GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Collinsella tanakaei YIT 12063

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 (11 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylT D-xylose transporter
xylA xylose isomerase
xylB xylulokinase
Alternative steps:
aldA (glycol)aldehyde dehydrogenase
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 HMPREF9452_RS06235 HMPREF9452_RS07145
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase HMPREF9452_RS00145
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase HMPREF9452_RS08900 HMPREF9452_RS00090
dopDH 2,5-dioxopentanonate dehydrogenase
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase
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 HMPREF9452_RS08560 HMPREF9452_RS03120
gyaR glyoxylate reductase HMPREF9452_RS05340 HMPREF9452_RS08490
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase HMPREF9452_RS00690 HMPREF9452_RS05330
xdh D-xylose dehydrogenase HMPREF9452_RS00595 HMPREF9452_RS08900
xdhA xylitol dehydrogenase HMPREF9452_RS08900 HMPREF9452_RS03390
xylC xylonolactonase
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
xylG ABC transporter for xylose, ATP-binding component xylG HMPREF9452_RS06110
xylH ABC transporter for xylose, permease component xylH
xylK_Tm ABC transporter for xylose, ATP binding component xylK HMPREF9452_RS06110
xyrA xylitol reductase HMPREF9452_RS03490 HMPREF9452_RS03485

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