GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Ochrobactrum thiophenivorans DSM 7216

Best path

livF, livG, livJ, livH, livM, 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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) CEV31_RS03670 CEV31_RS13095
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) CEV31_RS03675 CEV31_RS14825
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) CEV31_RS05815 CEV31_RS03660
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) CEV31_RS03685 CEV31_RS13110
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) CEV31_RS03680 CEV31_RS14830
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit CEV31_RS15005 CEV31_RS11960
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit CEV31_RS15010 CEV31_RS11955
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component CEV31_RS15015 CEV31_RS04690
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component CEV31_RS15020 CEV31_RS11945
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase CEV31_RS01035 CEV31_RS05790
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase CEV31_RS05620 CEV31_RS15760
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase CEV31_RS02655 CEV31_RS03445
fadA 2-methylacetoacetyl-CoA thiolase CEV31_RS03605 CEV31_RS02650
pccA propionyl-CoA carboxylase, alpha subunit CEV31_RS12235 CEV31_RS05800
pccB propionyl-CoA carboxylase, beta subunit CEV31_RS12230 CEV31_RS05795
epi methylmalonyl-CoA epimerase CEV31_RS10320
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit CEV31_RS12240
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit CEV31_RS12240
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase CEV31_RS06075
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) CEV31_RS06075
Bap2 L-isoleucine permease Bap2 CEV31_RS18290
bcaP L-isoleucine uptake transporter BcaP/CitA
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase CEV31_RS02710 CEV31_RS08355
hpcD 3-hydroxypropionyl-CoA dehydratase CEV31_RS04900 CEV31_RS05620
iolA malonate semialdehyde dehydrogenase (CoA-acylating) CEV31_RS03890 CEV31_RS08350
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components CEV31_RS12240
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) CEV31_RS14825 CEV31_RS02690
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) CEV31_RS14835 CEV31_RS02700
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) CEV31_RS03670 CEV31_RS17005
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
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit CEV31_RS12235 CEV31_RS10995
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pco propanyl-CoA oxidase CEV31_RS11735 CEV31_RS05790
prpB 2-methylisocitrate lyase CEV31_RS15595
prpC 2-methylcitrate synthase CEV31_RS12050
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase CEV31_RS04090
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