GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Pseudomonas fluorescens FW300-N2E3

Best path

livF, livG, livJ, livH, livM, 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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) AO353_17105 AO353_13360
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) AO353_17110 AO353_13355
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) AO353_17125 AO353_13340
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) AO353_17120 AO353_13345
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) AO353_17115 AO353_13350
ilvE L-leucine transaminase AO353_26655 AO353_20540
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit AO353_26635 AO353_15575
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit AO353_26640 AO353_15580
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component AO353_26645 AO353_15585
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component AO353_26650 AO353_01825
liuA isovaleryl-CoA dehydrogenase AO353_20350 AO353_06340
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit AO353_20335 AO353_19305
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit AO353_20345 AO353_19320
liuC 3-methylglutaconyl-CoA hydratase AO353_20340 AO353_25675
liuE hydroxymethylglutaryl-CoA lyase AO353_20365
atoA acetoacetyl-CoA transferase, A subunit AO353_27935
atoD acetoacetyl-CoA transferase, B subunit AO353_27940
atoB acetyl-CoA C-acetyltransferase AO353_25685 AO353_27945
Alternative steps:
aacS acetoacetyl-CoA synthetase AO353_21765 AO353_20355
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ AO353_04615
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) AO353_04605 AO353_12325
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP AO353_04600 AO353_16275
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) AO353_04610
Bap2 L-leucine permease Bap2 AO353_24825 AO353_16120
bcaP L-leucine uptake transporter BcaP
brnQ L-leucine:Na+ symporter BrnQ/BraB AO353_01810
leuT L-leucine:Na+ symporter LeuT
natA L-leucine ABC transporter, ATPase component 1 (NatA) AO353_17110 AO353_13530
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) AO353_17120
natE L-leucine ABC transporter, ATPase component 2 (NatE) AO353_17105 AO353_13360
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, 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