GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Brevibacterium jeotgali SJ5-8

Best path

leuT, 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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
leuT L-leucine:Na+ symporter LeuT BJEO58_RS06490
ilvE L-leucine transaminase BJEO58_RS04020 BJEO58_RS05775
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BJEO58_RS08660 BJEO58_RS13410
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BJEO58_RS08655 BJEO58_RS13405
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BJEO58_RS13400 BJEO58_RS08650
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BJEO58_RS13395 BJEO58_RS13775
liuA isovaleryl-CoA dehydrogenase BJEO58_RS00850 BJEO58_RS11280
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BJEO58_RS00855 BJEO58_RS09820
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit BJEO58_RS00860 BJEO58_RS10090
liuC 3-methylglutaconyl-CoA hydratase BJEO58_RS03580 BJEO58_RS08900
liuE hydroxymethylglutaryl-CoA lyase BJEO58_RS05305
atoA acetoacetyl-CoA transferase, A subunit BJEO58_RS10005
atoD acetoacetyl-CoA transferase, B subunit BJEO58_RS10010
atoB acetyl-CoA C-acetyltransferase BJEO58_RS06055 BJEO58_RS05920
Alternative steps:
aacS acetoacetyl-CoA synthetase BJEO58_RS01380 BJEO58_RS03695
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) BJEO58_RS10145
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BJEO58_RS03195 BJEO58_RS06850
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BJEO58_RS03185
Bap2 L-leucine permease Bap2 BJEO58_RS06510
bcaP L-leucine uptake transporter BcaP
brnQ L-leucine:Na+ symporter BrnQ/BraB
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) BJEO58_RS03195 BJEO58_RS05330
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) BJEO58_RS05330 BJEO58_RS05205
livH L-leucine ABC transporter, permease component 1 (LivH/BraD)
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-leucine ABC transporter, permease component 2 (LivM/BraE)
natA L-leucine ABC transporter, ATPase component 1 (NatA) BJEO58_RS13550 BJEO58_RS09465
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)
natE L-leucine ABC transporter, ATPase component 2 (NatE) BJEO58_RS04205 BJEO58_RS01195
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