GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Halomonas desiderata SP1

Best path

aapJ, aapQ, aapM, aapP, 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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aapJ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), substrate-binding component AapJ BZY95_RS06440
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) BZY95_RS06445
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) BZY95_RS06450 BZY95_RS12915
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP BZY95_RS02565 BZY95_RS12910
ilvE L-leucine transaminase BZY95_RS00615 BZY95_RS21775
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BZY95_RS09715
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BZY95_RS09720 BZY95_RS15035
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BZY95_RS18770 BZY95_RS09725
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BZY95_RS15335 BZY95_RS21050
liuA isovaleryl-CoA dehydrogenase BZY95_RS13300 BZY95_RS01015
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BZY95_RS13285 BZY95_RS03995
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit BZY95_RS13295
liuC 3-methylglutaconyl-CoA hydratase BZY95_RS13290 BZY95_RS17490
liuE hydroxymethylglutaryl-CoA lyase BZY95_RS13280 BZY95_RS01745
atoA* acetoacetyl-CoA transferase, A subunit BZY95_RS18560 with BZY95_RS18555 BZY95_RS02540
atoD acetoacetyl-CoA transferase, B subunit BZY95_RS18550 BZY95_RS02545
atoB acetyl-CoA C-acetyltransferase BZY95_RS13540 BZY95_RS02365
Alternative steps:
aacS acetoacetyl-CoA synthetase BZY95_RS09125 BZY95_RS21570
AAP1 L-leucine permease AAP1
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT BZY95_RS05825
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) BZY95_RS08160 BZY95_RS14695
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) BZY95_RS19340 BZY95_RS02780
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) BZY95_RS14710 BZY95_RS02765
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) BZY95_RS14935
livM L-leucine ABC transporter, permease component 2 (LivM/BraE)
natA L-leucine ABC transporter, ATPase component 1 (NatA) BZY95_RS14915 BZY95_RS14690
natB L-leucine ABC transporter, substrate-binding component NatB BZY95_RS14935
natC L-leucine ABC transporter, permease component 1 (NatC)
natD L-leucine ABC transporter, permease component 2 (NatD) BZY95_RS14925 BZY95_RS08775
natE L-leucine ABC transporter, ATPase component 2 (NatE) BZY95_RS14920 BZY95_RS02775
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 Apr 09 2024. 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