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Conserved domains on  [gi|333768599|gb|EGL45776|]
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radical SAM protein, BA_1875 family [Propionibacterium sp. 434-HC2]

Protein Classification

radical SAM/SPASM domain-containing protein( domain architecture ID 11499346)

radical SAM (S-adenosylmethionine) protein containing additional 4Fe4S-binding SPASM domain, similar to coenzyme PQQ synthesis protein E (PqqE) and anaerobic sulfatase-maturating enzyme (anSME)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
sam_11 TIGR04053
radical SAM protein, BA_1875 family; Members of this subfamily of the radical SAM domain ...
 40-407 0e+00

radical SAM protein, BA_1875 family; Members of this subfamily of the radical SAM domain superfamily show closer sequence relationships to peptide-modifying proteins of bacteriocin and PQQ biosynthesis than to other characterized radical SAM proteins. Within this subfamily, targets are likely to be diverse. [Unknown function, Enzymes of unknown specificity]


:

Pssm-ID: 274945 [Multi-domain]  Cd Length: 365  Bit Score: 641.64  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599   40 HDLNNKPFIVIWEVTRACALVCQHCRAEAQHHAAPGQLTNAQGHELINQLTSYERPYPMLILTGGDCFERPDLVDLIEYA 119
Cdd:TIGR04053   1 HDFNERPLIVIWEVTRACALACKHCRASAQPKPLPGELTTEEGKALLDQIAEFGDPYPLLVLTGGDPLMRPDLFELVDYA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599  120 VSKGLHVSISPSVTPLFTRDRVRAVQEAGVSIMSMSLDGGSATTHDAFRGFPGTFDHTVEACHMLRELGMKFQLNTVFTA 199
Cdd:TIGR04053  81 TSLGLRVSLSPSVTPNLTREAIAALKEAGVSAVSLSLDGATAETHDAFRGVPGSFDRTVNAIRAALELGIPVQINTTVTA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599  200 KNIHEAPQMLKNAIDLGAMMFYTFMLVPTGRGAQLDMLSPLEREDVLYWLHDNSTRIA--IKTTEAPQYRRIAFQRDAVR 277
Cdd:TIGR04053 161 ENVHELPDVAKLLKDLGVKLWSVFFLVPTGRGQALDDLTPEEAEDVLHWLYDVSDRYGfdVKTTEAPHYRRVALQRKGLE 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599  278 qgkERPVRHGELYEWLTRETNELLGEtiTEPRPPRTPLAINSGSGFAFIDHTGDVYPSGFLPIHCGSIKETPFPEIYRGS 357
Cdd:TIGR04053 241 ---KDELRGGELYRQLTEKLTELLGE--PVGRPPRRPMGTRDGNGFIFVSHTGDVYPSGFLPLSAGNVREESLVEIYRES 315

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|
gi 333768599  358 PVFQGLRNPNGFSGKCGACNFNHFCGGSRSTAYALTGDYLASDPSCAYVP 407
Cdd:TIGR04053 316 PLFKSLRDPDEFKGKCGRCEFRHVCGGSRARAYAVTGDPLAEDPACVYRP 365
 
Name Accession Description Interval E-value
sam_11 TIGR04053
radical SAM protein, BA_1875 family; Members of this subfamily of the radical SAM domain ...
 40-407 0e+00

radical SAM protein, BA_1875 family; Members of this subfamily of the radical SAM domain superfamily show closer sequence relationships to peptide-modifying proteins of bacteriocin and PQQ biosynthesis than to other characterized radical SAM proteins. Within this subfamily, targets are likely to be diverse. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 274945 [Multi-domain]  Cd Length: 365  Bit Score: 641.64  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599   40 HDLNNKPFIVIWEVTRACALVCQHCRAEAQHHAAPGQLTNAQGHELINQLTSYERPYPMLILTGGDCFERPDLVDLIEYA 119
Cdd:TIGR04053   1 HDFNERPLIVIWEVTRACALACKHCRASAQPKPLPGELTTEEGKALLDQIAEFGDPYPLLVLTGGDPLMRPDLFELVDYA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599  120 VSKGLHVSISPSVTPLFTRDRVRAVQEAGVSIMSMSLDGGSATTHDAFRGFPGTFDHTVEACHMLRELGMKFQLNTVFTA 199
Cdd:TIGR04053  81 TSLGLRVSLSPSVTPNLTREAIAALKEAGVSAVSLSLDGATAETHDAFRGVPGSFDRTVNAIRAALELGIPVQINTTVTA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599  200 KNIHEAPQMLKNAIDLGAMMFYTFMLVPTGRGAQLDMLSPLEREDVLYWLHDNSTRIA--IKTTEAPQYRRIAFQRDAVR 277
Cdd:TIGR04053 161 ENVHELPDVAKLLKDLGVKLWSVFFLVPTGRGQALDDLTPEEAEDVLHWLYDVSDRYGfdVKTTEAPHYRRVALQRKGLE 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599  278 qgkERPVRHGELYEWLTRETNELLGEtiTEPRPPRTPLAINSGSGFAFIDHTGDVYPSGFLPIHCGSIKETPFPEIYRGS 357
Cdd:TIGR04053 241 ---KDELRGGELYRQLTEKLTELLGE--PVGRPPRRPMGTRDGNGFIFVSHTGDVYPSGFLPLSAGNVREESLVEIYRES 315

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|
gi 333768599  358 PVFQGLRNPNGFSGKCGACNFNHFCGGSRSTAYALTGDYLASDPSCAYVP 407
Cdd:TIGR04053 316 PLFKSLRDPDEFKGKCGRCEFRHVCGGSRARAYAVTGDPLAEDPACVYRP 365
SkfB COG0535
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
 48-197 1.75e-41

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: 144.28  E-value: 1.75e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599  48 IVIWEVTRACALVCQHCRAEAqHHAAPGQLTNAQGHELINQLtsYERPYPMLILTGGDCFERPDLVDLIEYAVSKGLHVS 127
Cdd:COG0535    1 RLQIELTNRCNLRCKHCYADA-GPKRPGELSTEEAKRILDEL--AELGVKVVGLTGGEPLLRPDLFELVEYAKELGIRVN 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599 128 ISPSVTpLFTRDRVRAVQEAGVSIMSMSLDGGSATTHDAFRGFPGTFDHTVEACHMLRELGMKFQLNTVF 197
Cdd:COG0535   78 LSTNGT-LLTEELAERLAEAGLDHVTISLDGVDPETHDKIRGVPGAFDKVLEAIKLLKEAGIPVGINTVY 146
SPASM_MftC-like cd21123
Iron-sulfur cluster-binding SPASM domain of mycofactocin radical SAM maturase MftC and similar ...
 318-403 2.56e-35

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: 125.45  E-value: 2.56e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599 318 NSGSGFAFIDHTGDVYPSGFLPIHCGSIKETPFPEIYRGSPVFQGLRNPNGFSGKCGACNFNHFCGGSRSTAYALTGDYL 397
Cdd:cd21123    5 GAGRGIAFISPDGDVYPCGFLPFSAGNVREDSFKDIWENSELFKKLRDREFLKGKCGKCKYRNVCGGCRARAYAYTGDPL 84


                 ....*.
gi 333768599 398 ASDPSC 403
Cdd:cd21123   85 GEDPGC 90
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 53-190 2.94e-11

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: 61.39  E-value: 2.94e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599   53 VTRACALVCQHC-RAEAQHHAAPGQLTNAQGHELINQLtsYERPYPMLILTGGDCFERPDLVDLIEYAVSK----GLHVS 127
Cdd:pfam04055   1 ITRGCNLRCTYCaFPSIRARGKGRELSPEEILEEAKEL--KRLGVEVVILGGGEPLLLPDLVELLERLLKLelaeGIRIT 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 333768599  128 ISPSVTpLFTRDRVRAVQEAGVSIMSMSLDGGSATTHDAFRGfPGTFDHTVEACHMLRELGMK 190
Cdd:pfam04055  79 LETNGT-LLDEELLELLKEAGLDRVSIGLESGDDEVLKLINR-GHTFEEVLEALELLREAGIP 139
 
Name Accession Description Interval E-value
sam_11 TIGR04053
radical SAM protein, BA_1875 family; Members of this subfamily of the radical SAM domain ...
 40-407 0e+00

radical SAM protein, BA_1875 family; Members of this subfamily of the radical SAM domain superfamily show closer sequence relationships to peptide-modifying proteins of bacteriocin and PQQ biosynthesis than to other characterized radical SAM proteins. Within this subfamily, targets are likely to be diverse. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 274945 [Multi-domain]  Cd Length: 365  Bit Score: 641.64  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599   40 HDLNNKPFIVIWEVTRACALVCQHCRAEAQHHAAPGQLTNAQGHELINQLTSYERPYPMLILTGGDCFERPDLVDLIEYA 119
Cdd:TIGR04053   1 HDFNERPLIVIWEVTRACALACKHCRASAQPKPLPGELTTEEGKALLDQIAEFGDPYPLLVLTGGDPLMRPDLFELVDYA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599  120 VSKGLHVSISPSVTPLFTRDRVRAVQEAGVSIMSMSLDGGSATTHDAFRGFPGTFDHTVEACHMLRELGMKFQLNTVFTA 199
Cdd:TIGR04053  81 TSLGLRVSLSPSVTPNLTREAIAALKEAGVSAVSLSLDGATAETHDAFRGVPGSFDRTVNAIRAALELGIPVQINTTVTA 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599  200 KNIHEAPQMLKNAIDLGAMMFYTFMLVPTGRGAQLDMLSPLEREDVLYWLHDNSTRIA--IKTTEAPQYRRIAFQRDAVR 277
Cdd:TIGR04053 161 ENVHELPDVAKLLKDLGVKLWSVFFLVPTGRGQALDDLTPEEAEDVLHWLYDVSDRYGfdVKTTEAPHYRRVALQRKGLE 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599  278 qgkERPVRHGELYEWLTRETNELLGEtiTEPRPPRTPLAINSGSGFAFIDHTGDVYPSGFLPIHCGSIKETPFPEIYRGS 357
Cdd:TIGR04053 241 ---KDELRGGELYRQLTEKLTELLGE--PVGRPPRRPMGTRDGNGFIFVSHTGDVYPSGFLPLSAGNVREESLVEIYRES 315

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|
gi 333768599  358 PVFQGLRNPNGFSGKCGACNFNHFCGGSRSTAYALTGDYLASDPSCAYVP 407
Cdd:TIGR04053 316 PLFKSLRDPDEFKGKCGRCEFRHVCGGSRARAYAVTGDPLAEDPACVYRP 365
SkfB COG0535
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
 48-197 1.75e-41

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: 144.28  E-value: 1.75e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599  48 IVIWEVTRACALVCQHCRAEAqHHAAPGQLTNAQGHELINQLtsYERPYPMLILTGGDCFERPDLVDLIEYAVSKGLHVS 127
Cdd:COG0535    1 RLQIELTNRCNLRCKHCYADA-GPKRPGELSTEEAKRILDEL--AELGVKVVGLTGGEPLLRPDLFELVEYAKELGIRVN 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599 128 ISPSVTpLFTRDRVRAVQEAGVSIMSMSLDGGSATTHDAFRGFPGTFDHTVEACHMLRELGMKFQLNTVF 197
Cdd:COG0535   78 LSTNGT-LLTEELAERLAEAGLDHVTISLDGVDPETHDKIRGVPGAFDKVLEAIKLLKEAGIPVGINTVY 146
SPASM_MftC-like cd21123
Iron-sulfur cluster-binding SPASM domain of mycofactocin radical SAM maturase MftC and similar ...
 318-403 2.56e-35

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: 125.45  E-value: 2.56e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599 318 NSGSGFAFIDHTGDVYPSGFLPIHCGSIKETPFPEIYRGSPVFQGLRNPNGFSGKCGACNFNHFCGGSRSTAYALTGDYL 397
Cdd:cd21123    5 GAGRGIAFISPDGDVYPCGFLPFSAGNVREDSFKDIWENSELFKKLRDREFLKGKCGKCKYRNVCGGCRARAYAYTGDPL 84


                 ....*.
gi 333768599 398 ASDPSC 403
Cdd:cd21123   85 GEDPGC 90
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 51-251 5.92e-26

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: 104.34  E-value: 5.92e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599  51 WEVTRACALVCQHCRAEAQHHAAPGQLTNAqGHELINQLTSYERPYPMLILTGGDCFERPDLVDLIEYAVS--KGLHVSI 128
Cdd:cd01335    1 LELTRGCNLNCGFCSNPASKGRGPESPPEI-EEILDIVLEAKERGVEVVILTGGEPLLYPELAELLRRLKKelPGFEISI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599 129 SpSVTPLFTRDRVRAVQEAGVSIMSMSLDGGSATTHDAFRGFPGTFDHTVEACHMLRELGmkFQLNTVFTAKNIHE---- 204
Cdd:cd01335   80 E-TNGTLLTEELLKELKELGLDGVGVSLDSGDEEVADKIRGSGESFKERLEALKELREAG--LGLSTTLLVGLGDEdeed 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 333768599 205 -APQMLKNAIDLGAMMFYTFMLVPTGRGAQLDMLSPLEREDVLYWLHD 251
Cdd:cd01335  157 dLEELELLAEFRSPDRVSLFRLLPEEGTPLELAAPVVPAEKLLRLIAA 204
AslB COG0641
Sulfatase maturation enzyme AslB, radical SAM superfamily [Posttranslational modification, ...
 49-405 1.05e-20

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


Pssm-ID: 440406 [Multi-domain]  Cd Length: 349  Bit Score: 92.74  E-value: 1.05e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599  49 VIWEVTRACALVCQHCRAEAQHHAAPGQLTNAQGHELINQLTSYERPYPMLILT--GGDCFERPDLV-DLIEYAVSKGLH 125
Cdd:COG0641    3 LVLKPTSRCNLRCSYCYYSEGDEGSRRRMSEETAEKAIDFLIESSGPGKELTITffGGEPLLNFDFIkEIVEYARKYAKK 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599 126 -VSISPSVTP---LFTRDRVRAVQEAGVSImSMSLDGgSATTHDAFRGFP---GTFDHTVEACHMLRELGMKFQLNTVFT 198
Cdd:COG0641   83 gKKIRFSIQTngtLLDDEWIDFLKENGFSV-GISLDG-PKEIHDRNRVTKngkGSFDRVMRNIKLLKEHGVEVNIRCTVT 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599 199 AKNIHEAPQMLKNAIDLGAMMFYTFMLVPTGRGAQldmlsPLEREDVLYWLHdnstriaiktteapQYRRIAFQRDavrq 278
Cdd:COG0641  161 RENLDDPEELYDFLKELGFRSIQFNPVVEEGEADY-----SLTPEDYGEFLI--------------ELFDEWLERD---- 217

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599 279 GKERPVRHgelyewltretnelLGETITEPRPPRTPLAINSGSGFAFIDHTGDVYPSGFLPI----HCGSIKETPFPEIY 354
Cdd:COG0641  218 GGKIFVRE--------------FDILLAGLLPPCSSPCVGAGGNYLVVDPDGDIYPCDEFVGdpefRLGNVFDGSLAELL 283

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....
gi 333768599 355 RGSPVFQGLRNPNGF-SGKCGACNFNHFC-GGSRSTAYALTGDYLA-SDPSCAY 405
Cdd:COG0641  284 DSPKLRAFGREKNVLlDEECRSCPYLPLCgGGCPANRYAETGDGFKpYSYYCEL 337
SCM_rSAM_ScmF TIGR04251
SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in ...
 53-385 2.66e-16

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: 79.88  E-value: 2.66e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599   53 VTRACALVCQHCRAEAQHHAAPGQLTNAQgHELINQLTSYERPYPM--LILTGGDCFERPDLVDLIEYAVSKGLHVSISP 130
Cdd:TIGR04251  10 LTEGCNLKCRHCWIDPKYQGEGEQHPSLD-PSLFRSIIRQAIPLGLtsVKLTGGEPLLHPAIGEILECIGENNLQLSVET 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599  131 SVTpLFTRDRVRAVQEAGVSIMSMSLDGGSATTHDAFRGFPGTFDHTVEACHMLRELGMKFQLNTVFTAKNIHEAPQMLK 210
Cdd:TIGR04251  89 NGL-LCTPQTARDLASCETPFVSVSLDGVDAATHDWMRGVKGAFDKAVRGIHNLVEAGIHPQIIMTVTRRNVGQMEQIVR 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599  211 NAIDLGAMMFYTFMLVPTGRGAQL----DMLSPLEREDVLYWLHD---NSTRIAIKTTEAPQYRRIAfqrdavRQGKERP 283
Cdd:TIGR04251 168 LAESLGAESVKFNHVQPTSRGSKMhengETLSIGELVALGEWMERtliPSTALRIDFGHPPAFRPLG------RMFGEKP 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599  284 VRHGelyewltreTNELLGetiteprpprtPLAINSGSGFAFIDhTGDVYPSGFLpihcGSIKETPFPEIYRGSPVFQGL 363
Cdd:TIGR04251 242 GGCG---------LCGIFG-----------ILGVLSDGSYALCG-IGESIPELVF----GNAGSDRLDSVWSENPVLNEI 296

                         330       340
                  ....*....|....*....|....
gi 333768599  364 RN--PNGFSGKCGACNFNHFCGGS 385
Cdd:TIGR04251 297 RNgmPGRLEGVCGECLMKEKCLGS 320
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 53-190 2.94e-11

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: 61.39  E-value: 2.94e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599   53 VTRACALVCQHC-RAEAQHHAAPGQLTNAQGHELINQLtsYERPYPMLILTGGDCFERPDLVDLIEYAVSK----GLHVS 127
Cdd:pfam04055   1 ITRGCNLRCTYCaFPSIRARGKGRELSPEEILEEAKEL--KRLGVEVVILGGGEPLLLPDLVELLERLLKLelaeGIRIT 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 333768599  128 ISPSVTpLFTRDRVRAVQEAGVSIMSMSLDGGSATTHDAFRGfPGTFDHTVEACHMLRELGMK 190
Cdd:pfam04055  79 LETNGT-LLDEELLELLKEAGLDRVSIGLESGDDEVLKLINR-GHTFEEVLEALELLREAGIP 139
SCM_rSAM_ScmE TIGR04250
SynChlorMet cassette radical SAM/SPASM protein ScmE; A biosynthesis cassette found in ...
 52-204 9.37e-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: 50.63  E-value: 9.37e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599   52 EVTRACALVCQHCRAEAQHHAAPGQLTNAQGHELINQLTsyERPYPMLILTGGDCFERPDLVDLIEYAVSKGLHVSISPS 131
Cdd:TIGR04250   8 DITGRCNLRCRYCSHFSSAAETPTDLETAEWLRFFRELN--RCSVLRVVLSGGEPFMRSDFREIIDGIVKNRMRFSILSN 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 333768599  132 VTpLFTRDRVRAVQEAG-VSIMSMSLDGGSATTHDAFRGfPGTFDHTVEACHMLRELGMKFQLNTVFTAKNIHE 204
Cdd:TIGR04250  86 GT-LITDAIASFLAATRrCDYVQVSIDGSTPGTHDRLRG-TGSFLQAVEGIELLRKHAIPVVVRVTIHRWNVDD 157
SPASM_PqqE cd21119
Iron-sulfur cluster-binding SPASM domain of coenzyme PQQ synthesis protein E; Coenzyme PQQ ...
 320-407 1.53e-06

Iron-sulfur cluster-binding SPASM domain of coenzyme PQQ synthesis protein E; Coenzyme PQQ synthesis protein E (PqqE), also called pyrroloquinoline quinone (PQQ) biosynthesis protein E or PqqA peptide cyclase (EC 1.21.98.4), is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the formation of a C-C bond between C-4 of glutamate and C-3 of tyrosine residues of the PqqA protein, which is the first enzymatic step in the biosynthesis of the bacterial enzyme cofactor PQQ. 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 (RS) enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. PqqE contains two auxiliary Fe-S clusters in its SPASM domain: one nearest the RS site (AuxI) is in the form of a 2Fe-2S cluster ligated by four cysteines; and a more remote cluster (AuxII) in the form of a 4Fe-4S center that is ligated by three cysteine residues and one aspartate residue.


Pssm-ID: 410610 [Multi-domain]  Cd Length: 114  Bit Score: 46.53  E-value: 1.53e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599 320 GSGFAFIDHTGDVYP----SGFLPIHCGSIKETPFPEIYRGSPVFQGLRNPNGFSGKCGACNFNH--FcGGSRSTAYALT 393
Cdd:cd21119    9 GRIFLNVTPDGTVLPchaaETILPLEFPNVRDHSLAEIWYESFAFNRFRGTDWMPEPCRSCDEKEkdF-GGCRCQAFALT 87

                         90
                 ....*....|....
gi 333768599 394 GDYLASDPSCAYVP 407
Cdd:cd21119   88 GDAANTDPVCSKSP 101
SPASM_anSME cd21120
Iron-sulfur cluster-binding SPASM domain of anaerobic sulfatase maturating enzyme; Anaerobic ...
 320-384 1.43e-05

Iron-sulfur cluster-binding SPASM domain of anaerobic sulfatase maturating enzyme; Anaerobic sulfatase maturating enzyme (anSME) is a radical S-adenosylmethionine (SAM) enzyme that catalyzes, under anaerobic conditions, the co- or post-translational modification of arylsulfatases to form a catalytically essential formylglycine (FGly) residue to perform their hydrolysis function, removing sulfate groups from a wide array of substrates. 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 (RS) enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster; anSME contains two auxillary 4Fe-4S clusters in its SPASM domain.


Pssm-ID: 410611 [Multi-domain]  Cd Length: 107  Bit Score: 43.81  E-value: 1.43e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599 320 GSGFAfIDHTGDVYPSGF--LPIHC-GSIKETPFPEIYRgSPVFQ--GLRNPNgFSGKCGACNFNHFCGG 384
Cdd:cd21120    9 GDNLV-VEHNGDVYPCDHfvLPEYRlGNIQEQTLAELVD-SEKQQqfGAQKFK-LPAECKQCKYLFACHG 75
SPASM pfam13186
Iron-sulfur cluster-binding domain; This domain occurs as an additional C-terminal iron-sulfur ...
 320-377 1.84e-05

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


Pssm-ID: 433020 [Multi-domain]  Cd Length: 66  Bit Score: 42.47  E-value: 1.84e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 333768599  320 GSGFAFIDHTGDVYP----SGFLPIHCGSIKETPFPEIYRgSPVFQGLRNPNGFS--GKCGACN 377
Cdd:pfam13186   4 GWTSLVILPDGDVYPcfddDFVGPIVLGNIREQSLAEIWN-SPKYREFRKLGKFAliELCRDCP 66
rSAM_more_4Fe4S TIGR04085
radical SAM additional 4Fe4S-binding SPASM domain; This domain contains regions binding ...
 320-403 2.11e-05

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: 42.95  E-value: 2.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599  320 GSGFAFIDHTGDVYPSGFL---PIHCGSIKETPFPEIYRGSPVFQGLRNPNGF-SGKCGACNFNHFCGGS-RSTAYALTG 394
Cdd:TIGR04085   4 GRNSLVVDPDGDVYPCDHFvypEYKLGNIREDSLEEILNSSKQLEFGRWKSPKlPEECRSCKYLPLCGGGcPANRYLKTG 83

                          90
                  ....*....|
gi 333768599  395 DYLAS-DPSC 403
Cdd:TIGR04085  84 DINGPkNPLC 93
SPASM cd21109
Iron-sulfur cluster-binding SPASM domain; This iron-sulfur cluster-binding domain is named ...
 318-376 1.14e-03

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


Pssm-ID: 410609 [Multi-domain]  Cd Length: 65  Bit Score: 37.02  E-value: 1.14e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 333768599 318 NSGSGFAFIDHTGDVYPSGFLPIH---CGSIKETPFPEIYRgSPVFQGLRN--PNGFSGKCGAC 376
Cdd:cd21109    3 PAPWTSLYITPDGDVYPCCFDVNEelkLGNIREQSLKEIWN-SEKYREFRKllLDGKIKLCKNC 65
SPASM_AlbA-like cd21125
Iron-sulfur cluster-binding SPASM domain of antilisterial bacteriocin subtilosin biosynthesis ...
 326-403 8.86e-03

Iron-sulfur cluster-binding SPASM domain of antilisterial bacteriocin subtilosin biosynthesis protein AlbA and similar proteins; Bacillus subtilis antilisterial bacteriocin subtilosin biosynthesis protein AlbA is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the formation of three thioether bonds in the post-translational modification of a linear peptide into the cyclic peptide subtilosin A. The thioether bonds formed are between the sulfur of three cysteine residues and the alpha-carbons of two phenylalanines and one threonine to produce a rigid cyclic peptide. 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. AlbA appears to contain one auxillary Fe-S cluster, similar to the auxillary 4Fe-4S cluster in Bacillus circulans butirosin biosynthetic enzyme BtrN.


Pssm-ID: 410616 [Multi-domain]  Cd Length: 97  Bit Score: 35.54  E-value: 8.86e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 333768599 326 IDHTGDVYPSGFLPI---HCGSIKETPFPEIYRgSPV---FQGLRNPNGFSgkCGACNFNHFCG-GSRSTAYALTGDYLA 398
Cdd:cd21125   12 IDPDGEVYPCHLLHPtefKLGNIFEDSLASILK-NPVleiWQTYDPRFSEH--CKKCPFYGICGgGCIAKSLISYGRFDK 88


                 ....*
gi 333768599 399 SDPSC 403
Cdd:cd21125   89 PDPYC 93
 
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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