GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Nocardioides dokdonensis FR1436

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) I601_RS10465 I601_RS02130
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) I601_RS05910 I601_RS02125
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) I601_RS10450 I601_RS05905
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) I601_RS05895 I601_RS02140
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit I601_RS05215 I601_RS05890
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit I601_RS05210 I601_RS05885
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component I601_RS05880 I601_RS05205
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component I601_RS01085 I601_RS05875
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase I601_RS00925 I601_RS07220
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase I601_RS19165 I601_RS05525
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase I601_RS05790 I601_RS09355
fadA 2-methylacetoacetyl-CoA thiolase I601_RS03035 I601_RS17150
pccA propionyl-CoA carboxylase, alpha subunit I601_RS00935 I601_RS06760
pccB propionyl-CoA carboxylase, beta subunit I601_RS00885 I601_RS18425
epi methylmalonyl-CoA epimerase I601_RS19255
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit I601_RS01215 I601_RS19390
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit I601_RS01215 I601_RS19390
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase I601_RS17670
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) I601_RS17670
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase I601_RS09160 I601_RS02690
hpcD 3-hydroxypropionyl-CoA dehydratase I601_RS16330 I601_RS19165
iolA malonate semialdehyde dehydrogenase (CoA-acylating) I601_RS07030 I601_RS08960
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components I601_RS01215 I601_RS08155
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) I601_RS18175 I601_RS10945
natB L-isoleucine ABC transporter, substrate-binding component NatB
natC L-isoleucine ABC transporter, permease component 1 (NatC) I601_RS18180
natD L-isoleucine ABC transporter, permease component 2 (NatD) I601_RS18185
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) I601_RS18170 I601_RS10465
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 I601_RS03810
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit I601_RS00950 I601_RS00935
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit I601_RS05415
pco propanyl-CoA oxidase I601_RS08210 I601_RS10230
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase I601_RS09645 I601_RS03455
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 I601_RS03805
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 24 2021. 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