GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Arcobacter nitrofigilis DSM 7299

Best path

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

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.

39 steps (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) ARNIT_RS06940 ARNIT_RS08945
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) ARNIT_RS06935 ARNIT_RS08950
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) ARNIT_RS06920 ARNIT_RS08965
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) ARNIT_RS08960 ARNIT_RS06925
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) ARNIT_RS08955 ARNIT_RS06930
ilvE L-leucine transaminase ARNIT_RS01280 ARNIT_RS14135
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
liuA isovaleryl-CoA dehydrogenase
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit ARNIT_RS13965 ARNIT_RS00660
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit
liuC 3-methylglutaconyl-CoA hydratase ARNIT_RS06725
liuE hydroxymethylglutaryl-CoA lyase
aacS acetoacetyl-CoA synthetase
atoB acetyl-CoA C-acetyltransferase ARNIT_RS06730
Alternative steps:
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ ARNIT_RS02910
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) ARNIT_RS02900 ARNIT_RS16500
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP ARNIT_RS02895 ARNIT_RS13590
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) ARNIT_RS02905
atoA acetoacetyl-CoA transferase, A subunit
atoD acetoacetyl-CoA transferase, B subunit
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 ARNIT_RS13020
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component ARNIT_RS13025 ARNIT_RS09935
natA L-leucine ABC transporter, ATPase component 1 (NatA) ARNIT_RS08950 ARNIT_RS06935
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC)
natD L-leucine ABC transporter, permease component 2 (NatD) ARNIT_RS08960 ARNIT_RS06925
natE L-leucine ABC transporter, ATPase component 2 (NatE) ARNIT_RS08945 ARNIT_RS06940
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA ARNIT_RS10655
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB ARNIT_RS10660
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB ARNIT_RS10655
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 Apr 09 2024. 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