GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Mesorhizobium ciceri WSM1271

Best path

livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, 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) Mesci_1237 Mesci_6239
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) Mesci_1236 Mesci_6238
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) Mesci_1239 Mesci_4851
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) Mesci_1234 Mesci_0559
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) Mesci_1235 Mesci_6237
ilvE L-leucine transaminase Mesci_2940 Mesci_2177
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit Mesci_0881 Mesci_1463
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit Mesci_0882 Mesci_1464
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component Mesci_0883 Mesci_3697
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component Mesci_0884 Mesci_3699
liuA isovaleryl-CoA dehydrogenase Mesci_4845 Mesci_4014
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit Mesci_4850 Mesci_4168
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit Mesci_4846 Mesci_3668
liuC 3-methylglutaconyl-CoA hydratase Mesci_6037 Mesci_1860
liuE hydroxymethylglutaryl-CoA lyase
aacS acetoacetyl-CoA synthetase Mesci_2424 Mesci_2534
atoB acetyl-CoA C-acetyltransferase Mesci_1329 Mesci_1095
Alternative steps:
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ Mesci_4657 Mesci_2581
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) Mesci_4655 Mesci_2579
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP Mesci_4654 Mesci_2578
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) Mesci_4656 Mesci_2580
atoA acetoacetyl-CoA transferase, A subunit
atoD acetoacetyl-CoA transferase, B subunit
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
natA L-leucine ABC transporter, ATPase component 1 (NatA) Mesci_5232 Mesci_6238
natB L-leucine ABC transporter, substrate-binding component NatB Mesci_5226
natC L-leucine ABC transporter, permease component 1 (NatC) Mesci_5235 Mesci_6237
natD L-leucine ABC transporter, permease component 2 (NatD) Mesci_5234 Mesci_6236
natE L-leucine ABC transporter, ATPase component 2 (NatE) Mesci_5233 Mesci_1237
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused Mesci_0337
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