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Conserved domains on  [gi|429188957|gb|EKY29818|]
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radical SAM domain protein [Clostridium celatum DSM 1785]

Protein Classification

radical SAM protein( domain architecture ID 11425241)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SkfB COG0535
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
 25-169 1.78e-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: 143.51  E-value: 1.78e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  25 TFELSPCCNLDCRMCYVRKTKQEVNELggekTVEEWLELARECRDAGMLFLLLTGGEPFLYKDFKRLYLELKKMGFMISI 104
Cdd:COG0535    3 QIELTNRCNLRCKHCYADAGPKRPGEL----STEEAKRILDELAELGVKVVGLTGGEPLLRPDLFELVEYAKELGIRVNL 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 429188957 105 NTNGTLIDEEVVSWLSKNPPYRMQITLYGGSNETYERLCRDNKGFDKTTKAIKMLKEAGIAIKIN 169
Cdd:COG0535   79 STNGTLLTEELAERLAEAGLDHVTISLDGVDPETHDKIRGVPGAFDKVLEAIKLLKEAGIPVGIN 143
AslB super family cl33987
Sulfatase maturation enzyme AslB, radical SAM superfamily [Posttranslational modification, ...
 32-383 1.36e-26

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


The actual alignment was detected with superfamily member COG0641:

Pssm-ID: 440406 [Multi-domain]  Cd Length: 349  Bit Score: 108.92  E-value: 1.36e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  32 CNLDCRMCYVRKTKQEVNELGGEKTVEEWLE-LARECRDAGMLFLLLTGGEPFLYKDF-KRLYLELKKMG-----FMISI 104
Cdd:COG0641   11 CNLRCSYCYYSEGDEGSRRRMSEETAEKAIDfLIESSGPGKELTITFFGGEPLLNFDFiKEIVEYARKYAkkgkkIRFSI 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957 105 NTNGTLIDEEVVSWLSKNPpYRMQITLYGGS--NETYeRLCRDNKG-FDKTTKAIKMLKEAGIAIKINASMTQYNIEDLD 181
Cdd:COG0641   91 QTNGTLLDDEWIDFLKENG-FSVGISLDGPKeiHDRN-RVTKNGKGsFDRVMRNIKLLKEHGVEVNIRCTVTRENLDDPE 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957 182 KIYEFAKENNV-YVQatsymFPPTRrneeaigigdrftPQEAAHYSVKIDQLRLEKDEFSKRAIAMREGLIKFkSELEec 260
Cdd:COG0641  169 ELYDFLKELGFrSIQ-----FNPVV-------------EEGEADYSLTPEDYGEFLIELFDEWLERDGGKIFV-REFD-- 227

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957 261 esldssaedsdnienkNIIDNEETREKLKC-RAGKSSFWINWKGEMTACGMMnwpVAYP-FKEG-LIPAWYKIIDETDKL 337
Cdd:COG0641  228 ----------------ILLAGLLPPCSSPCvGAGGNYLVVDPDGDIYPCDEF---VGDPeFRLGnVFDGSLAELLDSPKL 288

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 429188957 338 RM---------PKKCTKCEKKFACTV-CGASVVTETGDFEKAPKYICKMTEKILEE 383
Cdd:COG0641  289 RAfgreknvllDEECRSCPYLPLCGGgCPANRYAETGDGFKPYSYYCELYKKLFEH 344
 
Name Accession Description Interval E-value
SkfB COG0535
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
 25-169 1.78e-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: 143.51  E-value: 1.78e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  25 TFELSPCCNLDCRMCYVRKTKQEVNELggekTVEEWLELARECRDAGMLFLLLTGGEPFLYKDFKRLYLELKKMGFMISI 104
Cdd:COG0535    3 QIELTNRCNLRCKHCYADAGPKRPGEL----STEEAKRILDELAELGVKVVGLTGGEPLLRPDLFELVEYAKELGIRVNL 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 429188957 105 NTNGTLIDEEVVSWLSKNPPYRMQITLYGGSNETYERLCRDNKGFDKTTKAIKMLKEAGIAIKIN 169
Cdd:COG0535   79 STNGTLLTEELAERLAEAGLDHVTISLDGVDPETHDKIRGVPGAFDKVLEAIKLLKEAGIPVGIN 143
AslB COG0641
Sulfatase maturation enzyme AslB, radical SAM superfamily [Posttranslational modification, ...
 32-383 1.36e-26

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


Pssm-ID: 440406 [Multi-domain]  Cd Length: 349  Bit Score: 108.92  E-value: 1.36e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  32 CNLDCRMCYVRKTKQEVNELGGEKTVEEWLE-LARECRDAGMLFLLLTGGEPFLYKDF-KRLYLELKKMG-----FMISI 104
Cdd:COG0641   11 CNLRCSYCYYSEGDEGSRRRMSEETAEKAIDfLIESSGPGKELTITFFGGEPLLNFDFiKEIVEYARKYAkkgkkIRFSI 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957 105 NTNGTLIDEEVVSWLSKNPpYRMQITLYGGS--NETYeRLCRDNKG-FDKTTKAIKMLKEAGIAIKINASMTQYNIEDLD 181
Cdd:COG0641   91 QTNGTLLDDEWIDFLKENG-FSVGISLDGPKeiHDRN-RVTKNGKGsFDRVMRNIKLLKEHGVEVNIRCTVTRENLDDPE 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957 182 KIYEFAKENNV-YVQatsymFPPTRrneeaigigdrftPQEAAHYSVKIDQLRLEKDEFSKRAIAMREGLIKFkSELEec 260
Cdd:COG0641  169 ELYDFLKELGFrSIQ-----FNPVV-------------EEGEADYSLTPEDYGEFLIELFDEWLERDGGKIFV-REFD-- 227

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957 261 esldssaedsdnienkNIIDNEETREKLKC-RAGKSSFWINWKGEMTACGMMnwpVAYP-FKEG-LIPAWYKIIDETDKL 337
Cdd:COG0641  228 ----------------ILLAGLLPPCSSPCvGAGGNYLVVDPDGDIYPCDEF---VGDPeFRLGnVFDGSLAELLDSPKL 288

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 429188957 338 RM---------PKKCTKCEKKFACTV-CGASVVTETGDFEKAPKYICKMTEKILEE 383
Cdd:COG0641  289 RAfgreknvllDEECRSCPYLPLCGGgCPANRYAETGDGFKPYSYYCELYKKLFEH 344
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 32-202 9.42e-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: 103.18  E-value: 9.42e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  32 CNLDCRMCYVRKTKQEVNELggEKTVEEWLELARECRDAGMLFLLLTGGEPFLYKDFKRLYLELKK--MGFMISINTNGT 109
Cdd:cd01335    7 CNLNCGFCSNPASKGRGPES--PPEIEEILDIVLEAKERGVEVVILTGGEPLLYPELAELLRRLKKelPGFEISIETNGT 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957 110 LIDEEVVSWLSKNPPYRMQITLYGGSNETYERLCRDNKGFDKTTKAIKMLKEAGIAIKINASMTQYNIEDLDKIYEFAKE 189
Cdd:cd01335   85 LLTEELLKELKELGLDGVGVSLDSGDEEVADKIRGSGESFKERLEALKELREAGLGLSTTLLVGLGDEDEEDDLEELELL 164

                        170
                 ....*....|...
gi 429188957 190 NNVYVQATSYMFP 202
Cdd:cd01335  165 AEFRSPDRVSLFR 177
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 28-183 9.49e-22

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: 91.05  E-value: 9.49e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957   28 LSPCCNLDCRMCYVRKTKQEVNelGGEKTVEEWLELARECRDAGMLFLLLTGGEPFLYKDFKRLYLELKKM----GFMIS 103
Cdd:pfam04055   1 ITRGCNLRCTYCAFPSIRARGK--GRELSPEEILEEAKELKRLGVEVVILGGGEPLLLPDLVELLERLLKLelaeGIRIT 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  104 INTNGTLIDEEVVSWLSKNPPYRMQITLYGGSNEtYERLCRDNKGFDKTTKAIKMLKEAGIAIKINASMTQ--YNIEDLD 181
Cdd:pfam04055  79 LETNGTLLDEELLELLKEAGLDRVSIGLESGDDE-VLKLINRGHTFEEVLEALELLREAGIPVVTDNIVGLpgETDEDLE 157


                  ..
gi 429188957  182 KI 183
Cdd:pfam04055 158 ET 159
SCM_rSAM_ScmE TIGR04250
SynChlorMet cassette radical SAM/SPASM protein ScmE; A biosynthesis cassette found in ...
 21-200 3.91e-21

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: 93.77  E-value: 3.91e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957   21 PLSGTFELSPCCNLDCRMCYVRKTKQEV-NELGgektVEEWLELARECRDAGMLFLLLTGGEPFLYKDFKRLY--LELKK 97
Cdd:TIGR04250   2 PRSVDIDITGRCNLRCRYCSHFSSAAETpTDLE----TAEWLRFFRELNRCSVLRVVLSGGEPFMRSDFREIIdgIVKNR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957   98 MGFmiSINTNGTLIDEEVVSWLSKNPPYR-MQITLYGGSNETYERlCRDNKGFDKTTKAIKMLKEAGIAIKINASMTQYN 176
Cdd:TIGR04250  78 MRF--SILSNGTLITDAIASFLAATRRCDyVQVSIDGSTPGTHDR-LRGTGSFLQAVEGIELLRKHAIPVVVRVTIHRWN 154

                         170       180
                  ....*....|....*....|....*...
gi 429188957  177 IEDLDKIYEFAKEN----NVYVQATSYM 200
Cdd:TIGR04250 155 VDDLRPIAALLLDDlglpAFSTNAASYM 182
N_Twi_rSAM NF033640
twitch domain-containing radical SAM protein; Members of this family are unusual among radical ...
 32-191 2.79e-10

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: 61.52  E-value: 2.79e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  32 CNLDCRMC---YVRKTKQEVNELGGEKTV----------EEWLELARECRDaGMLFLLLTGGEPFLYKDFKRLYLELKKM 98
Cdd:NF033640 120 CNLKCRMCgphSSSSWAKEAKKLGGPKLGdkkkiswfedEEFWKWLEELLP-SLKEIYFAGGEPLLIKEHYKLLEKLVEK 198

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  99 GFM----ISINTNGTLIDEEVVSWLSKNPPYRmQITLYG---GSNETYERLcRDNKGFDKTTKAIKMLKEAGIAIKINAS 171
Cdd:NF033640 199 GRAknieLRYNTNLTVLPDKLKDLLDLWKKFK-SVSISAsidGVGERNEYI-RYGSKWDEIEKNLKKLKEECPNVELRIN 276

                        170       180
                 ....*....|....*....|..
gi 429188957 172 MT-Q-YNIEDLDKIYEFAKENN 191
Cdd:NF033640 277 PTvSaLNVLHLPELLDWLLELG 298
Elp3 smart00729
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
 32-192 1.44e-08

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: 54.72  E-value: 1.44e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957    32 CNLDCRMCYVRKTKQEVNELGGEKTVEEWLELARECRDAGMLF-LLLTGGEPFL--YKDFKRLYLELKKMG-----FMIS 103
Cdd:smart00729  11 CPRRCTFCSFPSLRGKLRSRYLEALVREIELLAEKGEKEGLVGtVFIGGGTPTLlsPEQLEELLEAIREILglakdVEIT 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957   104 INTNGTLIDEEVVSWLSKNPPYRMQITLYGGSNETYERLCRdNKGFDKTTKAIKMLKEAGIaIKINASM-----TQyNIE 178
Cdd:smart00729  91 IETRPDTLTEELLEALKEAGVNRVSLGVQSGDDEVLKAINR-GHTVEDVLEAVELLREAGP-IKVSTDLivglpGE-TEE 167

                          170
                   ....*....|....
gi 429188957   179 DLDKIYEFAKENNV 192
Cdd:smart00729 168 DFEETLKLLKELGP 181
PRK13758 PRK13758
anaerobic sulfatase-maturase; Provisional
 29-191 2.48e-06

anaerobic sulfatase-maturase; Provisional


Pssm-ID: 172296 [Multi-domain]  Cd Length: 370  Bit Score: 49.14  E-value: 2.48e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  29 SPCCNLDCRMCYVRK--TKQEVNELGGEKtvEEWLE--LARECRDA-GMLFLLLTGGEPFLYK-DFKRLYLELKK----- 97
Cdd:PRK13758  12 SSGCNLKCTYCFYHSlsDNRNVKSYGIMR--DEVLEsmVKRVLNEAeGHCSFAFQGGEPTLAGlEFFEELMELQRkhnyk 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  98 -MGFMISINTNGTLIDEEVVSWLSKNpPYRMQITLYGGS--NETYERLCRDNKGFDKTTKAIKMLKEAGIAIKINASMTQ 174
Cdd:PRK13758  90 nLKIYNSLQTNGTLIDESWAKFLSEN-KFLVGLSMDGPKeiHNLNRKDCCGLDTFSKVERAAELFKKYKVEFNILCVVTS 168

                        170
                 ....*....|....*..
gi 429188957 175 YNIEDLDKIYEFAKENN 191
Cdd:PRK13758 169 NTARHVNKIYKYFKEKD 185
SPASM pfam13186
Iron-sulfur cluster-binding domain; This domain occurs as an additional C-terminal iron-sulfur ...
 290-346 4.80e-03

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: 35.53  E-value: 4.80e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 429188957  290 CRAGKSSFWINWKGEMTACGMMNWPVAYPF----KEGLIPAW----YKIIDETDKLRMPKKCTKC 346
Cdd:pfam13186   1 CFAGWTSLVILPDGDVYPCFDDDFVGPIVLgnirEQSLAEIWnspkYREFRKLGKFALIELCRDC 65
 
Name Accession Description Interval E-value
SkfB COG0535
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
 25-169 1.78e-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: 143.51  E-value: 1.78e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  25 TFELSPCCNLDCRMCYVRKTKQEVNELggekTVEEWLELARECRDAGMLFLLLTGGEPFLYKDFKRLYLELKKMGFMISI 104
Cdd:COG0535    3 QIELTNRCNLRCKHCYADAGPKRPGEL----STEEAKRILDELAELGVKVVGLTGGEPLLRPDLFELVEYAKELGIRVNL 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 429188957 105 NTNGTLIDEEVVSWLSKNPPYRMQITLYGGSNETYERLCRDNKGFDKTTKAIKMLKEAGIAIKIN 169
Cdd:COG0535   79 STNGTLLTEELAERLAEAGLDHVTISLDGVDPETHDKIRGVPGAFDKVLEAIKLLKEAGIPVGIN 143
AslB COG0641
Sulfatase maturation enzyme AslB, radical SAM superfamily [Posttranslational modification, ...
 32-383 1.36e-26

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


Pssm-ID: 440406 [Multi-domain]  Cd Length: 349  Bit Score: 108.92  E-value: 1.36e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  32 CNLDCRMCYVRKTKQEVNELGGEKTVEEWLE-LARECRDAGMLFLLLTGGEPFLYKDF-KRLYLELKKMG-----FMISI 104
Cdd:COG0641   11 CNLRCSYCYYSEGDEGSRRRMSEETAEKAIDfLIESSGPGKELTITFFGGEPLLNFDFiKEIVEYARKYAkkgkkIRFSI 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957 105 NTNGTLIDEEVVSWLSKNPpYRMQITLYGGS--NETYeRLCRDNKG-FDKTTKAIKMLKEAGIAIKINASMTQYNIEDLD 181
Cdd:COG0641   91 QTNGTLLDDEWIDFLKENG-FSVGISLDGPKeiHDRN-RVTKNGKGsFDRVMRNIKLLKEHGVEVNIRCTVTRENLDDPE 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957 182 KIYEFAKENNV-YVQatsymFPPTRrneeaigigdrftPQEAAHYSVKIDQLRLEKDEFSKRAIAMREGLIKFkSELEec 260
Cdd:COG0641  169 ELYDFLKELGFrSIQ-----FNPVV-------------EEGEADYSLTPEDYGEFLIELFDEWLERDGGKIFV-REFD-- 227

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957 261 esldssaedsdnienkNIIDNEETREKLKC-RAGKSSFWINWKGEMTACGMMnwpVAYP-FKEG-LIPAWYKIIDETDKL 337
Cdd:COG0641  228 ----------------ILLAGLLPPCSSPCvGAGGNYLVVDPDGDIYPCDEF---VGDPeFRLGnVFDGSLAELLDSPKL 288

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 429188957 338 RM---------PKKCTKCEKKFACTV-CGASVVTETGDFEKAPKYICKMTEKILEE 383
Cdd:COG0641  289 RAfgreknvllDEECRSCPYLPLCGGgCPANRYAETGDGFKPYSYYCELYKKLFEH 344
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 32-202 9.42e-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: 103.18  E-value: 9.42e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  32 CNLDCRMCYVRKTKQEVNELggEKTVEEWLELARECRDAGMLFLLLTGGEPFLYKDFKRLYLELKK--MGFMISINTNGT 109
Cdd:cd01335    7 CNLNCGFCSNPASKGRGPES--PPEIEEILDIVLEAKERGVEVVILTGGEPLLYPELAELLRRLKKelPGFEISIETNGT 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957 110 LIDEEVVSWLSKNPPYRMQITLYGGSNETYERLCRDNKGFDKTTKAIKMLKEAGIAIKINASMTQYNIEDLDKIYEFAKE 189
Cdd:cd01335   85 LLTEELLKELKELGLDGVGVSLDSGDEEVADKIRGSGESFKERLEALKELREAGLGLSTTLLVGLGDEDEEDDLEELELL 164

                        170
                 ....*....|...
gi 429188957 190 NNVYVQATSYMFP 202
Cdd:cd01335  165 AEFRSPDRVSLFR 177
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 28-183 9.49e-22

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: 91.05  E-value: 9.49e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957   28 LSPCCNLDCRMCYVRKTKQEVNelGGEKTVEEWLELARECRDAGMLFLLLTGGEPFLYKDFKRLYLELKKM----GFMIS 103
Cdd:pfam04055   1 ITRGCNLRCTYCAFPSIRARGK--GRELSPEEILEEAKELKRLGVEVVILGGGEPLLLPDLVELLERLLKLelaeGIRIT 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  104 INTNGTLIDEEVVSWLSKNPPYRMQITLYGGSNEtYERLCRDNKGFDKTTKAIKMLKEAGIAIKINASMTQ--YNIEDLD 181
Cdd:pfam04055  79 LETNGTLLDEELLELLKEAGLDRVSIGLESGDDE-VLKLINRGHTFEEVLEALELLREAGIPVVTDNIVGLpgETDEDLE 157


                  ..
gi 429188957  182 KI 183
Cdd:pfam04055 158 ET 159
SCM_rSAM_ScmE TIGR04250
SynChlorMet cassette radical SAM/SPASM protein ScmE; A biosynthesis cassette found in ...
 21-200 3.91e-21

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: 93.77  E-value: 3.91e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957   21 PLSGTFELSPCCNLDCRMCYVRKTKQEV-NELGgektVEEWLELARECRDAGMLFLLLTGGEPFLYKDFKRLY--LELKK 97
Cdd:TIGR04250   2 PRSVDIDITGRCNLRCRYCSHFSSAAETpTDLE----TAEWLRFFRELNRCSVLRVVLSGGEPFMRSDFREIIdgIVKNR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957   98 MGFmiSINTNGTLIDEEVVSWLSKNPPYR-MQITLYGGSNETYERlCRDNKGFDKTTKAIKMLKEAGIAIKINASMTQYN 176
Cdd:TIGR04250  78 MRF--SILSNGTLITDAIASFLAATRRCDyVQVSIDGSTPGTHDR-LRGTGSFLQAVEGIELLRKHAIPVVVRVTIHRWN 154

                         170       180
                  ....*....|....*....|....*...
gi 429188957  177 IEDLDKIYEFAKEN----NVYVQATSYM 200
Cdd:TIGR04250 155 VDDLRPIAALLLDDlglpAFSTNAASYM 182
SCM_rSAM_ScmF TIGR04251
SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in ...
 26-224 2.57e-13

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


Pssm-ID: 211974 [Multi-domain]  Cd Length: 353  Bit Score: 70.64  E-value: 2.57e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957   26 FELSPCCNLDCRMCYVRKTKQEVNELGGEKTVEEWLELARECRDAGMLFLLLTGGEPFLYKDFKRLYLELKKMGFMISIN 105
Cdd:TIGR04251   8 FYLTEGCNLKCRHCWIDPKYQGEGEQHPSLDPSLFRSIIRQAIPLGLTSVKLTGGEPLLHPAIGEILECIGENNLQLSVE 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  106 TNGTLIDEEVVSWLSKNPPYRMQITLYGGSNETYERLCRDNKGFDKTTKAIKMLKEAGIAIKINASMTQYNIEDLDKIYE 185
Cdd:TIGR04251  88 TNGLLCTPQTARDLASCETPFVSVSLDGVDAATHDWMRGVKGAFDKAVRGIHNLVEAGIHPQIIMTVTRRNVGQMEQIVR 167

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 429188957  186 FAKEnnvyVQATSYMF---PPTRRNEEAIGIGDRFTPQEAAH 224
Cdd:TIGR04251 168 LAES----LGAESVKFnhvQPTSRGSKMHENGETLSIGELVA 205
PflA COG1180
Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, ...
 32-191 1.37e-11

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


Pssm-ID: 440793 [Multi-domain]  Cd Length: 242  Bit Score: 64.05  E-value: 1.37e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  32 CNLDCRMCYVRKT-KQEVNELGGEKTVEEWLELARECRD-----AGMLFlllTGGEPFLYKDF-KRLYLELKKMGFMISI 104
Cdd:COG1180   31 CNLRCPYCHNPEIsQGRPDAAGRELSPEELVEEALKDRGfldscGGVTF---SGGEPTLQPEFlLDLAKLAKELGLHTAL 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957 105 NTNGTL---IDEEVVSWLSKnppyrMQITLYGGSNETYERLC-RDNKgfdKTTKAIKMLKEAGIAI--------KINASM 172
Cdd:COG1180  108 DTNGYIpeeALEELLPYLDA-----VNIDLKAFDDEFYRKLTgVSLE---PVLENLELLAESGVHVeirtlvipGLNDSE 179

                        170
                 ....*....|....*....
gi 429188957 173 tqyniEDLDKIYEFAKENN 191
Cdd:COG1180  180 -----EELEAIARFIAELG 193
QueE COG0602
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic ...
 32-120 5.69e-11

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: 61.31  E-value: 5.69e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  32 CNLDCRMCyvrKTKQEVNELGGEK-TVEEwleLARECRDAGMLFLLLTGGEPFLYKDFKRLYLELKKMGFMISINTNGTL 110
Cdd:COG0602   30 CNLRCSWC---DTKYAWDGEGGKRmSAEE---ILEEVAALGARHVVITGGEPLLQDDLAELLEALKDAGYEVALETNGTL 103

                         90
                 ....*....|
gi 429188957 111 IDEEVVSWLS 120
Cdd:COG0602  104 PIPAGIDWVT 113
NrdG2 TIGR02495
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
 32-195 6.80e-11

anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of the radical-SAM family (pfam04055). It is often gene clustered with the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, TIGR02487) and presumably fulfills the identical function as NrdG, which utilizes S-adenosyl methionine, an iron-sulfur cluster and a reductant (dihydroflavodoxin) to produce a glycine-centered radical in NrdD. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism, Protein fate, Protein modification and repair]


Pssm-ID: 274164 [Multi-domain]  Cd Length: 192  Bit Score: 60.84  E-value: 6.80e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957   32 CNLDCRMCY-----VRKTKQEVNElggeKTVEEWLElarecRDAGML-FLLLTGGEPFLYKDFKRLYLELKKMGFMISIN 105
Cdd:TIGR02495  26 CNLKCPYCHnplliPRRGSGEIEV----EELLEFLR-----RRRGLLdGVVITGGEPTLQAGLPDFLREVRELGFEVKLD 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  106 TNGT-------LIDEEVVSWLS---KNPPyrmqitlyggsnETYERLCRDNKGFDKTT--KAIKMLKEAGIAIKINASMT 173
Cdd:TIGR02495  97 TNGSnprrleeLLEEGLVDYVAmdvKAPP------------EKYGELYGLEKNGAAKNilKSLEILLESGIPFELRTTVV 164

                         170       180
                  ....*....|....*....|....
gi 429188957  174 QYNI--EDLDKIYEFAKENNVYVQ 195
Cdd:TIGR02495 165 RGFLteEDLAEIATRIKENGTYVL 188
N_Twi_rSAM NF033640
twitch domain-containing radical SAM protein; Members of this family are unusual among radical ...
 32-191 2.79e-10

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: 61.52  E-value: 2.79e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  32 CNLDCRMC---YVRKTKQEVNELGGEKTV----------EEWLELARECRDaGMLFLLLTGGEPFLYKDFKRLYLELKKM 98
Cdd:NF033640 120 CNLKCRMCgphSSSSWAKEAKKLGGPKLGdkkkiswfedEEFWKWLEELLP-SLKEIYFAGGEPLLIKEHYKLLEKLVEK 198

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  99 GFM----ISINTNGTLIDEEVVSWLSKNPPYRmQITLYG---GSNETYERLcRDNKGFDKTTKAIKMLKEAGIAIKINAS 171
Cdd:NF033640 199 GRAknieLRYNTNLTVLPDKLKDLLDLWKKFK-SVSISAsidGVGERNEYI-RYGSKWDEIEKNLKKLKEECPNVELRIN 276

                        170       180
                 ....*....|....*....|..
gi 429188957 172 MT-Q-YNIEDLDKIYEFAKENN 191
Cdd:NF033640 277 PTvSaLNVLHLPELLDWLLELG 298
Elp3 smart00729
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
 32-192 1.44e-08

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: 54.72  E-value: 1.44e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957    32 CNLDCRMCYVRKTKQEVNELGGEKTVEEWLELARECRDAGMLF-LLLTGGEPFL--YKDFKRLYLELKKMG-----FMIS 103
Cdd:smart00729  11 CPRRCTFCSFPSLRGKLRSRYLEALVREIELLAEKGEKEGLVGtVFIGGGTPTLlsPEQLEELLEAIREILglakdVEIT 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957   104 INTNGTLIDEEVVSWLSKNPPYRMQITLYGGSNETYERLCRdNKGFDKTTKAIKMLKEAGIaIKINASM-----TQyNIE 178
Cdd:smart00729  91 IETRPDTLTEELLEALKEAGVNRVSLGVQSGDDEVLKAINR-GHTVEDVLEAVELLREAGP-IKVSTDLivglpGE-TEE 167

                          170
                   ....*....|....
gi 429188957   179 DLDKIYEFAKENNV 192
Cdd:smart00729 168 DFEETLKLLKELGP 181
MoaA COG2896
GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) [Coenzyme transport and ...
 32-192 3.01e-08

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


Pssm-ID: 442141 [Multi-domain]  Cd Length: 329  Bit Score: 54.68  E-value: 3.01e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  32 CNLDCRMC-----YVRKTKQEVneLggekTVEEWLELARECRDAGMLFLLLTGGEPFLYKDFKRLYLELKKMGFM--ISI 104
Cdd:COG2896   24 CNFRCTYCmpeegYQFLPKEEL--L----SFEEIERLVRAFVELGVRKIRLTGGEPLLRKDLPELIARLAALPGIedLAL 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957 105 NTNGTLIDEEVVSW----LSknppyRMQI---TLyggSNETYERLCRDNKgFDKTTKAIKMLKEAGIA-IKINA-SMTQY 175
Cdd:COG2896   98 TTNGSLLARYAEALkaagLD-----RVNVsldSL---DPERFRRITRRDD-LDKVLAGIDAALAAGLTpVKINAvVMRGV 168

                        170
                 ....*....|....*..
gi 429188957 176 NIEDLDKIYEFAKENNV 192
Cdd:COG2896  169 NDDEILDLLEFAKERGI 185
Tyw1 COG0731
Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily [Translation, ribosomal ...
 27-204 4.53e-07

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: 50.58  E-value: 4.53e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  27 ELSP--CCNLDCRMCYVRKTKQEVNELGG----EKTVEEWLELARECRDAGMLF--LLLTG-GEPFLYKDFKRLYLELKK 97
Cdd:COG0731   27 NLIPnkTCNFDCVYCQRGRTTDLTRERREfddpEEILEELIEFLRKLPEEAREPdhITFSGsGEPTLYPNLGELIEEIKK 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  98 M-GFMISINTNGTLI-DEEVVSWLSK-NPPYrmqITLYGGSNETYERLCRDNKG--FDKTTKAIKMLKEAG---IAIKI- 168
Cdd:COG0731  107 LrGIKTALLTNGSLLhRPEVREELLKaDQVY---PSLDAADEETFRKINRPHPGlsWERIIEGLELFRKLYkgrTVIETm 183

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 429188957 169 ---NASMTQyniEDLDKIYEFAKENNV-YVQATSYMFPPT 204
Cdd:COG0731  184 lvkGINDSE---EELEAYAELIKRINPdFVELKTYMRPPA 220
PRK13758 PRK13758
anaerobic sulfatase-maturase; Provisional
 29-191 2.48e-06

anaerobic sulfatase-maturase; Provisional


Pssm-ID: 172296 [Multi-domain]  Cd Length: 370  Bit Score: 49.14  E-value: 2.48e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  29 SPCCNLDCRMCYVRK--TKQEVNELGGEKtvEEWLE--LARECRDA-GMLFLLLTGGEPFLYK-DFKRLYLELKK----- 97
Cdd:PRK13758  12 SSGCNLKCTYCFYHSlsDNRNVKSYGIMR--DEVLEsmVKRVLNEAeGHCSFAFQGGEPTLAGlEFFEELMELQRkhnyk 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  98 -MGFMISINTNGTLIDEEVVSWLSKNpPYRMQITLYGGS--NETYERLCRDNKGFDKTTKAIKMLKEAGIAIKINASMTQ 174
Cdd:PRK13758  90 nLKIYNSLQTNGTLIDESWAKFLSEN-KFLVGLSMDGPKeiHNLNRKDCCGLDTFSKVERAAELFKKYKVEFNILCVVTS 168

                        170
                 ....*....|....*..
gi 429188957 175 YNIEDLDKIYEFAKENN 191
Cdd:PRK13758 169 NTARHVNKIYKYFKEKD 185
TM0948 COG5014
Uncharacterized conserved protein TM0948, MoaA-related, radical SAM superfamily [General ...
 32-164 1.04e-05

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


Pssm-ID: 444038  Cd Length: 261  Bit Score: 46.52  E-value: 1.04e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  32 CNLDCRMCYVRKTKQEVNELGGEKTVEEWLE-LARECRDAGMLFLLLTGGEPFLYKDFKRLYLEL-KKMGFMISINTNGT 109
Cdd:COG5014   50 CNLRCGFCWSWRFRDFPLTIGKFYSPEEVAErLIEIARERGYRQVRLSGGEPTIGFEHLLKVLELfSERGLTFILETNGI 129

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 429188957 110 LI--DEEVVSWLSKNPPYRMQITLYGGSNETYERLC-RDNKGFDKTTKAIKMLKEAGI 164
Cdd:COG5014  130 LIgyDRELARELASFRNIVVRVSIKGCTPEEFSMLTgADPEFFELQLRALKNLVDAGL 187
rSAM_pep_methan TIGR04083
putative peptide-modifying radical SAM enzyme, Mhun_1560 family; Members of this family are ...
 32-190 1.49e-05

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: 46.64  E-value: 1.49e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957   32 CNLDCRMCYVRKTKQEVNELGGEKTVEEWLelaRECRDAGMLFLLlTGGEPFLY-KDFKRLYLE-----LKKMGFMISIN 105
Cdd:TIGR04083  10 CPSKCKYCWSSEETSPVMSIDTVKDIVEWL---KDFRDDRVTFTF-HGGEPLLAgADFYRQALPllsegLAHLKPEFAMQ 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  106 TNGTLIDEEVVSWLSKnppYRMQItlyGGSNETYERLCRDNKG---FDKTTKAIKMLKEAGIAIKINASMTQYNIEDLDK 182
Cdd:TIGR04083  86 TNLWLMTPELAEIFAE---YNVPI---GSSIDGPEEINDYQRGegyYQKTMKGYEIAKEHGLDVRFICTFTSYSVKQKEE 159


                  ....*...
gi 429188957  183 IYEFAKEN 190
Cdd:TIGR04083 160 IFNFFLEN 167
COG2100 COG2100
Uncharacterized Fe-S cluster-containing enzyme, radical SAM superfamily [General function ...
 32-190 7.60e-05

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


Pssm-ID: 441703 [Multi-domain]  Cd Length: 344  Bit Score: 44.51  E-value: 7.60e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  32 CNLDCRMCYV---RKTKQEVNE--LGGEKTVEEWLELAREcrDAGMLFLLLTG-GEPFLYKDFKRLYLELKKMGFM--IS 103
Cdd:COG2100   46 CNLNCIFCSVdagPHSRTRQAEyiVDPEYLVEWFEKVARF--KGKGVEAHIDGvGEPLLYPYIVELVKGLKEIKGVkvVS 123

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957 104 INTNGTLIDEEVVSWLSKNPPYRMQI---TLyggsNETYERLCRDNKGFD--KTTKAIK-MLKEAGIAIKINAS-MTQYN 176
Cdd:COG2100  124 MQTNGTLLSEKLIDELEEAGLDRINLsidTL----DPEKAKKLAGTKWYDveKVLELAEyIARETKIDLLIAPVwLPGIN 199

                        170
                 ....*....|....
gi 429188957 177 IEDLDKIYEFAKEN 190
Cdd:COG2100  200 DEDIPKIIEWALEI 213
PRK13745 PRK13745
anaerobic sulfatase-maturation protein;
32-189 8.03e-04

anaerobic sulfatase-maturation protein;


Pssm-ID: 237489 [Multi-domain]  Cd Length: 412  Bit Score: 41.38  E-value: 8.03e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  32 CNLDCRMC-YVRKTK---QEVNELGGEKTVEEWLELARECRDAGMLFLLLTGGEPFLYK-DFKRLYLELKKM---GFMI- 102
Cdd:PRK13745  24 CNLACDYCyYLEKSKlyqENPKHVMSDELLEKFIKEYINSQTMPQVLFTWHGGETLMRPlSFYKKALELQKKyarGRQId 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957 103 -SINTNGTLIDEEVVSWLSKNpPYRMQITLyGGSNETYERLCRDNKG---FDKTTKAIKMLKEAGIAIKINASMTQYNIE 178
Cdd:PRK13745 104 nCIQTNGTLLTDEWCEFFREN-NFLVGVSI-DGPQEFHDEYRKNKMGkpsFVKVMKGINLLKKHGVEWNAMAVVNDFNAD 181

                        170
                 ....*....|.
gi 429188957 179 DLDKIYEFAKE 189
Cdd:PRK13745 182 YPLDFYHFFKE 192
PLN02951 PLN02951
Molybderin biosynthesis protein CNX2
 28-200 9.23e-04

Molybderin biosynthesis protein CNX2


Pssm-ID: 215513 [Multi-domain]  Cd Length: 373  Bit Score: 40.89  E-value: 9.23e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957  28 LSPCCNLDCRMCY----VRKTKQEvnELggeKTVEEWLELARECRDAGMLFLLLTGGEPFLYKDFKRLYLELKK-MGF-M 101
Cdd:PLN02951  64 LTERCNLRCQYCMpeegVELTPKS--HL---LSQDEIVRLAGLFVAAGVDKIRLTGGEPTLRKDIEDICLQLSSlKGLkT 138

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957 102 ISINTNGTLideevvswLSKNPP-------YRMQITLYGGSNETYERLCRdNKGFDKTTKAIKMLKEAGI-AIKIN-ASM 172
Cdd:PLN02951 139 LAMTTNGIT--------LSRKLPrlkeaglTSLNISLDTLVPAKFEFLTR-RKGHDRVLESIDTAIELGYnPVKVNcVVM 209

                        170       180
                 ....*....|....*....|....*...
gi 429188957 173 TQYNIEDLDKIYEFAKENNVYVQATSYM 200
Cdd:PLN02951 210 RGFNDDEICDFVELTRDKPINVRFIEFM 237
Fer4_14 pfam13394
4Fe-4S single cluster domain;
32-113 1.30e-03

4Fe-4S single cluster domain;


Pssm-ID: 433171 [Multi-domain]  Cd Length: 115  Bit Score: 38.11  E-value: 1.30e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 429188957   32 CNLDCRMCYVRKTKqevNELGGEKTVEEwlELARECRDAGML-----FLLLTGGEPFLY---KDFKRLYLELKKMG--FM 101
Cdd:pfam13394   6 CNHSCPGCDNKETW---KFNYGEPFTEE--LEDQIIADLKDSyikrqGLVLTGGEPLHPwnlPVLLKLLKRVKEEYpsKD 80

                          90
                  ....*....|..
gi 429188957  102 ISINTNGTLIDE 113
Cdd:pfam13394  81 IWLETGYTLAID 92
SPASM pfam13186
Iron-sulfur cluster-binding domain; This domain occurs as an additional C-terminal iron-sulfur ...
 290-346 4.80e-03

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: 35.53  E-value: 4.80e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 429188957  290 CRAGKSSFWINWKGEMTACGMMNWPVAYPF----KEGLIPAW----YKIIDETDKLRMPKKCTKC 346
Cdd:pfam13186   1 CFAGWTSLVILPDGDVYPCFDDDFVGPIVLgnirEQSLAEIWnspkYREFRKLGKFALIELCRDC 65
 
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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