GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Pontibacter ramchanderi LP43

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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
leuT L-leucine:Na+ symporter LeuT BD749_RS08630
ilvE L-leucine transaminase BD749_RS07905 BD749_RS13360
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BD749_RS12665 BD749_RS11405
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BD749_RS12665 BD749_RS17720
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BD749_RS07170 BD749_RS18710
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BD749_RS18705 BD749_RS14590
liuA isovaleryl-CoA dehydrogenase BD749_RS09460 BD749_RS11220
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BD749_RS02955 BD749_RS17485
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit BD749_RS08175 BD749_RS15550
liuC 3-methylglutaconyl-CoA hydratase BD749_RS06390 BD749_RS17005
liuE hydroxymethylglutaryl-CoA lyase BD749_RS13095
atoA acetoacetyl-CoA transferase, A subunit BD749_RS17840 BD749_RS04210
atoD acetoacetyl-CoA transferase, B subunit BD749_RS17835 BD749_RS04210
atoB acetyl-CoA C-acetyltransferase BD749_RS13705 BD749_RS18285
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)
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BD749_RS18690 BD749_RS09725
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 BD749_RS18850
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) BD749_RS11320 BD749_RS14880
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) BD749_RS11320 BD749_RS17540
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) BD749_RS11320 BD749_RS14880
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) BD749_RS11320 BD749_RS12890
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