GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Pseudomonas fluorescens FW300-N2C3

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) AO356_05340 AO356_08480
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) AO356_05335 AO356_08485
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) AO356_05320 AO356_08500
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) AO356_05325 AO356_08495
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) AO356_05330 AO356_08490
ilvE L-leucine transaminase AO356_22970 AO356_21330
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit AO356_22990 AO356_24880
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit AO356_22985 AO356_24885
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component AO356_22980 AO356_08965
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component AO356_22975 AO356_19705
liuA isovaleryl-CoA dehydrogenase AO356_01580 AO356_15445
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit AO356_01595 AO356_02930
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit AO356_01585 AO356_02920
liuC 3-methylglutaconyl-CoA hydratase AO356_01590 AO356_24105
liuE hydroxymethylglutaryl-CoA lyase AO356_01570 AO356_24105
atoA acetoacetyl-CoA transferase, A subunit AO356_21650
atoD acetoacetyl-CoA transferase, B subunit AO356_21645
atoB acetyl-CoA C-acetyltransferase AO356_21640 AO356_26350
Alternative steps:
aacS acetoacetyl-CoA synthetase AO356_00425 AO356_01575
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ AO356_17380
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) AO356_17390 AO356_29675
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP AO356_17395 AO356_18215
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) AO356_17385
Bap2 L-leucine permease Bap2 AO356_17670 AO356_28340
bcaP L-leucine uptake transporter BcaP
brnQ L-leucine:Na+ symporter BrnQ/BraB AO356_19720
leuT L-leucine:Na+ symporter LeuT
natA L-leucine ABC transporter, ATPase component 1 (NatA) AO356_05335 AO356_29020
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC) AO356_05330
natD L-leucine ABC transporter, permease component 2 (NatD) AO356_08495 AO356_08345
natE L-leucine ABC transporter, ATPase component 2 (NatE) AO356_05340 AO356_08480
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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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