L-histidine catabolism hisM med Histidine transport system permease protein HisM (characterized) 45% 97% 192.2 AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter 53% 237.7
L-lysine catabolism hisM med Histidine transport system permease protein HisM (characterized) 45% 97% 192.2 AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter 53% 237.7
L-citrulline catabolism PS417_17600 med ABC transporter permease; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine ABC transporter permease HisM; SubName: Full=Histidine transport system permease protein; SubName: Full=Histidine/lysine/arginine/ornithine ABC transporter permease HisM (characterized, see rationale) 44% 92% 174.5 AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter 53% 237.7
L-histidine catabolism BPHYT_RS24010 lo Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale) 38% 89% 166.8 AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter 53% 237.7
L-lysine catabolism hisQ lo ABC transporter for L-Lysine, permease component 1 (characterized) 32% 94% 108.6 AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter 53% 237.7
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) 30% 88% 106.7 AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter 53% 237.7
L-asparagine catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 31% 85% 95.5 AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter 53% 237.7
L-aspartate catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 31% 85% 95.5 AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter 53% 237.7
L-glutamate catabolism gltJ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 31% 85% 95.5 AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter 53% 237.7

Sequence Analysis Tools

View GFF3090 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MPDFIAEWLNQNEIFTAMTIMEYWDGMVTTVHLVFLSLVIGLLVAVPLAILRTVRNPFVS
GPVWLYTYLFRGTPLLIQLYIIYYGLAQIEGIQETFWWEIFREPFYPALLAFTLNTAAYT
TEIIRGAIISTPNGEIEAAKAYGMNWFMRMRRIVLPSAARRAVQAYSNEVIFMLHASAIA
SVVTIVDLTGAARNIYSRFYAPFDAFIFVALCYMALTFILVFAFRKLETHLLKHQRPVNG

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, the preprint on GapMind for carbon sources, 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