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Conserved domains on  [gi|518093925|ref|WP_019264133|]
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MULTISPECIES: DNA-binding protein [Methanobrevibacter]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NrdD super family cl43387
Anaerobic ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]; ...
 8-41 3.75e-04

Anaerobic ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]; Anaerobic ribonucleoside-triphosphate reductase is part of the Pathway/BioSystem: Thymidylate biosynthesis


The actual alignment was detected with superfamily member COG1328:

Pssm-ID: 440939 [Multi-domain]  Cd Length: 671  Bit Score: 37.59  E-value: 3.75e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 518093925   8 VCKECGFnwitLNGEHHICPKCHSE-TIE-------YIGEVK 41
Cdd:COG1328  628 ICPKCGY----LGGEHDECPKCGNEdTVEvirrtcgYLGNVQ 665
 
Name Accession Description Interval E-value
NrdD COG1328
Anaerobic ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]; ...
 8-41 3.75e-04

Anaerobic ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]; Anaerobic ribonucleoside-triphosphate reductase is part of the Pathway/BioSystem: Thymidylate biosynthesis


Pssm-ID: 440939 [Multi-domain]  Cd Length: 671  Bit Score: 37.59  E-value: 3.75e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 518093925   8 VCKECGFnwitLNGEHHICPKCHSE-TIE-------YIGEVK 41
Cdd:COG1328  628 ICPKCGY----LGGEHDECPKCGNEdTVEvirrtcgYLGNVQ 665
NRDD pfam13597
Anaerobic ribonucleoside-triphosphate reductase;
8-42 3.82e-04

Anaerobic ribonucleoside-triphosphate reductase;


Pssm-ID: 463930 [Multi-domain]  Cd Length: 554  Bit Score: 37.47  E-value: 3.82e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 518093925    8 VCKECGFNwitlnGEHHICPKC--HSETIE-------YIGEVKD 42
Cdd:pfam13597 501 VCPDCGYT-----GEIEECPNCgnHDEKVEvirritgYLRPVSD 539
PRK08270 PRK08270
ribonucleoside triphosphate reductase;
8-33 3.97e-04

ribonucleoside triphosphate reductase;


Pssm-ID: 236212 [Multi-domain]  Cd Length: 656  Bit Score: 37.52  E-value: 3.97e-04
                         10        20
                 ....*....|....*....|....*.
gi 518093925   8 VCKECGFnwitLNGEHHICPKCHSET 33
Cdd:PRK08270 628 ICPKHGY----LSGEHEFCPKCGEET 649
RNR_III cd01675
Class III ribonucleotide reductase; Ribonucleotide reductase (RNR) catalyzes the reductive ...
 7-37 2.73e-03

Class III ribonucleotide reductase; Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit which contains the active and allosteric sites.


Pssm-ID: 153084 [Multi-domain]  Cd Length: 555  Bit Score: 34.96  E-value: 2.73e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 518093925   7 YVCKECGFnwiTLNGEHHICPKCHSETIEYI 37
Cdd:cd01675  519 DICNDCGY---IGEGEGFKCPKCGSEDVEVI 546
 
Name Accession Description Interval E-value
NrdD COG1328
Anaerobic ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]; ...
 8-41 3.75e-04

Anaerobic ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]; Anaerobic ribonucleoside-triphosphate reductase is part of the Pathway/BioSystem: Thymidylate biosynthesis


Pssm-ID: 440939 [Multi-domain]  Cd Length: 671  Bit Score: 37.59  E-value: 3.75e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 518093925   8 VCKECGFnwitLNGEHHICPKCHSE-TIE-------YIGEVK 41
Cdd:COG1328  628 ICPKCGY----LGGEHDECPKCGNEdTVEvirrtcgYLGNVQ 665
NRDD pfam13597
Anaerobic ribonucleoside-triphosphate reductase;
8-42 3.82e-04

Anaerobic ribonucleoside-triphosphate reductase;


Pssm-ID: 463930 [Multi-domain]  Cd Length: 554  Bit Score: 37.47  E-value: 3.82e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 518093925    8 VCKECGFNwitlnGEHHICPKC--HSETIE-------YIGEVKD 42
Cdd:pfam13597 501 VCPDCGYT-----GEIEECPNCgnHDEKVEvirritgYLRPVSD 539
PRK08270 PRK08270
ribonucleoside triphosphate reductase;
8-33 3.97e-04

ribonucleoside triphosphate reductase;


Pssm-ID: 236212 [Multi-domain]  Cd Length: 656  Bit Score: 37.52  E-value: 3.97e-04
                         10        20
                 ....*....|....*....|....*.
gi 518093925   8 VCKECGFnwitLNGEHHICPKCHSET 33
Cdd:PRK08270 628 ICPKHGY----LSGEHEFCPKCGEET 649
RNR_III cd01675
Class III ribonucleotide reductase; Ribonucleotide reductase (RNR) catalyzes the reductive ...
 7-37 2.73e-03

Class III ribonucleotide reductase; Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit which contains the active and allosteric sites.


Pssm-ID: 153084 [Multi-domain]  Cd Length: 555  Bit Score: 34.96  E-value: 2.73e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 518093925   7 YVCKECGFnwiTLNGEHHICPKCHSETIEYI 37
Cdd:cd01675  519 DICNDCGY---IGEGEGFKCPKCGSEDVEVI 546
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options: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.
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