GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Thiohalomonas denitrificans HLD2

Best path

Bap2, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, prpC, prpD, acn, prpB

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 (15 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 BLP65_RS07275 BLP65_RS06730
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BLP65_RS07270 BLP65_RS06725
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BLP65_RS07265
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BLP65_RS07260 BLP65_RS06720
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase BLP65_RS08625
fadA 2-methylacetoacetyl-CoA thiolase
prpC 2-methylcitrate synthase BLP65_RS02570
prpD 2-methylcitrate dehydratase
acn (2R,3S)-2-methylcitrate dehydratase BLP65_RS09165
prpB 2-methylisocitrate lyase
Alternative steps:
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
bcaP L-isoleucine uptake transporter BcaP/CitA
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BLP65_RS04695
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) BLP65_RS02265 BLP65_RS16320
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) BLP65_RS02265 BLP65_RS07555
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)
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) BLP65_RS02265 BLP65_RS05770
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) BLP65_RS02265 BLP65_RS16540
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
pccA propionyl-CoA carboxylase, alpha subunit BLP65_RS03235 BLP65_RS08595
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BLP65_RS08595 BLP65_RS03235
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit
pco propanyl-CoA oxidase BLP65_RS10735
prpF methylaconitate isomerase
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB
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