GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Desulfobacca acetoxidans DSM 11109

Best path

livF, livG, livJ, livH, livM, ilvE, ofoA, ofoB, 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
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) DESAC_RS09190 DESAC_RS10070
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) DESAC_RS09185 DESAC_RS06210
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) DESAC_RS10080 DESAC_RS07565
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) DESAC_RS09200 DESAC_RS06200
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) DESAC_RS01515 DESAC_RS09195
ilvE L-leucine transaminase DESAC_RS01095 DESAC_RS03760
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA DESAC_RS10780
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB DESAC_RS10785 DESAC_RS13300
liuA isovaleryl-CoA dehydrogenase DESAC_RS02715
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit DESAC_RS08025
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit DESAC_RS14020
liuC 3-methylglutaconyl-CoA hydratase
liuE hydroxymethylglutaryl-CoA lyase
aacS acetoacetyl-CoA synthetase DESAC_RS02235
atoB acetyl-CoA C-acetyltransferase
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)
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP DESAC_RS14065 DESAC_RS13085
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 DESAC_RS02020
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit DESAC_RS01240
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit DESAC_RS01235
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component DESAC_RS14420
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component DESAC_RS14070
natA L-leucine ABC transporter, ATPase component 1 (NatA) DESAC_RS10065 DESAC_RS09185
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC) DESAC_RS09195
natD L-leucine ABC transporter, permease component 2 (NatD) DESAC_RS06200 DESAC_RS09200
natE L-leucine ABC transporter, ATPase component 2 (NatE) DESAC_RS09190 DESAC_RS06215
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB DESAC_RS09130
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