GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Ruegeria conchae TW15

Best path

xylF, xylG, xylH, 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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylF ABC transporter for xylose, substrate binding component xylF G7G_RS0115585
xylG ABC transporter for xylose, ATP-binding component xylG G7G_RS0100415 G7G_RS0100435
xylH ABC transporter for xylose, permease component xylH G7G_RS0100410 G7G_RS0115590
xylA xylose isomerase G7G_RS0115600
xylB xylulokinase G7G_RS0115560
Alternative steps:
aldA (glycol)aldehyde dehydrogenase G7G_RS0118970 G7G_RS0103600
aldox-large (glycol)aldehyde oxidoreductase, large subunit G7G_RS0106435 G7G_RS0100870
aldox-med (glycol)aldehyde oxidoreductase, medium subunit G7G_RS0100880 G7G_RS0106440
aldox-small (glycol)aldehyde oxidoreductase, small subunit G7G_RS0100875 G7G_RS0106430
araS component of Arabinose, fructose, xylose porter
araT component of Arabinose, fructose, xylose porter
araU component of Arabinose, fructose, xylose porter G7G_RS0103680
araV component of Arabinose, fructose, xylose porter G7G_RS0115525 G7G_RS0114935
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase G7G_RS0110290
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase G7G_RS0110540 G7G_RS0120430
dopDH 2,5-dioxopentanonate dehydrogenase G7G_RS0110075 G7G_RS0110305
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase G7G_RS0117845
glcP glucose/mannose/xylose:H+ symporter
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA G7G_RS0103670 G7G_RS0117185
gtsB xylose ABC transporter, permease component 1 GtsB G7G_RS0103675 G7G_RS0117190
gtsC xylose ABC transporter, permease component 2 GtsC G7G_RS0103680 G7G_RS0117195
gtsD xylose ABC transporter, ATPase component GtsD G7G_RS0103685 G7G_RS0121175
gyaR glyoxylate reductase G7G_RS0120345 G7G_RS0112690
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase G7G_RS0110535 G7G_RS0100785
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase G7G_RS0100630 G7G_RS0117165
xdh D-xylose dehydrogenase G7G_RS0111310 G7G_RS0103500
xdhA xylitol dehydrogenase G7G_RS0116430 G7G_RS0120430
xylC xylonolactonase G7G_RS0100425 G7G_RS0111325
xylE_Tm ABC transporter for xylose, substrate binding component xylE G7G_RS0100405
xylF_Tm ABC transporter for xylose, permease component xylF G7G_RS0100410 G7G_RS0103330
xylK_Tm ABC transporter for xylose, ATP binding component xylK G7G_RS0100435 G7G_RS0100415
xylT D-xylose transporter
xyrA xylitol reductase

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