GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Moritella dasanensis ArB 0140

Best path

brnQ, ilvE, bkdA, bkdB, bkdC, lpd, liuA, liuB, liuD, liuC, liuE, aacS, 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
brnQ L-leucine:Na+ symporter BrnQ/BraB A923_RS0120070 A923_RS0115990
ilvE L-leucine transaminase A923_RS0119195 A923_RS0100145
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit A923_RS0101130
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit A923_RS0101135
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component A923_RS0101140 A923_RS22235
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component A923_RS0111095 A923_RS0119140
liuA isovaleryl-CoA dehydrogenase A923_RS0101015
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit A923_RS0101000 A923_RS0118365
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit A923_RS0101010
liuC 3-methylglutaconyl-CoA hydratase A923_RS0101005 A923_RS0104120
liuE hydroxymethylglutaryl-CoA lyase A923_RS0100995
aacS acetoacetyl-CoA synthetase A923_RS0100990 A923_RS0104565
atoB acetyl-CoA C-acetyltransferase A923_RS0119275 A923_RS0119825
Alternative steps:
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ A923_RS0106870
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) A923_RS0106860 A923_RS0119710
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP A923_RS0106855 A923_RS0109795
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) A923_RS22050
atoA acetoacetyl-CoA transferase, A subunit
atoD acetoacetyl-CoA transferase, B subunit
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
leuT L-leucine:Na+ symporter LeuT A923_RS0114590
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) A923_RS0116415 A923_RS0110810
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) A923_RS0110810 A923_RS0116420
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) A923_RS0116430
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) A923_RS0110810 A923_RS0116420
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) A923_RS0116415 A923_RS0106420
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
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