GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Marinobacter adhaerens HP15

Best path

livF, livG, livJ, livH, livM, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, atoB

Also see fitness data for the top candidates

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) HP15_3059 HP15_2703
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) HP15_3058 HP15_2704
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) HP15_3055
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) HP15_3056 HP15_2706
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) HP15_3057 HP15_2705
ilvE L-leucine transaminase HP15_436 HP15_858
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit HP15_61 HP15_1634
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit HP15_1633 HP15_63
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component HP15_1631 HP15_64
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component HP15_1523 HP15_65
liuA isovaleryl-CoA dehydrogenase HP15_2 HP15_1005
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit HP15_1002 HP15_4179
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit HP15_1004 HP15_2538
liuC 3-methylglutaconyl-CoA hydratase HP15_4180 HP15_1003
liuE hydroxymethylglutaryl-CoA lyase HP15_4178 HP15_1001
aacS acetoacetyl-CoA synthetase HP15_3799 HP15_4177
atoB acetyl-CoA C-acetyltransferase HP15_2996 HP15_5
Alternative steps:
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ HP15_2196
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) HP15_2194
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP HP15_2193 HP15_2920
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) HP15_2195
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 HP15_857 HP15_3916
natA L-leucine ABC transporter, ATPase component 1 (NatA) HP15_3058 HP15_2704
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC) HP15_3057
natD L-leucine ABC transporter, permease component 2 (NatD) HP15_3056 HP15_2015
natE L-leucine ABC transporter, ATPase component 2 (NatE) HP15_3059 HP15_4099
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused HP15_859
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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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