GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Photobacterium gaetbulicola Gung47

Best path

brnQ, bkdA, bkdB, bkdC, lpd, 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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB H744_RS25145 H744_RS09390
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit H744_RS04245 H744_RS26450
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit H744_RS04250 H744_RS26450
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component H744_RS04255 H744_RS15065
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component H744_RS12355 H744_RS03140
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase H744_RS04325 H744_RS04345
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase H744_RS10395 H744_RS14605
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase H744_RS04305 H744_RS22030
fadA 2-methylacetoacetyl-CoA thiolase H744_RS14600 H744_RS10390
prpC 2-methylcitrate synthase H744_RS05690 H744_RS21305
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) H744_RS05685
prpF methylaconitate isomerase H744_RS05680
acn (2R,3S)-2-methylcitrate dehydratase H744_RS05685 H744_RS12370
prpB 2-methylisocitrate lyase H744_RS24385 H744_RS05695
Alternative steps:
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
dddA 3-hydroxypropionate dehydrogenase H744_RS21070 H744_RS18120
epi methylmalonyl-CoA epimerase
hpcD 3-hydroxypropionyl-CoA dehydratase H744_RS04320 H744_RS14605
iolA malonate semialdehyde dehydrogenase (CoA-acylating) H744_RS03200 H744_RS04330
livF L-isoleucine ABC transporter, ATPase component 1 (LivF/BraG) H744_RS07085 H744_RS12065
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) H744_RS12065 H744_RS07090
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) H744_RS07100
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE)
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) H744_RS12065 H744_RS07090
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) H744_RS07085 H744_RS12065
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
pccA propionyl-CoA carboxylase, alpha subunit H744_RS09235
pccA1 propionyl-CoA carboxylase, biotin carboxyl carrier subunit H744_RS09235
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit
pccB propionyl-CoA carboxylase, beta subunit H744_RS04350
pco propanyl-CoA oxidase H744_RS04345
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