GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Cereibacter sphaeroides ATCC 17029

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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylT D-xylose transporter
xylA xylose isomerase RSPH17029_RS14310
xylB xylulokinase RSPH17029_RS14315
Alternative steps:
aldA (glycol)aldehyde dehydrogenase RSPH17029_RS04350 RSPH17029_RS13480
aldox-large (glycol)aldehyde oxidoreductase, large subunit RSPH17029_RS07705
aldox-med (glycol)aldehyde oxidoreductase, medium subunit RSPH17029_RS07700
aldox-small (glycol)aldehyde oxidoreductase, small subunit RSPH17029_RS07710 RSPH17029_RS19915
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 RSPH17029_RS10060 RSPH17029_RS17190
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase RSPH17029_RS12825 RSPH17029_RS15385
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase RSPH17029_RS20905 RSPH17029_RS09145
dopDH 2,5-dioxopentanonate dehydrogenase RSPH17029_RS17095 RSPH17029_RS04350
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase RSPH17029_RS03525 RSPH17029_RS13265
glcP glucose/mannose/xylose:H+ symporter
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA
gtsB xylose ABC transporter, permease component 1 GtsB RSPH17029_RS20300
gtsC xylose ABC transporter, permease component 2 GtsC RSPH17029_RS07675
gtsD xylose ABC transporter, ATPase component GtsD RSPH17029_RS17190 RSPH17029_RS20290
gyaR glyoxylate reductase RSPH17029_RS05035 RSPH17029_RS15170
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase RSPH17029_RS09140 RSPH17029_RS01090
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase RSPH17029_RS09155 RSPH17029_RS18285
xdh D-xylose dehydrogenase RSPH17029_RS00190 RSPH17029_RS05260
xdhA xylitol dehydrogenase RSPH17029_RS18305 RSPH17029_RS17935
xylC xylonolactonase RSPH17029_RS19585
xylE_Tm ABC transporter for xylose, substrate binding component xylE
xylF ABC transporter for xylose, substrate binding component xylF RSPH17029_RS14330 RSPH17029_RS17310
xylF_Tm ABC transporter for xylose, permease component xylF RSPH17029_RS14660 RSPH17029_RS17250
xylG ABC transporter for xylose, ATP-binding component xylG RSPH17029_RS14655 RSPH17029_RS15870
xylH ABC transporter for xylose, permease component xylH RSPH17029_RS14325 RSPH17029_RS17320
xylK_Tm ABC transporter for xylose, ATP binding component xylK RSPH17029_RS05240 RSPH17029_RS14655
xyrA xylitol reductase RSPH17029_RS05040 RSPH17029_RS19900

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 Apr 10 2024. 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