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Conserved domains on  [gi|1956819558|ref|WP_200597246|]
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radical SAM protein [Noviherbaspirillum pedocola]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rSAM_Geo_metal super family cl37417
putative metalloenzyme radical SAM/SPASM domain maturase; This model describes a family of ...
 7-332 6.39e-37

putative metalloenzyme radical SAM/SPASM domain maturase; This model describes a family of radical SAM/SPASM enzymes largely from the deltaproteobacteria. The family is most closely related to radical SAM enzyme family regularly in archaea in the vicinity of tungsten-containing oxidoreductases. A single member of the family in archaea may correspond to multiple tungsten enzymes, e.g. five in Pyrococcus furiosus. Therefore, the lack of a conserved gene neighborhood for members of this family in deltaprotebacteria suggests members may be involved in the maturation of multiple metalloenzymes.


The actual alignment was detected with superfamily member TIGR04311:

Pssm-ID: 275116 [Multi-domain]  Cd Length: 423  Bit Score: 137.07  E-value: 6.39e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558   7 LPRFVQIEPVGQCNLRCRMCpiafrPESAPGH--PAATMDVDVFKRLIDEFGAIEELHLQGMGEPMMHPRFFEMVSYAAG 84
Cdd:TIGR04311   1 YPSKLFVEVTTRCNLRCRMC-----VKQAGGSdiPEGDMTPETFRALEPALPHLEALVLNGIGEPLLHPDLEAFIALARQ 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558  85 RGIR---VSTNTNMTLMTEARAAKCVSSGLDTLHASLDAAEAEAYEAIRLRASFTKVLRNLRRIVAAKEAAASALPHVKL 161
Cdd:TIGR04311  76 AMPEtgwIGFQSNGLLLTEERARSLLDAGLDRICLSVDSLSPELFGKVRGGGDLGDLERAFAALAAARRRCGRPKLRLGV 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558 162 VAVVMRRNLTQLPALVRLAAREGVESLSVQHL---------------CHDFA---------------------------- 198
Cdd:TIGR04311 156 EFVLMRDNLRELPAVLRWAAARGADFALVSHLlpydaaaaeqslfgpNTDAAiaifqrwraraaeqgldlrryfdvvwky 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558 199 -----ESSLPEQYKPMRA-------FIDEETLLQDERERIAM---HFDAARIEAQRLGIELRLPNLTPRQHapdvpgpKR 263
Cdd:TIGR04311 236 gkspeEKRLVDFVRQMRAearrqgiFLNLPNLLQRDDGAVDDveaVFARAEAVAEECGLELRLPALAPRFE-------RR 308

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558 264 CDWPWRG-AYVSYDGSAMPC--------C-MVATPDRIN---FGNMAREGVAQVWNNTAYGEFRA-ALSSDTPpeVCSSC 329
Cdd:TIGR04311 309 CDFVEDGgAFISWDGKVHPCyflwhrysCfLDGWEKQVRpkvFGNVTERDLLEIWNGPEFRAFREeVLEYDYP--YCSNC 386


                  ...
gi 1956819558 330 AVY 332
Cdd:TIGR04311 387 TVA 389
 
Name Accession Description Interval E-value
rSAM_Geo_metal TIGR04311
putative metalloenzyme radical SAM/SPASM domain maturase; This model describes a family of ...
 7-332 6.39e-37

putative metalloenzyme radical SAM/SPASM domain maturase; This model describes a family of radical SAM/SPASM enzymes largely from the deltaproteobacteria. The family is most closely related to radical SAM enzyme family regularly in archaea in the vicinity of tungsten-containing oxidoreductases. A single member of the family in archaea may correspond to multiple tungsten enzymes, e.g. five in Pyrococcus furiosus. Therefore, the lack of a conserved gene neighborhood for members of this family in deltaprotebacteria suggests members may be involved in the maturation of multiple metalloenzymes.


Pssm-ID: 275116 [Multi-domain]  Cd Length: 423  Bit Score: 137.07  E-value: 6.39e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558   7 LPRFVQIEPVGQCNLRCRMCpiafrPESAPGH--PAATMDVDVFKRLIDEFGAIEELHLQGMGEPMMHPRFFEMVSYAAG 84
Cdd:TIGR04311   1 YPSKLFVEVTTRCNLRCRMC-----VKQAGGSdiPEGDMTPETFRALEPALPHLEALVLNGIGEPLLHPDLEAFIALARQ 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558  85 RGIR---VSTNTNMTLMTEARAAKCVSSGLDTLHASLDAAEAEAYEAIRLRASFTKVLRNLRRIVAAKEAAASALPHVKL 161
Cdd:TIGR04311  76 AMPEtgwIGFQSNGLLLTEERARSLLDAGLDRICLSVDSLSPELFGKVRGGGDLGDLERAFAALAAARRRCGRPKLRLGV 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558 162 VAVVMRRNLTQLPALVRLAAREGVESLSVQHL---------------CHDFA---------------------------- 198
Cdd:TIGR04311 156 EFVLMRDNLRELPAVLRWAAARGADFALVSHLlpydaaaaeqslfgpNTDAAiaifqrwraraaeqgldlrryfdvvwky 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558 199 -----ESSLPEQYKPMRA-------FIDEETLLQDERERIAM---HFDAARIEAQRLGIELRLPNLTPRQHapdvpgpKR 263
Cdd:TIGR04311 236 gkspeEKRLVDFVRQMRAearrqgiFLNLPNLLQRDDGAVDDveaVFARAEAVAEECGLELRLPALAPRFE-------RR 308

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558 264 CDWPWRG-AYVSYDGSAMPC--------C-MVATPDRIN---FGNMAREGVAQVWNNTAYGEFRA-ALSSDTPpeVCSSC 329
Cdd:TIGR04311 309 CDFVEDGgAFISWDGKVHPCyflwhrysCfLDGWEKQVRpkvFGNVTERDLLEIWNGPEFRAFREeVLEYDYP--YCSNC 386


                  ...
gi 1956819558 330 AVY 332
Cdd:TIGR04311 387 TVA 389
SkfB COG0535
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
 10-146 2.65e-33

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: 120.78  E-value: 2.65e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558  10 FVQIEPVGQCNLRCRMCPIAFRPEsapghPAATMDVDVFKRLIDEFGA--IEELHLQGmGEPMMHPRFFEMVSYAAGRGI 87
Cdd:COG0535     1 RLQIELTNRCNLRCKHCYADAGPK-----RPGELSTEEAKRILDELAElgVKVVGLTG-GEPLLRPDLFELVEYAKELGI 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558  88 RVSTNTNMTLMTEARAAKCVSSGLDTLHASLDAAEAEAYEAIR-LRASFTKVLRNLRRIV 146
Cdd:COG0535    75 RVNLSTNGTLLTEELAERLAEAGLDHVTISLDGVDPETHDKIRgVPGAFDKVLEAIKLLK 134
SPASM pfam13186
Iron-sulfur cluster-binding domain; This domain occurs as an additional C-terminal iron-sulfur ...
 264-329 8.30e-14

Iron-sulfur cluster-binding domain; This domain occurs as an additional C-terminal iron-sulfur cluster binding domain in many radical SAM domain, pfam04055 proteins. The domain occurs in a number of proteins that modify a protein to become an active enzyme, or a peptide to become a ribosomal natural product. The domain is named SPASM because it occurs in the maturases of Subilitosin, PQQ, Anaerobic Sulfatases, and Mycofactocin.


Pssm-ID: 433020 [Multi-domain]  Cd Length: 66  Bit Score: 65.58  E-value: 8.30e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1956819558 264 CDWPWRGAYVSYDGSAMPCCMVATPDRINFGNMAREGVAQVWNNTAYGEFRaALSSDTPPEVCSSC 329
Cdd:pfam13186   1 CFAGWTSLVILPDGDVYPCFDDDFVGPIVLGNIREQSLAEIWNSPKYREFR-KLGKFALIELCRDC 65
SPASM cd21109
Iron-sulfur cluster-binding SPASM domain; This iron-sulfur cluster-binding domain is named ...
 263-329 8.02e-13

Iron-sulfur cluster-binding SPASM domain; This iron-sulfur cluster-binding domain is named SPASM after the biochemically characterized members, AlbA, PqqE, anSME, and MftC, which are involved in Subtilosin A, Pyrroloquinoline quinone, Anaerobic Sulfatase, and Mycofactocin maturation, respectively. SPASM occurs as an additional C-terminal domain in many peptide-modifying enzymes of the radical S-adenosylmethionine (SAM) superfamily. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster.


Pssm-ID: 410609 [Multi-domain]  Cd Length: 65  Bit Score: 62.83  E-value: 8.02e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1956819558 263 RCDWPWRGAYVSYDGSAMPCCMvATPDRINFGNMAREGVAQVWNNTAYGEFRAALsSDTPPEVCSSC 329
Cdd:cd21109     1 PCPAPWTSLYITPDGDVYPCCF-DVNEELKLGNIREQSLKEIWNSEKYREFRKLL-LDGKIKLCKNC 65
N_Twi_rSAM NF033640
twitch domain-containing radical SAM protein; Members of this family are unusual among radical ...
 264-329 3.22e-09

twitch domain-containing radical SAM protein; Members of this family are unusual among radical SAM proteins in several ways. First, the N-terminal region consists of an iron-sulfur cluster-binding twitch domain (half of a SPASM domain), something usually found C-terminal to the radical SAM domain. Second, the radical SAM domains in many of the members of this family score poorly vs. the Pfam HMM, PF04055 (version 19), used to identify radical SAM. Lastly, the majority of members sequenced to date come from uncultured bacteria from marine or aquifer sources rather than from conventionally cultured bacterial isolates. The function is unknown.


Pssm-ID: 468123 [Multi-domain]  Cd Length: 396  Bit Score: 57.66  E-value: 3.22e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1956819558 264 CDWPWRGAYVSYDGSAMPCCMvATPDRINFGNMAREGVAQVWNNTAYGEFRAALSSDTPPEVCSSC 329
Cdd:NF033640    5 CPLPWTHLYIHPDGNVRPCCH-ARDDKGPLGNLKETSLEEIWNSDYMKKIRKKMLNGERPPGCEKC 69
PRK13745 PRK13745
anaerobic sulfatase-maturation protein;
6-100 1.84e-04

anaerobic sulfatase-maturation protein;


Pssm-ID: 237489 [Multi-domain]  Cd Length: 412  Bit Score: 42.93  E-value: 1.84e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558   6 ALPRFVQIEPVGQ-CNLRCRMCPIAFRPESAPGHPAATMDVDVFKRLIDEFgaIEELHLQGM------GEPMMHPRFFEM 78
Cdd:PRK13745   10 AKPLYIMLKPVGAvCNLACDYCYYLEKSKLYQENPKHVMSDELLEKFIKEY--INSQTMPQVlftwhgGETLMRPLSFYK 87

                          90       100
                  ....*....|....*....|....*...
gi 1956819558  79 VS------YAAGRGIRVSTNTNMTLMTE 100
Cdd:PRK13745   88 KAlelqkkYARGRQIDNCIQTNGTLLTD 115
 
Name Accession Description Interval E-value
rSAM_Geo_metal TIGR04311
putative metalloenzyme radical SAM/SPASM domain maturase; This model describes a family of ...
 7-332 6.39e-37

putative metalloenzyme radical SAM/SPASM domain maturase; This model describes a family of radical SAM/SPASM enzymes largely from the deltaproteobacteria. The family is most closely related to radical SAM enzyme family regularly in archaea in the vicinity of tungsten-containing oxidoreductases. A single member of the family in archaea may correspond to multiple tungsten enzymes, e.g. five in Pyrococcus furiosus. Therefore, the lack of a conserved gene neighborhood for members of this family in deltaprotebacteria suggests members may be involved in the maturation of multiple metalloenzymes.


Pssm-ID: 275116 [Multi-domain]  Cd Length: 423  Bit Score: 137.07  E-value: 6.39e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558   7 LPRFVQIEPVGQCNLRCRMCpiafrPESAPGH--PAATMDVDVFKRLIDEFGAIEELHLQGMGEPMMHPRFFEMVSYAAG 84
Cdd:TIGR04311   1 YPSKLFVEVTTRCNLRCRMC-----VKQAGGSdiPEGDMTPETFRALEPALPHLEALVLNGIGEPLLHPDLEAFIALARQ 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558  85 RGIR---VSTNTNMTLMTEARAAKCVSSGLDTLHASLDAAEAEAYEAIRLRASFTKVLRNLRRIVAAKEAAASALPHVKL 161
Cdd:TIGR04311  76 AMPEtgwIGFQSNGLLLTEERARSLLDAGLDRICLSVDSLSPELFGKVRGGGDLGDLERAFAALAAARRRCGRPKLRLGV 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558 162 VAVVMRRNLTQLPALVRLAAREGVESLSVQHL---------------CHDFA---------------------------- 198
Cdd:TIGR04311 156 EFVLMRDNLRELPAVLRWAAARGADFALVSHLlpydaaaaeqslfgpNTDAAiaifqrwraraaeqgldlrryfdvvwky 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558 199 -----ESSLPEQYKPMRA-------FIDEETLLQDERERIAM---HFDAARIEAQRLGIELRLPNLTPRQHapdvpgpKR 263
Cdd:TIGR04311 236 gkspeEKRLVDFVRQMRAearrqgiFLNLPNLLQRDDGAVDDveaVFARAEAVAEECGLELRLPALAPRFE-------RR 308

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558 264 CDWPWRG-AYVSYDGSAMPC--------C-MVATPDRIN---FGNMAREGVAQVWNNTAYGEFRA-ALSSDTPpeVCSSC 329
Cdd:TIGR04311 309 CDFVEDGgAFISWDGKVHPCyflwhrysCfLDGWEKQVRpkvFGNVTERDLLEIWNGPEFRAFREeVLEYDYP--YCSNC 386


                  ...
gi 1956819558 330 AVY 332
Cdd:TIGR04311 387 TVA 389
SkfB COG0535
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
 10-146 2.65e-33

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: 120.78  E-value: 2.65e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558  10 FVQIEPVGQCNLRCRMCPIAFRPEsapghPAATMDVDVFKRLIDEFGA--IEELHLQGmGEPMMHPRFFEMVSYAAGRGI 87
Cdd:COG0535     1 RLQIELTNRCNLRCKHCYADAGPK-----RPGELSTEEAKRILDELAElgVKVVGLTG-GEPLLRPDLFELVEYAKELGI 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558  88 RVSTNTNMTLMTEARAAKCVSSGLDTLHASLDAAEAEAYEAIR-LRASFTKVLRNLRRIV 146
Cdd:COG0535    75 RVNLSTNGTLLTEELAERLAEAGLDHVTISLDGVDPETHDKIRgVPGAFDKVLEAIKLLK 134
AslB COG0641
Sulfatase maturation enzyme AslB, radical SAM superfamily [Posttranslational modification, ...
 13-333 2.60e-21

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


Pssm-ID: 440406 [Multi-domain]  Cd Length: 349  Bit Score: 93.13  E-value: 2.60e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558  13 IEPVGQCNLRCRMCpiaFRPESAPGHPaATMDVDVFKRLID----EFGAIEELHL--QGmGEPMMHPRFF-EMVSYA--- 82
Cdd:COG0641     5 LKPTSRCNLRCSYC---YYSEGDEGSR-RRMSEETAEKAIDflieSSGPGKELTItfFG-GEPLLNFDFIkEIVEYArky 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558  83 --AGRGIRVSTNTNMTLMTEARAAKCVSSG------LD---TLHaslDaaeaeayeaiRLR------ASFTKVLRNLRRI 145
Cdd:COG0641    80 akKGKKIRFSIQTNGTLLDDEWIDFLKENGfsvgisLDgpkEIH---D----------RNRvtkngkGSFDRVMRNIKLL 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558 146 VAAKeaaasalPHVKLVAVVMRRNLTQLPALVRLAAREGVESLSVQHL-CHDFAESSL-PEQY-KPMRAFIDEetLLQDE 222
Cdd:COG0641   147 KEHG-------VEVNIRCTVTRENLDDPEELYDFLKELGFRSIQFNPVvEEGEADYSLtPEDYgEFLIELFDE--WLERD 217

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558 223 RERIA-MHFDAArieaqrlgielrLPNLTPRQHAPDVPGPKRCdwpwrgAYVSYDGSAMPC-CMVATPDRInFGNMAREG 300
Cdd:COG0641   218 GGKIFvREFDIL------------LAGLLPPCSSPCVGAGGNY------LVVDPDGDIYPCdEFVGDPEFR-LGNVFDGS 278

                         330       340       350
                  ....*....|....*....|....*....|...
gi 1956819558 301 VAQVWNNTAYGEFRAALSSDTPPEvCSSCAVYR 333
Cdd:COG0641   279 LAELLDSPKLRAFGREKNVLLDEE-CRSCPYLP 310
SPASM pfam13186
Iron-sulfur cluster-binding domain; This domain occurs as an additional C-terminal iron-sulfur ...
 264-329 8.30e-14

Iron-sulfur cluster-binding domain; This domain occurs as an additional C-terminal iron-sulfur cluster binding domain in many radical SAM domain, pfam04055 proteins. The domain occurs in a number of proteins that modify a protein to become an active enzyme, or a peptide to become a ribosomal natural product. The domain is named SPASM because it occurs in the maturases of Subilitosin, PQQ, Anaerobic Sulfatases, and Mycofactocin.


Pssm-ID: 433020 [Multi-domain]  Cd Length: 66  Bit Score: 65.58  E-value: 8.30e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1956819558 264 CDWPWRGAYVSYDGSAMPCCMVATPDRINFGNMAREGVAQVWNNTAYGEFRaALSSDTPPEVCSSC 329
Cdd:pfam13186   1 CFAGWTSLVILPDGDVYPCFDDDFVGPIVLGNIREQSLAEIWNSPKYREFR-KLGKFALIELCRDC 65
SCM_rSAM_ScmF TIGR04251
SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in ...
 19-193 1.04e-13

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: 71.02  E-value: 1.04e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558  19 CNLRCRMCPIAFRPESApGHPAATMDVDVFKRLIDEFG--AIEELHLQGmGEPMMHPRFFEMVSYAAGRGIRVSTNTNMT 96
Cdd:TIGR04251  14 CNLKCRHCWIDPKYQGE-GEQHPSLDPSLFRSIIRQAIplGLTSVKLTG-GEPLLHPAIGEILECIGENNLQLSVETNGL 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558  97 LMTEARAAKCVSSGLDTLHASLDAAEAEAYEAIR-LRASFTKVLRNLRRIVAAKEaaasalpHVKLVAVVMRRNLTQLPA 175
Cdd:TIGR04251  92 LCTPQTARDLASCETPFVSVSLDGVDAATHDWMRgVKGAFDKAVRGIHNLVEAGI-------HPQIIMTVTRRNVGQMEQ 164

                         170
                  ....*....|....*...
gi 1956819558 176 LVRLAAREGVESLSVQHL 193
Cdd:TIGR04251 165 IVRLAESLGAESVKFNHV 182
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 19-145 6.60e-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: 65.63  E-value: 6.60e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558  19 CNLRCRMCpiaFRPESAPGHPAATMDVDVFKRLIDEFGA--IEELHLqGMGEPMMHPRFFEMVSYAA----GRGIRVSTN 92
Cdd:pfam04055   5 CNLRCTYC---AFPSIRARGKGRELSPEEILEEAKELKRlgVEVVIL-GGGEPLLLPDLVELLERLLklelAEGIRITLE 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1956819558  93 TNMTLMTEARAAKCVSSGLDTLHASLDAAEAEAYEAIRLRASFTKVLRNLRRI 145
Cdd:pfam04055  81 TNGTLLDEELLELLKEAGLDRVSIGLESGDDEVLKLINRGHTFEEVLEALELL 133
SPASM cd21109
Iron-sulfur cluster-binding SPASM domain; This iron-sulfur cluster-binding domain is named ...
 263-329 8.02e-13

Iron-sulfur cluster-binding SPASM domain; This iron-sulfur cluster-binding domain is named SPASM after the biochemically characterized members, AlbA, PqqE, anSME, and MftC, which are involved in Subtilosin A, Pyrroloquinoline quinone, Anaerobic Sulfatase, and Mycofactocin maturation, respectively. SPASM occurs as an additional C-terminal domain in many peptide-modifying enzymes of the radical S-adenosylmethionine (SAM) superfamily. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster.


Pssm-ID: 410609 [Multi-domain]  Cd Length: 65  Bit Score: 62.83  E-value: 8.02e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1956819558 263 RCDWPWRGAYVSYDGSAMPCCMvATPDRINFGNMAREGVAQVWNNTAYGEFRAALsSDTPPEVCSSC 329
Cdd:cd21109     1 PCPAPWTSLYITPDGDVYPCCF-DVNEELKLGNIREQSLKEIWNSEKYREFRKLL-LDGKIKLCKNC 65
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 13-144 6.86e-10

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: 58.11  E-value: 6.86e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558  13 IEPVGQCNLRCRMCPIAFRPESAPGHPAATMDVDVFKRLIDEFGAieELHLQGMGEPMMHPRFFEMVSYAAGR--GIRVS 90
Cdd:cd01335     1 LELTRGCNLNCGFCSNPASKGRGPESPPEIEEILDIVLEAKERGV--EVVILTGGEPLLYPELAELLRRLKKElpGFEIS 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1956819558  91 TNTNMTLMTEARAAKCVSSGLDTLHASLDAAEAEAYEAIRLRA-SFTKVLRNLRR 144
Cdd:cd01335    79 IETNGTLLTEELLKELKELGLDGVGVSLDSGDEEVADKIRGSGeSFKERLEALKE 133
N_Twi_rSAM NF033640
twitch domain-containing radical SAM protein; Members of this family are unusual among radical ...
 264-329 3.22e-09

twitch domain-containing radical SAM protein; Members of this family are unusual among radical SAM proteins in several ways. First, the N-terminal region consists of an iron-sulfur cluster-binding twitch domain (half of a SPASM domain), something usually found C-terminal to the radical SAM domain. Second, the radical SAM domains in many of the members of this family score poorly vs. the Pfam HMM, PF04055 (version 19), used to identify radical SAM. Lastly, the majority of members sequenced to date come from uncultured bacteria from marine or aquifer sources rather than from conventionally cultured bacterial isolates. The function is unknown.


Pssm-ID: 468123 [Multi-domain]  Cd Length: 396  Bit Score: 57.66  E-value: 3.22e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1956819558 264 CDWPWRGAYVSYDGSAMPCCMvATPDRINFGNMAREGVAQVWNNTAYGEFRAALSSDTPPEVCSSC 329
Cdd:NF033640    5 CPLPWTHLYIHPDGNVRPCCH-ARDDKGPLGNLKETSLEEIWNSDYMKKIRKKMLNGERPPGCEKC 69
SCM_rSAM_ScmE TIGR04250
SynChlorMet cassette radical SAM/SPASM protein ScmE; A biosynthesis cassette found in ...
 8-307 2.93e-07

SynChlorMet cassette radical SAM/SPASM protein ScmE; 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 closer in sequence.


Pssm-ID: 211973 [Multi-domain]  Cd Length: 358  Bit Score: 51.40  E-value: 2.93e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558   8 PRFVQIEPVGQCNLRCRMCPIAfrpeSAPGHPAATMDVDVFKRLIDEFG--AIEELHLQGmGEPMMHPRFFEMVSYAAGR 85
Cdd:TIGR04250   2 PRSVDIDITGRCNLRCRYCSHF----SSAAETPTDLETAEWLRFFRELNrcSVLRVVLSG-GEPFMRSDFREIIDGIVKN 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558  86 GIRVSTNTNMTLMTEARAAKCVSSG-LDTLHASLDAAEAEAYEAIRLRASFTKVLRNLRRIvaakeaAASALPhVKLVAV 164
Cdd:TIGR04250  77 RMRFSILSNGTLITDAIASFLAATRrCDYVQVSIDGSTPGTHDRLRGTGSFLQAVEGIELL------RKHAIP-VVVRVT 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558 165 VMRRNLTQLPALVRLAARE------GVESLSVQHLCHDFAES---SLPEQYKPMrafideETLLQDERE---RIAMHFDA 232
Cdd:TIGR04250 150 IHRWNVDDLRPIAALLLDDlglpafSTNAASYMGLCRSNTDDvqlDTAERTLAM------EILLELEKEypgRISASAGP 223

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1956819558 233 ARIEAQRLGIELRLPNltprqHAPDVPGP---KRCDWPWRGAYVSYDGSAMPCCMVAtpdRINFGNMAREGVAQVWNN 307
Cdd:TIGR04250 224 LADARTWASMEQARID-----QQGNMPGRgylSGCGGIFMSLAVRADGVIVPCNQLS---HIELGRINRDSLRELWQN 293
SPASM_rSAM cd21126
Iron-sulfur cluster-binding SPASM domain of an uncharacterized group of radical SAM proteins; ...
 263-329 8.33e-07

Iron-sulfur cluster-binding SPASM domain of an uncharacterized group of radical SAM proteins; Members of this group are radical S-adenosylmethionine (SAM) enzymes with a SPASM domain, named after the biochemically characterized members, AlbA, PqqE, anSME, and MftC, which are involved in Subtilosin A, Pyrroloquinoline quinone, Anaerobic Sulfatase, and Mycofactocin maturation, respectively. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. This group appears to contain one auxillary Fe-S cluster, similar to the auxillary 4Fe-4S cluster in Bacillus circulans butirosin biosynthetic enzyme BtrN.


Pssm-ID: 410617 [Multi-domain]  Cd Length: 70  Bit Score: 45.92  E-value: 8.33e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1956819558 263 RCDWPWRGAYVSYDGSAMPCCMvatpDR---INFGNMAREGVAQVWNNTAYGEFRAA-LSSDTPPEVCSSC 329
Cdd:cd21126     2 HCWRMWHSCVITWDGKVVPCCF----DKdasHKLGDLKTQSFKELWCGKKYQQFRKQlLKSRSEIEICKNC 68
COG2100 COG2100
Uncharacterized Fe-S cluster-containing enzyme, radical SAM superfamily [General function ...
 12-119 2.75e-06

Uncharacterized Fe-S cluster-containing enzyme, radical SAM superfamily [General function prediction only];


Pssm-ID: 441703 [Multi-domain]  Cd Length: 344  Bit Score: 48.37  E-value: 2.75e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558  12 QIEPVGQCNLRCRMCPIAFRPESApgHPAATMDVDV------FKRLIDEFGAIEELHLQGMGEPMMHPRFFEMVSYAAG- 84
Cdd:COG2100    39 QVRPTTGCNLNCIFCSVDAGPHSR--TRQAEYIVDPeylvewFEKVARFKGKGVEAHIDGVGEPLLYPYIVELVKGLKEi 116

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1956819558  85 RGI-RVSTNTNMTLMTEARAAKCVSSGLDTLHASLD 119
Cdd:COG2100   117 KGVkVVSMQTNGTLLSEKLIDELEEAGLDRINLSID 152
MoaA COG2896
GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) [Coenzyme transport and ...
 19-186 2.21e-05

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: 45.44  E-value: 2.21e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558  19 CNLRCRMC----PIAFRPesapghPAATMDVDVFKRLIDEFGA--IEELHLQGmGEPMMH---PRFFEMVsyAAGRGIR- 88
Cdd:COG2896    24 CNFRCTYCmpeeGYQFLP------KEELLSFEEIERLVRAFVElgVRKIRLTG-GEPLLRkdlPELIARL--AALPGIEd 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558  89 VSTNTNMTLMTEaRAAKCVSSGLDTLHASLDAAEAEAYEAIRLRASFTKVLRNLRRIVaakeaaASALPHVKLVAVVMR- 167
Cdd:COG2896    95 LALTTNGSLLAR-YAEALKAAGLDRVNVSLDSLDPERFRRITRRDDLDKVLAGIDAAL------AAGLTPVKINAVVMRg 167

                         170
                  ....*....|....*....
gi 1956819558 168 RNLTQLPALVRLAAREGVE 186
Cdd:COG2896   168 VNDDEILDLLEFAKERGID 186
SPASM_Cmo-like cd21121
Iron-sulfur cluster-binding SPASM domain of tungsten-containing aldehyde ferredoxin ...
 269-329 4.72e-05

Iron-sulfur cluster-binding SPASM domain of tungsten-containing aldehyde ferredoxin oxidoreductase cofactor-modifying protein and similar proteins; This group is composed of Pyrococcus furiosus tungsten-containing aldehyde ferredoxin oxidoreductase (AOR; EC 1.2.7.5) cofactor-modifying protein, encoded by the cmo gene, and similar proteins. AOR cofactor-modifying protein is involved in the biosynthesis of a molybdopterin-based tungsten cofactor. Members of this group are radical S-adenosylmethionine (SAM) enzymes with a SPASM domain. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. This group appears to contain one auxillary Fe-S cluster, similar to the auxillary 4Fe-4S cluster in Bacillus circulans butirosin biosynthetic enzyme BtrN.


Pssm-ID: 410612 [Multi-domain]  Cd Length: 80  Bit Score: 41.13  E-value: 4.72e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1956819558 269 RGAYVSYDGSAMPCCMVATP------------DRINFGNMAREGVAQVWNNTAYGEFRAA-LSSDTPPevCSSC 329
Cdd:cd21121     9 RSAFIRVDGEVSPCYFLWHPyrsyingrekevKRVIFGNVKEESLLEIWNSPEYRAFRENvLRGDYPP--CRDC 80
rSAM_ocin_clost TIGR04068
Cys-rich peptide radical SAM maturase CcpM; Members of this family are radical SAM enzymes ...
 18-145 1.38e-04

Cys-rich peptide radical SAM maturase CcpM; Members of this family are radical SAM enzymes that occur next to clostridial Cys-rich predicted bacteriocin (or other class of ribosomal natural product) precursors (see families TIGR04065 and TIGR04067). They include a TIGR04085 C-terminal additional 4Fe4S cluster-binding domain that is associated with peptide modification by radical SAM enzymes, and they are proposed to be ribosomal natural product maturases. The gene symbol ccpM is assigned, for Clostridial Cys-rich Peptide Maturase. [Cellular processes, Toxin production and resistance]


Pssm-ID: 274958 [Multi-domain]  Cd Length: 459  Bit Score: 43.44  E-value: 1.38e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558  18 QCNLRCRMCPIAFRPESApGHPAATMDVDVFKRLIDEF----GAIEELHLQ--GmGEPMMHPRFF-EMVSYAA----GRG 86
Cdd:TIGR04068  91 QCNLRCKYCAYSGSYDNR-VHSNKRMSIETAKKAIDFLikhsEDTDELNLGfyG-GEPLLEFELIkECVEYAKekaeGKK 168

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1956819558  87 IRVSTNTNMTLMTEARAAKCVSSGLdTLHASLDAAEAEAYEAIRLRA---SFTKVLRNLRRI 145
Cdd:TIGR04068 169 INFNMTTNGTLLTEEIIEFLYDNEF-NLTISLDGPKEIHDKNRVFADgkgSFDKIMENIKMI 229
PRK13745 PRK13745
anaerobic sulfatase-maturation protein;
6-100 1.84e-04

anaerobic sulfatase-maturation protein;


Pssm-ID: 237489 [Multi-domain]  Cd Length: 412  Bit Score: 42.93  E-value: 1.84e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558   6 ALPRFVQIEPVGQ-CNLRCRMCPIAFRPESAPGHPAATMDVDVFKRLIDEFgaIEELHLQGM------GEPMMHPRFFEM 78
Cdd:PRK13745   10 AKPLYIMLKPVGAvCNLACDYCYYLEKSKLYQENPKHVMSDELLEKFIKEY--INSQTMPQVlftwhgGETLMRPLSFYK 87

                          90       100
                  ....*....|....*....|....*...
gi 1956819558  79 VS------YAAGRGIRVSTNTNMTLMTE 100
Cdd:PRK13745   88 KAlelqkkYARGRQIDNCIQTNGTLLTD 115
moaA PRK00164
GTP 3',8-cyclase MoaA;
19-186 4.87e-03

GTP 3',8-cyclase MoaA;


Pssm-ID: 234672 [Multi-domain]  Cd Length: 331  Bit Score: 38.20  E-value: 4.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558  19 CNLRCRMC----PIAFRPesapghPAATMDVDVFKRLIDEFGA--IEELHLQGmGEPMMHPRFFEMVSY-AAGRGIR-VS 90
Cdd:PRK00164   27 CNFRCTYCmpegYLPFLP------KEELLSLEEIERLVRAFVAlgVRKVRLTG-GEPLLRKDLEDIIAAlAALPGIRdLA 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1956819558  91 TNTNMTLMtEARAAKCVSSGLDTLHASLDAAEAEAYEAIRLRASFTKVLRNLRRIVaakeaaASALPHVKLVAVVMR-RN 169
Cdd:PRK00164  100 LTTNGYLL-ARRAAALKDAGLDRVNVSLDSLDPERFKAITGRDRLDQVLAGIDAAL------AAGLTPVKVNAVLMKgVN 172

                         170
                  ....*....|....*..
gi 1956819558 170 LTQLPALVRLAAREGVE 186
Cdd:PRK00164  173 DDEIPDLLEWAKDRGIQ 189
 
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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