GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Pseudarthrobacter sulfonivorans Ar51

Best path

natA, natB, natC, natD, natE, 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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
natA L-leucine ABC transporter, ATPase component 1 (NatA) AU252_RS04335 AU252_RS00660
natB L-leucine ABC transporter, substrate-binding component NatB AU252_RS04345
natC L-leucine ABC transporter, permease component 1 (NatC) AU252_RS04330
natD L-leucine ABC transporter, permease component 2 (NatD) AU252_RS04325
natE L-leucine ABC transporter, ATPase component 2 (NatE) AU252_RS04340 AU252_RS01290
ilvE L-leucine transaminase AU252_RS19160 AU252_RS10910
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit AU252_RS03450 AU252_RS10880
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit AU252_RS10885 AU252_RS15595
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component AU252_RS15600 AU252_RS02340
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component AU252_RS02335 AU252_RS03920
liuA isovaleryl-CoA dehydrogenase AU252_RS00840 AU252_RS01515
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit AU252_RS00815 AU252_RS03425
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit AU252_RS00810 AU252_RS03430
liuC 3-methylglutaconyl-CoA hydratase AU252_RS00745 AU252_RS00825
liuE hydroxymethylglutaryl-CoA lyase AU252_RS01445 AU252_RS01285
atoA acetoacetyl-CoA transferase, A subunit AU252_RS03415 AU252_RS07725
atoD acetoacetyl-CoA transferase, B subunit AU252_RS07730 AU252_RS03410
atoB acetyl-CoA C-acetyltransferase AU252_RS00950 AU252_RS16800
Alternative steps:
aacS acetoacetyl-CoA synthetase AU252_RS01520 AU252_RS16370
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) AU252_RS13390 AU252_RS15955
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP AU252_RS17760 AU252_RS15950
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) AU252_RS13390 AU252_RS17965
Bap2 L-leucine permease Bap2 AU252_RS05225 AU252_RS08100
bcaP L-leucine uptake transporter BcaP AU252_RS16215 AU252_RS04550
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) AU252_RS00890 AU252_RS04340
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) AU252_RS04335 AU252_RS00660
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) AU252_RS01305 AU252_RS04325
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) AU252_RS00900 AU252_RS04330
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 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