GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Lactobacillus silagei IWT126

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) CES79_RS10020 CES79_RS10015
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) CES79_RS10015 CES79_RS10020
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) CES79_RS10000
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) CES79_RS10005
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) CES79_RS10010
ilvE L-leucine transaminase CES79_RS05205 CES79_RS08185
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
liuA isovaleryl-CoA dehydrogenase
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit CES79_RS05880 CES79_RS03295
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit
liuC 3-methylglutaconyl-CoA hydratase
liuE hydroxymethylglutaryl-CoA lyase
aacS acetoacetyl-CoA synthetase
atoB acetyl-CoA C-acetyltransferase CES79_RS08555
Alternative steps:
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) CES79_RS09755 CES79_RS00820
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP CES79_RS00805 CES79_RS09760
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) CES79_RS00815
atoA acetoacetyl-CoA transferase, A subunit
atoD acetoacetyl-CoA transferase, B subunit
Bap2 L-leucine permease Bap2 CES79_RS01340 CES79_RS10735
bcaP L-leucine uptake transporter BcaP CES79_RS03120 CES79_RS02900
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit CES79_RS09610
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit CES79_RS09615
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component CES79_RS09620
brnQ L-leucine:Na+ symporter BrnQ/BraB CES79_RS10800 CES79_RS04070
leuT L-leucine:Na+ symporter LeuT
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component CES79_RS09625 CES79_RS04335
natA L-leucine ABC transporter, ATPase component 1 (NatA) CES79_RS10015 CES79_RS10020
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) CES79_RS10005
natE L-leucine ABC transporter, ATPase component 2 (NatE) CES79_RS10020 CES79_RS09760
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