GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Klebsiella michiganensis M5al

Best path

deoP, deoK, deoC, adh, ackA, pta

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 (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
deoP deoxyribose transporter BWI76_RS23685 BWI76_RS22920
deoK deoxyribokinase BWI76_RS00290 BWI76_RS00580
deoC deoxyribose-5-phosphate aldolase BWI76_RS04130 BWI76_RS23665
adh acetaldehyde dehydrogenase (not acylating) BWI76_RS21985 BWI76_RS15205
ackA acetate kinase BWI76_RS20235 BWI76_RS23200
pta phosphate acetyltransferase BWI76_RS20240 BWI76_RS20805
Alternative steps:
aacS acetoacetyl-CoA synthetase BWI76_RS17800 BWI76_RS23695
acs acetyl-CoA synthetase, AMP-forming BWI76_RS02095 BWI76_RS17800
ald-dh-CoA acetaldehyde dehydrogenase, acylating BWI76_RS17250 BWI76_RS20790
atoA acetoacetyl-CoA transferase, A subunit BWI76_RS16145
atoB acetyl-CoA C-acetyltransferase BWI76_RS23445 BWI76_RS01360
atoD acetoacetyl-CoA transferase, B subunit BWI76_RS16140
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase BWI76_RS16755 BWI76_RS23630
deoxyribonate-transport 2-deoxy-D-ribonate transporter BWI76_RS23725 BWI76_RS23715
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit BWI76_RS17570
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component
garK glycerate 2-kinase BWI76_RS24820 BWI76_RS07025
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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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