GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Sphingomonas indica Dd16

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 (30 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 B9N75_RS09025 B9N75_RS10410
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit B9N75_RS09030 B9N75_RS12980
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component B9N75_RS09035 B9N75_RS05030
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component B9N75_RS05895 B9N75_RS05035
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase B9N75_RS13445 B9N75_RS08665
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase B9N75_RS13460 B9N75_RS11255
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase B9N75_RS08655 B9N75_RS06390
fadA 2-methylacetoacetyl-CoA thiolase B9N75_RS12685 B9N75_RS13165
pccA propionyl-CoA carboxylase, alpha subunit B9N75_RS06755 B9N75_RS13145
pccB propionyl-CoA carboxylase, beta subunit B9N75_RS06795 B9N75_RS13150
epi methylmalonyl-CoA epimerase B9N75_RS06780
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit B9N75_RS06775
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit B9N75_RS06775
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase B9N75_RS04320
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) B9N75_RS04320
bcaP L-isoleucine uptake transporter BcaP/CitA B9N75_RS03485 B9N75_RS00325
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase B9N75_RS13465
hpcD 3-hydroxypropionyl-CoA dehydratase B9N75_RS13460 B9N75_RS11255
iolA malonate semialdehyde dehydrogenase (CoA-acylating) B9N75_RS13435 B9N75_RS04360
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) B9N75_RS06875 B9N75_RS12805
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) B9N75_RS06875 B9N75_RS06650
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 B9N75_RS06775
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) B9N75_RS06875 B9N75_RS03075
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) B9N75_RS06875 B9N75_RS05840
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 B9N75_RS09820
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit B9N75_RS11080 B9N75_RS06755
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase B9N75_RS12195
prpB 2-methylisocitrate lyase B9N75_RS04185
prpC 2-methylcitrate synthase B9N75_RS11750
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 B9N75_RS09810
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