L-leucine catabolism in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

L-leucine catabolism in Herbaspirillum seropedicae SmR1

Best path

livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB

Also see fitness data for the top candidates

Rules

Overview: Leucine degradation in GapMind is based on MetaCyc pathway L-leucine degradation I, via branched alpha-keto acid dehydrogenase (link). Other pathways for are not included here because they are not linked to sequence (link) or do not result in carbon incorporation.

all: leucine-transport, ilvE, BKD, liuA, liuB, liuD, liuC, liuE and acetoacetate-degradation

Comment: After transamination to 4-methyl-2-oxopentanoate by ilvE, kbd oxidatively decarboxylates it to isovaleryl-CoA (also known as 3-methylbutanoyl-CoA), liuA oxidizes it to 3-methylcrotonyl-CoA, liuBD carboxylates it to 3-methylglutaconyl-CoA, liuC hydrates it to hydroxymethylglutaryl-CoA, and liuE hydrolyzes it to acetoacetate and acetyl-CoA.

acetoacetate-degradation: acetoacetate-activation and atoB

Comment: The acetoacetate is activated to acetoacetyl-CoA, and cleaved by acetyl-CoA acetyltransferase, giving two acetyl-CoA.

acetoacetate-activation:

atoA and atoD
or aacS
Comment: acetyl-CoA:acetoacetyl-CoA transferase (sometimes given EC 2.8.3.9 or EC 2.8.3.8) or succinyl-CoA:acetoacetyl-CoA transferase (EC 2.8.3.5, also known as 3-oxoacid CoA-transferase) can activate acetoacetate. These have an A and B subunit. Alternatively, an ATP-dependent ligase (aacS) can activate acetoacetate (EC 6.2.1.16).

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).

leucine-transport:

livF, livG, livJ, livH and livM
or natA, natB, natC, natD and natE
or aapJ, aapQ, aapM and aapP
or leuT
or brnQ
or bcaP
or Bap2
or AAP1
Comment: Transporters were identified using query: transporter:leucine:L-leucine

39 steps (24 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
livF	L-leucine ABC transporter, ATPase component 1 (LivF/BraG)	HSERO_RS05975	HSERO_RS00900
livG	L-leucine ABC transporter, ATPase component 2 (LivG/BraF)	HSERO_RS05970	HSERO_RS00895
livJ	L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)	HSERO_RS08270	HSERO_RS17350
livH	L-leucine ABC transporter, permease component 1 (LivH/BraD)	HSERO_RS05960	HSERO_RS00885
livM	L-leucine ABC transporter, permease component 2 (LivM/BraE)	HSERO_RS08280	HSERO_RS05965
ilvE	L-leucine transaminase	HSERO_RS03330	HSERO_RS22025
ofo	branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused	HSERO_RS21380	HSERO_RS12755
liuA	isovaleryl-CoA dehydrogenase	HSERO_RS23440	HSERO_RS04905
liuB	3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit	HSERO_RS23460	HSERO_RS01925
liuD	3-methylcrotonyl-CoA carboxylase, beta subunit	HSERO_RS23455
liuC	3-methylglutaconyl-CoA hydratase	HSERO_RS15435	HSERO_RS23475
liuE	hydroxymethylglutaryl-CoA lyase	HSERO_RS23475
atoA	acetoacetyl-CoA transferase, A subunit	HSERO_RS23190	HSERO_RS20000
atoD	acetoacetyl-CoA transferase, B subunit	HSERO_RS23185	HSERO_RS19995
atoB	acetyl-CoA C-acetyltransferase	HSERO_RS01180	HSERO_RS04635
Alternative steps:
aacS	acetoacetyl-CoA synthetase
AAP1	L-leucine permease AAP1
aapJ	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ
aapM	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM)	HSERO_RS07530	HSERO_RS23030
aapP	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP	HSERO_RS19240	HSERO_RS17555
aapQ	ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)	HSERO_RS19340	HSERO_RS17565
Bap2	L-leucine permease Bap2
bcaP	L-leucine uptake transporter BcaP
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-leucine:Na+ symporter BrnQ/BraB
leuT	L-leucine:Na+ symporter LeuT
lpd	branched-chain alpha-ketoacid dehydrogenase, E3 component	HSERO_RS07315	HSERO_RS14875
natA	L-leucine ABC transporter, ATPase component 1 (NatA)	HSERO_RS14705	HSERO_RS08285
natB	L-leucine ABC transporter, substrate-binding component NatB
natC	L-leucine ABC transporter, permease component 1 (NatC)	HSERO_RS14700
natD	L-leucine ABC transporter, permease component 2 (NatD)	HSERO_RS05960	HSERO_RS00885
natE	L-leucine 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
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