GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Streptacidiphilus oryzae TH49

Best path

livF, livG, livJ, livH, livM, 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
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) BS73_RS29110 BS73_RS13620
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) BS73_RS29115 BS73_RS00335
livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3)
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) BS73_RS29125 BS73_RS13625
livM L-leucine ABC transporter, permease component 2 (LivM/BraE) BS73_RS29120 BS73_RS13630
ilvE L-leucine transaminase BS73_RS14690 BS73_RS05050
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit BS73_RS19265 BS73_RS01205
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit BS73_RS19260 BS73_RS19370
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component BS73_RS19375 BS73_RS19255
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component BS73_RS01320 BS73_RS28205
liuA isovaleryl-CoA dehydrogenase BS73_RS25270 BS73_RS10790
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit BS73_RS25280 BS73_RS23635
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit BS73_RS25285 BS73_RS00480
liuC 3-methylglutaconyl-CoA hydratase BS73_RS14910 BS73_RS33895
liuE hydroxymethylglutaryl-CoA lyase BS73_RS25275 BS73_RS01870
atoA acetoacetyl-CoA transferase, A subunit BS73_RS10025
atoD acetoacetyl-CoA transferase, B subunit BS73_RS10020
atoB acetyl-CoA C-acetyltransferase BS73_RS10365 BS73_RS08675
Alternative steps:
aacS acetoacetyl-CoA synthetase BS73_RS34115 BS73_RS06735
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 BS73_RS32880 BS73_RS15740
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
Bap2 L-leucine permease Bap2 BS73_RS16535 BS73_RS10785
bcaP L-leucine uptake transporter BcaP BS73_RS12665 BS73_RS16585
brnQ L-leucine:Na+ symporter BrnQ/BraB
leuT L-leucine:Na+ symporter LeuT
natA L-leucine ABC transporter, ATPase component 1 (NatA) BS73_RS00335 BS73_RS29115
natB L-leucine ABC transporter, substrate-binding component NatB
natC L-leucine ABC transporter, permease component 1 (NatC) BS73_RS29120
natD L-leucine ABC transporter, permease component 2 (NatD) BS73_RS29125
natE L-leucine ABC transporter, ATPase component 2 (NatE) BS73_RS00340 BS73_RS29110
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused BS73_RS06630
ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA
ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB BS73_RS21825
vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA
vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB BS73_RS21820 BS73_RS06405
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