GapMind for catabolism of small carbon sources

 

Protein WP_007701521.1 in Cronobacter universalis NCTC 9529

Annotation: NCBI__GCF_001277175.1:WP_007701521.1

Length: 464 amino acids

Source: GCF_001277175.1 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-cellobiose catabolism MFS-glucose hi Galactose-proton symporter; Galactose transporter (characterized) 89% 100% 830.9 Arabinose-proton symporter; Arabinose transporter 65% 587.0
D-galactose catabolism galP hi Galactose-proton symporter; Galactose transporter (characterized) 89% 100% 830.9 Glucose transporter GlcP; Glucose/H(+) symporter 38% 303.9
D-glucose catabolism MFS-glucose hi Galactose-proton symporter; Galactose transporter (characterized) 89% 100% 830.9 Arabinose-proton symporter; Arabinose transporter 65% 587.0
lactose catabolism MFS-glucose hi Galactose-proton symporter; Galactose transporter (characterized) 89% 100% 830.9 Arabinose-proton symporter; Arabinose transporter 65% 587.0
D-maltose catabolism MFS-glucose hi Galactose-proton symporter; Galactose transporter (characterized) 89% 100% 830.9 Arabinose-proton symporter; Arabinose transporter 65% 587.0
sucrose catabolism MFS-glucose hi Galactose-proton symporter; Galactose transporter (characterized) 89% 100% 830.9 Arabinose-proton symporter; Arabinose transporter 65% 587.0
trehalose catabolism MFS-glucose hi Galactose-proton symporter; Galactose transporter (characterized) 89% 100% 830.9 Arabinose-proton symporter; Arabinose transporter 65% 587.0
L-arabinose catabolism araE med Arabinose-proton symporter; Arabinose transporter (characterized) 65% 97% 587 Galactose-proton symporter; Galactose transporter 89% 830.9
D-xylose catabolism xylT med Arabinose-proton symporter; Arabinose transporter (characterized) 65% 97% 587 Galactose-proton symporter; Galactose transporter 89% 830.9
myo-inositol catabolism iolT lo Major myo-inositol transporter IolT (characterized) 37% 96% 288.1 Galactose-proton symporter; Galactose transporter 89% 830.9
D-fructose catabolism glcP lo D-fructose transporter, sugar porter family (characterized) 35% 94% 256.1 Galactose-proton symporter; Galactose transporter 89% 830.9
sucrose catabolism glcP lo D-fructose transporter, sugar porter family (characterized) 35% 94% 256.1 Galactose-proton symporter; Galactose transporter 89% 830.9
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) 34% 92% 251.5 Galactose-proton symporter; Galactose transporter 89% 830.9
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) 32% 92% 241.5 Galactose-proton symporter; Galactose transporter 89% 830.9
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) 32% 92% 241.5 Galactose-proton symporter; Galactose transporter 89% 830.9
myo-inositol catabolism HMIT lo Probable inositol transporter 2 (characterized) 40% 59% 240 Galactose-proton symporter; Galactose transporter 89% 830.9
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) 31% 89% 239.2 Galactose-proton symporter; Galactose transporter 89% 830.9
D-fructose catabolism STP6 lo sugar transport protein 6 (characterized) 32% 91% 225.7 Galactose-proton symporter; Galactose transporter 89% 830.9
sucrose catabolism STP6 lo sugar transport protein 6 (characterized) 32% 91% 225.7 Galactose-proton symporter; Galactose transporter 89% 830.9
D-galacturonate catabolism gatA lo The galacturonic acid (galacturonate) uptake porter, GatA, of 518 aas and 12 TMSs (characterized) 34% 91% 222.2 Galactose-proton symporter; Galactose transporter 89% 830.9
trehalose catabolism TRET1 lo Facilitated trehalose transporter Tret1; BmTRET1 (characterized) 31% 93% 221.1 Galactose-proton symporter; Galactose transporter 89% 830.9
D-fructose catabolism frt1 lo Fructose:H+ symporter, Frt1 (characterized) 30% 80% 186.4 Galactose-proton symporter; Galactose transporter 89% 830.9
D-glucosamine (chitosamine) catabolism SLC2A2 lo Solute carrier family 2, facilitated glucose transporter member 2; Glucose transporter type 2, liver; GLUT-2 (characterized) 31% 75% 186.4 Galactose-proton symporter; Galactose transporter 89% 830.9
sucrose catabolism frt1 lo Fructose:H+ symporter, Frt1 (characterized) 30% 80% 186.4 Galactose-proton symporter; Galactose transporter 89% 830.9

Sequence Analysis Tools

View WP_007701521.1 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

MPDNKKQGRSHKAMTFFVCFLAALAGLLFGLDIGVIAGALPFIAKDFNITPHQQEWVVSS
MMFGAAVGAVGSGWLSSRLGRKYSLMIGSVLFVIGSLCSAFAPNAEVLIISRVLLGLAVG
IASYTAPLYLSEIAPEKIRGSMISMYQLMITIGILGAYLSDTAFSYSGAWRWMLGVITIP
AILLLIGVFFLPDSPRWFAAKRRFHDAERVLLRLRDSSAEAKRELEEIRESLKVKQGGWA
LFKDNSNFRRAVFLGILLQVMQQFTGMNVIMYYAPKIFELAGYSNTTEQMWGTVIVGLTN
VLATFIAIGLVDRWGRKPTLILGFIVMAAGMGILGTMLHMGIDSPAGQYFAVAMLLMFII
GFAMSAGPLIWVLCSEIQPLKGRDFGITLSTTTNWIANMIVGATFLTMLNTLGNAPTFWV
YAGLNLFFIVLTVWLVPETKHVSLEHIERNLMQGRKLRDIGSND

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