GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Salinicoccus carnicancri Crm

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
leuT L-leucine:Na+ symporter LeuT
ilvE L-leucine transaminase C792_RS0112120 C792_RS0109150
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit C792_RS0107730 C792_RS0105245
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit C792_RS0107735 C792_RS0108925
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component C792_RS0107740 C792_RS0108920
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component C792_RS0105260 C792_RS0107725
liuA isovaleryl-CoA dehydrogenase C792_RS0109335
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit C792_RS0107655 C792_RS0110520
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit
liuC 3-methylglutaconyl-CoA hydratase C792_RS0108985 C792_RS0109005
liuE hydroxymethylglutaryl-CoA lyase
atoA acetoacetyl-CoA transferase, A subunit C792_RS0112540
atoD acetoacetyl-CoA transferase, B subunit C792_RS0112535
atoB acetyl-CoA C-acetyltransferase C792_RS0112545 C792_RS0109325
Alternative steps:
aacS acetoacetyl-CoA synthetase
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) C792_RS0101010 C792_RS0103290
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP C792_RS0103280 C792_RS14100
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
brnQ L-leucine:Na+ symporter BrnQ/BraB C792_RS0108210
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) C792_RS0100130 C792_RS0112505
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) C792_RS0112050 C792_RS0112505
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) C792_RS0112050 C792_RS0112505
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) C792_RS0113665 C792_RS0107500
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA C792_RS0106080
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB C792_RS0106085
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB C792_RS0106080
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