GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Azospirillum brasilense Sp245

Best path

deoP, deoK, deoC, adh, acs

Also see fitness data for the top candidates

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
deoP deoxyribose transporter
deoK deoxyribokinase
deoC deoxyribose-5-phosphate aldolase
adh acetaldehyde dehydrogenase (not acylating) AZOBR_RS22315 AZOBR_RS26825
acs acetyl-CoA synthetase, AMP-forming AZOBR_RS00270 AZOBR_RS06340
Alternative steps:
aacS acetoacetyl-CoA synthetase AZOBR_RS31155 AZOBR_RS09405
ackA acetate kinase AZOBR_RS12495 AZOBR_RS04605
ald-dh-CoA acetaldehyde dehydrogenase, acylating AZOBR_RS32240 AZOBR_RS32475
atoA acetoacetyl-CoA transferase, A subunit
atoB acetyl-CoA C-acetyltransferase AZOBR_RS30610 AZOBR_RS28180
atoD acetoacetyl-CoA transferase, B subunit
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase AZOBR_RS25730 AZOBR_RS16640
deoxyribonate-transport 2-deoxy-D-ribonate transporter
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit AZOBR_RS30035 AZOBR_RS27485
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit AZOBR_RS30030
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component
garK glycerate 2-kinase AZOBR_RS07950
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme AZOBR_RS23055 AZOBR_RS27000
pta phosphate acetyltransferase AZOBR_RS04600 AZOBR_RS12500

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.

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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