GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Herbaspirillum seropedicae SmR1

Best path

xylF, xylG, xylH, xdh, xylC, xad, DKDP-dehydrog, HDOP-hydrol, gyaR, glcB

Also see fitness data for the top candidates

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 HSERO_RS05190 HSERO_RS22460
xylG ABC transporter for xylose, ATP-binding component xylG HSERO_RS05195 HSERO_RS22465
xylH ABC transporter for xylose, permease component xylH HSERO_RS05200 HSERO_RS22470
xdh D-xylose dehydrogenase HSERO_RS22475 HSERO_RS05210
xylC xylonolactonase HSERO_RS19370 HSERO_RS05225
xad D-xylonate dehydratase HSERO_RS22480 HSERO_RS16705
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase HSERO_RS19365 HSERO_RS12955
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase HSERO_RS06355 HSERO_RS17860
gyaR glyoxylate reductase HSERO_RS08110 HSERO_RS19280
glcB malate synthase HSERO_RS15200
Alternative steps:
aldA (glycol)aldehyde dehydrogenase HSERO_RS05395 HSERO_RS05645
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit HSERO_RS16320
aldox-small (glycol)aldehyde oxidoreductase, small subunit HSERO_RS06620 HSERO_RS16320
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 HSERO_RS16715 HSERO_RS22645
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase HSERO_RS16395
dopDH 2,5-dioxopentanonate dehydrogenase HSERO_RS00735 HSERO_RS07235
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcP glucose/mannose/xylose:H+ symporter
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA HSERO_RS22730
gtsB xylose ABC transporter, permease component 1 GtsB HSERO_RS18950 HSERO_RS01340
gtsC xylose ABC transporter, permease component 2 GtsC HSERO_RS01335
gtsD xylose ABC transporter, ATPase component GtsD HSERO_RS16715 HSERO_RS18940
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase HSERO_RS19360 HSERO_RS06355
xdhA xylitol dehydrogenase HSERO_RS17015 HSERO_RS05485
xylA xylose isomerase
xylB xylulokinase HSERO_RS02220 HSERO_RS17030
xylE_Tm ABC transporter for xylose, substrate binding component xylE
xylF_Tm ABC transporter for xylose, permease component xylF HSERO_RS05255 HSERO_RS05325
xylK_Tm ABC transporter for xylose, ATP binding component xylK HSERO_RS05250 HSERO_RS22220
xylT D-xylose transporter
xyrA xylitol reductase HSERO_RS16785 HSERO_RS13585

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 17 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