GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Desulfoscipio geothermicus DSM 3669

Best path

leuT, 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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
leuT L-leucine:Na+ symporter LeuT BM299_RS01110
ilvE L-leucine transaminase BM299_RS08275 BM299_RS14600
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
liuA isovaleryl-CoA dehydrogenase BM299_RS06015 BM299_RS06045
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BM299_RS06260
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit BM299_RS10410 BM299_RS09155
liuC 3-methylglutaconyl-CoA hydratase BM299_RS10405 BM299_RS07795
liuE hydroxymethylglutaryl-CoA lyase BM299_RS10395 BM299_RS00910
aacS acetoacetyl-CoA synthetase BM299_RS14405 BM299_RS10805
atoB acetyl-CoA C-acetyltransferase BM299_RS18350 BM299_RS11340
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) BM299_RS18040
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BM299_RS08585 BM299_RS18035
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
atoA acetoacetyl-CoA transferase, A subunit
atoD acetoacetyl-CoA transferase, B subunit
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP BM299_RS10185
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BM299_RS04425
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BM299_RS04430
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BM299_RS04440
brnQ L-leucine:Na+ symporter BrnQ/BraB
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) BM299_RS15855 BM299_RS11075
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) BM299_RS15860 BM299_RS12340
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
natA L-leucine ABC transporter, ATPase component 1 (NatA) BM299_RS15860 BM299_RS05470
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) BM299_RS15855 BM299_RS11075
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA BM299_RS04815 BM299_RS08890
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB BM299_RS12845 BM299_RS08885
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA BM299_RS06120
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB BM299_RS06125 BM299_RS07360
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