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Conserved domains on  [gi|1319856081|gb|PLL41302|]
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ribonucleotide-diphosphate reductase subunit alpha, partial [Klebsiella pneumoniae]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNR_1b_NrdE super family cl33280
ribonucleoside-diphosphate reductase, class 1b, alpha subunit; Members of this family are NrdE, ...
 14-181 2.76e-85

ribonucleoside-diphosphate reductase, class 1b, alpha subunit; Members of this family are NrdE, the alpha subunit of class 1b ribonucleotide reductase. This form uses a dimanganese moiety associated with a tyrosine radical to reduce the cellular requirement for iron.


The actual alignment was detected with superfamily member TIGR04170:

Pssm-ID: 211905 [Multi-domain]  Cd Length: 698  Bit Score: 264.70  E-value: 2.76e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1319856081  14 DFHALNAMLNLYDSEGRIPFEKDRQAVEAFMATQVQPNALTFPSQEDKLSWLVSEGYYDPQVLAGYDRGFVLALFAHARR 93
Cdd:TIGR04170   1 DYHALNNELNLYDDNGKIQFDKDKEALDAYFLEHVNQNTVFFHNLKEKLDYLVENNYYEEEVLDKYSFEFVIELFEHAYA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1319856081  94 APFRFQTFLGAWKFYTSYALKTFDGKHYLEDFAERSVMVALTLARGDEQQARQLTEEILSGRFQPATPTFLNAGKQQRGE 173
Cdd:TIGR04170  81 SKFRFPSFMGAFKFYTSYALKTNDGKRYLERYEDRVCMVALTLANGDEELAKQLVDEMISQRYQPATPTFLNAGRARRGE 160


                  ....*...
gi 1319856081 174 LISCFLLR 181
Cdd:TIGR04170 161 LVSCFLLR 168
 
Name Accession Description Interval E-value
RNR_1b_NrdE TIGR04170
ribonucleoside-diphosphate reductase, class 1b, alpha subunit; Members of this family are NrdE, ...
 14-181 2.76e-85

ribonucleoside-diphosphate reductase, class 1b, alpha subunit; Members of this family are NrdE, the alpha subunit of class 1b ribonucleotide reductase. This form uses a dimanganese moiety associated with a tyrosine radical to reduce the cellular requirement for iron.


Pssm-ID: 211905 [Multi-domain]  Cd Length: 698  Bit Score: 264.70  E-value: 2.76e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1319856081  14 DFHALNAMLNLYDSEGRIPFEKDRQAVEAFMATQVQPNALTFPSQEDKLSWLVSEGYYDPQVLAGYDRGFVLALFAHARR 93
Cdd:TIGR04170   1 DYHALNNELNLYDDNGKIQFDKDKEALDAYFLEHVNQNTVFFHNLKEKLDYLVENNYYEEEVLDKYSFEFVIELFEHAYA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1319856081  94 APFRFQTFLGAWKFYTSYALKTFDGKHYLEDFAERSVMVALTLARGDEQQARQLTEEILSGRFQPATPTFLNAGKQQRGE 173
Cdd:TIGR04170  81 SKFRFPSFMGAFKFYTSYALKTNDGKRYLERYEDRVCMVALTLANGDEELAKQLVDEMISQRYQPATPTFLNAGRARRGE 160


                  ....*...
gi 1319856081 174 LISCFLLR 181
Cdd:TIGR04170 161 LVSCFLLR 168
RNR_N pfam08343
Ribonucleotide reductase N-terminal; This domain is found at the N-terminus of bacterial ...
 15-96 1.12e-33

Ribonucleotide reductase N-terminal; This domain is found at the N-terminus of bacterial ribonucleoside-diphosphate reductases (ribonucleotide reductases, RNRs) which catalyze the formation of deoxyribonucleotides. It occurs together with the RNR all-alpha domain (pfam00317) and the RNR barrel domain (pfam02867).


Pssm-ID: 429933  Cd Length: 82  Bit Score: 114.47  E-value: 1.12e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1319856081  15 FHALNAMLNLYDSEGRIPFEKDRQAVEAFMATQVQPNALTFPSQEDKLSWLVSEGYYDPQVLAGYDRGFVLALFAHARRA 94
Cdd:pfam08343   1 YIALNNELNLYDENGKIQFDKDKEALEAYFKEHVNPNTVFFHSLKEKLDYLVENDYYEEEFLNKYSFEFIEELYKYAYSY 80


                  ..
gi 1319856081  95 PF 96
Cdd:pfam08343  81 KF 82
NrdA COG0209
Ribonucleotide reductase alpha subunit [Nucleotide transport and metabolism]; Ribonucleotide ...
 55-181 3.11e-27

Ribonucleotide reductase alpha subunit [Nucleotide transport and metabolism]; Ribonucleotide reductase alpha subunit is part of the Pathway/BioSystem: Pyrimidine salvage


Pssm-ID: 439979 [Multi-domain]  Cd Length: 665  Bit Score: 107.19  E-value: 3.11e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1319856081  55 FPSQEDKLSWlVSEGYYDPQVLagydRGFVLALFAHARRAPFRFQTFLGAWKFYTSYALKTFDGKhYLEDFAERSVMVAL 134
Cdd:COG0209    10 YKSFSEKIKY-VEEGLYDERLL----EEDLEELAAAIDPERDRFFSYNALKTLYDRYLLKDEDGK-PLETPQDLFMRVAM 83

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1319856081 135 TLARGD-----EQQARQLTEEILSGRFQPATPTFLNAGKqQRGELISCFLLR 181
Cdd:COG0209    84 GLAAAEkpedrEEWAKEFYDLLSSLRFLPATPTLFNAGT-PRGQLSSCFVLP 134
RNR_I cd01679
Class I ribonucleotide reductase; Ribonucleotide reductase (RNR) catalyzes the reductive ...
 127-181 2.08e-16

Class I 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 many viruses, 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 anaerobic bacteria, bacteriophages, 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). Class I RNR is oxygen-dependent and can be subdivided into classes Ia (eukaryotes, prokaryotes, viruses and phages) and Ib (which is found in prokaryotes only). It is a tetrameric enzyme of two alpha and two beta subunits; this model covers the major part of the alpha or large subunit, called R1 in class Ia and R1E in class Ib.


Pssm-ID: 153088 [Multi-domain]  Cd Length: 460  Bit Score: 75.66  E-value: 2.08e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1319856081 127 ERSVMVALTLARGDEQQARQLTEEILSGRFQPATPTFLNAGKqQRGELISCFLLR 181
Cdd:cd01679     3 DRLMRVALGLASGDLEWAKEFYDLLSKQRFTPATPTLFNAGT-PRGQLSSCFLLT 56
PRK09209 PRK09209
ribonucleoside-diphosphate reductase subunit alpha;
65-179 1.54e-06

ribonucleoside-diphosphate reductase subunit alpha;


Pssm-ID: 181700 [Multi-domain]  Cd Length: 761  Bit Score: 47.41  E-value: 1.54e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1319856081  65 LVSEGYYDPQVLAGYDRGFVLALFAHARRAPFRFQTFLGAWKFYTSYALKTFDGKHYlEDFAERSVMVALTLARGDEQQA 144
Cdd:PRK09209  122 LAERGIYSNDLLKRYSKEELIEAGKMIDPERDKLFTYIGLYLLADRYLATDSDRNVY-ELPQERWLTIALYLMQNEPRER 200

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1319856081 145 R-QLTEE---ILSGRFQP-ATPTFLNAGKQQrGELISCFL 179
Cdd:PRK09209  201 RmQLVKEaywALSNLYMTvATPTLANAGKVG-GQLSSCFI 239
 
Name Accession Description Interval E-value
RNR_1b_NrdE TIGR04170
ribonucleoside-diphosphate reductase, class 1b, alpha subunit; Members of this family are NrdE, ...
 14-181 2.76e-85

ribonucleoside-diphosphate reductase, class 1b, alpha subunit; Members of this family are NrdE, the alpha subunit of class 1b ribonucleotide reductase. This form uses a dimanganese moiety associated with a tyrosine radical to reduce the cellular requirement for iron.


Pssm-ID: 211905 [Multi-domain]  Cd Length: 698  Bit Score: 264.70  E-value: 2.76e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1319856081  14 DFHALNAMLNLYDSEGRIPFEKDRQAVEAFMATQVQPNALTFPSQEDKLSWLVSEGYYDPQVLAGYDRGFVLALFAHARR 93
Cdd:TIGR04170   1 DYHALNNELNLYDDNGKIQFDKDKEALDAYFLEHVNQNTVFFHNLKEKLDYLVENNYYEEEVLDKYSFEFVIELFEHAYA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1319856081  94 APFRFQTFLGAWKFYTSYALKTFDGKHYLEDFAERSVMVALTLARGDEQQARQLTEEILSGRFQPATPTFLNAGKQQRGE 173
Cdd:TIGR04170  81 SKFRFPSFMGAFKFYTSYALKTNDGKRYLERYEDRVCMVALTLANGDEELAKQLVDEMISQRYQPATPTFLNAGRARRGE 160


                  ....*...
gi 1319856081 174 LISCFLLR 181
Cdd:TIGR04170 161 LVSCFLLR 168
RNR_N pfam08343
Ribonucleotide reductase N-terminal; This domain is found at the N-terminus of bacterial ...
 15-96 1.12e-33

Ribonucleotide reductase N-terminal; This domain is found at the N-terminus of bacterial ribonucleoside-diphosphate reductases (ribonucleotide reductases, RNRs) which catalyze the formation of deoxyribonucleotides. It occurs together with the RNR all-alpha domain (pfam00317) and the RNR barrel domain (pfam02867).


Pssm-ID: 429933  Cd Length: 82  Bit Score: 114.47  E-value: 1.12e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1319856081  15 FHALNAMLNLYDSEGRIPFEKDRQAVEAFMATQVQPNALTFPSQEDKLSWLVSEGYYDPQVLAGYDRGFVLALFAHARRA 94
Cdd:pfam08343   1 YIALNNELNLYDENGKIQFDKDKEALEAYFKEHVNPNTVFFHSLKEKLDYLVENDYYEEEFLNKYSFEFIEELYKYAYSY 80


                  ..
gi 1319856081  95 PF 96
Cdd:pfam08343  81 KF 82
NrdA COG0209
Ribonucleotide reductase alpha subunit [Nucleotide transport and metabolism]; Ribonucleotide ...
 55-181 3.11e-27

Ribonucleotide reductase alpha subunit [Nucleotide transport and metabolism]; Ribonucleotide reductase alpha subunit is part of the Pathway/BioSystem: Pyrimidine salvage


Pssm-ID: 439979 [Multi-domain]  Cd Length: 665  Bit Score: 107.19  E-value: 3.11e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1319856081  55 FPSQEDKLSWlVSEGYYDPQVLagydRGFVLALFAHARRAPFRFQTFLGAWKFYTSYALKTFDGKhYLEDFAERSVMVAL 134
Cdd:COG0209    10 YKSFSEKIKY-VEEGLYDERLL----EEDLEELAAAIDPERDRFFSYNALKTLYDRYLLKDEDGK-PLETPQDLFMRVAM 83

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1319856081 135 TLARGD-----EQQARQLTEEILSGRFQPATPTFLNAGKqQRGELISCFLLR 181
Cdd:COG0209    84 GLAAAEkpedrEEWAKEFYDLLSSLRFLPATPTLFNAGT-PRGQLSSCFVLP 134
RNR_I cd01679
Class I ribonucleotide reductase; Ribonucleotide reductase (RNR) catalyzes the reductive ...
 127-181 2.08e-16

Class I 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 many viruses, 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 anaerobic bacteria, bacteriophages, 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). Class I RNR is oxygen-dependent and can be subdivided into classes Ia (eukaryotes, prokaryotes, viruses and phages) and Ib (which is found in prokaryotes only). It is a tetrameric enzyme of two alpha and two beta subunits; this model covers the major part of the alpha or large subunit, called R1 in class Ia and R1E in class Ib.


Pssm-ID: 153088 [Multi-domain]  Cd Length: 460  Bit Score: 75.66  E-value: 2.08e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1319856081 127 ERSVMVALTLARGDEQQARQLTEEILSGRFQPATPTFLNAGKqQRGELISCFLLR 181
Cdd:cd01679     3 DRLMRVALGLASGDLEWAKEFYDLLSKQRFTPATPTLFNAGT-PRGQLSSCFLLT 56
Ribonuc_red_lgN pfam00317
Ribonucleotide reductase, all-alpha domain;
100-168 3.87e-13

Ribonucleotide reductase, all-alpha domain;


Pssm-ID: 459758 [Multi-domain]  Cd Length: 75  Bit Score: 61.48  E-value: 3.87e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1319856081 100 TFLGAWKFYTSYALKTFDGKhYLEDFAERSVMVALTLAR-----GDEQQARQLTEEILSGRFQPATPTFLNAGK 168
Cdd:pfam00317   2 TYLGAKVLEDRYLLKDEDGE-LLETPQDMFMRVALALAGaeleeDRLELAEEFYDLLSSLKFLPATPTLMNAGT 74
PRK09209 PRK09209
ribonucleoside-diphosphate reductase subunit alpha;
65-179 1.54e-06

ribonucleoside-diphosphate reductase subunit alpha;


Pssm-ID: 181700 [Multi-domain]  Cd Length: 761  Bit Score: 47.41  E-value: 1.54e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1319856081  65 LVSEGYYDPQVLAGYDRGFVLALFAHARRAPFRFQTFLGAWKFYTSYALKTFDGKHYlEDFAERSVMVALTLARGDEQQA 144
Cdd:PRK09209  122 LAERGIYSNDLLKRYSKEELIEAGKMIDPERDKLFTYIGLYLLADRYLATDSDRNVY-ELPQERWLTIALYLMQNEPRER 200

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1319856081 145 R-QLTEE---ILSGRFQP-ATPTFLNAGKQQrGELISCFL 179
Cdd:PRK09209  201 RmQLVKEaywALSNLYMTvATPTLANAGKVG-GQLSSCFI 239
PRK09102 PRK09102
ribonucleoside-diphosphate reductase subunit alpha;
112-179 2.62e-04

ribonucleoside-diphosphate reductase subunit alpha;


Pssm-ID: 236378 [Multi-domain]  Cd Length: 601  Bit Score: 40.71  E-value: 2.62e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1319856081 112 ALKTFDGKHYL--------EDFAERSVMVALTLARGDEQQARQLTEEILSGRFQPATPTFLNAGKQqRGELISCFL 179
Cdd:PRK09102   19 AWLTEFGKATLrdryllegESYQDLFARIAEAYADIDPEHAQRFYDYMSRGWFMPATPVLSNGGTD-RGLPISCFL 93
RNR_II_dimer cd02888
Class II ribonucleotide reductase, dimeric form; Ribonucleotide reductase (RNR) catalyzes the ...
 144-180 2.01e-03

Class II ribonucleotide reductase, dimeric form; 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 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). Class II RNRs are found in bacteria that can live under both aerobic and anaerobic conditions. Many, but not all members of this class are found to be homodimers. Adenosylcobalamin interacts directly with an active site cysteine to form the reactive cysteine radical.


Pssm-ID: 153089 [Multi-domain]  Cd Length: 464  Bit Score: 37.98  E-value: 2.01e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1319856081 144 ARQLTEEILSGRFQPATPTFLNAGKQQRGELISCFLL 180
Cdd:cd02888     1 ADEFFYLLLSQGFIPNSPTLMNAGTGELGQLSACFVL 37
 
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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