Component_60599 |
Source of aspartate-semialdehyde |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
GenProp0193 |
lysine biosynthesis via alpha-aminoadipate (AAA pathway)~Lysine biosynthesis in fungi has been characterized and begins with the condensation of 2-oxoglutarate and acetyl-CoA to homocitrate and continues through the distinctive intermediate, alpha-aminoadipate. This pathway is distinct in every respect from the diaminopimelate pathway commonly found in bacteria and animals. Recently, an alpha-aminoadipate pathway closely related to the fungal version has been characterized in Thermus thermophilus [1] and appears to be widely distributed among the archaea. |
None - {{∅}} |
Both - {{t},{f}} |
Unconfirmed contradictory |
|
Evidence_55126 |
TIGR00761 HMM |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
Component_60600 |
Source of aspartate-semialdehyde |
True - {{∅},{t}} |
True - {{t}} |
Confirmed presence |
|
Evidence_55128 |
TIGR02087 HMM |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Evidence_82146 |
TIGR03535 HMM |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Component_42742 |
epsilon-dehydrogenase (proposed) |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
Evidence_82150 |
TIGR03539 HMM |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Evidence_82147 |
TIGR03536 HMM |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Evidence_2245 |
TIGR00674 HMM |
True - {{∅},{t}} |
True - {{t}} |
Confirmed presence |
|
Component_60595 |
diaminopimelate decarboxylase |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
Component_42736 |
homocitrate synthase |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Evidence_82139 |
GenProp0160 GENPROP |
True - {{∅},{t}} |
True - {{t}} |
Confirmed presence |
|
Component_35603 |
aspartate-semialdehyde dehydrogenase |
True - {{t}} |
True - {{t}} |
Confirmed presence |
|
Component_270 |
diaminopimelate epimerase |
True - {{∅},{t}} |
True - {{t}} |
Confirmed presence |
|
Evidence_47945 |
TIGR00656 HMM |
True - {{t}} |
True - {{t}} |
Confirmed presence |
|
Component_35602 |
aspartate kinase |
True - {{t}} |
True - {{t}} |
Confirmed presence |
|
Evidence_55118 |
TIGR02144 HMM |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Evidence_82152 |
TIGR03542 HMM |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Evidence_82140 |
GenProp0787 GENPROP |
None - {{∅}} |
None - {{∅}} |
Unexplained |
|
Evidence_47949 |
TIGR01745 HMM |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
GenProp0786 |
lysine biosynthesis via diaminopimelate (DAP), succinylated branch~ |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Component_271 |
diaminopimelate decarboxylase |
True - {{∅},{t}} |
True - {{t}} |
Confirmed presence |
|
Evidence_55124 |
TIGR00707 HMM |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
Evidence_55127 |
TIGR02083 HMM |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Component_42737 |
homoaconitate hydratase, LysT subunit |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Component_42743 |
aminotransferase |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
Evidence_47946 |
TIGR00657 HMM |
True - {{t}} |
True - {{t}} |
Confirmed presence |
|
GenProp0125 |
lysine biosynthesis via diaminopimelate (DAP)~The basic amino acid lysine is synthesized in most bacteria and plants via a nine step pathway from aspartate (via aspartate semialdehyde which is also used in a number of other pathways). Most species utilize succinate (from succinyl-CoA) to make an important amide linkage in the ring-opening of piperidine dicarboxylate. The succinate is then hydrolyzed several steps later. Other species carry out analogous transformations with acetate (from acetyl-CoA). Chlamydia and cyanobacteria have been shown to utilize a direct aminotransferase path without the acylation/deacylation steps, and a number of other species apparently also use this variant. Each of these variants are included within this property. A closely related variant (GenProp0788) utilizes the NADPH-dependent enzyme diaminopimelate dehydrogenase (ddh) which incorporates ammonia directly and creates the meso-isomer of diaminopimelate, bypassing the need for the epimerase, DapE. A completely different pathway via alpha-amino adipate exists in fungi and certain bacteria (GenProp0193). Certain obligate intracellular organisms such as Coxiella, Rickettsia and Wolbachia contain all but the final step of this pathway (diaminopimelate decarboxylase). Presumably these organisms have no need of lysine biosynthesis, being able to obtain it from their hosts. The products of the penultimate two steps, however, (LL- and meso-diaminopimelate) are required components of the bacterial cell wall and so the rest of the pathway persists. The formal possibility that the decarboxylase exists in these organsims but is undetected requires that the state of this property remain 'some evidence' as opposed to 'NO'. |
True - {{∅},{t}} |
True - {{t}} |
Confirmed presence |
|
Evidence_55120 |
TIGR02146 HMM |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Component_42741 |
epsilon-carboxykinase (proposed) |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
GenProp0788 |
lysine biosynthesis via diaminopimelate (DAP) utilizing ammonia and NADPH~This pathway for the biosynthesis of L-lysine differs from the more common diaminopimelate pathway by the action of diaminopimelate dehydrogenase (ddh). This enzyme requires both ammonia as a nitrogen source (instead of an amino acid via a transaminase) and reductive power in the form of NADPH. Additionally, this pathway does not require the acetyl/succinyl protecting group transformations found in the standard pathway, nor does it require the action of diaminopimelate epimerase. This enzyme has been best characterized in Corynebacterium glutamicum and Bacillus sphaericus. One should note that the ddh enzyme is shown acting on the compound L-2-amino-6-oxoheptanedioate in EC and KEGG representations. This is merely the ring-opened form of 2,3,4,5-tetrahydropicolinate with which it is in equilibrium, and upon which the acyltransferases of the common pathway act. |
None - {{∅}} |
Both - {{t},{f}} |
Unconfirmed contradictory |
|
Component_60593 |
dihydrodipicolinate synthase |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
Evidence_82131 |
TIGR01921 HMM |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Evidence_55116 |
TIGR00977 HMM |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Evidence_82133 |
TIGR00036 HMM |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
GenProp0160 |
aspartate semialdehyde biosynthesis from aspartate~The aspartate semialdehyde biosynthesis is a two step pathway. [2] The product of this pathway can be used in the lysine biosynthesis or in the pathway leading to homoserine involved in the threonine, isoleucine and methionine biosynthesis. There are three different isozymes differed in their sensitivity to regulation by Lys, Met and Thr in Escherichia coli. [1] |
True - {{t}} |
True - {{t}} |
Confirmed presence |
|
Evidence_47947 |
TIGR00978 HMM |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Evidence_82135 |
GenProp0125 GENPROP |
True - {{t}} |
True - {{t}} |
Confirmed presence |
|
Evidence_2246 |
TIGR00036 HMM |
True - {{∅},{t}} |
True - {{t}} |
Confirmed presence |
|
Component_42738 |
homoaconitate hydratase, LysU subunit |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Evidence_2247 |
TIGR00965 HMM |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Component_60594 |
dihydrodipicolinate reductase |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
Evidence_82132 |
TIGR00674 HMM |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
Evidence_82151 |
TIGR03540 HMM |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Component_60591 |
succinyl-diaminopimelate transaminase |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Component_42744 |
acylase |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Evidence_2249 |
TIGR01246 HMM |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Component_265 |
dihydrodipicolinate synthase |
True - {{∅},{t}} |
True - {{t}} |
Confirmed presence |
|
Evidence_2250 |
TIGR01900 HMM |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Component_60592 |
diaminopimelate dehydrogenase |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Component_60587 |
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Evidence_82138 |
GenProp0160 GENPROP |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
Component_60596 |
lysine biosynthesis pathways |
True - {{t}} |
True - {{t}} |
Confirmed presence |
|
GenProp0199 |
lysine biosynthesis~The basic amino acid lysine may be synthesized by one of two types of pathways pathways in prokaryotes, the diaminopimelate (DAP) pathways and the alpha-aminoadipate (AAA) pathway. The DAP pathway has several variants including the dehydrogenase (reductive) pathway which requires ammonia and NADPH and the acetylated and succinylated pathways which do not. A non-reductive pathway which uses neither acetate or succinate protecting groups is found in plants but has not been observed in prokaryotes. The AAA pathway has a variant found in fungi and plants which has not been observed in prokaryotes. |
True - {{t}} |
True - {{t}} |
Confirmed presence |
|
Evidence_2252 |
TIGR01048 HMM |
True - {{∅},{t}} |
True - {{t}} |
Confirmed presence |
|
Evidence_47948 |
TIGR01296 HMM |
True - {{t}} |
True - {{t}} |
Confirmed presence |
|
Evidence_82136 |
GenProp0193 GENPROP |
None - {{∅}} |
Both - {{t},{f}} |
Unconfirmed contradictory |
|
Evidence_82134 |
TIGR01048 HMM |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
Component_267 |
aminotransferase pathways |
None - {{∅}} |
None - {{∅}} |
Unexplained |
|
Evidence_55119 |
TIGR01850 HMM |
None - {{∅}} |
True - {{t}} |
Unconfirmed presence |
|
Component_60588 |
succinyl-diaminopimelate desuccinylase (DapE) |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Evidence_82141 |
GenProp0786 GENPROP |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Component_42740 |
alpha-aminoadipate acylase (proposed) |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Evidence_55084 |
TIGR02130 HMM |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Evidence_82137 |
GenProp0788 GENPROP |
None - {{∅}} |
Both - {{t},{f}} |
Unconfirmed contradictory |
|
Evidence_55129 |
TIGR01343 HMM |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Evidence_82149 |
TIGR03538 HMM |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Evidence_82148 |
TIGR03537 HMM |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Evidence_55117 |
TIGR02090 HMM |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Evidence_2251 |
TIGR00652 HMM |
True - {{∅},{t}} |
True - {{t}} |
Confirmed presence |
|
Component_266 |
dihydrodipicolinate reductase |
True - {{∅},{t}} |
True - {{t}} |
Confirmed presence |
|
Evidence_47951 |
TIGR02078 HMM |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|
Evidence_55125 |
TIGR01902 HMM |
None - {{∅}} |
False - {{f}} |
Unconfirmed absence |
|