GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Sinorhizobium fredii NGR234

Best path

livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, 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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) NGR_RS23730 NGR_RS21555
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) NGR_RS23735 NGR_RS21550
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) NGR_RS23720 NGR_RS14075
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) NGR_RS23745 NGR_RS21540
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) NGR_RS23740 NGR_RS10930
ilvE L-leucine transaminase NGR_RS28850 NGR_RS21050
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit NGR_RS26080 NGR_RS17680
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit NGR_RS26085 NGR_RS05450
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component NGR_RS26090 NGR_RS09295
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component NGR_RS26095 NGR_RS17710
liuA isovaleryl-CoA dehydrogenase NGR_RS05525 NGR_RS16735
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit NGR_RS05540 NGR_RS10035
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit NGR_RS05530 NGR_RS10025
liuC 3-methylglutaconyl-CoA hydratase NGR_RS05550 NGR_RS14350
liuE hydroxymethylglutaryl-CoA lyase NGR_RS05545
aacS acetoacetyl-CoA synthetase NGR_RS13035 NGR_RS01395
atoB acetyl-CoA C-acetyltransferase NGR_RS27475 NGR_RS26100
Alternative steps:
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ NGR_RS17855
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) NGR_RS17845 NGR_RS23815
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP NGR_RS17840 NGR_RS10540
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) NGR_RS17850 NGR_RS02885
atoA acetoacetyl-CoA transferase, A subunit
atoD acetoacetyl-CoA transferase, B subunit
Bap2 L-leucine permease Bap2 NGR_RS11085
bcaP L-leucine uptake transporter BcaP
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
natA L-leucine ABC transporter, ATPase component 1 (NatA) NGR_RS10935 NGR_RS28290
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC) NGR_RS10930
natD L-leucine ABC transporter, permease component 2 (NatD) NGR_RS28280 NGR_RS10455
natE L-leucine ABC transporter, ATPase component 2 (NatE) NGR_RS10940 NGR_RS23730
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
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 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