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Conserved domains on  [gi|446079869|ref|WP_000157724|]
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MULTISPECIES: 7-carboxy-7-deazaguanine synthase QueE [Acinetobacter]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rSAM_QueE_gams super family cl30230
putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, gammaproteobacterial type; ...
 18-236 1.42e-141

putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, gammaproteobacterial type; Members of this radical SAM domain protein family appear to be a form of the queuosine biosynthesis protein QueE. QueE is involved in making preQ0 (7-cyano-7-deazaquanine), a precursor of both the bacterial/eukaryotic modified tRNA base queuosine and the archaeal modified base archaeosine. Members occur in preQ0 operons species that lack members of related protein family TIGR03365.


The actual alignment was detected with superfamily member TIGR04349:

Pssm-ID: 275145 [Multi-domain]  Cd Length: 210  Bit Score: 394.66  E-value: 1.42e-141
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869   18 LRITEIFYSLQGEANASGLPTVFIRLTGCPLRCSYCDTTYSFEGGERLSLEHIIETAEKYQTPYICVTGGEPLAQPNCLI 97
Cdd:TIGR04349   1 LRITEIFYSLQGETSTVGLPTVFVRLTGCPLRCVYCDTAYAFSGGERMSLDDILAQVASYGARYVTVTGGEPLAQPACLP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869   98 LLQRLCDAGFDVSLETSGALDVSRVDPRVSKVLDLKTPTSGEEHRNLISNLDHLTPRDQIKFVICNREDYEWSKQQVEQY 177
Cdd:TIGR04349  81 LLTALCDAGYEVSLETSGALDISGVDPRVVKVMDLKTPGSGEVARNLWENLALLTPHDQIKFVLCDRADYDWARQKLREH 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 446079869  178 QLQTKVStVWFSPAFAVEKgavglprlARDLAQWILDDKLPVRFQLQLHKLLWNDESGR 236
Cdd:TIGR04349 161 ALAERCE-VLFSPVYGQLA--------PADLAEWILADRLPVRFQLQLHKLLWGDAPGR 210
 
Name Accession Description Interval E-value
rSAM_QueE_gams TIGR04349
putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, gammaproteobacterial type; ...
 18-236 1.42e-141

putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, gammaproteobacterial type; Members of this radical SAM domain protein family appear to be a form of the queuosine biosynthesis protein QueE. QueE is involved in making preQ0 (7-cyano-7-deazaquanine), a precursor of both the bacterial/eukaryotic modified tRNA base queuosine and the archaeal modified base archaeosine. Members occur in preQ0 operons species that lack members of related protein family TIGR03365.


Pssm-ID: 275145 [Multi-domain]  Cd Length: 210  Bit Score: 394.66  E-value: 1.42e-141
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869   18 LRITEIFYSLQGEANASGLPTVFIRLTGCPLRCSYCDTTYSFEGGERLSLEHIIETAEKYQTPYICVTGGEPLAQPNCLI 97
Cdd:TIGR04349   1 LRITEIFYSLQGETSTVGLPTVFVRLTGCPLRCVYCDTAYAFSGGERMSLDDILAQVASYGARYVTVTGGEPLAQPACLP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869   98 LLQRLCDAGFDVSLETSGALDVSRVDPRVSKVLDLKTPTSGEEHRNLISNLDHLTPRDQIKFVICNREDYEWSKQQVEQY 177
Cdd:TIGR04349  81 LLTALCDAGYEVSLETSGALDISGVDPRVVKVMDLKTPGSGEVARNLWENLALLTPHDQIKFVLCDRADYDWARQKLREH 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 446079869  178 QLQTKVStVWFSPAFAVEKgavglprlARDLAQWILDDKLPVRFQLQLHKLLWNDESGR 236
Cdd:TIGR04349 161 ALAERCE-VLFSPVYGQLA--------PADLAEWILADRLPVRFQLQLHKLLWGDAPGR 210
QueE COG0602
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic ...
 18-229 3.27e-90

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: 264.31  E-value: 3.27e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869  18 LRITEIFYSLQGEANASGLPTVFIRLTGCPLRCSYCDTTYSFEG--GERLSLEHIIETAEKYQTPYICVTGGEPLAQPNC 95
Cdd:COG0602    2 LPIVEIFYSIQGEGALAGRPAVFVRLAGCNLRCSWCDTKYAWDGegGKRMSAEEILEEVAALGARHVVITGGEPLLQDDL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869  96 LILLQRLCDAGFDVSLETSGALDVSRVDPRVSkvLDLKTPTSGEEHRNlISNLDHLTPRDQIKFVICNREDYEWSKQQVE 175
Cdd:COG0602   82 AELLEALKDAGYEVALETNGTLPIPAGIDWVT--VSPKLPSSGEEEDN-RENLEVLRRADELKFVVADETDLEEAEELLA 158

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446079869 176 QYQLQTKvstVWFSPAFAVEkgavgLPRLARDLAQWILDDKlPVRFQLQLHKLL 229
Cdd:COG0602  159 RLDFRCP---VYLQPVWGNK-----LEENTELLAEWCLAHP-NVRLSPQLHKLL 203
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 44-175 5.22e-10

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: 56.38  E-value: 5.22e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869   44 TGCPLRCSYCDTTYSFEGGER--LSLEHIIETAEKYQ---TPYICVTGGEPLAQPNCLILLQRLC----DAGFDVSLETS 114
Cdd:pfam04055   3 RGCNLRCTYCAFPSIRARGKGreLSPEEILEEAKELKrlgVEVVILGGGEPLLLPDLVELLERLLklelAEGIRITLETN 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446079869  115 GaldvSRVDPRVSKVLDlktptsgEEHRNLIS-NLDHLTPRdqIKFVICNREDYEWSKQQVE 175
Cdd:pfam04055  83 G----TLLDEELLELLK-------EAGLDRVSiGLESGDDE--VLKLINRGHTFEEVLEALE 131
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 44-117 1.47e-08

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: 53.11  E-value: 1.47e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869  44 TGCPLRCSYC--DTTYSFEGGERLSLEHIIE---TAEKYQTPYICVTGGEPLAQPNCLILLQRLCD--AGFDVSLETSGA 116
Cdd:cd01335    5 RGCNLNCGFCsnPASKGRGPESPPEIEEILDivlEAKERGVEVVILTGGEPLLYPELAELLRRLKKelPGFEISIETNGT 84


                 .
gi 446079869 117 L 117
Cdd:cd01335   85 L 85
pflA PRK11145
pyruvate formate lyase 1-activating protein;
43-161 2.08e-06

pyruvate formate lyase 1-activating protein;


Pssm-ID: 182994 [Multi-domain]  Cd Length: 246  Bit Score: 47.33  E-value: 2.08e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869  43 LTGCPLRCSYCDT--TYSFEGGERLSLEHIIETAEKYQtPY-------ICVTGGEPLAQPNCLILLQRLCDA-GFDVSLE 112
Cdd:PRK11145  27 FQGCLMRCLYCHNrdTWDTHGGKEVTVEELMKEVVTYR-HFmnasgggVTASGGEAILQAEFVRDWFRACKKeGIHTCLD 105

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446079869 113 TSGAldVSRVDPRVSKV--------LDLKTpTSGEEHRNLI--SN---LD---HLTPRDQ---IKFVI 161
Cdd:PRK11145 106 TNGF--VRRYDPVIDELldvtdlvmLDLKQ-MNDEIHQNLVgvSNhrtLEfarYLAKRNQktwIRYVV 170
 
Name Accession Description Interval E-value
rSAM_QueE_gams TIGR04349
putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, gammaproteobacterial type; ...
 18-236 1.42e-141

putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, gammaproteobacterial type; Members of this radical SAM domain protein family appear to be a form of the queuosine biosynthesis protein QueE. QueE is involved in making preQ0 (7-cyano-7-deazaquanine), a precursor of both the bacterial/eukaryotic modified tRNA base queuosine and the archaeal modified base archaeosine. Members occur in preQ0 operons species that lack members of related protein family TIGR03365.


Pssm-ID: 275145 [Multi-domain]  Cd Length: 210  Bit Score: 394.66  E-value: 1.42e-141
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869   18 LRITEIFYSLQGEANASGLPTVFIRLTGCPLRCSYCDTTYSFEGGERLSLEHIIETAEKYQTPYICVTGGEPLAQPNCLI 97
Cdd:TIGR04349   1 LRITEIFYSLQGETSTVGLPTVFVRLTGCPLRCVYCDTAYAFSGGERMSLDDILAQVASYGARYVTVTGGEPLAQPACLP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869   98 LLQRLCDAGFDVSLETSGALDVSRVDPRVSKVLDLKTPTSGEEHRNLISNLDHLTPRDQIKFVICNREDYEWSKQQVEQY 177
Cdd:TIGR04349  81 LLTALCDAGYEVSLETSGALDISGVDPRVVKVMDLKTPGSGEVARNLWENLALLTPHDQIKFVLCDRADYDWARQKLREH 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 446079869  178 QLQTKVStVWFSPAFAVEKgavglprlARDLAQWILDDKLPVRFQLQLHKLLWNDESGR 236
Cdd:TIGR04349 161 ALAERCE-VLFSPVYGQLA--------PADLAEWILADRLPVRFQLQLHKLLWGDAPGR 210
QueE COG0602
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic ...
 18-229 3.27e-90

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: 264.31  E-value: 3.27e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869  18 LRITEIFYSLQGEANASGLPTVFIRLTGCPLRCSYCDTTYSFEG--GERLSLEHIIETAEKYQTPYICVTGGEPLAQPNC 95
Cdd:COG0602    2 LPIVEIFYSIQGEGALAGRPAVFVRLAGCNLRCSWCDTKYAWDGegGKRMSAEEILEEVAALGARHVVITGGEPLLQDDL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869  96 LILLQRLCDAGFDVSLETSGALDVSRVDPRVSkvLDLKTPTSGEEHRNlISNLDHLTPRDQIKFVICNREDYEWSKQQVE 175
Cdd:COG0602   82 AELLEALKDAGYEVALETNGTLPIPAGIDWVT--VSPKLPSSGEEEDN-RENLEVLRRADELKFVVADETDLEEAEELLA 158

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446079869 176 QYQLQTKvstVWFSPAFAVEkgavgLPRLARDLAQWILDDKlPVRFQLQLHKLL 229
Cdd:COG0602  159 RLDFRCP---VYLQPVWGNK-----LEENTELLAEWCLAHP-NVRLSPQLHKLL 203
rSAM_QueE_Clost TIGR03963
putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, clostridial; Members of ...
 19-233 3.37e-51

putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, clostridial; Members of this radical SAM domain protein family appear to be the Clostridial form of the queuosine biosynthesis protein QueE. QueE is involved in making preQ0 (7-cyano-7-deazaquanine), a precursor of both the bacterial/eukaryotic modified tRNA base queuosine and the archaeal modified base archaeosine. Members occur in preQ0 operons species that lack members of related protein family TIGR03365. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 188478 [Multi-domain]  Cd Length: 219  Bit Score: 165.64  E-value: 3.37e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869   19 RITEIFYSLQGEANASGLPTVFIRLTGCPLRCSYCDTTYSFEGG---ERLSLEHIIETAEKYQTPYICVTGGEPLAQPNC 95
Cdd:TIGR03963   2 KVVEKFVSINGEGKRAGELATFIRFAGCNLNCSYCDTTWANDKDcpyELLSADEIYDYIKETGVKNVTLTGGEPLLQENI 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869   96 LILLQ-RLCDAGFDVSLETSGALDVS---RVDPRVSKVLDLKTPTSGEEHRNLISNLDHLTPRDQIKFVICNREDYEWSK 171
Cdd:TIGR03963  82 DELIElLLGDAGLEVEIETNGSVDIApfkERPDRLIFTMDYKLPSSGMENNMCLDNLSYLTKKDVVKFVVGSIEDLEKAK 161

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446079869  172 QQVEQYQLQTKvSTVWFSPAFavekGAVGLprlaRDLAQWILDDKL-PVRFQLQLHKLLWNDE 233
Cdd:TIGR03963 162 EIISKYNLTEK-CQVYFSPVF----GKIEP----EEIVEFMKEHHLnGVRLQLQLHKVIWDPE 215
Bsubt_queE TIGR03365
7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; This uncharacterized enzyme, ...
 16-235 5.63e-23

7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; This uncharacterized enzyme, designated QueE, participates in the biosynthesis, from GTP, of 7-cyano-7-deazaguanosine, also called preQ0 because in many species it is a precursor of queuosine. In most Archaea, it is instead the precursor of a different tRNA modified base, archaeosine. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 274545  Cd Length: 238  Bit Score: 93.19  E-value: 5.63e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869   16 SGLRITEIF-YSLQGEANASGLPTVFIRLTGCPLRCSYCDTTYSFEGGER-----LSLEHIIETAEKY--QTP-YICVTG 86
Cdd:TIGR03365   1 KKIPVLEIFgPTIQGEGMVIGQKTMFVRTAGCDYRCSWCDSAFTWDGSAKddwrpMTAEEIWQELKALggGTFlHVTLSG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869   87 GEPLAQPNCLILLQRLCDAGFDVSLETSGaldvSRVDPRVSKVLDL----KTPTSGEEHR-----NLISNLDHlTPRDQI 157
Cdd:TIGR03365  81 GNPALQKPLGELIDLLHEKGYRFALETQG----SVWQDWFTDIDDLtlspKPPSSGMETDwqkldDCIERLGP-GPQISL 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869  158 KFVICNREDYEWSKQQVEQYQ-----LQTKVSTVwfsPAFAVEKGAVGLPRLARDLAQWILDDKL--PVRFQLQLHKLLW 230
Cdd:TIGR03365 156 KVVVFDDADYAYAKTVHARYPhlpfyLQPGNHTP---PPSDDDDLIDGLLDRMEWLVDKVAADREwfDVRVLPQLHTLLW 232


                  ....*
gi 446079869  231 NDESG 235
Cdd:TIGR03365 233 GNKRG 237
PflA COG1180
Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, ...
 38-145 1.30e-16

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


Pssm-ID: 440793 [Multi-domain]  Cd Length: 242  Bit Score: 75.99  E-value: 1.30e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869  38 TVFirLTGCPLRCSYC---DTTYS--FEGGERLSLEHIIETAEKYQTPY-----ICVTGGEPLAQPNCLI-LLQRLCDAG 106
Cdd:COG1180   25 SVF--TQGCNLRCPYChnpEISQGrpDAAGRELSPEELVEEALKDRGFLdscggVTFSGGEPTLQPEFLLdLAKLAKELG 102

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 446079869 107 FDVSLETSGALDVSRVD---PRVSKV-LDLKTPTSgEEHRNLI 145
Cdd:COG1180  103 LHTALDTNGYIPEEALEellPYLDAVnIDLKAFDD-EFYRKLT 144
SkfB COG0535
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
 38-117 4.26e-13

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: 64.92  E-value: 4.26e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869  38 TVFIRLTG-CPLRCSYCDTTYSFEGGERLSLE---HIIETAEKYQTPYICVTGGEPLAQPNCLILLQRLCDAGFDVSLET 113
Cdd:COG0535    1 RLQIELTNrCNLRCKHCYADAGPKRPGELSTEeakRILDELAELGVKVVGLTGGEPLLRPDLFELVEYAKELGIRVNLST 80


                 ....
gi 446079869 114 SGAL 117
Cdd:COG0535   81 NGTL 84
PFLA TIGR02493
pyruvate formate-lyase 1-activating enzyme; An iron-sulfur protein with a radical-SAM domain ...
 38-132 2.31e-10

pyruvate formate-lyase 1-activating enzyme; An iron-sulfur protein with a radical-SAM domain (pfam04055). A single glycine residue in EC 2.3.1.54, formate C-acetyltransferase (formate-pyruvate lyase), is oxidized to the corresponding radical by transfer of H from its CH2 to AdoMet with concomitant cleavage of the latter. The reaction requires Fe2+. The first stage is reduction of the AdoMet to give methionine and the 5'-deoxyadenosin-5-yl radical, which then abstracts a hydrogen radical from the glycine residue. [Energy metabolism, Anaerobic, Protein fate, Protein modification and repair]


Pssm-ID: 131546 [Multi-domain]  Cd Length: 235  Bit Score: 58.53  E-value: 2.31e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869   38 TVFirLTGCPLRCSYCDT--TYSFEGGERLSLEHIIETAEKYQTPY------ICVTGGEPLAQPNCLILLQRLC-DAGFD 108
Cdd:TIGR02493  19 VVF--MQGCPLRCQYCHNpdTWDLKGGTEVTPEELIKEVGSYKDFFkasgggVTFSGGEPLLQPEFLSELFKACkELGIH 96

                          90       100
                  ....*....|....*....|....*
gi 446079869  109 VSLETSGAL-DVSRVDPRVSKVLDL 132
Cdd:TIGR02493  97 TCLDTSGFLgGCTEAADELLEYTDL 121
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 44-175 5.22e-10

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: 56.38  E-value: 5.22e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869   44 TGCPLRCSYCDTTYSFEGGER--LSLEHIIETAEKYQ---TPYICVTGGEPLAQPNCLILLQRLC----DAGFDVSLETS 114
Cdd:pfam04055   3 RGCNLRCTYCAFPSIRARGKGreLSPEEILEEAKELKrlgVEVVILGGGEPLLLPDLVELLERLLklelAEGIRITLETN 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446079869  115 GaldvSRVDPRVSKVLDlktptsgEEHRNLIS-NLDHLTPRdqIKFVICNREDYEWSKQQVE 175
Cdd:pfam04055  83 G----TLLDEELLELLK-------EAGLDRVSiGLESGDDE--VLKLINRGHTFEEVLEALE 131
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 44-117 1.47e-08

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: 53.11  E-value: 1.47e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869  44 TGCPLRCSYC--DTTYSFEGGERLSLEHIIE---TAEKYQTPYICVTGGEPLAQPNCLILLQRLCD--AGFDVSLETSGA 116
Cdd:cd01335    5 RGCNLNCGFCsnPASKGRGPESPPEIEEILDivlEAKERGVEVVILTGGEPLLYPELAELLRRLKKelPGFEISIETNGT 84


                 .
gi 446079869 117 L 117
Cdd:cd01335   85 L 85
Fer4_14 pfam13394
4Fe-4S single cluster domain;
45-151 1.91e-08

4Fe-4S single cluster domain;


Pssm-ID: 433171 [Multi-domain]  Cd Length: 115  Bit Score: 51.21  E-value: 1.91e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869   45 GCPLRCSYCD--TTYSFEGGERLSLE---HIIETAEKYQTP--YICVTGGEPLA---QPNCLILLQRL---CDaGFDVSL 111
Cdd:pfam13394   5 GCNHSCPGCDnkETWKFNYGEPFTEEledQIIADLKDSYIKrqGLVLTGGEPLHpwnLPVLLKLLKRVkeeYP-SKDIWL 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 446079869  112 ETSGALDvsrvdprvskvLDLKTPTSgEEHRNLISNLDHL 151
Cdd:pfam13394  84 ETGYTLA-----------IDFEYPDT-EEQLFTLSVIDVL 111
NrdG2 TIGR02495
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
 35-115 4.63e-08

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: 51.60  E-value: 4.63e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869   35 GLPTVFIRLTGCPLRCSYCDTTY--SFEGGERLSLEHIIETAEKYQ--TPYICVTGGEPLAQPNCLILLQRLCDAGFDVS 110
Cdd:TIGR02495  15 GKLAFTIFLQGCNLKCPYCHNPLliPRRGSGEIEVEELLEFLRRRRglLDGVVITGGEPTLQAGLPDFLREVRELGFEVK 94


                  ....*
gi 446079869  111 LETSG 115
Cdd:TIGR02495  95 LDTNG 99
pflA PRK11145
pyruvate formate lyase 1-activating protein;
43-161 2.08e-06

pyruvate formate lyase 1-activating protein;


Pssm-ID: 182994 [Multi-domain]  Cd Length: 246  Bit Score: 47.33  E-value: 2.08e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869  43 LTGCPLRCSYCDT--TYSFEGGERLSLEHIIETAEKYQtPY-------ICVTGGEPLAQPNCLILLQRLCDA-GFDVSLE 112
Cdd:PRK11145  27 FQGCLMRCLYCHNrdTWDTHGGKEVTVEELMKEVVTYR-HFmnasgggVTASGGEAILQAEFVRDWFRACKKeGIHTCLD 105

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446079869 113 TSGAldVSRVDPRVSKV--------LDLKTpTSGEEHRNLI--SN---LD---HLTPRDQ---IKFVI 161
Cdd:PRK11145 106 TNGF--VRRYDPVIDELldvtdlvmLDLKQ-MNDEIHQNLVgvSNhrtLEfarYLAKRNQktwIRYVV 170
Fer4_12 pfam13353
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
 39-102 2.68e-05

4Fe-4S single cluster domain; This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.


Pssm-ID: 433138 [Multi-domain]  Cd Length: 137  Bit Score: 42.54  E-value: 2.68e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869   39 VFIRLTGCPLRCSYC--DTTYSFEGGERLS---LEHIIETAEKYQTPYICVTGGEPLAQ-PNCLILLQRL 102
Cdd:pfam13353   8 CSLFVSGCNHHCKGCfnPETWDFKYGKPFTeelEDEIIEDLAKPYIQGLTLSGGEPLLNaEALLELVKRV 77
SCM_rSAM_ScmF TIGR04251
SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in ...
 36-131 1.25e-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: 42.52  E-value: 1.25e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869   36 LPTVFIRLT-GCPLRCSYC--DTTYSFEGGERLSLE-----HIIETAEKYQTPYICVTGGEPLAQPNCLILLQRLCDAGF 107
Cdd:TIGR04251   3 LHQIYFYLTeGCNLKCRHCwiDPKYQGEGEQHPSLDpslfrSIIRQAIPLGLTSVKLTGGEPLLHPAIGEILECIGENNL 82

                          90       100       110
                  ....*....|....*....|....*....|..
gi 446079869  108 DVSLETSGAL---DVSRV-----DPRVSKVLD 131
Cdd:TIGR04251  83 QLSVETNGLLctpQTARDlasceTPFVSVSLD 114
moaA TIGR02666
molybdenum cofactor biosynthesis protein A, bacterial; The model for this family describes ...
 46-117 1.56e-04

molybdenum cofactor biosynthesis protein A, bacterial; The model for this family describes molybdenum cofactor biosynthesis protein A, or MoaA, as found in bacteria. It does not include the family of probable functional equivalent proteins from the archaea. MoaA works together with MoaC to synthesize precursor Z from guanine. [Biosynthesis of cofactors, prosthetic groups, and carriers, Molybdopterin]


Pssm-ID: 274250 [Multi-domain]  Cd Length: 334  Bit Score: 41.83  E-value: 1.56e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869   46 CPLRCSYC---DTTYSFEGGERL----SLEHIIETAEKYQTPYICVTGGEPLAQPNCLILLQRL--CDAGFDVSLETSGA 116
Cdd:TIGR02666  20 CNLRCVYCmpeGGGLDFLPKEELltfeEIERLVRAFVGLGVRKVRLTGGEPLLRKDLVELVARLaaLPGIEDIALTTNGL 99


                  .
gi 446079869  117 L 117
Cdd:TIGR02666 100 L 100
AslB COG0641
Sulfatase maturation enzyme AslB, radical SAM superfamily [Posttranslational modification, ...
 46-117 2.63e-04

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


Pssm-ID: 440406 [Multi-domain]  Cd Length: 349  Bit Score: 41.51  E-value: 2.63e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869  46 CPLRCSYC---------DTTYSFEGGERLsLEHIIETAEKYQTPYICVTGGEPLAQP----NCLILLQRLCDAG--FDVS 110
Cdd:COG0641   11 CNLRCSYCyysegdegsRRRMSEETAEKA-IDFLIESSGPGKELTITFFGGEPLLNFdfikEIVEYARKYAKKGkkIRFS 89


                 ....*..
gi 446079869 111 LETSGAL 117
Cdd:COG0641   90 IQTNGTL 96
TM0948 COG5014
Uncharacterized conserved protein TM0948, MoaA-related, radical SAM superfamily [General ...
 45-117 1.47e-03

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


Pssm-ID: 444038  Cd Length: 261  Bit Score: 38.82  E-value: 1.47e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869  45 GCPLRCSYC----DTTYSFEGGERLS----LEHIIETAEKYQTPYICVTGGEPLAQPNCLI-LLQRLCDAGFDVSLETSG 115
Cdd:COG5014   49 GCNLRCGFCwswrFRDFPLTIGKFYSpeevAERLIEIARERGYRQVRLSGGEPTIGFEHLLkVLELFSERGLTFILETNG 128


                 ..
gi 446079869 116 AL 117
Cdd:COG5014  129 IL 130
COG2108 COG2108
Uncharacterized radical SAM domain-containing protein [Function unknown];
38-117 2.35e-03

Uncharacterized radical SAM domain-containing protein [Function unknown];


Pssm-ID: 441711 [Multi-domain]  Cd Length: 361  Bit Score: 38.41  E-value: 2.35e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869  38 TVFIrlTG-CPLRCSYC---------DTTYSfegGERL--SLEHIIETAEKYQTPYICVTGGEPLAQP----NCLILLQR 101
Cdd:COG2108   30 VLFI--TGlCNRNCFYCplseerkgkDVIYA---NERPveSDEDVIEEARRMGALGAGITGGEPLLVLdrtlEYIRLLKE 104

                         90
                 ....*....|....*.
gi 446079869 102 LCDAGFDVSLETSGAL 117
Cdd:COG2108  105 EFGPDHHIHLYTNGIL 120
YgiQ COG1032
Radical SAM superfamily enzyme YgiQ, UPF0313 family [General function prediction only];
45-126 5.28e-03

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


Pssm-ID: 440655 [Multi-domain]  Cd Length: 394  Bit Score: 37.62  E-value: 5.28e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446079869  45 GCPLRCSYCDTTYSFEGGERL-SLEHIIETAE----KYQTPYICVTGGEPLAQPNCLI-LLQRLCDAGFDVSLetSGALD 118
Cdd:COG1032  183 GCPFGCSFCSISALYGRKVRYrSPESVVEEIEelvkRYGIREIFFVDDNFNVDKKRLKeLLEELIERGLNVSF--PSEVR 260


                 ....*...
gi 446079869 119 VSRVDPRV 126
Cdd:COG1032  261 VDLLDEEL 268
moaA PRK00164
GTP 3',8-cyclase MoaA;
46-90 6.50e-03

GTP 3',8-cyclase MoaA;


Pssm-ID: 234672 [Multi-domain]  Cd Length: 331  Bit Score: 37.04  E-value: 6.50e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446079869  46 CPLRCSYC--DTTYSFEGGER-LSLEHIIETA--------EKyqtpyICVTGGEPL 90
Cdd:PRK00164  27 CNFRCTYCmpEGYLPFLPKEElLSLEEIERLVrafvalgvRK-----VRLTGGEPL 77
 
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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