GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Herbaspirillum seropedicae SmR1

Best path

drdehyd-alpha, drdehyd-beta, drdehyd-cytc, deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, atoA, atoD, atoB

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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit HSERO_RS06620 HSERO_RS16320
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component HSERO_RS16735 HSERO_RS22390
deoxyribonate-transport 2-deoxy-D-ribonate transporter HSERO_RS05805 HSERO_RS05735
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase HSERO_RS17235 HSERO_RS12375
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme HSERO_RS17240
garK glycerate 2-kinase HSERO_RS10055
atoA acetoacetyl-CoA transferase, A subunit HSERO_RS23190 HSERO_RS20000
atoD acetoacetyl-CoA transferase, B subunit HSERO_RS23185 HSERO_RS19995
atoB acetyl-CoA C-acetyltransferase HSERO_RS01180 HSERO_RS04635
Alternative steps:
aacS acetoacetyl-CoA synthetase
ackA acetate kinase HSERO_RS01305 HSERO_RS11090
acs acetyl-CoA synthetase, AMP-forming HSERO_RS07770 HSERO_RS23535
adh acetaldehyde dehydrogenase (not acylating) HSERO_RS05115 HSERO_RS09465
ald-dh-CoA acetaldehyde dehydrogenase, acylating
deoC deoxyribose-5-phosphate aldolase HSERO_RS05120
deoK deoxyribokinase HSERO_RS11500 HSERO_RS05105
deoP deoxyribose transporter
pta phosphate acetyltransferase HSERO_RS12030 HSERO_RS01300

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