GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Acidovorax caeni R-24608

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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) BN2503_RS06720 BN2503_RS02275
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) BN2503_RS06725 BN2503_RS02270
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BN2503_RS04725 BN2503_RS02255
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) BN2503_RS06735 BN2503_RS02260
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) BN2503_RS06730 BN2503_RS02265
ilvE L-leucine transaminase BN2503_RS13460 BN2503_RS07910
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused BN2503_RS02910
liuA isovaleryl-CoA dehydrogenase BN2503_RS15695 BN2503_RS07075
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BN2503_RS06975 BN2503_RS07525
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit BN2503_RS06995 BN2503_RS14690
liuC 3-methylglutaconyl-CoA hydratase BN2503_RS06985 BN2503_RS06965
liuE hydroxymethylglutaryl-CoA lyase BN2503_RS06965
atoA acetoacetyl-CoA transferase, A subunit BN2503_RS02630
atoD acetoacetyl-CoA transferase, B subunit BN2503_RS02625
atoB acetyl-CoA C-acetyltransferase BN2503_RS17070 BN2503_RS12305
Alternative steps:
aacS acetoacetyl-CoA synthetase BN2503_RS07000 BN2503_RS02705
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) BN2503_RS00885
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BN2503_RS14975 BN2503_RS00880
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BN2503_RS14985
Bap2 L-leucine permease Bap2 BN2503_RS15280
bcaP L-leucine uptake transporter BcaP
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BN2503_RS17110 BN2503_RS03820
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
lpd* branched-chain alpha-ketoacid dehydrogenase, E3 component BN2503_RS17105 with BN2503_RS11830 BN2503_RS03815
natA L-leucine ABC transporter, ATPase component 1 (NatA) BN2503_RS06725 BN2503_RS01080
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC) BN2503_RS02265
natD L-leucine ABC transporter, permease component 2 (NatD) BN2503_RS06735 BN2503_RS02260
natE L-leucine ABC transporter, ATPase component 2 (NatE) BN2503_RS06720 BN2503_RS02275
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