GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Bacteroides fluxus YIT 12057

Best path

leuT, ilvE, vorA*, vorB, vorC, 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
leuT L-leucine:Na+ symporter LeuT HMPREF9446_RS14715
ilvE L-leucine transaminase HMPREF9446_RS11165
vorA* branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA HMPREF9446_RS03160 with HMPREF9446_RS03165
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB HMPREF9446_RS03155 HMPREF9446_RS13130
vorC branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC HMPREF9446_RS03150
liuA isovaleryl-CoA dehydrogenase HMPREF9446_RS00545
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit HMPREF9446_RS10475
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit HMPREF9446_RS00070 HMPREF9446_RS10485
liuC 3-methylglutaconyl-CoA hydratase HMPREF9446_RS13610
liuE hydroxymethylglutaryl-CoA lyase
aacS acetoacetyl-CoA synthetase HMPREF9446_RS08555
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
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM)
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP HMPREF9446_RS15165 HMPREF9446_RS00290
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
bcaP L-leucine uptake transporter BcaP HMPREF9446_RS06370
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit HMPREF9446_RS06135
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit HMPREF9446_RS06135
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component HMPREF9446_RS06130
brnQ L-leucine:Na+ symporter BrnQ/BraB
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) HMPREF9446_RS09630 HMPREF9446_RS13805
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) HMPREF9446_RS09630 HMPREF9446_RS13805
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)
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component HMPREF9446_RS12300 HMPREF9446_RS05445
natA L-leucine ABC transporter, ATPase component 1 (NatA) HMPREF9446_RS09630 HMPREF9446_RS00290
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) HMPREF9446_RS09630 HMPREF9446_RS13805
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 HMPREF9446_RS13125

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