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Conserved domains on  [gi|1697057048|gb|QDH57590|]
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radical SAM protein [Bacteroides xylanisolvens]

Protein Classification

7-carboxy-7-deazaguanine synthase QueE( domain architecture ID 11427350)

7-carboxy-7-deazaguanine synthase QueE is a radical SAM protein that catalyzes the complex heterocyclic radical-mediated conversion of 6-carboxy-5,6,7,8-tetrahydropterin (CPH4) to 7-carboxy-7-deazaguanine (CDG), a common step in the biosynthesis of all 7-deazapurine-containing compounds

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
QueE COG0602
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic ...
 3-180 9.76e-83

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: 243.12  E-value: 9.76e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048   3 KINEIFYSLQGEGYHTGTPAIFVRFSGCNLKCDFCDTQH----EEGKMMTDDEIIAEVKKYPAVTVVLTGGEPSLWID-D 77
Cdd:COG0602     3 PIVEIFYSIQGEGALAGRPAVFVRLAGCNLRCSWCDTKYawdgEGGKRMSAEEILEEVAALGARHVVITGGEPLLQDDlA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048  78 ELIDRLHQAGKYVTIETNGTRPLPAAIDWVTCSPKQGAKL----------AIDRMDEVKVVYEGQ-DISIFELLPAEH-- 144
Cdd:COG0602    83 ELLEALKDAGYEVALETNGTLPIPAGIDWVTVSPKLPSSGeeednrenleVLRRADELKFVVADEtDLEEAEELLARLdf 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1697057048 145 ---FFLQPCSCN----NTASTVDCVMRHPKWRLSLQTHKLIDI 180
Cdd:COG0602   163 rcpVYLQPVWGNkleeNTELLAEWCLAHPNVRLSPQLHKLLGV 205
 
Name Accession Description Interval E-value
QueE COG0602
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic ...
 3-180 9.76e-83

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: 243.12  E-value: 9.76e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048   3 KINEIFYSLQGEGYHTGTPAIFVRFSGCNLKCDFCDTQH----EEGKMMTDDEIIAEVKKYPAVTVVLTGGEPSLWID-D 77
Cdd:COG0602     3 PIVEIFYSIQGEGALAGRPAVFVRLAGCNLRCSWCDTKYawdgEGGKRMSAEEILEEVAALGARHVVITGGEPLLQDDlA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048  78 ELIDRLHQAGKYVTIETNGTRPLPAAIDWVTCSPKQGAKL----------AIDRMDEVKVVYEGQ-DISIFELLPAEH-- 144
Cdd:COG0602    83 ELLEALKDAGYEVALETNGTLPIPAGIDWVTVSPKLPSSGeeednrenleVLRRADELKFVVADEtDLEEAEELLARLdf 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1697057048 145 ---FFLQPCSCN----NTASTVDCVMRHPKWRLSLQTHKLIDI 180
Cdd:COG0602   163 rcpVYLQPVWGNkleeNTELLAEWCLAHPNVRLSPQLHKLLGV 205
queE_Cx14CxxC TIGR04508
7-carboxy-7-deazaguanine synthase, Cx14CxxC type; In the pathway of 7-cyano-7-deazaquanine ...
 4-181 8.73e-68

7-carboxy-7-deazaguanine synthase, Cx14CxxC type; In the pathway of 7-cyano-7-deazaquanine (preQ0) biosynthesis, the radical SAM enzyme QueE is quite variable. This model describes a variant form in which the three-Cys motif that binds the signature 4Fe-4S cluster takes the form Cx14CxxC, as in Burkholderia multivorans ATCC 17616. The crystal structure is known.


Pssm-ID: 275301  Cd Length: 208  Bit Score: 205.32  E-value: 8.73e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048   4 INEIFYSLQGEGYHTGTPAIFVRFSGCNL-----------KCDFCDTQ------HEEGKMMTDDEIIAEVKK-YPAVT-- 63
Cdd:TIGR04508   3 VKEIFYTLQGEGAQAGRAAVFCRFAGCNLwsgreqdrakaVCRFCDTDfvgtdgENGGKFADADALAAHIAAlWPGGGat 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048  64 --VVLTGGEPSLWIDDELIDRLHQAGKYVTIETNGTRPLPAAIDWVTCSPKQGAKLAIDRMDEVKVVY--EGQDISIFEL 139
Cdd:TIGR04508  83 pyVVCTGGEPLLQLDDALIDALHARGFEVAIETNGTLPAPEGIDWICVSPKAGAPLVQTSGDELKLVYpqPGLLPELFEA 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1697057048 140 LPAEHFFLQPC----SCNNTASTVDCVMRHPKWRLSLQTHKLIDIR 181
Cdd:TIGR04508 163 LDFEHFLLQPMdgpqRAANTQAAIDYCLAHPRWRLSLQTHKYLGIP 208
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 29-105 7.71e-13

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: 62.93  E-value: 7.71e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048  29 GCNLKCDFCDT----QHEEGKMMTDDEIIAEVKKY---PAVTVVLTGGEPSLWID-----DELIDRLHQAGKYVTIETNG 96
Cdd:pfam04055   4 GCNLRCTYCAFpsirARGKGRELSPEEILEEAKELkrlGVEVVILGGGEPLLLPDlvellERLLKLELAEGIRITLETNG 83


                  ....*....
gi 1697057048  97 TRPLPAAID 105
Cdd:pfam04055  84 TLLDEELLE 92
moaA PRK00164
GTP 3',8-cyclase MoaA;
30-98 5.75e-06

GTP 3',8-cyclase MoaA;


Pssm-ID: 234672 [Multi-domain]  Cd Length: 331  Bit Score: 45.13  E-value: 5.75e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048  30 CNLKCDFCdtqHEEGKM--------MTDDEI-------IAE-VKKypavtVVLTGGEPSLWID-DELIDRLHQ--AGKYV 90
Cdd:PRK00164   27 CNFRCTYC---MPEGYLpflpkeelLSLEEIerlvrafVALgVRK-----VRLTGGEPLLRKDlEDIIAALAAlpGIRDL 98


                  ....*...
gi 1697057048  91 TIETNGTR 98
Cdd:PRK00164   99 ALTTNGYL 106
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 29-105 1.11e-05

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: 43.86  E-value: 1.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048  29 GCNLKCDFCDTQHEEGKMM-------TDDEIIAEVKKYPAVTVVLTGGEPSLWIDD-ELIDRLHQ--AGKYVTIETNGTR 98
Cdd:cd01335     6 GCNLNCGFCSNPASKGRGPesppeieEILDIVLEAKERGVEVVILTGGEPLLYPELaELLRRLKKelPGFEISIETNGTL 85


                  ....*..
gi 1697057048  99 PLPAAID 105
Cdd:cd01335    86 LTEELLK 92
 
Name Accession Description Interval E-value
QueE COG0602
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic ...
 3-180 9.76e-83

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: 243.12  E-value: 9.76e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048   3 KINEIFYSLQGEGYHTGTPAIFVRFSGCNLKCDFCDTQH----EEGKMMTDDEIIAEVKKYPAVTVVLTGGEPSLWID-D 77
Cdd:COG0602     3 PIVEIFYSIQGEGALAGRPAVFVRLAGCNLRCSWCDTKYawdgEGGKRMSAEEILEEVAALGARHVVITGGEPLLQDDlA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048  78 ELIDRLHQAGKYVTIETNGTRPLPAAIDWVTCSPKQGAKL----------AIDRMDEVKVVYEGQ-DISIFELLPAEH-- 144
Cdd:COG0602    83 ELLEALKDAGYEVALETNGTLPIPAGIDWVTVSPKLPSSGeeednrenleVLRRADELKFVVADEtDLEEAEELLARLdf 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1697057048 145 ---FFLQPCSCN----NTASTVDCVMRHPKWRLSLQTHKLIDI 180
Cdd:COG0602   163 rcpVYLQPVWGNkleeNTELLAEWCLAHPNVRLSPQLHKLLGV 205
queE_Cx14CxxC TIGR04508
7-carboxy-7-deazaguanine synthase, Cx14CxxC type; In the pathway of 7-cyano-7-deazaquanine ...
 4-181 8.73e-68

7-carboxy-7-deazaguanine synthase, Cx14CxxC type; In the pathway of 7-cyano-7-deazaquanine (preQ0) biosynthesis, the radical SAM enzyme QueE is quite variable. This model describes a variant form in which the three-Cys motif that binds the signature 4Fe-4S cluster takes the form Cx14CxxC, as in Burkholderia multivorans ATCC 17616. The crystal structure is known.


Pssm-ID: 275301  Cd Length: 208  Bit Score: 205.32  E-value: 8.73e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048   4 INEIFYSLQGEGYHTGTPAIFVRFSGCNL-----------KCDFCDTQ------HEEGKMMTDDEIIAEVKK-YPAVT-- 63
Cdd:TIGR04508   3 VKEIFYTLQGEGAQAGRAAVFCRFAGCNLwsgreqdrakaVCRFCDTDfvgtdgENGGKFADADALAAHIAAlWPGGGat 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048  64 --VVLTGGEPSLWIDDELIDRLHQAGKYVTIETNGTRPLPAAIDWVTCSPKQGAKLAIDRMDEVKVVY--EGQDISIFEL 139
Cdd:TIGR04508  83 pyVVCTGGEPLLQLDDALIDALHARGFEVAIETNGTLPAPEGIDWICVSPKAGAPLVQTSGDELKLVYpqPGLLPELFEA 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1697057048 140 LPAEHFFLQPC----SCNNTASTVDCVMRHPKWRLSLQTHKLIDIR 181
Cdd:TIGR04508 163 LDFEHFLLQPMdgpqRAANTQAAIDYCLAHPRWRLSLQTHKYLGIP 208
rSAM_QueE_Clost TIGR03963
putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, clostridial; Members of ...
 3-100 8.44e-24

putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, clostridial; Members of this radical SAM domain protein family appear to be the Clostridial form of the queuosine biosynthesis protein QueE. QueE is involved in making preQ0 (7-cyano-7-deazaquanine), a precursor of both the bacterial/eukaryotic modified tRNA base queuosine and the archaeal modified base archaeosine. Members occur in preQ0 operons species that lack members of related protein family TIGR03365. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 188478 [Multi-domain]  Cd Length: 219  Bit Score: 93.22  E-value: 8.44e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048   3 KINEIFYSLQGEGYHTGTPAIFVRFSGCNLKCDFCDTQHEEGK-----MMTDDEIIAEVKKYPAVTVVLTGGEPSLWID- 76
Cdd:TIGR03963   2 KVVEKFVSINGEGKRAGELATFIRFAGCNLNCSYCDTTWANDKdcpyeLLSADEIYDYIKETGVKNVTLTGGEPLLQENi 81

                          90       100
                  ....*....|....*....|....*
gi 1697057048  77 DELID-RLHQAGKYVTIETNGTRPL 100
Cdd:TIGR03963  82 DELIElLLGDAGLEVEIETNGSVDI 106
PflA COG1180
Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, ...
 7-107 5.73e-15

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


Pssm-ID: 440793 [Multi-domain]  Cd Length: 242  Bit Score: 70.21  E-value: 5.73e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048   7 IFYSLQGEGYH--TGTPA--IFvrFSGCNLKCDFC---DTQHEE----GKMMTDDEIIAEVKKYPAVT-----VVLTGGE 70
Cdd:COG1180     6 RIYGISPFSTVdgPGSIRlsVF--TQGCNLRCPYChnpEISQGRpdaaGRELSPEELVEEALKDRGFLdscggVTFSGGE 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1697057048  71 PSLWIDD--ELIDRLHQAGKYVTIETNGTRPLPAA------IDWV 107
Cdd:COG1180    84 PTLQPEFllDLAKLAKELGLHTALDTNGYIPEEALeellpyLDAV 128
SkfB COG0535
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
 30-110 1.59e-14

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: 67.24  E-value: 1.59e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048  30 CNLKCDFC--DTQHEEGKMMTDDE---IIAEVKKYPAVTVVLTGGEPSLWID-DELIDRLHQAGKYVTIETNGT------ 97
Cdd:COG0535    10 CNLRCKHCyaDAGPKRPGELSTEEakrILDELAELGVKVVGLTGGEPLLRPDlFELVEYAKELGIRVNLSTNGTllteel 89

                          90
                  ....*....|....*
gi 1697057048  98 --RPLPAAIDWVTCS 110
Cdd:COG0535    90 aeRLAEAGLDHVTIS 104
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 29-105 7.71e-13

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: 62.93  E-value: 7.71e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048  29 GCNLKCDFCDT----QHEEGKMMTDDEIIAEVKKY---PAVTVVLTGGEPSLWID-----DELIDRLHQAGKYVTIETNG 96
Cdd:pfam04055   4 GCNLRCTYCAFpsirARGKGRELSPEEILEEAKELkrlGVEVVILGGGEPLLLPDlvellERLLKLELAEGIRITLETNG 83


                  ....*....
gi 1697057048  97 TRPLPAAID 105
Cdd:pfam04055  84 TLLDEELLE 92
AslB COG0641
Sulfatase maturation enzyme AslB, radical SAM superfamily [Posttranslational modification, ...
 28-97 2.72e-08

Sulfatase maturation enzyme AslB, radical SAM superfamily [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440406 [Multi-domain]  Cd Length: 349  Bit Score: 52.30  E-value: 2.72e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048  28 SGCNLKCDFC---DTQHEEGKMMTD-------DEIIAEVKKYPAVTVVLTGGEPSLWID--DELIDRLHQAGKY-----V 90
Cdd:COG0641     9 SRCNLRCSYCyysEGDEGSRRRMSEetaekaiDFLIESSGPGKELTITFFGGEPLLNFDfiKEIVEYARKYAKKgkkirF 88


                  ....*..
gi 1697057048  91 TIETNGT 97
Cdd:COG0641    89 SIQTNGT 95
Fer4_14 pfam13394
4Fe-4S single cluster domain;
23-97 4.00e-08

4Fe-4S single cluster domain;


Pssm-ID: 433171 [Multi-domain]  Cd Length: 115  Bit Score: 49.28  E-value: 4.00e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048  23 IFVrfSGCNLKCDFCDTQ-------HEEGKMMTDDEIIAEVKK--YPAVTVVLTGGEPSLWIDDE----LIDRLHQ--AG 87
Cdd:pfam13394   1 LFV--SGCNHSCPGCDNKetwkfnyGEPFTEELEDQIIADLKDsyIKRQGLVLTGGEPLHPWNLPvllkLLKRVKEeyPS 78

                          90
                  ....*....|
gi 1697057048  88 KYVTIETNGT 97
Cdd:pfam13394  79 KDIWLETGYT 88
NrdG2 TIGR02495
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
 18-107 5.97e-08

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: 50.05  E-value: 5.97e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048  18 TGTPAIFVRFSGCNLKCDFCDTQH----EEGKMMTDDEIIAEVKKYPAVT--VVLTGGEPSLWID-DELIDRLHQAGKYV 90
Cdd:TIGR02495  14 PGKLAFTIFLQGCNLKCPYCHNPLliprRGSGEIEVEELLEFLRRRRGLLdgVVITGGEPTLQAGlPDFLREVRELGFEV 93

                          90       100
                  ....*....|....*....|....
gi 1697057048  91 TIETNGTRPLPAA-------IDWV 107
Cdd:TIGR02495  94 KLDTNGSNPRRLEelleeglVDYV 117
TM0948 COG5014
Uncharacterized conserved protein TM0948, MoaA-related, radical SAM superfamily [General ...
 29-97 9.10e-07

Uncharacterized conserved protein TM0948, MoaA-related, radical SAM superfamily [General function prediction only];


Pssm-ID: 444038  Cd Length: 261  Bit Score: 47.29  E-value: 9.10e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048  29 GCNLKCDFC------DTQHEEGKMMTDDEI------IAEVKKYPAVTvvLTGGEPSLWIDD--ELIDRLHQAGKYVTIET 94
Cdd:COG5014    49 GCNLRCGFCwswrfrDFPLTIGKFYSPEEVaerlieIARERGYRQVR--LSGGEPTIGFEHllKVLELFSERGLTFILET 126


                  ...
gi 1697057048  95 NGT 97
Cdd:COG5014   127 NGI 129
moaA PRK00164
GTP 3',8-cyclase MoaA;
30-98 5.75e-06

GTP 3',8-cyclase MoaA;


Pssm-ID: 234672 [Multi-domain]  Cd Length: 331  Bit Score: 45.13  E-value: 5.75e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048  30 CNLKCDFCdtqHEEGKM--------MTDDEI-------IAE-VKKypavtVVLTGGEPSLWID-DELIDRLHQ--AGKYV 90
Cdd:PRK00164   27 CNFRCTYC---MPEGYLpflpkeelLSLEEIerlvrafVALgVRK-----VRLTGGEPLLRKDlEDIIAALAAlpGIRDL 98


                  ....*...
gi 1697057048  91 TIETNGTR 98
Cdd:PRK00164   99 ALTTNGYL 106
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 29-105 1.11e-05

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: 43.86  E-value: 1.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048  29 GCNLKCDFCDTQHEEGKMM-------TDDEIIAEVKKYPAVTVVLTGGEPSLWIDD-ELIDRLHQ--AGKYVTIETNGTR 98
Cdd:cd01335     6 GCNLNCGFCSNPASKGRGPesppeieEILDIVLEAKERGVEVVILTGGEPLLYPELaELLRRLKKelPGFEISIETNGTL 85


                  ....*..
gi 1697057048  99 PLPAAID 105
Cdd:cd01335    86 LTEELLK 92
Fer4_12 pfam13353
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
 11-98 8.81e-05

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: 40.62  E-value: 8.81e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048  11 LQGEGYHTgtpAIFVrfSGCNLKCDFC---DTQH-EEGKMMTD---DEIIAEVKKYPAVTVVLTGGEPSLWIDD--ELID 81
Cdd:pfam13353   1 VNGPGVRC---SLFV--SGCNHHCKGCfnpETWDfKYGKPFTEeleDEIIEDLAKPYIQGLTLSGGEPLLNAEAllELVK 75

                          90
                  ....*....|....*...
gi 1697057048  82 RLHQAGKYVTI-ETNGTR 98
Cdd:pfam13353  76 RVREECPEKDIwLWTGYT 93
SCM_rSAM_ScmF TIGR04251
SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in ...
 29-133 2.11e-04

SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in Syntrophobacter fumaroxidans MPOB, Chlorobium limicola DSM 245, Methanocella paludicola SANAE, and delta proteobacterium NaphS2 contains two PqqE-like radical SAM/SPASM domain proteins, a PqqD homolog, and a conserved hypothetical protein. These components suggest modification of a ribosomally produced peptide precursor, but the precursor has not been identified. Of the two PqqE homologs of the cassette, this family is the more distant in sequence.


Pssm-ID: 211974 [Multi-domain]  Cd Length: 353  Bit Score: 40.59  E-value: 2.11e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048  29 GCNLKCDFC--DTQHEEGKMMTDD-------EIIAEVKKYPAVTVVLTGGEPSLWID-DELIDRLHQAGKYVTIETNGTr 98
Cdd:TIGR04251  13 GCNLKCRHCwiDPKYQGEGEQHPSldpslfrSIIRQAIPLGLTSVKLTGGEPLLHPAiGEILECIGENNLQLSVETNGL- 91

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1697057048  99 plpaaidwvTCSPKQGAKLAIDRMDEVKVVYEGQD 133
Cdd:TIGR04251  92 ---------LCTPQTARDLASCETPFVSVSLDGVD 117
MoaA COG2896
GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) [Coenzyme transport and ...
 30-98 3.82e-04

GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) [Coenzyme transport and metabolism]; GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) is part of the Pathway/BioSystem: Molybdopterin biosynthesis


Pssm-ID: 442141 [Multi-domain]  Cd Length: 329  Bit Score: 40.04  E-value: 3.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048  30 CNLKCDFCdtqHEEGKM--------MTDDEI--IAE------VKKypavtVVLTGGEPSLWID-DELIDRLHQAG--KYV 90
Cdd:COG2896    24 CNFRCTYC---MPEEGYqflpkeelLSFEEIerLVRafvelgVRK-----IRLTGGEPLLRKDlPELIARLAALPgiEDL 95


                  ....*...
gi 1697057048  91 TIETNGTR 98
Cdd:COG2896    96 ALTTNGSL 103
PLN02951 PLN02951
Molybderin biosynthesis protein CNX2
 30-102 7.45e-04

Molybderin biosynthesis protein CNX2


Pssm-ID: 215513 [Multi-domain]  Cd Length: 373  Bit Score: 38.97  E-value: 7.45e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1697057048  30 CNLKCDFCdtQHEEG-------KMMTDDEIIAEVKKYPAVTVV---LTGGEPSLWID-DELIDRLHQAG--KYVTIETNG 96
Cdd:PLN02951   68 CNLRCQYC--MPEEGveltpksHLLSQDEIVRLAGLFVAAGVDkirLTGGEPTLRKDiEDICLQLSSLKglKTLAMTTNG 145


                  ....*....
gi 1697057048  97 ---TRPLPA 102
Cdd:PLN02951  146 itlSRKLPR 154
 
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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