GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Pseudomonas fluorescens FW300-N1B4

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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) Pf1N1B4_3214 Pf1N1B4_1378
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) Pf1N1B4_3215 Pf1N1B4_1379
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) Pf1N1B4_3218 Pf1N1B4_1382
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) Pf1N1B4_3217 Pf1N1B4_1381
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) Pf1N1B4_3216 Pf1N1B4_1380
ilvE L-leucine transaminase Pf1N1B4_4476 Pf1N1B4_27
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Pf1N1B4_4480 Pf1N1B4_1020
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Pf1N1B4_4479 Pf1N1B4_1019
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component Pf1N1B4_4478 Pf1N1B4_1018
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Pf1N1B4_4477 Pf1N1B4_3683
liuA isovaleryl-CoA dehydrogenase Pf1N1B4_3987 Pf1N1B4_2720
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit Pf1N1B4_3984 Pf1N1B4_225
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit Pf1N1B4_3986 Pf1N1B4_222
liuC 3-methylglutaconyl-CoA hydratase Pf1N1B4_3985 Pf1N1B4_4788
liuE hydroxymethylglutaryl-CoA lyase Pf1N1B4_3990
atoA acetoacetyl-CoA transferase, A subunit Pf1N1B4_5833
atoD acetoacetyl-CoA transferase, B subunit Pf1N1B4_5834
atoB acetyl-CoA C-acetyltransferase Pf1N1B4_4786 Pf1N1B4_5835
Alternative steps:
aacS acetoacetyl-CoA synthetase Pf1N1B4_5634 Pf1N1B4_3988
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ Pf1N1B4_917
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) Pf1N1B4_915 Pf1N1B4_4805
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Pf1N1B4_914 Pf1N1B4_774
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) Pf1N1B4_916 Pf1N1B4_772
Bap2 L-leucine permease Bap2 Pf1N1B4_801 Pf1N1B4_1639
bcaP L-leucine uptake transporter BcaP
brnQ L-leucine:Na+ symporter BrnQ/BraB Pf1N1B4_3686
leuT L-leucine:Na+ symporter LeuT
natA L-leucine ABC transporter, ATPase component 1 (NatA) Pf1N1B4_3215 Pf1N1B4_1346
natB L-leucine ABC transporter, substrate-binding component NatB Pf1N1B4_1382
natC L-leucine ABC transporter, permease component 1 (NatC) Pf1N1B4_3216
natD L-leucine ABC transporter, permease component 2 (NatD)
natE L-leucine ABC transporter, ATPase component 2 (NatE) Pf1N1B4_3214 Pf1N1B4_1378
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 Aug 02 2021. The underlying query database was built on Aug 02 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