GapMind for catabolism of small carbon sources

 

Protein 353923 in Bacteroides thetaiotaomicron VPI-5482

Annotation: BT4397 xylose/H+ symporter (NCBI ptt file)

Length: 460 amino acids

Source: Btheta in FitnessBrowser

Candidate for 22 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-xylose catabolism xylT med D-xylose-proton symporter (characterized) 39% 96% 332.4 D-fructose transporter, sugar porter family 36% 288.5
L-arabinose catabolism araE lo Arabinose-proton symporter; Arabinose transporter (characterized) 37% 97% 327.4 D-xylose-proton symporter 39% 332.4
D-galactose catabolism galP lo Arabinose-proton symporter; Arabinose transporter (characterized) 37% 97% 327.4 D-xylose-proton symporter 39% 332.4
D-fructose catabolism glcP lo D-fructose transporter, sugar porter family (characterized) 36% 93% 288.5 D-xylose-proton symporter 39% 332.4
sucrose catabolism glcP lo D-fructose transporter, sugar porter family (characterized) 36% 93% 288.5 D-xylose-proton symporter 39% 332.4
D-cellobiose catabolism MFS-glucose lo The glucose uptake porter, GluP (characterized) 37% 95% 285.8 D-xylose-proton symporter 39% 332.4
D-glucose catabolism MFS-glucose lo The glucose uptake porter, GluP (characterized) 37% 95% 285.8 D-xylose-proton symporter 39% 332.4
lactose catabolism MFS-glucose lo The glucose uptake porter, GluP (characterized) 37% 95% 285.8 D-xylose-proton symporter 39% 332.4
D-maltose catabolism MFS-glucose lo The glucose uptake porter, GluP (characterized) 37% 95% 285.8 D-xylose-proton symporter 39% 332.4
sucrose catabolism MFS-glucose lo The glucose uptake porter, GluP (characterized) 37% 95% 285.8 D-xylose-proton symporter 39% 332.4
trehalose catabolism MFS-glucose lo The glucose uptake porter, GluP (characterized) 37% 95% 285.8 D-xylose-proton symporter 39% 332.4
myo-inositol catabolism iolT lo Major myo-inositol transporter IolT (characterized) 37% 95% 258.8 D-xylose-proton symporter 39% 332.4
D-sorbitol (glucitol) catabolism SOT lo Sorbitol (D-Glucitol):H+ co-transporter, SOT1 (Km for sorbitol of 0.64 mM) of 509 aas and 12 TMSs (Gao et al. 2003). SOT1 of P. cerasus is expressed throughout fruit development, but especially when growth and sorbitol accumulation rates are highest. In leaves, PcSOT1 expression is highest in young, expanding tissues, but substantially less in mature leaves (characterized) 30% 92% 211.8 D-xylose-proton symporter 39% 332.4
xylitol catabolism PLT5 lo Polyol (xylitol):H+ symporter, PLT4 (characterized) 31% 90% 209.1 D-xylose-proton symporter 39% 332.4
D-galactose catabolism gal2 lo galactose transporter (characterized) 30% 80% 199.1 D-xylose-proton symporter 39% 332.4
D-xylose catabolism gal2 lo galactose transporter (characterized) 30% 80% 199.1 D-xylose-proton symporter 39% 332.4
trehalose catabolism TRET1 lo Facilitated trehalose transporter Tret1; BmTRET1 (characterized) 31% 77% 198.4 D-xylose-proton symporter 39% 332.4
D-fructose catabolism Slc2a5 lo sugar transport protein 13 (characterized) 30% 88% 189.9 D-xylose-proton symporter 39% 332.4
sucrose catabolism Slc2a5 lo sugar transport protein 13 (characterized) 30% 88% 189.9 D-xylose-proton symporter 39% 332.4
D-galacturonate catabolism gatA lo The galacturonic acid (galacturonate) uptake porter, GatA, of 518 aas and 12 TMSs (characterized) 30% 91% 180.6 D-xylose-proton symporter 39% 332.4
D-gluconate catabolism ght3 lo high-affinity gluconate transporter ght3 (characterized) 31% 84% 179.5 D-xylose-proton symporter 39% 332.4
myo-inositol catabolism HMIT lo Proton myo-inositol cotransporter; H(+)-myo-inositol cotransporter; Hmit; H(+)-myo-inositol symporter; Solute carrier family 2 member 13 (characterized) 34% 52% 176.4 D-xylose-proton symporter 39% 332.4

Sequence Analysis Tools

View 353923 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

MKSYNKKFVYSICLVSAMGGLLFGYDWVVIGGAKPFYELYFGIADSPTMQGLAMSVALLG
CLIGAMVAGMMADRYGRKPLLLISAFIFLSSAYATGAFSVFSWFLAARFLGGIGIGIASG
LSPMYIAEVAPTSIRGKLVSLNQLTIVLGILGAQIANWLIAEPIPADFTPADICASWNGQ
MGWRWMFWGAAFPAAVFLLLACFIPESPRWLAMKGKREKAWSVLSRIGGNRYAEQELQMV
EQTSASKSEGGLKLLFSRPFRKVLVLGVIVAVFQQWCGTNVIFNYAQEIFQSAGYSLGDV
LFNIVVTGVANVIFTFVAIYTVERLGRRALMLLGAGGLAGIYLVLGTCYFFQVSGFFMVV
LVVLAIACYAMSLGPITWVLLAEIFPNRVRGVAMATCTFALWVGSFTLTYTFPLLNTALG
SYGTFWIYSAICVFGFLFFLRALPETKGKSLETLEKDLIK

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