GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_1228 in Dyella japonica UNC79MFTsu3.2

Annotation: N515DRAFT_1228 MFS transporter, SP family, galactose:H+ symporter

Length: 463 amino acids

Source: Dyella79 in FitnessBrowser

Candidate for 28 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism MFS-glucose hi Galactose-proton symporter; Galactose transporter (characterized) 67% 97% 605.9 Arabinose-proton symporter; Arabinose transporter 57% 507.3
D-galactose catabolism galP hi Galactose-proton symporter; Galactose transporter (characterized) 67% 97% 605.9 D-xylose transporter; D-xylose-proton symporter 40% 296.6
D-glucose catabolism MFS-glucose hi Galactose-proton symporter; Galactose transporter (characterized) 67% 97% 605.9 Arabinose-proton symporter; Arabinose transporter 57% 507.3
lactose catabolism MFS-glucose hi Galactose-proton symporter; Galactose transporter (characterized) 67% 97% 605.9 Arabinose-proton symporter; Arabinose transporter 57% 507.3
D-maltose catabolism MFS-glucose hi Galactose-proton symporter; Galactose transporter (characterized) 67% 97% 605.9 Arabinose-proton symporter; Arabinose transporter 57% 507.3
sucrose catabolism MFS-glucose hi Galactose-proton symporter; Galactose transporter (characterized) 67% 97% 605.9 Arabinose-proton symporter; Arabinose transporter 57% 507.3
trehalose catabolism MFS-glucose hi Galactose-proton symporter; Galactose transporter (characterized) 67% 97% 605.9 Arabinose-proton symporter; Arabinose transporter 57% 507.3
L-arabinose catabolism araE med Arabinose-proton symporter; Arabinose transporter (characterized) 57% 99% 507.3 Galactose-proton symporter; Galactose transporter 67% 605.9
D-xylose catabolism xylT med Arabinose-proton symporter; Arabinose transporter (characterized) 57% 99% 507.3 Galactose-proton symporter; Galactose transporter 67% 605.9
myo-inositol catabolism iolT lo Inositol transporter 1 (characterized) 35% 88% 283.9 Galactose-proton symporter; Galactose transporter 67% 605.9
D-fructose catabolism glcP lo D-fructose transporter, sugar porter family (characterized) 35% 98% 265 Galactose-proton symporter; Galactose transporter 67% 605.9
sucrose catabolism glcP lo D-fructose transporter, sugar porter family (characterized) 35% 98% 265 Galactose-proton symporter; Galactose transporter 67% 605.9
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) 32% 91% 250.8 Galactose-proton symporter; Galactose transporter 67% 605.9
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% 92% 247.7 Galactose-proton symporter; Galactose transporter 67% 605.9
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% 95% 245 Galactose-proton symporter; Galactose transporter 67% 605.9
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% 95% 245 Galactose-proton symporter; Galactose transporter 67% 605.9
D-fructose catabolism STP6 lo sugar transport protein 6 (characterized) 32% 93% 241.5 Galactose-proton symporter; Galactose transporter 67% 605.9
sucrose catabolism STP6 lo sugar transport protein 6 (characterized) 32% 93% 241.5 Galactose-proton symporter; Galactose transporter 67% 605.9
glycerol catabolism PLT5 lo polyol transporter 5 (characterized) 30% 91% 233.8 Galactose-proton symporter; Galactose transporter 67% 605.9
D-mannitol catabolism PLT5 lo polyol transporter 5 (characterized) 30% 91% 233.8 Galactose-proton symporter; Galactose transporter 67% 605.9
D-ribose catabolism PLT5 lo polyol transporter 5 (characterized) 30% 91% 233.8 Galactose-proton symporter; Galactose transporter 67% 605.9
xylitol catabolism PLT5 lo polyol transporter 5 (characterized) 30% 91% 233.8 Galactose-proton symporter; Galactose transporter 67% 605.9
trehalose catabolism TRET1 lo Facilitated trehalose transporter Tret1; BmTRET1 (characterized) 32% 90% 222.2 Galactose-proton symporter; Galactose transporter 67% 605.9
myo-inositol catabolism HMIT lo Probable inositol transporter 3 (characterized) 35% 59% 212.6 Galactose-proton symporter; Galactose transporter 67% 605.9
D-galacturonate catabolism gatA lo The galacturonic acid (galacturonate) uptake porter, GatA, of 518 aas and 12 TMSs (characterized) 31% 90% 200.3 Galactose-proton symporter; Galactose transporter 67% 605.9
D-fructose catabolism frt1 lo Fructose:H+ symporter, Frt1 (characterized) 30% 79% 188.7 Galactose-proton symporter; Galactose transporter 67% 605.9
sucrose catabolism frt1 lo Fructose:H+ symporter, Frt1 (characterized) 30% 79% 188.7 Galactose-proton symporter; Galactose transporter 67% 605.9
glycerol catabolism stl1 lo glycerol permease (characterized) 30% 85% 183.3 Galactose-proton symporter; Galactose transporter 67% 605.9

Sequence Analysis Tools

View N515DRAFT_1228 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

MNSQAIATPTAHVKGTVIYTCVLAALAGLMFGLDIGVISGASQFIKAEFAISDHTIEWIV
SSMMFGAAVGALGAGWLSSHLGRKRSLILGAILFVIGSLLCGLAWSPETLIAARVILGLA
IGIATFTAPLYLAEVAPEHIRGAMISTYQLMITIGILVAFLSDTALSYHGAWRWMLGVIA
IPGALFLLGVLGLPDSPRWLMMRGRRDEAIDVLRRLRGDEVVVAREAADIEEQLKTPQRG
WDLFAENPNFRRSVFLGALLQIMQQFTGMNVVMYYAPRIFQEMGYDTAAQMWFTALVGLT
NVLATFIAIALIDRWGRKPILYTGFAVMAVGLGVVGALMNGGINGQTEQYTCVAMLLFFI
VGFAMSAGPLVWTLCSEIQPLKGRDFGIGVSTFTNWITNMVVGFTFLSLLNTIGNASTFW
LYAALNAVFIVLTFWLVPETKGVTLEQIERNLMAGKRLRDIGR

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