GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Phaeobacter inhibens BS107

Best path

xylF, xylG, xylH, xylA, xylB

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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
xylF ABC transporter for xylose, substrate binding component xylF PGA1_262p00430
xylG ABC transporter for xylose, ATP-binding component xylG PGA1_c23060 PGA1_c03960
xylH ABC transporter for xylose, permease component xylH PGA1_262p00440 PGA1_c28050
xylA xylose isomerase PGA1_c14000
xylB xylulokinase PGA1_c14010
Alternative steps:
aldA (glycol)aldehyde dehydrogenase PGA1_c29650 PGA1_c23170
aldox-large (glycol)aldehyde oxidoreductase, large subunit PGA1_c20870 PGA1_c11660
aldox-med (glycol)aldehyde oxidoreductase, medium subunit PGA1_c20860
aldox-small (glycol)aldehyde oxidoreductase, small subunit PGA1_c20880 PGA1_c16210
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 PGA1_c02740 PGA1_c07900
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase PGA1_c13170 PGA1_c08430
dopDH 2,5-dioxopentanonate dehydrogenase PGA1_c05130 PGA1_262p01460
Echvi_1871 sodium/xylose cotransporter
gal2 galactose/glucose/xylose uniporter
glcB malate synthase PGA1_c09900 PGA1_c03680
glcP glucose/mannose/xylose:H+ symporter
gtsA xylose ABC transporter, periplasmic substrate-binding component GtsA PGA1_78p00160 PGA1_c19500
gtsB xylose ABC transporter, permease component 1 GtsB PGA1_c19490 PGA1_78p00170
gtsC xylose ABC transporter, permease component 2 GtsC PGA1_c19480 PGA1_78p00180
gtsD xylose ABC transporter, ATPase component GtsD PGA1_c02740 PGA1_c19470
gyaR glyoxylate reductase PGA1_c28260 PGA1_c24680
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase PGA1_c04530 PGA1_c33930
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase
xad D-xylonate dehydratase PGA1_c07380 PGA1_c04540
xdh D-xylose dehydrogenase PGA1_c07370 PGA1_c27390
xdhA xylitol dehydrogenase PGA1_c34320 PGA1_c13170
xylC xylonolactonase
xylE_Tm ABC transporter for xylose, substrate binding component xylE
xylF_Tm ABC transporter for xylose, permease component xylF PGA1_c23080 PGA1_c23070
xylK_Tm ABC transporter for xylose, ATP binding component xylK PGA1_c23060 PGA1_c26910
xylT D-xylose transporter
xyrA xylitol reductase

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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