GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Mesorhizobium ciceri biovar biserrulae 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_RS06160 MESCI_RS31070
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) MESCI_RS06155 MESCI_RS31065
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) MESCI_RS06170 MESCI_RS24305
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) MESCI_RS06145 MESCI_RS02785
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) MESCI_RS06150 MESCI_RS31060
ilvE L-leucine transaminase MESCI_RS14795 MESCI_RS10940
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit MESCI_RS04380 MESCI_RS07285
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit MESCI_RS04385 MESCI_RS07290
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component MESCI_RS04390 MESCI_RS18620
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component MESCI_RS04395 MESCI_RS18630
liuA isovaleryl-CoA dehydrogenase MESCI_RS24275 MESCI_RS20160
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit MESCI_RS24300 MESCI_RS20920
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit MESCI_RS24280 MESCI_RS18485
liuC 3-methylglutaconyl-CoA hydratase MESCI_RS30135 MESCI_RS09340
liuE hydroxymethylglutaryl-CoA lyase
aacS acetoacetyl-CoA synthetase MESCI_RS12210 MESCI_RS12760
atoB acetyl-CoA C-acetyltransferase MESCI_RS06630 MESCI_RS05450
Alternative steps:
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ MESCI_RS23340 MESCI_RS12995
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) MESCI_RS23330 MESCI_RS12985
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP MESCI_RS23325 MESCI_RS12980
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) MESCI_RS23335 MESCI_RS12990
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_RS26210 MESCI_RS31065
natB L-leucine ABC transporter, substrate-binding component NatB MESCI_RS26180
natC L-leucine ABC transporter, permease component 1 (NatC) MESCI_RS26225 MESCI_RS31060
natD L-leucine ABC transporter, permease component 2 (NatD) MESCI_RS26220 MESCI_RS31055
natE L-leucine ABC transporter, ATPase component 2 (NatE) MESCI_RS26215 MESCI_RS06160
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused MESCI_RS01690
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 Apr 09 2024. 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