GapMind for catabolism of small carbon sources

 

Protein WP_061535122.1 in Collimonas arenae Ter10

Annotation: NCBI__GCF_001584165.1:WP_061535122.1

Length: 367 amino acids

Source: GCF_001584165.1 in NCBI

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism aapM hi 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) 46% 98% 340.1 ABC transporter for D-Alanine, permease component 1 44% 299.7
L-aspartate catabolism aapM hi 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) 46% 98% 340.1 ABC transporter for D-Alanine, permease component 1 44% 299.7
L-glutamate catabolism aapM hi 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) 46% 98% 340.1 ABC transporter for D-Alanine, permease component 1 44% 299.7
L-histidine catabolism aapM hi 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) 46% 98% 340.1 ABC transporter for D-Alanine, permease component 1 44% 299.7
L-leucine catabolism aapM hi 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) 46% 98% 340.1 ABC transporter for D-Alanine, permease component 1 44% 299.7
L-proline catabolism aapM hi 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) 46% 98% 340.1 ABC transporter for D-Alanine, permease component 1 44% 299.7
D-alanine catabolism Pf6N2E2_5404 med ABC transporter for D-Alanine, permease component 1 (characterized) 44% 98% 299.7 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) 46% 340.1
L-asparagine catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 45% 69% 229.2 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) 46% 340.1
L-aspartate catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 45% 69% 229.2 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) 46% 340.1
L-asparagine catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 40% 68% 211.8 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) 46% 340.1
L-aspartate catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 40% 68% 211.8 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) 46% 340.1
L-glutamate catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 40% 68% 211.8 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) 46% 340.1

Sequence Analysis Tools

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MKSSCAASSVKPRTSSLSKAWLWCRKNLFGGVFNTVVTCVIVVLALSVLPSAFNWAIRNA
VFAPDSAACRAAAEHGACWGVIAAKYRIMLFGRYPFPEQWRPLCVTIALVFLLVLSCWRR
MWRAGLLVVWLVTLLSAFFMLRGGLFGLDPVETERWGGLPLTMLLSMVSLALSFPLAVMI
ALGRRSRMPVIKALCVLFVEIVRGVPLISVLFMASFMFPFLLPQGVSIDVLVRVLVGLTL
FTGAYLAEAVRAGLQAIPKGQVEAAHAIGLSTWQTNRKIVLPQALRLVVPSMMNTLIGTF
KDTSLVTIVGLFELTGALQLALADAEWRRFYIEGQLFMAAIYFVFCFSMSRYSRWIERHL
NRGTRRQ

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