GapMind for catabolism of small carbon sources

 

Protein WP_054254746.1 in Acidovorax caeni R-24608

Annotation: NCBI__GCF_001298675.1:WP_054254746.1

Length: 217 amino acids

Source: GCF_001298675.1 in NCBI

Candidate for 34 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-glutamate catabolism gltK med 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) 41% 98% 147.1 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
L-asparagine catabolism aatM lo PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized) 40% 99% 148.3 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
L-aspartate catabolism aatM lo PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized) 40% 99% 148.3 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
L-histidine catabolism Ac3H11_2554 lo ABC transporter for L-Histidine, permease component 1 (characterized) 35% 89% 136.7 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
L-lysine catabolism hisQ lo ABC transporter for L-Lysine, permease component 1 (characterized) 38% 91% 134 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
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) 39% 91% 132.9 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
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) 39% 91% 132.9 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
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) 39% 91% 132.9 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
D-glucosamine (chitosamine) catabolism AO353_21715 lo ABC transporter for D-Glucosamine, permease component 2 (characterized) 36% 93% 124.8 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
L-asparagine catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 32% 80% 123.6 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
L-aspartate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 32% 80% 123.6 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
L-glutamate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 32% 80% 123.6 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
L-arginine catabolism artQ lo Histidine transport system permease protein HisQ (characterized) 35% 96% 120.9 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
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) 37% 92% 120.9 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
L-histidine catabolism hisQ lo Histidine transport system permease protein HisQ (characterized) 35% 96% 120.9 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
L-histidine catabolism aapM lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized) 35% 53% 117.9 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
L-citrulline catabolism AO353_03045 lo ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized) 34% 92% 117.1 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
L-citrulline catabolism PS417_17600 lo 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) 34% 95% 114.4 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
L-asparagine catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 36% 54% 112.1 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
L-aspartate catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 36% 54% 112.1 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
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% 53% 109.8 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
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% 53% 109.8 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
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% 53% 109.8 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
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% 53% 109.8 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
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% 53% 109.8 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
D-alanine catabolism Pf6N2E2_5404 lo ABC transporter for D-Alanine, permease component 1 (characterized) 33% 55% 107.8 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
L-citrulline catabolism AO353_03050 lo ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized) 32% 92% 107.5 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
L-histidine catabolism BPHYT_RS24010 lo Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale) 33% 88% 106.7 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
L-histidine catabolism BPHYT_RS24005 lo Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale) 32% 93% 104 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
L-glutamate catabolism gluC lo GluC aka CGL1952, component of Glutamate porter (characterized) 31% 96% 100.1 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
L-glutamate catabolism gluD lo GluD aka CGL1953, component of Glutamate porter (characterized) 30% 73% 92 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
L-asparagine catabolism peb1D lo Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) 31% 92% 90.9 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
L-aspartate catabolism peb1D lo Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) 31% 92% 90.9 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3
L-histidine catabolism aapQ lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized) 30% 52% 85.9 BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter 39% 153.3

Sequence Analysis Tools

View WP_054254746.1 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

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Sequence

MDYALSLLGPLGQGALVTLKLFVITLVLAVPLGLVLALARLSRLKLLSAGVNGYIWLMRG
TPLMLQMLFIYFALPFVPVIGVRLPDFPAAVAAFALNYAAYFAEIFRAGIQSVDRGQYEA
AKVLGMNYGQTMRRVVLPQMVRNILPPMSNETITLVKDTSLIYVLALNDLLRAARGIVQR
DFTTTPFIVAAAFYLVMTLVLTWAFQRLEQRYAKFDQ

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