GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Erythrobacter gangjinensis K7-2

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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
leuT L-leucine:Na+ symporter LeuT AAW01_RS01765
ilvE L-leucine transaminase AAW01_RS00160 AAW01_RS10325
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit AAW01_RS01595 AAW01_RS02710
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit AAW01_RS01600 AAW01_RS02700
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component AAW01_RS01605 AAW01_RS02590
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component AAW01_RS02605 AAW01_RS00490
liuA isovaleryl-CoA dehydrogenase AAW01_RS07145 AAW01_RS10540
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit AAW01_RS10650 AAW01_RS04050
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit AAW01_RS07130 AAW01_RS04080
liuC 3-methylglutaconyl-CoA hydratase AAW01_RS13205 AAW01_RS11465
liuE hydroxymethylglutaryl-CoA lyase AAW01_RS11300
atoA acetoacetyl-CoA transferase, A subunit AAW01_RS09475
atoD acetoacetyl-CoA transferase, B subunit AAW01_RS09460
atoB acetyl-CoA C-acetyltransferase AAW01_RS02970 AAW01_RS00830
Alternative steps:
aacS acetoacetyl-CoA synthetase AAW01_RS06755 AAW01_RS00835
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 AAW01_RS07155 AAW01_RS11525
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
brnQ L-leucine:Na+ symporter BrnQ/BraB
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) AAW01_RS09360 AAW01_RS06625
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) AAW01_RS09360 AAW01_RS07155
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) AAW01_RS09360
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) AAW01_RS09360 AAW01_RS06625
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA AAW01_RS01480
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB AAW01_RS01485
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB AAW01_RS01480
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