livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, atoA, atoD, atoB
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.
Or see definitions of steps
Step | Description | Best candidate | 2nd candidate |
---|---|---|---|
livF | L-leucine ABC transporter, ATPase component 1 (LivF/BraG) | BN2503_RS06720 | BN2503_RS02275 |
livG | L-leucine ABC transporter, ATPase component 2 (LivG/BraF) | BN2503_RS06725 | BN2503_RS02270 |
livJ | L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) | BN2503_RS04725 | BN2503_RS02255 |
livH | L-leucine ABC transporter, permease component 1 (LivH/BraD) | BN2503_RS06735 | BN2503_RS02260 |
livM | L-leucine ABC transporter, permease component 2 (LivM/BraE) | BN2503_RS06730 | BN2503_RS02265 |
ilvE | L-leucine transaminase | BN2503_RS13460 | BN2503_RS07910 |
ofo | branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused | BN2503_RS02910 | |
liuA | isovaleryl-CoA dehydrogenase | BN2503_RS15695 | BN2503_RS07075 |
liuB | 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit | BN2503_RS06975 | BN2503_RS07525 |
liuD | 3-methylcrotonyl-CoA carboxylase, beta subunit | BN2503_RS06995 | BN2503_RS14690 |
liuC | 3-methylglutaconyl-CoA hydratase | BN2503_RS06985 | BN2503_RS06965 |
liuE | hydroxymethylglutaryl-CoA lyase | BN2503_RS06965 | |
atoA | acetoacetyl-CoA transferase, A subunit | BN2503_RS02630 | |
atoD | acetoacetyl-CoA transferase, B subunit | BN2503_RS02625 | |
atoB | acetyl-CoA C-acetyltransferase | BN2503_RS17070 | BN2503_RS12305 |
Alternative steps: | |||
aacS | acetoacetyl-CoA synthetase | BN2503_RS07000 | BN2503_RS02705 |
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) | BN2503_RS00885 | |
aapP | ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP | BN2503_RS14975 | BN2503_RS00880 |
aapQ | ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) | BN2503_RS14985 | |
Bap2 | L-leucine permease Bap2 | BN2503_RS15280 | |
bcaP | L-leucine uptake transporter BcaP | ||
bkdA | branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit | ||
bkdB | branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit | ||
bkdC | branched-chain alpha-ketoacid dehydrogenase, E2 component | BN2503_RS17110 | BN2503_RS03820 |
brnQ | L-leucine:Na+ symporter BrnQ/BraB | ||
leuT | L-leucine:Na+ symporter LeuT | ||
lpd* | branched-chain alpha-ketoacid dehydrogenase, E3 component | BN2503_RS17105 with BN2503_RS11830 | BN2503_RS03815 |
natA | L-leucine ABC transporter, ATPase component 1 (NatA) | BN2503_RS06725 | BN2503_RS01080 |
natB | L-leucine ABC transporter, substrate-binding component NatB | ||
natC | L-leucine ABC transporter, permease component 1 (NatC) | BN2503_RS02265 | |
natD | L-leucine ABC transporter, permease component 2 (NatD) | BN2503_RS06735 | BN2503_RS02260 |
natE | L-leucine ABC transporter, ATPase component 2 (NatE) | BN2503_RS06720 | BN2503_RS02275 |
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.
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:
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