GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Pseudomonas benzenivorans DSM 8628

Best path

livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB

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) BLS63_RS09635 BLS63_RS23795
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) BLS63_RS09640 BLS63_RS23790
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BLS63_RS09655 BLS63_RS23775
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) BLS63_RS09650 BLS63_RS23780
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) BLS63_RS09645 BLS63_RS23785
ilvE L-leucine transaminase BLS63_RS05050 BLS63_RS23260
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused BLS63_RS19365
liuA isovaleryl-CoA dehydrogenase BLS63_RS24330 BLS63_RS13640
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BLS63_RS24345 BLS63_RS18330
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit BLS63_RS24335 BLS63_RS18315
liuC 3-methylglutaconyl-CoA hydratase BLS63_RS24340 BLS63_RS17665
liuE hydroxymethylglutaryl-CoA lyase BLS63_RS24350 BLS63_RS17665
atoA acetoacetyl-CoA transferase, A subunit BLS63_RS25510 BLS63_RS21205
atoD acetoacetyl-CoA transferase, B subunit BLS63_RS25505 BLS63_RS21195
atoB acetyl-CoA C-acetyltransferase BLS63_RS22810 BLS63_RS21120
Alternative steps:
aacS acetoacetyl-CoA synthetase BLS63_RS25520 BLS63_RS24315
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ BLS63_RS08600
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) BLS63_RS08610 BLS63_RS18545
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BLS63_RS08615 BLS63_RS23600
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BLS63_RS08605 BLS63_RS11280
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BLS63_RS24845 BLS63_RS02715
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BLS63_RS24850 BLS63_RS19020
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BLS63_RS24855 BLS63_RS05065
brnQ L-leucine:Na+ symporter BrnQ/BraB BLS63_RS00215
leuT L-leucine:Na+ symporter LeuT
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BLS63_RS00200 BLS63_RS25065
natA L-leucine ABC transporter, ATPase component 1 (NatA) BLS63_RS09640 BLS63_RS23790
natB L-leucine ABC transporter, substrate-binding component NatB BLS63_RS23775
natC L-leucine ABC transporter, permease component 1 (NatC)
natD L-leucine ABC transporter, permease component 2 (NatD) BLS63_RS09650 BLS63_RS23780
natE L-leucine ABC transporter, ATPase component 2 (NatE) BLS63_RS09635 BLS63_RS23795
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 24 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:

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