GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Rhizobium leguminosarum bv. trifolii WSM1325

Best path

deoP, deoK, deoC, adh, acs

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase RLEG_RS00345 RLEG_RS11285
deoC deoxyribose-5-phosphate aldolase RLEG_RS11270 RLEG_RS22155
adh acetaldehyde dehydrogenase (not acylating) RLEG_RS11275 RLEG_RS18780
acs acetyl-CoA synthetase, AMP-forming RLEG_RS21015 RLEG_RS21030
Alternative steps:
aacS acetoacetyl-CoA synthetase RLEG_RS02080 RLEG_RS03060
ackA acetate kinase RLEG_RS17140
ald-dh-CoA acetaldehyde dehydrogenase, acylating
atoA acetoacetyl-CoA transferase, A subunit RLEG_RS27925
atoB acetyl-CoA C-acetyltransferase RLEG_RS20540 RLEG_RS35140
atoD acetoacetyl-CoA transferase, B subunit RLEG_RS27920
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase RLEG_RS15460 RLEG_RS18620
deoxyribonate-transport 2-deoxy-D-ribonate transporter RLEG_RS29595
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit RLEG_RS32870 RLEG_RS23140
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component RLEG_RS32865 RLEG_RS04805
garK glycerate 2-kinase RLEG_RS08115
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme RLEG_RS34775
pta phosphate acetyltransferase RLEG_RS00240 RLEG_RS10915

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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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