GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Streptomyces kebangsaanensis SUK12

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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylF ABC transporter for xylose, substrate binding component xylF RH94_RS32830 RH94_RS09355
xylG ABC transporter for xylose, ATP-binding component xylG RH94_RS32835 RH94_RS04605
xylH ABC transporter for xylose, permease component xylH RH94_RS32840 RH94_RS33575
xylA xylose isomerase RH94_RS23920
xylB xylulokinase RH94_RS23915 RH94_RS32950
Alternative steps:
aldA (glycol)aldehyde dehydrogenase RH94_RS37005 RH94_RS20650
aldox-large (glycol)aldehyde oxidoreductase, large subunit RH94_RS33125 RH94_RS37555
aldox-med (glycol)aldehyde oxidoreductase, medium subunit RH94_RS33130 RH94_RS37565
aldox-small (glycol)aldehyde oxidoreductase, small subunit RH94_RS33120 RH94_RS37560
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 RH94_RS27405 RH94_RS20645
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase RH94_RS21155
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase RH94_RS18480 RH94_RS29205
dopDH 2,5-dioxopentanonate dehydrogenase RH94_RS35230 RH94_RS37005
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase RH94_RS16670 RH94_RS14430
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 RH94_RS13700 RH94_RS35540
gtsD xylose ABC transporter, ATPase component GtsD RH94_RS27405 RH94_RS20645
gyaR glyoxylate reductase RH94_RS12895 RH94_RS08650
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase RH94_RS37320 RH94_RS25080
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase RH94_RS35300 RH94_RS32815
xdh D-xylose dehydrogenase RH94_RS38075 RH94_RS32155
xdhA xylitol dehydrogenase RH94_RS35355 RH94_RS10610
xylC xylonolactonase RH94_RS32890
xylE_Tm ABC transporter for xylose, substrate binding component xylE
xylF_Tm ABC transporter for xylose, permease component xylF RH94_RS04595 RH94_RS33575
xylK_Tm ABC transporter for xylose, ATP binding component xylK RH94_RS04605 RH94_RS32835
xylT D-xylose transporter RH94_RS25280
xyrA xylitol reductase RH94_RS31490 RH94_RS23765

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