GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Novosphingobium barchaimii LL02

Best path

leuT, ilvE, bkdA, bkdB, bkdC, lpd, 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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
leuT L-leucine:Na+ symporter LeuT
ilvE L-leucine transaminase V474_RS06130 V474_RS22725
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit V474_RS02435 V474_RS09600
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit V474_RS02440 V474_RS19420
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component V474_RS02445 V474_RS07635
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component V474_RS03825 V474_RS11040
liuA isovaleryl-CoA dehydrogenase V474_RS05240 V474_RS01300
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit V474_RS18360 V474_RS05365
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit V474_RS18370 V474_RS05395
liuC 3-methylglutaconyl-CoA hydratase V474_RS01310 V474_RS16345
liuE hydroxymethylglutaryl-CoA lyase V474_RS10040 V474_RS08255
atoA acetoacetyl-CoA transferase, A subunit V474_RS17305 V474_RS21635
atoD acetoacetyl-CoA transferase, B subunit V474_RS21640 V474_RS17310
atoB acetyl-CoA C-acetyltransferase V474_RS02980 V474_RS05390
Alternative steps:
aacS acetoacetyl-CoA synthetase V474_RS16650 V474_RS07610
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)
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP V474_RS07795 V474_RS19195
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP V474_RS08715 V474_RS02665
brnQ L-leucine:Na+ symporter BrnQ/BraB
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) V474_RS15730 V474_RS07795
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) V474_RS07795 V474_RS15730
livH L-leucine ABC transporter, permease component 1 (LivH/BraD)
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livM L-leucine ABC transporter, permease component 2 (LivM/BraE)
natA L-leucine ABC transporter, ATPase component 1 (NatA) V474_RS15730 V474_RS07795
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)
natE L-leucine ABC transporter, ATPase component 2 (NatE) V474_RS15730 V474_RS07795
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 V474_RS04820
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.

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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