GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Nitratifractor salsuginis DSM 16511

Best path

livF, livG, livJ, livH, livM, ilvE, ofo, 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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) NITSA_RS04140 NITSA_RS09465
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) NITSA_RS04145 NITSA_RS09465
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) NITSA_RS04160
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) NITSA_RS04155
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) NITSA_RS04150
ilvE L-leucine transaminase NITSA_RS02975
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
liuA isovaleryl-CoA dehydrogenase
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit NITSA_RS10075
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit
liuC 3-methylglutaconyl-CoA hydratase
liuE hydroxymethylglutaryl-CoA lyase
aacS acetoacetyl-CoA synthetase NITSA_RS10155
atoB acetyl-CoA C-acetyltransferase
Alternative steps:
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ NITSA_RS08630
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) NITSA_RS08640
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP NITSA_RS08645 NITSA_RS02650
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) NITSA_RS08635
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 NITSA_RS05070
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit NITSA_RS05075
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component NITSA_RS11705 NITSA_RS05090
natA L-leucine ABC transporter, ATPase component 1 (NatA) NITSA_RS04145 NITSA_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) NITSA_RS04155
natE L-leucine ABC transporter, ATPase component 2 (NatE) NITSA_RS04140 NITSA_RS09465
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA NITSA_RS01900
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB NITSA_RS01905
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB NITSA_RS01900
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