GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Carboxydothermus pertinax Ug1

Best path

livF, livG, livJ, livH, livM, vorA*, vorB, vorC, 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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) cpu_RS01320 cpu_RS01325
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) cpu_RS01325 cpu_RS11745
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) cpu_RS01340 cpu_RS13285
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) cpu_RS01335
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) cpu_RS01330
vorA* branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA cpu_RS03820 with cpu_RS03815
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB cpu_RS03825 cpu_RS08605
vorC branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase cpu_RS11860 cpu_RS02525
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase cpu_RS10405 cpu_RS10860
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase cpu_RS11320 cpu_RS09085
fadA 2-methylacetoacetyl-CoA thiolase cpu_RS10880 cpu_RS10705
pccA propionyl-CoA carboxylase, alpha subunit cpu_RS04525 cpu_RS07800
pccB propionyl-CoA carboxylase, beta subunit cpu_RS07795 cpu_RS01750
epi methylmalonyl-CoA epimerase cpu_RS07790
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit cpu_RS04735 cpu_RS07780
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit cpu_RS04730 cpu_RS07785
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
Bap2 L-isoleucine permease Bap2 cpu_RS11915
bcaP L-isoleucine uptake transporter BcaP/CitA cpu_RS07250
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
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase cpu_RS10405 cpu_RS10860
iolA malonate semialdehyde dehydrogenase (CoA-acylating)
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component cpu_RS02370
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components cpu_RS04735 cpu_RS07780
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) cpu_RS01325 cpu_RS01320
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) cpu_RS01335
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) cpu_RS01320 cpu_RS01325
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 cpu_RS03820
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit cpu_RS04525 cpu_RS07800
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase cpu_RS01705 cpu_RS10430
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase

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