GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Sphingopyxis indica DS15

Best path

Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small

Rules

Overview: Isoleucine degradation in GapMind is based on MetaCyc pathway L-isoleucine degradation I (link). The other pathways are fermentative and do not lead to carbon incorporation (link, link).

45 steps (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Bap2 L-isoleucine permease Bap2
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit CHB69_RS04235 CHB69_RS18910
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit CHB69_RS04230 CHB69_RS18905
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component CHB69_RS04225 CHB69_RS07995
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component CHB69_RS02765 CHB69_RS08010
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase CHB69_RS13685 CHB69_RS03045
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase CHB69_RS13675 CHB69_RS12770
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase CHB69_RS16340 CHB69_RS02805
fadA 2-methylacetoacetyl-CoA thiolase CHB69_RS02585 CHB69_RS08555
pccA propionyl-CoA carboxylase, alpha subunit CHB69_RS03015 CHB69_RS00455
pccB propionyl-CoA carboxylase, beta subunit CHB69_RS02650 CHB69_RS03025
epi methylmalonyl-CoA epimerase CHB69_RS02655
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit CHB69_RS02660
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit CHB69_RS02660 CHB69_RS06455
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase CHB69_RS16520
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) CHB69_RS16520
bcaP L-isoleucine uptake transporter BcaP/CitA CHB69_RS13745
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase CHB69_RS09450
hpcD 3-hydroxypropionyl-CoA dehydratase CHB69_RS13675 CHB69_RS12770
iolA malonate semialdehyde dehydrogenase (CoA-acylating) CHB69_RS13705 CHB69_RS13105
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) CHB69_RS09975 CHB69_RS00845
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) CHB69_RS14435 CHB69_RS09975
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD)
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE)
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components CHB69_RS02660
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) CHB69_RS09975
natB L-isoleucine ABC transporter, substrate-binding component NatB
natC L-isoleucine ABC transporter, permease component 1 (NatC)
natD L-isoleucine ABC transporter, permease component 2 (NatD)
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) CHB69_RS09975 CHB69_RS11895
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB CHB69_RS02935
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit CHB69_RS00455 CHB69_RS03015
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase CHB69_RS11225 CHB69_RS08545
prpB 2-methylisocitrate lyase CHB69_RS07425
prpC 2-methylcitrate synthase CHB69_RS18155
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB CHB69_RS02930
vorC branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC

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.

Links

Downloads

Related tools

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