GapMind for catabolism of small carbon sources

 

Protein Ga0059261_1777 in Sphingomonas koreensis DSMZ 15582

Annotation: Ga0059261_1777 MFS transporter, sugar porter (SP) family

Length: 458 amino acids

Source: Korea 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
D-fructose catabolism glcP hi D-fructose transporter, sugar porter family (characterized) 100% 100% 885.9 D-xylose-proton symporter 36% 303.5
sucrose catabolism glcP hi D-fructose transporter, sugar porter family (characterized) 100% 100% 885.9 D-xylose-proton symporter 36% 303.5
D-xylose catabolism xylT lo D-xylose-proton symporter (characterized) 36% 93% 303.5 D-fructose transporter, sugar porter family 100% 885.9
D-cellobiose catabolism MFS-glucose lo The glucose uptake porter, GluP (characterized) 37% 98% 285.8 D-fructose transporter, sugar porter family 100% 885.9
D-glucose catabolism MFS-glucose lo The glucose uptake porter, GluP (characterized) 37% 98% 285.8 D-fructose transporter, sugar porter family 100% 885.9
lactose catabolism MFS-glucose lo The glucose uptake porter, GluP (characterized) 37% 98% 285.8 D-fructose transporter, sugar porter family 100% 885.9
D-maltose catabolism MFS-glucose lo The glucose uptake porter, GluP (characterized) 37% 98% 285.8 D-fructose transporter, sugar porter family 100% 885.9
sucrose catabolism MFS-glucose lo The glucose uptake porter, GluP (characterized) 37% 98% 285.8 D-fructose transporter, sugar porter family 100% 885.9
trehalose catabolism MFS-glucose lo The glucose uptake porter, GluP (characterized) 37% 98% 285.8 D-fructose transporter, sugar porter family 100% 885.9
L-arabinose catabolism araE lo Arabinose-proton symporter; Arabinose transporter (characterized) 35% 94% 282 D-fructose transporter, sugar porter family 100% 885.9
D-galactose catabolism galP lo Arabinose-proton symporter; Arabinose transporter (characterized) 35% 94% 282 D-fructose transporter, sugar porter family 100% 885.9
myo-inositol catabolism iolT lo Major myo-inositol transporter, IolT1, of 456 aas (characterized) 33% 95% 261.5 D-fructose transporter, sugar porter family 100% 885.9
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) 33% 92% 237.3 D-fructose transporter, sugar porter family 100% 885.9
glycerol catabolism PLT5 lo polyol transporter 5 (characterized) 33% 84% 226.5 D-fructose transporter, sugar porter family 100% 885.9
D-mannitol catabolism PLT5 lo polyol transporter 5 (characterized) 33% 84% 226.5 D-fructose transporter, sugar porter family 100% 885.9
D-ribose catabolism PLT5 lo polyol transporter 5 (characterized) 33% 84% 226.5 D-fructose transporter, sugar porter family 100% 885.9
xylitol catabolism PLT5 lo polyol transporter 5 (characterized) 33% 84% 226.5 D-fructose transporter, sugar porter family 100% 885.9
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) 30% 90% 209.5 D-fructose transporter, sugar porter family 100% 885.9
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) 30% 90% 209.5 D-fructose transporter, sugar porter family 100% 885.9
trehalose catabolism TRET1 lo Facilitated trehalose transporter Tret1; PvTret1 (characterized) 30% 88% 193.7 D-fructose transporter, sugar porter family 100% 885.9
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% 57% 183.3 D-fructose transporter, sugar porter family 100% 885.9

Sequence Analysis Tools

View Ga0059261_1777 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

MHSVSASFAGAPDEEARATVAIILSAAGAALGGLLFGFDTAVISGATQALQLQFGLTDAM
LGFTVASALIGTVLGSLIAGAPADRFGRKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRF
MGGLAIGAASVVTPIYIAEVSPARFRGRLVAMNQLNIVLGILIAFLSNYIIAGLVQYDVA
WRWMFGIVAVPSTIFLLVTLLLPESPRWLAIHGQADRARDVMQRLGFADPRAELARIELA
EAREEAAGKPRLFQRSHFTPVACAIAIAMFNQLSGINALLYYAPRIFELAGAGADSALLQ
SIAVGGTNLVFTVAALFLIDRFGRRPLLFVGSVICAATLLLVGWQLESAKPDGTLILFGL
LGFIAAFAMSQGAVIWVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVGGW
VFAFFGAMMLLQLLWTWKFMPETNGIALEDMNLGSARA

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