GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Mucilaginibacter mallensis MP1X4

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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylT D-xylose transporter BLU33_RS04945 BLU33_RS04860
xylA xylose isomerase BLU33_RS13290 BLU33_RS02750
xylB xylulokinase BLU33_RS13285 BLU33_RS09605
Alternative steps:
aldA (glycol)aldehyde dehydrogenase BLU33_RS14055 BLU33_RS06915
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 BLU33_RS00530 BLU33_RS19840
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase BLU33_RS09730 BLU33_RS06275
dopDH 2,5-dioxopentanonate dehydrogenase BLU33_RS02870 BLU33_RS14055
Echvi_1871 sodium/xylose cotransporter BLU33_RS02975 BLU33_RS02755
gal2 galactose/glucose/xylose uniporter BLU33_RS04945
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 BLU33_RS00530 BLU33_RS19840
gyaR glyoxylate reductase BLU33_RS05855 BLU33_RS10820
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase BLU33_RS09735 BLU33_RS05560
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase BLU33_RS06575 BLU33_RS19300
xdh D-xylose dehydrogenase BLU33_RS15210 BLU33_RS09730
xdhA xylitol dehydrogenase BLU33_RS08240 BLU33_RS13085
xylC xylonolactonase BLU33_RS17565
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
xylH ABC transporter for xylose, permease component xylH
xylK_Tm ABC transporter for xylose, ATP binding component xylK
xyrA xylitol reductase BLU33_RS02595 BLU33_RS24165

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