nitrogenase cofactor biosynthesis protein NifB; This model describes NifB, a protein required ...
22-445
0e+00
nitrogenase cofactor biosynthesis protein NifB; This model describes NifB, a protein required for the biosynthesis of the iron-molybdenum (or iron-vanadium) cofactor used by the nitrogen-fixing enzyme nitrogenase. NifB belongs to the radical SAM family, and the FeMo cluster biosynthesis process requires S-adenosylmethionine. Archaeal homologs lack the most C-terminal region and score between the trusted and noise cutoffs of this model. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Central intermediary metabolism, Nitrogen fixation]
The actual alignment was detected with superfamily member TIGR01290:
Pssm-ID: 273539 [Multi-domain] Cd Length: 442 Bit Score: 609.54 E-value: 0e+00
nitrogenase cofactor biosynthesis protein NifB; This model describes NifB, a protein required ...
22-445
0e+00
nitrogenase cofactor biosynthesis protein NifB; This model describes NifB, a protein required for the biosynthesis of the iron-molybdenum (or iron-vanadium) cofactor used by the nitrogen-fixing enzyme nitrogenase. NifB belongs to the radical SAM family, and the FeMo cluster biosynthesis process requires S-adenosylmethionine. Archaeal homologs lack the most C-terminal region and score between the trusted and noise cutoffs of this model. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Central intermediary metabolism, Nitrogen fixation]
Pssm-ID: 273539 [Multi-domain] Cd Length: 442 Bit Score: 609.54 E-value: 0e+00
NifB belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, and ...
343-451
7.30e-34
NifB belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme as part of nitrogen fixation in bacteria. This domain is sometimes found fused to a N-terminal domain (the Radical SAM domain) in nifB-like proteins.
Pssm-ID: 238432 Cd Length: 106 Bit Score: 123.11 E-value: 7.30e-34
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
45-216
1.91e-32
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: 120.78 E-value: 1.91e-32
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
50-228
6.40e-17
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: 77.95 E-value: 6.40e-17
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
48-255
2.20e-06
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: 48.55 E-value: 2.20e-06
nitrogenase cofactor biosynthesis protein NifB; This model describes NifB, a protein required ...
22-445
0e+00
nitrogenase cofactor biosynthesis protein NifB; This model describes NifB, a protein required for the biosynthesis of the iron-molybdenum (or iron-vanadium) cofactor used by the nitrogen-fixing enzyme nitrogenase. NifB belongs to the radical SAM family, and the FeMo cluster biosynthesis process requires S-adenosylmethionine. Archaeal homologs lack the most C-terminal region and score between the trusted and noise cutoffs of this model. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Central intermediary metabolism, Nitrogen fixation]
Pssm-ID: 273539 [Multi-domain] Cd Length: 442 Bit Score: 609.54 E-value: 0e+00
NifB belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, and ...
343-451
7.30e-34
NifB belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme as part of nitrogen fixation in bacteria. This domain is sometimes found fused to a N-terminal domain (the Radical SAM domain) in nifB-like proteins.
Pssm-ID: 238432 Cd Length: 106 Bit Score: 123.11 E-value: 7.30e-34
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
45-216
1.91e-32
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: 120.78 E-value: 1.91e-32
This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, ...
343-450
5.96e-22
This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This domain is a predicted small-molecule-binding domain (SMBD) with an alpha/beta fold that is present either as a stand-alone domain (e.g. NifX and NifY) or fused to another conserved domain (e.g. NifB) however, its function is still undetermined.The SCOP database suggests that this domain is most similar to structures within the ribonuclease H superfamily. This conserved domain is represented in two of the three major divisions of life (bacteria and archaea).
Pssm-ID: 238315 Cd Length: 102 Bit Score: 90.00 E-value: 5.96e-22
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
50-228
6.40e-17
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: 77.95 E-value: 6.40e-17
molybdenum cofactor biosynthesis protein A, bacterial; The model for this family describes ...
42-245
3.53e-13
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: 70.33 E-value: 3.53e-13
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
48-244
7.00e-13
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: 67.36 E-value: 7.00e-13
GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) [Coenzyme transport and ...
54-223
1.90e-11
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: 65.08 E-value: 1.90e-11
Dinitrogenase iron-molybdenum cofactor; This family contains several NIF (B, Y and X) proteins ...
351-451
2.84e-11
Dinitrogenase iron-molybdenum cofactor; This family contains several NIF (B, Y and X) proteins which are iron-molybdenum cofactors (FeMo-co) in the dinitrogenase enzyme which catalyzes the reduction of dinitrogen to ammonium. Dinitrogenase is a hetero-tetrameric (alpha(2)beta(2)) enzyme which contains the iron-molybdenum cofactor (FeMo-co) at its active site.
Pssm-ID: 460602 Cd Length: 93 Bit Score: 59.58 E-value: 2.84e-11
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
48-255
2.20e-06
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: 48.55 E-value: 2.20e-06
NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and ...
344-447
7.70e-05
NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. The protein is part of the nitrogen fixation gene cluster in nitrogen-fixing bacteria and has sequence similarity to other members of the cluster.
Pssm-ID: 238433 Cd Length: 102 Bit Score: 41.82 E-value: 7.70e-05
SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in ...
54-237
2.98e-03
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: 39.82 E-value: 2.98e-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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