GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Phyllobacterium brassicacearum STM 196

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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylF ABC transporter for xylose, substrate binding component xylF CU102_RS11770 CU102_RS17160
xylG ABC transporter for xylose, ATP-binding component xylG CU102_RS11775 CU102_RS28785
xylH ABC transporter for xylose, permease component xylH CU102_RS11780 CU102_RS21095
xylA xylose isomerase CU102_RS17145
xylB xylulokinase CU102_RS17150 CU102_RS17135
Alternative steps:
aldA (glycol)aldehyde dehydrogenase CU102_RS05845 CU102_RS20940
aldox-large (glycol)aldehyde oxidoreductase, large subunit CU102_RS14045
aldox-med (glycol)aldehyde oxidoreductase, medium subunit CU102_RS14050 CU102_RS00855
aldox-small (glycol)aldehyde oxidoreductase, small subunit CU102_RS14040 CU102_RS24330
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 CU102_RS19470 CU102_RS08100
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase CU102_RS15345 CU102_RS04995
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase CU102_RS28870 CU102_RS05200
dopDH 2,5-dioxopentanonate dehydrogenase CU102_RS05845 CU102_RS19905
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase CU102_RS13355 CU102_RS22610
glcP glucose/mannose/xylose:H+ symporter
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA CU102_RS18490 CU102_RS20290
gtsB xylose ABC transporter, permease component 1 GtsB CU102_RS18495 CU102_RS20285
gtsC xylose ABC transporter, permease component 2 GtsC CU102_RS18500 CU102_RS20280
gtsD xylose ABC transporter, ATPase component GtsD CU102_RS18505 CU102_RS22280
gyaR glyoxylate reductase CU102_RS13520 CU102_RS09940
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase CU102_RS28865 CU102_RS18365
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase CU102_RS09610
xad D-xylonate dehydratase CU102_RS18375 CU102_RS07305
xdh D-xylose dehydrogenase CU102_RS21630 CU102_RS23015
xdhA xylitol dehydrogenase CU102_RS17560 CU102_RS23605
xylC xylonolactonase
xylE_Tm ABC transporter for xylose, substrate binding component xylE CU102_RS25525
xylF_Tm ABC transporter for xylose, permease component xylF CU102_RS04470 CU102_RS21095
xylK_Tm ABC transporter for xylose, ATP binding component xylK CU102_RS28785 CU102_RS11775
xylT D-xylose transporter
xyrA xylitol reductase CU102_RS04460 CU102_RS23005

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