GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Chlorobaculum parvum NCIB 8327

Best path

Bap2, ofo, 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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Bap2 L-isoleucine permease Bap2
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase CPAR_RS01845
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase CPAR_RS00690 CPAR_RS11375
fadA 2-methylacetoacetyl-CoA thiolase
pccA propionyl-CoA carboxylase, alpha subunit CPAR_RS09535
pccB propionyl-CoA carboxylase, beta subunit
epi methylmalonyl-CoA epimerase CPAR_RS04265
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit CPAR_RS04250
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit CPAR_RS04250
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase CPAR_RS07295
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
bcaP L-isoleucine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase CPAR_RS01845
iolA malonate semialdehyde dehydrogenase (CoA-acylating) CPAR_RS01995
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) CPAR_RS01555 CPAR_RS05330
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) CPAR_RS01555 CPAR_RS05790
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)
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component CPAR_RS03710
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components CPAR_RS04250
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) CPAR_RS01555 CPAR_RS02770
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) CPAR_RS05970 CPAR_RS05920
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA CPAR_RS09505
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB CPAR_RS09510
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit CPAR_RS09535
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase CPAR_RS07585
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase CPAR_RS01905
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 CPAR_RS09505
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 Apr 09 2024. 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