GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Xanthobacter autotrophicus Py2

Best path

livF, livG, livJ, livH, livM, ilvE, ofo, 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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) XAUT_RS19750 XAUT_RS04450
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) XAUT_RS19745 XAUT_RS20495
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) XAUT_RS19760 XAUT_RS07820
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) XAUT_RS19735 XAUT_RS03235
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) XAUT_RS19740 XAUT_RS20495
ilvE L-leucine transaminase XAUT_RS12870 XAUT_RS22260
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused XAUT_RS01975
liuA isovaleryl-CoA dehydrogenase XAUT_RS21625 XAUT_RS06340
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit XAUT_RS09310 XAUT_RS23950
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit XAUT_RS09320 XAUT_RS23945
liuC 3-methylglutaconyl-CoA hydratase XAUT_RS09315 XAUT_RS04570
liuE hydroxymethylglutaryl-CoA lyase XAUT_RS09305
atoA acetoacetyl-CoA transferase, A subunit XAUT_RS11815 XAUT_RS05620
atoD acetoacetyl-CoA transferase, B subunit XAUT_RS11820 XAUT_RS05615
atoB acetyl-CoA C-acetyltransferase XAUT_RS23630 XAUT_RS15615
Alternative steps:
aacS acetoacetyl-CoA synthetase XAUT_RS20600 XAUT_RS14125
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ XAUT_RS23020 XAUT_RS08225
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) XAUT_RS23030 XAUT_RS10440
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP XAUT_RS23035 XAUT_RS12270
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) XAUT_RS23025
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit XAUT_RS19675 XAUT_RS07870
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit XAUT_RS20440 XAUT_RS19685
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component XAUT_RS00790 XAUT_RS19690
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component XAUT_RS19705 XAUT_RS00800
natA L-leucine ABC transporter, ATPase component 1 (NatA) XAUT_RS20495 XAUT_RS04455
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) XAUT_RS03235 XAUT_RS08110
natE L-leucine ABC transporter, ATPase component 2 (NatE) XAUT_RS19750 XAUT_RS20500
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.

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