GapMind for catabolism of small carbon sources

 

Protein BWI76_RS23425 in Klebsiella michiganensis M5al

Annotation: BWI76_RS23425 MFS transporter

Length: 472 amino acids

Source: Koxy in FitnessBrowser

Candidate for 15 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arabinose catabolism araE hi Arabinose-proton symporter; Arabinose transporter (characterized) 93% 100% 875.9 Galactose-proton symporter; Galactose transporter 65% 594.7
D-galactose catabolism galP hi Arabinose-proton symporter; Arabinose transporter (characterized) 93% 100% 875.9 Inositol transporter 1 37% 283.9
D-xylose catabolism xylT hi Arabinose-proton symporter; Arabinose transporter (characterized) 93% 100% 875.9 Galactose-proton symporter; Galactose transporter 65% 594.7
D-cellobiose catabolism MFS-glucose med Galactose-proton symporter; Galactose transporter (characterized) 65% 98% 594.7 Arabinose-proton symporter; Arabinose transporter 93% 875.9
D-glucose catabolism MFS-glucose med Galactose-proton symporter; Galactose transporter (characterized) 65% 98% 594.7 Arabinose-proton symporter; Arabinose transporter 93% 875.9
lactose catabolism MFS-glucose med Galactose-proton symporter; Galactose transporter (characterized) 65% 98% 594.7 Arabinose-proton symporter; Arabinose transporter 93% 875.9
D-maltose catabolism MFS-glucose med Galactose-proton symporter; Galactose transporter (characterized) 65% 98% 594.7 Arabinose-proton symporter; Arabinose transporter 93% 875.9
sucrose catabolism MFS-glucose med Galactose-proton symporter; Galactose transporter (characterized) 65% 98% 594.7 Arabinose-proton symporter; Arabinose transporter 93% 875.9
trehalose catabolism MFS-glucose med Galactose-proton symporter; Galactose transporter (characterized) 65% 98% 594.7 Arabinose-proton symporter; Arabinose transporter 93% 875.9
D-mannose catabolism STP6 lo The high affinity sugar:H+ symporter (sugar uptake) porter of 514 aas and 12 TMSs, STP10. It transports glucose, galactose and mannose, and is therefore a hexose transporter (Rottmann et al. 2016). The 2.4 (characterized) 30% 89% 225.7 Arabinose-proton symporter; Arabinose transporter 93% 875.9
trehalose catabolism TRET1 lo Facilitated trehalose transporter Tret1-2 homolog; DmTret1-2 (characterized) 31% 98% 223.8 Arabinose-proton symporter; Arabinose transporter 93% 875.9
myo-inositol catabolism HMIT lo Probable inositol transporter 2 (characterized) 36% 57% 220.3 Arabinose-proton symporter; Arabinose transporter 93% 875.9
D-fructose catabolism Slc2a5 lo sugar transport protein 13 (characterized) 31% 88% 204.5 Arabinose-proton symporter; Arabinose transporter 93% 875.9
sucrose catabolism Slc2a5 lo sugar transport protein 13 (characterized) 31% 88% 204.5 Arabinose-proton symporter; Arabinose transporter 93% 875.9
D-galacturonate catabolism gatA lo The galacturonic acid (galacturonate) uptake porter, GatA, of 518 aas and 12 TMSs (characterized) 31% 87% 200.7 Arabinose-proton symporter; Arabinose transporter 93% 875.9

Sequence Analysis Tools

View BWI76_RS23425 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

MTSISHDSTTMPRTQRDTRRMNQFVSVAAAVAGLLFGLDIGVIAGALPFITDHFVLSSRL
QEWVVSSMMLGAAIGALFNGWLSFRLGRKYSLMVGAVLFVAGSVGSAFAGSVEMLLAARI
VLGVAVGIASYTAPLYLSEMASENVRGKMISMYQLMVTLGIVMAFLSDTAFSYSGNWRAM
LGVLALPALVLIILVIFLPNSPRWLAEKGRHVEAEEVLRMLRDTSEKARDELNEIRESLK
LKQGGWALFKVNRNVRRAVFLGMLLQAMQQFTGMNIIMYYAPRIFKMAGFTTTEQQMVAT
LVVGLTFMFATFIAVFTVDKAGRKPALKIGFSVMAIGTLVLGYCLMQFDNGTASSGLSWL
SVGMTMMCIAGYAMSAAPVVWILCSEIQPLKCRDFGITCSTTTNWVSNMIIGATFLTLLD
AIGAAGTFWLYTALNVAFIGVTFWLIPETKNVTLEHIERKLMSGEKLRNIGN

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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