GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Martelella endophytica YC6887

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 (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter
deoK deoxyribokinase TM49_RS19450 TM49_RS03305
deoC deoxyribose-5-phosphate aldolase TM49_RS09210 TM49_RS03310
adh acetaldehyde dehydrogenase (not acylating) TM49_RS22260 TM49_RS20575
acs acetyl-CoA synthetase, AMP-forming TM49_RS04845 TM49_RS00160
Alternative steps:
aacS acetoacetyl-CoA synthetase TM49_RS00160
ackA acetate kinase TM49_RS17995
ald-dh-CoA acetaldehyde dehydrogenase, acylating TM49_RS20575
atoA acetoacetyl-CoA transferase, A subunit
atoB acetyl-CoA C-acetyltransferase TM49_RS01995 TM49_RS17855
atoD acetoacetyl-CoA transferase, B subunit
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase TM49_RS22185 TM49_RS02095
deoxyribonate-transport 2-deoxy-D-ribonate transporter
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit TM49_RS03245
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component TM49_RS19810
garK glycerate 2-kinase TM49_RS21040
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme TM49_RS22215
pta phosphate acetyltransferase TM49_RS05720 TM49_RS08310

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