lysine-2,3-aminomutase; This model describes lysine-2,3-aminomutase as found along with ...
22-435
0e+00
lysine-2,3-aminomutase; This model describes lysine-2,3-aminomutase as found along with beta-lysine acetyltransferase in a two-enzyme pathway for making the compatible solute N-epsilon-acetyl-beta-lysine. This compatible solute, or osmolyte, is known to protect a number of methanogenic archaea against salt stress. The trusted cutoff distinguishes a tight clade with essentially full-length homology from additional homologs that are shorter or highly diverged in the C-terminal region. All members of this family have the radical SAM motif CXXXCXXC, while some but not all have a second copy of the motif in the C-terminal region.
:
Pssm-ID: 163532 [Multi-domain] Cd Length: 417 Bit Score: 852.07 E-value: 0e+00
lysine-2,3-aminomutase; This model describes lysine-2,3-aminomutase as found along with ...
22-435
0e+00
lysine-2,3-aminomutase; This model describes lysine-2,3-aminomutase as found along with beta-lysine acetyltransferase in a two-enzyme pathway for making the compatible solute N-epsilon-acetyl-beta-lysine. This compatible solute, or osmolyte, is known to protect a number of methanogenic archaea against salt stress. The trusted cutoff distinguishes a tight clade with essentially full-length homology from additional homologs that are shorter or highly diverged in the C-terminal region. All members of this family have the radical SAM motif CXXXCXXC, while some but not all have a second copy of the motif in the C-terminal region.
Pssm-ID: 163532 [Multi-domain] Cd Length: 417 Bit Score: 852.07 E-value: 0e+00
Lysine-2,3-aminomutase; This domain family is found in bacteria, archaea and eukaryotes, and ...
323-443
1.91e-52
Lysine-2,3-aminomutase; This domain family is found in bacteria, archaea and eukaryotes, and is typically between 111 and 127 amino acids in length. The family is found in association with pfam04055. LAM catalyzes the interconversion of L-alpha-lysine and L-beta-lysine, which proceeds by migration of the amino group from C2 to C3 concomitant with cross-migration of the 3-pro-R hydrogen of L-alpha-lysine to the 2-pro-R position of L-beta-lysine.
Pssm-ID: 378876 Cd Length: 127 Bit Score: 172.24 E-value: 1.91e-52
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
130-327
4.36e-14
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin.
Pssm-ID: 100105 [Multi-domain] Cd Length: 204 Bit Score: 70.83 E-value: 4.36e-14
lysine-2,3-aminomutase; This model describes lysine-2,3-aminomutase as found along with ...
22-435
0e+00
lysine-2,3-aminomutase; This model describes lysine-2,3-aminomutase as found along with beta-lysine acetyltransferase in a two-enzyme pathway for making the compatible solute N-epsilon-acetyl-beta-lysine. This compatible solute, or osmolyte, is known to protect a number of methanogenic archaea against salt stress. The trusted cutoff distinguishes a tight clade with essentially full-length homology from additional homologs that are shorter or highly diverged in the C-terminal region. All members of this family have the radical SAM motif CXXXCXXC, while some but not all have a second copy of the motif in the C-terminal region.
Pssm-ID: 163532 [Multi-domain] Cd Length: 417 Bit Score: 852.07 E-value: 0e+00
glutamate 2,3-aminomutase; Members of this family are glutamate 2,3-aminomutase, a radical SAM ...
23-377
1.31e-166
glutamate 2,3-aminomutase; Members of this family are glutamate 2,3-aminomutase, a radical SAM enzyme with a pyridoxal phosphate group. It is closely related to lysine 2,3-aminomutase, but distinguished by architecture (longer N-terminal region, shorter C-terminal region) and replacement of key lysine-binding residues Asp293 and Asp330 (inferred from the crystal structure) by glutamate-binding residues Lys and Asn. Activity was demonstrated for sequences from Clostridium difficile, Thermoanaerobacter tengcongensis MB4, and Syntrophomonas wolfei str. Goettingen. The action of this enzyme creates beta-glutamate, an osmolyte. [Cellular processes, Adaptations to atypical conditions]
Pssm-ID: 275161 Cd Length: 404 Bit Score: 474.45 E-value: 1.31e-166
arginine 2,3-aminomutase; Members of this family are arginine 2,3-aminomutase, a radical SAM ...
25-371
9.41e-123
arginine 2,3-aminomutase; Members of this family are arginine 2,3-aminomutase, a radical SAM enzyme more closely related to lysine 2,3-aminomutase than to glutamate 2,3-aminomutase. The enzyme makes L-beta-arginine, sometimes in the context of antibiotic biosynthesis (blasticidin S, mildiomycin, etc). Activity is proven in Streptomyces griseochromogenes, which makes blasticidin S.
Pssm-ID: 275261 Cd Length: 351 Bit Score: 360.97 E-value: 9.41e-123
KamA family protein; This model represents essentially the whole of E. coli YjeK and of some ...
25-344
2.94e-116
KamA family protein; This model represents essentially the whole of E. coli YjeK and of some of its apparent orthologs. YodO in Bacillus subtilis, a family member which is longer protein by an additional 100 residues, is characterized as a lysine 2,3-aminomutase with iron, sulphide and pyridoxal 5'-phosphate groups. The homolog MJ0634 from M. jannaschii is preceded by nearly 200 C-terminal residues. This family shows similarity to molybdenum cofactor biosynthesis protein MoaA and related proteins. Note that the E. coli homolog was expressed in E. coli and purified and found not to display display lysine 2,3-aminomutase activity. Active site residues are found in 100 residue extension in B. subtilis. Name changed to KamA family protein. [Cellular processes, Adaptations to atypical conditions]
Pssm-ID: 272980 Cd Length: 331 Bit Score: 343.74 E-value: 2.94e-116
lysine-2,3-aminomutase-related protein; Members of this protein form a distinctive clade, ...
51-356
8.83e-102
lysine-2,3-aminomutase-related protein; Members of this protein form a distinctive clade, homologous to lysine-2,3-aminomutase (of Bacillus, Clostridium, and methanogenic archaea) and likely similar in function. Members of this family are found in Rhodopseudomonas, Caulobacter crescentus, Bradyrhizobium, etc.
Pssm-ID: 163534 Cd Length: 321 Bit Score: 306.30 E-value: 8.83e-102
Lysine-2,3-aminomutase; This domain family is found in bacteria, archaea and eukaryotes, and ...
323-443
1.91e-52
Lysine-2,3-aminomutase; This domain family is found in bacteria, archaea and eukaryotes, and is typically between 111 and 127 amino acids in length. The family is found in association with pfam04055. LAM catalyzes the interconversion of L-alpha-lysine and L-beta-lysine, which proceeds by migration of the amino group from C2 to C3 concomitant with cross-migration of the 3-pro-R hydrogen of L-alpha-lysine to the 2-pro-R position of L-beta-lysine.
Pssm-ID: 378876 Cd Length: 127 Bit Score: 172.24 E-value: 1.91e-52
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
130-327
4.36e-14
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin.
Pssm-ID: 100105 [Multi-domain] Cd Length: 204 Bit Score: 70.83 E-value: 4.36e-14
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
132-278
1.10e-11
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.
Pssm-ID: 427681 [Multi-domain] Cd Length: 159 Bit Score: 62.93 E-value: 1.10e-11
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
127-284
7.55e-08
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, chromosome partitioning, Coenzyme transport and metabolism];
Pssm-ID: 440301 [Multi-domain] Cd Length: 159 Bit Score: 51.83 E-value: 7.55e-08
2-iminoacetate synthase ThiH/Menaquinone biosynthesis enzymes MqnC and MqnE [Coenzyme ...
123-207
1.25e-04
2-iminoacetate synthase ThiH/Menaquinone biosynthesis enzymes MqnC and MqnE [Coenzyme transport and metabolism]; 2-iminoacetate synthase ThiH/Menaquinone biosynthesis enzymes MqnC and MqnE is part of the Pathway/BioSystem: Thiamine biosynthesis
Pssm-ID: 440680 [Multi-domain] Cd Length: 351 Bit Score: 43.96 E-value: 1.25e-04
SynChlorMet cassette radical SAM/SPASM protein ScmE; A biosynthesis cassette found in ...
125-189
5.54e-03
SynChlorMet cassette radical SAM/SPASM protein ScmE; A biosynthesis cassette found in Syntrophobacter fumaroxidans MPOB, Chlorobium limicola DSM 245, Methanocella paludicola SANAE, and delta proteobacterium NaphS2 contains two PqqE-like radical SAM/SPASM domain proteins, a PqqD homolog, and a conserved hypothetical protein. These components suggest modification of a ribosomally produced peptide precursor, but the precursor has not been identified. Of the two PqqE homologs of the cassette, this family is the closer in sequence.
Pssm-ID: 211973 [Multi-domain] Cd Length: 358 Bit Score: 38.68 E-value: 5.54e-03
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
127-186
5.65e-03
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.
Pssm-ID: 433138 [Multi-domain] Cd Length: 137 Bit Score: 37.15 E-value: 5.65e-03
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
of the residues that compose this conserved feature have been mapped to the query sequence.
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