GapMind for catabolism of small carbon sources

 

Protein GFF4197 in Pseudomonas stutzeri RCH2

Annotation: Psest_4270 TRAP transporter, DctM subunit

Length: 426 amino acids

Source: psRCH2 in FitnessBrowser

Candidate for 8 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-malate catabolism dctM hi C4-dicarboxylate TRAP transporter large permease protein DctM (characterized) 86% 100% 718.4 Sialic acid TRAP transporter large permease protein SiaM 36% 298.9
fumarate catabolism dctM hi C4-dicarboxylate TRAP transporter large permease protein DctM (characterized) 86% 100% 718.4 Sialic acid TRAP transporter large permease protein SiaM 36% 298.9
succinate catabolism dctM hi C4-dicarboxylate TRAP transporter large permease protein DctM (characterized) 86% 100% 718.4 Sialic acid TRAP transporter large permease protein SiaM 36% 298.9
2-oxoglutarate (alpha-ketoglutarate) catabolism dctM hi dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized) 50% 99% 408.7 Sialic acid TRAP transporter large permease protein SiaM 36% 298.9
D-glucuronate catabolism dctM med Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale) 42% 100% 335.5 C4-dicarboxylate TRAP transporter large permease protein DctM 86% 718.4
D-gluconate catabolism gntB med TRAP-type large permease component (characterized, see rationale) 40% 99% 330.5 C4-dicarboxylate TRAP transporter large permease protein DctM 86% 718.4
pyruvate catabolism dctM lo Alr3027 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids (characterized) 34% 97% 219.9 C4-dicarboxylate TRAP transporter large permease protein DctM 86% 718.4
L-glutamate catabolism gtrB lo GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized) 31% 97% 202.2 C4-dicarboxylate TRAP transporter large permease protein DctM 86% 718.4

Sequence Analysis Tools

View GFF4197 at FitnessBrowser

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

MTILFLFAALFVLMFIGVPVAVSLGLAGSLTIMIFSQDSVRSLAIKLFETSEHYTLLAIP
FFLLAGAFMTTGGVARRLIDFANACVGHIRGGLAIGAVLACMLFAALSGSSPATVAAVGS
IAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSVVMVVYAAATETSVGKLFMAGVVPGIL
LGGALMIAIYIIAVKKNLPALPRASFREWLSAARKAIWGLLLMVIILGGIYSGMFTPTEA
AAVAAVYSAFVALFVYKDISLRDCPKVLLESGKLSIMLMFIIANAMLFAHVLTTEQIPQA
ITAWVIEAGLQPWMFLLVVNIVLLIAGAFMEPSAIILILAPILFPIAIQLGIDPIHLGII
MVVNMEIGLITPPVGLNLFVASAVTGMPVTQVIRAVLPWLALMLSFLVIITYVPSISLAL
PNMLGM

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