GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Erythrobacter marinus HWDM-33

Best path

Bap2, 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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
Bap2 L-isoleucine permease Bap2
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit AAV99_RS08475 AAV99_RS09615
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit AAV99_RS08480 AAV99_RS09610
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component AAV99_RS08485 AAV99_RS09200
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component AAV99_RS09190 AAV99_RS07335
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase AAV99_RS13300 AAV99_RS03120
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase AAV99_RS05725 AAV99_RS05720
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase AAV99_RS00990 AAV99_RS03635
fadA 2-methylacetoacetyl-CoA thiolase AAV99_RS09865 AAV99_RS12435
pccA propionyl-CoA carboxylase, alpha subunit AAV99_RS05715 AAV99_RS13205
pccB propionyl-CoA carboxylase, beta subunit AAV99_RS05680 AAV99_RS03105
epi methylmalonyl-CoA epimerase AAV99_RS05690 AAV99_RS12455
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit AAV99_RS05695
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit AAV99_RS05695 AAV99_RS11005
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase AAV99_RS02180
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) AAV99_RS02180
bcaP L-isoleucine uptake transporter BcaP/CitA AAV99_RS13360
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase
hpcD 3-hydroxypropionyl-CoA dehydratase AAV99_RS05725 AAV99_RS12275
iolA malonate semialdehyde dehydrogenase (CoA-acylating) AAV99_RS05730 AAV99_RS05570
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) AAV99_RS05200 AAV99_RS12745
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) AAV99_RS05200 AAV99_RS12745
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD)
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE)
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components AAV99_RS05695
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) AAV99_RS05200
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)
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) AAV99_RS12745 AAV99_RS05200
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA AAV99_RS08370
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB AAV99_RS08375
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit AAV99_RS05715 AAV99_RS10750
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit AAV99_RS05715
pco propanyl-CoA oxidase AAV99_RS06380 AAV99_RS03120
prpB 2-methylisocitrate lyase
prpC 2-methylcitrate synthase AAV99_RS09730
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 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