GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) [Coenzyme transport and ...
3-338
2.73e-173
GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) [Coenzyme transport and metabolism]; GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) is part of the Pathway/BioSystem: Molybdopterin biosynthesis
:
Pssm-ID: 442141 [Multi-domain] Cd Length: 329 Bit Score: 483.79 E-value: 2.73e-173
GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) [Coenzyme transport and ...
3-338
2.73e-173
GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) [Coenzyme transport and metabolism]; GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) is part of the Pathway/BioSystem: Molybdopterin biosynthesis
Pssm-ID: 442141 [Multi-domain] Cd Length: 329 Bit Score: 483.79 E-value: 2.73e-173
molybdenum cofactor biosynthesis protein A, bacterial; The model for this family describes ...
6-338
4.77e-153
molybdenum cofactor biosynthesis protein A, bacterial; The model for this family describes molybdenum cofactor biosynthesis protein A, or MoaA, as found in bacteria. It does not include the family of probable functional equivalent proteins from the archaea. MoaA works together with MoaC to synthesize precursor Z from guanine. [Biosynthesis of cofactors, prosthetic groups, and carriers, Molybdopterin]
Pssm-ID: 274250 [Multi-domain] Cd Length: 334 Bit Score: 432.81 E-value: 4.77e-153
Molybdenum Cofactor Synthesis C; This region contains two iron-sulphur (3Fe-4S) binding sites. ...
190-317
5.99e-50
Molybdenum Cofactor Synthesis C; This region contains two iron-sulphur (3Fe-4S) binding sites. Mutations in this region of Swiss:O14940 cause MOCOD (Molybdenum Co-Factor Deficiency) type A.
Pssm-ID: 428955 [Multi-domain] Cd Length: 127 Bit Score: 162.77 E-value: 5.99e-50
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
19-221
1.89e-23
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: 95.86 E-value: 1.89e-23
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
19-190
3.37e-15
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.
Pssm-ID: 214792 [Multi-domain] Cd Length: 216 Bit Score: 73.59 E-value: 3.37e-15
viperin family antiviral radical SAM protein; Homologs of a viral defense radical SAM enzyme ...
21-169
9.64e-13
viperin family antiviral radical SAM protein; Homologs of a viral defense radical SAM enzyme found in Homo sapiens, viperin (RSAD2), occur in prokaryotes with a strong bias toward placement in phage defense islands, encoded next to CRISPR system and restriction enzyme genes. Further investigation shows members indeed perform the anti-viral function of synthesizing modified ribonucleotides such as ddhCTP, ddh-guanosine triphosphate (ddhGTP) and ddh-uridine triphosphate (ddhUTP). Those non-standard ribonucleotides can interfere with viral replication machinery.
Pssm-ID: 468450 [Multi-domain] Cd Length: 280 Bit Score: 67.57 E-value: 9.64e-13
twitch domain-containing radical SAM protein; Members of this family are unusual among radical ...
16-197
9.40e-10
twitch domain-containing radical SAM protein; Members of this family are unusual among radical SAM proteins in several ways. First, the N-terminal region consists of an iron-sulfur cluster-binding twitch domain (half of a SPASM domain), something usually found C-terminal to the radical SAM domain. Second, the radical SAM domains in many of the members of this family score poorly vs. the Pfam HMM, PF04055 (version 19), used to identify radical SAM. Lastly, the majority of members sequenced to date come from uncultured bacteria from marine or aquifer sources rather than from conventionally cultured bacterial isolates. The function is unknown.
Pssm-ID: 468123 [Multi-domain] Cd Length: 396 Bit Score: 59.20 E-value: 9.40e-10
GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) [Coenzyme transport and ...
3-338
2.73e-173
GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) [Coenzyme transport and metabolism]; GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) is part of the Pathway/BioSystem: Molybdopterin biosynthesis
Pssm-ID: 442141 [Multi-domain] Cd Length: 329 Bit Score: 483.79 E-value: 2.73e-173
molybdenum cofactor biosynthesis protein A, bacterial; The model for this family describes ...
6-338
4.77e-153
molybdenum cofactor biosynthesis protein A, bacterial; The model for this family describes molybdenum cofactor biosynthesis protein A, or MoaA, as found in bacteria. It does not include the family of probable functional equivalent proteins from the archaea. MoaA works together with MoaC to synthesize precursor Z from guanine. [Biosynthesis of cofactors, prosthetic groups, and carriers, Molybdopterin]
Pssm-ID: 274250 [Multi-domain] Cd Length: 334 Bit Score: 432.81 E-value: 4.77e-153
probable molybdenum cofactor biosynthesis protein A, archaeal; This model describes an ...
8-299
5.51e-72
probable molybdenum cofactor biosynthesis protein A, archaeal; This model describes an archaeal family related, and predicted to be functionally equivalent, to molybdenum cofactor biosynthesis protein A (MoaA) of bacteria (see TIGR02666). [Biosynthesis of cofactors, prosthetic groups, and carriers, Molybdopterin]
Pssm-ID: 274251 [Multi-domain] Cd Length: 302 Bit Score: 225.26 E-value: 5.51e-72
Molybdenum Cofactor Synthesis C; This region contains two iron-sulphur (3Fe-4S) binding sites. ...
190-317
5.99e-50
Molybdenum Cofactor Synthesis C; This region contains two iron-sulphur (3Fe-4S) binding sites. Mutations in this region of Swiss:O14940 cause MOCOD (Molybdenum Co-Factor Deficiency) type A.
Pssm-ID: 428955 [Multi-domain] Cd Length: 127 Bit Score: 162.77 E-value: 5.99e-50
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
17-168
1.21e-30
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: 113.84 E-value: 1.21e-30
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
21-178
9.18e-27
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: 103.37 E-value: 9.18e-27
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
19-221
1.89e-23
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: 95.86 E-value: 1.89e-23
Iron-sulfur cluster-binding Twitch domain of GTP 3',8-cyclase; The iron-sulfur cluster-binding ...
257-326
6.14e-21
Iron-sulfur cluster-binding Twitch domain of GTP 3',8-cyclase; The iron-sulfur cluster-binding Twitch domain is found at the C-terminus of GTP 3',8-cyclase (EC 4.1.99.22), which is also called molybdenum cofactor biosynthesis protein A (MoaA) in bacteria and archaea, molybdenum cofactor biosynthesis protein 1 (MOCS1) in most eukaryotes, and molybdenum cofactor biosynthesis enzyme CNX2 in plants. GTP 3',8-cyclase is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the first step in molybdopterin biosynthesis, the cyclization of guanosine triphosphate to (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate, which is then converted to molybdopterin in subsequent steps. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. GTP 3',8-cyclase contains an additional iron-sulfur cluster at the C-terminal Twitch domain that is involved in substrate binding. The Twitch domain may be related to another iron-sulfur cluster-binding domain found at the C-terminus of some radical SAM enzymes, the SPASM domain, named after the biochemically characterized members, AlbA, PqqE, anSMEs, and MftC, which are involved in Subtilosin A, Pyrroloquinoline quinone, Anaerobic Sulfatase, and Mycofactocin maturation, respectively.
Pssm-ID: 411052 [Multi-domain] Cd Length: 70 Bit Score: 84.90 E-value: 6.14e-21
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
19-190
3.37e-15
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.
Pssm-ID: 214792 [Multi-domain] Cd Length: 216 Bit Score: 73.59 E-value: 3.37e-15
viperin family antiviral radical SAM protein; Homologs of a viral defense radical SAM enzyme ...
21-169
9.64e-13
viperin family antiviral radical SAM protein; Homologs of a viral defense radical SAM enzyme found in Homo sapiens, viperin (RSAD2), occur in prokaryotes with a strong bias toward placement in phage defense islands, encoded next to CRISPR system and restriction enzyme genes. Further investigation shows members indeed perform the anti-viral function of synthesizing modified ribonucleotides such as ddhCTP, ddh-guanosine triphosphate (ddhGTP) and ddh-uridine triphosphate (ddhUTP). Those non-standard ribonucleotides can interfere with viral replication machinery.
Pssm-ID: 468450 [Multi-domain] Cd Length: 280 Bit Score: 67.57 E-value: 9.64e-13
Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily [Translation, ribosomal ...
24-246
2.05e-10
Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily [Translation, ribosomal structure and biogenesis]; Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily is part of the Pathway/BioSystem: tRNA modification
Pssm-ID: 440495 [Multi-domain] Cd Length: 248 Bit Score: 60.21 E-value: 2.05e-10
twitch domain-containing radical SAM protein; Members of this family are unusual among radical ...
16-197
9.40e-10
twitch domain-containing radical SAM protein; Members of this family are unusual among radical SAM proteins in several ways. First, the N-terminal region consists of an iron-sulfur cluster-binding twitch domain (half of a SPASM domain), something usually found C-terminal to the radical SAM domain. Second, the radical SAM domains in many of the members of this family score poorly vs. the Pfam HMM, PF04055 (version 19), used to identify radical SAM. Lastly, the majority of members sequenced to date come from uncultured bacteria from marine or aquifer sources rather than from conventionally cultured bacterial isolates. The function is unknown.
Pssm-ID: 468123 [Multi-domain] Cd Length: 396 Bit Score: 59.20 E-value: 9.40e-10
SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in ...
14-189
1.10e-09
SynChlorMet cassette radical SAM/SPASM protein ScmF; 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 more distant in sequence.
Pssm-ID: 211974 [Multi-domain] Cd Length: 353 Bit Score: 59.08 E-value: 1.10e-09
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic ...
25-91
3.94e-07
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic radical activating enzyme NrdG/QueE is part of the Pathway/BioSystem: tRNA modification
Pssm-ID: 440367 [Multi-domain] Cd Length: 205 Bit Score: 49.75 E-value: 3.94e-07
SynChlorMet cassette radical SAM/SPASM protein ScmE; A biosynthesis cassette found in ...
19-89
3.40e-06
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: 48.31 E-value: 3.40e-06
radical SAM peptide maturase, GG-Bacteroidales family; Members of this protein family are ...
14-111
8.31e-06
radical SAM peptide maturase, GG-Bacteroidales family; Members of this protein family are radical SAM enzymes (pfam04055) with the additional C-terminal region (TIGR04085) that is frequently a marker of peptide modification. Many members of this family are found in the vicinity of one or several ORFs encoding short polypeptides with a Gly-Gly motif (common for bacteriocin leader peptide cleavage), followed by a Cys-rich patch and then poorly conserved sequences.
Pssm-ID: 200399 [Multi-domain] Cd Length: 411 Bit Score: 46.99 E-value: 8.31e-06
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
25-129
1.28e-05
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: 44.08 E-value: 1.28e-05
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
25-121
1.81e-05
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of the radical-SAM family (pfam04055). It is often gene clustered with the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, TIGR02487) and presumably fulfills the identical function as NrdG, which utilizes S-adenosyl methionine, an iron-sulfur cluster and a reductant (dihydroflavodoxin) to produce a glycine-centered radical in NrdD. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism, Protein fate, Protein modification and repair]
Pssm-ID: 274164 [Multi-domain] Cd Length: 192 Bit Score: 44.66 E-value: 1.81e-05
2-iminoacetate synthase ThiH/Menaquinone biosynthesis enzymes MqnC and MqnE [Coenzyme ...
19-77
6.09e-03
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: 38.19 E-value: 6.09e-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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Functional characterization of the conserved domain architecture found on the query.
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if a domain or superfamily has been annotated with functional sites (conserved features),
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click on the bars or triangles to view your query sequence embedded in a multiple sequence alignment of the proteins used to develop the corresponding domain model.
The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores.
Click on the domain model's accession number to view the multiple sequence alignment of the proteins used to develop the corresponding domain model.
To view your query sequence embedded in that multiple sequence alignment, click on the colored bars in the Graphical Summary portion of the search results page,
or click on the triangles, if present, that represent functional sites (conserved features)
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Concise Display shows only the best scoring domain model, in each hit category listed below except non-specific hits, for each region on the query sequence.
(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
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(labeled illustration) Four types of hits can be shown, as available,
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and represent a very high confidence that the query sequence belongs to the same protein family as the sequences use to create the domain model
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