GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Sinorhizobium fredii NGR234

Best path

livF, livG, livJ, livH, livM, 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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) NGR_RS23730 NGR_RS21555
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) NGR_RS23735 NGR_RS21550
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) NGR_RS14075 NGR_RS23720
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) NGR_RS23745 NGR_RS21540
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) NGR_RS23740 NGR_RS10930
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit NGR_RS26080 NGR_RS17680
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit NGR_RS26085 NGR_RS05450
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component NGR_RS26090 NGR_RS09295
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component NGR_RS26095 NGR_RS17710
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase NGR_RS10015 NGR_RS05525
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase NGR_RS29675 NGR_RS12210
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase NGR_RS01290 NGR_RS14530
fadA 2-methylacetoacetyl-CoA thiolase NGR_RS27475 NGR_RS26100
pccA propionyl-CoA carboxylase, alpha subunit NGR_RS10035 NGR_RS05540
pccB propionyl-CoA carboxylase, beta subunit NGR_RS10025 NGR_RS05530
epi methylmalonyl-CoA epimerase NGR_RS16610
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit NGR_RS10040
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit NGR_RS10040
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase NGR_RS27315 NGR_RS03745
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) NGR_RS27315 NGR_RS03745
Bap2 L-isoleucine permease Bap2 NGR_RS11085
bcaP L-isoleucine uptake transporter BcaP/CitA
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase NGR_RS02360 NGR_RS03665
hpcD 3-hydroxypropionyl-CoA dehydratase NGR_RS29675 NGR_RS27640
iolA malonate semialdehyde dehydrogenase (CoA-acylating) NGR_RS13065 NGR_RS23205
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components NGR_RS10040
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) NGR_RS10935 NGR_RS28290
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) NGR_RS28280 NGR_RS10455
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) NGR_RS10940 NGR_RS23730
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
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit NGR_RS10035 NGR_RS16825
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase NGR_RS06370
prpB 2-methylisocitrate lyase NGR_RS18405
prpC 2-methylcitrate synthase NGR_RS18005
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase NGR_RS02985
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