GapMind for catabolism of small carbon sources

 

2-deoxy-D-ribose catabolism in Burkholderia phytofirmans PsJN

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
drdehyd-alpha 2-deoxy-D-ribose dehydrogenase, alpha subunit BPHYT_RS24630 BPHYT_RS32800
drdehyd-beta 2-deoxy-D-ribose dehydrogenase, beta subunit BPHYT_RS24635 BPHYT_RS32805
drdehyd-cytc 2-deoxyribose-D dehydrogenase, cytochrome c component BPHYT_RS24640 BPHYT_RS10075
deoxyribonate-transport 2-deoxy-D-ribonate transporter BPHYT_RS04765 BPHYT_RS31140
deoxyribonate-dehyd 2-deoxy-D-ribonate 3-dehydrogenase BPHYT_RS04775 BPHYT_RS35475
ketodeoxyribonate-cleavage 2-deoxy-3-keto-D-ribonate cleavage enzyme BPHYT_RS04760 BPHYT_RS22385
garK glycerate 2-kinase BPHYT_RS09440
atoA acetoacetyl-CoA transferase, A subunit BPHYT_RS13675 BPHYT_RS21415
atoD acetoacetyl-CoA transferase, B subunit BPHYT_RS13670 BPHYT_RS21420
atoB acetyl-CoA C-acetyltransferase BPHYT_RS09150 BPHYT_RS09180
Alternative steps:
aacS acetoacetyl-CoA synthetase BPHYT_RS19375 BPHYT_RS23420
ackA acetate kinase BPHYT_RS06125 BPHYT_RS26200
acs acetyl-CoA synthetase, AMP-forming BPHYT_RS07000 BPHYT_RS27780
adh acetaldehyde dehydrogenase (not acylating) BPHYT_RS25810 BPHYT_RS00120
ald-dh-CoA acetaldehyde dehydrogenase, acylating BPHYT_RS07245 BPHYT_RS21770
deoC deoxyribose-5-phosphate aldolase BPHYT_RS25815
deoK deoxyribokinase BPHYT_RS25805 BPHYT_RS20695
deoP deoxyribose transporter
pta phosphate acetyltransferase BPHYT_RS21700 BPHYT_RS27695

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