GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Pseudomonas litoralis 2SM5

Best path

livF, livG, livJ, livH, livM, ilvE, ofo, 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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) BLU11_RS03750 BLU11_RS01420
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) BLU11_RS03755 BLU11_RS01420
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BLU11_RS03770
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) BLU11_RS03765
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) BLU11_RS03760
ilvE L-leucine transaminase BLU11_RS11780 BLU11_RS06275
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused BLU11_RS15475
liuA isovaleryl-CoA dehydrogenase BLU11_RS15705 BLU11_RS15480
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BLU11_RS15720 BLU11_RS15495
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit BLU11_RS15710 BLU11_RS15485
liuC 3-methylglutaconyl-CoA hydratase BLU11_RS15715 BLU11_RS15490
liuE hydroxymethylglutaryl-CoA lyase BLU11_RS15725 BLU11_RS15500
atoA acetoacetyl-CoA transferase, A subunit BLU11_RS15730 BLU11_RS15505
atoD acetoacetyl-CoA transferase, B subunit BLU11_RS15735 BLU11_RS15510
atoB acetyl-CoA C-acetyltransferase BLU11_RS15740 BLU11_RS15515
Alternative steps:
aacS acetoacetyl-CoA synthetase BLU11_RS06220 BLU11_RS15900
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 BLU11_RS14500 BLU11_RS18455
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
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BLU11_RS15975
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BLU11_RS15970
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BLU11_RS15965 BLU11_RS11795
brnQ L-leucine:Na+ symporter BrnQ/BraB BLU11_RS04790
leuT L-leucine:Na+ symporter LeuT
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BLU11_RS04775 BLU11_RS17200
natA L-leucine ABC transporter, ATPase component 1 (NatA) BLU11_RS03755 BLU11_RS01420
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) BLU11_RS03765
natE L-leucine ABC transporter, ATPase component 2 (NatE) BLU11_RS03750 BLU11_RS01420
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