GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Acidovorax sp. GW101-3H11

Best path

livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB

Also see fitness data for the top candidates

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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) Ac3H11_1692 Ac3H11_1936
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) Ac3H11_1693 Ac3H11_4983
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) Ac3H11_2396 Ac3H11_552
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) Ac3H11_1695 Ac3H11_1939
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) Ac3H11_1694 Ac3H11_4628
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused Ac3H11_1196 Ac3H11_2707
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase Ac3H11_2996 Ac3H11_2359
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase Ac3H11_1914 Ac3H11_4006
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase Ac3H11_2606 Ac3H11_3411
fadA 2-methylacetoacetyl-CoA thiolase Ac3H11_2994 Ac3H11_178
prpC 2-methylcitrate synthase Ac3H11_2322 Ac3H11_3161
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) Ac3H11_2323 Ac3H11_1140
prpF methylaconitate isomerase Ac3H11_2325 Ac3H11_4370
acn (2R,3S)-2-methylcitrate dehydratase Ac3H11_1140 Ac3H11_2323
prpB 2-methylisocitrate lyase Ac3H11_2831 Ac3H11_2326
Alternative steps:
Bap2 L-isoleucine permease Bap2
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 Ac3H11_2466 Ac3H11_4092
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase Ac3H11_3320 Ac3H11_4659
epi methylmalonyl-CoA epimerase Ac3H11_2274
hpcD 3-hydroxypropionyl-CoA dehydratase Ac3H11_2775 Ac3H11_4006
iolA malonate semialdehyde dehydrogenase (CoA-acylating) Ac3H11_4340 Ac3H11_2357
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Ac3H11_4091 Ac3H11_2465
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit Ac3H11_2278
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit Ac3H11_2278
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components Ac3H11_2278
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) Ac3H11_1693 Ac3H11_104
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) Ac3H11_1695
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) Ac3H11_1692 Ac3H11_1936
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 Ac3H11_2275 Ac3H11_3016
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit Ac3H11_2275 Ac3H11_4028
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit Ac3H11_2276 Ac3H11_3010
pco propanyl-CoA oxidase Ac3H11_3533
prpD 2-methylcitrate dehydratase
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 Sep 17 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 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