GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Limnohabitans curvus MWH-C5

Best path

drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB

Rules

Overview: Deoxyribose utilization in GapMind is based on MetaCyc pathways 2-deoxy-D-ribose degradation I via deoxyribose 5-phosphate aldolase (link) and pathway II via oxidation to 2-deoxy-3-dehydro-D-ribonate (link).

19 steps (12 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit B9Z44_RS10955 B9Z44_RS10265
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit B9Z44_RS10960
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component
deoxyribonate-transport 2-deoxy-D-ribonate transporter
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase B9Z44_RS11555 B9Z44_RS13785
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme
garK glycerate 2-kinase B9Z44_RS10585
atoA acetoacetyl-CoA transferase, A subunit B9Z44_RS11635 B9Z44_RS03445
atoD acetoacetyl-CoA transferase, B subunit B9Z44_RS11640 B9Z44_RS03440
atoB acetyl-CoA C-acetyltransferase B9Z44_RS11030 B9Z44_RS12465
Alternative steps:
aacS acetoacetyl-CoA synthetase B9Z44_RS06550 B9Z44_RS01335
ackA acetate kinase B9Z44_RS09890
acs acetyl-CoA synthetase, AMP-forming B9Z44_RS10305 B9Z44_RS13605
adh acetaldehyde dehydrogenase (not acylating) B9Z44_RS11745 B9Z44_RS11550
ald-dh-CoA acetaldehyde dehydrogenase, acylating
deoC deoxyribose-5-phosphate aldolase
deoK deoxyribokinase
deoP deoxyribose transporter
pta phosphate acetyltransferase B9Z44_RS09885 B9Z44_RS07290

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