GapMind for catabolism of small carbon sources

 

Protein WP_012112845.1 in Xanthobacter autotrophicus Py2

Annotation: NCBI__GCF_000017645.1:WP_012112845.1

Length: 444 amino acids

Source: GCF_000017645.1 in NCBI

Candidate for 19 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 med Galactose-proton symporter; Galactose transporter (characterized) 35% 95% 267.7 Arabinose-proton symporter; Arabinose transporter 32% 240.7
D-galactose catabolism galP med Galactose-proton symporter; Galactose transporter (characterized) 35% 95% 267.7 D-fructose transporter, sugar porter family 35% 236.9
D-glucose catabolism MFS-glucose med Galactose-proton symporter; Galactose transporter (characterized) 35% 95% 267.7 Arabinose-proton symporter; Arabinose transporter 32% 240.7
lactose catabolism MFS-glucose med Galactose-proton symporter; Galactose transporter (characterized) 35% 95% 267.7 Arabinose-proton symporter; Arabinose transporter 32% 240.7
D-maltose catabolism MFS-glucose med Galactose-proton symporter; Galactose transporter (characterized) 35% 95% 267.7 Arabinose-proton symporter; Arabinose transporter 32% 240.7
sucrose catabolism MFS-glucose med Galactose-proton symporter; Galactose transporter (characterized) 35% 95% 267.7 Arabinose-proton symporter; Arabinose transporter 32% 240.7
trehalose catabolism MFS-glucose med Galactose-proton symporter; Galactose transporter (characterized) 35% 95% 267.7 Arabinose-proton symporter; Arabinose transporter 32% 240.7
L-arabinose catabolism araE lo Arabinose-proton symporter; Arabinose transporter (characterized) 32% 93% 240.7 Galactose-proton symporter; Galactose transporter 35% 267.7
D-xylose catabolism xylT lo Arabinose-proton symporter; Arabinose transporter (characterized) 32% 93% 240.7 Galactose-proton symporter; Galactose transporter 35% 267.7
D-fructose catabolism glcP lo D-fructose transporter, sugar porter family (characterized) 35% 94% 236.9 Galactose-proton symporter; Galactose transporter 35% 267.7
sucrose catabolism glcP lo D-fructose transporter, sugar porter family (characterized) 35% 94% 236.9 Galactose-proton symporter; Galactose transporter 35% 267.7
myo-inositol catabolism iolT lo Myoinositol:H+ symporter, MIT (characterized) 31% 80% 204.9 Galactose-proton symporter; Galactose transporter 35% 267.7
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) 30% 90% 199.9 Galactose-proton symporter; Galactose transporter 35% 267.7
D-fructose catabolism STP6 lo sugar transport protein 6 (characterized) 30% 79% 180.6 Galactose-proton symporter; Galactose transporter 35% 267.7
D-mannose catabolism STP6 lo sugar transport protein 6 (characterized) 30% 79% 180.6 Galactose-proton symporter; Galactose transporter 35% 267.7
sucrose catabolism STP6 lo sugar transport protein 6 (characterized) 30% 79% 180.6 Galactose-proton symporter; Galactose transporter 35% 267.7
D-fructose catabolism Slc2a5 lo sugar transport protein 13 (characterized) 31% 78% 168.7 Galactose-proton symporter; Galactose transporter 35% 267.7
sucrose catabolism Slc2a5 lo sugar transport protein 13 (characterized) 31% 78% 168.7 Galactose-proton symporter; Galactose transporter 35% 267.7
myo-inositol catabolism HMIT lo Probable inositol transporter 2 (characterized) 32% 55% 159.5 Galactose-proton symporter; Galactose transporter 35% 267.7

Sequence Analysis Tools

View WP_012112845.1 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

MKTLLLTASLVLLFGILFGFSTASIAGVVEAIAQAFALSTRATEMVVTSLLVGCFIGAAA
AAPVSARIGRRPACLLAAVLAMAGYSLIPLGQGVAPGAGMLVAARILIGLGVGLSSMVVP
MYAAEVTPARHRGAVVSLFQLAITLGILAGYAVPLALIGRASWQQMLGGGVLVAAACAAI
VLLLPESPRWLRSRGMSARADAAARALGISDEMGEEHAPDGANWRAVLGRGATGAVLVLC
SVLFVLQNFSGIDGILYYAPHIFTELGFPAGTAALAATFGLGLFNVIATIAAMALVDRLG
RRPLLIVGSAAMAVSLGAVIVAALADWPWVALAGLCAYIVAFALSLGPLPYVLMSELFPS
AIRERGIAVASATSWLFNGIVAGTFLSVVQGIGLAGTIGIFFVVCVLSLVVSVLFVPETR
RIGLEEIEADVLDGRPLRQLGAGG

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