GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Mucilaginibacter mallensis MP1X4

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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
leuT L-leucine:Na+ symporter LeuT
ilvE L-leucine transaminase BLU33_RS01980 BLU33_RS07390
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BLU33_RS24660 BLU33_RS19455
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BLU33_RS24660 BLU33_RS18750
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BLU33_RS10760 BLU33_RS18030
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BLU33_RS07565 BLU33_RS18175
liuA isovaleryl-CoA dehydrogenase BLU33_RS17775 BLU33_RS24850
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BLU33_RS09750 BLU33_RS23025
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit BLU33_RS08985 BLU33_RS16640
liuC 3-methylglutaconyl-CoA hydratase BLU33_RS22635 BLU33_RS04380
liuE hydroxymethylglutaryl-CoA lyase BLU33_RS13655
atoA acetoacetyl-CoA transferase, A subunit BLU33_RS08095
atoD acetoacetyl-CoA transferase, B subunit BLU33_RS08100
atoB acetyl-CoA C-acetyltransferase BLU33_RS09250 BLU33_RS24945
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)
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BLU33_RS00530 BLU33_RS17915
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 BLU33_RS17855
brnQ L-leucine:Na+ symporter BrnQ/BraB
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) BLU33_RS23120 BLU33_RS15970
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) BLU33_RS23120 BLU33_RS00530
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) BLU33_RS23120 BLU33_RS00530
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) BLU33_RS23120 BLU33_RS19365
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
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