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Conserved domains on  [gi|16132196|ref|NP_418796|]
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putative glycyl-radical enzyme activating enzyme YjjW [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

YjjW family glycine radical enzyme activase( domain architecture ID 11499336)

YjjW family glycine radical enzyme activase is a radical SAM protein that is paired with and appears to activate a glycyl radical enzyme of unknown function, designated YjjI

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
activase_YjjW TIGR04041
glycine radical enzyme activase, YjjW family; Members of this family are radical SAM enzymes, ...
 5-283 1.38e-168

glycine radical enzyme activase, YjjW family; Members of this family are radical SAM enzymes, designated YjjW in E. coli, that are paired with and appear to activate a glycyl radical enzyme of unknown function, designated YjjI. This activase and its target are found in Clostridial species as well as E. coli and cousins. Members of this family may be misannotated as pyruvate formate lyase activating enzyme. [Protein fate, Protein modification and repair]


:

Pssm-ID: 274938 [Multi-domain]  Cd Length: 276  Bit Score: 467.88  E-value: 1.38e-168
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196     5 CALVSKIIPFSCVDGPGSRLALFLQGCNLRCKNCHNPWTMGRCNDCGECVPQCPHQALQIVDGKVVWNAVVCEQCDTCLK 84
Cdd:TIGR04041   1 KALVNKIIPFSCVDGPGNRLAIFLQGCNFDCKYCHNPETINHCDHCGDCVAGCPAGALSLVDGKVVWDKERCIGCDTCIK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196    85 RCPQHATPMAQSMSVDEVLSHVRKAVLFIEGITVSGGEATTQLPFVVALFTAIKNdpqlRHLTCLVDSNGMLSETGWEKL 164
Cdd:TIGR04041  81 VCPHQSSPKTKEYTVEELLDRIRKNMPFIRGITVSGGECTLQLDFLTELFKAIKA----AGLTCFIDSNGSLDLTGWPKL 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196   165 LPVCDGAMLDLKAWGSECHQQLTGRDNQQIKRSIYLLAERGKLAELRLLVIPGQVDYLQHIEELAAFIKGLG-DVPVRLN 243
Cdd:TIGR04041 157 LPVLDGAMLDLKAWDSETHRWLTGRDNHRVLKNIRFLAELGKLYEVRLVHIPGLSDLEQEIDGLARFLGDLPsDTRIKLI 236

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 16132196   244 AFHAHGVYGEAQSWASATPEDVEPLADALKVRGVSRLIFP 283
Cdd:TIGR04041 237 AFRHHGVRGEALEWPSPTDEQMEELAEALIKRGFRDIILP 276
 
Name Accession Description Interval E-value
activase_YjjW TIGR04041
glycine radical enzyme activase, YjjW family; Members of this family are radical SAM enzymes, ...
 5-283 1.38e-168

glycine radical enzyme activase, YjjW family; Members of this family are radical SAM enzymes, designated YjjW in E. coli, that are paired with and appear to activate a glycyl radical enzyme of unknown function, designated YjjI. This activase and its target are found in Clostridial species as well as E. coli and cousins. Members of this family may be misannotated as pyruvate formate lyase activating enzyme. [Protein fate, Protein modification and repair]


Pssm-ID: 274938 [Multi-domain]  Cd Length: 276  Bit Score: 467.88  E-value: 1.38e-168
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196     5 CALVSKIIPFSCVDGPGSRLALFLQGCNLRCKNCHNPWTMGRCNDCGECVPQCPHQALQIVDGKVVWNAVVCEQCDTCLK 84
Cdd:TIGR04041   1 KALVNKIIPFSCVDGPGNRLAIFLQGCNFDCKYCHNPETINHCDHCGDCVAGCPAGALSLVDGKVVWDKERCIGCDTCIK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196    85 RCPQHATPMAQSMSVDEVLSHVRKAVLFIEGITVSGGEATTQLPFVVALFTAIKNdpqlRHLTCLVDSNGMLSETGWEKL 164
Cdd:TIGR04041  81 VCPHQSSPKTKEYTVEELLDRIRKNMPFIRGITVSGGECTLQLDFLTELFKAIKA----AGLTCFIDSNGSLDLTGWPKL 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196   165 LPVCDGAMLDLKAWGSECHQQLTGRDNQQIKRSIYLLAERGKLAELRLLVIPGQVDYLQHIEELAAFIKGLG-DVPVRLN 243
Cdd:TIGR04041 157 LPVLDGAMLDLKAWDSETHRWLTGRDNHRVLKNIRFLAELGKLYEVRLVHIPGLSDLEQEIDGLARFLGDLPsDTRIKLI 236

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 16132196   244 AFHAHGVYGEAQSWASATPEDVEPLADALKVRGVSRLIFP 283
Cdd:TIGR04041 237 AFRHHGVRGEALEWPSPTDEQMEELAEALIKRGFRDIILP 276
PflA COG1180
Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, ...
 6-279 1.54e-69

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


Pssm-ID: 440793 [Multi-domain]  Cd Length: 242  Bit Score: 215.05  E-value: 1.54e-69
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196   6 ALVSKIIPFSCVDGPGS-RLALFLQGCNLRCKNCHNPWTMGRcndcgecvpqcphqalqivdgkvvwnavvceqcdtclk 84
Cdd:COG1180   5 GRIYGISPFSTVDGPGSiRLSVFTQGCNLRCPYCHNPEISQG-------------------------------------- 46

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196  85 rcpqHATPMAQSMSVDEVLSHVRKAVLFIE---GITVSGGEATTQLPFVVALFTAIKNdpqlRHLTCLVDSNGMLSETGW 161
Cdd:COG1180  47 ----RPDAAGRELSPEELVEEALKDRGFLDscgGVTFSGGEPTLQPEFLLDLAKLAKE----LGLHTALDTNGYIPEEAL 118

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196 162 EKLLPVCDGAMLDLKAWGSECHQQLTGRDNQQIKRSIYLLAERGKLAELRLLVIPGQVDYLQHIEELAAFIKGLGDV-PV 240
Cdd:COG1180 119 EELLPYLDAVNIDLKAFDDEFYRKLTGVSLEPVLENLELLAESGVHVEIRTLVIPGLNDSEEELEAIARFIAELGDViPV 198

                       250       260       270
                ....*....|....*....|....*....|....*....
gi 16132196 241 RLNAFHAHgvyGEAQSWASATPEDVEPLADALKVRGVSR 279
Cdd:COG1180 199 HLLPFHPL---YKLEDVPPPSPETLERAREIAREYGLKY 234
pflA PRK11145
pyruvate formate lyase 1-activating protein;
15-249 7.78e-26

pyruvate formate lyase 1-activating protein;


Pssm-ID: 182994 [Multi-domain]  Cd Length: 246  Bit Score: 102.41  E-value: 7.78e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196   15 SC--VDGPGSRLALFLQGCNLRCKNCHNPWTmgrcndcgecvpqcphqalqivdgkvvWnavvceqcDTclkrcpqHAtp 92
Cdd:PRK11145  12 SCgtVDGPGIRFITFFQGCLMRCLYCHNRDT---------------------------W--------DT-------HG-- 47

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196   93 mAQSMSVDEVLSHVRKAVLFIE----GITVSGGEATTQLPFVVALFTAIKNdpQLRHlTCLvDSNGMLS--ETGWEKLLP 166
Cdd:PRK11145  48 -GKEVTVEELMKEVVTYRHFMNasggGVTASGGEAILQAEFVRDWFRACKK--EGIH-TCL-DTNGFVRryDPVIDELLD 122

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196  167 VCDGAMLDLKAWGSECHQQLTGRDNQQIKRSIYLLAERGKLAELRLLVIPGQVDYLQHIEELAAFIKGLGDV-PVRLNAF 245
Cdd:PRK11145 123 VTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFARYLAKRNQKTWIRYVVVPGWTDDDDSAHRLGEFIKDMGNIeKIELLPY 202


                 ....
gi 16132196  246 HAHG 249
Cdd:PRK11145 203 HELG 206
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 27-271 2.21e-15

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: 73.14  E-value: 2.21e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196  27 FLQGCNLRCKNCHNPWTMGRCNDCGECVpqcphqalqivdgkvvwnavvceqcdtclkrcpqhatpmaqsmsVDEVLSHV 106
Cdd:cd01335   3 LTRGCNLNCGFCSNPASKGRGPESPPEI--------------------------------------------EEILDIVL 38

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196 107 RKAVLFIEGITVSGGEATTQLPFVVALFTAIKNDPqlrHLTCLVDSNGM-LSETGWEKLLP---VCDGAMLDLKAWGSEC 182
Cdd:cd01335  39 EAKERGVEVVILTGGEPLLYPELAELLRRLKKELP---GFEISIETNGTlLTEELLKELKElglDGVGVSLDSGDEEVAD 115

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196 183 HQQLTGRDNQQIKRSIYLLAERGKLAELRLLVIPGQVDYLQHIEELAAFIKGLGDVPVRLNAFHAHGVYGEAQSWASATP 262
Cdd:cd01335 116 KIRGSGESFKERLEALKELREAGLGLSTTLLVGLGDEDEEDDLEELELLAEFRSPDRVSLFRLLPEEGTPLELAAPVVPA 195


                ....*....
gi 16132196 263 EDVEPLADA 271
Cdd:cd01335 196 EKLLRLIAA 204
Fer4_12 pfam13353
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
 17-169 3.85e-09

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: 54.10  E-value: 3.85e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196    17 VDGPGSRLALFLQGCNLRCKNCHNPWTmgrcndcgecvpqcphqalqivdgkvvWNavvceqcdtclkrcPQHATPMAQS 96
Cdd:pfam13353   1 VNGPGVRCSLFVSGCNHHCKGCFNPET---------------------------WD--------------FKYGKPFTEE 39

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16132196    97 MsVDEVLSHVRKAvlFIEGITVSGGEATTQLPFVVALFTAIKN-DPQLRHLTCLVDSNGMLSETGWEKLLPVCD 169
Cdd:pfam13353  40 L-EDEIIEDLAKP--YIQGLTLSGGEPLLNAEALLELVKRVREeCPEKDIWLWTGYTFEELQSKDQLELLKLID 110
ferrodoxin_EFR1 NF038196
EFR1 family ferrodoxin; Members of the family have a C-terminal ferrodoxin domain, with eight ...
 46-90 3.53e-07

EFR1 family ferrodoxin; Members of the family have a C-terminal ferrodoxin domain, with eight conserved Cys residues in two CxxCxxCxxxCP motifs, each of which binds a 4Fe-4S cluster. The N-terminal region resembles flavodoxin domains, with some members of the family recognized by Pfam models PF12724 (Flavodoxin_5) or PF00258 (Flavodoxin_1).


Pssm-ID: 468407 [Multi-domain]  Cd Length: 243  Bit Score: 50.24  E-value: 3.53e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 16132196   46 RCNDCGECVPQCPHQALQIVDGKVVW--NavvCEQCDTCLKRCPQHA 90
Cdd:NF038196 186 KCIGCGICAKVCPVNNIEMEDGKPVWghN---CTHCLACIHRCPKEA 229
 
Name Accession Description Interval E-value
activase_YjjW TIGR04041
glycine radical enzyme activase, YjjW family; Members of this family are radical SAM enzymes, ...
 5-283 1.38e-168

glycine radical enzyme activase, YjjW family; Members of this family are radical SAM enzymes, designated YjjW in E. coli, that are paired with and appear to activate a glycyl radical enzyme of unknown function, designated YjjI. This activase and its target are found in Clostridial species as well as E. coli and cousins. Members of this family may be misannotated as pyruvate formate lyase activating enzyme. [Protein fate, Protein modification and repair]


Pssm-ID: 274938 [Multi-domain]  Cd Length: 276  Bit Score: 467.88  E-value: 1.38e-168
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196     5 CALVSKIIPFSCVDGPGSRLALFLQGCNLRCKNCHNPWTMGRCNDCGECVPQCPHQALQIVDGKVVWNAVVCEQCDTCLK 84
Cdd:TIGR04041   1 KALVNKIIPFSCVDGPGNRLAIFLQGCNFDCKYCHNPETINHCDHCGDCVAGCPAGALSLVDGKVVWDKERCIGCDTCIK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196    85 RCPQHATPMAQSMSVDEVLSHVRKAVLFIEGITVSGGEATTQLPFVVALFTAIKNdpqlRHLTCLVDSNGMLSETGWEKL 164
Cdd:TIGR04041  81 VCPHQSSPKTKEYTVEELLDRIRKNMPFIRGITVSGGECTLQLDFLTELFKAIKA----AGLTCFIDSNGSLDLTGWPKL 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196   165 LPVCDGAMLDLKAWGSECHQQLTGRDNQQIKRSIYLLAERGKLAELRLLVIPGQVDYLQHIEELAAFIKGLG-DVPVRLN 243
Cdd:TIGR04041 157 LPVLDGAMLDLKAWDSETHRWLTGRDNHRVLKNIRFLAELGKLYEVRLVHIPGLSDLEQEIDGLARFLGDLPsDTRIKLI 236

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 16132196   244 AFHAHGVYGEAQSWASATPEDVEPLADALKVRGVSRLIFP 283
Cdd:TIGR04041 237 AFRHHGVRGEALEWPSPTDEQMEELAEALIKRGFRDIILP 276
PflA COG1180
Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, ...
 6-279 1.54e-69

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


Pssm-ID: 440793 [Multi-domain]  Cd Length: 242  Bit Score: 215.05  E-value: 1.54e-69
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196   6 ALVSKIIPFSCVDGPGS-RLALFLQGCNLRCKNCHNPWTMGRcndcgecvpqcphqalqivdgkvvwnavvceqcdtclk 84
Cdd:COG1180   5 GRIYGISPFSTVDGPGSiRLSVFTQGCNLRCPYCHNPEISQG-------------------------------------- 46

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196  85 rcpqHATPMAQSMSVDEVLSHVRKAVLFIE---GITVSGGEATTQLPFVVALFTAIKNdpqlRHLTCLVDSNGMLSETGW 161
Cdd:COG1180  47 ----RPDAAGRELSPEELVEEALKDRGFLDscgGVTFSGGEPTLQPEFLLDLAKLAKE----LGLHTALDTNGYIPEEAL 118

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196 162 EKLLPVCDGAMLDLKAWGSECHQQLTGRDNQQIKRSIYLLAERGKLAELRLLVIPGQVDYLQHIEELAAFIKGLGDV-PV 240
Cdd:COG1180 119 EELLPYLDAVNIDLKAFDDEFYRKLTGVSLEPVLENLELLAESGVHVEIRTLVIPGLNDSEEELEAIARFIAELGDViPV 198

                       250       260       270
                ....*....|....*....|....*....|....*....
gi 16132196 241 RLNAFHAHgvyGEAQSWASATPEDVEPLADALKVRGVSR 279
Cdd:COG1180 199 HLLPFHPL---YKLEDVPPPSPETLERAREIAREYGLKY 234
PFLE_PFLC TIGR02494
glycyl-radical enzyme activating protein; This subset of the radical-SAM family (pfam04055) ...
 14-250 1.08e-42

glycyl-radical enzyme activating protein; This subset of the radical-SAM family (pfam04055) includes a number of probable activating proteins acting on different enzymes all requiring an amino-acid-centered radical. The closest relatives to this family are the pyruvate-formate lyase activating enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic ribonucleotide reductase activating enzyme (TIGR02491). Included within this subfamily are activators of hydroxyphenyl acetate decarboxylase (HdpA), benzylsuccinate synthase (BssD), gycerol dehydratase (DhaB2) as well as enzymes annotated in E. coli as activators of different isozymes of pyruvate-formate lyase (PFLC and PFLE) however, these appear to lack characterization and may activate enzymes with distinctive functions. Most of the sequence-level variability between these forms is concentrated within an N-terminal domain which follows a conserved group of three cysteines and contains a variable pattern of 0 to 8 additional cysteines.


Pssm-ID: 274163 [Multi-domain]  Cd Length: 295  Bit Score: 147.87  E-value: 1.08e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196    14 FSCVDGPGSRLALFLQGCNLRCKNCHNP--WTM--------GRCNDCGECVPQCPHQALQIV---DGKVV--WNAVVCEQ 78
Cdd:TIGR02494   7 YSVHDGPGIRTTVFLKGCPLRCKWCSNPesQRKspellfkeNRCLGCGKCVEVCPAGTARLSelaDGRNRiiIRREKCTH 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196    79 CDTCLKRCPQHATPM-AQSMSVDEVLSHVRKAVLFIE----GITVSGGEATTQLPFVVALFTAIKNdpqlRHLTCLVDSN 153
Cdd:TIGR02494  87 CGKCTEACPSGALSIvGEEMTVEEVMRVVLRDSIFYRnsggGVTLSGGEPLLQPEFALALLQACHE----RGIHTAVETS 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196   154 GMLSETGWEKLLPVCDGAMLDLKAWGSECHQQLTGRDNQQIKRSIYLLAERGKLAELRLLVIPGQVDYLQHIEELAAFIK 233
Cdd:TIGR02494 163 GFTPWETIEKVLPYVDLFLFDIKHLDDERHKEVTGVDNEPILENLEALAAAGKNVVIRIPVIPGFNDSEENIEAIAAFLR 242

                         250
                  ....*....|....*....
gi 16132196   234 GLGDVPVRLN--AFHAHGV 250
Cdd:TIGR02494 243 KLEPGVDEIDllPYHRLGE 261
PFLA TIGR02493
pyruvate formate-lyase 1-activating enzyme; An iron-sulfur protein with a radical-SAM domain ...
 14-251 1.11e-39

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: 138.27  E-value: 1.11e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196    14 FSCVDGPGSRLALFLQGCNLRCKNCHNPWTmgrcndcgecvpqcphqalqivdgkvvWnavvceqcdtclkrCPQHATPm 93
Cdd:TIGR02493   8 MGTVDGPGIRFVVFMQGCPLRCQYCHNPDT---------------------------W--------------DLKGGTE- 45

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196    94 aqsMSVDEVLSHVRKAVLFIE----GITVSGGEATTQLPFVVALFTAIKndpQLRHLTCLvDSNGMLSETG--WEKLLPV 167
Cdd:TIGR02493  46 ---VTPEELIKEVGSYKDFFKasggGVTFSGGEPLLQPEFLSELFKACK---ELGIHTCL-DTSGFLGGCTeaADELLEY 118

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196   168 CDGAMLDLKAWGSECHQQLTGRDNQQIKRSIYLLAERGKLAELRLLVIPGQVDYLQHIEELAAFIKGLGDVP-VRLNAFH 246
Cdd:TIGR02493 119 TDLVLLDIKHFNPEKYKKLTGVSLQPTLDFAKYLAKRNKPIWIRYVLVPGYTDSEEDIEALAEFVKTLPNVErVEVLPYH 198


                  ....*
gi 16132196   247 AHGVY 251
Cdd:TIGR02493 199 QLGVY 203
pflA PRK11145
pyruvate formate lyase 1-activating protein;
15-249 7.78e-26

pyruvate formate lyase 1-activating protein;


Pssm-ID: 182994 [Multi-domain]  Cd Length: 246  Bit Score: 102.41  E-value: 7.78e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196   15 SC--VDGPGSRLALFLQGCNLRCKNCHNPWTmgrcndcgecvpqcphqalqivdgkvvWnavvceqcDTclkrcpqHAtp 92
Cdd:PRK11145  12 SCgtVDGPGIRFITFFQGCLMRCLYCHNRDT---------------------------W--------DT-------HG-- 47

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196   93 mAQSMSVDEVLSHVRKAVLFIE----GITVSGGEATTQLPFVVALFTAIKNdpQLRHlTCLvDSNGMLS--ETGWEKLLP 166
Cdd:PRK11145  48 -GKEVTVEELMKEVVTYRHFMNasggGVTASGGEAILQAEFVRDWFRACKK--EGIH-TCL-DTNGFVRryDPVIDELLD 122

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196  167 VCDGAMLDLKAWGSECHQQLTGRDNQQIKRSIYLLAERGKLAELRLLVIPGQVDYLQHIEELAAFIKGLGDV-PVRLNAF 245
Cdd:PRK11145 123 VTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFARYLAKRNQKTWIRYVVVPGWTDDDDSAHRLGEFIKDMGNIeKIELLPY 202


                 ....
gi 16132196  246 HAHG 249
Cdd:PRK11145 203 HELG 206
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 27-271 2.21e-15

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: 73.14  E-value: 2.21e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196  27 FLQGCNLRCKNCHNPWTMGRCNDCGECVpqcphqalqivdgkvvwnavvceqcdtclkrcpqhatpmaqsmsVDEVLSHV 106
Cdd:cd01335   3 LTRGCNLNCGFCSNPASKGRGPESPPEI--------------------------------------------EEILDIVL 38

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196 107 RKAVLFIEGITVSGGEATTQLPFVVALFTAIKNDPqlrHLTCLVDSNGM-LSETGWEKLLP---VCDGAMLDLKAWGSEC 182
Cdd:cd01335  39 EAKERGVEVVILTGGEPLLYPELAELLRRLKKELP---GFEISIETNGTlLTEELLKELKElglDGVGVSLDSGDEEVAD 115

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196 183 HQQLTGRDNQQIKRSIYLLAERGKLAELRLLVIPGQVDYLQHIEELAAFIKGLGDVPVRLNAFHAHGVYGEAQSWASATP 262
Cdd:cd01335 116 KIRGSGESFKERLEALKELREAGLGLSTTLLVGLGDEDEEDDLEELELLAEFRSPDRVSLFRLLPEEGTPLELAAPVVPA 195


                ....*....
gi 16132196 263 EDVEPLADA 271
Cdd:cd01335 196 EKLLRLIAA 204
NrdG2 TIGR02495
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
 7-233 5.33e-14

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: 68.93  E-value: 5.33e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196     7 LVSKIIPFSCVDGPG-SRLALFLQGCNLRCKNCHNPwtmgrcndcgecvpqcPHQALQivdgkvvwnavVCEQcdtclkr 85
Cdd:TIGR02495   1 RIAGLVPFSTVDYPGkLAFTIFLQGCNLKCPYCHNP----------------LLIPRR-----------GSGE------- 46

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196    86 cpqhatpmaqsMSVDEVLSHVRKAVLFIEGITVSGGEATTQlpfvVALFTAIKNDPQLRHLTCLvDSNG----MLSETGW 161
Cdd:TIGR02495  47 -----------IEVEELLEFLRRRRGLLDGVVITGGEPTLQ----AGLPDFLREVRELGFEVKL-DTNGsnprRLEELLE 110

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 16132196   162 EKLLpvcDGAMLDLKAwGSECHQQLTGRD----NQQIKRSIYLLAERGKLAELRLLVIPGQVDyLQHIEELAAFIK 233
Cdd:TIGR02495 111 EGLV---DYVAMDVKA-PPEKYGELYGLEkngaAKNILKSLEILLESGIPFELRTTVVRGFLT-EEDLAEIATRIK 181
PRK10076 PRK10076
pyruvate formate lyase II activase; Provisional
 86-268 5.84e-12

pyruvate formate lyase II activase; Provisional


Pssm-ID: 182224 [Multi-domain]  Cd Length: 213  Bit Score: 63.63  E-value: 5.84e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196   86 CPQHA-TPMAQSMSVDEVLSHVRKAVLFIE----GITVSGGEATTQLPFVVALFTaikndpQLRHL--TCLVDSNGMLSE 158
Cdd:PRK10076   7 CPSGAfERIGRDITLDALEREVMKDDIFFRtsggGVTLSGGEVLMQAEFATRFLQ------RLRLWgvSCAIETAGDAPA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196  159 TgweKLLPV---CDGAMLDLKAWGSECHQQLTGRDNQQIKRSIYLLAERGKLAELRLLVIPGQVDYLQHIEELAAFIKGL 235
Cdd:PRK10076  81 S---KLLPLaklCDEVLFDLKIMDATQARDVVKMNLPRVLENLRLLVSEGVNVIPRLPLIPGFTLSRENMQQALDVLIPL 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 16132196  236 GDVPVRLNAFHAhgvYGEA------QSWASA-----TPEDVEPL 268
Cdd:PRK10076 158 GIKQIHLLPFHQ---YGEPkyrllgKTWSMKevpapSSADVATM 198
DsrA COG2221
Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Inorganic ion ...
 46-90 2.07e-09

Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Inorganic ion transport and metabolism];


Pssm-ID: 441823 [Multi-domain]  Cd Length: 69  Bit Score: 52.75  E-value: 2.07e-09
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 16132196  46 RCNDCGECVPQCPHQALQIVDGKVVWNAVVCEQCDTCLKRCPQHA 90
Cdd:COG2221  16 KCIGCGLCVAVCPTGAISLDDGKLVIDEEKCIGCGACIRVCPTGA 60
Fer4_12 pfam13353
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
 17-169 3.85e-09

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: 54.10  E-value: 3.85e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196    17 VDGPGSRLALFLQGCNLRCKNCHNPWTmgrcndcgecvpqcphqalqivdgkvvWNavvceqcdtclkrcPQHATPMAQS 96
Cdd:pfam13353   1 VNGPGVRCSLFVSGCNHHCKGCFNPET---------------------------WD--------------FKYGKPFTEE 39

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16132196    97 MsVDEVLSHVRKAvlFIEGITVSGGEATTQLPFVVALFTAIKN-DPQLRHLTCLVDSNGMLSETGWEKLLPVCD 169
Cdd:pfam13353  40 L-EDEIIEDLAKP--YIQGLTLSGGEPLLNAEALLELVKRVREeCPEKDIWLWTGYTFEELQSKDQLELLKLID 110
COG1149 COG1149
MinD superfamily P-loop ATPase, contains an inserted ferredoxin domain [General function ...
 46-90 4.16e-09

MinD superfamily P-loop ATPase, contains an inserted ferredoxin domain [General function prediction only];


Pssm-ID: 440763 [Multi-domain]  Cd Length: 68  Bit Score: 52.04  E-value: 4.16e-09
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 16132196  46 RCNDCGECVPQCPHQALQIVDGK-VVWNAVVCEQCDTCLKRCPQHA 90
Cdd:COG1149  12 KCIGCGLCVEVCPEGAIKLDDGGaPVVDPDLCTGCGACVGVCPTGA 57
NrdG TIGR02491
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
 8-122 4.43e-09

anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of the radical-SAM family (pfam04055) and utilizes S-adenosyl methionine, an iron-sulfur cluster and a reductant (dihydroflavodoxin) to produce a glycine-centered radical in the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, TIGR02487). The two components form an alpha-2/beta-2 heterodimer. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism, Protein fate, Protein modification and repair]


Pssm-ID: 274161 [Multi-domain]  Cd Length: 154  Bit Score: 54.28  E-value: 4.43e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196     8 VSKIIPFSCVDGPGSRLALFLQGCNLRCKNCHNPWTmgrcndcgecvpqcphqalqivdgkvvWNavvceqcdtclkrcP 87
Cdd:TIGR02491   2 YMNIKPDDIVNGEGIRVSLFVAGCKHHCEGCFNKET---------------------------WN--------------F 40

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 16132196    88 QHATPMAQSMsVDEVLSHVRKAVlFIEGITVSGGE 122
Cdd:TIGR02491  41 NGGKEFTEAL-EKEIIRDLNDNP-LIDGLTLSGGD 73
COG2768 COG2768
Uncharacterized Fe-S cluster protein [Function unknown];
46-90 5.36e-09

Uncharacterized Fe-S cluster protein [Function unknown];


Pssm-ID: 442050 [Multi-domain]  Cd Length: 74  Bit Score: 52.04  E-value: 5.36e-09
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 16132196  46 RCNDCGECVPQCPHQALQIVDGKVVWNAVVCEQCDTCLKRCPQHA 90
Cdd:COG2768  12 KCIGCGACVKVCPVGAISIEDGKAVIDPEKCIGCGACIEVCPVGA 56
IorA COG4231
TPP-dependent indolepyruvate ferredoxin oxidoreductase, alpha subunit [Energy production and ...
 46-90 1.15e-07

TPP-dependent indolepyruvate ferredoxin oxidoreductase, alpha subunit [Energy production and conversion];


Pssm-ID: 443375 [Multi-domain]  Cd Length: 76  Bit Score: 48.12  E-value: 1.15e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 16132196  46 RCNDCGECVPQCPHQALQIVDGKVVWNAVVCEQCDTCLKRCPQHA 90
Cdd:COG4231  23 KCTGCGACVKVCPADAIEEGDGKAVIDPDLCIGCGSCVQVCPVDA 67
HdrA COG1148
Heterodisulfide reductase, subunit A (polyferredoxin) [Energy production and conversion];
46-111 1.85e-07

Heterodisulfide reductase, subunit A (polyferredoxin) [Energy production and conversion];


Pssm-ID: 440762 [Multi-domain]  Cd Length: 563  Bit Score: 51.78  E-value: 1.85e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 16132196  46 RCNDCGECVPQCPHQALQIVDGKVVW-NAVVCEQCDTCLKRCPQHATPMaQSMSVDEVLSHVrKAVL 111
Cdd:COG1148 497 KCTGCGRCVEVCPYGAISIDEKGVAEvNPALCKGCGTCAAACPSGAISL-KGFTDDQILAQI-DALL 561
ferrodoxin_EFR1 NF038196
EFR1 family ferrodoxin; Members of the family have a C-terminal ferrodoxin domain, with eight ...
 46-90 3.53e-07

EFR1 family ferrodoxin; Members of the family have a C-terminal ferrodoxin domain, with eight conserved Cys residues in two CxxCxxCxxxCP motifs, each of which binds a 4Fe-4S cluster. The N-terminal region resembles flavodoxin domains, with some members of the family recognized by Pfam models PF12724 (Flavodoxin_5) or PF00258 (Flavodoxin_1).


Pssm-ID: 468407 [Multi-domain]  Cd Length: 243  Bit Score: 50.24  E-value: 3.53e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 16132196   46 RCNDCGECVPQCPHQALQIVDGKVVW--NavvCEQCDTCLKRCPQHA 90
Cdd:NF038196 186 KCIGCGICAKVCPVNNIEMEDGKPVWghN---CTHCLACIHRCPKEA 229
NapF COG1145
Ferredoxin [Energy production and conversion];
11-90 6.86e-07

Ferredoxin [Energy production and conversion];


Pssm-ID: 440760 [Multi-domain]  Cd Length: 238  Bit Score: 49.34  E-value: 6.86e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196  11 IIPFSCVDGPGSRLALFLQGCNLRCKNCHNPWT--MGRCNDCGECVPQCPHQALQIVDGK--VVWNAVVCEQCDTCLKRC 86
Cdd:COG1145 146 ILGAAAPVDALAISGGKKIEEELKIAIKKAKAVidAEKCIGCGLCVKVCPTGAIRLKDGKpqIVVDPDKCIGCGACVKVC 225


                ....
gi 16132196  87 PQHA 90
Cdd:COG1145 226 PVGA 229
PRK00783 PRK00783
DNA-directed RNA polymerase subunit D; Provisional
 45-90 5.32e-06

DNA-directed RNA polymerase subunit D; Provisional


Pssm-ID: 234837 [Multi-domain]  Cd Length: 263  Bit Score: 46.80  E-value: 5.32e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 16132196   45 GRCNDCGECVPQCPHQALQIVDGK-VVWNAVVCEQCDTCLKRCPQHA 90
Cdd:PRK00783 169 EDCDECEKCVEACPRGVLELKEGKlVVTDLLNCSLCKLCERACPGKA 215
Fer4_9 pfam13187
4Fe-4S dicluster domain;
46-90 6.43e-06

4Fe-4S dicluster domain;


Pssm-ID: 463801 [Multi-domain]  Cd Length: 50  Bit Score: 42.54  E-value: 6.43e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 16132196    46 RCNDCGECVPQCPHQALQIVDGKVVWNAVV----CEQCDTCLKRCPQHA 90
Cdd:pfam13187   1 KCTGCGACVAACPAGAIVPDLVGQTIRGDIaglaCIGCGACVDACPRGA 49
Nar1 COG4624
Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];
46-90 9.74e-06

Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];


Pssm-ID: 443663 [Multi-domain]  Cd Length: 450  Bit Score: 46.56  E-value: 9.74e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 16132196  46 RCNDCGECVPQCPHQALQIVDGKVVWNAVVCEQCDTCLKRCPQHA 90
Cdd:COG4624  92 KCKNCYPCVRACPVKAIKVDDGKAEIDEEKCISCGQCVAVCPFGA 136
PreA COG1146
NAD-dependent dihydropyrimidine dehydrogenase, PreA subunit [Nucleotide transport and ...
 46-90 4.61e-05

NAD-dependent dihydropyrimidine dehydrogenase, PreA subunit [Nucleotide transport and metabolism];


Pssm-ID: 440761 [Multi-domain]  Cd Length: 67  Bit Score: 40.85  E-value: 4.61e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 16132196  46 RCNDCGECVPQCPHQALQIVDGKvvWNAVV-----CEQCDTCLKRCPQHA 90
Cdd:COG1146   9 KCIGCGACVEVCPVDVLELDEEG--KKALVinpeeCIGCGACELVCPVGA 56
PRK13795 PRK13795
hypothetical protein; Provisional
 46-87 4.63e-05

hypothetical protein; Provisional


Pssm-ID: 237510 [Multi-domain]  Cd Length: 636  Bit Score: 44.60  E-value: 4.63e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 16132196   46 RCNDCGECVPQCPHQALQIVDGK--VVWNAVVCEQCDTCLKRCP 87
Cdd:PRK13795 582 ECVGCGVCVGACPTGAIRIEEGKrkISVDEEKCIHCGKCTEVCP 625
Fer4_7 pfam12838
4Fe-4S dicluster domain; Superfamily includes proteins containing domains which bind to ...
 47-87 5.75e-04

4Fe-4S dicluster domain; Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.


Pssm-ID: 463724 [Multi-domain]  Cd Length: 51  Bit Score: 37.12  E-value: 5.75e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 16132196    47 CNDCGECVPQCPHQAL-----QIVDGKVVW--NAVVCEQCDTCLKRCP 87
Cdd:pfam12838   1 CIGCGACVAACPVGAItldevGEKKGTKTVviDPERCVGCGACVAVCP 48
PRK07118 PRK07118
Fe-S cluster domain-containing protein;
47-90 9.48e-04

Fe-S cluster domain-containing protein;


Pssm-ID: 235941 [Multi-domain]  Cd Length: 280  Bit Score: 39.92  E-value: 9.48e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 16132196   47 CNDCGECVPQCPHQALQIVDGKVVWNAVVCEQCDTCLKRCPQHA 90
Cdd:PRK07118 215 CIGCGKCVKACPAGAITMENNLAVIDQEKCTSCGKCVEKCPTKA 258
HycB COG1142
Fe-S-cluster-containing hydrogenase component 2 [Energy production and conversion];
46-90 1.96e-03

Fe-S-cluster-containing hydrogenase component 2 [Energy production and conversion];


Pssm-ID: 440757 [Multi-domain]  Cd Length: 138  Bit Score: 37.71  E-value: 1.96e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 16132196  46 RCNDCGECVPQCPHQALQIVDGKVVWNAVVCEQCDT------CLKRCPQHA 90
Cdd:COG1142  82 KCIGCGLCVLACPFGAITMVGEKSRAVAVKCDLCGGreggpaCVEACPTGA 132
RNR_activ_nrdG3 TIGR02826
anaerobic ribonucleoside-triphosphate reductase activating protein; Members of this family ...
 24-43 2.68e-03

anaerobic ribonucleoside-triphosphate reductase activating protein; Members of this family represent a set of radical SAM enzymes related to, yet architecturally different from, the activating protein for the glycine radical-containing, oxygen-sensitive ribonucleoside-triphosphate reductase (RNR) as described in model TIGR02491. Members of this family are found paired with members of a similarly divergent set of anaerobic ribonucleoside-triphosphate reductases. Identification of this protein as an RNR activitating protein is partly from pairing with a candidate RNR. It is further supported by our finding that upstream of these operons are examples of a conserved regulatory element (described Rodionov and Gelfand) that is found in nearly all bacteria and that occurs specifically upstream of operons for all three classes of RNR genes. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism]


Pssm-ID: 274317  Cd Length: 147  Bit Score: 37.33  E-value: 2.68e-03
                          10        20
                  ....*....|....*....|
gi 16132196    24 LALFLQGCNLRCKNCHNPWT 43
Cdd:TIGR02826  18 LAFYISGCPLGCPGCHSPEL 37
AmmeMemoSam_rS TIGR04337
AmmeMemoRadiSam system radical SAM enzyme; Members of this protein family are uncharacterized ...
 169-246 2.75e-03

AmmeMemoRadiSam system radical SAM enzyme; Members of this protein family are uncharacterized radical SAM enzymes that occur in a prokaryotic three-gene system along with homologs of mammalian proteins Memo (Mediator of ErbB2-driven cell MOtility) and AMMERCR1 (Alport syndrome, Mental Retardation, Midface hypoplasia, and Elliptocytosis). Among radical SAM enzymes that have been experimentally characterized, the most closely related in sequence include activases of pyruvate formate-lyase and of benzylsuccinate synthase.


Pssm-ID: 275136 [Multi-domain]  Cd Length: 349  Bit Score: 38.82  E-value: 2.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16132196   169 DGAMLDLKAWGSECHQQLTGRDNQQIKRS-IYLLAERGKLAELRLLVIPGQVDYLQHIEELAAFI-KGLG-DVPVRLNAF 245
Cdd:TIGR04337 170 DAANVDLKAFTEDFYHKLCGGHLQPVLDTlRYLRHETDVWLEITTLLIPGENDSDAELEAMCEWIvENLGpDVPLHFTAF 249


                  .
gi 16132196   246 H 246
Cdd:TIGR04337 250 H 250
PRK12809 PRK12809
putative oxidoreductase Fe-S binding subunit; Reviewed
 36-98 3.33e-03

putative oxidoreductase Fe-S binding subunit; Reviewed


Pssm-ID: 183762 [Multi-domain]  Cd Length: 639  Bit Score: 38.85  E-value: 3.33e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16132196   36 KNCHNPWTMGRCNDcGECVPQCPHQALQIVDGKVVWNAVVCEQCDTCLKRCPQHATPMAQSMS 98
Cdd:PRK12809  48 GQAANPVACHHCNN-APCVTACPVNALTFQSDSVQLDEQKCIGCKRCAIACPFGVVEMVDTIA 109
nrdG PRK11121
anaerobic ribonucleoside-triphosphate reductase-activating protein;
13-40 4.12e-03

anaerobic ribonucleoside-triphosphate reductase-activating protein;


Pssm-ID: 236853  Cd Length: 154  Bit Score: 36.89  E-value: 4.12e-03
                         10        20
                 ....*....|....*....|....*...
gi 16132196   13 PFSCVDGPGSRLALFLQGCNLRCKNCHN 40
Cdd:PRK11121   8 PVDVVNGPGTRCTLFVSGCVHQCPGCYN 35
DMSOR_beta_like cd16372
uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the ...
 47-87 4.31e-03

uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.


Pssm-ID: 319894 [Multi-domain]  Cd Length: 125  Bit Score: 36.54  E-value: 4.31e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 16132196  47 CNDCGECVPQCPHQALQIVDGKVVW-NAVVCEQCDTCLKRCP 87
Cdd:cd16372  49 CNQCGECIDVCPTGAITRDANGVVMiNKKLCVGCLMCVGFCP 90
napF TIGR00402
ferredoxin-type protein NapF; The gene codes for a ferredoxin-type cytosolic protein, NapF, of ...
 41-90 5.60e-03

ferredoxin-type protein NapF; The gene codes for a ferredoxin-type cytosolic protein, NapF, of the periplasmic nitrate reductase system, as in Escherichia coli. NapF interacts with the catalytic subunit, NapA, and may be an accessory protein for NapA maturation. [Energy metabolism, Electron transport]


Pssm-ID: 273060 [Multi-domain]  Cd Length: 101  Bit Score: 35.69  E-value: 5.60e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 16132196    41 PWT------MGRCNDCGECVPQCPHQALQIVDG---KVVWNAVVCEQCDTCLKRCPQHA 90
Cdd:TIGR00402  24 PWSareslfSAVCTRCGECASACENNILQLGQQgqpTVEFDNAECDFCGKCAEACPTNA 82
DMSOR_beta_like cd16370
uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the ...
 46-93 8.26e-03

uncharacterized subfamily of DMSO Reductase beta subunit family; This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system.


Pssm-ID: 319892 [Multi-domain]  Cd Length: 131  Bit Score: 35.71  E-value: 8.26e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 16132196  46 RCNDCGECVPQCPHQALQIVDGKVVwnAVVCEQCDTCLKRCPQHATPM 93
Cdd:cd16370  84 KCIGCGNCVKACIVGAIFWDEETNK--PIICIHCGYCARYCPHDVLAM 129
PRK07118 PRK07118
Fe-S cluster domain-containing protein;
47-89 9.22e-03

Fe-S cluster domain-containing protein;


Pssm-ID: 235941 [Multi-domain]  Cd Length: 280  Bit Score: 36.83  E-value: 9.22e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 16132196   47 CNDCGECVPQCPHQALQIVDGKVVWNAVVCEQCDTCLKRCPQH 89
Cdd:PRK07118 141 CLGLGSCVAACPFDAIHIENGLPVVDEDKCTGCGACVKACPRN 183
MtMvhB_like cd10549
Uncharacterized polyferredoxin-like protein; This family contains uncharacterized ...
 46-90 9.40e-03

Uncharacterized polyferredoxin-like protein; This family contains uncharacterized polyferredoxin protein similar to Methanobacterium thermoautotrophicum MvhB. The mvhB is a gene of the methylviologen-reducing hydrogenase operon. It is predicted to contain 12 [4Fe-4S] clusters, and was therefore suggested to be a polyferredoxin. As a subfamily of the beta subunit of the DMSO Reductase (DMSOR) family, it is predicted to function as electron carrier in the reducing reaction.


Pssm-ID: 319871 [Multi-domain]  Cd Length: 128  Bit Score: 35.45  E-value: 9.40e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 16132196  46 RCNDCGECVPQCPHQALQIVDGK-----VVWNAVVCEQCDTCLKRCPQHA 90
Cdd:cd10549   7 KCIGCGICVKACPTDAIELGPNGaiargPEIDEDKCVFCGACVEVCPTGA 56
 
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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