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Conserved domains on  [gi|446789820|ref|WP_000867076|]
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MULTISPECIES: anaerobic ribonucleoside-triphosphate reductase activating protein [Bacillus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NrdG super family cl37123
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
 2-149 8.70e-62

anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of the radical-SAM family (pfam04055) and utilizes S-adenosyl methionine, an iron-sulfur cluster and a reductant (dihydroflavodoxin) to produce a glycine-centered radical in the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, TIGR02487). The two components form an alpha-2/beta-2 heterodimer. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism, Protein fate, Protein modification and repair]


The actual alignment was detected with superfamily member TIGR02491:

Pssm-ID: 274161 [Multi-domain]  Cd Length: 154  Bit Score: 186.79  E-value: 8.70e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446789820    2 KVMNIIHDSVVDGEGLRTVVFFAGCPHRCVGCHNPKSWNICNGTEMT---VEEIVKEIASNPLTD-VTFSGGDPFFQaAE 77
Cdd:TIGR02491   1 NYMNIKPDDIVNGEGIRVSLFVAGCKHHCEGCFNKETWNFNGGKEFTealEKEIIRDLNDNPLIDgLTLSGGDPLYP-RN 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446789820   78 VKKVAKIVKDLK-----KNLWMYTGYTLEEIQSSQNNdmIELLHYGDVLVDGRFEIEEKDLTLPFRGSSNQRIIRLK 149
Cdd:TIGR02491  80 VEELIELVKKIKaefpeKDIWLWTGYTWEEILEDEKH--LEVLKYIDVLVDGKFELSKKDLKLKFRGSSNQRIIDLK 154
 
Name Accession Description Interval E-value
NrdG TIGR02491
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
 2-149 8.70e-62

anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of the radical-SAM family (pfam04055) and utilizes S-adenosyl methionine, an iron-sulfur cluster and a reductant (dihydroflavodoxin) to produce a glycine-centered radical in the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, TIGR02487). The two components form an alpha-2/beta-2 heterodimer. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism, Protein fate, Protein modification and repair]


Pssm-ID: 274161 [Multi-domain]  Cd Length: 154  Bit Score: 186.79  E-value: 8.70e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446789820    2 KVMNIIHDSVVDGEGLRTVVFFAGCPHRCVGCHNPKSWNICNGTEMT---VEEIVKEIASNPLTD-VTFSGGDPFFQaAE 77
Cdd:TIGR02491   1 NYMNIKPDDIVNGEGIRVSLFVAGCKHHCEGCFNKETWNFNGGKEFTealEKEIIRDLNDNPLIDgLTLSGGDPLYP-RN 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446789820   78 VKKVAKIVKDLK-----KNLWMYTGYTLEEIQSSQNNdmIELLHYGDVLVDGRFEIEEKDLTLPFRGSSNQRIIRLK 149
Cdd:TIGR02491  80 VEELIELVKKIKaefpeKDIWLWTGYTWEEILEDEKH--LEVLKYIDVLVDGKFELSKKDLKLKFRGSSNQRIIDLK 154
Fer4_12 pfam13353
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
 12-146 2.86e-56

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: 172.36  E-value: 2.86e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446789820   12 VDGEGLRTVVFFAGCPHRCVGCHNPKSWNICNGTEMTVE---EIVKEIASNPLTDVTFSGGDPFFQAAEVKKVAKIVK-- 86
Cdd:pfam13353   1 VNGPGVRCSLFVSGCNHHCKGCFNPETWDFKYGKPFTEEledEIIEDLAKPYIQGLTLSGGEPLLNAEALLELVKRVRee 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446789820   87 DLKKNLWMYTGYTLEEIQssqNNDMIELLHYGDVLVDGRFEIEEKDLTLPFRGSSNQRII 146
Cdd:pfam13353  81 CPEKDIWLWTGYTFEELQ---SKDQLELLKLIDVLVDGKFEQSLKDPSLRFRGSSNQRII 137
nrdG PRK11121
anaerobic ribonucleoside-triphosphate reductase-activating protein;
11-149 3.11e-39

anaerobic ribonucleoside-triphosphate reductase-activating protein;


Pssm-ID: 236853  Cd Length: 154  Bit Score: 129.73  E-value: 3.11e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446789820  11 VVDGEGLRTVVFFAGCPHRCVGCHNPKSWNICNGTEMTvEEIVKEIASNpLTD-------VTFSGGDPFFqAAEVKKVAK 83
Cdd:PRK11121  11 VVNGPGTRCTLFVSGCVHQCPGCYNKSTWRLNSGHPFT-KEMEDQIIAD-LNDtrikrqgLSLSGGDPLH-PQNVPDILK 87

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446789820  84 IVKDLK-----KNLWMYTGYTLEEIQSSQNndmiELLHYGDVLVDGRFEIEEKDLTLPFRGSSNQRIIRLK 149
Cdd:PRK11121  88 LVQRVKaecpgKDIWVWTGYKLDELNAAQR----QVVDLIDVLVDGKFVQDLADPSLIWRGSSNQVIHRLR 154
PflA COG1180
Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, ...
 1-123 2.92e-23

Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440793 [Multi-domain]  Cd Length: 242  Bit Score: 91.01  E-value: 2.92e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446789820   1 MKVMNIIHD----SVVDGEG-LRTVVFFAGCPHRCVGCHNPKSWNI---CNGTEMTVEEIVKEIASN-PLTD----VTFS 67
Cdd:COG1180    1 EEVRGRIYGispfSTVDGPGsIRLSVFTQGCNLRCPYCHNPEISQGrpdAAGRELSPEELVEEALKDrGFLDscggVTFS 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446789820  68 GGDPFFQAAEVKKVAKIVKDLKknlwMYT-----GYTLEEIqssqnndMIELLHYGD-VLVD 123
Cdd:COG1180   81 GGEPTLQPEFLLDLAKLAKELG----LHTaldtnGYIPEEA-------LEELLPYLDaVNID 131
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 20-90 4.70e-07

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: 47.33  E-value: 4.70e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446789820  20 VVFFAGCPHRCVGCHNPKSWNICNGT---EMTVEEIVKEIASNPLTDVTFSGGDPFFQAAEVKKVAKIVKDLKK 90
Cdd:cd01335    1 LELTRGCNLNCGFCSNPASKGRGPESppeIEEILDIVLEAKERGVEVVILTGGEPLLYPELAELLRRLKKELPG 74
 
Name Accession Description Interval E-value
NrdG TIGR02491
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
 2-149 8.70e-62

anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of the radical-SAM family (pfam04055) and utilizes S-adenosyl methionine, an iron-sulfur cluster and a reductant (dihydroflavodoxin) to produce a glycine-centered radical in the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, TIGR02487). The two components form an alpha-2/beta-2 heterodimer. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism, Protein fate, Protein modification and repair]


Pssm-ID: 274161 [Multi-domain]  Cd Length: 154  Bit Score: 186.79  E-value: 8.70e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446789820    2 KVMNIIHDSVVDGEGLRTVVFFAGCPHRCVGCHNPKSWNICNGTEMT---VEEIVKEIASNPLTD-VTFSGGDPFFQaAE 77
Cdd:TIGR02491   1 NYMNIKPDDIVNGEGIRVSLFVAGCKHHCEGCFNKETWNFNGGKEFTealEKEIIRDLNDNPLIDgLTLSGGDPLYP-RN 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446789820   78 VKKVAKIVKDLK-----KNLWMYTGYTLEEIQSSQNNdmIELLHYGDVLVDGRFEIEEKDLTLPFRGSSNQRIIRLK 149
Cdd:TIGR02491  80 VEELIELVKKIKaefpeKDIWLWTGYTWEEILEDEKH--LEVLKYIDVLVDGKFELSKKDLKLKFRGSSNQRIIDLK 154
Fer4_12 pfam13353
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
 12-146 2.86e-56

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: 172.36  E-value: 2.86e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446789820   12 VDGEGLRTVVFFAGCPHRCVGCHNPKSWNICNGTEMTVE---EIVKEIASNPLTDVTFSGGDPFFQAAEVKKVAKIVK-- 86
Cdd:pfam13353   1 VNGPGVRCSLFVSGCNHHCKGCFNPETWDFKYGKPFTEEledEIIEDLAKPYIQGLTLSGGEPLLNAEALLELVKRVRee 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446789820   87 DLKKNLWMYTGYTLEEIQssqNNDMIELLHYGDVLVDGRFEIEEKDLTLPFRGSSNQRII 146
Cdd:pfam13353  81 CPEKDIWLWTGYTFEELQ---SKDQLELLKLIDVLVDGKFEQSLKDPSLRFRGSSNQRII 137
nrdG PRK11121
anaerobic ribonucleoside-triphosphate reductase-activating protein;
11-149 3.11e-39

anaerobic ribonucleoside-triphosphate reductase-activating protein;


Pssm-ID: 236853  Cd Length: 154  Bit Score: 129.73  E-value: 3.11e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446789820  11 VVDGEGLRTVVFFAGCPHRCVGCHNPKSWNICNGTEMTvEEIVKEIASNpLTD-------VTFSGGDPFFqAAEVKKVAK 83
Cdd:PRK11121  11 VVNGPGTRCTLFVSGCVHQCPGCYNKSTWRLNSGHPFT-KEMEDQIIAD-LNDtrikrqgLSLSGGDPLH-PQNVPDILK 87

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446789820  84 IVKDLK-----KNLWMYTGYTLEEIQSSQNndmiELLHYGDVLVDGRFEIEEKDLTLPFRGSSNQRIIRLK 149
Cdd:PRK11121  88 LVQRVKaecpgKDIWVWTGYKLDELNAAQR----QVVDLIDVLVDGKFVQDLADPSLIWRGSSNQVIHRLR 154
PFLA TIGR02493
pyruvate formate-lyase 1-activating enzyme; An iron-sulfur protein with a radical-SAM domain ...
 12-147 3.85e-24

pyruvate formate-lyase 1-activating enzyme; An iron-sulfur protein with a radical-SAM domain (pfam04055). A single glycine residue in EC 2.3.1.54, formate C-acetyltransferase (formate-pyruvate lyase), is oxidized to the corresponding radical by transfer of H from its CH2 to AdoMet with concomitant cleavage of the latter. The reaction requires Fe2+. The first stage is reduction of the AdoMet to give methionine and the 5'-deoxyadenosin-5-yl radical, which then abstracts a hydrogen radical from the glycine residue. [Energy metabolism, Anaerobic, Protein fate, Protein modification and repair]


Pssm-ID: 131546 [Multi-domain]  Cd Length: 235  Bit Score: 93.20  E-value: 3.85e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446789820   12 VDGEGLRTVVFFAGCPHRCVGCHNPKSWNICNGTEMTVEEIVKEIAS-NPLTD-----VTFSGGDPFFQAAEVKKVAKIV 85
Cdd:TIGR02493  11 VDGPGIRFVVFMQGCPLRCQYCHNPDTWDLKGGTEVTPEELIKEVGSyKDFFKasgggVTFSGGEPLLQPEFLSELFKAC 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446789820   86 KDLKKNLWMYT-GYTLEeiqssQNNDMIELLHYGD-VLVDGRFEIEEKDLTLPfrGSSNQRIIR 147
Cdd:TIGR02493  91 KELGIHTCLDTsGFLGG-----CTEAADELLEYTDlVLLDIKHFNPEKYKKLT--GVSLQPTLD 147
PflA COG1180
Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, ...
 1-123 2.92e-23

Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440793 [Multi-domain]  Cd Length: 242  Bit Score: 91.01  E-value: 2.92e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446789820   1 MKVMNIIHD----SVVDGEG-LRTVVFFAGCPHRCVGCHNPKSWNI---CNGTEMTVEEIVKEIASN-PLTD----VTFS 67
Cdd:COG1180    1 EEVRGRIYGispfSTVDGPGsIRLSVFTQGCNLRCPYCHNPEISQGrpdAAGRELSPEELVEEALKDrGFLDscggVTFS 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446789820  68 GGDPFFQAAEVKKVAKIVKDLKknlwMYT-----GYTLEEIqssqnndMIELLHYGD-VLVD 123
Cdd:COG1180   81 GGEPTLQPEFLLDLAKLAKELG----LHTaldtnGYIPEEA-------LEELLPYLDaVNID 131
Fer4_14 pfam13394
4Fe-4S single cluster domain;
21-125 3.08e-19

4Fe-4S single cluster domain;


Pssm-ID: 433171 [Multi-domain]  Cd Length: 115  Bit Score: 77.40  E-value: 3.08e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446789820   21 VFFAGCPHRCVGCHNPKSWNICNGTEMTVEEIVKEIASNPLTD-----VTFSGGDPFFQA--AEVKKVAKIVKD--LKKN 91
Cdd:pfam13394   1 LFVSGCNHSCPGCDNKETWKFNYGEPFTEELEDQIIADLKDSYikrqgLVLTGGEPLHPWnlPVLLKLLKRVKEeyPSKD 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 446789820   92 LWMYTGYTLE-EIQSSQNNDMIELLHYGDVLVDGR 125
Cdd:pfam13394  81 IWLETGYTLAiDFEYPDTEEQLFTLSVIDVLVDGK 115
RNR_activ_nrdG3 TIGR02826
anaerobic ribonucleoside-triphosphate reductase activating protein; Members of this family ...
 21-150 1.20e-15

anaerobic ribonucleoside-triphosphate reductase activating protein; Members of this family represent a set of radical SAM enzymes related to, yet architecturally different from, the activating protein for the glycine radical-containing, oxygen-sensitive ribonucleoside-triphosphate reductase (RNR) as described in model TIGR02491. Members of this family are found paired with members of a similarly divergent set of anaerobic ribonucleoside-triphosphate reductases. Identification of this protein as an RNR activitating protein is partly from pairing with a candidate RNR. It is further supported by our finding that upstream of these operons are examples of a conserved regulatory element (described Rodionov and Gelfand) that is found in nearly all bacteria and that occurs specifically upstream of operons for all three classes of RNR genes. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism]


Pssm-ID: 274317  Cd Length: 147  Bit Score: 68.91  E-value: 1.20e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446789820   21 VFFAGCPHRCVGCHNPKSWNICNGTEMTVEEIVKEIA--SNPLTDVTFSGGDpfFQAAEVKKVAKIVK---DLKKNLwmY 95
Cdd:TIGR02826  20 FYISGCPLGCPGCHSPELWHEDEGTPLTPEVLAQLLDkyRSLITCVLFLGGE--WEPEALLSLLKYVKehaGLKVCL--Y 95

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446789820   96 TGYTleeiqssqNNDMIELLHYGDVLVDGRFEIEEKDLTLPfrgSSNQRIIRLKE 150
Cdd:TIGR02826  96 TGRE--------PKDPLELVQHLDYLKTGPWIETLGGLDSP---TTNQRFYDIRT 139
pflA PRK11145
pyruvate formate lyase 1-activating protein;
1-79 5.77e-15

pyruvate formate lyase 1-activating protein;


Pssm-ID: 182994 [Multi-domain]  Cd Length: 246  Bit Score: 69.29  E-value: 5.77e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446789820   1 MKVMNIIHD----SVVDGEGLRTVVFFAGCPHRCVGCHNPKSWNICNGTEMTVEEIVKEIAS-NPLTD-----VTFSGGD 70
Cdd:PRK11145   1 MSVIGRIHSfescGTVDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEELMKEVVTyRHFMNasgggVTASGGE 80


                 ....*....
gi 446789820  71 PFFQAAEVK 79
Cdd:PRK11145  81 AILQAEFVR 89
activase_YjjW TIGR04041
glycine radical enzyme activase, YjjW family; Members of this family are radical SAM enzymes, ...
 2-69 2.63e-14

glycine radical enzyme activase, YjjW family; Members of this family are radical SAM enzymes, designated YjjW in E. coli, that are paired with and appear to activate a glycyl radical enzyme of unknown function, designated YjjI. This activase and its target are found in Clostridial species as well as E. coli and cousins. Members of this family may be misannotated as pyruvate formate lyase activating enzyme. [Protein fate, Protein modification and repair]


Pssm-ID: 274938 [Multi-domain]  Cd Length: 276  Bit Score: 67.66  E-value: 2.63e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446789820    2 KVMNIIHDSVVDGEGLRTVVFFAGCPHRCVGCHNPKSWNICNG------------------------------------- 44
Cdd:TIGR04041   3 LVNKIIPFSCVDGPGNRLAIFLQGCNFDCKYCHNPETINHCDHcgdcvagcpagalslvdgkvvwdkercigcdtcikvc 82

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 446789820   45 --------TEMTVEEIVKEIASNP--LTDVTFSGG 69
Cdd:TIGR04041  83 phqsspktKEYTVEELLDRIRKNMpfIRGITVSGG 117
PFLE_PFLC TIGR02494
glycyl-radical enzyme activating protein; This subset of the radical-SAM family (pfam04055) ...
 3-75 2.26e-12

glycyl-radical enzyme activating protein; This subset of the radical-SAM family (pfam04055) includes a number of probable activating proteins acting on different enzymes all requiring an amino-acid-centered radical. The closest relatives to this family are the pyruvate-formate lyase activating enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic ribonucleotide reductase activating enzyme (TIGR02491). Included within this subfamily are activators of hydroxyphenyl acetate decarboxylase (HdpA), benzylsuccinate synthase (BssD), gycerol dehydratase (DhaB2) as well as enzymes annotated in E. coli as activators of different isozymes of pyruvate-formate lyase (PFLC and PFLE) however, these appear to lack characterization and may activate enzymes with distinctive functions. Most of the sequence-level variability between these forms is concentrated within an N-terminal domain which follows a conserved group of three cysteines and contains a variable pattern of 0 to 8 additional cysteines.


Pssm-ID: 274163 [Multi-domain]  Cd Length: 295  Bit Score: 62.74  E-value: 2.26e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446789820    3 VMNIIHDSVVDGEGLRTVVFFAGCPHRCVGCHNPKSW------------------------------------------- 39
Cdd:TIGR02494   1 IFNIQRYSVHDGPGIRTTVFLKGCPLRCKWCSNPESQrkspellfkenrclgcgkcvevcpagtarlseladgrnriiir 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446789820   40 -----------NIC-------NGTEMTVEEIVKEIasnpLTD----------VTFSGGDPFFQA 75
Cdd:TIGR02494  81 rekcthcgkctEACpsgalsiVGEEMTVEEVMRVV----LRDsifyrnsgggVTLSGGEPLLQP 140
QueE COG0602
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic ...
 14-75 2.64e-12

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: 61.31  E-value: 2.64e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446789820  14 GEGLRT---VVF--FAGCPHRCVGCHNPKSWNICNGTEMTVEEIVKEIASNPLTDVTFSGGDPFFQA 75
Cdd:COG0602   13 GEGALAgrpAVFvrLAGCNLRCSWCDTKYAWDGEGGKRMSAEEILEEVAALGARHVVITGGEPLLQD 79
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 22-99 3.02e-09

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: 52.53  E-value: 3.02e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446789820   22 FFAGCPHRCVGCHNPKSWNICNGTEMTVEEIVKEI---ASNPLTDVTFSGGDPFFQAAEVKKVAKIVKDLKKNLWMYTGY 98
Cdd:pfam04055   1 ITRGCNLRCTYCAFPSIRARGKGRELSPEEILEEAkelKRLGVEVVILGGGEPLLLPDLVELLERLLKLELAEGIRITLE 80


                  .
gi 446789820   99 T 99
Cdd:pfam04055  81 T 81
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 20-90 4.70e-07

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: 47.33  E-value: 4.70e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446789820  20 VVFFAGCPHRCVGCHNPKSWNICNGT---EMTVEEIVKEIASNPLTDVTFSGGDPFFQAAEVKKVAKIVKDLKK 90
Cdd:cd01335    1 LELTRGCNLNCGFCSNPASKGRGPESppeIEEILDIVLEAKERGVEVVILTGGEPLLYPELAELLRRLKKELPG 74
SkfB COG0535
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
 26-100 5.98e-07

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: 46.43  E-value: 5.98e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446789820  26 CPHRCVGCHNPKSWNicNGTEMTVEE---IVKEIASNPLTDVTFSGGDPFFqAAEVKKVAKIVKDLKKNLWMYTGYTL 100
Cdd:COG0535   10 CNLRCKHCYADAGPK--RPGELSTEEakrILDELAELGVKVVGLTGGEPLL-RPDLFELVEYAKELGIRVNLSTNGTL 84
NrdG2 TIGR02495
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
 10-86 1.99e-06

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: 45.43  E-value: 1.99e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446789820   10 SVVDGEGLRT-VVFFAGCPHRCVGCHNPKSWNICNGTEMTVEEIVKEI-ASNPLTD-VTFSGGDPFFQAAEVKKVAKIVK 86
Cdd:TIGR02495   9 STVDYPGKLAfTIFLQGCNLKCPYCHNPLLIPRRGSGEIEVEELLEFLrRRRGLLDgVVITGGEPTLQAGLPDFLREVRE 88
PflX COG1313
Radical SAM superfamily enzyme PflX [General function prediction only];
21-53 8.75e-04

Radical SAM superfamily enzyme PflX [General function prediction only];


Pssm-ID: 440924  Cd Length: 295  Bit Score: 38.20  E-value: 8.75e-04
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 446789820  21 VFFAGCPHRCVGCHNpksWNI---CNGTEMTVEEIV 53
Cdd:COG1313   57 IFFSGCNLRCVFCQN---YEIsqeGEGKEISVEELA 89
 
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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