GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Azospirillum humicireducens SgZ-5

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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase A6A40_RS17295 A6A40_RS23020
deoC deoxyribose-5-phosphate aldolase A6A40_RS17265 A6A40_RS20695
adh acetaldehyde dehydrogenase (not acylating) A6A40_RS26775 A6A40_RS21130
acs acetyl-CoA synthetase, AMP-forming A6A40_RS10075 A6A40_RS08675
Alternative steps:
aacS acetoacetyl-CoA synthetase A6A40_RS05525 A6A40_RS15700
ackA acetate kinase A6A40_RS02540 A6A40_RS29385
ald-dh-CoA acetaldehyde dehydrogenase, acylating A6A40_RS21750
atoA acetoacetyl-CoA transferase, A subunit A6A40_RS26060 A6A40_RS22045
atoB acetyl-CoA C-acetyltransferase A6A40_RS09435 A6A40_RS28855
atoD acetoacetyl-CoA transferase, B subunit A6A40_RS26065 A6A40_RS22040
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase A6A40_RS28835 A6A40_RS27210
deoxyribonate-transport 2-deoxy-D-ribonate transporter A6A40_RS15710 A6A40_RS14875
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit A6A40_RS13065 A6A40_RS14910
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit A6A40_RS13070
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component A6A40_RS14915 A6A40_RS13970
garK glycerate 2-kinase A6A40_RS26420 A6A40_RS16675
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme
pta phosphate acetyltransferase A6A40_RS02535 A6A40_RS29930

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