GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Chromobacterium vaccinii MWU205

Best path

livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, prpC, acnD, prpF, acn, prpB

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
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) VL52_RS15485 VL52_RS03360
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) VL52_RS15490 VL52_RS03360
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) VL52_RS09675 VL52_RS22490
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) VL52_RS15500
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) VL52_RS15495
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused VL52_RS19015
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase VL52_RS21025 VL52_RS19965
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase VL52_RS10360 VL52_RS21030
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase VL52_RS17095 VL52_RS02940
fadA 2-methylacetoacetyl-CoA thiolase VL52_RS14225 VL52_RS21005
prpC 2-methylcitrate synthase VL52_RS06910 VL52_RS01125
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) VL52_RS06920 VL52_RS13705
prpF methylaconitate isomerase VL52_RS06925 VL52_RS07045
acn (2R,3S)-2-methylcitrate dehydratase VL52_RS06920 VL52_RS16820
prpB 2-methylisocitrate lyase VL52_RS13445 VL52_RS06905
Alternative steps:
Bap2 L-isoleucine permease Bap2 VL52_RS10410 VL52_RS13800
bcaP L-isoleucine uptake transporter BcaP/CitA VL52_RS03530
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component VL52_RS01115
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase VL52_RS11315
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase VL52_RS18865 VL52_RS21030
iolA malonate semialdehyde dehydrogenase (CoA-acylating) VL52_RS11940 VL52_RS21020
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component VL52_RS06780 VL52_RS01105
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) VL52_RS15490 VL52_RS03360
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) VL52_RS15500
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) VL52_RS15485 VL52_RS03360
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB
pccA propionyl-CoA carboxylase, alpha subunit VL52_RS19945 VL52_RS01580
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit VL52_RS01580 VL52_RS19945
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit VL52_RS19955
pco propanyl-CoA oxidase VL52_RS20895 VL52_RS19965
prpD 2-methylcitrate dehydratase
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