GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Dinoroseobacter shibae DFL-12

Best path

aapJ, aapQ, aapM, aapP, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB

Also see fitness data for the top candidates

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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ Dshi_0318
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) Dshi_0319
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) Dshi_0320
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Dshi_0321 Dshi_2221
ilvE L-leucine transaminase Dshi_3301 Dshi_4206
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused Dshi_1762
liuA isovaleryl-CoA dehydrogenase Dshi_1297 Dshi_0838
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit Dshi_1301 Dshi_0723
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit Dshi_1300 Dshi_0718
liuC 3-methylglutaconyl-CoA hydratase Dshi_1304 Dshi_1048
liuE hydroxymethylglutaryl-CoA lyase Dshi_1303
atoA acetoacetyl-CoA transferase, A subunit Dshi_1136
atoD acetoacetyl-CoA transferase, B subunit Dshi_1134
atoB acetyl-CoA C-acetyltransferase Dshi_3066 Dshi_3331
Alternative steps:
aacS acetoacetyl-CoA synthetase Dshi_3403 Dshi_0833
AAP1 L-leucine permease AAP1
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Dshi_2158 Dshi_0534
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Dshi_2159 Dshi_0535
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component Dshi_1967 Dshi_2884
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) Dshi_0381 Dshi_3728
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) Dshi_0375 Dshi_3727
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) Dshi_3725 Dshi_0861
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) Dshi_0379 Dshi_1978
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Dshi_1966 Dshi_2886
natA L-leucine ABC transporter, ATPase component 1 (NatA) Dshi_1521 Dshi_1981
natB L-leucine ABC transporter, substrate-binding component NatB Dshi_1977
natC L-leucine ABC transporter, permease component 1 (NatC)
natD L-leucine ABC transporter, permease component 2 (NatD) Dshi_1518 Dshi_1979
natE L-leucine ABC transporter, ATPase component 2 (NatE) Dshi_1520 Dshi_1980
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 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, 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