GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Shewanella halifaxensis HAW-EB4

Best path

deoP, deoK, deoC, adh, ackA, pta

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 (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase SHAL_RS02955
deoC deoxyribose-5-phosphate aldolase SHAL_RS16180
adh acetaldehyde dehydrogenase (not acylating) SHAL_RS01660 SHAL_RS11740
ackA acetate kinase SHAL_RS13495 SHAL_RS14195
pta phosphate acetyltransferase SHAL_RS13500 SHAL_RS14190
Alternative steps:
aacS acetoacetyl-CoA synthetase SHAL_RS10965 SHAL_RS17595
acs acetyl-CoA synthetase, AMP-forming SHAL_RS08815 SHAL_RS15005
ald-dh-CoA acetaldehyde dehydrogenase, acylating SHAL_RS11740 SHAL_RS10915
atoA acetoacetyl-CoA transferase, A subunit SHAL_RS15045 SHAL_RS15280
atoB acetyl-CoA C-acetyltransferase SHAL_RS14895 SHAL_RS14245
atoD acetoacetyl-CoA transferase, B subunit SHAL_RS15050 SHAL_RS15285
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase
deoxyribonate-transport 2-deoxy-D-ribonate transporter
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit SHAL_RS03335
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component
garK glycerate 2-kinase SHAL_RS14520
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme

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