GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Herbaspirillum seropedicae SmR1

Best path

livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, 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 (24 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) HSERO_RS05975 HSERO_RS00900
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) HSERO_RS05970 HSERO_RS00895
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) HSERO_RS08270 HSERO_RS17350
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) HSERO_RS05960 HSERO_RS00885
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) HSERO_RS08280 HSERO_RS05965
ilvE L-leucine transaminase HSERO_RS03330 HSERO_RS22025
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused HSERO_RS21380 HSERO_RS12755
liuA isovaleryl-CoA dehydrogenase HSERO_RS23440 HSERO_RS04905
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit HSERO_RS23460 HSERO_RS01925
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit HSERO_RS23455
liuC 3-methylglutaconyl-CoA hydratase HSERO_RS15435 HSERO_RS23475
liuE hydroxymethylglutaryl-CoA lyase HSERO_RS23475
atoA acetoacetyl-CoA transferase, A subunit HSERO_RS23190 HSERO_RS20000
atoD acetoacetyl-CoA transferase, B subunit HSERO_RS23185 HSERO_RS19995
atoB acetyl-CoA C-acetyltransferase HSERO_RS01180 HSERO_RS04635
Alternative steps:
aacS acetoacetyl-CoA synthetase
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) HSERO_RS07530 HSERO_RS23030
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP HSERO_RS19240 HSERO_RS17555
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) HSERO_RS19340 HSERO_RS17565
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component HSERO_RS14880 HSERO_RS07310
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component HSERO_RS07315 HSERO_RS14875
natA L-leucine ABC transporter, ATPase component 1 (NatA) HSERO_RS14705 HSERO_RS08285
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC) HSERO_RS14700
natD L-leucine ABC transporter, permease component 2 (NatD) HSERO_RS05960 HSERO_RS00885
natE L-leucine ABC transporter, ATPase component 2 (NatE) HSERO_RS08290 HSERO_RS08925
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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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