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Conserved domains on  [gi|651250891|ref|WP_026385731|]
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putative 7-carboxy-7-deazaguanine synthase QueE [Acidaminococcus intestini]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rSAM_QueE_Clost TIGR03963
putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, clostridial; Members of ...
 6-218 4.71e-136

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: 380.19  E-value: 4.71e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891    6 FPVVEIFDSIDGEGKRTGYMATFVRFAGCNLRCSYCDTAYAWDASQAKEWLSEDNLFQQITAYPWKRVTLTGGEPMLQP- 84
Cdd:TIGR03963   1 FKVVEKFVSINGEGKRAGELATFIRFAGCNLNCSYCDTTWANDKDCPYELLSADEIYDYIKETGVKNVTLTGGEPLLQEn 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891   85 IETLCR-RLGDAGYEVNIETNGAAAL--FLERPDRLFYTMDIKSPSSGEKDRMRWENLSLLTADDVLKFVVGSVEDLRYM 161
Cdd:TIGR03963  81 IDELIElLLGDAGLEVEIETNGSVDIapFKERPDRLIFTMDYKLPSSGMENNMCLDNLSYLTKKDVVKFVVGSIEDLEKA 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 651250891  162 ETILSTYSI--KAQIYVSPVFGKIEPVALVDFVKHHQLSRVCVQVQLHKVIWDPEARGV 218
Cdd:TIGR03963 161 KEIISKYNLteKCQVYFSPVFGKIEPEEIVEFMKEHHLNGVRLQLQLHKVIWDPEMRGV 219
 
Name Accession Description Interval E-value
rSAM_QueE_Clost TIGR03963
putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, clostridial; Members of ...
 6-218 4.71e-136

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: 380.19  E-value: 4.71e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891    6 FPVVEIFDSIDGEGKRTGYMATFVRFAGCNLRCSYCDTAYAWDASQAKEWLSEDNLFQQITAYPWKRVTLTGGEPMLQP- 84
Cdd:TIGR03963   1 FKVVEKFVSINGEGKRAGELATFIRFAGCNLNCSYCDTTWANDKDCPYELLSADEIYDYIKETGVKNVTLTGGEPLLQEn 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891   85 IETLCR-RLGDAGYEVNIETNGAAAL--FLERPDRLFYTMDIKSPSSGEKDRMRWENLSLLTADDVLKFVVGSVEDLRYM 161
Cdd:TIGR03963  81 IDELIElLLGDAGLEVEIETNGSVDIapFKERPDRLIFTMDYKLPSSGMENNMCLDNLSYLTKKDVVKFVVGSIEDLEKA 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 651250891  162 ETILSTYSI--KAQIYVSPVFGKIEPVALVDFVKHHQLSRVCVQVQLHKVIWDPEARGV 218
Cdd:TIGR03963 161 KEIISKYNLteKCQVYFSPVFGKIEPEEIVEFMKEHHLNGVRLQLQLHKVIWDPEMRGV 219
QueE COG0602
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic ...
 5-210 2.03e-79

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: 236.19  E-value: 2.03e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891   5 RFPVVEIFDSIDGEGKRTGYMATFVRFAGCNLRCSYCDTAYAWDASqAKEWLSEDNLFQQITAYPWKRVTLTGGEPMLQP 84
Cdd:COG0602    1 TLPIVEIFYSIQGEGALAGRPAVFVRLAGCNLRCSWCDTKYAWDGE-GGKRMSAEEILEEVAALGARHVVITGGEPLLQD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891  85 -IETLCRRLGDAGYEVNIETNGAAALFLERpDRLfyTMDIKSPSSGEKDRMrWENLSLLTADDVLKFVVGSVEDLRYMET 163
Cdd:COG0602   80 dLAELLEALKDAGYEVALETNGTLPIPAGI-DWV--TVSPKLPSSGEEEDN-RENLEVLRRADELKFVVADETDLEEAEE 155

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 651250891 164 ILSTYSIKAQIYVSPVFG-KIE--PVALVDFVKHHQlsRVCVQVQLHKVI 210
Cdd:COG0602  156 LLARLDFRCPVYLQPVWGnKLEenTELLAEWCLAHP--NVRLSPQLHKLL 203
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 33-151 2.92e-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: 56.77  E-value: 2.92e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891   33 GCNLRCSYCDTAYAWDASQAKEwLSEDNLFQQITAY---PWKRVTLTGGEPMLQP-----IETLCRRLGDAGYEVNIETN 104
Cdd:pfam04055   4 GCNLRCTYCAFPSIRARGKGRE-LSPEEILEEAKELkrlGVEVVILGGGEPLLLPdlvelLERLLKLELAEGIRITLETN 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 651250891  105 GaAALFLERPDRL------FYTMDIKSPSSGEKDRMRWENlsllTADDVLKFV 151
Cdd:pfam04055  83 G-TLLDEELLELLkeagldRVSIGLESGDDEVLKLINRGH----TFEEVLEAL 130
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 33-165 2.13e-07

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: 49.64  E-value: 2.13e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891  33 GCNLRCSYCdtAYAWDASQAKEWLSEDNLFQQITAYPWKR----VTLTGGEPMLQP-----IETLCRRLGdaGYEVNIET 103
Cdd:cd01335    6 GCNLNCGFC--SNPASKGRGPESPPEIEEILDIVLEAKERgvevVILTGGEPLLYPelaelLRRLKKELP--GFEISIET 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891 104 NG-------AAALFLERPDRLFYTMDIKSP-------SSGEKDRMRWENLSLLTADDVlKFVVGSV------EDLRYMET 163
Cdd:cd01335   82 NGtllteelLKELKELGLDGVGVSLDSGDEevadkirGSGESFKERLEALKELREAGL-GLSTTLLvglgdeDEEDDLEE 160


                 ..
gi 651250891 164 IL 165
Cdd:cd01335  161 LE 162
pflA PRK11145
pyruvate formate lyase 1-activating protein;
1-105 4.28e-07

pyruvate formate lyase 1-activating protein;


Pssm-ID: 182994 [Multi-domain]  Cd Length: 246  Bit Score: 48.87  E-value: 4.28e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891   1 MKTERFPVVEIFDSIDGEGKRtgymatFVRF-AGCNLRCSYCDTAYAWDASQAKEwLSEDNLFQQITAYpwkR------- 72
Cdd:PRK11145   2 SVIGRIHSFESCGTVDGPGIR------FITFfQGCLMRCLYCHNRDTWDTHGGKE-VTVEELMKEVVTY---Rhfmnasg 71

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 651250891  73 --VTLTGGEPMLQP--IETLCRRLGDAGYEVNIETNG 105
Cdd:PRK11145  72 ggVTASGGEAILQAefVRDWFRACKKEGIHTCLDTNG 108
N_Twi_rSAM NF033640
twitch domain-containing radical SAM protein; Members of this family are unusual among radical ...
 34-105 4.51e-04

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: 40.33  E-value: 4.51e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891  34 CNLRCSYCDTAY--AWDASQAK------------EWLSEDNLFQQItaYPW----KRVTLTGGEPMLQPiET-----LCR 90
Cdd:NF033640 120 CNLKCRMCGPHSssSWAKEAKKlggpklgdkkkiSWFEDEEFWKWL--EELlpslKEIYFAGGEPLLIK-EHyklleKLV 196

                         90
                 ....*....|....*.
gi 651250891  91 RLGDAGY-EVNIETNG 105
Cdd:NF033640 197 EKGRAKNiELRYNTNL 212
 
Name Accession Description Interval E-value
rSAM_QueE_Clost TIGR03963
putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, clostridial; Members of ...
 6-218 4.71e-136

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: 380.19  E-value: 4.71e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891    6 FPVVEIFDSIDGEGKRTGYMATFVRFAGCNLRCSYCDTAYAWDASQAKEWLSEDNLFQQITAYPWKRVTLTGGEPMLQP- 84
Cdd:TIGR03963   1 FKVVEKFVSINGEGKRAGELATFIRFAGCNLNCSYCDTTWANDKDCPYELLSADEIYDYIKETGVKNVTLTGGEPLLQEn 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891   85 IETLCR-RLGDAGYEVNIETNGAAAL--FLERPDRLFYTMDIKSPSSGEKDRMRWENLSLLTADDVLKFVVGSVEDLRYM 161
Cdd:TIGR03963  81 IDELIElLLGDAGLEVEIETNGSVDIapFKERPDRLIFTMDYKLPSSGMENNMCLDNLSYLTKKDVVKFVVGSIEDLEKA 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 651250891  162 ETILSTYSI--KAQIYVSPVFGKIEPVALVDFVKHHQLSRVCVQVQLHKVIWDPEARGV 218
Cdd:TIGR03963 161 KEIISKYNLteKCQVYFSPVFGKIEPEEIVEFMKEHHLNGVRLQLQLHKVIWDPEMRGV 219
QueE COG0602
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic ...
 5-210 2.03e-79

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: 236.19  E-value: 2.03e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891   5 RFPVVEIFDSIDGEGKRTGYMATFVRFAGCNLRCSYCDTAYAWDASqAKEWLSEDNLFQQITAYPWKRVTLTGGEPMLQP 84
Cdd:COG0602    1 TLPIVEIFYSIQGEGALAGRPAVFVRLAGCNLRCSWCDTKYAWDGE-GGKRMSAEEILEEVAALGARHVVITGGEPLLQD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891  85 -IETLCRRLGDAGYEVNIETNGAAALFLERpDRLfyTMDIKSPSSGEKDRMrWENLSLLTADDVLKFVVGSVEDLRYMET 163
Cdd:COG0602   80 dLAELLEALKDAGYEVALETNGTLPIPAGI-DWV--TVSPKLPSSGEEEDN-RENLEVLRRADELKFVVADETDLEEAEE 155

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 651250891 164 ILSTYSIKAQIYVSPVFG-KIE--PVALVDFVKHHQlsRVCVQVQLHKVI 210
Cdd:COG0602  156 LLARLDFRCPVYLQPVWGnKLEenTELLAEWCLAHP--NVRLSPQLHKLL 203
rSAM_QueE_gams TIGR04349
putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, gammaproteobacterial type; ...
 8-217 7.54e-62

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: 192.05  E-value: 7.54e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891    8 VVEIFDSIDGEGKRTGYMATFVRFAGCNLRCSYCDTAYAWdasQAKEWLSEDNLFQQITAYPWKRVTLTGGEPMLQP-IE 86
Cdd:TIGR04349   3 ITEIFYSLQGETSTVGLPTVFVRLTGCPLRCVYCDTAYAF---SGGERMSLDDILAQVASYGARYVTVTGGEPLAQPaCL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891   87 TLCRRLGDAGYEVNIETNGaaALFLERPD-RLFYTMDIKSPSSGEKDRMRWENLSLLTADDVLKFVVGSVEDLRYMETIL 165
Cdd:TIGR04349  80 PLLTALCDAGYEVSLETSG--ALDISGVDpRVVKVMDLKTPGSGEVARNLWENLALLTPHDQIKFVLCDRADYDWARQKL 157

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 651250891  166 STYSI--KAQIYVSPVFGKIEPVALVDFVKHHQLsRVCVQVQLHKVIWDpEARG 217
Cdd:TIGR04349 158 REHALaeRCEVLFSPVYGQLAPADLAEWILADRL-PVRFQLQLHKLLWG-DAPG 209
Bsubt_queE TIGR03365
7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; This uncharacterized enzyme, ...
 4-218 3.48e-30

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: 111.68  E-value: 3.48e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891    4 ERFPVVEIFD-SIDGEGKRTGYMATFVRFAGCNLRCSYCDTAYAWDASQAKEW--LSEDNLFQQITAYPWKR---VTLTG 77
Cdd:TIGR03365   1 KKIPVLEIFGpTIQGEGMVIGQKTMFVRTAGCDYRCSWCDSAFTWDGSAKDDWrpMTAEEIWQELKALGGGTflhVTLSG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891   78 GEPMLQ-PIETLCRRLGDAGYEVNIETNGAAAL-FLERPDRLfyTMDIKSPSSGEKdrMRWENLS--LLTADD----VLK 149
Cdd:TIGR03365  81 GNPALQkPLGELIDLLHEKGYRFALETQGSVWQdWFTDIDDL--TLSPKPPSSGME--TDWQKLDdcIERLGPgpqiSLK 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891  150 FVVGSVEDLRYMETILSTYSiKAQIYVSP----------------VFGKIEpvALVDFV-KHHQLSRVCVQVQLHKVIWD 212
Cdd:TIGR03365 157 VVVFDDADYAYAKTVHARYP-HLPFYLQPgnhtpppsddddlidgLLDRME--WLVDKVaADREWFDVRVLPQLHTLLWG 233


                  ....*.
gi 651250891  213 PEaRGV 218
Cdd:TIGR03365 234 NK-RGV 238
SkfB COG0535
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
 34-117 2.27e-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: 62.61  E-value: 2.27e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891  34 CNLRCSYCdtaYAWDASQAKEWLSED---NLFQQITAYPWKRVTLTGGEPMLQP-IETLCRRLGDAGYEVNIETNGaAAL 109
Cdd:COG0535   10 CNLRCKHC---YADAGPKRPGELSTEeakRILDELAELGVKVVGLTGGEPLLRPdLFELVEYAKELGIRVNLSTNG-TLL 85


                 ....*...
gi 651250891 110 FLERPDRL 117
Cdd:COG0535   86 TEELAERL 93
PflA COG1180
Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, ...
 12-142 2.38e-12

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


Pssm-ID: 440793 [Multi-domain]  Cd Length: 242  Bit Score: 64.05  E-value: 2.38e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891  12 FDSIDGEGKRTgyMATFvrFAGCNLRCSYCdtaYAWDASQAK-----EWLSEDNLFQQITAY-PWKR----VTLTGGEPM 81
Cdd:COG1180   13 FSTVDGPGSIR--LSVF--TQGCNLRCPYC---HNPEISQGRpdaagRELSPEELVEEALKDrGFLDscggVTFSGGEPT 85

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 651250891  82 LQP--IETLCRRLGDAGYEVNIETNGaaALFLERPDRLF-YT----MDIKSPSS-------GEKDRMRWENLSLL 142
Cdd:COG1180   86 LQPefLLDLAKLAKELGLHTALDTNG--YIPEEALEELLpYLdavnIDLKAFDDefyrkltGVSLEPVLENLELL 158
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 33-151 2.92e-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: 56.77  E-value: 2.92e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891   33 GCNLRCSYCDTAYAWDASQAKEwLSEDNLFQQITAY---PWKRVTLTGGEPMLQP-----IETLCRRLGDAGYEVNIETN 104
Cdd:pfam04055   4 GCNLRCTYCAFPSIRARGKGRE-LSPEEILEEAKELkrlGVEVVILGGGEPLLLPdlvelLERLLKLELAEGIRITLETN 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 651250891  105 GaAALFLERPDRL------FYTMDIKSPSSGEKDRMRWENlsllTADDVLKFV 151
Cdd:pfam04055  83 G-TLLDEELLELLkeagldRVSIGLESGDDEVLKLINRGH----TFEEVLEAL 130
Fer4_12 pfam13353
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
 15-92 4.01e-08

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: 50.25  E-value: 4.01e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891   15 IDGEGKRTgymatFVRFAGCNLRCSYCDTAYAWDASQAKEWlsEDNLFQQITAYPWKR----VTLTGGEPMLQPIET--L 88
Cdd:pfam13353   1 VNGPGVRC-----SLFVSGCNHHCKGCFNPETWDFKYGKPF--TEELEDEIIEDLAKPyiqgLTLSGGEPLLNAEALleL 73


                  ....
gi 651250891   89 CRRL 92
Cdd:pfam13353  74 VKRV 77
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 33-165 2.13e-07

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: 49.64  E-value: 2.13e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891  33 GCNLRCSYCdtAYAWDASQAKEWLSEDNLFQQITAYPWKR----VTLTGGEPMLQP-----IETLCRRLGdaGYEVNIET 103
Cdd:cd01335    6 GCNLNCGFC--SNPASKGRGPESPPEIEEILDIVLEAKERgvevVILTGGEPLLYPelaelLRRLKKELP--GFEISIET 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891 104 NG-------AAALFLERPDRLFYTMDIKSP-------SSGEKDRMRWENLSLLTADDVlKFVVGSV------EDLRYMET 163
Cdd:cd01335   82 NGtllteelLKELKELGLDGVGVSLDSGDEevadkirGSGESFKERLEALKELREAGL-GLSTTLLvglgdeDEEDDLEE 160


                 ..
gi 651250891 164 IL 165
Cdd:cd01335  161 LE 162
NrdG2 TIGR02495
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
 22-126 3.59e-07

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: 48.51  E-value: 3.59e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891   22 TGYMATFVRFAGCNLRCSYCDTAYAWDAsQAKEWLSEDNLFQQITaypwKR------VTLTGGEPMLQP-IETLCRRLGD 94
Cdd:TIGR02495  14 PGKLAFTIFLQGCNLKCPYCHNPLLIPR-RGSGEIEVEELLEFLR----RRrglldgVVITGGEPTLQAgLPDFLREVRE 88

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 651250891   95 AGYEVNIETNG----AAALFLERPDRLFYTMDIKSP 126
Cdd:TIGR02495  89 LGFEVKLDTNGsnprRLEELLEEGLVDYVAMDVKAP 124
Fer4_14 pfam13394
4Fe-4S single cluster domain;
31-115 3.66e-07

4Fe-4S single cluster domain;


Pssm-ID: 433171 [Multi-domain]  Cd Length: 115  Bit Score: 47.36  E-value: 3.66e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891   31 FAGCNLRCSYCDTAYAWDaSQAKEWLSEDNLFQQITA-----YPWKRVTLTGGEPM----LQPIETLCRRLGD--AGYEV 99
Cdd:pfam13394   3 VSGCNHSCPGCDNKETWK-FNYGEPFTEELEDQIIADlkdsyIKRQGLVLTGGEPLhpwnLPVLLKLLKRVKEeyPSKDI 81

                          90
                  ....*....|....*.
gi 651250891  100 NIETNGAAALFLERPD 115
Cdd:pfam13394  82 WLETGYTLAIDFEYPD 97
moaA TIGR02666
molybdenum cofactor biosynthesis protein A, bacterial; The model for this family describes ...
 34-113 4.27e-07

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: 49.53  E-value: 4.27e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891   34 CNLRCSYC---DTAYAWdaSQAKEWLSEDNLFQQITAYP---WKRVTLTGGEPMLQP-IETLCRRLG--DAGYEVNIETN 104
Cdd:TIGR02666  20 CNLRCVYCmpeGGGLDF--LPKEELLTFEEIERLVRAFVglgVRKVRLTGGEPLLRKdLVELVARLAalPGIEDIALTTN 97


                  ....*....
gi 651250891  105 GaaaLFLER 113
Cdd:TIGR02666  98 G---LLLAR 103
pflA PRK11145
pyruvate formate lyase 1-activating protein;
1-105 4.28e-07

pyruvate formate lyase 1-activating protein;


Pssm-ID: 182994 [Multi-domain]  Cd Length: 246  Bit Score: 48.87  E-value: 4.28e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891   1 MKTERFPVVEIFDSIDGEGKRtgymatFVRF-AGCNLRCSYCDTAYAWDASQAKEwLSEDNLFQQITAYpwkR------- 72
Cdd:PRK11145   2 SVIGRIHSFESCGTVDGPGIR------FITFfQGCLMRCLYCHNRDTWDTHGGKE-VTVEELMKEVVTY---Rhfmnasg 71

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 651250891  73 --VTLTGGEPMLQP--IETLCRRLGDAGYEVNIETNG 105
Cdd:PRK11145  72 ggVTASGGEAILQAefVRDWFRACKKEGIHTCLDTNG 108
SCM_rSAM_ScmF TIGR04251
SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in ...
 33-105 1.93e-06

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: 47.53  E-value: 1.93e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 651250891   33 GCNLRCSYCDTAYAWDASQAKEWLSEDNLFQQIT--AYPW--KRVTLTGGEPMLQP-IETLCRRLGDAGYEVNIETNG 105
Cdd:TIGR04251  13 GCNLKCRHCWIDPKYQGEGEQHPSLDPSLFRSIIrqAIPLglTSVKLTGGEPLLHPaIGEILECIGENNLQLSVETNG 90
PLN02951 PLN02951
Molybderin biosynthesis protein CNX2
 34-105 2.14e-06

Molybderin biosynthesis protein CNX2


Pssm-ID: 215513 [Multi-domain]  Cd Length: 373  Bit Score: 47.44  E-value: 2.14e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 651250891  34 CNLRCSYCDTAYAWDASQAKEWLSEDNLFQQITAYPWKRVT---LTGGEPMLQP-IETLCRRL-GDAG-YEVNIETNG 105
Cdd:PLN02951  68 CNLRCQYCMPEEGVELTPKSHLLSQDEIVRLAGLFVAAGVDkirLTGGEPTLRKdIEDICLQLsSLKGlKTLAMTTNG 145
moaA PRK00164
GTP 3',8-cyclase MoaA;
34-110 8.03e-06

GTP 3',8-cyclase MoaA;


Pssm-ID: 234672 [Multi-domain]  Cd Length: 331  Bit Score: 45.52  E-value: 8.03e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891  34 CNLRCSYC--DTAYAWDASQakEWLSEDNLFQQITA---YPWKRVTLTGGEPMLQP-IETLCRRLGDAGY--EVNIETNG 105
Cdd:PRK00164  27 CNFRCTYCmpEGYLPFLPKE--ELLSLEEIERLVRAfvaLGVRKVRLTGGEPLLRKdLEDIIAALAALPGirDLALTTNG 104

                         90
                 ....*....|.
gi 651250891 106 ------AAALF 110
Cdd:PRK00164 105 yllarrAAALK 115
AslB COG0641
Sulfatase maturation enzyme AslB, radical SAM superfamily [Posttranslational modification, ...
 34-105 8.98e-06

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


Pssm-ID: 440406 [Multi-domain]  Cd Length: 349  Bit Score: 45.36  E-value: 8.98e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891  34 CNLRCSYCdtaYAWD-ASQAKEWLSE-------DNLFQQITAYPWKRVTLTGGEPMLQP--IETLC---RRLGDAGYEVN 100
Cdd:COG0641   11 CNLRCSYC---YYSEgDEGSRRRMSEetaekaiDFLIESSGPGKELTITFFGGEPLLNFdfIKEIVeyaRKYAKKGKKIR 87


                 ....*..
gi 651250891 101 --IETNG 105
Cdd:COG0641   88 fsIQTNG 94
MoaA COG2896
GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) [Coenzyme transport and ...
 34-109 2.22e-05

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: 44.28  E-value: 2.22e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891  34 CNLRCSYC--DTAYAWDASqaKEWLSednlFQQITaypwkRVT------------LTGGEPMLQP-IETLCRRLGDAG-- 96
Cdd:COG2896   24 CNFRCTYCmpEEGYQFLPK--EELLS----FEEIE-----RLVrafvelgvrkirLTGGEPLLRKdLPELIARLAALPgi 92

                         90
                 ....*....|....*....
gi 651250891  97 YEVNIETNG------AAAL 109
Cdd:COG2896   93 EDLALTTNGsllaryAEAL 111
N_Twi_rSAM NF033640
twitch domain-containing radical SAM protein; Members of this family are unusual among radical ...
 34-105 4.51e-04

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: 40.33  E-value: 4.51e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891  34 CNLRCSYCDTAY--AWDASQAK------------EWLSEDNLFQQItaYPW----KRVTLTGGEPMLQPiET-----LCR 90
Cdd:NF033640 120 CNLKCRMCGPHSssSWAKEAKKlggpklgdkkkiSWFEDEEFWKWL--EELlpslKEIYFAGGEPLLIK-EHyklleKLV 196

                         90
                 ....*....|....*.
gi 651250891  91 RLGDAGY-EVNIETNG 105
Cdd:NF033640 197 EKGRAKNiELRYNTNL 212
TM0948 COG5014
Uncharacterized conserved protein TM0948, MoaA-related, radical SAM superfamily [General ...
 33-105 1.36e-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: 1.36e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 651250891  33 GCNLRCSYCDT-AYAWDASQAKEWLSEDNLFQQITAYPWKR----VTLTGGEP------MLQPIETlcrrLGDAGYEVNI 101
Cdd:COG5014   49 GCNLRCGFCWSwRFRDFPLTIGKFYSPEEVAERLIEIARERgyrqVRLSGGEPtigfehLLKVLEL----FSERGLTFIL 124


                 ....
gi 651250891 102 ETNG 105
Cdd:COG5014  125 ETNG 128
sulfatase_rSAM TIGR03942
anaerobic sulfatase-maturating enzyme; Members of this protein family are radical SAM family ...
 32-86 3.35e-03

anaerobic sulfatase-maturating enzyme; Members of this protein family are radical SAM family enzymes, maturases that prepare the oxygen-sensitive radical required in the active site of anaerobic sulfatases. This maturase role has led to many misleading legacy annotations suggesting that this enzyme maturase is instead a sulfatase regulatory protein. All members of the seed alignment are radical SAM enzymes encoded next to or near an anaerobic sulfatase. Note that a single genome may encode more than one sulfatase/maturase pair. [Protein fate, Protein modification and repair]


Pssm-ID: 188457 [Multi-domain]  Cd Length: 363  Bit Score: 37.59  E-value: 3.35e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 651250891   32 AGCNLRCSYC-----DTAYAwdasQAKEWLSEDNL--F--QQITAYPWKRVTLT--GGEPMLQPIE 86
Cdd:TIGR03942   9 AKCNLDCDYCfylekEDLYP----KPKPKMSDETLetFikQYIASQDGPEVNFAwqGGEPTLAGLD 70
SCM_rSAM_ScmE TIGR04250
SynChlorMet cassette radical SAM/SPASM protein ScmE; A biosynthesis cassette found in ...
 34-80 9.38e-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: 36.37  E-value: 9.38e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 651250891   34 CNLRCSYCdTAYAWDASQAK-----EWLsedNLFQQITAYPWKRVTLTGGEP 80
Cdd:TIGR04250  13 CNLRCRYC-SHFSSAAETPTdletaEWL---RFFRELNRCSVLRVVLSGGEP 60
 
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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