GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Nocardiopsis baichengensis YIM 90130

Best path

natA, natB, natC, natD, natE, 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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) C892_RS0115130 C892_RS0110655
natB L-isoleucine ABC transporter, substrate-binding component NatB C892_RS0115140
natC L-isoleucine ABC transporter, permease component 1 (NatC) C892_RS0115125
natD L-isoleucine ABC transporter, permease component 2 (NatD) C892_RS0115120 C892_RS0104280
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) C892_RS0115135 C892_RS0110660
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit C892_RS0105120 C892_RS0112230
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit C892_RS0109110 C892_RS0105115
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component C892_RS0109115 C892_RS0105110
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component C892_RS0123470 C892_RS0114110
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase C892_RS0127300 C892_RS0124975
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase C892_RS0110920 C892_RS0113150
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase C892_RS0103765 C892_RS0113775
fadA 2-methylacetoacetyl-CoA thiolase C892_RS0126720 C892_RS0106330
pccA propionyl-CoA carboxylase, alpha subunit C892_RS0123485 C892_RS0127295
pccB propionyl-CoA carboxylase, beta subunit C892_RS0123495 C892_RS0127290
epi methylmalonyl-CoA epimerase C892_RS0118240
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit C892_RS0104600 C892_RS0118195
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit C892_RS0128095 C892_RS0104600
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase C892_RS0113040
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) C892_RS0113040
Bap2 L-isoleucine permease Bap2 C892_RS0102390
bcaP L-isoleucine uptake transporter BcaP/CitA C892_RS0120615
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase C892_RS0105225
hpcD 3-hydroxypropionyl-CoA dehydratase C892_RS0126825 C892_RS0107320
iolA malonate semialdehyde dehydrogenase (CoA-acylating) C892_RS0108545 C892_RS0126085
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) C892_RS0110660 C892_RS0115135
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) C892_RS0115130 C892_RS0110655
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) C892_RS0115120 C892_RS0104280
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) C892_RS0115125 C892_RS0110670
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components C892_RS0104600 C892_RS0118195
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 C892_RS0115965
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit C892_RS0127295 C892_RS0123485
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase C892_RS0110455 C892_RS0114500
prpB 2-methylisocitrate lyase C892_RS0122210
prpC 2-methylcitrate synthase C892_RS0125305 C892_RS0103950
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 C892_RS0115970
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