GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Halomonas titanicae BH1

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 (28 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 HALTITAN_RS07485 HALTITAN_RS02835
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ) HALTITAN_RS02840 HALTITAN_RS07490
aapM ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 2 (AapM) HALTITAN_RS02845 HALTITAN_RS07495
aapP ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), ATPase component AapP HALTITAN_RS02850 HALTITAN_RS07500
ilvE L-leucine transaminase HALTITAN_RS22815 HALTITAN_RS07475
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit HALTITAN_RS16760
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit HALTITAN_RS16765
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component HALTITAN_RS16770 HALTITAN_RS13360
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component HALTITAN_RS12210 HALTITAN_RS09625
liuA isovaleryl-CoA dehydrogenase HALTITAN_RS05155 HALTITAN_RS00790
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit HALTITAN_RS05140 HALTITAN_RS02185
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit HALTITAN_RS05150
liuC 3-methylglutaconyl-CoA hydratase HALTITAN_RS05145 HALTITAN_RS11900
liuE hydroxymethylglutaryl-CoA lyase HALTITAN_RS05135 HALTITAN_RS13915
atoA acetoacetyl-CoA transferase, A subunit HALTITAN_RS07015
atoD acetoacetyl-CoA transferase, B subunit HALTITAN_RS07020
atoB acetyl-CoA C-acetyltransferase HALTITAN_RS18010 HALTITAN_RS18730
Alternative steps:
aacS acetoacetyl-CoA synthetase HALTITAN_RS05130 HALTITAN_RS18625
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
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) HALTITAN_RS02305 HALTITAN_RS22535
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) HALTITAN_RS02310 HALTITAN_RS03355
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) HALTITAN_RS02320 HALTITAN_RS05180
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) HALTITAN_RS19895
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) HALTITAN_RS02315
natA L-leucine ABC transporter, ATPase component 1 (NatA) HALTITAN_RS19870 HALTITAN_RS05165
natB L-leucine ABC transporter, substrate-binding component NatB HALTITAN_RS19895
natC L-leucine ABC transporter, permease component 1 (NatC)
natD L-leucine ABC transporter, permease component 2 (NatD) HALTITAN_RS19880 HALTITAN_RS02320
natE L-leucine ABC transporter, ATPase component 2 (NatE) HALTITAN_RS19875 HALTITAN_RS02305
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused HALTITAN_RS01790
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