GapMind for catabolism of small carbon sources

 

Protein 200106 in Shewanella oneidensis MR-1

Annotation: FitnessBrowser__MR1:200106

Length: 424 amino acids

Source: MR1 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-glutamate catabolism gltP hi Na+/H+ dicarboxylate symporter (characterized, see rationale) 58% 96% 470.7 The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up 35% 277.3
L-asparagine catabolism glt hi Sodium:dicarboxylate symporter (characterized, see rationale) 47% 93% 369.8 The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up 35% 277.3
L-aspartate catabolism glt hi Sodium:dicarboxylate symporter (characterized, see rationale) 47% 93% 369.8 The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up 35% 277.3
L-malate catabolism dctA lo The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized) 35% 94% 277.3 Glutamate transporter homolog; Glt(Ph); Sodium-aspartate symporter Glt(Ph); Sodium-dependent aspartate transporter 47% 359.0
fumarate catabolism dctA lo The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized) 35% 94% 277.3 Glutamate transporter homolog; Glt(Ph); Sodium-aspartate symporter Glt(Ph); Sodium-dependent aspartate transporter 47% 359.0
succinate catabolism dctA lo The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized) 35% 94% 277.3 Glutamate transporter homolog; Glt(Ph); Sodium-aspartate symporter Glt(Ph); Sodium-dependent aspartate transporter 47% 359.0
acetate catabolism dctA lo Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized) 35% 92% 263.8 Glutamate transporter homolog; Glt(Ph); Sodium-aspartate symporter Glt(Ph); Sodium-dependent aspartate transporter 47% 359.0
L-alanine catabolism SLC1A4 lo neutral amino acid transporter B(0) (characterized) 36% 54% 189.5 Glutamate transporter homolog; Glt(Ph); Sodium-aspartate symporter Glt(Ph); Sodium-dependent aspartate transporter 47% 359.0

Sequence Analysis Tools

View 200106 at FitnessBrowser

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

Fitness BLAST: loading...

Sequence

MSVPLWLQIFVGMVLGILVGVTLGEQASYLKPIGTLFVNTIKMLIVPLVFCSLIVGVTSM
EDTAKMGRIGFKSFSFYLCTTAIAISLGLVVGYVIQPGAGVPLLQHEAVNTAKEVPSVMQ
TLIDIVPTNPVAALASGQILQVIVFAVALGIALVLIGDHGKPAIKVFESLAEAMYKLTDM
VMKLAPYGVFGLMAWVAGEYGIDMLWPLIKVIIAVYIGCIIHVLGFYSIVLRLFAKLNPL
HFFKGISNAMAVAFTTSSSAGTLPASMKCASEYLGVNKKISSFVLPLGTTINMDGTALYQ
GVTALFVAQAFGIDLTWVDYLTIILTATLASIGTAGVPGAGLVMLTLVLSTVGLPLEGVA
LIAGIDRILDMARTVVNVSGDLVATTVIAKSENELDVEHYNADMVQSAVIAEQNAANESA
ATQR

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:

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