GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Kocuria flava HO-9041

Best path

xylT, xylA, xylB

Rules

Overview: Xylose degradation in GapMind is based on MetaCyc pathways I via D-xylulose (link), II via xylitol (link), III or V via 2-dehydro-3-deoxy-D-arabinonate (DKDP) dehydratase (link, link), IV via DKDP aldolase (link), as well as another pathway via DKDP dehydrogenase (PMC6336799).

36 steps (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylT D-xylose transporter AS188_RS02770 AS188_RS06680
xylA xylose isomerase
xylB xylulokinase
Alternative steps:
aldA (glycol)aldehyde dehydrogenase AS188_RS05910 AS188_RS01305
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit
araS component of Arabinose, fructose, xylose porter
araT component of Arabinose, fructose, xylose porter
araU component of Arabinose, fructose, xylose porter
araV component of Arabinose, fructose, xylose porter AS188_RS14700 AS188_RS10405
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase AS188_RS08430 AS188_RS09680
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase AS188_RS03480 AS188_RS15385
dopDH 2,5-dioxopentanonate dehydrogenase AS188_RS05910 AS188_RS01305
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase AS188_RS14500 AS188_RS04920
glcP glucose/mannose/xylose:H+ symporter
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA
gtsB xylose ABC transporter, permease component 1 GtsB
gtsC xylose ABC transporter, permease component 2 GtsC
gtsD xylose ABC transporter, ATPase component GtsD AS188_RS14700 AS188_RS10405
gyaR glyoxylate reductase AS188_RS05455 AS188_RS04900
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase AS188_RS11385 AS188_RS12500
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase AS188_RS04760 AS188_RS00785
xdh D-xylose dehydrogenase AS188_RS06880 AS188_RS03480
xdhA xylitol dehydrogenase AS188_RS07440 AS188_RS03420
xylC xylonolactonase AS188_RS05230
xylE_Tm ABC transporter for xylose, substrate binding component xylE
xylF ABC transporter for xylose, substrate binding component xylF
xylF_Tm ABC transporter for xylose, permease component xylF AS188_RS10230 AS188_RS06770
xylG ABC transporter for xylose, ATP-binding component xylG AS188_RS10235 AS188_RS06775
xylH ABC transporter for xylose, permease component xylH AS188_RS10230
xylK_Tm ABC transporter for xylose, ATP binding component xylK AS188_RS10235 AS188_RS06775
xyrA xylitol reductase AS188_RS02695 AS188_RS08400

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

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