L-valine catabolism in Azospirillum humicireducens SgZ-5

GapMind for catabolism of small carbon sources

L-valine catabolism in Azospirillum humicireducens SgZ-5

Best path

livF, livG, livJ, livH, livM, ofo, acdH, ech, bch, mmsB, mmsA, pccA, pccB, epi, mcm-large, mcm-small

Rules

Overview: Valine degradation in GapMind is based on MetaCyc pathway L-valine degradation I (link). The other pathways do not produce any fixed carbon and are not included.

all: valine-transport, BKD, acdH, ech, bch, mmsB, mmsA and propionyl-CoA-degradation

Comment: An aminotransferase (not represented) forms 3-methyl-2-oxobutanoate, the decarboxylating alpha-ketoacid dehydrogenase (BKD) forms isobutanoyl-CoA, dehydrogenase acdH forms methylacrylyl-CoA (2-methylprop-2-enoyl-CoA), the hydratase ech forms (S)-3-hydroxy-isobutaonoyl-CoA, a hydrolase forms (S)-3-hydroxy-isobutanoate, a dehydrogenase forms (S)-methylmalonate semialdehyde (2-methyl-3-oxopropanoate), and a decarboxylating dehydrogenase forms propionyl-CoA.

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.

valine-transport:

livF, livG, livJ, livH and livM
or natA, natB, natC, natD and natE
or Bap2
or brnQ
or phtJ
or bcaP
Comment: Transporters were identified using query: transporter:valine:L-valine:val

47 steps (36 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
livF	L-valine ABC transporter, ATPase component 1 (LivF/BraG)	A6A40_RS13375	A6A40_RS10195
livG	L-valine ABC transporter, ATPase component 2 (LivG/BraF)	A6A40_RS13380	A6A40_RS10200
livJ	L-valine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)	A6A40_RS13365	A6A40_RS30135
livH	L-valine ABC transporter, permease component 1 (LivH/BraD)	A6A40_RS13390	A6A40_RS09880
livM	L-valine ABC transporter, permease component 2 (LivM/BraE)	A6A40_RS13385	A6A40_RS10205
ofo	branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused	A6A40_RS06170
acdH	isobutyryl-CoA dehydrogenase	A6A40_RS19630	A6A40_RS25755
ech	(S)-3-hydroxybutanoyl-CoA hydro-lyase	A6A40_RS14715	A6A40_RS26600
bch	3-hydroxyisobutyryl-CoA hydrolase	A6A40_RS04755	A6A40_RS14715
mmsB	3-hydroxyisobutyrate dehydrogenase	A6A40_RS25760	A6A40_RS21835
mmsA	methylmalonate-semialdehyde dehydrogenase	A6A40_RS18190	A6A40_RS25750
pccA	propionyl-CoA carboxylase, alpha subunit	A6A40_RS28245	A6A40_RS19645
pccB	propionyl-CoA carboxylase, beta subunit	A6A40_RS28240	A6A40_RS19635
epi	methylmalonyl-CoA epimerase	A6A40_RS08555
mcm-large	methylmalonyl-CoA mutase, large (catalytic) subunit	A6A40_RS28250
mcm-small	methylmalonyl-CoA mutase, small (adenosylcobamide-binding) subunit	A6A40_RS28250
Alternative steps:
acn	(2R,3S)-2-methylcitrate dehydratase	A6A40_RS30175	A6A40_RS10110
acnD	2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)	A6A40_RS10110
Bap2	L-valine permease Bap2
bcaP	L-valine uptake transporter BcaP/CitA
bkdA	branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit	A6A40_RS05300	A6A40_RS28475
bkdB	branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit	A6A40_RS03060	A6A40_RS05295
bkdC	branched-chain alpha-ketoacid dehydrogenase, E2 component	A6A40_RS00800	A6A40_RS05290
brnQ	L-valine:cation symporter BrnQ/BraZ/BraB
dddA	3-hydroxypropionate dehydrogenase	A6A40_RS28085	A6A40_RS13555
hpcD	3-hydroxypropionyl-CoA dehydratase	A6A40_RS14715	A6A40_RS26605
iolA	malonate semialdehyde dehydrogenase (CoA-acylating)	A6A40_RS18190	A6A40_RS25750
lpd	branched-chain alpha-ketoacid dehydrogenase, E3 component	A6A40_RS10440	A6A40_RS20715
mcmA	methylmalonyl-CoA mutase, fused catalytic and adenosylcobamide-binding components	A6A40_RS28250
natA	L-valine ABC transporter, ATPase component 1 (NatA)	A6A40_RS22590	A6A40_RS21790
natB	L-valine ABC transporter, substrate-binding component NatB
natC	L-valine ABC transporter, permease component 1 (NatC)	A6A40_RS22595	A6A40_RS15195
natD	L-valine ABC transporter, permease component 2 (NatD)	A6A40_RS15190	A6A40_RS10210
natE	L-valine ABC transporter, ATPase component 2 (NatE)	A6A40_RS21795	A6A40_RS29805
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	A6A40_RS28245	A6A40_RS04105
pccA2	propionyl-CoA carboxylase, biotin carboxylase subunit	A6A40_RS19645
pco	propanyl-CoA oxidase	A6A40_RS26290
phtJ	L-valine uptake permease PhtJ
prpB	2-methylisocitrate lyase	A6A40_RS25400	A6A40_RS21800
prpC	2-methylcitrate synthase	A6A40_RS13735	A6A40_RS04630
prpD	2-methylcitrate dehydratase
prpF	methylaconitate isomerase
vorA	branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB	branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB	A6A40_RS22220
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.

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