GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Saccharomonospora cyanea NA-134

Best path

leuT, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, 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
leuT L-leucine:Na+ symporter LeuT SACCYDRAFT_RS08685
ilvE L-leucine transaminase SACCYDRAFT_RS06020 SACCYDRAFT_RS25305
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit SACCYDRAFT_RS24865 SACCYDRAFT_RS10835
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit SACCYDRAFT_RS24870 SACCYDRAFT_RS10830
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component SACCYDRAFT_RS24875 SACCYDRAFT_RS10825
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component SACCYDRAFT_RS06380 SACCYDRAFT_RS10840
liuA isovaleryl-CoA dehydrogenase SACCYDRAFT_RS19835 SACCYDRAFT_RS24720
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit SACCYDRAFT_RS19840 SACCYDRAFT_RS09880
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit SACCYDRAFT_RS09875 SACCYDRAFT_RS19845
liuC 3-methylglutaconyl-CoA hydratase SACCYDRAFT_RS07390 SACCYDRAFT_RS10655
liuE hydroxymethylglutaryl-CoA lyase SACCYDRAFT_RS03430 SACCYDRAFT_RS10655
aacS acetoacetyl-CoA synthetase SACCYDRAFT_RS01150 SACCYDRAFT_RS21975
atoB acetyl-CoA C-acetyltransferase SACCYDRAFT_RS18430 SACCYDRAFT_RS20715
Alternative steps:
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) SACCYDRAFT_RS12025 SACCYDRAFT_RS19200
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP SACCYDRAFT_RS17805 SACCYDRAFT_RS24845
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
atoA acetoacetyl-CoA transferase, A subunit
atoD acetoacetyl-CoA transferase, B subunit
Bap2 L-leucine permease Bap2 SACCYDRAFT_RS20860 SACCYDRAFT_RS13365
bcaP L-leucine uptake transporter BcaP SACCYDRAFT_RS10940
brnQ L-leucine:Na+ symporter BrnQ/BraB
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) SACCYDRAFT_RS15020 SACCYDRAFT_RS20255
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) SACCYDRAFT_RS15025 SACCYDRAFT_RS15380
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) SACCYDRAFT_RS15015
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) SACCYDRAFT_RS15010
natA L-leucine ABC transporter, ATPase component 1 (NatA) SACCYDRAFT_RS15025 SACCYDRAFT_RS10270
natB L-leucine ABC transporter, substrate-binding component NatB SACCYDRAFT_RS18990
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) SACCYDRAFT_RS15020 SACCYDRAFT_RS18405
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 SACCYDRAFT_RS02020
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB SACCYDRAFT_RS02025
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.

Links

Downloads

Related tools

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