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Conserved domains on  [gi|2182182963|ref|WP_235585823|]
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radical SAM protein [Lactococcus lactis]

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; transfers 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:1904047|GO:0051539|GO:0003824
PubMed:  11222759|18307109|17936058
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, ...
 10-154 2.04e-28

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: 107.30  E-value: 2.04e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  10 FLTWMLTNKCNLRCKFCY--LEDYQGKELELDEINQVLDIIQDKEFTHVSLLGGEPTECEYFEYIIIQLEKLRISYSFST 87
Cdd:COG0535     1 RLQIELTNRCNLRCKHCYadAGPKRPGELSTEEAKRILDELAELGVKVVGLTGGEPLLRPDLFELVEYAKELGIRVNLST 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2182182963  88 NDQKLfrNEELIRILSKSKyLKEVLISLESPQKLINDAVRGK-GTFESAIKSVELLVKENVPTRLAMV 154
Cdd:COG0535    81 NGTLL--TEELAERLAEAG-LDHVTISLDGVDPETHDKIRGVpGAFDKVLEAIKLLKEAGIPVGINTV 145
mycofact_rSAM super family cl33223
mycofactocin radical SAM maturase; Members of this family are uncharacterized radical SAM ...
 5-306 2.11e-23

mycofactocin radical SAM maturase; Members of this family are uncharacterized radical SAM proteins from the Mycobacterium tuberculosis and many other Actinobacteria, as well as some deltaproteobacteria (e.g. Geobacter uraniireducens), firmicutes (Pelotomaculum thermopropionicum and Desulfotomaculum acetoxidans), and Chloroflexi (Thermomicrobium roseum DSM 5159 and Sphaerobacter thermophilus DSM 20745). They resemble several characterized radical SAM enzymes of peptide modification (PqqE, AlbA), and are always found next to the proposed target, TIGR03969, the putative mycofactocin precursor. [Unknown function, Enzymes of unknown specificity]


The actual alignment was detected with superfamily member TIGR03962:

Pssm-ID: 188477 [Multi-domain]  Cd Length: 339  Bit Score: 97.99  E-value: 2.11e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963   5 LKNPLFLTWMLTNKCNLRCKFCYleDYQGK----ELELDEINQVLDIIQDKEFTHVSLLGGEPT-ECEYFEYIIIQLEKl 79
Cdd:TIGR03962   8 LDAPICLTWELTYACNLACVHCL--SSSGKrdprELTTAECKRLIDELAAMQVFYVNIGGGEPTvRPDFWELMDYATAH- 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  80 RISYSFSTNDQKLfrNEELIRILSKSKYLkEVLISLESPQKLINDAVRGKGTFESAIKSVELLVKENVPT-RLAMVVTKE 158
Cdd:TIGR03962  85 GVGVKFSTNGVRI--DPEVADRLAATDYV-DVQISLDGATAEVNDAVRGAGSFDLARRAMDNLAAAGFRGfKISVVLTRR 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963 159 NNSTIQQMIDMCATLGCrELRLMPFMPMGTG--LLEKERLFMD-----YEGLVRAcsdlkiPDNLIV-TTYLKEENTAET 230
Cdd:TIGR03962 162 NFGQLDEFYALADRYGA-QLRLTRLRPSGRGadVWDELHPTAAqqrqlYDWLVAH------GERVLTgDSFFHLAALGQP 234

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963 231 LG----CGAGTAACVINSDLTLSACPVVSQTQKsieKLGN--DCSSFDYIWGTSSIFNIWRagKYRKSTSCNLCPLFEEC 304
Cdd:TIGR03962 235 LPglnmCGAGRVVCLIDPVGDVYACPFVIHEEF---LAGNvrEDGGFAGVWRTSPLFRRLR--EPQSGGACQSCSAYDSC 309


                  ..
gi 2182182963 305 GG 306
Cdd:TIGR03962 310 RG 311
 
Name Accession Description Interval E-value
SkfB COG0535
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
 10-154 2.04e-28

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: 107.30  E-value: 2.04e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  10 FLTWMLTNKCNLRCKFCY--LEDYQGKELELDEINQVLDIIQDKEFTHVSLLGGEPTECEYFEYIIIQLEKLRISYSFST 87
Cdd:COG0535     1 RLQIELTNRCNLRCKHCYadAGPKRPGELSTEEAKRILDELAELGVKVVGLTGGEPLLRPDLFELVEYAKELGIRVNLST 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2182182963  88 NDQKLfrNEELIRILSKSKyLKEVLISLESPQKLINDAVRGK-GTFESAIKSVELLVKENVPTRLAMV 154
Cdd:COG0535    81 NGTLL--TEELAERLAEAG-LDHVTISLDGVDPETHDKIRGVpGAFDKVLEAIKLLKEAGIPVGINTV 145
mycofact_rSAM TIGR03962
mycofactocin radical SAM maturase; Members of this family are uncharacterized radical SAM ...
 5-306 2.11e-23

mycofactocin radical SAM maturase; Members of this family are uncharacterized radical SAM proteins from the Mycobacterium tuberculosis and many other Actinobacteria, as well as some deltaproteobacteria (e.g. Geobacter uraniireducens), firmicutes (Pelotomaculum thermopropionicum and Desulfotomaculum acetoxidans), and Chloroflexi (Thermomicrobium roseum DSM 5159 and Sphaerobacter thermophilus DSM 20745). They resemble several characterized radical SAM enzymes of peptide modification (PqqE, AlbA), and are always found next to the proposed target, TIGR03969, the putative mycofactocin precursor. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 188477 [Multi-domain]  Cd Length: 339  Bit Score: 97.99  E-value: 2.11e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963   5 LKNPLFLTWMLTNKCNLRCKFCYleDYQGK----ELELDEINQVLDIIQDKEFTHVSLLGGEPT-ECEYFEYIIIQLEKl 79
Cdd:TIGR03962   8 LDAPICLTWELTYACNLACVHCL--SSSGKrdprELTTAECKRLIDELAAMQVFYVNIGGGEPTvRPDFWELMDYATAH- 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  80 RISYSFSTNDQKLfrNEELIRILSKSKYLkEVLISLESPQKLINDAVRGKGTFESAIKSVELLVKENVPT-RLAMVVTKE 158
Cdd:TIGR03962  85 GVGVKFSTNGVRI--DPEVADRLAATDYV-DVQISLDGATAEVNDAVRGAGSFDLARRAMDNLAAAGFRGfKISVVLTRR 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963 159 NNSTIQQMIDMCATLGCrELRLMPFMPMGTG--LLEKERLFMD-----YEGLVRAcsdlkiPDNLIV-TTYLKEENTAET 230
Cdd:TIGR03962 162 NFGQLDEFYALADRYGA-QLRLTRLRPSGRGadVWDELHPTAAqqrqlYDWLVAH------GERVLTgDSFFHLAALGQP 234

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963 231 LG----CGAGTAACVINSDLTLSACPVVSQTQKsieKLGN--DCSSFDYIWGTSSIFNIWRagKYRKSTSCNLCPLFEEC 304
Cdd:TIGR03962 235 LPglnmCGAGRVVCLIDPVGDVYACPFVIHEEF---LAGNvrEDGGFAGVWRTSPLFRRLR--EPQSGGACQSCSAYDSC 309


                  ..
gi 2182182963 305 GG 306
Cdd:TIGR03962 310 RG 311
AslB COG0641
Sulfatase maturation enzyme AslB, radical SAM superfamily [Posttranslational modification, ...
 11-306 2.46e-22

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


Pssm-ID: 440406 [Multi-domain]  Cd Length: 349  Bit Score: 95.44  E-value: 2.46e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  11 LTWMLTNKCNLRCKFCYL---EDYQGKELELDEINQVLDII----QDKEFTHVSLLGGEPT-ECEYFEYIIIQLEKL--- 79
Cdd:COG0641     3 LVLKPTSRCNLRCSYCYYsegDEGSRRRMSEETAEKAIDFLiessGPGKELTITFFGGEPLlNFDFIKEIVEYARKYakk 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  80 --RISYSFSTNDQKLfrNEELIRILSKSKYLkeVLISLESPQKlINDAVR----GKGTFESAIKSVELLVKENVPTRLAM 153
Cdd:COG0641    83 gkKIRFSIQTNGTLL--DDEWIDFLKENGFS--VGISLDGPKE-IHDRNRvtknGKGSFDRVMRNIKLLKEHGVEVNIRC 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963 154 VVTKENNSTIQQMIDMCATLGCRELRLMPFMPMGTGLL-----EKERLFMDYEGLVRACSDLKIPDNLIvTTYLKEENTA 228
Cdd:COG0641   158 TVTRENLDDPEELYDFLKELGFRSIQFNPVVEEGEADYsltpeDYGEFLIELFDEWLERDGGKIFVREF-DILLAGLLPP 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963 229 ETLGC-GAGTAACVINSDLTLSACPVVSQTQKsiEKLGN-DCSSFDYIWGTSSIFNIWRAGKYRKSTSCNLCPLFEECGG 306
Cdd:COG0641   237 CSSPCvGAGGNYLVVDPDGDIYPCDEFVGDPE--FRLGNvFDGSLAELLDSPKLRAFGREKNVLLDEECRSCPYLPLCGG 314
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 15-166 2.28e-18

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: 80.26  E-value: 2.28e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  15 LTNKCNLRCKFCYLEDYQ----GKELELDEINQVLDIIQDKEFTHVSLLGGEPTECEYFEYIIIQLEKLR----ISYSFS 86
Cdd:pfam04055   1 ITRGCNLRCTYCAFPSIRargkGRELSPEEILEEAKELKRLGVEVVILGGGEPLLLPDLVELLERLLKLElaegIRITLE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  87 TNDQKLfrNEELIRILSKSKyLKEVLISLESPQKLINDAVRGKGTFESAIKSVELLVKENVPTR--LAMVVTKENNSTIQ 164
Cdd:pfam04055  81 TNGTLL--DEELLELLKEAG-LDRVSIGLESGDDEVLKLINRGHTFEEVLEALELLREAGIPVVtdNIVGLPGETDEDLE 157


                  ..
gi 2182182963 165 QM 166
Cdd:pfam04055 158 ET 159
rSAM_skfB TIGR04403
sporulation killing factor system radical SAM maturase; Members of this family are a radical ...
 8-266 4.20e-16

sporulation killing factor system radical SAM maturase; Members of this family are a radical SAM enzyme of post-translational modification of ribosomally translated peptides. In Bacillus subtilis, the enzyme SkfB creates a sactipeptide (sulfur-to-alpha-carbon) crosslink of Cys-4 to Met-12 of the mature form of sporulation killing factor (SkfA). In Paenibacillus larvae subsp. larvae B-3650, the Met is replaced by Leu, so the modification must be different. SkfB has 2 4Fe-4S clusters, one in its radical SAM domain (pfam04055) and one in a region that somewhat resembles the SPASM domain (TIGR04085).


Pssm-ID: 275196 [Multi-domain]  Cd Length: 402  Bit Score: 78.04  E-value: 4.20e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963   8 PLFLTWMLTNKCNLRCKFCYLEdyQGK----ELELDEINQVLDIIQDKEFTHVSLLGGEPTECEYFEYIIIQLEKLRISY 83
Cdd:TIGR04403 103 PISCTLQLTNACNLSCSFCYAS--SGKpypeELATDQWIQVMQKLAAVGVADVTLTGGEAKLIKGFKEIVTVASSLFTNV 180

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  84 SFSTNDQKlFRNEElIRILSKSKYLkEVLISLESPQKlINDAVRG-KGTFESAIKSVELLVKENVPTRLAMVVTKENNST 162
Cdd:TIGR04403 181 NVFSNGLN-WRDEE-VELLSHLGNV-SVQISIDGTPE-THNLLRGrKGAFEESMNTIKRLAEANIPVIVAMTINEKNADT 256

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963 163 IQQMIDMCATLGCRELRLMPFMPMGTGLLEKERLFMDYEGLVRAC---SDLKIPDNLIVTTYLKEENTAETLGCGAGTAA 239
Cdd:TIGR04403 257 VKDVVKDCANAGARIFRAGKTLSVGRATEGFKALTDEFESCVQQQlkeARRKWGDQLNIIDWEHEESSFTTDFCTPGYLA 336

                         250       260       270
                  ....*....|....*....|....*....|..
gi 2182182963 240 CVINSDLTLSACPVVSQT-----QKSIEKLGN 266
Cdd:TIGR04403 337 WYIRADGYVTPCQLEDEPlghilRDSIGDIGS 368
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 13-205 1.34e-14

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: 71.21  E-value: 1.34e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  13 WMLTNKCNLRCKFCY-LEDYQGKELELDEINQVLDIIQDKEF---THVSLLGGEPTECEYFEYIIIQL--EKLRISYSFS 86
Cdd:cd01335     1 LELTRGCNLNCGFCSnPASKGRGPESPPEIEEILDIVLEAKErgvEVVILTGGEPLLYPELAELLRRLkkELPGFEISIE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  87 TNDQKLfrNEELIRILSKSKyLKEVLISLESPQKLINDAVRGKG-TFESAIKSVELLVKENVPTRLAMVVTKENNSTIQQ 165
Cdd:cd01335    81 TNGTLL--TEELLKELKELG-LDGVGVSLDSGDEEVADKIRGSGeSFKERLEALKELREAGLGLSTTLLVGLGDEDEEDD 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2182182963 166 MIDMCATL---GCRELRLMPFMPMGTGLLEKERLFMDYEGLVR 205
Cdd:cd01335   158 LEELELLAefrSPDRVSLFRLLPEEGTPLELAAPVVPAEKLLR 200
viperin_w_prok NF038283
viperin family antiviral radical SAM protein; Homologs of a viral defense radical SAM enzyme ...
 13-159 3.11e-07

viperin family antiviral radical SAM protein; Homologs of a viral defense radical SAM enzyme found in Homo sapiens, viperin (RSAD2), occur in prokaryotes with a strong bias toward placement in phage defense islands, encoded next to CRISPR system and restriction enzyme genes. Further investigation shows members indeed perform the anti-viral function of synthesizing modified ribonucleotides such as ddhCTP, ddh-guanosine triphosphate (ddhGTP) and ddh-uridine triphosphate (ddhUTP). Those non-standard ribonucleotides can interfere with viral replication machinery.


Pssm-ID: 468450 [Multi-domain]  Cd Length: 280  Bit Score: 50.63  E-value: 3.11e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  13 WMLTNKCNLRCKFCY-------LEDYQGKELELDEINQVLDIIQDKEFTHVSL--LGGEPTECeyfEYIIIQLEKLRISY 83
Cdd:NF038283    6 WHLTEACNYRCKYCFakwndvkSPRHHDKGHLEKLLEELAEFFKLLSYGFVRInfAGGEPLLY---PDRLLDLIKLAKEL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  84 SFS----TNDQKLfrNEELIRILskSKYLKEVLISLESPQKLINDA---VRGKG---TFESAIKSVELLVKENVPTRLAM 153
Cdd:NF038283   83 GFKtsiiTNGSLL--TEEFLEEL--APYLDWIGISIDSANEETNRKigrVDRKGrvlSLEELLELIALIRQINPNIKLKI 158


                  ....*...
gi 2182182963 154 --VVTKEN 159
Cdd:NF038283  159 ntVVNRLN 166
Elp3 smart00729
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
 16-188 2.65e-06

Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.


Pssm-ID: 214792 [Multi-domain]  Cd Length: 216  Bit Score: 47.40  E-value: 2.65e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963   16 TNKCNLRCKFCYLEDYQGKELE--LDEINQVLDIIQDK-----EFTHVSLLGGEPT--ECEYFEYII-----IQLEKLRI 81
Cdd:smart00729   8 TRGCPRRCTFCSFPSLRGKLRSryLEALVREIELLAEKgekegLVGTVFIGGGTPTllSPEQLEELLeaireILGLAKDV 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963   82 SYSFSTNDqkLFRNEELIRILSKSKyLKEVLISLESPQKLINDAVRGKGTFESAIKSVELLvKENVPTRLAMVVT----K 157
Cdd:smart00729  88 EITIETRP--DTLTEELLEALKEAG-VNRVSLGVQSGDDEVLKAINRGHTVEDVLEAVELL-REAGPIKVSTDLIvglpG 163

                          170       180       190
                   ....*....|....*....|....*....|..
gi 2182182963  158 ENNSTIQQMIDMCATLGCRELRLMPFMPM-GT 188
Cdd:smart00729 164 ETEEDFEETLKLLKELGPDRVSIFPLSPRpGT 195
PRK13758 PRK13758
anaerobic sulfatase-maturase; Provisional
 16-166 1.99e-05

anaerobic sulfatase-maturase; Provisional


Pssm-ID: 172296 [Multi-domain]  Cd Length: 370  Bit Score: 45.68  E-value: 1.99e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  16 TNKCNLRCKFCYLEDY-QGKELELDEI--NQVLDIIQDKEFTHV------SLLGGEPT--ECEYFEYIIIQLEK-----L 79
Cdd:PRK13758   12 SSGCNLKCTYCFYHSLsDNRNVKSYGImrDEVLESMVKRVLNEAeghcsfAFQGGEPTlaGLEFFEELMELQRKhnyknL 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  80 RISYSFSTNDQKLfrNEELIRILSKSKYLkeVLISLESPqKLINDAVR----GKGTFESAIKSVELLVKENVPTRLAMVV 155
Cdd:PRK13758   92 KIYNSLQTNGTLI--DESWAKFLSENKFL--VGLSMDGP-KEIHNLNRkdccGLDTFSKVERAAELFKKYKVEFNILCVV 166

                         170
                  ....*....|.
gi 2182182963 156 TKENNSTIQQM 166
Cdd:PRK13758  167 TSNTARHVNKI 177
SPASM_MftC-like cd21123
Iron-sulfur cluster-binding SPASM domain of mycofactocin radical SAM maturase MftC and similar ...
 230-306 1.45e-04

Iron-sulfur cluster-binding SPASM domain of mycofactocin radical SAM maturase MftC and similar proteins; This group is composed of Mycobacterium tuberculosis putative mycofactocin radical SAM maturase MftC and similar proteins. MftC is a radical S-adenosylmethionine (SAM) enzyme that may function to modify mycofactocin, a conserved polypeptide that might serve as an electron carrier. 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 that is similar to the second auxillary 4Fe-4S cluster (AuxII) of Clostridium perfringens anaerobic sulfatase-maturating enzyme (anSME).


Pssm-ID: 410614 [Multi-domain]  Cd Length: 91  Bit Score: 39.93  E-value: 1.45e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2182182963 230 TLGCGAGTAACVINSDLTLSACPVVSQTQKSIEKlgndcSSFDYIWGTSSIFNIWRAGKYRKStSCNLCPLFEECGG 306
Cdd:cd21123     1 TGGCGAGRGIAFISPDGDVYPCGFLPFSAGNVRE-----DSFKDIWENSELFKKLRDREFLKG-KCGKCKYRNVCGG 71
N_Twi_rSAM NF033640
twitch domain-containing radical SAM protein; Members of this family are unusual among radical ...
 6-115 2.98e-03

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: 38.79  E-value: 2.98e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963   6 KNPLFLTWMLTNKCNLRCKFCY-------LEDYQGKELELDEINQVLDIIQDKEF-----------THVSLLGGEPTECE 67
Cdd:NF033640  107 VNPRYLDLRFGNLCNLKCRMCGphsssswAKEAKKLGGPKLGDKKKISWFEDEEFwkwleellpslKEIYFAGGEPLLIK 186

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2182182963  68 YFeYIIiqLEKLR-------ISYSFSTNDQKLfrNEELIRILSKSKYLKEVLISL 115
Cdd:NF033640  187 EH-YKL--LEKLVekgraknIELRYNTNLTVL--PDKLKDLLDLWKKFKSVSISA 236
 
Name Accession Description Interval E-value
SkfB COG0535
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
 10-154 2.04e-28

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: 107.30  E-value: 2.04e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  10 FLTWMLTNKCNLRCKFCY--LEDYQGKELELDEINQVLDIIQDKEFTHVSLLGGEPTECEYFEYIIIQLEKLRISYSFST 87
Cdd:COG0535     1 RLQIELTNRCNLRCKHCYadAGPKRPGELSTEEAKRILDELAELGVKVVGLTGGEPLLRPDLFELVEYAKELGIRVNLST 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2182182963  88 NDQKLfrNEELIRILSKSKyLKEVLISLESPQKLINDAVRGK-GTFESAIKSVELLVKENVPTRLAMV 154
Cdd:COG0535    81 NGTLL--TEELAERLAEAG-LDHVTISLDGVDPETHDKIRGVpGAFDKVLEAIKLLKEAGIPVGINTV 145
mycofact_rSAM TIGR03962
mycofactocin radical SAM maturase; Members of this family are uncharacterized radical SAM ...
 5-306 2.11e-23

mycofactocin radical SAM maturase; Members of this family are uncharacterized radical SAM proteins from the Mycobacterium tuberculosis and many other Actinobacteria, as well as some deltaproteobacteria (e.g. Geobacter uraniireducens), firmicutes (Pelotomaculum thermopropionicum and Desulfotomaculum acetoxidans), and Chloroflexi (Thermomicrobium roseum DSM 5159 and Sphaerobacter thermophilus DSM 20745). They resemble several characterized radical SAM enzymes of peptide modification (PqqE, AlbA), and are always found next to the proposed target, TIGR03969, the putative mycofactocin precursor. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 188477 [Multi-domain]  Cd Length: 339  Bit Score: 97.99  E-value: 2.11e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963   5 LKNPLFLTWMLTNKCNLRCKFCYleDYQGK----ELELDEINQVLDIIQDKEFTHVSLLGGEPT-ECEYFEYIIIQLEKl 79
Cdd:TIGR03962   8 LDAPICLTWELTYACNLACVHCL--SSSGKrdprELTTAECKRLIDELAAMQVFYVNIGGGEPTvRPDFWELMDYATAH- 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  80 RISYSFSTNDQKLfrNEELIRILSKSKYLkEVLISLESPQKLINDAVRGKGTFESAIKSVELLVKENVPT-RLAMVVTKE 158
Cdd:TIGR03962  85 GVGVKFSTNGVRI--DPEVADRLAATDYV-DVQISLDGATAEVNDAVRGAGSFDLARRAMDNLAAAGFRGfKISVVLTRR 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963 159 NNSTIQQMIDMCATLGCrELRLMPFMPMGTG--LLEKERLFMD-----YEGLVRAcsdlkiPDNLIV-TTYLKEENTAET 230
Cdd:TIGR03962 162 NFGQLDEFYALADRYGA-QLRLTRLRPSGRGadVWDELHPTAAqqrqlYDWLVAH------GERVLTgDSFFHLAALGQP 234

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963 231 LG----CGAGTAACVINSDLTLSACPVVSQTQKsieKLGN--DCSSFDYIWGTSSIFNIWRagKYRKSTSCNLCPLFEEC 304
Cdd:TIGR03962 235 LPglnmCGAGRVVCLIDPVGDVYACPFVIHEEF---LAGNvrEDGGFAGVWRTSPLFRRLR--EPQSGGACQSCSAYDSC 309


                  ..
gi 2182182963 305 GG 306
Cdd:TIGR03962 310 RG 311
AslB COG0641
Sulfatase maturation enzyme AslB, radical SAM superfamily [Posttranslational modification, ...
 11-306 2.46e-22

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


Pssm-ID: 440406 [Multi-domain]  Cd Length: 349  Bit Score: 95.44  E-value: 2.46e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  11 LTWMLTNKCNLRCKFCYL---EDYQGKELELDEINQVLDII----QDKEFTHVSLLGGEPT-ECEYFEYIIIQLEKL--- 79
Cdd:COG0641     3 LVLKPTSRCNLRCSYCYYsegDEGSRRRMSEETAEKAIDFLiessGPGKELTITFFGGEPLlNFDFIKEIVEYARKYakk 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  80 --RISYSFSTNDQKLfrNEELIRILSKSKYLkeVLISLESPQKlINDAVR----GKGTFESAIKSVELLVKENVPTRLAM 153
Cdd:COG0641    83 gkKIRFSIQTNGTLL--DDEWIDFLKENGFS--VGISLDGPKE-IHDRNRvtknGKGSFDRVMRNIKLLKEHGVEVNIRC 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963 154 VVTKENNSTIQQMIDMCATLGCRELRLMPFMPMGTGLL-----EKERLFMDYEGLVRACSDLKIPDNLIvTTYLKEENTA 228
Cdd:COG0641   158 TVTRENLDDPEELYDFLKELGFRSIQFNPVVEEGEADYsltpeDYGEFLIELFDEWLERDGGKIFVREF-DILLAGLLPP 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963 229 ETLGC-GAGTAACVINSDLTLSACPVVSQTQKsiEKLGN-DCSSFDYIWGTSSIFNIWRAGKYRKSTSCNLCPLFEECGG 306
Cdd:COG0641   237 CSSPCvGAGGNYLVVDPDGDIYPCDEFVGDPE--FRLGNvFDGSLAELLDSPKLRAFGREKNVLLDEECRSCPYLPLCGG 314
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 15-166 2.28e-18

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: 80.26  E-value: 2.28e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  15 LTNKCNLRCKFCYLEDYQ----GKELELDEINQVLDIIQDKEFTHVSLLGGEPTECEYFEYIIIQLEKLR----ISYSFS 86
Cdd:pfam04055   1 ITRGCNLRCTYCAFPSIRargkGRELSPEEILEEAKELKRLGVEVVILGGGEPLLLPDLVELLERLLKLElaegIRITLE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  87 TNDQKLfrNEELIRILSKSKyLKEVLISLESPQKLINDAVRGKGTFESAIKSVELLVKENVPTR--LAMVVTKENNSTIQ 164
Cdd:pfam04055  81 TNGTLL--DEELLELLKEAG-LDRVSIGLESGDDEVLKLINRGHTFEEVLEALELLREAGIPVVtdNIVGLPGETDEDLE 157


                  ..
gi 2182182963 165 QM 166
Cdd:pfam04055 158 ET 159
rSAM_skfB TIGR04403
sporulation killing factor system radical SAM maturase; Members of this family are a radical ...
 8-266 4.20e-16

sporulation killing factor system radical SAM maturase; Members of this family are a radical SAM enzyme of post-translational modification of ribosomally translated peptides. In Bacillus subtilis, the enzyme SkfB creates a sactipeptide (sulfur-to-alpha-carbon) crosslink of Cys-4 to Met-12 of the mature form of sporulation killing factor (SkfA). In Paenibacillus larvae subsp. larvae B-3650, the Met is replaced by Leu, so the modification must be different. SkfB has 2 4Fe-4S clusters, one in its radical SAM domain (pfam04055) and one in a region that somewhat resembles the SPASM domain (TIGR04085).


Pssm-ID: 275196 [Multi-domain]  Cd Length: 402  Bit Score: 78.04  E-value: 4.20e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963   8 PLFLTWMLTNKCNLRCKFCYLEdyQGK----ELELDEINQVLDIIQDKEFTHVSLLGGEPTECEYFEYIIIQLEKLRISY 83
Cdd:TIGR04403 103 PISCTLQLTNACNLSCSFCYAS--SGKpypeELATDQWIQVMQKLAAVGVADVTLTGGEAKLIKGFKEIVTVASSLFTNV 180

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  84 SFSTNDQKlFRNEElIRILSKSKYLkEVLISLESPQKlINDAVRG-KGTFESAIKSVELLVKENVPTRLAMVVTKENNST 162
Cdd:TIGR04403 181 NVFSNGLN-WRDEE-VELLSHLGNV-SVQISIDGTPE-THNLLRGrKGAFEESMNTIKRLAEANIPVIVAMTINEKNADT 256

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963 163 IQQMIDMCATLGCRELRLMPFMPMGTGLLEKERLFMDYEGLVRAC---SDLKIPDNLIVTTYLKEENTAETLGCGAGTAA 239
Cdd:TIGR04403 257 VKDVVKDCANAGARIFRAGKTLSVGRATEGFKALTDEFESCVQQQlkeARRKWGDQLNIIDWEHEESSFTTDFCTPGYLA 336

                         250       260       270
                  ....*....|....*....|....*....|..
gi 2182182963 240 CVINSDLTLSACPVVSQT-----QKSIEKLGN 266
Cdd:TIGR04403 337 WYIRADGYVTPCQLEDEPlghilRDSIGDIGS 368
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 13-205 1.34e-14

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: 71.21  E-value: 1.34e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  13 WMLTNKCNLRCKFCY-LEDYQGKELELDEINQVLDIIQDKEF---THVSLLGGEPTECEYFEYIIIQL--EKLRISYSFS 86
Cdd:cd01335     1 LELTRGCNLNCGFCSnPASKGRGPESPPEIEEILDIVLEAKErgvEVVILTGGEPLLYPELAELLRRLkkELPGFEISIE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  87 TNDQKLfrNEELIRILSKSKyLKEVLISLESPQKLINDAVRGKG-TFESAIKSVELLVKENVPTRLAMVVTKENNSTIQQ 165
Cdd:cd01335    81 TNGTLL--TEELLKELKELG-LDGVGVSLDSGDEEVADKIRGSGeSFKERLEALKELREAGLGLSTTLLVGLGDEDEEDD 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 2182182963 166 MIDMCATL---GCRELRLMPFMPMGTGLLEKERLFMDYEGLVR 205
Cdd:cd01335   158 LEELELLAefrSPDRVSLFRLLPEEGTPLELAAPVVPAEKLLR 200
SCM_rSAM_ScmE TIGR04250
SynChlorMet cassette radical SAM/SPASM protein ScmE; A biosynthesis cassette found in ...
 15-159 3.49e-13

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: 69.11  E-value: 3.49e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  15 LTNKCNLRCKFCYLEDYQG---KELELDEINQVLDIIQDKEFTHVSLLGGEPTECEYFEYIIIQLEKLRISYSFSTNDQK 91
Cdd:TIGR04250   9 ITGRCNLRCRYCSHFSSAAetpTDLETAEWLRFFRELNRCSVLRVVLSGGEPFMRSDFREIIDGIVKNRMRFSILSNGTL 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2182182963  92 LfrNEELIRILSKSKYLKEVLISLESPQKLINDAVRGKGTFESAIKSVELLVKENVPTRLAMVVTKEN 159
Cdd:TIGR04250  89 I--TDAIASFLAATRRCDYVQVSIDGSTPGTHDRLRGTGSFLQAVEGIELLRKHAIPVVVRVTIHRWN 154
SCM_rSAM_ScmF TIGR04251
SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in ...
 15-189 3.92e-09

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: 56.77  E-value: 3.92e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  15 LTNKCNLRCKFCYLE-DYQGKE-----LELDEINQVLDIIQDKEFTHVSLLGGEPTECEYFEYIIIQLEKLRISYSFSTN 88
Cdd:TIGR04251  10 LTEGCNLKCRHCWIDpKYQGEGeqhpsLDPSLFRSIIRQAIPLGLTSVKLTGGEPLLHPAIGEILECIGENNLQLSVETN 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  89 DqkLFRNEELIRILSKSKYLKeVLISLESPQKLINDAVRG-KGTFESAIKSVELLVKENVPTRLAMVVTKENNSTIQQMI 167
Cdd:TIGR04251  90 G--LLCTPQTARDLASCETPF-VSVSLDGVDAATHDWMRGvKGAFDKAVRGIHNLVEAGIHPQIIMTVTRRNVGQMEQIV 166

                         170       180
                  ....*....|....*....|..
gi 2182182963 168 DMCATLGCRELRLMPFMPMGTG 189
Cdd:TIGR04251 167 RLAESLGAESVKFNHVQPTSRG 188
rSAM_ocin_clost TIGR04068
Cys-rich peptide radical SAM maturase CcpM; Members of this family are radical SAM enzymes ...
 3-146 6.41e-08

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: 53.46  E-value: 6.41e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963   3 NYLKNPL-FLTWMLTNKCNLRCKFC-YLEDYQ-----GKELELDEINQVLDII----QDKEFTHVSLLGGEP-------T 64
Cdd:TIGR04068  75 YYLENKIqMLILQVTQQCNLRCKYCaYSGSYDnrvhsNKRMSIETAKKAIDFLikhsEDTDELNLGFYGGEPllefeliK 154

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  65 ECeyFEYIIIQLEKLRISYSFSTNDQKLfrNEELIRILSKSKYlkEVLISLESPQKlINDAVR----GKGTFESAIKSVE 140
Cdd:TIGR04068 155 EC--VEYAKEKAEGKKINFNMTTNGTLL--TEEIIEFLYDNEF--NLTISLDGPKE-IHDKNRvfadGKGSFDKIMENIK 227


                  ....*.
gi 2182182963 141 LLVKEN 146
Cdd:TIGR04068 228 MIKKKY 233
rSAM_Cxxx_rpt TIGR04115
radical SAM peptide maturase, CXXX-repeat target family; Members of this radical SAM domain ...
 11-145 1.24e-07

radical SAM peptide maturase, CXXX-repeat target family; Members of this radical SAM domain protein are predicted peptide maturases, similar to PqqE, AlbA, the mycofactocin radical SAM maturase, and many others that share the peptide modification radical SAM protein C-terminal additional 4Fe4S-binding domain (TIGR04085). Members co-occur with a protein of unknown function that may be a chaperone or immunity protein and with a peptide that may have twelve or more cysteines occurring regularly spaced every fourth residue. These Cys residues tend to be flanked by residues with small side chains that provide minimal steric hindrance to crosslink formation by the radical SAM enzyme as in the subtilosin A system.


Pssm-ID: 200366 [Multi-domain]  Cd Length: 359  Bit Score: 52.58  E-value: 1.24e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  11 LTWMLTNKCNLRCKFCYL-EDYQGKELELDEINQVLDII--QDKEFTHVSL----LGGEP-TECEYFE----YIIIQLEK 78
Cdd:TIGR04115   4 ITFIVTDDCQLACKYCYQtGKNKNKRMSFETAKKAVDYIlsGNKGFGEPSViwdfIGGEPlLEIELIDricdYIKNRMIE 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2182182963  79 L------RISYSFSTNDQkLFRNEELIRILSKSKYLKEVLISLESPQKLiNDAVR----GKGTFESAIKSVELLVKE 145
Cdd:TIGR04115  84 LnhpwfnSYRFSFSTNGV-CYFEEKVQRFIQKNNQHLSISITIDGTKEK-HDSCRvfpdGRGSYDLVVSNAPLWLNQ 158
viperin_w_prok NF038283
viperin family antiviral radical SAM protein; Homologs of a viral defense radical SAM enzyme ...
 13-159 3.11e-07

viperin family antiviral radical SAM protein; Homologs of a viral defense radical SAM enzyme found in Homo sapiens, viperin (RSAD2), occur in prokaryotes with a strong bias toward placement in phage defense islands, encoded next to CRISPR system and restriction enzyme genes. Further investigation shows members indeed perform the anti-viral function of synthesizing modified ribonucleotides such as ddhCTP, ddh-guanosine triphosphate (ddhGTP) and ddh-uridine triphosphate (ddhUTP). Those non-standard ribonucleotides can interfere with viral replication machinery.


Pssm-ID: 468450 [Multi-domain]  Cd Length: 280  Bit Score: 50.63  E-value: 3.11e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  13 WMLTNKCNLRCKFCY-------LEDYQGKELELDEINQVLDIIQDKEFTHVSL--LGGEPTECeyfEYIIIQLEKLRISY 83
Cdd:NF038283    6 WHLTEACNYRCKYCFakwndvkSPRHHDKGHLEKLLEELAEFFKLLSYGFVRInfAGGEPLLY---PDRLLDLIKLAKEL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  84 SFS----TNDQKLfrNEELIRILskSKYLKEVLISLESPQKLINDA---VRGKG---TFESAIKSVELLVKENVPTRLAM 153
Cdd:NF038283   83 GFKtsiiTNGSLL--TEEFLEEL--APYLDWIGISIDSANEETNRKigrVDRKGrvlSLEELLELIALIRQINPNIKLKI 158


                  ....*...
gi 2182182963 154 --VVTKEN 159
Cdd:NF038283  159 ntVVNRLN 166
PflA COG1180
Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, ...
 19-186 4.21e-07

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


Pssm-ID: 440793 [Multi-domain]  Cd Length: 242  Bit Score: 50.18  E-value: 4.21e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  19 CNLRCKFCY-------LEDYQGKELELDEInqVLDIIQDKEFTH----VSLLGGEPT-ECEYFEYIIIQLEKLRISYSFS 86
Cdd:COG1180    31 CNLRCPYCHnpeisqgRPDAAGRELSPEEL--VEEALKDRGFLDscggVTFSGGEPTlQPEFLLDLAKLAKELGLHTALD 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  87 TNdqkLFRNEELIRILskSKYLKEVLISLespqKLINDAVRGKGT---FESAIKSVELLVKENVPTRLAM-VVTKENNS- 161
Cdd:COG1180   109 TN---GYIPEEALEEL--LPYLDAVNIDL----KAFDDEFYRKLTgvsLEPVLENLELLAESGVHVEIRTlVIPGLNDSe 179

                         170       180
                  ....*....|....*....|....*..
gi 2182182963 162 -TIQQMIDMCATLG-CRELRLMPFMPM 186
Cdd:COG1180   180 eELEAIARFIAELGdVIPVHLLPFHPL 206
rSAM_GlyRichRpt TIGR04261
radical SAM/SPASM domain protein, GRRM system; Members of this protein family are radical SAM ...
 16-158 6.05e-07

radical SAM/SPASM domain protein, GRRM system; Members of this protein family are radical SAM/SPASM domain proteins (see pfam04055 and TIGR04085) related to anaeroboic sulfatase maturating enzymes and the peptide modification enzyme PqqE. Members are found primarily in Cyanobacteria adjacent to a short protein, ~150 residues, in which the last ~60 residues tends to be repetitive and highly glycine-rich (see TIGR04260). The arrangement suggests modifications to the repetitive C-terminal region by this radical SAM domain enzyme, but the purpose of this system on the whole is unknown.


Pssm-ID: 211984 [Multi-domain]  Cd Length: 363  Bit Score: 50.42  E-value: 6.05e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  16 TNKCNLRCKFCYLEDYQGKE-LELDEINQVLDIIQDKEFT--HVSLL--GGEP--TECEY----FEYIIIQLEKLR---- 80
Cdd:TIGR04261   4 TSFCNLDCDYCYLPDRQLKNrLSLDLIEPILKRILESPFVgpGFTICwhAGEPltVPISFydeaTEIIREALEEYNqqpv 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  81 -ISYSFSTN----DQ---KLFRneelirilsksKYLKEVLISLESPQkLINDAVR----GKGTFESAIKSVELLVKENVP 148
Cdd:TIGR04261  84 qIEQSVQTNgtliNQawcDCFK-----------RNRIVVGVSLDGPA-FIHDAHRrtrtGRGSHAATMRGIRALQKNEIP 151

                         170
                  ....*....|
gi 2182182963 149 TRLAMVVTKE 158
Cdd:TIGR04261 152 FSVIAVLTED 161
YgiQ COG1032
Radical SAM superfamily enzyme YgiQ, UPF0313 family [General function prediction only];
19-201 1.35e-06

Radical SAM superfamily enzyme YgiQ, UPF0313 family [General function prediction only];


Pssm-ID: 440655 [Multi-domain]  Cd Length: 394  Bit Score: 49.17  E-value: 1.35e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  19 CNLRCKFC-----YLEDYQGKELE--LDEINQvldIIQDKEFTHVSLLGGEPTE-CEYFEYIIIQLEKLRISYSFSTNdq 90
Cdd:COG1032   184 CPFGCSFCsisalYGRKVRYRSPEsvVEEIEE---LVKRYGIREIFFVDDNFNVdKKRLKELLEELIERGLNVSFPSE-- 258

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  91 klFR----NEELIRILSKSKyLKEVLISLESPQKLINDAVRGKGTFESAIKSVELLVKENVPTRLAMVV-----TKEnns 161
Cdd:COG1032   259 --VRvdllDEELLELLKKAG-CRGLFIGIESGSQRVLKAMNKGITVEDILEAVRLLKKAGIRVKLYFIIglpgeTEE--- 332

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2182182963 162 TIQQMIDMCATLGCRELRLMPFMPM-GTGL---LEKERLFMDYE 201
Cdd:COG1032   333 DIEETIEFIKELGPDQAQVSIFTPLpGTPLyeeLEKEGRLYDWE 376
Elp3 smart00729
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
 16-188 2.65e-06

Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.


Pssm-ID: 214792 [Multi-domain]  Cd Length: 216  Bit Score: 47.40  E-value: 2.65e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963   16 TNKCNLRCKFCYLEDYQGKELE--LDEINQVLDIIQDK-----EFTHVSLLGGEPT--ECEYFEYII-----IQLEKLRI 81
Cdd:smart00729   8 TRGCPRRCTFCSFPSLRGKLRSryLEALVREIELLAEKgekegLVGTVFIGGGTPTllSPEQLEELLeaireILGLAKDV 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963   82 SYSFSTNDqkLFRNEELIRILSKSKyLKEVLISLESPQKLINDAVRGKGTFESAIKSVELLvKENVPTRLAMVVT----K 157
Cdd:smart00729  88 EITIETRP--DTLTEELLEALKEAG-VNRVSLGVQSGDDEVLKAINRGHTVEDVLEAVELL-REAGPIKVSTDLIvglpG 163

                          170       180       190
                   ....*....|....*....|....*....|..
gi 2182182963  158 ENNSTIQQMIDMCATLGCRELRLMPFMPM-GT 188
Cdd:smart00729 164 ETEEDFEETLKLLKELGPDRVSIFPLSPRpGT 195
QueE COG0602
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic ...
 19-109 1.33e-05

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: 45.13  E-value: 1.33e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  19 CNLRCKFC---Y-LEDYQGKELELDEInqvLDIIQDKEFTHVSLLGGEPTECEYFEYIIIQLEKLRISYSFSTN------ 88
Cdd:COG0602    30 CNLRCSWCdtkYaWDGEGGKRMSAEEI---LEEVAALGARHVVITGGEPLLQDDLAELLEALKDAGYEVALETNgtlpip 106

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2182182963  89 --------DQKLF------RNEELIRILSKSKYLK 109
Cdd:COG0602   107 agidwvtvSPKLPssgeeeDNRENLEVLRRADELK 141
PRK13758 PRK13758
anaerobic sulfatase-maturase; Provisional
 16-166 1.99e-05

anaerobic sulfatase-maturase; Provisional


Pssm-ID: 172296 [Multi-domain]  Cd Length: 370  Bit Score: 45.68  E-value: 1.99e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  16 TNKCNLRCKFCYLEDY-QGKELELDEI--NQVLDIIQDKEFTHV------SLLGGEPT--ECEYFEYIIIQLEK-----L 79
Cdd:PRK13758   12 SSGCNLKCTYCFYHSLsDNRNVKSYGImrDEVLESMVKRVLNEAeghcsfAFQGGEPTlaGLEFFEELMELQRKhnyknL 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  80 RISYSFSTNDQKLfrNEELIRILSKSKYLkeVLISLESPqKLINDAVR----GKGTFESAIKSVELLVKENVPTRLAMVV 155
Cdd:PRK13758   92 KIYNSLQTNGTLI--DESWAKFLSENKFL--VGLSMDGP-KEIHNLNRkdccGLDTFSKVERAAELFKKYKVEFNILCVV 166

                         170
                  ....*....|.
gi 2182182963 156 TKENNSTIQQM 166
Cdd:PRK13758  167 TSNTARHVNKI 177
moaA PRK00164
GTP 3',8-cyclase MoaA;
15-200 5.52e-05

GTP 3',8-cyclase MoaA;


Pssm-ID: 234672 [Multi-domain]  Cd Length: 331  Bit Score: 43.98  E-value: 5.52e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  15 LTNKCNLRCKFCYLEDYQ-----GKELELDEINQVLDIIQDKEFTHVSLLGGEPTECEYFEYIIIQLEKLR--ISYSFST 87
Cdd:PRK00164   23 VTDRCNFRCTYCMPEGYLpflpkEELLSLEEIERLVRAFVALGVRKVRLTGGEPLLRKDLEDIIAALAALPgiRDLALTT 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  88 NDQKLFRneelirilsKSKYLKE-----VLISLES--PQ--KLINdavrGKGTFESAIKSVELL-------VKENvptrl 151
Cdd:PRK00164  103 NGYLLAR---------RAAALKDagldrVNVSLDSldPErfKAIT----GRDRLDQVLAGIDAAlaagltpVKVN----- 164

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2182182963 152 aMVVTKENNST-IQQMIDMCATLGCrELRLMPFMPMGTGllekERLFMDY 200
Cdd:PRK00164  165 -AVLMKGVNDDeIPDLLEWAKDRGI-QLRFIELMPTGEG----NEWFRKH 208
ThiH COG1060
2-iminoacetate synthase ThiH/Menaquinone biosynthesis enzymes MqnC and MqnE [Coenzyme ...
 15-73 8.41e-05

2-iminoacetate synthase ThiH/Menaquinone biosynthesis enzymes MqnC and MqnE [Coenzyme transport and metabolism]; 2-iminoacetate synthase ThiH/Menaquinone biosynthesis enzymes MqnC and MqnE is part of the Pathway/BioSystem: Thiamine biosynthesis


Pssm-ID: 440680 [Multi-domain]  Cd Length: 351  Bit Score: 43.58  E-value: 8.41e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2182182963  15 LTNKCNLRCKFC----YLEDYQGKELELDEINQVLDIIQDKEFTHVSLLGGEPTEC--EYFEYII 73
Cdd:COG1060    57 LTNVCVNGCKFCafsrDNGDIDRYTLSPEEILEEAEEAKALGATEILLVGGEHPDLplEYYLDLL 121
SPASM_MftC-like cd21123
Iron-sulfur cluster-binding SPASM domain of mycofactocin radical SAM maturase MftC and similar ...
 230-306 1.45e-04

Iron-sulfur cluster-binding SPASM domain of mycofactocin radical SAM maturase MftC and similar proteins; This group is composed of Mycobacterium tuberculosis putative mycofactocin radical SAM maturase MftC and similar proteins. MftC is a radical S-adenosylmethionine (SAM) enzyme that may function to modify mycofactocin, a conserved polypeptide that might serve as an electron carrier. 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 that is similar to the second auxillary 4Fe-4S cluster (AuxII) of Clostridium perfringens anaerobic sulfatase-maturating enzyme (anSME).


Pssm-ID: 410614 [Multi-domain]  Cd Length: 91  Bit Score: 39.93  E-value: 1.45e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2182182963 230 TLGCGAGTAACVINSDLTLSACPVVSQTQKSIEKlgndcSSFDYIWGTSSIFNIWRAGKYRKStSCNLCPLFEECGG 306
Cdd:cd21123     1 TGGCGAGRGIAFISPDGDVYPCGFLPFSAGNVRE-----DSFKDIWENSELFKKLRDREFLKG-KCGKCKYRNVCGG 71
PLN02951 PLN02951
Molybderin biosynthesis protein CNX2
 15-79 1.83e-04

Molybderin biosynthesis protein CNX2


Pssm-ID: 215513 [Multi-domain]  Cd Length: 373  Bit Score: 42.82  E-value: 1.83e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2182182963  15 LTNKCNLRCKFCYLEDyqGKEL----EL---DEINQVLDIIQDKEFTHVSLLGGEPTECEYFEYIIIQLEKL 79
Cdd:PLN02951   64 LTERCNLRCQYCMPEE--GVELtpksHLlsqDEIVRLAGLFVAAGVDKIRLTGGEPTLRKDIEDICLQLSSL 133
rSAM_pep_methan TIGR04083
putative peptide-modifying radical SAM enzyme, Mhun_1560 family; Members of this family are ...
 19-146 3.00e-04

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: 42.02  E-value: 3.00e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  19 CNLRCKFCYLEDYQGKELELDEINQVLDIIQD--KEFTHVSLLGGEPTEC------EYFEYIIIQLEKLRISYSFSTNDQ 90
Cdd:TIGR04083  10 CPSKCKYCWSSEETSPVMSIDTVKDIVEWLKDfrDDRVTFTFHGGEPLLAgadfyrQALPLLSEGLAHLKPEFAMQTNLW 89

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2182182963  91 KLfrNEELIRILSKskYLKEVLISLESPQKlINDAVRGKGTFESAIKSVElLVKEN 146
Cdd:TIGR04083  90 LM--TPELAEIFAE--YNVPIGSSIDGPEE-INDYQRGEGYYQKTMKGYE-IAKEH 139
TM0948 COG5014
Uncharacterized conserved protein TM0948, MoaA-related, radical SAM superfamily [General ...
 19-148 9.67e-04

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: 9.67e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  19 CNLRCKFCY---LEDYQ---GKELELDEINQVL-DIIQDKEFTHVSLLGGEPTECeyFEYIIIQLEKL---RISYSFSTN 88
Cdd:COG5014    50 CNLRCGFCWswrFRDFPltiGKFYSPEEVAERLiEIARERGYRQVRLSGGEPTIG--FEHLLKVLELFserGLTFILETN 127

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2182182963  89 DQKLFRNEELIRILSKSKYLkEVLISLE--SPQK--LINDAvrGKGTFESAIKSVELLVKENVP 148
Cdd:COG5014   128 GILIGYDRELARELASFRNI-VVRVSIKgcTPEEfsMLTGA--DPEFFELQLRALKNLVDAGLE 188
N_Twi_rSAM NF033640
twitch domain-containing radical SAM protein; Members of this family are unusual among radical ...
 6-115 2.98e-03

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: 38.79  E-value: 2.98e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963   6 KNPLFLTWMLTNKCNLRCKFCY-------LEDYQGKELELDEINQVLDIIQDKEF-----------THVSLLGGEPTECE 67
Cdd:NF033640  107 VNPRYLDLRFGNLCNLKCRMCGphsssswAKEAKKLGGPKLGDKKKISWFEDEEFwkwleellpslKEIYFAGGEPLLIK 186

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2182182963  68 YFeYIIiqLEKLR-------ISYSFSTNDQKLfrNEELIRILSKSKYLKEVLISL 115
Cdd:NF033640  187 EH-YKL--LEKLVekgraknIELRYNTNLTVL--PDKLKDLLDLWKKFKSVSISA 236
Tyw1 COG0731
Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily [Translation, ribosomal ...
 14-145 7.37e-03

Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily [Translation, ribosomal structure and biogenesis]; Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440495 [Multi-domain]  Cd Length: 248  Bit Score: 37.09  E-value: 7.37e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2182182963  14 MLTNK-CNLRCKFCYL---EDYQGKELELDEINQVLD---------IIQDKEFTHVSLLG-GEPTECEYFEYIIIQLEKL 79
Cdd:COG0731    28 LIPNKtCNFDCVYCQRgrtTDLTRERREFDDPEEILEelieflrklPEEAREPDHITFSGsGEPTLYPNLGELIEEIKKL 107

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2182182963  80 R-ISYSFSTNDQkLFRNEELIRILSKskyLKEVLISLESPQ----KLINDAVrGKGTFESAIKSVELLVKE 145
Cdd:COG0731   108 RgIKTALLTNGS-LLHRPEVREELLK---ADQVYPSLDAADeetfRKINRPH-PGLSWERIIEGLELFRKL 173
rSAM_more_4Fe4S TIGR04085
radical SAM additional 4Fe4S-binding SPASM domain; This domain contains regions binding ...
 233-306 9.77e-03

radical SAM additional 4Fe4S-binding SPASM domain; This domain contains regions binding additional 4Fe4S clusters found in various radical SAM proteins C-terminal to the domain described by model pfam04055. Radical SAM enzymes with this domain tend to be involved in protein modification, including anaerobic sulfatase maturation proteins, a quinohemoprotein amine dehydrogenase biogenesis protein, the Pep1357-cyclizing radical SAM enzyme, and various bacteriocin biosynthesis proteins. The motif CxxCxxxxxCxxxC is nearly invariant for members of this family, although PqqE has a variant form. We name this domain SPASM for Subtilosin, PQQ, Anaerobic Sulfatase, and Mycofactocin.


Pssm-ID: 274968 [Multi-domain]  Cd Length: 93  Bit Score: 34.86  E-value: 9.77e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2182182963 233 CGAGTAACVINSDLTLSACPVVSQTQksiEKLGN-DCSSFDYIWGTSSIFNIWRAGKYRKSTSCNLCPLFEECGG 306
Cdd:TIGR04085   1 CGAGRNSLVVDPDGDVYPCDHFVYPE---YKLGNiREDSLEEILNSSKQLEFGRWKSPKLPEECRSCKYLPLCGG 72
 
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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