GapMind for catabolism of small carbon sources

 

L-isoleucine catabolism in Sinorhizobium meliloti 1021

Best path

livF, livG, livJ, livH, livM, bkdA, bkdB, bkdC, lpd, acdH, ech, ivdG, fadA, pccA, pccB, epi, mcm-large, mcm-small

Also see fitness data for the top candidates

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) SMc01948 SMc02358
livG L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF) SMc01949 SMc02357
livJ L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) SMc00078 SMc01946
livH L-isoleucine ABC transporter, permease component 1 (LivH/BraD) SMc01951 SMc02359
livM L-isoleucine ABC transporter, permease component 2 (LivM/BraE) SMc01950
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit SMc03201 SMc01030
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit SMc03202 SM_b20020
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component SMc03203 SM_b20019
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component SMc03204 SMc01035
acdH (2S)-2-methylbutanoyl-CoA dehydrogenase SM_b20753 SMa1400
ech 2-methyl-3-hydroxybutyryl-CoA hydro-lyase SMc01153 SMc02227
ivdG 3-hydroxy-2-methylbutyryl-CoA dehydrogenase SMa1452 SMc00572
fadA 2-methylacetoacetyl-CoA thiolase SMc03879 SMa1450
pccA propionyl-CoA carboxylase, alpha subunit SM_b20756 SM_b21124
pccB propionyl-CoA carboxylase, beta subunit SM_b20755 SM_b21122
epi methylmalonyl-CoA epimerase SMc01930
mcm-large methylmalonyl-CoA mutase, large (catalytic) subunit SM_b20757
mcm-small methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit SM_b20757
Alternative steps:
acn (2R,3S)-2-methylcitrate dehydratase SMc03846
acnD 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) SMc03846
Bap2 L-isoleucine permease Bap2
bcaP L-isoleucine uptake transporter BcaP/CitA
brnQ L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA 3-hydroxypropionate dehydrogenase SMc03116 SM_b20496
hpcD 3-hydroxypropionyl-CoA dehydratase SMc01153 SMc04398
iolA malonate semialdehyde dehydrogenase (CoA-acylating) SMc00781 SM_b20891
mcmA methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components SM_b20757
natA L-isoleucine ABC transporter, ATPase component 1 (NatA) SMc03120 SMc01949
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) SM_b20604
natE L-isoleucine ABC transporter, ATPase component 2 (NatE) SMc01948 SMc02358
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 SM_b20756 SMc01345
pccA2 propionyl-CoA carboxylase, biotin carboxylase subunit SMc03895
pco propanyl-CoA oxidase SM_b21181 SM_b21121
prpB 2-methylisocitrate lyase SMc00768
prpC 2-methylcitrate synthase SMc02087
prpD 2-methylcitrate dehydratase
prpF methylaconitate isomerase SMc00497
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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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