GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Shewanella sp. ANA-3

Best path

brnQ, ilvE, bkdA, bkdB, bkdC, lpd, 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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
brnQ L-leucine:Na+ symporter BrnQ/BraB Shewana3_3332
ilvE L-leucine transaminase Shewana3_3830 Shewana3_2121
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Shewana3_2131
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Shewana3_2130
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component Shewana3_2129 Shewana3_0427
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Shewana3_0428 Shewana3_4345
liuA isovaleryl-CoA dehydrogenase Shewana3_1672 Shewana3_2769
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit Shewana3_1669 Shewana3_3438
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit Shewana3_1671
liuC 3-methylglutaconyl-CoA hydratase Shewana3_1670 Shewana3_1668
liuE hydroxymethylglutaryl-CoA lyase Shewana3_1668
atoA acetoacetyl-CoA transferase, A subunit Shewana3_3467 Shewana3_1667
atoD acetoacetyl-CoA transferase, B subunit Shewana3_1666 Shewana3_3468
atoB acetyl-CoA C-acetyltransferase Shewana3_2771 Shewana3_0023
Alternative steps:
aacS acetoacetyl-CoA synthetase Shewana3_2475 Shewana3_2386
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) Shewana3_0881
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Shewana3_0880 Shewana3_3096
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) Shewana3_0673 Shewana3_0880
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) Shewana3_0673 Shewana3_3192
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) Shewana3_0673 Shewana3_1620
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) Shewana3_0880 Shewana3_2749
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 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