GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Sporolactobacillus vineae SL153

Best path

bcaP, ilvE, bkdA, bkdB, bkdC, lpd, 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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
bcaP L-leucine uptake transporter BcaP RH97_RS02450 RH97_RS05565
ilvE L-leucine transaminase RH97_RS02175 RH97_RS07205
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit RH97_RS10575 RH97_RS04120
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit RH97_RS10580 RH97_RS04115
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component RH97_RS10585 RH97_RS04110
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component RH97_RS04105 RH97_RS10570
liuA isovaleryl-CoA dehydrogenase RH97_RS08905
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit RH97_RS09550 RH97_RS08700
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit
liuC 3-methylglutaconyl-CoA hydratase RH97_RS08930 RH97_RS07390
liuE hydroxymethylglutaryl-CoA lyase
atoA acetoacetyl-CoA transferase, A subunit RH97_RS08945 RH97_RS04720
atoD acetoacetyl-CoA transferase, B subunit RH97_RS08950 RH97_RS04725
atoB acetyl-CoA C-acetyltransferase RH97_RS08940 RH97_RS04710
Alternative steps:
aacS acetoacetyl-CoA synthetase RH97_RS08925
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) RH97_RS02560
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP RH97_RS07910 RH97_RS08095
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
Bap2 L-leucine permease Bap2 RH97_RS02150 RH97_RS12570
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) RH97_RS07250 RH97_RS07245
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) RH97_RS07245 RH97_RS08020
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) RH97_RS07235
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) RH97_RS07230
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) RH97_RS07240
natA L-leucine ABC transporter, ATPase component 1 (NatA) RH97_RS07245 RH97_RS07250
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) RH97_RS07235
natE L-leucine ABC transporter, ATPase component 2 (NatE) RH97_RS07250 RH97_RS08365
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 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