GapMind for catabolism of small carbon sources

 

Protein Ac3H11_4900 in Acidovorax sp. GW101-3H11

Annotation: FitnessBrowser__acidovorax_3H11:Ac3H11_4900

Length: 217 amino acids

Source: acidovorax_3H11 in FitnessBrowser

Candidate for 14 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% 97% 136.7 L-cystine transport system permease protein YecS 36% 146.0
L-lysine catabolism hisM lo ABC transporter for L-Lysine, permease component 2 (characterized) 36% 96% 127.5 L-cystine transport system permease protein YecS 36% 146.0
L-histidine catabolism BPHYT_RS24010 lo Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale) 35% 88% 125.6 L-cystine transport system permease protein YecS 36% 146.0
L-arginine catabolism artM 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) 31% 97% 114 L-cystine transport system permease protein YecS 36% 146.0
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) 31% 97% 114 L-cystine transport system permease protein YecS 36% 146.0
L-asparagine catabolism natH lo Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) 33% 51% 113.6 L-cystine transport system permease protein YecS 36% 146.0
L-aspartate catabolism natH lo Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) 33% 51% 113.6 L-cystine transport system permease protein YecS 36% 146.0
L-glutamate catabolism gltJ lo Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized) 33% 83% 112.8 L-cystine transport system permease protein YecS 36% 146.0
L-asparagine catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 32% 83% 107.1 L-cystine transport system permease protein YecS 36% 146.0
L-aspartate catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 32% 83% 107.1 L-cystine transport system permease protein YecS 36% 146.0
L-glutamate catabolism gluC lo GluC aka CGL1952, component of Glutamate porter (characterized) 33% 97% 105.1 L-cystine transport system permease protein YecS 36% 146.0
L-asparagine catabolism aatM lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized) 31% 90% 103.2 L-cystine transport system permease protein YecS 36% 146.0
L-aspartate catabolism aatM lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized) 31% 90% 103.2 L-cystine transport system permease protein YecS 36% 146.0
L-glutamate catabolism gltK lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized) 31% 90% 103.2 L-cystine transport system permease protein YecS 36% 146.0

Sequence Analysis Tools

View Ac3H11_4900 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

MVEFSLWDILRNLLLAARWTVSLSLIAFIGGGLVGLLLLVLRLSKVRGVDRAVGAYVQVF
QGTPLLMQLFLAYFGIALFGIKTSPWTAAAVALTLYTSAYLTEIWRGCVASIPKGQWEAA
QSLAFNFGEQLRHVVLPQALRIAVPPTVGFLVQVIKGTALASVIGFVELTKAGSMISNAT
YKPFLVYACVALLYFVLCFPVSLVAQSLERKLHGNRR

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