GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Brucella inopinata BO1

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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) BIBO1_RS12235 BIBO1_RS14990
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) BIBO1_RS12240 BIBO1_RS14985
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BIBO1_RS12225 BIBO1_RS06815
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) BIBO1_RS12250 BIBO1_RS19000
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) BIBO1_RS12245 BIBO1_RS0105460
ilvE L-leucine transaminase BIBO1_RS09965 BIBO1_RS16680
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BIBO1_RS17495 BIBO1_RS08625
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BIBO1_RS17500 BIBO1_RS08620
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BIBO1_RS17505 BIBO1_RS05695
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BIBO1_RS17510 BIBO1_RS08610
liuA isovaleryl-CoA dehydrogenase BIBO1_RS06840 BIBO1_RS17775
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BIBO1_RS06830 BIBO1_RS09065
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit BIBO1_RS06835 BIBO1_RS09060
liuC 3-methylglutaconyl-CoA hydratase BIBO1_RS06820 BIBO1_RS15870
liuE hydroxymethylglutaryl-CoA lyase BIBO1_RS06825
aacS acetoacetyl-CoA synthetase BIBO1_RS06845 BIBO1_RS13010
atoB acetyl-CoA C-acetyltransferase BIBO1_RS17190 BIBO1_RS16830
Alternative steps:
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ BIBO1_RS07165 BIBO1_RS18960
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) BIBO1_RS07175 BIBO1_RS19985
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BIBO1_RS07180 BIBO1_RS20000
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BIBO1_RS07170 BIBO1_RS19985
atoA acetoacetyl-CoA transferase, A subunit BIBO1_RS16820
atoD acetoacetyl-CoA transferase, B subunit BIBO1_RS16825
Bap2 L-leucine permease Bap2 BIBO1_RS14845
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) BIBO1_RS19765 BIBO1_RS12240
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) BIBO1_RS19000
natE L-leucine ABC transporter, ATPase component 2 (NatE) BIBO1_RS12235 BIBO1_RS14990
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.

Links

Downloads

Related tools

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