GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Lacinutrix algicola AKS293

Best path

brnQ, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, atoA, atoD, 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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
brnQ L-leucine:Na+ symporter BrnQ/BraB ASC41_RS09265
ilvE L-leucine transaminase ASC41_RS02375 ASC41_RS06740
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit ASC41_RS13240 ASC41_RS03545
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit ASC41_RS13240 ASC41_RS01930
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component ASC41_RS04735 ASC41_RS03540
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component ASC41_RS12550 ASC41_RS16385
liuA isovaleryl-CoA dehydrogenase ASC41_RS03630 ASC41_RS03050
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit ASC41_RS11580 ASC41_RS08120
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit ASC41_RS14455 ASC41_RS11575
liuC 3-methylglutaconyl-CoA hydratase ASC41_RS09525 ASC41_RS02310
liuE hydroxymethylglutaryl-CoA lyase ASC41_RS03965
atoA acetoacetyl-CoA transferase, A subunit ASC41_RS09660
atoD acetoacetyl-CoA transferase, B subunit ASC41_RS09655
atoB acetyl-CoA C-acetyltransferase ASC41_RS12920 ASC41_RS02340
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)
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP ASC41_RS06935 ASC41_RS13385
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
leuT L-leucine:Na+ symporter LeuT
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) ASC41_RS04105 ASC41_RS06375
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) ASC41_RS04105 ASC41_RS13455
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)
natA L-leucine ABC transporter, ATPase component 1 (NatA) ASC41_RS04105 ASC41_RS06790
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) ASC41_RS04105 ASC41_RS06375
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 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