GapMind for catabolism of small carbon sources

 

Protein CA265_RS10595 in Pedobacter sp. GW460-11-11-14-LB5

Annotation: CA265_RS10595 dicarboxylate/amino acid:cation symporter

Length: 458 amino acids

Source: Pedo557 in FitnessBrowser

Candidate for 7 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism glt hi Uncharacterized protein (characterized, see rationale) 55% 85% 419.9 C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) 40% 287.7
L-aspartate catabolism glt hi Uncharacterized protein (characterized, see rationale) 55% 85% 419.9 C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) 40% 287.7
L-glutamate catabolism gltP hi proton/sodium-glutamate symport protein GltT (characterized) 43% 90% 312 C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) 40% 287.7
L-malate catabolism dctA lo C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized) 40% 83% 287.7 proton/sodium-glutamate symport protein GltT 43% 312.0
fumarate catabolism dctA lo C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized) 40% 83% 287.7 proton/sodium-glutamate symport protein GltT 43% 312.0
succinate catabolism dctA lo C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized) 40% 83% 287.7 proton/sodium-glutamate symport protein GltT 43% 312.0
acetate catabolism dctA lo Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized) 38% 84% 265.4 proton/sodium-glutamate symport protein GltT 43% 312.0

Sequence Analysis Tools

View CA265_RS10595 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MKKNKLTLFIFLALIAGIALGYILNVNSINVYNQNILTADAKVKSIEVRIAKSTDTTSIG
YTQLKAERKANAKIKKENEDIREKKLEYFTLLSDIFLRLIKMIVAPLVFTTLVVGVAKVG
DIKAVGRIGGKTLGWFLAMSLMSLVLGMVLVNLFEPGRHMKLSLPDQLVNTGIQKAAMSV
KDFIAHVFPKSIAESMSTNEILQIVVFSLFFGVATAAIGDLGQIVIKAFDAIAHVILKMT
GYVMNFAPLAVFGAMTAIVAKQGLNVLNTYAIFIGEFYLGLAILWAVLIFLGFLVLKKRI
FRLVNDMKEPALLAFSTASSEAAYPKTMMLLERFGCKDKIVSFVLPLGYSFNLDGSMMYM
TFASLFIAQAYGIHLGFEQQISMLLILMLTSKGIAGVPRASLVVIAGTIASFNIPEAGLA
LLIGIDPLLDMGRSATNVVGNSIATAVVSKWEGELKES

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