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Conserved domains on  [gi|492499074|ref|WP_005866833|]
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MULTISPECIES: radical SAM protein [Parabacteroides]

Protein Classification

radical SAM protein( domain architecture ID 11425241)

radical SAM protein generates radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity; contains a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; transfer of a single electron from the iron-sulfur cluster to SAM leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical

Gene Ontology:  GO:0003824|GO:0051539|GO:1904047
PubMed:  17936058|11222759|18307109|17291766|15450488
SCOP:  3000308

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SkfB COG0535
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
 57-193 4.54e-37

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: 131.95  E-value: 4.54e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074  57 FVMISITESCNLSCSGCWVSAGGRKA--LSIAQLNGIITESKRQGSYFFGILGGEPLMYKGLLETMEKHSD--CYFQLFT 132
Cdd:COG0535    1 RLQIELTNRCNLRCKHCYADAGPKRPgeLSTEEAKRILDELAELGVKVVGLTGGEPLLRPDLFELVEYAKElgIRVNLST 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 492499074 133 NATLLTEEVAFRLKKMGNVTPLISIEGLKDES-DIRRGKDGVLDRTIRGVRACRKARLIFGV 193
Cdd:COG0535   81 NGTLLTEELAERLAEAGLDHVTISLDGVDPEThDKIRGVPGAFDKVLEAIKLLKEAGIPVGI 142
AslB super family cl33987
Sulfatase maturation enzyme AslB, radical SAM superfamily [Posttranslational modification, ...
 58-336 1.92e-20

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


The actual alignment was detected with superfamily member COG0641:

Pssm-ID: 440406 [Multi-domain]  Cd Length: 349  Bit Score: 91.59  E-value: 1.92e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074  58 VMISITESCNLSCSGCWVSAG---GRKALSIAQLNGII----TESKRQGSYFFGILGGEPLM----YKGLLETMEKHS-- 124
Cdd:COG0641    3 LVLKPTSRCNLRCSYCYYSEGdegSRRRMSEETAEKAIdfliESSGPGKELTITFFGGEPLLnfdfIKEIVEYARKYAkk 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074 125 --DCYFQLFTNATLLTEEVAFRLKKMgNVTPLISIEGLKDESDIRR----GKdGVLDRTIRGVRACRKARLIFGVAASIC 198
Cdd:COG0641   83 gkKIRFSIQTNGTLLDDEWIDFLKEN-GFSVGISLDGPKEIHDRNRvtknGK-GSFDRVMRNIKLLKEHGVEVNIRCTVT 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074 199 RSNYEDLVSRahIERMAREGtlylWYYIY-RPVGAVPNVENALTKEQIRDF-----RRFIVEQRRDAPLFIIDTYWDD-- 270
Cdd:COG0641  161 RENLDDPEEL--YDFLKELG----FRSIQfNPVVEEGEADYSLTPEDYGEFlielfDEWLERDGGKIFVREFDILLAGll 234

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 492499074 271 -KGKALCPAATGMSHHISPSGAVEFCPPLQMARDFINGD--ASNLVELFRDSMFLADLRKMTAETSRGC 336
Cdd:COG0641  235 pPCSSPCVGAGGNYLVVDPDGDIYPCDEFVGDPEFRLGNvfDGSLAELLDSPKLRAFGREKNVLLDEEC 303
 
Name Accession Description Interval E-value
SkfB COG0535
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
 57-193 4.54e-37

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: 131.95  E-value: 4.54e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074  57 FVMISITESCNLSCSGCWVSAGGRKA--LSIAQLNGIITESKRQGSYFFGILGGEPLMYKGLLETMEKHSD--CYFQLFT 132
Cdd:COG0535    1 RLQIELTNRCNLRCKHCYADAGPKRPgeLSTEEAKRILDELAELGVKVVGLTGGEPLLRPDLFELVEYAKElgIRVNLST 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 492499074 133 NATLLTEEVAFRLKKMGNVTPLISIEGLKDES-DIRRGKDGVLDRTIRGVRACRKARLIFGV 193
Cdd:COG0535   81 NGTLLTEELAERLAEAGLDHVTISLDGVDPEThDKIRGVPGAFDKVLEAIKLLKEAGIPVGI 142
AslB COG0641
Sulfatase maturation enzyme AslB, radical SAM superfamily [Posttranslational modification, ...
 58-336 1.92e-20

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


Pssm-ID: 440406 [Multi-domain]  Cd Length: 349  Bit Score: 91.59  E-value: 1.92e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074  58 VMISITESCNLSCSGCWVSAG---GRKALSIAQLNGII----TESKRQGSYFFGILGGEPLM----YKGLLETMEKHS-- 124
Cdd:COG0641    3 LVLKPTSRCNLRCSYCYYSEGdegSRRRMSEETAEKAIdfliESSGPGKELTITFFGGEPLLnfdfIKEIVEYARKYAkk 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074 125 --DCYFQLFTNATLLTEEVAFRLKKMgNVTPLISIEGLKDESDIRR----GKdGVLDRTIRGVRACRKARLIFGVAASIC 198
Cdd:COG0641   83 gkKIRFSIQTNGTLLDDEWIDFLKEN-GFSVGISLDGPKEIHDRNRvtknGK-GSFDRVMRNIKLLKEHGVEVNIRCTVT 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074 199 RSNYEDLVSRahIERMAREGtlylWYYIY-RPVGAVPNVENALTKEQIRDF-----RRFIVEQRRDAPLFIIDTYWDD-- 270
Cdd:COG0641  161 RENLDDPEEL--YDFLKELG----FRSIQfNPVVEEGEADYSLTPEDYGEFlielfDEWLERDGGKIFVREFDILLAGll 234

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 492499074 271 -KGKALCPAATGMSHHISPSGAVEFCPPLQMARDFINGD--ASNLVELFRDSMFLADLRKMTAETSRGC 336
Cdd:COG0641  235 pPCSSPCVGAGGNYLVVDPDGDIYPCDEFVGDPEFRLGNvfDGSLAELLDSPKLRAFGREKNVLLDEEC 303
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 60-252 6.02e-15

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: 73.14  E-value: 6.02e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074  60 ISITESCNLSCSGCWVSAGGRKALSIAQLNGIITESKRQ----GSYFFGILGGEPLMYKGLLETME---KHSDC-YFQLF 131
Cdd:cd01335    1 LELTRGCNLNCGFCSNPASKGRGPESPPEIEEILDIVLEakerGVEVVILTGGEPLLYPELAELLRrlkKELPGfEISIE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074 132 TNATLLTEEVAFRLKKMGNVTPLISIEGL-KDESDIRRGKDGVLDRTIRGVRACRKARLIFGVAASICRSNYEDLVSRAH 210
Cdd:cd01335   81 TNGTLLTEELLKELKELGLDGVGVSLDSGdEEVADKIRGSGESFKERLEALKELREAGLGLSTTLLVGLGDEDEEDDLEE 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 492499074 211 IERMAREGTLYLWY-YIYRPVGAVPNvENALTKEQIRDFRRFI 252
Cdd:cd01335  161 LELLAEFRSPDRVSlFRLLPEEGTPL-ELAAPVVPAEKLLRLI 202
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 62-193 2.40e-14

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: 70.25  E-value: 2.40e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074   62 ITESCNLSCSGCWVSA----GGRKALSIAQLNGIITESKRQGSYFFGILGGEPLMYKGLLE------TMEKHSDCYFQLF 131
Cdd:pfam04055   1 ITRGCNLRCTYCAFPSirarGKGRELSPEEILEEAKELKRLGVEVVILGGGEPLLLPDLVEllerllKLELAEGIRITLE 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 492499074  132 TNATLLTEEVAFRLKKMGNVTPLISIEGLKDESDIRRGKDGVLDRTIRGVRACRKARLIFGV 193
Cdd:pfam04055  81 TNGTLLDEELLELLKEAGLDRVSIGLESGDDEVLKLINRGHTFEEVLEALELLREAGIPVVT 142
SCM_rSAM_ScmF TIGR04251
SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in ...
 62-216 9.95e-11

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: 62.55  E-value: 9.95e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074   62 ITESCNLSCSGCWV-----SAGGR-KALSIAQLNGIITESKRQGSYFFGILGGEPLMYKGLLETME--KHSDCYFQLFTN 133
Cdd:TIGR04251  10 LTEGCNLKCRHCWIdpkyqGEGEQhPSLDPSLFRSIIRQAIPLGLTSVKLTGGEPLLHPAIGEILEciGENNLQLSVETN 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074  134 ATLLTEEVAFRLKKMGNVTPLISIEGLKDES-DIRRGKDGVLDRTIRGVRACRKARLIFGVAASICRSNyedlvsRAHIE 212
Cdd:TIGR04251  90 GLLCTPQTARDLASCETPFVSVSLDGVDAAThDWMRGVKGAFDKAVRGIHNLVEAGIHPQIIMTVTRRN------VGQME 163


                  ....
gi 492499074  213 RMAR 216
Cdd:TIGR04251 164 QIVR 167
SPASM_rSAM cd21128
Iron-sulfur cluster-binding SPASM domain of an uncharacterized group of radical SAM proteins; ...
 274-342 2.24e-06

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 may contain one auxillary Fe-S cluster with an open coordination site, similar to the auxillary 4Fe-4S cluster in Bacillus circulans butirosin biosynthetic enzyme BtrN, but missing one conserved cysteine in the binding site.


Pssm-ID: 410619 [Multi-domain]  Cd Length: 65  Bit Score: 44.67  E-value: 2.24e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 492499074 274 ALCPAATGMSHHISPSGAVEFCPPLQMARDFINGDAsnLVELFRDSMFLAdLRKMTAEtSRGCILLEDP 342
Cdd:cd21128    1 GGCIAGRRRYLHVNPDGDVEPCPFVPFSFGNIKEKS--LKEAWNSPFFRE-YRKQQPF-LRPCPMIDPP 65
N_Twi_rSAM NF033640
twitch domain-containing radical SAM protein; Members of this family are unusual among radical ...
 21-171 3.36e-04

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: 42.64  E-value: 3.36e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074  21 SPRLIwkfmYNFGWRNFRNMAAFEKRQALGAPFFPAFVMISITESCNLSCSGCWvsaggrKALS------IAQLNGIITE 94
Cdd:NF033640  79 SLRQE----SNERWAKHIEDAIKSTDEDGSDDVNPRYLDLRFGNLCNLKCRMCG------PHSSsswakeAKKLGGPKLG 148

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074  95 SKRQGSYF------------------FGILGGEPLMYKG---LLETMEKH---SDCYFQLFTNATLLTEEVAF---RLKK 147
Cdd:NF033640 149 DKKKISWFedeefwkwleellpslkeIYFAGGEPLLIKEhykLLEKLVEKgraKNIELRYNTNLTVLPDKLKDlldLWKK 228

                        170       180
                 ....*....|....*....|....*
gi 492499074 148 MGNVTPLISIEGLKDESD-IRRGKD 171
Cdd:NF033640 229 FKSVSISASIDGVGERNEyIRYGSK 253
 
Name Accession Description Interval E-value
SkfB COG0535
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
 57-193 4.54e-37

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: 131.95  E-value: 4.54e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074  57 FVMISITESCNLSCSGCWVSAGGRKA--LSIAQLNGIITESKRQGSYFFGILGGEPLMYKGLLETMEKHSD--CYFQLFT 132
Cdd:COG0535    1 RLQIELTNRCNLRCKHCYADAGPKRPgeLSTEEAKRILDELAELGVKVVGLTGGEPLLRPDLFELVEYAKElgIRVNLST 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 492499074 133 NATLLTEEVAFRLKKMGNVTPLISIEGLKDES-DIRRGKDGVLDRTIRGVRACRKARLIFGV 193
Cdd:COG0535   81 NGTLLTEELAERLAEAGLDHVTISLDGVDPEThDKIRGVPGAFDKVLEAIKLLKEAGIPVGI 142
AslB COG0641
Sulfatase maturation enzyme AslB, radical SAM superfamily [Posttranslational modification, ...
 58-336 1.92e-20

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


Pssm-ID: 440406 [Multi-domain]  Cd Length: 349  Bit Score: 91.59  E-value: 1.92e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074  58 VMISITESCNLSCSGCWVSAG---GRKALSIAQLNGII----TESKRQGSYFFGILGGEPLM----YKGLLETMEKHS-- 124
Cdd:COG0641    3 LVLKPTSRCNLRCSYCYYSEGdegSRRRMSEETAEKAIdfliESSGPGKELTITFFGGEPLLnfdfIKEIVEYARKYAkk 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074 125 --DCYFQLFTNATLLTEEVAFRLKKMgNVTPLISIEGLKDESDIRR----GKdGVLDRTIRGVRACRKARLIFGVAASIC 198
Cdd:COG0641   83 gkKIRFSIQTNGTLLDDEWIDFLKEN-GFSVGISLDGPKEIHDRNRvtknGK-GSFDRVMRNIKLLKEHGVEVNIRCTVT 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074 199 RSNYEDLVSRahIERMAREGtlylWYYIY-RPVGAVPNVENALTKEQIRDF-----RRFIVEQRRDAPLFIIDTYWDD-- 270
Cdd:COG0641  161 RENLDDPEEL--YDFLKELG----FRSIQfNPVVEEGEADYSLTPEDYGEFlielfDEWLERDGGKIFVREFDILLAGll 234

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 492499074 271 -KGKALCPAATGMSHHISPSGAVEFCPPLQMARDFINGD--ASNLVELFRDSMFLADLRKMTAETSRGC 336
Cdd:COG0641  235 pPCSSPCVGAGGNYLVVDPDGDIYPCDEFVGDPEFRLGNvfDGSLAELLDSPKLRAFGREKNVLLDEEC 303
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 60-252 6.02e-15

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: 73.14  E-value: 6.02e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074  60 ISITESCNLSCSGCWVSAGGRKALSIAQLNGIITESKRQ----GSYFFGILGGEPLMYKGLLETME---KHSDC-YFQLF 131
Cdd:cd01335    1 LELTRGCNLNCGFCSNPASKGRGPESPPEIEEILDIVLEakerGVEVVILTGGEPLLYPELAELLRrlkKELPGfEISIE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074 132 TNATLLTEEVAFRLKKMGNVTPLISIEGL-KDESDIRRGKDGVLDRTIRGVRACRKARLIFGVAASICRSNYEDLVSRAH 210
Cdd:cd01335   81 TNGTLLTEELLKELKELGLDGVGVSLDSGdEEVADKIRGSGESFKERLEALKELREAGLGLSTTLLVGLGDEDEEDDLEE 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 492499074 211 IERMAREGTLYLWY-YIYRPVGAVPNvENALTKEQIRDFRRFI 252
Cdd:cd01335  161 LELLAEFRSPDRVSlFRLLPEEGTPL-ELAAPVVPAEKLLRLI 202
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 62-193 2.40e-14

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: 70.25  E-value: 2.40e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074   62 ITESCNLSCSGCWVSA----GGRKALSIAQLNGIITESKRQGSYFFGILGGEPLMYKGLLE------TMEKHSDCYFQLF 131
Cdd:pfam04055   1 ITRGCNLRCTYCAFPSirarGKGRELSPEEILEEAKELKRLGVEVVILGGGEPLLLPDLVEllerllKLELAEGIRITLE 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 492499074  132 TNATLLTEEVAFRLKKMGNVTPLISIEGLKDESDIRRGKDGVLDRTIRGVRACRKARLIFGV 193
Cdd:pfam04055  81 TNGTLLDEELLELLKEAGLDRVSIGLESGDDEVLKLINRGHTFEEVLEALELLREAGIPVVT 142
SCM_rSAM_ScmF TIGR04251
SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in ...
 62-216 9.95e-11

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: 62.55  E-value: 9.95e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074   62 ITESCNLSCSGCWV-----SAGGR-KALSIAQLNGIITESKRQGSYFFGILGGEPLMYKGLLETME--KHSDCYFQLFTN 133
Cdd:TIGR04251  10 LTEGCNLKCRHCWIdpkyqGEGEQhPSLDPSLFRSIIRQAIPLGLTSVKLTGGEPLLHPAIGEILEciGENNLQLSVETN 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074  134 ATLLTEEVAFRLKKMGNVTPLISIEGLKDES-DIRRGKDGVLDRTIRGVRACRKARLIFGVAASICRSNyedlvsRAHIE 212
Cdd:TIGR04251  90 GLLCTPQTARDLASCETPFVSVSLDGVDAAThDWMRGVKGAFDKAVRGIHNLVEAGIHPQIIMTVTRRN------VGQME 163


                  ....
gi 492499074  213 RMAR 216
Cdd:TIGR04251 164 QIVR 167
rSAM_pep_methan TIGR04083
putative peptide-modifying radical SAM enzyme, Mhun_1560 family; Members of this family are ...
 58-185 2.40e-09

putative peptide-modifying radical SAM enzyme, Mhun_1560 family; Members of this family are radical SAM enzymes, homologous to a variety of other peptide-modifying radical SAM, and found primarily in methanogenic archaea.


Pssm-ID: 274966 [Multi-domain]  Cd Length: 376  Bit Score: 58.59  E-value: 2.40e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074   58 VMISITESCNLSCSGCWVSAGGRKALSIAQLNGIITESK--RQGSYFFGILGGEPLM-----YKGLLETMEK---HSDCY 127
Cdd:TIGR04083   2 VMIIPTLGCPSKCKYCWSSEETSPVMSIDTVKDIVEWLKdfRDDRVTFTFHGGEPLLagadfYRQALPLLSEglaHLKPE 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 492499074  128 FQLFTNATLLTEEVAFRLKKMgNVTPLISIEGLKDESDIRRGkDGVLDRTIRGVRACR 185
Cdd:TIGR04083  82 FAMQTNLWLMTPELAEIFAEY-NVPIGSSIDGPEEINDYQRG-EGYYQKTMKGYEIAK 137
SCM_rSAM_ScmE TIGR04250
SynChlorMet cassette radical SAM/SPASM protein ScmE; A biosynthesis cassette found in ...
 55-209 6.06e-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: 51.01  E-value: 6.06e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074   55 PAFVMISITESCNLSCSGC--WVSAGG-RKALSIAQLNGIITESKRQGSYFFGILGGEPLMYKGLLETMEK--HSDCYFQ 129
Cdd:TIGR04250   2 PRSVDIDITGRCNLRCRYCshFSSAAEtPTDLETAEWLRFFRELNRCSVLRVVLSGGEPFMRSDFREIIDGivKNRMRFS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074  130 LFTNATLLTEEVAFRLKKMGNV-TPLISIEGLKDES-DIRRGkDGVLDRTIRGVRACRKARLIFGVAASICRSNYEDLVS 207
Cdd:TIGR04250  82 ILSNGTLITDAIASFLAATRRCdYVQVSIDGSTPGThDRLRG-TGSFLQAVEGIELLRKHAIPVVVRVTIHRWNVDDLRP 160


                  ..
gi 492499074  208 RA 209
Cdd:TIGR04250 161 IA 162
SPASM_rSAM cd21128
Iron-sulfur cluster-binding SPASM domain of an uncharacterized group of radical SAM proteins; ...
 274-342 2.24e-06

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 may contain one auxillary Fe-S cluster with an open coordination site, similar to the auxillary 4Fe-4S cluster in Bacillus circulans butirosin biosynthetic enzyme BtrN, but missing one conserved cysteine in the binding site.


Pssm-ID: 410619 [Multi-domain]  Cd Length: 65  Bit Score: 44.67  E-value: 2.24e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 492499074 274 ALCPAATGMSHHISPSGAVEFCPPLQMARDFINGDAsnLVELFRDSMFLAdLRKMTAEtSRGCILLEDP 342
Cdd:cd21128    1 GGCIAGRRRYLHVNPDGDVEPCPFVPFSFGNIKEKS--LKEAWNSPFFRE-YRKQQPF-LRPCPMIDPP 65
N_Twi_rSAM NF033640
twitch domain-containing radical SAM protein; Members of this family are unusual among radical ...
 21-171 3.36e-04

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: 42.64  E-value: 3.36e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074  21 SPRLIwkfmYNFGWRNFRNMAAFEKRQALGAPFFPAFVMISITESCNLSCSGCWvsaggrKALS------IAQLNGIITE 94
Cdd:NF033640  79 SLRQE----SNERWAKHIEDAIKSTDEDGSDDVNPRYLDLRFGNLCNLKCRMCG------PHSSsswakeAKKLGGPKLG 148

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074  95 SKRQGSYF------------------FGILGGEPLMYKG---LLETMEKH---SDCYFQLFTNATLLTEEVAF---RLKK 147
Cdd:NF033640 149 DKKKISWFedeefwkwleellpslkeIYFAGGEPLLIKEhykLLEKLVEKgraKNIELRYNTNLTVLPDKLKDlldLWKK 228

                        170       180
                 ....*....|....*....|....*
gi 492499074 148 MGNVTPLISIEGLKDESD-IRRGKD 171
Cdd:NF033640 229 FKSVSISASIDGVGERNEyIRYGSK 253
TM0948 COG5014
Uncharacterized conserved protein TM0948, MoaA-related, radical SAM superfamily [General ...
 66-163 1.36e-03

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


Pssm-ID: 444038  Cd Length: 261  Bit Score: 39.97  E-value: 1.36e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492499074  66 CNLSCSGCWVSAGGRKALSIAQL-------NGIITESKRQGSYFFGILGGEP-LMYKGLLETME--KHSDCYFQLFTNAT 135
Cdd:COG5014   50 CNLRCGFCWSWRFRDFPLTIGKFyspeevaERLIEIARERGYRQVRLSGGEPtIGFEHLLKVLElfSERGLTFILETNGI 129

                         90       100       110
                 ....*....|....*....|....*....|
gi 492499074 136 LLT--EEVAFRLKKMGNVTPLISIEGLKDE 163
Cdd:COG5014  130 LIGydRELARELASFRNIVVRVSIKGCTPE 159
 
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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