GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Photobacterium jeanii R-40508

Best path

brnQ, 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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
brnQ L-leucine:Na+ symporter BrnQ/BraB A3K86_RS11180 A3K86_RS09495
ilvE L-leucine transaminase A3K86_RS17165 A3K86_RS04690
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
liuA isovaleryl-CoA dehydrogenase A3K86_RS15945 A3K86_RS15925
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit A3K86_RS09575
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit A3K86_RS15950
liuC 3-methylglutaconyl-CoA hydratase A3K86_RS15955 A3K86_RS15960
liuE hydroxymethylglutaryl-CoA lyase A3K86_RS15960
aacS acetoacetyl-CoA synthetase A3K86_RS18920
atoB acetyl-CoA C-acetyltransferase A3K86_RS19875 A3K86_RS15935
Alternative steps:
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ A3K86_RS01705
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) A3K86_RS01695 A3K86_RS17300
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP A3K86_RS01690 A3K86_RS21200
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) A3K86_RS01700 A3K86_RS21185
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 A3K86_RS15830
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit A3K86_RS15835
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component A3K86_RS10520 A3K86_RS06310
leuT L-leucine:Na+ symporter LeuT A3K86_RS01975 A3K86_RS13930
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) A3K86_RS10225 A3K86_RS04635
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) A3K86_RS10225 A3K86_RS10255
livH L-leucine ABC transporter, permease component 1 (LivH/BraD)
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-leucine ABC transporter, permease component 2 (LivM/BraE)
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component A3K86_RS10525 A3K86_RS01850
natA L-leucine ABC transporter, ATPase component 1 (NatA) A3K86_RS10225 A3K86_RS12240
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)
natE L-leucine ABC transporter, ATPase component 2 (NatE) A3K86_RS10225 A3K86_RS04635
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 24 2021. 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