GapMind for catabolism of small carbon sources

 

Protein WP_007703466.1 in Cronobacter universalis NCTC 9529

Annotation: NCBI__GCF_001277175.1:WP_007703466.1

Length: 472 amino acids

Source: GCF_001277175.1 in NCBI

Candidate for 18 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) 85% 99% 797.3 Galactose-proton symporter; Galactose transporter 64% 595.5
D-galactose catabolism galP hi Arabinose-proton symporter; Arabinose transporter (characterized) 85% 99% 797.3 D-xylose transporter; D-xylose-proton symporter 40% 287.0
D-xylose catabolism xylT hi Arabinose-proton symporter; Arabinose transporter (characterized) 85% 99% 797.3 Galactose-proton symporter; Galactose transporter 64% 595.5
D-cellobiose catabolism MFS-glucose med Galactose-proton symporter; Galactose transporter (characterized) 64% 99% 595.5 Arabinose-proton symporter; Arabinose transporter 85% 797.3
D-glucose catabolism MFS-glucose med Galactose-proton symporter; Galactose transporter (characterized) 64% 99% 595.5 Arabinose-proton symporter; Arabinose transporter 85% 797.3
lactose catabolism MFS-glucose med Galactose-proton symporter; Galactose transporter (characterized) 64% 99% 595.5 Arabinose-proton symporter; Arabinose transporter 85% 797.3
D-maltose catabolism MFS-glucose med Galactose-proton symporter; Galactose transporter (characterized) 64% 99% 595.5 Arabinose-proton symporter; Arabinose transporter 85% 797.3
sucrose catabolism MFS-glucose med Galactose-proton symporter; Galactose transporter (characterized) 64% 99% 595.5 Arabinose-proton symporter; Arabinose transporter 85% 797.3
trehalose catabolism MFS-glucose med Galactose-proton symporter; Galactose transporter (characterized) 64% 99% 595.5 Arabinose-proton symporter; Arabinose transporter 85% 797.3
myo-inositol catabolism iolT lo Major myo-inositol transporter IolT (characterized) 36% 93% 267.7 Arabinose-proton symporter; Arabinose transporter 85% 797.3
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) 31% 89% 227.3 Arabinose-proton symporter; Arabinose transporter 85% 797.3
trehalose catabolism TRET1 lo Facilitated trehalose transporter Tret1; BmTRET1 (characterized) 32% 92% 226.9 Arabinose-proton symporter; Arabinose transporter 85% 797.3
myo-inositol catabolism HMIT lo Probable inositol transporter 2 (characterized) 36% 57% 219.5 Arabinose-proton symporter; Arabinose transporter 85% 797.3
D-fructose catabolism Slc2a5 lo sugar transport protein 13 (characterized) 31% 90% 208.4 Arabinose-proton symporter; Arabinose transporter 85% 797.3
sucrose catabolism Slc2a5 lo sugar transport protein 13 (characterized) 31% 90% 208.4 Arabinose-proton symporter; Arabinose transporter 85% 797.3
D-fructose catabolism STP6 lo sugar transport protein 6 (characterized) 31% 92% 202.6 Arabinose-proton symporter; Arabinose transporter 85% 797.3
sucrose catabolism STP6 lo sugar transport protein 6 (characterized) 31% 92% 202.6 Arabinose-proton symporter; Arabinose transporter 85% 797.3
D-galacturonate catabolism gatA lo The galacturonic acid (galacturonate) uptake porter, GatA, of 518 aas and 12 TMSs (characterized) 31% 88% 198.4 Arabinose-proton symporter; Arabinose transporter 85% 797.3

Sequence Analysis Tools

View WP_007703466.1 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

Fitness BLAST: loading...

Sequence

MSSVSEVTPAVSAQERKARRMNLFVSFSAAVAGLLFGLDIGVIAGALPFITDHFSLSSRA
QEWVVSSMMLGAALGALFNGWLSSRLGRKYSLLAGAALFIIGSLGSAFAHSLEILLAARV
ILGVAVGIASYTAPLYLSEMASEKVRGKMISLYQLMVTLGILLAFLSDTALSYSGNWRAM
LGVLALPAVVLLVMVVFLPNSPRWLAAKGMNIEAERVLRMLRDTSEKAREELNEIRESLK
VKQGGWALFTANRNVRRAVFLGMLLQAMQQFTGMNIIMYYAPKIFQMAGFASTEEQMIAT
VVVGLTFMLATFIAVFTVDKAGRKPALKIGFSVMAIGTLVLGYCLMKVDHGEISGGISWL
SVGMTMMCIAGYAMSAAPVVWILCSEIQPLKCRDFGVTCSTTTNWVSNMIIGATFLTLID
HIGAAGTFWLYTALNLVFVGVTFWLIPETKNVTLEHIEKNLMAGKKLRDIGQ

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