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Conserved domains on  [gi|1595694710|ref|WP_133302805|]
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radical SAM protein, partial [Bacteroides sp. AF04-22]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SkfB super family cl43172
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
 6-104 2.41e-12

Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, chromosome partitioning, Coenzyme transport and metabolism];


The actual alignment was detected with superfamily member COG0535:

Pssm-ID: 440301 [Multi-domain]  Cd Length: 159  Bit Score: 60.69  E-value: 2.41e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1595694710   6 IIEVDITHRCNLICRHCNRlcnaenqYAIVRNSLDMDMRHIDYLCREIKSIRkgsIETIRILGGEPLLSK-ILEpavqAF 84
Cdd:COG0535     1 RLQIELTNRCNLRCKHCYA-------DAGPKRPGELSTEEAKRILDELAELG---VKVVGLTGGEPLLRPdLFE----LV 66

                          90       100
                  ....*....|....*....|
gi 1595694710  85 ELLKDEGYIsnINIVTNGTL 104
Cdd:COG0535    67 EYAKELGIR--VNLSTNGTL 84
 
Name Accession Description Interval E-value
SkfB COG0535
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
 6-104 2.41e-12

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: 60.69  E-value: 2.41e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1595694710   6 IIEVDITHRCNLICRHCNRlcnaenqYAIVRNSLDMDMRHIDYLCREIKSIRkgsIETIRILGGEPLLSK-ILEpavqAF 84
Cdd:COG0535     1 RLQIELTNRCNLRCKHCYA-------DAGPKRPGELSTEEAKRILDELAELG---VKVVGLTGGEPLLRPdLFE----LV 66

                          90       100
                  ....*....|....*....|
gi 1595694710  85 ELLKDEGYIsnINIVTNGTL 104
Cdd:COG0535    67 EYAKELGIR--VNLSTNGTL 84
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 11-110 2.36e-06

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: 44.44  E-value: 2.36e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1595694710  11 ITHRCNLICRHCNRlcnaeNQYAIVRNSLDMDMRHIDylcREIKSIRKGSIETIRILGGEPLLSKILEPAVQAFELLKDE 90
Cdd:pfam04055   1 ITRGCNLRCTYCAF-----PSIRARGKGRELSPEEIL---EEAKELKRLGVEVVILGGGEPLLLPDLVELLERLLKLELA 72

                          90       100
                  ....*....|....*....|
gi 1595694710  91 GYISnINIVTNGTLPIPAYC 110
Cdd:pfam04055  73 EGIR-ITLETNGTLLDEELL 91
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 9-107 3.46e-06

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: 44.63  E-value: 3.46e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1595694710   9 VDITHRCNLICRHCNRlcNAENQYAIVRNSLDMDMRHIDYlcreikSIRKGSIETIRILGGEPLLskiLEPAVQAFELLK 88
Cdd:cd01335     1 LELTRGCNLNCGFCSN--PASKGRGPESPPEIEEILDIVL------EAKERGVEVVILTGGEPLL---YPELAELLRRLK 69

                          90
                  ....*....|....*....
gi 1595694710  89 DEGYISNINIVTNGTLPIP 107
Cdd:cd01335    70 KELPGFEISIETNGTLLTE 88
moaA PRK00164
GTP 3',8-cyclase MoaA;
11-104 4.88e-05

GTP 3',8-cyclase MoaA;


Pssm-ID: 234672 [Multi-domain]  Cd Length: 331  Bit Score: 41.67  E-value: 4.88e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1595694710  11 ITHRCNLICRHCNRlcnaENQYAIVRNSLDMDMRHIDYLCREikSIRKGsIETIRILGGEPLLSKILEPAVQAfelLKDE 90
Cdd:PRK00164   23 VTDRCNFRCTYCMP----EGYLPFLPKEELLSLEEIERLVRA--FVALG-VRKVRLTGGEPLLRKDLEDIIAA---LAAL 92

                          90
                  ....*....|....
gi 1595694710  91 GYISNINIVTNGTL 104
Cdd:PRK00164   93 PGIRDLALTTNGYL 106
SCM_rSAM_ScmF TIGR04251
SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in ...
 11-112 1.97e-04

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: 40.21  E-value: 1.97e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1595694710  11 ITHRCNLICRHC---NRLCNAENQYAivrnSLDMDM-RHIdylcreIKSIRKGSIETIRILGGEPLlskiLEPAV-QAFE 85
Cdd:TIGR04251  10 LTEGCNLKCRHCwidPKYQGEGEQHP----SLDPSLfRSI------IRQAIPLGLTSVKLTGGEPL----LHPAIgEILE 75

                          90       100
                  ....*....|....*....|....*..
gi 1595694710  86 LLKDEGYisNINIVTNGTLpipayCSP 112
Cdd:TIGR04251  76 CIGENNL--QLSVETNGLL-----CTP 95
 
Name Accession Description Interval E-value
SkfB COG0535
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
 6-104 2.41e-12

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: 60.69  E-value: 2.41e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1595694710   6 IIEVDITHRCNLICRHCNRlcnaenqYAIVRNSLDMDMRHIDYLCREIKSIRkgsIETIRILGGEPLLSK-ILEpavqAF 84
Cdd:COG0535     1 RLQIELTNRCNLRCKHCYA-------DAGPKRPGELSTEEAKRILDELAELG---VKVVGLTGGEPLLRPdLFE----LV 66

                          90       100
                  ....*....|....*....|
gi 1595694710  85 ELLKDEGYIsnINIVTNGTL 104
Cdd:COG0535    67 EYAKELGIR--VNLSTNGTL 84
AslB COG0641
Sulfatase maturation enzyme AslB, radical SAM superfamily [Posttranslational modification, ...
 11-104 1.13e-06

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


Pssm-ID: 440406 [Multi-domain]  Cd Length: 349  Bit Score: 46.52  E-value: 1.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1595694710  11 ITHRCNLICRHcnrlCNAENQYAIVRNSLDMDM--RHIDYLcreIKSIRKGSIETIRILGGEPLLS-KILEPAVQAFELL 87
Cdd:COG0641     7 PTSRCNLRCSY----CYYSEGDEGSRRRMSEETaeKAIDFL---IESSGPGKELTITFFGGEPLLNfDFIKEIVEYARKY 79

                          90
                  ....*....|....*..
gi 1595694710  88 KDEGYISNINIVTNGTL 104
Cdd:COG0641    80 AKKGKKIRFSIQTNGTL 96
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 11-110 2.36e-06

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: 44.44  E-value: 2.36e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1595694710  11 ITHRCNLICRHCNRlcnaeNQYAIVRNSLDMDMRHIDylcREIKSIRKGSIETIRILGGEPLLSKILEPAVQAFELLKDE 90
Cdd:pfam04055   1 ITRGCNLRCTYCAF-----PSIRARGKGRELSPEEIL---EEAKELKRLGVEVVILGGGEPLLLPDLVELLERLLKLELA 72

                          90       100
                  ....*....|....*....|
gi 1595694710  91 GYISnINIVTNGTLPIPAYC 110
Cdd:pfam04055  73 EGIR-ITLETNGTLLDEELL 91
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 9-107 3.46e-06

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: 44.63  E-value: 3.46e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1595694710   9 VDITHRCNLICRHCNRlcNAENQYAIVRNSLDMDMRHIDYlcreikSIRKGSIETIRILGGEPLLskiLEPAVQAFELLK 88
Cdd:cd01335     1 LELTRGCNLNCGFCSN--PASKGRGPESPPEIEEILDIVL------EAKERGVEVVILTGGEPLL---YPELAELLRRLK 69

                          90
                  ....*....|....*....
gi 1595694710  89 DEGYISNINIVTNGTLPIP 107
Cdd:cd01335    70 KELPGFEISIETNGTLLTE 88
moaA PRK00164
GTP 3',8-cyclase MoaA;
11-104 4.88e-05

GTP 3',8-cyclase MoaA;


Pssm-ID: 234672 [Multi-domain]  Cd Length: 331  Bit Score: 41.67  E-value: 4.88e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1595694710  11 ITHRCNLICRHCNRlcnaENQYAIVRNSLDMDMRHIDYLCREikSIRKGsIETIRILGGEPLLSKILEPAVQAfelLKDE 90
Cdd:PRK00164   23 VTDRCNFRCTYCMP----EGYLPFLPKEELLSLEEIERLVRA--FVALG-VRKVRLTGGEPLLRKDLEDIIAA---LAAL 92

                          90
                  ....*....|....
gi 1595694710  91 GYISNINIVTNGTL 104
Cdd:PRK00164   93 PGIRDLALTTNGYL 106
QueE COG0602
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic ...
 15-118 5.98e-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: 41.28  E-value: 5.98e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1595694710  15 CNLICRHCNrlcnaenqyaiVRNSLDMD---MRHIDYLCREIKSIRKGSIEtirILGGEPLLSKILEPAVQAfelLKDEG 91
Cdd:COG0602    30 CNLRCSWCD-----------TKYAWDGEggkRMSAEEILEEVAALGARHVV---ITGGEPLLQDDLAELLEA---LKDAG 92

                          90       100
                  ....*....|....*....|....*..
gi 1595694710  92 YisNINIVTNGTLPIPAYCsPYIVFAP 118
Cdd:COG0602    93 Y--EVALETNGTLPIPAGI-DWVTVSP 116
PflA COG1180
Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, ...
 15-105 1.60e-04

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


Pssm-ID: 440793 [Multi-domain]  Cd Length: 242  Bit Score: 40.17  E-value: 1.60e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1595694710  15 CNLICRHCnrlCNAEnqyaIVRNSLDMDMRHI--DYLCREIKSiRKGSIETIR---ILGGEPLLSkiLEPAVQAFELLKD 89
Cdd:COG1180    31 CNLRCPYC---HNPE----ISQGRPDAAGRELspEELVEEALK-DRGFLDSCGgvtFSGGEPTLQ--PEFLLDLAKLAKE 100

                          90
                  ....*....|....*.
gi 1595694710  90 EGYisNINIVTNGTLP 105
Cdd:COG1180   101 LGL--HTALDTNGYIP 114
SCM_rSAM_ScmF TIGR04251
SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in ...
 11-112 1.97e-04

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: 40.21  E-value: 1.97e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1595694710  11 ITHRCNLICRHC---NRLCNAENQYAivrnSLDMDM-RHIdylcreIKSIRKGSIETIRILGGEPLlskiLEPAV-QAFE 85
Cdd:TIGR04251  10 LTEGCNLKCRHCwidPKYQGEGEQHP----SLDPSLfRSI------IRQAIPLGLTSVKLTGGEPL----LHPAIgEILE 75

                          90       100
                  ....*....|....*....|....*..
gi 1595694710  86 LLKDEGYisNINIVTNGTLpipayCSP 112
Cdd:TIGR04251  76 CIGENNL--QLSVETNGLL-----CTP 95
PLN02951 PLN02951
Molybderin biosynthesis protein CNX2
 9-102 2.27e-03

Molybderin biosynthesis protein CNX2


Pssm-ID: 215513 [Multi-domain]  Cd Length: 373  Bit Score: 37.04  E-value: 2.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1595694710   9 VDITHRCNLICRHCNrlcnAENQYAIVRNSldmDMRHIDYLCREIKSIRKGSIETIRILGGEPLLSKILEPAVQAFELLK 88
Cdd:PLN02951   62 ISLTERCNLRCQYCM----PEEGVELTPKS---HLLSQDEIVRLAGLFVAAGVDKIRLTGGEPTLRKDIEDICLQLSSLK 134

                          90
                  ....*....|....
gi 1595694710  89 DegyISNINIVTNG 102
Cdd:PLN02951  135 G---LKTLAMTTNG 145
SCM_rSAM_ScmE TIGR04250
SynChlorMet cassette radical SAM/SPASM protein ScmE; A biosynthesis cassette found in ...
 7-104 4.96e-03

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: 35.99  E-value: 4.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1595694710   7 IEVDITHRCNLICRHCNRLCNAenqyaivrNSLDMDMRHIDYLcREIKSIRKGSIETIRILGGEPLLSKILEpavqafEL 86
Cdd:TIGR04250   5 VDIDITGRCNLRCRYCSHFSSA--------AETPTDLETAEWL-RFFRELNRCSVLRVVLSGGEPFMRSDFR------EI 69

                          90       100
                  ....*....|....*....|.
gi 1595694710  87 LkdEGYISN---INIVTNGTL 104
Cdd:TIGR04250  70 I--DGIVKNrmrFSILSNGTL 88
rSAM_w_lipo TIGR04133
radical SAM enzyme, rSAM/lipoprotein system; Members of this protein family are radical SAM ...
 12-102 6.33e-03

radical SAM enzyme, rSAM/lipoprotein system; Members of this protein family are radical SAM enzymes with an additional 4Fe4S cluster-binding C-terminal domain (TIGR04085) shared with PqqE and many other peptide and protein-modifying radical SAM enzymes. All members occur in the context of a predicted lipoprotein that usually is encoded by an adjacent gene.


Pssm-ID: 200384 [Multi-domain]  Cd Length: 350  Bit Score: 35.47  E-value: 6.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1595694710  12 THRCNLICRHCNRLCnaenqyaiVRNSLDMDMRHIDYL--CREIKSIRKGSIETIRILGGEPLLSKILEPAVQAfelLKD 89
Cdd:TIGR04133  31 TLRCNLACLHCGSDC--------KKDSSVPDMPLEDFLkvLDSITPHVDPHDVLVIITGGEPLVRPDLEEIGRE---LYR 99

                          90
                  ....*....|...
gi 1595694710  90 EGYisNINIVTNG 102
Cdd:TIGR04133 100 RGY--PWGMVTNG 110
MoaA COG2896
GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) [Coenzyme transport and ...
 11-104 9.01e-03

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: 35.04  E-value: 9.01e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1595694710  11 ITHRCNLICRHCNrlcnAENQYAIVRN----SLDmdmrHIDYLCREikSIRKGsIETIRILGGEPLLSKILEPAVQAfel 86
Cdd:COG2896    20 VTDRCNFRCTYCM----PEEGYQFLPKeellSFE----EIERLVRA--FVELG-VRKIRLTGGEPLLRKDLPELIAR--- 85

                          90
                  ....*....|....*...
gi 1595694710  87 LKDEGYISNINIVTNGTL 104
Cdd:COG2896    86 LAALPGIEDLALTTNGSL 103
 
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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