GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Rhizobium etli CFN 42

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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) RHE_RS16995 RHE_RS25475
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) RHE_RS17000 RHE_RS25470
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) RHE_RS15820 RHE_RS16985
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) RHE_RS17010 RHE_RS25480
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) RHE_RS17005
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit RHE_RS23200 RHE_RS09870
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit RHE_RS23205 RHE_RS09875
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component RHE_RS23210 RHE_RS19880
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component RHE_RS23215 RHE_RS09895
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase RHE_RS23195 RHE_RS23165
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase RHE_RS01800 RHE_RS02825
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase RHE_RS23185 RHE_RS07365
fadA 2-methylacetoacetyl-CoA thiolase RHE_RS20545 RHE_RS23190
pccA propionyl-CoA carboxylase, alpha subunit RHE_RS11385 RHE_RS23155
pccB propionyl-CoA carboxylase, beta subunit RHE_RS11415 RHE_RS23160
epi methylmalonyl-CoA epimerase RHE_RS08290
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit RHE_RS22800
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit RHE_RS22800
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase RHE_RS20170
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) RHE_RS20170
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase RHE_RS25490 RHE_RS22360
hpcD 3-hydroxypropionyl-CoA dehydratase RHE_RS01800 RHE_RS08795
iolA malonate semialdehyde dehydrogenase (CoA-acylating) RHE_RS03695 RHE_RS16180
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components RHE_RS22800
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) RHE_RS25470 RHE_RS17000
natB L-isoleucine ABC transporter, substrate-binding component NatB RHE_RS15140
natC L-isoleucine ABC transporter, permease component 1 (NatC) RHE_RS17005
natD L-isoleucine ABC transporter, permease component 2 (NatD) RHE_RS25480
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) RHE_RS16995 RHE_RS17625
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 RHE_RS11385 RHE_RS09550
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit RHE_RS23155
pco propanyl-CoA oxidase RHE_RS25445
prpB 2-methylisocitrate lyase RHE_RS03605
prpC 2-methylcitrate synthase RHE_RS09835 RHE_RS11160
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
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