GapMind for catabolism of small carbon sources

 

Protein WP_091374691.1 in Mucilaginibacter mallensis MP1X4

Annotation: NCBI__GCF_900105165.1:WP_091374691.1

Length: 445 amino acids

Source: GCF_900105165.1 in NCBI

Candidate for 24 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-fructose catabolism glcP hi D-fructose transporter, sugar porter family (characterized) 51% 93% 414.8 D-xylose-proton symporter 36% 295.4
sucrose catabolism glcP hi D-fructose transporter, sugar porter family (characterized) 51% 93% 414.8 D-xylose-proton symporter 36% 295.4
D-xylose catabolism xylT lo D-xylose-proton symporter (characterized) 36% 95% 295 D-fructose transporter, sugar porter family 51% 414.8
L-arabinose catabolism araE lo Arabinose-proton symporter; Arabinose transporter (characterized) 38% 96% 294.7 D-fructose transporter, sugar porter family 51% 414.8
D-galactose catabolism galP lo Arabinose-proton symporter; Arabinose transporter (characterized) 38% 96% 294.7 D-fructose transporter, sugar porter family 51% 414.8
D-cellobiose catabolism MFS-glucose lo The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) (characterized) 37% 85% 261.9 D-fructose transporter, sugar porter family 51% 414.8
D-glucose catabolism MFS-glucose lo The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) (characterized) 37% 85% 261.9 D-fructose transporter, sugar porter family 51% 414.8
lactose catabolism MFS-glucose lo The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) (characterized) 37% 85% 261.9 D-fructose transporter, sugar porter family 51% 414.8
D-maltose catabolism MFS-glucose lo The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) (characterized) 37% 85% 261.9 D-fructose transporter, sugar porter family 51% 414.8
sucrose catabolism MFS-glucose lo The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) (characterized) 37% 85% 261.9 D-fructose transporter, sugar porter family 51% 414.8
trehalose catabolism MFS-glucose lo The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) (characterized) 37% 85% 261.9 D-fructose transporter, sugar porter family 51% 414.8
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) 33% 90% 250 D-fructose transporter, sugar porter family 51% 414.8
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) 33% 91% 237.7 D-fructose transporter, sugar porter family 51% 414.8
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) 33% 91% 237.7 D-fructose transporter, sugar porter family 51% 414.8
glycerol catabolism PLT5 lo polyol transporter 5 (characterized) 30% 86% 230.7 D-fructose transporter, sugar porter family 51% 414.8
D-mannitol catabolism PLT5 lo polyol transporter 5 (characterized) 30% 86% 230.7 D-fructose transporter, sugar porter family 51% 414.8
myo-inositol catabolism iolT lo polyol transporter 5 (characterized) 30% 86% 230.7 D-fructose transporter, sugar porter family 51% 414.8
D-ribose catabolism PLT5 lo polyol transporter 5 (characterized) 30% 86% 230.7 D-fructose transporter, sugar porter family 51% 414.8
xylitol catabolism PLT5 lo polyol transporter 5 (characterized) 30% 86% 230.7 D-fructose transporter, sugar porter family 51% 414.8
D-fructose catabolism STP6 lo sugar transport protein 6 (characterized) 30% 91% 207.6 D-fructose transporter, sugar porter family 51% 414.8
D-mannose catabolism STP6 lo sugar transport protein 6 (characterized) 30% 91% 207.6 D-fructose transporter, sugar porter family 51% 414.8
sucrose catabolism STP6 lo sugar transport protein 6 (characterized) 30% 91% 207.6 D-fructose transporter, sugar porter family 51% 414.8
glycerol catabolism stl1 lo glycerol permease (characterized) 31% 83% 181.8 D-fructose transporter, sugar porter family 51% 414.8
myo-inositol catabolism HMIT lo Probable inositol transporter 3 (characterized) 32% 58% 174.9 D-fructose transporter, sugar porter family 51% 414.8

Sequence Analysis Tools

View WP_091374691.1 at NCBI

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

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Sequence

MRKHSVMAWSMVVALGGFLFGFDTAVISGAEKSIQQFWHLSAFEHGLTISIALIGTVIGS
LLGSRPSDRFGRKNTLYFVAIAYLLSSLGTALADSWSIFLVFRFLGGLGVGASSVTAPIY
ISEVSPADNRGKLVGLFQFNVVLGILVSYLSNYLISQGGDNSWRWMLGVQAVPAFIFLCL
IYLIPESPRWLILKKGDTKRALEILRIINPLNCEQELVSIQKSGTDDQGNKHAKESLFSG
KYKTPIILVVLFAFFNQVSGINAIIYYAPRIFEMAGLGPHSSLLSTVGIGMINFIFTLLG
INIIDKVGRRVLMLVGSVGLIASLFAVAFTFYSGHLSGFAIPVYMMVFIAFFAFSQGAVI
WVFISEIFPNQVRAKGQTLGSSTHWIMAAIIAFGFPSVAESLGGAPTFFFFGFMMMLQLI
FVWFFMPETKGTSLEQIDAKIAVLH

This GapMind analysis is from Sep 24 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