GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Photobacterium gaetbulicola Gung47

Best path

brnQ, 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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
brnQ L-leucine:Na+ symporter BrnQ/BraB H744_RS25145 H744_RS09390
ilvE L-leucine transaminase H744_RS10170 H744_RS16340
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit H744_RS04245 H744_RS26450
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit H744_RS04250 H744_RS26450
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component H744_RS04255 H744_RS15065
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component H744_RS12355 H744_RS03140
liuA isovaleryl-CoA dehydrogenase H744_RS04345 H744_RS04325
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit H744_RS09235
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit H744_RS04350
liuC 3-methylglutaconyl-CoA hydratase H744_RS04355 H744_RS04360
liuE hydroxymethylglutaryl-CoA lyase H744_RS04360
atoA acetoacetyl-CoA transferase, A subunit H744_RS02900
atoD acetoacetyl-CoA transferase, B subunit H744_RS02895
atoB acetyl-CoA C-acetyltransferase H744_RS02875 H744_RS04335
Alternative steps:
aacS acetoacetyl-CoA synthetase H744_RS02730 H744_RS03935
AAP1 L-leucine permease AAP1
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ H744_RS20715 H744_RS06585
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) H744_RS20725 H744_RS06575
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP H744_RS20730 H744_RS06570
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) H744_RS20720 H744_RS06580
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
leuT L-leucine:Na+ symporter LeuT H744_RS20220 H744_RS22565
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) H744_RS07085 H744_RS12065
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) H744_RS12065 H744_RS07090
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) H744_RS07100
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) H744_RS07090 H744_RS12065
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) H744_RS07085 H744_RS12065
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.

Links

Downloads

Related tools

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