GapMind for catabolism of small carbon sources

 

D-xylose catabolism in Algoriphagus aquaeductus T4

Best path

Echvi_1871, 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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Echvi_1871 sodium/xylose cotransporter CLV31_RS02275 CLV31_RS07755
xylA xylose isomerase CLV31_RS02285
xylB xylulokinase CLV31_RS02280
Alternative steps:
aldA (glycol)aldehyde dehydrogenase CLV31_RS07110
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit CLV31_RS13005 CLV31_RS04730
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 CLV31_RS01090 CLV31_RS07770
DKDP-aldolase 2-dehydro-3-deoxy-D-arabinonate aldolase CLV31_RS16845
DKDP-dehydrog D-2-keto-3-deoxypentoate dehydrogenase CLV31_RS07895 CLV31_RS01685
dopDH 2,5-dioxopentanonate dehydrogenase CLV31_RS15190 CLV31_RS07110
gal2 galactose/glucose/xylose uniporter CLV31_RS13825
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 CLV31_RS00030 CLV31_RS07165
gyaR glyoxylate reductase CLV31_RS15460 CLV31_RS01025
HDOP-hydrol 5-hydroxy-2,4-dioxopentanonate hydrolase CLV31_RS01680
kdaD 2-keto-3-deoxy-D-arabinonate dehydratase CLV31_RS02940
xad D-xylonate dehydratase CLV31_RS20790 CLV31_RS20160
xdh D-xylose dehydrogenase CLV31_RS12640 CLV31_RS01685
xdhA xylitol dehydrogenase CLV31_RS06290 CLV31_RS07350
xylC xylonolactonase CLV31_RS18705
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
xylT D-xylose transporter CLV31_RS17305 CLV31_RS13825
xyrA xylitol reductase CLV31_RS10670 CLV31_RS06035

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