L-isoleucine catabolism in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

L-isoleucine catabolism in Herbaspirillum seropedicae SmR1

Best path

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

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).

all: isoleucine-transport, BKD, acdH, ech, ivdG, fadA and propionyl-CoA-degradation

Comment: A transaminase (which is not represented) converts isoleucine to (3S)-3-methyl-2-oxopentanoate, the decarboxylating dehydrogenase BKD forms (2S)-2-methylbutanoyl-CoA, dehydrogenase acdH forms (E)-2-methylcrotonyl-CoA, hydratase ech forms (2S,3S)-3-hydroxy-2-methylbutanoyl-CoA, dehydrogenase ivdG forms 2-methylacetoacetyl-CoA, and a thiolase forms propanioyl-CoA and acetyl-CoA. (The initial transaminase is not represented because amino-acid aminotransferases are often non-specific.)

BKD:

bkdA, bkdB, bkdC and lpd
or vorA, vorB and vorC
or ofoA and ofoB
or ofo
Comment: These decarboxylating dehydrogenases act on 4-methyl-2-oxopentanoate, 3-methyl-2-oxobutanoate (2-oxoisovalerate) and (S)-3-methyl-2-oxopentanoate and are known as the branched-chain alpha-ketoacid dehydrogenases. They can pass electrons to NAD (EC 1.2.1.25) or to ferredoxin (EC 1.2.7.7). The NAD-dependent enzyme is the sum of three activities: EC 1.2.4.4 (the 4-methyl-2-oxopentanoate dehydrogenase, with transfer to the lipopoyllysine residue of 2.3.1.168) which is itself heteromeric, with alpha and beta subunits; EC 2.3.1.168 (dihydrolipoyllysine-residue (3-methylbutanoyl)transferase); and EC 1.8.1.4 (dihydrolipoyl dehydrogenase, transferring electrons to NAD). The well-characterized ferredoxin-dependent enzymes have 3 subunits (vorABC) or 2 subunits (ofoAB). Genetic data identified a fused ferredoxin-dependent enzyme with just 1 subunit (ofo).

propionyl-CoA-degradation:

prpC, prpD, acn and prpB
or prpC, acnD, prpF, acn and prpB
or propionyl-CoA-carboxylase, epi and methylmalonyl-CoA-mutase
or pco, hpcD, dddA and iolA
Comment: In 2-methylcitrate cycle I, propionyl-CoA is combined with oxalacetate (by prpC) to give methylcitrate, dehydrated to cis-2-methylaconitate by prpD, hydrated to (2R,3S)-2-methylisocitrate, and a lyase produces pyruvate and succinate. (We consider succinate as a central intermediate, as most organisms can activate it to succinyl-CoA or can oxidize it to fumarate and convert that to oxaloacetate.) In 2-methylcitrate cycle II, a different dehydratase (acnD) and an isomerase (prpF) replace the dehydratase prpD; acnD dehydrates (2S,3S)-2-methylcitrate to 2-methyl-trans-aconitate, and prpF isomerizes it to cis-2-methylaconitate. In propanoyl CoA degradation I, propionyl-CoA carboxylase forms (S)-methylmalonyl-CoA, methylmalonyl-CoA epimerase forms (R)-methylmalonyl-CoA, and methylmalonyl-CoA mutase forms succinyl-CoA, which is a central metabolite. (Note that methylmalonyl-CoA mutase requires adenosylcobamide, a form of vitamin B12, for activity.) In propanoyl-CoA degradation II: propionyl-CoA is oxidized to acrylyl-CoA by pco, hydrated to 3-hydroxypropionyl-CoA, hydrolzed to 3-hydroxypropionate, oxidized to 3-oxopropionate (malonate semialdehyde), and oxidized to acetyl-CoA and CO2.

methylmalonyl-CoA-mutase:

mcmA
or mcm-large and mcm-small
Comment: methylmalonyl-CoA mutase has a catalytic domain and a B12-binding domain. These are usually found in the same protein, which we call mcmA. In Metallosphaera and Pyrococcus, the B12-binding domain is a separate subunit. In Propionibacterium and Methylorubrum, there is an additional subunit with a catalytic domain only; this may have a protective role (PMID:14734568) and is not described here. There's also a mcm-interacting GTPase (known as MeaB or YgfD) that loads B12 onto mcm and protects it from inactivation (see PMC4631608); this is not described here. Some fused mcm proteins include a MeaB domain as well (i.e., Q8F222, Q8Y2U5).

propionyl-CoA-carboxylase:

pccA and pccB
or pccA1, pccA2 and pccB
Comment: propionyl-CoA carboxylase is a heteromer, usually with alpha and beta subunits pccAB. Haloferax mediterranei has a third subunit as well (pccX), which is not described here. Acidianus brierleyi has a diverged pccA split into two pieces.

isoleucine-transport:

livF, livG, livJ, livH and livM
or natA, natB, natC, natD and natE
or Bap2
or brnQ
or bcaP
Comment: Transporters were identified using query: transporter:isoleucine:L-isoleucine:ile and non-specific large neutral amino acid tranpsorters from mammals were ignored.

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)	HSERO_RS05975	HSERO_RS00900
livG	L-isoleucine ABC transporter, ATPase component 2 (LivG/BraF)	HSERO_RS05970	HSERO_RS00895
livJ	L-isoleucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)	HSERO_RS08270	HSERO_RS17350
livH	L-isoleucine ABC transporter, permease component 1 (LivH/BraD)	HSERO_RS05960	HSERO_RS00885
livM	L-isoleucine ABC transporter, permease component 2 (LivM/BraE)	HSERO_RS08280	HSERO_RS05965
ofo	branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused	HSERO_RS21380	HSERO_RS12755
acdH	(2S)-2-methylbutanoyl-CoA dehydrogenase	HSERO_RS12750	HSERO_RS04640
ech	2-methyl-3-hydroxybutyryl-CoA hydro-lyase	HSERO_RS01260	HSERO_RS19405
ivdG	3-hydroxy-2-methylbutyryl-CoA dehydrogenase	HSERO_RS05890	HSERO_RS04630
fadA	2-methylacetoacetyl-CoA thiolase	HSERO_RS01180	HSERO_RS04635
prpC	2-methylcitrate synthase	HSERO_RS15655	HSERO_RS14890
acnD	2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)	HSERO_RS11425	HSERO_RS14940
prpF	methylaconitate isomerase	HSERO_RS11420	HSERO_RS07335
acn	(2R,3S)-2-methylcitrate dehydratase	HSERO_RS11425	HSERO_RS14940
prpB	2-methylisocitrate lyase	HSERO_RS10565	HSERO_RS15660
Alternative steps:
Bap2	L-isoleucine permease Bap2
bcaP	L-isoleucine uptake transporter BcaP/CitA
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	HSERO_RS14880	HSERO_RS07310
brnQ	L-isoleucine:cation symporter BrnQ/BraZ/BraB
dddA	3-hydroxypropionate dehydrogenase	HSERO_RS24000	HSERO_RS23855
epi	methylmalonyl-CoA epimerase
hpcD	3-hydroxypropionyl-CoA dehydratase	HSERO_RS19405	HSERO_RS12745
iolA	malonate semialdehyde dehydrogenase (CoA-acylating)	HSERO_RS24005	HSERO_RS23245
lpd	branched-chain alpha-ketoacid dehydrogenase, E3 component	HSERO_RS07315	HSERO_RS14875
mcm-large	methylmalonyl-CoA mutase, large (catalytic) subunit
mcm-small	methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit	HSERO_RS21740
mcmA	methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components
natA	L-isoleucine ABC transporter, ATPase component 1 (NatA)	HSERO_RS08920	HSERO_RS14705
natB	L-isoleucine ABC transporter, substrate-binding component NatB
natC	L-isoleucine ABC transporter, permease component 1 (NatC)	HSERO_RS14700
natD	L-isoleucine ABC transporter, permease component 2 (NatD)	HSERO_RS05960	HSERO_RS00885
natE	L-isoleucine ABC transporter, ATPase component 2 (NatE)	HSERO_RS08290	HSERO_RS08925
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	HSERO_RS23460	HSERO_RS01925
pccA1	propionyl-CoA carboxylase, biotin carboxyl carrier subunit	HSERO_RS01925	HSERO_RS20550
pccA2	propionyl-CoA carboxylase, biotin carboxylase subunit
pccB	propionyl-CoA carboxylase, beta subunit	HSERO_RS23455
pco	propanyl-CoA oxidase	HSERO_RS23440
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 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources