GapMind for catabolism of small carbon sources

 

Protein 16922 in Escherichia coli BW25113

Annotation: FitnessBrowser__Keio:16922

Length: 472 amino acids

Source: Keio in FitnessBrowser

Candidate for 21 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) 100% 100% 917.5 Galactose-proton symporter; Galactose transporter 65% 597.0
D-galactose catabolism galP hi Arabinose-proton symporter; Arabinose transporter (characterized) 100% 100% 917.5 D-xylose transporter; D-xylose-proton symporter 39% 285.0
D-xylose catabolism xylT hi Arabinose-proton symporter; Arabinose transporter (characterized) 100% 100% 917.5 Galactose-proton symporter; Galactose transporter 65% 597.0
D-cellobiose catabolism MFS-glucose med Galactose-proton symporter; Galactose transporter (characterized) 65% 98% 597 Arabinose-proton symporter; Arabinose transporter 100% 917.5
D-glucose catabolism MFS-glucose med Galactose-proton symporter; Galactose transporter (characterized) 65% 98% 597 Arabinose-proton symporter; Arabinose transporter 100% 917.5
lactose catabolism MFS-glucose med Galactose-proton symporter; Galactose transporter (characterized) 65% 98% 597 Arabinose-proton symporter; Arabinose transporter 100% 917.5
D-maltose catabolism MFS-glucose med Galactose-proton symporter; Galactose transporter (characterized) 65% 98% 597 Arabinose-proton symporter; Arabinose transporter 100% 917.5
sucrose catabolism MFS-glucose med Galactose-proton symporter; Galactose transporter (characterized) 65% 98% 597 Arabinose-proton symporter; Arabinose transporter 100% 917.5
trehalose catabolism MFS-glucose med Galactose-proton symporter; Galactose transporter (characterized) 65% 98% 597 Arabinose-proton symporter; Arabinose transporter 100% 917.5
myo-inositol catabolism iolT lo Inositol transporter 1 (characterized) 37% 90% 279.6 Arabinose-proton symporter; Arabinose transporter 100% 917.5
myo-inositol catabolism HMIT lo Probable inositol transporter 2 (characterized) 38% 57% 227.3 Arabinose-proton symporter; Arabinose transporter 100% 917.5
trehalose catabolism TRET1 lo Facilitated trehalose transporter Tret1; AmTRET1 (characterized) 30% 93% 223.8 Arabinose-proton symporter; Arabinose transporter 100% 917.5
D-sorbitol (glucitol) catabolism SOT lo Sorbitol (glucitol):H+ co-transporter, SOT2 (Km for sorbitol of 0.81 mM) of 491 aas and 12 TMSs (Gao et al. 2003). SOT2 of Prunus cerasus is mainly expressed only early in fruit development and not in leaves (characterized) 30% 92% 223 Arabinose-proton symporter; Arabinose transporter 100% 917.5
D-fructose catabolism glcP lo Glucose/fructose:H+ symporter, GlcP (characterized) 33% 96% 221.9 Arabinose-proton symporter; Arabinose transporter 100% 917.5
sucrose catabolism glcP lo Glucose/fructose:H+ symporter, GlcP (characterized) 33% 96% 221.9 Arabinose-proton symporter; Arabinose transporter 100% 917.5
D-fructose catabolism Slc2a5 lo The fructose/xylose:H+ symporter, PMT1 (polyol monosaccharide transporter-1). Also transports other substrates at lower rates. PMT2 is largely of the same sequence and function. Both are present in pollen and young xylem cells (Klepek et al., 2005). A similar ortholog has been identifed in pollen grains of Petunia hybrida (characterized) 31% 92% 221.1 Arabinose-proton symporter; Arabinose transporter 100% 917.5
sucrose catabolism Slc2a5 lo The fructose/xylose:H+ symporter, PMT1 (polyol monosaccharide transporter-1). Also transports other substrates at lower rates. PMT2 is largely of the same sequence and function. Both are present in pollen and young xylem cells (Klepek et al., 2005). A similar ortholog has been identifed in pollen grains of Petunia hybrida (characterized) 31% 92% 221.1 Arabinose-proton symporter; Arabinose transporter 100% 917.5
xylitol catabolism PLT5 lo Polyol (xylitol):H+ symporter, PLT4 (characterized) 31% 88% 217.6 Arabinose-proton symporter; Arabinose transporter 100% 917.5
D-fructose catabolism frt1 lo Fructose:H+ symporter, Frt1 (characterized) 31% 82% 193.4 Arabinose-proton symporter; Arabinose transporter 100% 917.5
sucrose catabolism frt1 lo Fructose:H+ symporter, Frt1 (characterized) 31% 82% 193.4 Arabinose-proton symporter; Arabinose transporter 100% 917.5
glycerol catabolism stl1 lo glycerol permease (characterized) 30% 85% 183 Arabinose-proton symporter; Arabinose transporter 100% 917.5

Sequence Analysis Tools

View 16922 at FitnessBrowser

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MVTINTESALTPRSLRDTRRMNMFVSVAAAVAGLLFGLDIGVIAGALPFITDHFVLTSRL
QEWVVSSMMLGAAIGALFNGWLSFRLGRKYSLMAGAILFVLGSIGSAFATSVEMLIAARV
VLGIAVGIASYTAPLYLSEMASENVRGKMISMYQLMVTLGIVLAFLSDTAFSYSGNWRAM
LGVLALPAVLLIILVVFLPNSPRWLAEKGRHIEAEEVLRMLRDTSEKAREELNEIRESLK
LKQGGWALFKINRNVRRAVFLGMLLQAMQQFTGMNIIMYYAPRIFKMAGFTTTEQQMIAT
LVVGLTFMFATFIAVFTVDKAGRKPALKIGFSVMALGTLVLGYCLMQFDNGTASSGLSWL
SVGMTMMCIAGYAMSAAPVVWILCSEIQPLKCRDFGITCSTTTNWVSNMIIGATFLTLLD
SIGAAGTFWLYTALNIAFVGITFWLIPETKNVTLEHIERKLMAGEKLRNIGV

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