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Conserved domains on  [gi|818695931|gb|KKT40771|]
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Ribonucleoside-triphosphate reductase [Candidatus Collierbacteria bacterium GW2011_GWC2_44_13]

Protein Classification

glycyl radical enzyme family protein( domain architecture ID 1562547)

glycyl radical enzyme family protein such as ribonucleotide reductase (RNR) and pyruvate formate lyase (PFL), which have diverged from a common ancestor. They have a structurally similar ten-stranded alpha-beta barrel domain that hosts the active site, and are radical enzymes. RNRs are found in all organisms and provide the only mechanism by which nucleotides are converted to deoxynucleotides. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs use a diiron-tyrosyl radical while Class II RNRs use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. PFL, an essential enzyme in anaerobic bacteria, catalyzes the conversion of pyruvate and CoA to acteylCoA and formate in a mechanism that uses a glycyl radical.

CATH:  3.20.70.20
PubMed:  10574800
SCOP:  3001069

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNR_PFL super family cl38938
Ribonucleotide reductase and Pyruvate formate lyase; Ribonucleotide reductase (RNR) and ...
 140-752 1.07e-94

Ribonucleotide reductase and Pyruvate formate lyase; Ribonucleotide reductase (RNR) and pyruvate formate lyase (PFL) are believed to have diverged from a common ancestor. They have a structurally similar ten-stranded alpha-beta barrel domain that hosts the active site, and are radical enzymes. RNRs are found in all organisms and provide the only mechanism by which nucleotides are converted to deoxynucleotides. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs use a diiron-tyrosyl radical while Class II RNRs use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. PFL, an essential enzyme in anaerobic bacteria, catalyzes the conversion of pyruvate and CoA to acteylCoA and formate in a mechanism that uses a glycyl radical.


The actual alignment was detected with superfamily member cd01676:

Pssm-ID: 476821 [Multi-domain]  Cd Length: 658  Bit Score: 308.67  E-value: 1.07e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 140 FFDKYSRFNYDlGRRETWKETVDRSVDFLRELSGGKLESGVY----------KRIRNSILEMKATPSMRLLAMAG-PAAR 208
Cdd:cd01676    5 YYRTYSRPKEE-GQNENWDQTVERVVEGTFELWERHLGNPLRwlnekaeeeaEELRSLIFELKALPPGRGLWLGGtDYSR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 209 -RNNISIYNCSYQPV-DSIDSFVEALIISMNGCGVGFSVENRYVENLPRVK----------------------RQDGLET 264
Cdd:cd01676   84 qRRFASLNNCAFVSTeDVVYPFVFLMDLLMQGCGVGFDTAGSNISQIPRPLqeikvqrvnrtekggiqnnvetYDPTQHT 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 265 KQMLIEDSTEGWADALRTGLHTWFDGG-DIKFDYSALRPAGAILRTKGGRSSGPEPLRKMMEFVRERIFTRQGSFLRAID 343
Cdd:cd01676  164 WIIKVPDSREGWVKSVQLLLDLYFNPAqTLIFDYSDIRPAGERLKGFGGIASGPEPLKKLHKAIAAILNDRSGKPLTSVD 243

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 344 AHDIMCEVGNAAVSGGMRRTAMISLFDFDDKEMWDSKSGDFERDN-SQRWNANNSAVWPlSGLTQLEVTKQMLEIvkSGR 422
Cdd:cd01676  244 IVDLMNLIGVCVVSGNVRRSAEIAFGQPEDEDFADLKQYQWNPGRrEHGWASNNSVVFE-SKPDRLEYSFACMLI--RGN 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 423 GEPGIFNRQSA-------LDMRPARRAPAEfGTNPCGEIILRPYEFCNLS-IAIARREDTYETLKDKVEVASIIGTIQAM 494
Cdd:cd01676  321 GEPGIAWLDNMkayarmvLLTTPYHDLRAK-GGNPCGEISLESYELCNLVeVFPLKHEGDLEDLQETLYLAGRYAKTVTL 399

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 495 A-TNFSGLRPAWKNNceeeRLLGVDINGQMDS-----PVAQDSAVQNRLRQV---AIETNREVAEKLGINQAAAVTCVKP 565
Cdd:cd01676  400 LpLHWEITNEIILRN----RRIGVSMSGIADFivragGDLTLHDLKRWRNIGyeaVYQYDERLSKWLGIPLSIKVTCVKP 475

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 566 SGNSSQLFNCSSGIHARWSPYYVRNIRVSTHSSIFKVLKSGGVPMDPEngqtLESANTWVIHFPVKSPDGAVTRKSFSAT 645
Cdd:cd01676  476 SGTISLLAGASPGMHYPLGKYLIRRIRFQKHDPLAPALIAAGYHVEPD----IYDPTSVLVEFPVKAGNADRTANTVSIV 551

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 646 AQCEYWLKNKINWTEHNPSVTITYHP-DEVIDLIKWVWEHRNLIGGMSFLPAFDAAYS--QMPYQEIERDDYEKLKAGFP 722
Cdd:cd01676  552 EQLSLLAFLQTYWADNQVSNTISFDPsPEGPALIQALQQFQYQYKSVSLLPRFDTTKNaaQMPFEPITKERYEQRIAKLK 631

                        650       660       670
                 ....*....|....*....|....*....|.
gi 818695931 723 PIDFSKLYRYEEEDytkaAQELACVAG-CDI 752
Cdd:cd01676  632 DVDYSGDYISPLEE----DLQTFCDSGaCPI 658
PRK08270 super family cl35671
ribonucleoside triphosphate reductase;
20-114 3.22e-24

ribonucleoside triphosphate reductase;


The actual alignment was detected with superfamily member PRK08270:

Pssm-ID: 236212 [Multi-domain]  Cd Length: 656  Bit Score: 108.40  E-value: 3.22e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  20 PKTIVKRDGRVVPFEIQKIEKAISSCFEDLGKNPLTPVGELAQRVVNIIgAKYTKPTVEQVQDTVELVLQAAGEFEAAKN 99
Cdd:PRK08270   2 PTKIIKRDGRIVPFDAEKITEAIAKAFKATGEFDPSEAERLALRVIEKL-EDEDIPSVEEIQDIVEKVLIEAGYFKTAKA 80

                         90
                 ....*....|....*
gi 818695931 100 YIIYRVEHAKLRDSR 114
Cdd:PRK08270  81 YILYREQHARLRNDK 95
 
Name Accession Description Interval E-value
RNR_II_monomer cd01676
Class II ribonucleotide reductase, monomeric form; Ribonucleotide reductase (RNR) catalyzes ...
 140-752 1.07e-94

Class II ribonucleotide reductase, monomeric 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. This particular subfamily is found to be active as a monomer. Adenosylcobalamin interacts directly with an active site cysteine to form the reactive cysteine radical.


Pssm-ID: 153085 [Multi-domain]  Cd Length: 658  Bit Score: 308.67  E-value: 1.07e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 140 FFDKYSRFNYDlGRRETWKETVDRSVDFLRELSGGKLESGVY----------KRIRNSILEMKATPSMRLLAMAG-PAAR 208
Cdd:cd01676    5 YYRTYSRPKEE-GQNENWDQTVERVVEGTFELWERHLGNPLRwlnekaeeeaEELRSLIFELKALPPGRGLWLGGtDYSR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 209 -RNNISIYNCSYQPV-DSIDSFVEALIISMNGCGVGFSVENRYVENLPRVK----------------------RQDGLET 264
Cdd:cd01676   84 qRRFASLNNCAFVSTeDVVYPFVFLMDLLMQGCGVGFDTAGSNISQIPRPLqeikvqrvnrtekggiqnnvetYDPTQHT 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 265 KQMLIEDSTEGWADALRTGLHTWFDGG-DIKFDYSALRPAGAILRTKGGRSSGPEPLRKMMEFVRERIFTRQGSFLRAID 343
Cdd:cd01676  164 WIIKVPDSREGWVKSVQLLLDLYFNPAqTLIFDYSDIRPAGERLKGFGGIASGPEPLKKLHKAIAAILNDRSGKPLTSVD 243

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 344 AHDIMCEVGNAAVSGGMRRTAMISLFDFDDKEMWDSKSGDFERDN-SQRWNANNSAVWPlSGLTQLEVTKQMLEIvkSGR 422
Cdd:cd01676  244 IVDLMNLIGVCVVSGNVRRSAEIAFGQPEDEDFADLKQYQWNPGRrEHGWASNNSVVFE-SKPDRLEYSFACMLI--RGN 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 423 GEPGIFNRQSA-------LDMRPARRAPAEfGTNPCGEIILRPYEFCNLS-IAIARREDTYETLKDKVEVASIIGTIQAM 494
Cdd:cd01676  321 GEPGIAWLDNMkayarmvLLTTPYHDLRAK-GGNPCGEISLESYELCNLVeVFPLKHEGDLEDLQETLYLAGRYAKTVTL 399

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 495 A-TNFSGLRPAWKNNceeeRLLGVDINGQMDS-----PVAQDSAVQNRLRQV---AIETNREVAEKLGINQAAAVTCVKP 565
Cdd:cd01676  400 LpLHWEITNEIILRN----RRIGVSMSGIADFivragGDLTLHDLKRWRNIGyeaVYQYDERLSKWLGIPLSIKVTCVKP 475

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 566 SGNSSQLFNCSSGIHARWSPYYVRNIRVSTHSSIFKVLKSGGVPMDPEngqtLESANTWVIHFPVKSPDGAVTRKSFSAT 645
Cdd:cd01676  476 SGTISLLAGASPGMHYPLGKYLIRRIRFQKHDPLAPALIAAGYHVEPD----IYDPTSVLVEFPVKAGNADRTANTVSIV 551

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 646 AQCEYWLKNKINWTEHNPSVTITYHP-DEVIDLIKWVWEHRNLIGGMSFLPAFDAAYS--QMPYQEIERDDYEKLKAGFP 722
Cdd:cd01676  552 EQLSLLAFLQTYWADNQVSNTISFDPsPEGPALIQALQQFQYQYKSVSLLPRFDTTKNaaQMPFEPITKERYEQRIAKLK 631

                        650       660       670
                 ....*....|....*....|....*....|.
gi 818695931 723 PIDFSKLYRYEEEDytkaAQELACVAG-CDI 752
Cdd:cd01676  632 DVDYSGDYISPLEE----DLQTFCDSGaCPI 658
RTPR TIGR02505
ribonucleoside-triphosphate reductase, adenosylcobalamin-dependent; This model represents a ...
 144-719 2.73e-83

ribonucleoside-triphosphate reductase, adenosylcobalamin-dependent; This model represents a group of adenosylcobalamin(B12)-dependent ribonucleotide reductases (RNR) related to the characterized species from Lactococcus leichmannii. RNR's are responsible for the conversion of the ribose sugar of RNA into the deoxyribose sugar of DNA. This is the rate-limiting step of DNA biosynthesis. Thus model identifies NrdJ enzymes only in cyanobacteria, lactococcus and certain bacteriophage. A separate model (TIGR02504) identifies a larger group of divergent B12-dependent RNR's. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism]


Pssm-ID: 274169 [Multi-domain]  Cd Length: 713  Bit Score: 279.50  E-value: 2.73e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  144 YSRFNYDLGRRETWKETVDRSVDFLREL----------SGGKLESGVYKRIRNSILEMKATPSMRLLAMAGPA-ARRNNI 212
Cdd:TIGR02505  20 YARWLPEKGRSENWDETVERVVSGNRNLwprlqdrpllELQQSLTEEAERLYRLIYELKALPSGRNLWIGGTDyQRRTED 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  213 SIYNCSYQPVDSIDSFVEALIISMNGCGVGFSVENRYVENLPRVKR---------------QDGLETKQML--------- 268
Cdd:TIGR02505 100 SLFNCWFTAIRPQKPFSFLFDLLMKGCGVGFSVARSNISQIPRVDQeikvqlvvdetsesyDASVEVGAVSknedvqdvd 179

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  269 IEDSTEGWADALRTGLHTWFD----GGDIK--FDYSALRPAGAILRTKGGRSSGPEPLRKMMEFVRERIFTRQGSFLRAI 342
Cdd:TIGR02505 180 LPDTREGWVLANALLIDLHFAqtnaDRKQKlvLDLSDIRPAGAELKGFGGTASGPVPLAKMLTDVAEILSNKAGGRLTAV 259

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  343 DAHDIMCEVGNAAVSGGMRRTAMISLFDFDDKEmWDSKSGDFERDNSQRWNANN-----SAVWPLS----GLTQLEVTKQ 413
Cdd:TIGR02505 260 DAADICNLIGKAVVAGNVRRSAEMALFSNDDPE-FESFKQAKEKLMHHRWASNNsvavdSAFSGLArsaaDILENGEPGQ 338

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  414 mlEIVKSGRGEPGIFNRQSAldmrpARRAPAEFGTNPCGEIILRPYEFCNLS-IAIArredTYETLKDKVEVASIIGTIQ 492
Cdd:TIGR02505 339 --VNLDLSKSEGRIVNGRYQ-----AGEDGDVEGTNPCGEILLANGEPCNLFeVNLL----AFEEDGWGLQRAFALAARY 407

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  493 AMATNFSGLR-PAWKNNCEEERLLGVDINGQMD-----------------------SPVAQDSAVQ--NRLRQVAIETNR 546
Cdd:TIGR02505 408 AKRVTFSPYDdEISREIIQKNRRIGVSMSGIQDflllrggtgfkddfdpetheaikVRVYDKRAAKflDRMYKIVVKAAQ 487

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  547 EVAEKLGINQAAAVTCVKPSGNSSQLFNCSSGIHARWSPYYVRNIRVSTHSSIFKVLKSGGV-----PMDPENGQTLESA 621
Cdd:TIGR02505 488 DYSKELGCPEPIKHTTVKPSGTISKLAGASEGIHPPYGAYLIRRITFSKSDPLAPALKACGYtveadQYDKNEQGRLPPC 567

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  622 NTWVIHFPVKS-----PD-GAVTRKSFSATAQCEYWLKNKINWTEHNPSVTITYHPDEVIDLIKWVWEHRNLIGG----- 690
Cdd:TIGR02505 568 KTTLVEFPIKAvgadnPNiAEVGINTVSAAAQFAFYAFLQTYWSDNNVSCTITFDPSEGEQVESALRQYRDNSEGyfstk 647

                         650       660       670
                  ....*....|....*....|....*....|
gi 818695931  691 -MSFLPAFDAAYSQMPYQEIERDDYEKLKA 719
Cdd:TIGR02505 648 sTSLLPAFGGSFPQLPKEPIDKETYEKRSA 677
PRK08270 PRK08270
ribonucleoside triphosphate reductase;
20-114 3.22e-24

ribonucleoside triphosphate reductase;


Pssm-ID: 236212 [Multi-domain]  Cd Length: 656  Bit Score: 108.40  E-value: 3.22e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  20 PKTIVKRDGRVVPFEIQKIEKAISSCFEDLGKNPLTPVGELAQRVVNIIgAKYTKPTVEQVQDTVELVLQAAGEFEAAKN 99
Cdd:PRK08270   2 PTKIIKRDGRIVPFDAEKITEAIAKAFKATGEFDPSEAERLALRVIEKL-EDEDIPSVEEIQDIVEKVLIEAGYFKTAKA 80

                         90
                 ....*....|....*
gi 818695931 100 YIIYRVEHAKLRDSR 114
Cdd:PRK08270  81 YILYREQHARLRNDK 95
NrdD COG1328
Anaerobic ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]; ...
 20-128 3.97e-23

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: 105.00  E-value: 3.97e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  20 PKTIVKRDGRVVPFEIQKIEKAISSCFEDLGKNPLTP--VGELAQRVVNIIGAKYTK--PTVEQVQDTVELVLQAAGEFE 95
Cdd:COG1328    2 MLKVIKRDGRVVPFDPEKIANAIKKAAKAVGGEDRDEelAEEIADEVEKELERLGGGgtITVEEIQDIVEKVLMESGHPE 81

                         90       100       110
                 ....*....|....*....|....*....|...
gi 818695931  96 AAKNYIIYRVEHAKLRDSRPIPKEVAKAFSESD 128
Cdd:COG1328   82 VAKAYILYREQRTRLREARTTLVDDIELLDEYD 114
ATP-cone pfam03477
ATP cone domain;
21-109 3.03e-18

ATP cone domain;


Pssm-ID: 397513 [Multi-domain]  Cd Length: 86  Bit Score: 80.00  E-value: 3.03e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931   21 KTIVKRDGRVVPFEIQKIEKAISSCFEDLGKNpltpVGELAQRVVNIIGAKYTK-PTVEQVQDTVELVLQAAGEFEAAKN 99
Cdd:pfam03477   1 MKVIKRDGRREPFDKEKIRRAIEKACEKSPDQ----ADELASEVEEELEKSLEDgISTEEIQDLVEKTLAEHPDYAVARA 76

                          90
                  ....*....|
gi 818695931  100 YIIYRVEHAK 109
Cdd:pfam03477  77 YILYRNLRKE 86
PRK06406 PRK06406
vitamin B12-dependent ribonucleotide reductase;
20-591 3.44e-17

vitamin B12-dependent ribonucleotide reductase;


Pssm-ID: 235796 [Multi-domain]  Cd Length: 771  Bit Score: 86.06  E-value: 3.44e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  20 PKTIVKRDGRVVPFEIQKIEKAISSCFEDLGKNPLTPVGELAQRVVNIIgAKYTKPTVEQVQDTVELVLQAAGEF----- 94
Cdd:PRK06406   4 VKEVIKRDGTVVPFDKKKIAMAIYKAMLSVKNGSMEDAEELTDKVVERL-KKYERPTVEQIQDIVEKVLMTKKINgkdft 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  95 EAAKNYIIYRVEHAKLRDSRPIP------KEVAKAFS--ESDVYFENQIQKF-----QFFDKYSRF------NYDLGRRE 155
Cdd:PRK06406  83 DVAKSYILYREKRRKIREEKELIgvkddlKLTLNAIKvlEARYLLKDEDGKIietprQMFRRVARHiaiveaLYDDEVYD 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 156 TWKETVDRSVDFlrelsgGKLESGVYKRIRNSILEMKATPSMRLL---AMAGPAARRNNISIYNCSYQPVDSIDSFVEAL 232
Cdd:PRK06406 163 KTGKQKENAEVI------GKLSVTQEDMLKRAFRYLKEEGIMKGDfeeFLDFLKTKWDSIEEYINKFEEVMSNLKFVPNS 236

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 233 IISMNGCGVGFSVENRYVenLPrvkrqdgletkqmlIEDSTEGWADALRTGLHTWFDGGDIKFDYSALRPAGAILRTKGG 312
Cdd:PRK06406 237 PTLMNAGTKLGQLSACFV--LP--------------VPDSIEGIFNALKYTAMIHKSGGGTGFSFSRLRPKDDIVASTKG 300

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 313 RSSGPEplrkmmefvreriftrqgSFLRAID-AHDIMCEvgnaavsGGMRRTAMISLFDFDDKEMWD-SKSGDFERDNSQ 390
Cdd:PRK06406 301 VASGPL------------------SFMRIFDvTTDVIKQ-------GGKRRGANMGILSYHHPDIMEfITSKDSENKVLS 355

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 391 RWNAN------------NSAVWPLSGLTQLEVTKQM-------LEIVKSGR-GEPG-IF----NRQSaldmrPARRAPAE 445
Cdd:PRK06406 356 NFNISvavtdeffdkldNDDYYPLRNPRNGKEVKRIkarqvwdLIITQAWKtGDPGvIFldeiNRKN-----PVKNLGEI 430

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 446 FGTNPCGEIILRPYEFC-----NLSIAIARREDTYETLKDKVEVASIIGTIQAMATNFSglRPAWKNNCEEERLLGVDIN 520
Cdd:PRK06406 431 ESTNPCGEQPLLPYESCnlgsiNLSKFVENGKIDWDRLRETVHIATRFLDNVIDANKFP--VPQIKEMTRMTRKIGLGVM 508

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 521 G------QMDSPVAQDSAV---QNRLRQVAIETNRE---VAEKLGINQA---------------AAVTCVKPSGNSSQLF 573
Cdd:PRK06406 509 GfadmliKLGIPYNSEEALeiaEKVMKFINEESHRAsqkLAEERGVFPAwygsewekkgikmrnSTTTTIAPTGTISIIA 588

                        650
                 ....*....|....*...
gi 818695931 574 NCSSGIHARWSPYYVRNI 591
Cdd:PRK06406 589 GCSSSIEPLFAIAFVRHV 606
NrdA COG0209
Ribonucleotide reductase alpha subunit [Nucleotide transport and metabolism]; Ribonucleotide ...
 269-485 1.41e-12

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: 70.99  E-value: 1.41e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 269 IEDSTEGWADALRTG--LHTWfdGGDIKFDYSALRPAGAILRTKGGRSSGPeplrkmmefVreriftrqgSFLRAIDAhd 346
Cdd:COG0209  135 VEDSLESIFDALKDAalLSKS--GGGVGFNFSRLRPKGSPIKGTGGVSSGP---------V---------PFMKVFDD-- 192

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 347 iMCEvgnAAVSGGMRRTA-MISLfdfddkEMW--------DSK--SGDFERdnsqRW-NANNS---------AV-----W 400
Cdd:COG0209  193 -AAV---AVNQGGKRRGAnMVYL------RVWhpdieeflDLKknNGDERR----RLhNFNISvwipdlfmeAVeededW 258

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 401 PL---------SGLTQLEVTKQMLEIVKSGR---------------------GEPGIF-----NRQSALDmrparrapaE 445
Cdd:COG0209  259 TLfsprevpdlYGLYGEEFEEAYEEYEADGRvyktikarelwrkilesawetGEPGILfkdtiNRRNPLP---------H 329

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 818695931 446 FG----TNPCGEIILRPYEF----CNL-SIAIAR--REDT--YETLKDKVEVA 485
Cdd:COG0209  330 LGvihsSNLCGEIPLLPYESedasCNLgSINLAKfvKDGEfdWEKLEETVRTA 382
Ribonuc_red_lgC pfam02867
Ribonucleotide reductase, barrel domain;
267-601 1.03e-09

Ribonucleotide reductase, barrel domain;


Pssm-ID: 460729 [Multi-domain]  Cd Length: 487  Bit Score: 61.45  E-value: 1.03e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  267 MLIEDSTEGWADALRTGLHTWFDGGDIKFDYSALRPAGAILRTKGGRSSGPEPlrkmmefvreriftrqgsFLRAIDAhd 346
Cdd:pfam02867   6 LSVEDSLDSIYDTLKEAALLSKGGGGIGLNLSKLRAKGSPIRGTGGASSGVVP------------------FLKLFDD-- 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  347 iMCEVGNaavSGGMRRTA-MISLfdfddkEMWDSKSGDF------ERDNSQRW-NANNSAV--------------WPL-- 402
Cdd:pfam02867  66 -SARYVN---QGGKRRGAaAVYL------EVWHPDIEEFldlkknNGDEEVRArNLNLGVWvpdlfmerveadedWTLfs 135

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  403 ----SGLTQL---EVTKQMLEIVKSGR----------------------GEPGIF-----NRQSALDMRPARRApaefgT 448
Cdd:pfam02867 136 preaPDLEDLygeEFEKEYYEREENEGirkktvkarelwfkiaksqietGYPYILfkdavNRKNPQKHLGTIKS-----S 210

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  449 NPCGEIILRPYEF----CNL-SIAIARredtYETLKDKVEVASIIGTIQAMAT--------NFSGLRPAWKNNcEEERLL 515
Cdd:pfam02867 211 NLCTEIVQPTSPSeiavCNLaSINLAK----FVEFGGTFDFEKLREVVKLAVRaldnvidiNDYPVPEARRSN-KRHRPI 285

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  516 GVDING----------QMDSPVAQD--SAVQNRLRQVAIETNREVAEKLGI----NQAAA-------------------- 559
Cdd:pfam02867 286 GLGVMGladalaklgiPYDSEEARDlnDKIFETMYYYALKASSELAKEKGPfpgfEGSKYskgilqfdkyvktdfapkas 365

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 818695931  560 ----------------------VTCVKPSGNSSQLFNCSSGIHARWSPYYVRNIRVSTHSSIFK 601
Cdd:pfam02867 366 ktredweelredikkyglrnsqLTAIAPTGSISQIAGATESIEPIFSNVYSRKVLSEETKEYYK 429
 
Name Accession Description Interval E-value
RNR_II_monomer cd01676
Class II ribonucleotide reductase, monomeric form; Ribonucleotide reductase (RNR) catalyzes ...
 140-752 1.07e-94

Class II ribonucleotide reductase, monomeric 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. This particular subfamily is found to be active as a monomer. Adenosylcobalamin interacts directly with an active site cysteine to form the reactive cysteine radical.


Pssm-ID: 153085 [Multi-domain]  Cd Length: 658  Bit Score: 308.67  E-value: 1.07e-94
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 140 FFDKYSRFNYDlGRRETWKETVDRSVDFLRELSGGKLESGVY----------KRIRNSILEMKATPSMRLLAMAG-PAAR 208
Cdd:cd01676    5 YYRTYSRPKEE-GQNENWDQTVERVVEGTFELWERHLGNPLRwlnekaeeeaEELRSLIFELKALPPGRGLWLGGtDYSR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 209 -RNNISIYNCSYQPV-DSIDSFVEALIISMNGCGVGFSVENRYVENLPRVK----------------------RQDGLET 264
Cdd:cd01676   84 qRRFASLNNCAFVSTeDVVYPFVFLMDLLMQGCGVGFDTAGSNISQIPRPLqeikvqrvnrtekggiqnnvetYDPTQHT 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 265 KQMLIEDSTEGWADALRTGLHTWFDGG-DIKFDYSALRPAGAILRTKGGRSSGPEPLRKMMEFVRERIFTRQGSFLRAID 343
Cdd:cd01676  164 WIIKVPDSREGWVKSVQLLLDLYFNPAqTLIFDYSDIRPAGERLKGFGGIASGPEPLKKLHKAIAAILNDRSGKPLTSVD 243

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 344 AHDIMCEVGNAAVSGGMRRTAMISLFDFDDKEMWDSKSGDFERDN-SQRWNANNSAVWPlSGLTQLEVTKQMLEIvkSGR 422
Cdd:cd01676  244 IVDLMNLIGVCVVSGNVRRSAEIAFGQPEDEDFADLKQYQWNPGRrEHGWASNNSVVFE-SKPDRLEYSFACMLI--RGN 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 423 GEPGIFNRQSA-------LDMRPARRAPAEfGTNPCGEIILRPYEFCNLS-IAIARREDTYETLKDKVEVASIIGTIQAM 494
Cdd:cd01676  321 GEPGIAWLDNMkayarmvLLTTPYHDLRAK-GGNPCGEISLESYELCNLVeVFPLKHEGDLEDLQETLYLAGRYAKTVTL 399

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 495 A-TNFSGLRPAWKNNceeeRLLGVDINGQMDS-----PVAQDSAVQNRLRQV---AIETNREVAEKLGINQAAAVTCVKP 565
Cdd:cd01676  400 LpLHWEITNEIILRN----RRIGVSMSGIADFivragGDLTLHDLKRWRNIGyeaVYQYDERLSKWLGIPLSIKVTCVKP 475

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 566 SGNSSQLFNCSSGIHARWSPYYVRNIRVSTHSSIFKVLKSGGVPMDPEngqtLESANTWVIHFPVKSPDGAVTRKSFSAT 645
Cdd:cd01676  476 SGTISLLAGASPGMHYPLGKYLIRRIRFQKHDPLAPALIAAGYHVEPD----IYDPTSVLVEFPVKAGNADRTANTVSIV 551

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 646 AQCEYWLKNKINWTEHNPSVTITYHP-DEVIDLIKWVWEHRNLIGGMSFLPAFDAAYS--QMPYQEIERDDYEKLKAGFP 722
Cdd:cd01676  552 EQLSLLAFLQTYWADNQVSNTISFDPsPEGPALIQALQQFQYQYKSVSLLPRFDTTKNaaQMPFEPITKERYEQRIAKLK 631

                        650       660       670
                 ....*....|....*....|....*....|.
gi 818695931 723 PIDFSKLYRYEEEDytkaAQELACVAG-CDI 752
Cdd:cd01676  632 DVDYSGDYISPLEE----DLQTFCDSGaCPI 658
RTPR TIGR02505
ribonucleoside-triphosphate reductase, adenosylcobalamin-dependent; This model represents a ...
 144-719 2.73e-83

ribonucleoside-triphosphate reductase, adenosylcobalamin-dependent; This model represents a group of adenosylcobalamin(B12)-dependent ribonucleotide reductases (RNR) related to the characterized species from Lactococcus leichmannii. RNR's are responsible for the conversion of the ribose sugar of RNA into the deoxyribose sugar of DNA. This is the rate-limiting step of DNA biosynthesis. Thus model identifies NrdJ enzymes only in cyanobacteria, lactococcus and certain bacteriophage. A separate model (TIGR02504) identifies a larger group of divergent B12-dependent RNR's. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism]


Pssm-ID: 274169 [Multi-domain]  Cd Length: 713  Bit Score: 279.50  E-value: 2.73e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  144 YSRFNYDLGRRETWKETVDRSVDFLREL----------SGGKLESGVYKRIRNSILEMKATPSMRLLAMAGPA-ARRNNI 212
Cdd:TIGR02505  20 YARWLPEKGRSENWDETVERVVSGNRNLwprlqdrpllELQQSLTEEAERLYRLIYELKALPSGRNLWIGGTDyQRRTED 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  213 SIYNCSYQPVDSIDSFVEALIISMNGCGVGFSVENRYVENLPRVKR---------------QDGLETKQML--------- 268
Cdd:TIGR02505 100 SLFNCWFTAIRPQKPFSFLFDLLMKGCGVGFSVARSNISQIPRVDQeikvqlvvdetsesyDASVEVGAVSknedvqdvd 179

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  269 IEDSTEGWADALRTGLHTWFD----GGDIK--FDYSALRPAGAILRTKGGRSSGPEPLRKMMEFVRERIFTRQGSFLRAI 342
Cdd:TIGR02505 180 LPDTREGWVLANALLIDLHFAqtnaDRKQKlvLDLSDIRPAGAELKGFGGTASGPVPLAKMLTDVAEILSNKAGGRLTAV 259

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  343 DAHDIMCEVGNAAVSGGMRRTAMISLFDFDDKEmWDSKSGDFERDNSQRWNANN-----SAVWPLS----GLTQLEVTKQ 413
Cdd:TIGR02505 260 DAADICNLIGKAVVAGNVRRSAEMALFSNDDPE-FESFKQAKEKLMHHRWASNNsvavdSAFSGLArsaaDILENGEPGQ 338

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  414 mlEIVKSGRGEPGIFNRQSAldmrpARRAPAEFGTNPCGEIILRPYEFCNLS-IAIArredTYETLKDKVEVASIIGTIQ 492
Cdd:TIGR02505 339 --VNLDLSKSEGRIVNGRYQ-----AGEDGDVEGTNPCGEILLANGEPCNLFeVNLL----AFEEDGWGLQRAFALAARY 407

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  493 AMATNFSGLR-PAWKNNCEEERLLGVDINGQMD-----------------------SPVAQDSAVQ--NRLRQVAIETNR 546
Cdd:TIGR02505 408 AKRVTFSPYDdEISREIIQKNRRIGVSMSGIQDflllrggtgfkddfdpetheaikVRVYDKRAAKflDRMYKIVVKAAQ 487

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  547 EVAEKLGINQAAAVTCVKPSGNSSQLFNCSSGIHARWSPYYVRNIRVSTHSSIFKVLKSGGV-----PMDPENGQTLESA 621
Cdd:TIGR02505 488 DYSKELGCPEPIKHTTVKPSGTISKLAGASEGIHPPYGAYLIRRITFSKSDPLAPALKACGYtveadQYDKNEQGRLPPC 567

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  622 NTWVIHFPVKS-----PD-GAVTRKSFSATAQCEYWLKNKINWTEHNPSVTITYHPDEVIDLIKWVWEHRNLIGG----- 690
Cdd:TIGR02505 568 KTTLVEFPIKAvgadnPNiAEVGINTVSAAAQFAFYAFLQTYWSDNNVSCTITFDPSEGEQVESALRQYRDNSEGyfstk 647

                         650       660       670
                  ....*....|....*....|....*....|
gi 818695931  691 -MSFLPAFDAAYSQMPYQEIERDDYEKLKA 719
Cdd:TIGR02505 648 sTSLLPAFGGSFPQLPKEPIDKETYEKRSA 677
PRK08270 PRK08270
ribonucleoside triphosphate reductase;
20-114 3.22e-24

ribonucleoside triphosphate reductase;


Pssm-ID: 236212 [Multi-domain]  Cd Length: 656  Bit Score: 108.40  E-value: 3.22e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  20 PKTIVKRDGRVVPFEIQKIEKAISSCFEDLGKNPLTPVGELAQRVVNIIgAKYTKPTVEQVQDTVELVLQAAGEFEAAKN 99
Cdd:PRK08270   2 PTKIIKRDGRIVPFDAEKITEAIAKAFKATGEFDPSEAERLALRVIEKL-EDEDIPSVEEIQDIVEKVLIEAGYFKTAKA 80

                         90
                 ....*....|....*
gi 818695931 100 YIIYRVEHAKLRDSR 114
Cdd:PRK08270  81 YILYREQHARLRNDK 95
NrdD COG1328
Anaerobic ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]; ...
 20-128 3.97e-23

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: 105.00  E-value: 3.97e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  20 PKTIVKRDGRVVPFEIQKIEKAISSCFEDLGKNPLTP--VGELAQRVVNIIGAKYTK--PTVEQVQDTVELVLQAAGEFE 95
Cdd:COG1328    2 MLKVIKRDGRVVPFDPEKIANAIKKAAKAVGGEDRDEelAEEIADEVEKELERLGGGgtITVEEIQDIVEKVLMESGHPE 81

                         90       100       110
                 ....*....|....*....|....*....|...
gi 818695931  96 AAKNYIIYRVEHAKLRDSRPIPKEVAKAFSESD 128
Cdd:COG1328   82 VAKAYILYREQRTRLREARTTLVDDIELLDEYD 114
PRK07111 PRK07111
anaerobic ribonucleoside triphosphate reductase; Provisional
 21-114 5.41e-19

anaerobic ribonucleoside triphosphate reductase; Provisional


Pssm-ID: 235937 [Multi-domain]  Cd Length: 735  Bit Score: 91.93  E-value: 5.41e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  21 KTIVKRDGRVVPFEIQKIEKAISSCFEDLGKNP-LTPVGELAQRVVNIIGAKY-TKPTVEQVQDTVELVLQAAGEFEAAK 98
Cdd:PRK07111   3 LYIVKRDGREVPFDEEKITNAIFKAAEAVGGELdESEAIELTQKVIKYLEEKYkEEVTVEDIQDLVEKVLIENGHAETAK 82

                         90
                 ....*....|....*.
gi 818695931  99 NYIIYRVEHAKLRDSR 114
Cdd:PRK07111  83 AYILYRAERTRIREIK 98
PRK12364 PRK12364
ribonucleoside-diphosphate reductase subunit alpha;
23-143 9.40e-19

ribonucleoside-diphosphate reductase subunit alpha;


Pssm-ID: 237077 [Multi-domain]  Cd Length: 842  Bit Score: 91.35  E-value: 9.40e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  23 IVKRDGRVVPFEIQKIEKAISSCFEDLGKnPLTP--VGELAQRVVNIIGAKYTKP---TVEQVQDTVELVLQAAGEFEAA 97
Cdd:PRK12364   3 IIKRNGTTEPYDREKIEVAIRKAFASVGK-PISDeiIYSLVAEVERFIKEKYPNGhnvSVEEIQDLVEKTLMEHGHYAEV 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 818695931  98 KNYIIYRVEHAKLRDSRP-------------IPKEVAKAFSESDVYFENQIQKFQFFDK 143
Cdd:PRK12364  82 KSYILYRAQRTEKRKAREqiikffdddtvlgVLKEIQKDFPSDEYSLDLLAEKFLSFCK 140
ATP-cone pfam03477
ATP cone domain;
21-109 3.03e-18

ATP cone domain;


Pssm-ID: 397513 [Multi-domain]  Cd Length: 86  Bit Score: 80.00  E-value: 3.03e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931   21 KTIVKRDGRVVPFEIQKIEKAISSCFEDLGKNpltpVGELAQRVVNIIGAKYTK-PTVEQVQDTVELVLQAAGEFEAAKN 99
Cdd:pfam03477   1 MKVIKRDGRREPFDKEKIRRAIEKACEKSPDQ----ADELASEVEEELEKSLEDgISTEEIQDLVEKTLAEHPDYAVARA 76

                          90
                  ....*....|
gi 818695931  100 YIIYRVEHAK 109
Cdd:pfam03477  77 YILYRNLRKE 86
NrdJ_Z TIGR02504
ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; This model represents a ...
 269-683 2.78e-17

ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent; This model represents a group of adenosylcobalamin(B12)-dependent ribonucleotide reductases (Class II RNRs) related to the characterized species from Pyrococcus, Thermoplasma, Corynebacterium, and Deinococcus. RNR's are responsible for the conversion of the ribose sugar of RNA into the deoxyribose sugar of DNA. This is the rate-limiting step of DNA biosynthesis. This model identifies genes in a wide range of deeply branching bacteria. All are structurally related to the class I (non-heme iron dependent) RNRs. In most species this gene is known as NrdJ, while in mycobacteria it is called NrdZ. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism]


Pssm-ID: 274168 [Multi-domain]  Cd Length: 575  Bit Score: 85.84  E-value: 2.78e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  269 IEDSTEGWADALRTGLHTWFDGGDIKFDYSALRPAGAILRTKGGRSSGPEplrkmmefvreriftrqgSFLRAIDAhdiM 348
Cdd:TIGR02504  84 VEDSMEDIFEALKEAALIFKRGGGVGYNFSTLRPKGDLVSGTGGVASGPV------------------SFMRVFDS---A 142

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  349 CEVgnaAVSGGMRRTA-MISLfdfddkEMWDSKSGDF---ERDNSQRWNANNS---------AV---------WPLSGLT 406
Cdd:TIGR02504 143 AGV---VKQGGTRRGAqMGIL------DVWHPDIEEFieaKAKEGKLQNFNISvgvtdefmeAVendeeyelrNPRTGEY 213

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  407 QLEVTKQML-EIVKSG--RGEPGIF-----NRQSALDMRPARRApaefgTNPCGEIILRPYEFCNL-SIAIAR--REDT- 474
Cdd:TIGR02504 214 KEVDARELWdKIVESAwkSAEPGVLfidtiNKWHTCPYGGRINA-----TNPCGEQPLLPYESCNLgSINLAKfvKNDFg 288

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  475 ------YETLKDKVEVASIIGTIQAMATNFSglRPAWKNNCEEERLLGVDING------QM----DSPVAQDSA--VQNR 536
Cdd:TIGR02504 289 deasfdFERLREVVRLATRFLDNVIDINVFP--LPEIAENTKKTRRIGLGIMGladlliKLgipyDSEEARELAeeVMEF 366

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  537 LRQVAIETNREVAEKLG-------------------INQA----------------AAVTCVKPSGNSSQLFNCSSGIHA 581
Cdd:TIGR02504 367 IADAAYRASAELAKERGafplydaskypmgramgarIPSAlpaeireairkygirnAQLTTIAPTGTISLIAGTSSGIEP 446

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  582 RWSPYYVRNIRVS-----THSSIFKVLKSGGVPMDPENGQTLESANTWVIHFPVKSPDGAVTRKSFS--------ATAQc 648
Cdd:TIGR02504 447 VFALVYFRNVTVGgelleVNPLVELALRELGYYSDEIVKYVDEKGTVEGAPGPEELPKVFVTAMDISpedhvlmqAAIQ- 525

                         490       500       510
                  ....*....|....*....|....*....|....*....
gi 818695931  649 eywlknkiNWTEHNPSVTI----TYHPDEVIDLIKWVWE 683
Cdd:TIGR02504 526 --------PWVDSSISKTInmpsDATVEDVKAVYLEAWK 556
PRK06406 PRK06406
vitamin B12-dependent ribonucleotide reductase;
20-591 3.44e-17

vitamin B12-dependent ribonucleotide reductase;


Pssm-ID: 235796 [Multi-domain]  Cd Length: 771  Bit Score: 86.06  E-value: 3.44e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  20 PKTIVKRDGRVVPFEIQKIEKAISSCFEDLGKNPLTPVGELAQRVVNIIgAKYTKPTVEQVQDTVELVLQAAGEF----- 94
Cdd:PRK06406   4 VKEVIKRDGTVVPFDKKKIAMAIYKAMLSVKNGSMEDAEELTDKVVERL-KKYERPTVEQIQDIVEKVLMTKKINgkdft 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  95 EAAKNYIIYRVEHAKLRDSRPIP------KEVAKAFS--ESDVYFENQIQKF-----QFFDKYSRF------NYDLGRRE 155
Cdd:PRK06406  83 DVAKSYILYREKRRKIREEKELIgvkddlKLTLNAIKvlEARYLLKDEDGKIietprQMFRRVARHiaiveaLYDDEVYD 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 156 TWKETVDRSVDFlrelsgGKLESGVYKRIRNSILEMKATPSMRLL---AMAGPAARRNNISIYNCSYQPVDSIDSFVEAL 232
Cdd:PRK06406 163 KTGKQKENAEVI------GKLSVTQEDMLKRAFRYLKEEGIMKGDfeeFLDFLKTKWDSIEEYINKFEEVMSNLKFVPNS 236

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 233 IISMNGCGVGFSVENRYVenLPrvkrqdgletkqmlIEDSTEGWADALRTGLHTWFDGGDIKFDYSALRPAGAILRTKGG 312
Cdd:PRK06406 237 PTLMNAGTKLGQLSACFV--LP--------------VPDSIEGIFNALKYTAMIHKSGGGTGFSFSRLRPKDDIVASTKG 300

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 313 RSSGPEplrkmmefvreriftrqgSFLRAID-AHDIMCEvgnaavsGGMRRTAMISLFDFDDKEMWD-SKSGDFERDNSQ 390
Cdd:PRK06406 301 VASGPL------------------SFMRIFDvTTDVIKQ-------GGKRRGANMGILSYHHPDIMEfITSKDSENKVLS 355

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 391 RWNAN------------NSAVWPLSGLTQLEVTKQM-------LEIVKSGR-GEPG-IF----NRQSaldmrPARRAPAE 445
Cdd:PRK06406 356 NFNISvavtdeffdkldNDDYYPLRNPRNGKEVKRIkarqvwdLIITQAWKtGDPGvIFldeiNRKN-----PVKNLGEI 430

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 446 FGTNPCGEIILRPYEFC-----NLSIAIARREDTYETLKDKVEVASIIGTIQAMATNFSglRPAWKNNCEEERLLGVDIN 520
Cdd:PRK06406 431 ESTNPCGEQPLLPYESCnlgsiNLSKFVENGKIDWDRLRETVHIATRFLDNVIDANKFP--VPQIKEMTRMTRKIGLGVM 508

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 521 G------QMDSPVAQDSAV---QNRLRQVAIETNRE---VAEKLGINQA---------------AAVTCVKPSGNSSQLF 573
Cdd:PRK06406 509 GfadmliKLGIPYNSEEALeiaEKVMKFINEESHRAsqkLAEERGVFPAwygsewekkgikmrnSTTTTIAPTGTISIIA 588

                        650
                 ....*....|....*...
gi 818695931 574 NCSSGIHARWSPYYVRNI 591
Cdd:PRK06406 589 GCSSSIEPLFAIAFVRHV 606
RNR_II_dimer cd02888
Class II ribonucleotide reductase, dimeric form; Ribonucleotide reductase (RNR) catalyzes the ...
 271-587 1.20e-16

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: 83.44  E-value: 1.20e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 271 DSTEGWADALRTGLHTWFDGGDIKFDYSALRPAGAILRTKGGRSSGPeplrkmmefVreriftrqgSFLRAIDAhdiMCE 350
Cdd:cd02888   42 DSIEGIFDALKEAALIFKRGGGVGYNFSRLRPKGDIVKSTGGVASGP---------V---------SFMRVFDA---ATG 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 351 VgnaAVSGGMRRTA-MISL-------FDFDDKEMWDSKSGDFErdnsqrwNANNS---------AV-----WPLSGLTQ- 407
Cdd:cd02888  101 V---IKQGGTRRGAnMGVLdvdhpdiEEFIDAKMKEEKTVVLQ-------NFNISvavtdafmeAVendepWELRNPREp 170

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 408 --LEVTKQML------EIVKSGR--GEPGIF-----NRQSALDMRPARRApaefgTNPCGEIILRPYEFCNL-SIAIAR- 470
Cdd:cd02888  171 dtGKVYRTVParelwdKIVEAAWdsADPGVLfidtiNRWNPLPGLGRINA-----TNPCGEQPLLPYESCNLgSINLSKf 245

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 471 -REDT------YETLKDKVEVASIIGTIQAMATNFSglRPAWKNNCEEERLLGVDING------QM----DSPVAQD--S 531
Cdd:cd02888  246 vKNPFggasfdFERLREAVRLAVRFLDNVIDVNRYP--LPEIAEETKATRRIGLGVMGladmliKLgipyDSEEARElaE 323

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 532 AVQNRLRQVAIETNREVAEKLG------INQA---------------------------AAVTCVKPSGNSSQLFNCSSG 578
Cdd:cd02888  324 RIMSFIRDAAYRASAELAKERGpfplfdASRYlmlkvivnakelpddvleeiekygirnAHLTTIAPTGTISLIAGTSSG 403


                 ....*....
gi 818695931 579 IHarwsPYY 587
Cdd:cd02888  404 IE----PIF 408
PRK09263 PRK09263
anaerobic ribonucleoside triphosphate reductase; Provisional
 20-114 3.93e-16

anaerobic ribonucleoside triphosphate reductase; Provisional


Pssm-ID: 236436 [Multi-domain]  Cd Length: 711  Bit Score: 82.62  E-value: 3.93e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  20 PKTIVKRDGRVVPFEIQKIEKAISSCFEDLGKNPLTPVGELAQRVVNIIgAKYTKPTVEQVQDTVELVLQAAGEFEAAKN 99
Cdd:PRK09263   2 MPKVIKRDGRKVPFDSEKIKNAIEKAAKAVEVDDEDYCATVAAEIASRV-EGRDEVDIEEIQDAVENQLMAGPYKALARA 80

                         90
                 ....*....|....*
gi 818695931 100 YIIYRVEHAKLRDSR 114
Cdd:PRK09263  81 YIEYRHDRDIAREKA 95
PRK08332 PRK08332
vitamin B12-dependent ribonucleotide reductase;
23-199 1.52e-13

vitamin B12-dependent ribonucleotide reductase;


Pssm-ID: 181392 [Multi-domain]  Cd Length: 1740  Bit Score: 74.80  E-value: 1.52e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931   23 IVKRDGRVVPFEIQKIEKAISSCFEDLGKNPLTPVGELAQRVVNIIGAKYTK--PTVEQVQDTVELVLQAAGEFEAAKNY 100
Cdd:PRK08332    6 VMKRDGRIVPFDESRIRWAVQRAMWEVGVRDEKKLDEVVKRIVQRINELYDGkiPHIENIQDIVELELMRAGLFEVAKAY 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  101 IIYRVEHAKLRDS--RPIPK----EVAKAFS---------------ESDVYFENQIQKFQ----------------FFDK 143
Cdd:PRK08332   86 ILYRKKKAEIREEkkRILNKkeldEIDKRFSinalrvlasrylkkdENGNIIESPRELFErvailavipdllyderVFDK 165

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 818695931  144 YSRFNYDLGRRETWKETVDrsvDFLRELSGGKLESGVY--KRIRNSILEMKATPSMRL 199
Cdd:PRK08332  166 NGNYSQDLKRVEYYLENFE---EFDGKYSIGKYKLNKYhfERMVNLYRELAEKGKMKV 220
NrdA COG0209
Ribonucleotide reductase alpha subunit [Nucleotide transport and metabolism]; Ribonucleotide ...
 269-485 1.41e-12

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: 70.99  E-value: 1.41e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 269 IEDSTEGWADALRTG--LHTWfdGGDIKFDYSALRPAGAILRTKGGRSSGPeplrkmmefVreriftrqgSFLRAIDAhd 346
Cdd:COG0209  135 VEDSLESIFDALKDAalLSKS--GGGVGFNFSRLRPKGSPIKGTGGVSSGP---------V---------PFMKVFDD-- 192

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 347 iMCEvgnAAVSGGMRRTA-MISLfdfddkEMW--------DSK--SGDFERdnsqRW-NANNS---------AV-----W 400
Cdd:COG0209  193 -AAV---AVNQGGKRRGAnMVYL------RVWhpdieeflDLKknNGDERR----RLhNFNISvwipdlfmeAVeededW 258

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 401 PL---------SGLTQLEVTKQMLEIVKSGR---------------------GEPGIF-----NRQSALDmrparrapaE 445
Cdd:COG0209  259 TLfsprevpdlYGLYGEEFEEAYEEYEADGRvyktikarelwrkilesawetGEPGILfkdtiNRRNPLP---------H 329

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
gi 818695931 446 FG----TNPCGEIILRPYEF----CNL-SIAIAR--REDT--YETLKDKVEVA 485
Cdd:COG0209  330 LGvihsSNLCGEIPLLPYESedasCNLgSINLAKfvKDGEfdWEKLEETVRTA 382
PRK12365 PRK12365
ribonucleoside-diphosphate reductase subunit alpha;
22-146 3.39e-11

ribonucleoside-diphosphate reductase subunit alpha;


Pssm-ID: 171440 [Multi-domain]  Cd Length: 1046  Bit Score: 66.89  E-value: 3.39e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931   22 TIVKRDGRVVPFEIQKIEKAISSCFEDLGKNP-------LTPVGELAQRVVNIIGAKYTKPT---VEQVQDTVELVLQAA 91
Cdd:PRK12365  119 SVIRRDGTVVHFNPMKISAALEKAFRATDKIEgmtpssvLEEINALTQNIVEEILECCSQEDridIEKIQDIVEQQLMVV 198

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 818695931   92 GEFEAAKNYIIYRVEHAKLRDSRPIPKEVAKAFSES--DVYFEN----QIQKFQFFDKYSR 146
Cdd:PRK12365  199 GHYDVAKNYILYREARARVRDNKEEDGSTEKTIAEEayEVLSKDgstyTMTKSQLLAHFAW 259
PRK07207 PRK07207
ribonucleoside-diphosphate reductase subunit alpha;
23-123 7.97e-10

ribonucleoside-diphosphate reductase subunit alpha;


Pssm-ID: 235966 [Multi-domain]  Cd Length: 965  Bit Score: 62.67  E-value: 7.97e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  23 IVKRDGRVVPFEIQKIEKAISSCF--------------EDLgknpltpVGELAQRVVNIIgaKYTKPT-----VEQVQDT 83
Cdd:PRK07207  36 VIRRNGSVVPFEPSKIAVAMTKAFlaveggqaaasarvRET-------VEQLTEQVVRAL--VRRRPSggtfhIEDIQDQ 106

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 818695931  84 VELVLQAAGEFEAAKNYIIYRVEHAKLRDSRPIPKEVAKA 123
Cdd:PRK07207 107 VELALMRSGEHKVARAYVLYREKRAQERAAEAEAAAAEAH 146
Ribonuc_red_lgC pfam02867
Ribonucleotide reductase, barrel domain;
267-601 1.03e-09

Ribonucleotide reductase, barrel domain;


Pssm-ID: 460729 [Multi-domain]  Cd Length: 487  Bit Score: 61.45  E-value: 1.03e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  267 MLIEDSTEGWADALRTGLHTWFDGGDIKFDYSALRPAGAILRTKGGRSSGPEPlrkmmefvreriftrqgsFLRAIDAhd 346
Cdd:pfam02867   6 LSVEDSLDSIYDTLKEAALLSKGGGGIGLNLSKLRAKGSPIRGTGGASSGVVP------------------FLKLFDD-- 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  347 iMCEVGNaavSGGMRRTA-MISLfdfddkEMWDSKSGDF------ERDNSQRW-NANNSAV--------------WPL-- 402
Cdd:pfam02867  66 -SARYVN---QGGKRRGAaAVYL------EVWHPDIEEFldlkknNGDEEVRArNLNLGVWvpdlfmerveadedWTLfs 135

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  403 ----SGLTQL---EVTKQMLEIVKSGR----------------------GEPGIF-----NRQSALDMRPARRApaefgT 448
Cdd:pfam02867 136 preaPDLEDLygeEFEKEYYEREENEGirkktvkarelwfkiaksqietGYPYILfkdavNRKNPQKHLGTIKS-----S 210

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  449 NPCGEIILRPYEF----CNL-SIAIARredtYETLKDKVEVASIIGTIQAMAT--------NFSGLRPAWKNNcEEERLL 515
Cdd:pfam02867 211 NLCTEIVQPTSPSeiavCNLaSINLAK----FVEFGGTFDFEKLREVVKLAVRaldnvidiNDYPVPEARRSN-KRHRPI 285

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931  516 GVDING----------QMDSPVAQD--SAVQNRLRQVAIETNREVAEKLGI----NQAAA-------------------- 559
Cdd:pfam02867 286 GLGVMGladalaklgiPYDSEEARDlnDKIFETMYYYALKASSELAKEKGPfpgfEGSKYskgilqfdkyvktdfapkas 365

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 818695931  560 ----------------------VTCVKPSGNSSQLFNCSSGIHARWSPYYVRNIRVSTHSSIFK 601
Cdd:pfam02867 366 ktredweelredikkyglrnsqLTAIAPTGSISQIAGATESIEPIFSNVYSRKVLSEETKEYYK 429
PRK12365 PRK12365
ribonucleoside-diphosphate reductase subunit alpha;
22-112 1.30e-09

ribonucleoside-diphosphate reductase subunit alpha;


Pssm-ID: 171440 [Multi-domain]  Cd Length: 1046  Bit Score: 61.89  E-value: 1.30e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931   22 TIVKRDGRVVPFEIQKIEKAISSCFED---------LGKNPLTPVGELAQRVVNIIGAKYTKP---TVEQVQDTVELVLQ 89
Cdd:PRK12365   10 TIVKRNGMFVPFNQNRIFQALEAAFRDtrsledhspLPEDLESSIRSITHQVVKEVVQKITEGqvvTVERIQDMVESQLY 89

                          90       100
                  ....*....|....*....|...
gi 818695931   90 AAGEFEAAKNYIIYRVEHAKLRD 112
Cdd:PRK12365   90 VNGLQDVARDYIVYRDDRKAHRK 112
PRK08665 PRK08665
vitamin B12-dependent ribonucleotide reductase;
269-485 4.86e-09

vitamin B12-dependent ribonucleotide reductase;


Pssm-ID: 236330 [Multi-domain]  Cd Length: 752  Bit Score: 59.95  E-value: 4.86e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 269 IEDSTEGWADALR-TGL-HTwfDGGDIKFDYSALRPAGAILRTKGGRSSGPeplrkmMEFVRerIF-----------TRQ 335
Cdd:PRK08665 102 VGDSIEEIFDAVKhAALiHK--SGGGTGFSFSRLRPKNDRVGSTGGVASGP------VSFMR--VFdaateaikqggTRR 171

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 336 GS---FLRaIDAHDIM----C-----EVGNAAVSGGMRRTAMISLFDFDDKEMWDSKSGDFerdnSQRWNAnnSAVWPLs 403
Cdd:PRK08665 172 GAnmgILR-VDHPDIMefitCkedngELTNFNISVAITEAFMEAVEADEEYDLINPRTGEV----VGRLNA--REVFDL- 243

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931 404 gltqlevtkqmleIVKS--GRGEPGIFnrqsALDmRPARRAPA-EFG----TNPCGEIILRPYEFCNL-SIAIAR--RED 473
Cdd:PRK08665 244 -------------IVEMawENGEPGIV----FID-RINRDNPTpHLGeiesTNPCGEQPLLPYESCNLgSINLSKmvKNG 305

                        250
                 ....*....|....
gi 818695931 474 T--YETLKDKVEVA 485
Cdd:PRK08665 306 DvdWEKLREVVHLA 319
PRK08115 PRK08115
vitamin B12-dependent ribonucleotide reductase;
424-484 9.56e-05

vitamin B12-dependent ribonucleotide reductase;


Pssm-ID: 236152 [Multi-domain]  Cd Length: 858  Bit Score: 45.99  E-value: 9.56e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 818695931 424 EPGIFNRQSALDMRPARR-APAEFGTNPCGEIILRPYEFCNL-SIAIARREDT------YETLKDKVEV 484
Cdd:PRK08115 451 EPGIFFIDNANEMTNAKAyGQKVVATNPCGEQPLAPYSVCNLaAINLANMADKetktvdYEKLKRTVEV 519
RRF pfam01765
Ribosome recycling factor; The ribosome recycling factor (RRF / ribosome release factor) ...
 12-144 9.16e-04

Ribosome recycling factor; The ribosome recycling factor (RRF / ribosome release factor) dissociates the ribosome from the mRNA after termination of translation, and is essential bacterial growth. Thus ribosomes are "recycled" and ready for another round of protein synthesis.


Pssm-ID: 460316  Cd Length: 158  Bit Score: 40.50  E-value: 9.16e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818695931   12 IDRIKIEFPKT---------IVKRDGR---VVPFE---IQKIEKAISSCfeDLGKNPltpvgelaQRVVNIIGAKYTKPT 76
Cdd:pfam01765  14 LDNIKVDYYGSptplnqlaqVSVPEARtlvITPWDksmLKAIEKAILAS--DLGLNP--------QNDGQVIRLPIPPLT 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 818695931   77 VEQVQdtvELVLQAAGEFEAAKNYI--IYRVEHAKLRdsrpipKEVAKAFSESDV-YFENQIQKFQffDKY 144
Cdd:pfam01765  84 EERRK---ELVKQAKKLAEEAKVAIrnIRRDANDKLK------KLEKDEISEDELkKAEKEIQKLT--DKY 143
RNR_Alpha pfam17975
Ribonucleotide reductase alpha domain; This is the alpha helical domain of ribonucleotide ...
 144-202 1.06e-03

Ribonucleotide reductase alpha domain; This is the alpha helical domain of ribonucleotide reductases. Family members include Ribonucleotide reductase (RNR, EC:1.17.4.1), which catalyze the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs divide into three classes on the basis of their metallocofactor usage. This domain is found in Class II. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Many organizms have more than one class of RNR present in their genomes. Ribonucleotide reductase is an oligomeric enzyme composed of a large sub-unit (700 to 1000 residues) and a small sub-unit (300 to 400 residues) - class II RNRs are less complex, using the small molecule B12 in place of the small chain. Some family members carry ATP cone domain which acts as a functional regulator. Competitive binding of ATP and dATP to an N-terminal ATP-cone domain determines enzyme activity. As the ratio of dATP to ATP increases above a certain threshold, the enzyme activity is turned off. Substrate nucleotides are recognized by relatively simple H-bonding interactions at the N-terminus of one or more alpha helices. In the monomeric class II RNR, the effector binds in a pocket formed by helices in a 130 amino acid insertion which constitutes this domain.


Pssm-ID: 465599 [Multi-domain]  Cd Length: 101  Bit Score: 39.15  E-value: 1.06e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 818695931  144 YSRFNYDLGRRETWKETVDRSVD----FLRELSGGKLESGVYKRIRNS-------ILEMKATPSMR-LLAM 202
Cdd:pfam17975  29 YSRWKPDEGRNENWWETVKRVVEgninLQPRWIEDHGLGWDQSKAQKEaqelydrIYGMKFLPPGRgLWIM 99
 
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.
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