GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Chromobacterium vaccinii MWU205

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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) VL52_RS15485 VL52_RS03360
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) VL52_RS15490 VL52_RS03360
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) VL52_RS09675 VL52_RS22490
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) VL52_RS15500
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) VL52_RS15495
ilvE L-leucine transaminase VL52_RS16135 VL52_RS03625
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused VL52_RS19015
liuA isovaleryl-CoA dehydrogenase VL52_RS19965 VL52_RS13095
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit VL52_RS19945 VL52_RS01580
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit VL52_RS19955
liuC 3-methylglutaconyl-CoA hydratase VL52_RS11135 VL52_RS19950
liuE hydroxymethylglutaryl-CoA lyase VL52_RS19930
aacS acetoacetyl-CoA synthetase VL52_RS19925 VL52_RS11845
atoB acetyl-CoA C-acetyltransferase VL52_RS14225 VL52_RS21005
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) VL52_RS08850 VL52_RS19745
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP VL52_RS19750 VL52_RS06130
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) VL52_RS19740 VL52_RS19745
atoA acetoacetyl-CoA transferase, A subunit
atoD acetoacetyl-CoA transferase, B subunit
Bap2 L-leucine permease Bap2 VL52_RS10410 VL52_RS13800
bcaP L-leucine uptake transporter BcaP VL52_RS03530
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component VL52_RS01115
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT VL52_RS13310
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component VL52_RS06780 VL52_RS01105
natA L-leucine ABC transporter, ATPase component 1 (NatA) VL52_RS15490 VL52_RS03360
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC) VL52_RS15495
natD L-leucine ABC transporter, permease component 2 (NatD) VL52_RS15500
natE L-leucine ABC transporter, ATPase component 2 (NatE) VL52_RS15485 VL52_RS03360
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB
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