GapMind for catabolism of small carbon sources

 

Protein 207828 in Desulfovibrio vulgaris Hildenborough

Annotation: DVU2341 amino acid ABC transproter, permease protein, His/Glu/Gln/Arg/opine family

Length: 233 amino acids

Source: 882 in MicrobesOnline

Candidate for 18 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism aatQ med PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 40% 94% 171.8 Basic amino acid uptake transporter, BgtAB 40% 152.9
L-aspartate catabolism aatQ med PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 40% 94% 171.8 Basic amino acid uptake transporter, BgtAB 40% 152.9
L-glutamate catabolism gltJ med PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 40% 94% 171.8 Basic amino acid uptake transporter, BgtAB 40% 152.9
L-asparagine catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 37% 73% 141 PP1070, component of Acidic amino acid uptake porter, AatJMQP 40% 171.8
L-aspartate catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 37% 73% 141 PP1070, component of Acidic amino acid uptake porter, AatJMQP 40% 171.8
L-asparagine catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 32% 98% 129 PP1070, component of Acidic amino acid uptake porter, AatJMQP 40% 171.8
L-aspartate catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 32% 98% 129 PP1070, component of Acidic amino acid uptake porter, AatJMQP 40% 171.8
L-glutamate catabolism gltK lo Glutamate/aspartate import permease protein GltK (characterized) 32% 98% 129 PP1070, component of Acidic amino acid uptake porter, AatJMQP 40% 171.8
L-asparagine catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 31% 84% 120.2 PP1070, component of Acidic amino acid uptake porter, AatJMQP 40% 171.8
L-aspartate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 31% 84% 120.2 PP1070, component of Acidic amino acid uptake porter, AatJMQP 40% 171.8
L-glutamate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 31% 84% 120.2 PP1070, component of Acidic amino acid uptake porter, AatJMQP 40% 171.8
D-alanine catabolism Pf6N2E2_5403 lo ABC transporter for D-Alanine, permease component 2 (characterized) 38% 53% 106.7 PP1070, component of Acidic amino acid uptake porter, AatJMQP 40% 171.8
L-asparagine catabolism aapQ lo AapQ, 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) 34% 50% 100.9 PP1070, component of Acidic amino acid uptake porter, AatJMQP 40% 171.8
L-aspartate catabolism aapQ lo AapQ, 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) 34% 50% 100.9 PP1070, component of Acidic amino acid uptake porter, AatJMQP 40% 171.8
L-glutamate catabolism aapQ lo AapQ, 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) 34% 50% 100.9 PP1070, component of Acidic amino acid uptake porter, AatJMQP 40% 171.8
L-histidine catabolism aapQ lo AapQ, 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) 34% 50% 100.9 PP1070, component of Acidic amino acid uptake porter, AatJMQP 40% 171.8
L-leucine catabolism aapQ lo AapQ, 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) 34% 50% 100.9 PP1070, component of Acidic amino acid uptake porter, AatJMQP 40% 171.8
L-proline catabolism aapQ lo AapQ, 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) 34% 50% 100.9 PP1070, component of Acidic amino acid uptake porter, AatJMQP 40% 171.8

Sequence Analysis Tools

View 207828 at MicrobesOnline

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

MQYTFDWNLVLSGERLDWIVQGVITTCQLSGLSLVLAMLLGTLIAVMRLSGVRPFVWFSV
AFTEFFRNTPLLVQIFFWYFGSDAVLPDAVNQWLYKQNFEFAAGVISLTVYTAAFIAEEI
RSGIFSIPRTQLEASRACGLSFMQAMSYVVLPQAFRIIVPPLISQALNLFKNSSLCMTIG
VMELTYMARQIESYTFHGFEAFTVSTLIYLCISLMVSLLINLYNTHFLRTIKY

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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