As text, or see rules and steps
# Leucine degradation in GapMind is based on MetaCyc pathway L-leucine degradation I, # via branched alpha-keto acid dehydrogenase (metacyc:LEU-DEG2-PWY). # Other pathways for are not included here because they are not linked to sequence # (metacyc:PWY-5075) or do not result in carbon incorporation. # ABC transporters: # E. coli livFGHMJ or livFGHMK (livK and livJ are alternate SBPs); # and livJFGHM from Streptococcus pneumoniae; # and braCDEFG from Pseudomonas aeruginosa (braC is the SBP); # and braDEFG/braC3 from R. leguminosarum; braC3 (RL3540; Q1MDE9) is a secondary # SBP that transports leucine/isoleucine/valine/alanine (PMID:19597156); the # proximal braC (Q9L3M3) is also thought to be involved in leucine transport (PMC135202); # LivH/BraD = RL3750/Q1MCU0; LivM/BraE = RL3749/Q1MCU1; # LivG/BraF = RL3748/Q1MCU2; LivF/BraG = RL3747/Q1MCU3; # and in Acidovorax sp. GW101-3H11: # LivF = Ac3H11_1692 (A0A165KC78), LivG = Ac3H11_1693 (A0A165KC86), # LivJ = Ac3H11_2396 (A0A165KTD4; not near the other components, but strong phenotype on leucine and cofitness), # LivH = Ac3H11_1695 (A0A165KC95), LivM = Ac3H11_1694 (A0A165KER0); livF L-leucine ABC transporter, ATPase component 1 (LivF/BraG) curated:CharProtDB::CH_003736 curated:TCDB::P21630 curated:TCDB::Q8DQH7 uniprot:Q1MCU3 uniprot:A0A165KC78 livG L-leucine ABC transporter, ATPase component 2 (LivG/BraF) curated:TCDB::P0A9S7 curated:TCDB::P21629 curated:TCDB::Q8DQH8 uniprot:Q1MCU2 uniprot:A0A165KC86 livJ L-leucine ABC transporter, substrate-binding component (LivJ/LivK/BraC/BraC3) curated:SwissProt::P21175 curated:CharProtDB::CH_107418 curated:TCDB::P0AD96 curated:TCDB::Q8DQI1 uniprot:Q1MDE9 curated:TCDB::Q9L3M3 uniprot:A0A165KTD4 livH L-leucine ABC transporter, permease component 1 (LivH/BraD) curated:TCDB::P21627 curated:TCDB::Q8DQI0 curated:ecocyc::LIVH-MONOMER uniprot:Q1MCU0 uniprot:A0A165KC95 # LivM from Streptococcus pneumoniae lacks an N-terminal domain of unknown # function (DUF3382) that is found in E.coli and P. aeruginosa livM L-leucine ABC transporter, permease component 2 (LivM/BraE) curated:SwissProt::P22729 curated:TCDB::P21628 curated:TCDB::Q8DQH9 uniprot:Q1MCU1 uniprot:A0A165KER0 # Transporters were identified using # query: transporter:leucine:L-leucine leucine-transport: livF livG livJ livH livM # Synechocystis natABCDE and a related system in Anabaena (annotated with "leu" not leucine as the substrate) natA L-leucine ABC transporter, ATPase component 1 (NatA) curated:TCDB::Q55164 curated:TCDB::Q7A2H0 natB L-leucine ABC transporter, substrate-binding component NatB curated:TCDB::Q55387 curated:TCDB::Q8YVY4 natC L-leucine ABC transporter, permease component 1 (NatC) curated:TCDB::P74455 curated:TCDB::Q8YY08 natD L-leucine ABC transporter, permease component 2 (NatD) curated:TCDB::P74318 curated:TCDB::Q8YXD0 natE L-leucine ABC transporter, ATPase component 2 (NatE) curated:TCDB::P73650 curated:TCDB::Q8YT15 leucine-transport: natA natB natC natD natE # AapJQMP from Rhizobium leguminosarum is described in glutamate.steps import glutamate.steps:aapJ aapQ aapM aapP leucine-transport: aapJ aapQ aapM aapP # Homomeric transporters: leuT L-leucine:Na+ symporter LeuT curated:TCDB::O67854 leucine-transport: leuT brnQ L-leucine:Na+ symporter BrnQ/BraB curated:TCDB::P0AD99 curated:TCDB::P19072 leucine-transport: brnQ bcaP L-leucine uptake transporter BcaP curated:TCDB::S6EX81 leucine-transport: bcaP Bap2 L-leucine permease Bap2 curated:CharProtDB::CH_091448 curated:TCDB::Q2VQZ4 leucine-transport: Bap2 AAP1 L-leucine permease AAP1 curated:CharProtDB::CH_091601 leucine-transport: AAP1 # Ignore heteromeric systems found only in animals (i.e., TC 2.A.3.8.25) # Ignore regulatory proteins such as SC16B_HUMAN, SSY1_YEAST # Ignore amino acid exporters such as leuE, yjeH, brnEF # These enzymes transfer the amino group to 2-oxoglutarate to form # glutamate; glutamate dehydrogenase (not included in the pathway # definition) can then release the ammonia. Many other paths are # possible but do not seem to be known (i.e., transfer to oxaloacetate # followed by aspartate-ammonia lyase). ilvE L-leucine transaminase EC:2.6.1.6 EC:2.6.1.42 bkdA branched-chain alpha-ketoacid dehydrogenase, E1 component alpha subunit curated:SwissProt::P12694 curated:BRENDA::Q72GU1 curated:CharProtDB::CH_121278 curated:SwissProt::O45924 curated:SwissProt::P11178 curated:SwissProt::P9WIS3 curated:SwissProt::Q5SLR4 curated:SwissProt::Q84JL2 curated:SwissProt::Q9LPL5 curated:reanno::Smeli:SMc03201 curated:reanno::pseudo13_GW456_L13:PfGW456L13_3540 curated:reanno::pseudo3_N2E3:AO353_26635 curated:reanno::pseudo5_N2C3_1:AO356_22990 curated:reanno::pseudo6_N2E2:Pf6N2E2_481 curated:metacyc::MONOMER-11683 bkdB branched-chain alpha-ketoacid dehydrogenase, E1 component beta subunit curated:CharProtDB::CH_121283 curated:SwissProt::P21953 curated:SwissProt::P9WIS1 curated:SwissProt::Q5SLR3 curated:SwissProt::Q9LDY2 curated:metacyc::MONOMER-11684 curated:reanno::Smeli:SMc03202 curated:reanno::WCS417:GFF3430 curated:reanno::pseudo13_GW456_L13:PfGW456L13_3541 curated:reanno::pseudo5_N2C3_1:AO356_22985 curated:reanno::pseudo6_N2E2:Pf6N2E2_480 curated:BRENDA::Q9HIA4 bkdC branched-chain alpha-ketoacid dehydrogenase, E2 component EC:2.3.1.168 lpd branched-chain alpha-ketoacid dehydrogenase, E3 component EC:1.8.1.4 vorA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit VorA curated:SwissProt::P80907 ignore_other:1.2.7.7 vorB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit VorB curated:SwissProt::P80908 ignore_other:1.2.7.7 vorC branched-chain alpha-ketoacid:ferredoxin oxidoreductase, gamma subunit VorC curated:SwissProt::P80909 ignore_other:1.2.7.7 # ofoAB is similar to low-specificity 2-oxoacid oxidoreductases (EC:1.2.7.11); it is generally # not certain if these act on 4-methyl-2-oxopentanoate or not, but they probably do. ofoA branched-chain alpha-ketoacid:ferredoxin oxidoreductase, alpha subunit OfoA curated:SwissProt::P72578 ignore_other:1.2.7.7 ignore_other:1.2.7.11 ofoB branched-chain alpha-ketoacid:ferredoxin oxidoreductase, beta subunit OfoB curated:SwissProt::P72579 ignore_other:1.2.7.7 ignore_other:1.2.7.11 ofo branched-chain alpha-ketoacid:ferredoxin oxidoreductase, fused curated:reanno::Cup4G11:RR42_RS19540 curated:reanno::psRCH2:GFF3452 ignore_other:1.2.7.7 ignore_other:1.2.7.11 # These decarboxylating dehydrogenases act on # 4-methyl-2-oxopentanoate, # 3-methyl-2-oxobutanoate (2-oxoisovalerate) # and (S)-3-methyl-2-oxopentanoate and are known as the branched-chain # alpha-ketoacid dehydrogenases. # They can pass electrons to NAD (EC:1.2.1.25) or to ferredoxin (EC:1.2.7.7). # The NAD-dependent enzyme is the sum of three activities: # EC:1.2.4.4 (the 4-methyl-2-oxopentanoate dehydrogenase, with transfer to the lipopoyllysine residue of 2.3.1.168) # which is itself heteromeric, with alpha and beta subunits; # EC:2.3.1.168 (dihydrolipoyllysine-residue (3-methylbutanoyl)transferase); # and EC:1.8.1.4 (dihydrolipoyl dehydrogenase, transferring electrons to NAD). BKD: bkdA bkdB bkdC lpd # The well-characterized ferredoxin-dependent enzymes have 3 subunits (vorABC) or 2 subunits (ofoAB). BKD: vorA vorB vorC BKD: ofoA ofoB # Genetic data identified a fused ferredoxin-dependent enzyme with just 1 subunit (ofo). BKD: ofo liuA isovaleryl-CoA dehydrogenase EC:1.3.8.4 EC:1.3.99.10 # 3-methylcrotonyl-CoA carboxylase has 2 subunits liuB 3-methylcrotonyl-CoA carboxylase, alpha (biotin-containing) subunit curated:CharProtDB::CH_122249 curated:BRENDA::Q42523 curated:BRENDA::Q9I299 curated:SwissProt::Q2QMG2 curated:SwissProt::Q96RQ3 curated:SwissProt::Q99MR8 curated:reanno::SB2B:6937189 curated:reanno::Smeli:SM_b21124 curated:reanno::pseudo1_N1B4:Pf1N1B4_3984 curated:reanno::pseudo5_N2C3_1:AO356_01595 curated:reanno::pseudo6_N2E2:Pf6N2E2_2194 ignore_other:6.4.1.4 liuD 3-methylcrotonyl-CoA carboxylase, beta subunit curated:BRENDA::Q9I297 curated:BRENDA::Q9LDD8 curated:CharProtDB::CH_122289 curated:SwissProt::Q9HCC0 curated:SwissProt::Q9V9A7 curated:reanno::SB2B:6937191 curated:reanno::Smeli:SM_b21122 curated:reanno::psRCH2:GFF1050 curated:reanno::pseudo5_N2C3_1:AO356_01585 curated:reanno::pseudo6_N2E2:Pf6N2E2_2192 ignore_other:6.4.1.4 # SM_b21126 (Q92VJ6) is a bit diverged and is confirmed by fitness data liuC 3-methylglutaconyl-CoA hydratase EC:4.2.1.18 uniprot:Q92VJ6 liuE hydroxymethylglutaryl-CoA lyase EC:4.1.3.4 atoA acetoacetyl-CoA transferase, A subunit curated:ecocyc::ATOD-MONOMER curated:metacyc::HP0691-MONOMER curated:reanno::psRCH2:GFF1045 curated:reanno::pseudo6_N2E2:Pf6N2E2_2111 ignore_other:2.8.3.5 atoD acetoacetyl-CoA transferase, B subunit curated:ecocyc::ATOA-MONOMER curated:metacyc::HP0692-MONOMER curated:reanno::psRCH2:GFF1044 curated:reanno::pseudo6_N2E2:Pf6N2E2_2112 ignore_other:2.8.3.5 aacS acetoacetyl-CoA synthetase EC:6.2.1.16 # acetyl-CoA:acetoacetyl-CoA transferase (sometimes given EC:2.8.3.9 or EC:2.8.3.8) # or succinyl-CoA:acetoacetyl-CoA transferase (EC:2.8.3.5, also known as 3-oxoacid CoA-transferase) # can activate acetoacetate. # These have an A and B subunit. acetoacetate-activation: atoA atoD # Alternatively, an ATP-dependent ligase (aacS) can activate acetoacetate (EC:6.2.1.16). acetoacetate-activation: aacS # Produces two acetyl-CoA from acetoacetyl-CoA and CoA. # EC:2.3.1.16 describes a broader range of beta-ketothiolases. # This enzyme is usually homomeric, but uniprot:I3R3D0 and uniprot:I3RA71 are non-catalytic subunits # of an enzyme from Haloferax mediterranei that also contains a # "normal" catalytic subunit (uniprot:I3R3D1, uniprot:I3RA72). # Inclusion of uniprot:P07256 was an error in BRENDA. # And CharProtDB includes an odd annotation of the form "similar to acetyl-CoA acetyltransferase" atoB acetyl-CoA C-acetyltransferase EC:2.3.1.9 ignore_other:2.3.1.16 ignore:BRENDA::P07256 ignore:BRENDA::I3R3D0 ignore:BRENDA::I3RA71 ignore_other:similar to acetyl-CoA acetyltransferase # The acetoacetate is activated to acetoacetyl-CoA, # and cleaved by acetyl-CoA acetyltransferase, # giving two acetyl-CoA. acetoacetate-degradation: acetoacetate-activation atoB # After transamination to 4-methyl-2-oxopentanoate by ilvE, # kbd oxidatively decarboxylates it to isovaleryl-CoA (also known as 3-methylbutanoyl-CoA), # liuA oxidizes it to 3-methylcrotonyl-CoA, # liuBD carboxylates it to 3-methylglutaconyl-CoA, # liuC hydrates it to hydroxymethylglutaryl-CoA, # and liuE hydrolyzes it to acetoacetate and acetyl-CoA. all: leucine-transport ilvE BKD liuA liuB liuD liuC liuE acetoacetate-degradation
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