GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Alkalihalobacterium alkalinitrilicum DSM 22532

Best path

brnQ, 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
brnQ L-leucine:Na+ symporter BrnQ/BraB BK574_RS22150
ilvE L-leucine transaminase BK574_RS09430 BK574_RS22720
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BK574_RS11490 BK574_RS15530
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BK574_RS11485 BK574_RS15525
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BK574_RS25480 BK574_RS11480
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BK574_RS25485 BK574_RS11495
liuA isovaleryl-CoA dehydrogenase BK574_RS02975 BK574_RS14045
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BK574_RS23295 BK574_RS08370
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit BK574_RS14015 BK574_RS02990
liuC 3-methylglutaconyl-CoA hydratase BK574_RS14020 BK574_RS02155
liuE hydroxymethylglutaryl-CoA lyase BK574_RS14025 BK574_RS03550
atoA acetoacetyl-CoA transferase, A subunit BK574_RS18855 BK574_RS00550
atoD acetoacetyl-CoA transferase, B subunit BK574_RS00555 BK574_RS18860
atoB acetyl-CoA C-acetyltransferase BK574_RS10695 BK574_RS19085
Alternative steps:
aacS acetoacetyl-CoA synthetase BK574_RS06955 BK574_RS14040
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) BK574_RS01585
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BK574_RS11415 BK574_RS18745
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
leuT L-leucine:Na+ symporter LeuT BK574_RS21030 BK574_RS14090
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) BK574_RS08055 BK574_RS14050
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) BK574_RS08060 BK574_RS14075
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) BK574_RS14065 BK574_RS08070
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) BK574_RS08065 BK574_RS14060
natA L-leucine ABC transporter, ATPase component 1 (NatA) BK574_RS08060 BK574_RS14075
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) BK574_RS14065
natE L-leucine ABC transporter, ATPase component 2 (NatE) BK574_RS08055 BK574_RS14050
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA BK574_RS00115 BK574_RS09150
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB BK574_RS09145 BK574_RS00120
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB BK574_RS09150
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