GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Bradyrhizobium sp. BTAi1

Best path

livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcmA

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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) BBTA_RS24920 BBTA_RS13465
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) BBTA_RS24915 BBTA_RS33150
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BBTA_RS24925 BBTA_RS13980
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) BBTA_RS24905 BBTA_RS28020
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) BBTA_RS24910 BBTA_RS33165
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused BBTA_RS23430
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase BBTA_RS16750 BBTA_RS31195
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase BBTA_RS14030 BBTA_RS33140
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase BBTA_RS33225 BBTA_RS36315
fadA 2-methylacetoacetyl-CoA thiolase BBTA_RS35760 BBTA_RS35630
pccA propionyl-CoA carboxylase, alpha subunit BBTA_RS22990 BBTA_RS18960
pccB propionyl-CoA carboxylase, beta subunit BBTA_RS23485 BBTA_RS18955
epi methylmalonyl-CoA epimerase BBTA_RS21240
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components BBTA_RS14110
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase BBTA_RS01825
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) BBTA_RS01825
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BBTA_RS20850
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BBTA_RS20845
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BBTA_RS01895 BBTA_RS20835
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase BBTA_RS13920 BBTA_RS10200
hpcD 3-hydroxypropionyl-CoA dehydratase BBTA_RS14030 BBTA_RS08325
iolA malonate semialdehyde dehydrogenase (CoA-acylating) BBTA_RS16745 BBTA_RS30410
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BBTA_RS20830 BBTA_RS01905
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit BBTA_RS14110
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit BBTA_RS14110 BBTA_RS33075
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) BBTA_RS28610 BBTA_RS28010
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) BBTA_RS11930 BBTA_RS28620
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) BBTA_RS28605 BBTA_RS24920
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB BBTA_RS29555
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit BBTA_RS22990 BBTA_RS19730
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase BBTA_RS11430 BBTA_RS31195
prpB 2-methylisocitrate lyase BBTA_RS05345 BBTA_RS28000
prpC 2-methylcitrate synthase BBTA_RS35405 BBTA_RS21030
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase BBTA_RS29435 BBTA_RS04630
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB BBTA_RS29550
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