GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Azospirillum brasilense Sp245

Best path

livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB

Also see fitness data for the top candidates

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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) AZOBR_RS08250 AZOBR_RS29685
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) AZOBR_RS08245 AZOBR_RS32405
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) AZOBR_RS08260 AZOBR_RS25645
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) AZOBR_RS08235 AZOBR_RS03565
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) AZOBR_RS08240 AZOBR_RS25635
ilvE L-leucine transaminase AZOBR_RS06555 AZOBR_RS16425
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
liuA isovaleryl-CoA dehydrogenase AZOBR_RS22310 AZOBR_RS22300
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit AZOBR_RS22285 AZOBR_RS21105
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit AZOBR_RS22295 AZOBR_RS21100
liuC 3-methylglutaconyl-CoA hydratase AZOBR_RS22290 AZOBR_RS26485
liuE hydroxymethylglutaryl-CoA lyase AZOBR_RS22280
aacS acetoacetyl-CoA synthetase AZOBR_RS31155 AZOBR_RS09405
atoB acetyl-CoA C-acetyltransferase AZOBR_RS30610 AZOBR_RS28180
Alternative steps:
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ AZOBR_RS08655 AZOBR_RS00530
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) AZOBR_RS08665 AZOBR_RS18065
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP AZOBR_RS08670 AZOBR_RS15690
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) AZOBR_RS08660 AZOBR_RS15675
atoA acetoacetyl-CoA transferase, A subunit
atoD acetoacetyl-CoA transferase, B subunit
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit AZOBR_RS22245 AZOBR_RS04795
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit AZOBR_RS04800 AZOBR_RS22250
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component AZOBR_RS14080
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component AZOBR_RS14390 AZOBR_RS03960
natA L-leucine ABC transporter, ATPase component 1 (NatA) AZOBR_RS32405 AZOBR_RS04130
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC) AZOBR_RS29675
natD L-leucine ABC transporter, permease component 2 (NatD) AZOBR_RS29670 AZOBR_RS21005
natE L-leucine ABC transporter, ATPase component 2 (NatE) AZOBR_RS19790 AZOBR_RS29685
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB AZOBR_RS02380
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB AZOBR_RS02385
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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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