GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Desulfovibrio vulgaris Hildenborough

Best path

livF, livG, livJ, livH, livM, ilvE, vorA*, vorB, vorC, 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
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) DVU0551 DVU0716
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) DVU2741 DVU0550
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) DVU0547 DVU0712
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) DVU2743 DVU0548
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) DVU0549 DVU0714
ilvE L-leucine transaminase DVU3197 DVU2364
vorA* branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA DVU3348 with DVU3347 DVU1946
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB DVU3349 DVU1945
vorC branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC
liuA isovaleryl-CoA dehydrogenase
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit DVU1834 DVU2226
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit
liuC 3-methylglutaconyl-CoA hydratase
liuE hydroxymethylglutaryl-CoA lyase
aacS acetoacetyl-CoA synthetase DVU3065 DVU0748
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 DVU2342
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) DVU0967 DVU0751
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP DVU0753 DVU2343
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) DVU2341
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
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT DVU1092
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component DVU1423 DVU1037
natA L-leucine ABC transporter, ATPase component 1 (NatA) DVU2741 DVU0715
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC) DVU0549
natD L-leucine ABC transporter, permease component 2 (NatD) DVU0713 DVU0548
natE L-leucine ABC transporter, ATPase component 2 (NatE) DVU0551 DVU0716
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA DVU1569 DVU1945
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB DVU1570 DVU1946

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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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