GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Pseudomonas simiae WCS417

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) PS417_06595 PS417_02675
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) PS417_06600 PS417_02670
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) PS417_06615 PS417_02655
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) PS417_06610 PS417_02660
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) PS417_06605 PS417_02665
ilvE L-leucine transaminase PS417_17565 PS417_18690
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit PS417_17545 PS417_11765
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit PS417_17550 PS417_11770
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component PS417_17555 PS417_02215
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component PS417_17560 PS417_08905
liuA isovaleryl-CoA dehydrogenase PS417_17015 PS417_24590
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit PS417_17030 PS417_19595
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit PS417_17020 PS417_19580
liuC 3-methylglutaconyl-CoA hydratase PS417_17025 PS417_13845
liuE hydroxymethylglutaryl-CoA lyase PS417_17005 PS417_06935
atoA acetoacetyl-CoA transferase, A subunit PS417_10525
atoD acetoacetyl-CoA transferase, B subunit PS417_10520
atoB acetyl-CoA C-acetyltransferase PS417_10515 PS417_13855
Alternative steps:
aacS acetoacetyl-CoA synthetase PS417_12145 PS417_17010
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ PS417_23345 PS417_04900
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) PS417_04910 PS417_01810
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP PS417_04915 PS417_26115
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) PS417_04905
Bap2 L-leucine permease Bap2 PS417_01505 PS417_05405
bcaP L-leucine uptake transporter BcaP
brnQ L-leucine:Na+ symporter BrnQ/BraB PS417_08920
leuT L-leucine:Na+ symporter LeuT
natA L-leucine ABC transporter, ATPase component 1 (NatA) PS417_06600 PS417_16795
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC) PS417_02665
natD L-leucine ABC transporter, permease component 2 (NatD) PS417_06610 PS417_02660
natE L-leucine ABC transporter, ATPase component 2 (NatE) PS417_06595 PS417_02675
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