GapMind for catabolism of small carbon sources

 

L-leucine catabolism in Sphingobium czechense LL01

Best path

leuT, 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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
leuT L-leucine:Na+ symporter LeuT
ilvE L-leucine transaminase V473_RS15150 V473_RS16535
bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit V473_RS07890 V473_RS09780
bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit V473_RS07885 V473_RS09775
bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component V473_RS07880 V473_RS02805
lpd branched-chain alpha-ketoacid dehydrogenase, E3 component V473_RS06640 V473_RS22020
liuA isovaleryl-CoA dehydrogenase V473_RS17395 V473_RS17555
liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit V473_RS17405 V473_RS08265
liuD 3-methylcrotonyl-CoA carboxylase, beta subunit V473_RS17400 V473_RS08285
liuC 3-methylglutaconyl-CoA hydratase V473_RS08215 V473_RS18100
liuE hydroxymethylglutaryl-CoA lyase
atoA acetoacetyl-CoA transferase, A subunit V473_RS02865 V473_RS08605
atoD acetoacetyl-CoA transferase, B subunit V473_RS00560 V473_RS08315
atoB acetyl-CoA C-acetyltransferase V473_RS07145 V473_RS00635
Alternative steps:
aacS acetoacetyl-CoA synthetase V473_RS14610 V473_RS18475
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 V473_RS04645 V473_RS03740
aapQ ABC transporter for amino acids (Asp/Asn/Glu/Pro/Leu), permease component 1 (AapQ)
Bap2 L-leucine permease Bap2
bcaP L-leucine uptake transporter BcaP V473_RS03185 V473_RS00330
brnQ L-leucine:Na+ symporter BrnQ/BraB
livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) V473_RS04120 V473_RS13485
livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) V473_RS04115 V473_RS13485
livH L-leucine ABC transporter, permease component 1 (LivH/BraD) V473_RS04105
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) V473_RS04115 V473_RS13485
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) V473_RS04105
natE L-leucine ABC transporter, ATPase component 2 (NatE) V473_RS04120 V473_RS13485
ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused V473_RS08130
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