GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Tistlia consotensis USBA 355

Best path

livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, 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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) B9O00_RS11410 B9O00_RS18195
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) B9O00_RS11415 B9O00_RS18190
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) B9O00_RS11400 B9O00_RS18210
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) B9O00_RS18200 B9O00_RS11425
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) B9O00_RS11420 B9O00_RS18235
ilvE L-leucine transaminase B9O00_RS22765 B9O00_RS29405
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused B9O00_RS18295
liuA isovaleryl-CoA dehydrogenase B9O00_RS18920 B9O00_RS05885
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit B9O00_RS18055 B9O00_RS26095
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit B9O00_RS18010 B9O00_RS26085
liuC 3-methylglutaconyl-CoA hydratase B9O00_RS26090 B9O00_RS14075
liuE hydroxymethylglutaryl-CoA lyase B9O00_RS18065
aacS acetoacetyl-CoA synthetase B9O00_RS16180 B9O00_RS21920
atoB acetyl-CoA C-acetyltransferase B9O00_RS02255 B9O00_RS06430
Alternative steps:
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ B9O00_RS10695 B9O00_RS06680
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) B9O00_RS30245 B9O00_RS00465
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP B9O00_RS06665 B9O00_RS30340
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) B9O00_RS30240 B9O00_RS06675
atoA acetoacetyl-CoA transferase, A subunit B9O00_RS13585
atoD acetoacetyl-CoA transferase, B subunit B9O00_RS13580
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit B9O00_RS33825 B9O00_RS29555
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit B9O00_RS19175 B9O00_RS29390
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component B9O00_RS19180 B9O00_RS06975
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component B9O00_RS29400 B9O00_RS06970
natA L-leucine ABC transporter, ATPase component 1 (NatA) B9O00_RS18780 B9O00_RS25265
natB L-leucine ABC transporter, substrate-binding component NatB B9O00_RS19590
natC L-leucine ABC transporter, permease component 1 (NatC)
natD L-leucine ABC transporter, permease component 2 (NatD) B9O00_RS19585 B9O00_RS18200
natE L-leucine ABC transporter, ATPase component 2 (NatE) B9O00_RS19570 B9O00_RS11410
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB B9O00_RS10285
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB B9O00_RS10290
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 Apr 09 2024. 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