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Conserved domains on  [gi|16128869|ref|NP_415422|]
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pyruvate formate-lyase activating enzyme [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

pyruvate formate lyase 1-activating protein( domain architecture ID 11485227)

pyruvate formate lyase 1-activating protein is a radical SAM protein that activates pyruvate formate-lyase 1 under anaerobic conditions by generation of an organic free radical, using S-adenosylmethionine and reduced flavodoxin as cosubstrates to produce 5'-deoxy-adenosine

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
pflA PRK11145
pyruvate formate lyase 1-activating protein;
1-246 0e+00

pyruvate formate lyase 1-activating protein;


:

Pssm-ID: 182994 [Multi-domain]  Cd Length: 246  Bit Score: 567.73  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869    1 MSVIGRIHSFESCGTVDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEDLMKEVVTYRHFMNASGGGVTASGGE 80
Cdd:PRK11145   1 MSVIGRIHSFESCGTVDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEELMKEVVTYRHFMNASGGGVTASGGE 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869   81 AILQAEFVRDWFRACKKEGIHTCLDTNGFVRRYDPVIDELLEVTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFAKYLANK 160
Cdd:PRK11145  81 AILQAEFVRDWFRACKKEGIHTCLDTNGFVRRYDPVIDELLDVTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFARYLAKR 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869  161 NVKVWIRYVVVPGWSDDDDSAHRLGEFTRDMGNVEKIELLPYHELGKHKWVAMGEEYKLDGVKPPKKETMERVKGILEQY 240
Cdd:PRK11145 161 NQKTWIRYVVVPGWTDDDDSAHRLGEFIKDMGNIEKIELLPYHELGKHKWEAMGEEYKLDGVKPPSKETMERVKGILEQY 240

                 ....*.
gi 16128869  241 GHKVMF 246
Cdd:PRK11145 241 GHKVMY 246
 
Name Accession Description Interval E-value
pflA PRK11145
pyruvate formate lyase 1-activating protein;
1-246 0e+00

pyruvate formate lyase 1-activating protein;


Pssm-ID: 182994 [Multi-domain]  Cd Length: 246  Bit Score: 567.73  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869    1 MSVIGRIHSFESCGTVDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEDLMKEVVTYRHFMNASGGGVTASGGE 80
Cdd:PRK11145   1 MSVIGRIHSFESCGTVDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEELMKEVVTYRHFMNASGGGVTASGGE 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869   81 AILQAEFVRDWFRACKKEGIHTCLDTNGFVRRYDPVIDELLEVTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFAKYLANK 160
Cdd:PRK11145  81 AILQAEFVRDWFRACKKEGIHTCLDTNGFVRRYDPVIDELLDVTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFARYLAKR 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869  161 NVKVWIRYVVVPGWSDDDDSAHRLGEFTRDMGNVEKIELLPYHELGKHKWVAMGEEYKLDGVKPPKKETMERVKGILEQY 240
Cdd:PRK11145 161 NQKTWIRYVVVPGWTDDDDSAHRLGEFIKDMGNIEKIELLPYHELGKHKWEAMGEEYKLDGVKPPSKETMERVKGILEQY 240

                 ....*.
gi 16128869  241 GHKVMF 246
Cdd:PRK11145 241 GHKVMY 246
PFLA TIGR02493
pyruvate formate-lyase 1-activating enzyme; An iron-sulfur protein with a radical-SAM domain ...
6-240 2.27e-146

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: 408.30  E-value: 2.27e-146
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869     6 RIHSFESCGTVDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEDLMKEVVTYRHFMNASGGGVTASGGEAILQA 85
Cdd:TIGR02493   1 RIHSTESMGTVDGPGIRFVVFMQGCPLRCQYCHNPDTWDLKGGTEVTPEELIKEVGSYKDFFKASGGGVTFSGGEPLLQP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869    86 EFVRDWFRACKKEGIHTCLDTNGFVRRYDPVIDELLEVTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFAKYLANKNVKVW 165
Cdd:TIGR02493  81 EFLSELFKACKELGIHTCLDTSGFLGGCTEAADELLEYTDLVLLDIKHFNPEKYKKLTGVSLQPTLDFAKYLAKRNKPIW 160
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16128869   166 IRYVVVPGWSDDDDSAHRLGEFTRDMGNVEKIELLPYHELGKHKWVAMGEEYKLDGVKPPKKETMERVKGILEQY 240
Cdd:TIGR02493 161 IRYVLVPGYTDSEEDIEALAEFVKTLPNVERVEVLPYHQLGVYKWEALGIEYPLEGVKPPNKEQLERAAEIFKEY 235
PflA COG1180
Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, ...
1-243 1.65e-101

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


Pssm-ID: 440793 [Multi-domain]  Cd Length: 242  Bit Score: 294.78  E-value: 1.65e-101
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869   1 MSVIGRIHSFESCGTVDGPG-IRFITFFQGCLMRCLYCHNRDTWDTH---GGKEVTVEDLMKEVVTYRHFMNaSGGGVTA 76
Cdd:COG1180   1 EEVRGRIYGISPFSTVDGPGsIRLSVFTQGCNLRCPYCHNPEISQGRpdaAGRELSPEELVEEALKDRGFLD-SCGGVTF 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869  77 SGGEAILQAEFVRDWFRACKKEGIHTCLDTNGFVrrYDPVIDELLEVTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFAKY 156
Cdd:COG1180  80 SGGEPTLQPEFLLDLAKLAKELGLHTALDTNGYI--PEEALEELLPYLDAVNIDLKAFDDEFYRKLTGVSLEPVLENLEL 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869 157 LANKNVKVWIRYVVVPGWSDDDDSAHRLGEFTRDMGNVEKIELLPYHELgkhkwvamgeeYKLDGVKPPKKETMERVKGI 236
Cdd:COG1180 158 LAESGVHVEIRTLVIPGLNDSEEELEAIARFIAELGDVIPVHLLPFHPL-----------YKLEDVPPPSPETLERAREI 226

                ....*..
gi 16128869 237 LEQYGHK 243
Cdd:COG1180 227 AREYGLK 233
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
26-178 1.69e-19

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: 82.19  E-value: 1.69e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869    26 FFQGCLMRCLYCHNRDTWDTHGGKEVTVEDLMKEVVTYRhfmNASGGGVTASGGEAILQAEFVRDWFRACKK---EGIHT 102
Cdd:pfam04055   1 ITRGCNLRCTYCAFPSIRARGKGRELSPEEILEEAKELK---RLGVEVVILGGGEPLLLPDLVELLERLLKLelaEGIRI 77
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16128869   103 CLDTNGFVRRYDpVIDELLEVT-DLVMLDLKQMNDEIHQNL-VGVSNHRTLEFAKYLANKNVKV-WIRYVVVPGWSDDD 178
Cdd:pfam04055  78 TLETNGTLLDEE-LLELLKEAGlDRVSIGLESGDDEVLKLInRGHTFEEVLEALELLREAGIPVvTDNIVGLPGETDED 155
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
24-208 3.94e-10

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: 57.73  E-value: 3.94e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869  24 ITFFQGCLMRCLYCHNRdtWDTHGGKEVTVE-DLMKEVVTYRHFMNASGggVTASGGEAILQAEFVRDWFRACK-KEGIH 101
Cdd:cd01335   1 LELTRGCNLNCGFCSNP--ASKGRGPESPPEiEEILDIVLEAKERGVEV--VILTGGEPLLYPELAELLRRLKKeLPGFE 76
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869 102 TCLDTNGFVRRYDPV--IDELLEVTDLVMLDLKqmnDEIHQNLVGVSNH---RTLEFAKYLANKNVKVWIRYVVVPGWSD 176
Cdd:cd01335  77 ISIETNGTLLTEELLkeLKELGLDGVGVSLDSG---DEEVADKIRGSGEsfkERLEALKELREAGLGLSTTLLVGLGDED 153
                       170       180       190
                ....*....|....*....|....*....|..
gi 16128869 177 DDDSAhRLGEFTRDMGNVEKIELLPYHELGKH 208
Cdd:cd01335 154 EEDDL-EELELLAEFRSPDRVSLFRLLPEEGT 184
viperin_w_prok NF038283
viperin family antiviral radical SAM protein; Homologs of a viral defense radical SAM enzyme ...
30-118 8.43e-04

viperin family antiviral radical SAM protein; Homologs of a viral defense radical SAM enzyme found in Homo sapiens, viperin (RSAD2), occur in prokaryotes with a strong bias toward placement in phage defense islands, encoded next to CRISPR system and restriction enzyme genes. Further investigation shows members indeed perform the anti-viral function of synthesizing modified ribonucleotides such as ddhCTP, ddh-guanosine triphosphate (ddhGTP) and ddh-uridine triphosphate (ddhUTP). Those non-standard ribonucleotides can interfere with viral replication machinery.


Pssm-ID: 468450 [Multi-domain]  Cd Length: 280  Bit Score: 39.84  E-value: 8.43e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869   30 CLMRCLYC--HNRDTWDTHGGKEVTVEDLMKEVVTYRHFMNASGGGVTASGGEAILQAEFVRDWFRACKKEGIHTCLDTN 107
Cdd:NF038283  12 CNYRCKYCfaKWNDVKSPRHHDKGHLEKLLEELAEFFKLLSYGFVRINFAGGEPLLYPDRLLDLIKLAKELGFKTSIITN 91
                         90
                 ....*....|....*..
gi 16128869  108 G------FVRRYDPVID 118
Cdd:NF038283  92 GsllteeFLEELAPYLD 108
 
Name Accession Description Interval E-value
pflA PRK11145
pyruvate formate lyase 1-activating protein;
1-246 0e+00

pyruvate formate lyase 1-activating protein;


Pssm-ID: 182994 [Multi-domain]  Cd Length: 246  Bit Score: 567.73  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869    1 MSVIGRIHSFESCGTVDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEDLMKEVVTYRHFMNASGGGVTASGGE 80
Cdd:PRK11145   1 MSVIGRIHSFESCGTVDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEELMKEVVTYRHFMNASGGGVTASGGE 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869   81 AILQAEFVRDWFRACKKEGIHTCLDTNGFVRRYDPVIDELLEVTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFAKYLANK 160
Cdd:PRK11145  81 AILQAEFVRDWFRACKKEGIHTCLDTNGFVRRYDPVIDELLDVTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFARYLAKR 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869  161 NVKVWIRYVVVPGWSDDDDSAHRLGEFTRDMGNVEKIELLPYHELGKHKWVAMGEEYKLDGVKPPKKETMERVKGILEQY 240
Cdd:PRK11145 161 NQKTWIRYVVVPGWTDDDDSAHRLGEFIKDMGNIEKIELLPYHELGKHKWEAMGEEYKLDGVKPPSKETMERVKGILEQY 240

                 ....*.
gi 16128869  241 GHKVMF 246
Cdd:PRK11145 241 GHKVMY 246
PFLA TIGR02493
pyruvate formate-lyase 1-activating enzyme; An iron-sulfur protein with a radical-SAM domain ...
6-240 2.27e-146

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: 408.30  E-value: 2.27e-146
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869     6 RIHSFESCGTVDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEDLMKEVVTYRHFMNASGGGVTASGGEAILQA 85
Cdd:TIGR02493   1 RIHSTESMGTVDGPGIRFVVFMQGCPLRCQYCHNPDTWDLKGGTEVTPEELIKEVGSYKDFFKASGGGVTFSGGEPLLQP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869    86 EFVRDWFRACKKEGIHTCLDTNGFVRRYDPVIDELLEVTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFAKYLANKNVKVW 165
Cdd:TIGR02493  81 EFLSELFKACKELGIHTCLDTSGFLGGCTEAADELLEYTDLVLLDIKHFNPEKYKKLTGVSLQPTLDFAKYLAKRNKPIW 160
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16128869   166 IRYVVVPGWSDDDDSAHRLGEFTRDMGNVEKIELLPYHELGKHKWVAMGEEYKLDGVKPPKKETMERVKGILEQY 240
Cdd:TIGR02493 161 IRYVLVPGYTDSEEDIEALAEFVKTLPNVERVEVLPYHQLGVYKWEALGIEYPLEGVKPPNKEQLERAAEIFKEY 235
PflA COG1180
Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, ...
1-243 1.65e-101

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


Pssm-ID: 440793 [Multi-domain]  Cd Length: 242  Bit Score: 294.78  E-value: 1.65e-101
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869   1 MSVIGRIHSFESCGTVDGPG-IRFITFFQGCLMRCLYCHNRDTWDTH---GGKEVTVEDLMKEVVTYRHFMNaSGGGVTA 76
Cdd:COG1180   1 EEVRGRIYGISPFSTVDGPGsIRLSVFTQGCNLRCPYCHNPEISQGRpdaAGRELSPEELVEEALKDRGFLD-SCGGVTF 79
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869  77 SGGEAILQAEFVRDWFRACKKEGIHTCLDTNGFVrrYDPVIDELLEVTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFAKY 156
Cdd:COG1180  80 SGGEPTLQPEFLLDLAKLAKELGLHTALDTNGYI--PEEALEELLPYLDAVNIDLKAFDDEFYRKLTGVSLEPVLENLEL 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869 157 LANKNVKVWIRYVVVPGWSDDDDSAHRLGEFTRDMGNVEKIELLPYHELgkhkwvamgeeYKLDGVKPPKKETMERVKGI 236
Cdd:COG1180 158 LAESGVHVEIRTLVIPGLNDSEEELEAIARFIAELGDVIPVHLLPFHPL-----------YKLEDVPPPSPETLERAREI 226

                ....*..
gi 16128869 237 LEQYGHK 243
Cdd:COG1180 227 AREYGLK 233
PFLE_PFLC TIGR02494
glycyl-radical enzyme activating protein; This subset of the radical-SAM family (pfam04055) ...
17-241 4.41e-65

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: 204.10  E-value: 4.41e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869    17 DGPGIRFITFFQGCLMRCLYCHNRDTWD----------------------------------------------THG--- 47
Cdd:TIGR02494  11 DGPGIRTTVFLKGCPLRCKWCSNPESQRkspellfkenrclgcgkcvevcpagtarlseladgrnriiirrekcTHCgkc 90
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869    48 ------------GKEVTVEDLMKEVVTYRHFMNASGGGVTASGGEAILQAEFVRDWFRACKKEGIHTCLDTNGFVRRydP 115
Cdd:TIGR02494  91 teacpsgalsivGEEMTVEEVMRVVLRDSIFYRNSGGGVTLSGGEPLLQPEFALALLQACHERGIHTAVETSGFTPW--E 168
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869   116 VIDELLEVTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFAKYLANKNVKVWIRYVVVPGWSDDDDSAHRLGEFTRDMGN-V 194
Cdd:TIGR02494 169 TIEKVLPYVDLFLFDIKHLDDERHKEVTGVDNEPILENLEALAAAGKNVVIRIPVIPGFNDSEENIEAIAAFLRKLEPgV 248
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 16128869   195 EKIELLPYHELGKHKWVAMGEEYKLDGVKPPKKETMERVKGILEQYG 241
Cdd:TIGR02494 249 DEIDLLPYHRLGENKYRQLGREYPDSEIPDPAEEQLLELKEIFESKG 295
activase_YjjW TIGR04041
glycine radical enzyme activase, YjjW family; Members of this family are radical SAM enzymes, ...
1-241 6.00e-51

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: 167.43  E-value: 6.00e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869     1 MSVIGRIHSFeSCgtVDGPGIRFITFFQGCLMRCLYCHNRDTWDT------------------HGGK------------- 49
Cdd:TIGR04041   1 KALVNKIIPF-SC--VDGPGNRLAIFLQGCNFDCKYCHNPETINHcdhcgdcvagcpagalslVDGKvvwdkercigcdt 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869    50 --------------EVTVEDLMKEVVTYRHFMNasggGVTASGGEAILQAEFVRDWFRACKKEGIhTCL-DTNGFV--RR 112
Cdd:TIGR04041  78 cikvcphqsspktkEYTVEELLDRIRKNMPFIR----GITVSGGECTLQLDFLTELFKAIKAAGL-TCFiDSNGSLdlTG 152
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869   113 YdpviDELLEVTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFAKYLANKNVKVWIRYVVVPGWSDDDDSAHRLGEFTRDMG 192
Cdd:TIGR04041 153 W----PKLLPVLDGAMLDLKAWDSETHRWLTGRDNHRVLKNIRFLAELGKLYEVRLVHIPGLSDLEQEIDGLARFLGDLP 228
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*....
gi 16128869   193 NVEKIELLPYHELGkhkwvaMGEEYKldGVKPPKKETMERVKGILEQYG 241
Cdd:TIGR04041 229 SDTRIKLIAFRHHG------VRGEAL--EWPSPTDEQMEELAEALIKRG 269
PRK10076 PRK10076
pyruvate formate lyase II activase; Provisional
48-244 3.68e-30

pyruvate formate lyase II activase; Provisional


Pssm-ID: 182224 [Multi-domain]  Cd Length: 213  Bit Score: 111.78  E-value: 3.68e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869   48 GKEVTVEDLMKEVVTYRHFMNASGGGVTASGGEAILQAEFVRDWFRACKKEGIHTCLDTNGFVRRydpviDELL---EVT 124
Cdd:PRK10076  16 GRDITLDALEREVMKDDIFFRTSGGGVTLSGGEVLMQAEFATRFLQRLRLWGVSCAIETAGDAPA-----SKLLplaKLC 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869  125 DLVMLDLKQMNDEIHQNLVGVSNHRTLEFAKYLANKNVKVWIRYVVVPGWSDDDDSAHRLGEFTRDMGnVEKIELLPYHE 204
Cdd:PRK10076  91 DEVLFDLKIMDATQARDVVKMNLPRVLENLRLLVSEGVNVIPRLPLIPGFTLSRENMQQALDVLIPLG-IKQIHLLPFHQ 169
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 16128869  205 LGKHKWVAMGEEYKLDGVKPPKKETMERVKGILEQYGHKV 244
Cdd:PRK10076 170 YGEPKYRLLGKTWSMKEVPAPSSADVATMREMAERAGFQV 209
NrdG2 TIGR02495
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
6-179 1.30e-19

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: 83.18  E-value: 1.30e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869     6 RIHSFESCGTVDGPG-IRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEDLMKEVVTYRHFMNasggGVTASGGEAILQ 84
Cdd:TIGR02495   1 RIAGLVPFSTVDYPGkLAFTIFLQGCNLKCPYCHNPLLIPRRGSGEIEVEELLEFLRRRRGLLD----GVVITGGEPTLQ 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869    85 AEFVrDWFRACKKEGIHTCLDTNG-FVRRYDPVIDELLevTDLVMLDLK---QMNDEIHQNLVGVSNHRTLEFAKYLANK 160
Cdd:TIGR02495  77 AGLP-DFLREVRELGFEVKLDTNGsNPRRLEELLEEGL--VDYVAMDVKappEKYGELYGLEKNGAAKNILKSLEILLES 153
                         170
                  ....*....|....*....
gi 16128869   161 NVKVWIRYVVVPGWSDDDD 179
Cdd:TIGR02495 154 GIPFELRTTVVRGFLTEED 172
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
26-178 1.69e-19

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: 82.19  E-value: 1.69e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869    26 FFQGCLMRCLYCHNRDTWDTHGGKEVTVEDLMKEVVTYRhfmNASGGGVTASGGEAILQAEFVRDWFRACKK---EGIHT 102
Cdd:pfam04055   1 ITRGCNLRCTYCAFPSIRARGKGRELSPEEILEEAKELK---RLGVEVVILGGGEPLLLPDLVELLERLLKLelaEGIRI 77
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16128869   103 CLDTNGFVRRYDpVIDELLEVT-DLVMLDLKQMNDEIHQNL-VGVSNHRTLEFAKYLANKNVKV-WIRYVVVPGWSDDD 178
Cdd:pfam04055  78 TLETNGTLLDEE-LLELLKEAGlDRVSIGLESGDDEVLKLInRGHTFEEVLEALELLREAGIPVvTDNIVGLPGETDED 155
Fer4_12 pfam13353
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
16-149 1.19e-18

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: 79.14  E-value: 1.19e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869    16 VDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEdLMKEVVTYrhFMNASGGGVTASGGEAILQAEFVRDWFRAC 95
Cdd:pfam13353   1 VNGPGVRCSLFVSGCNHHCKGCFNPETWDFKYGKPFTEE-LEDEIIED--LAKPYIQGLTLSGGEPLLNAEALLELVKRV 77
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 16128869    96 KKEGIH-TCLDTNGFvrRYD----PVIDELLEVTDlVMLDLKQMND--EIHQNLVGVSNHR 149
Cdd:pfam13353  78 REECPEkDIWLWTGY--TFEelqsKDQLELLKLID-VLVDGKFEQSlkDPSLRFRGSSNQR 135
NrdG TIGR02491
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
6-94 1.58e-13

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: 66.22  E-value: 1.58e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869     6 RIHSFESCGTVDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTvEDLMKEVVtyRHFM-NASGGGVTASGGEAILQ 84
Cdd:TIGR02491   1 NYMNIKPDDIVNGEGIRVSLFVAGCKHHCEGCFNKETWNFNGGKEFT-EALEKEII--RDLNdNPLIDGLTLSGGDPLYP 77
                          90
                  ....*....|....*.
gi 16128869    85 A------EFVRdWFRA 94
Cdd:TIGR02491  78 RnveeliELVK-KIKA 92
QueE COG0602
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic ...
27-132 2.38e-10

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: 58.23  E-value: 2.38e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869  27 FQGCLMRCLYChnrDT---WDTHGGKEVTVEDLMKEVVTYRHFMnasgggVTASGGEAILQAEFvRDWFRACKKEGIHTC 103
Cdd:COG0602  27 LAGCNLRCSWC---DTkyaWDGEGGKRMSAEEILEEVAALGARH------VVITGGEPLLQDDL-AELLEALKDAGYEVA 96
                        90       100
                ....*....|....*....|....*....
gi 16128869 104 LDTNGFVRRYDPVidellevtDLVMLDLK 132
Cdd:COG0602  97 LETNGTLPIPAGI--------DWVTVSPK 117
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
24-208 3.94e-10

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: 57.73  E-value: 3.94e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869  24 ITFFQGCLMRCLYCHNRdtWDTHGGKEVTVE-DLMKEVVTYRHFMNASGggVTASGGEAILQAEFVRDWFRACK-KEGIH 101
Cdd:cd01335   1 LELTRGCNLNCGFCSNP--ASKGRGPESPPEiEEILDIVLEAKERGVEV--VILTGGEPLLYPELAELLRRLKKeLPGFE 76
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869 102 TCLDTNGFVRRYDPV--IDELLEVTDLVMLDLKqmnDEIHQNLVGVSNH---RTLEFAKYLANKNVKVWIRYVVVPGWSD 176
Cdd:cd01335  77 ISIETNGTLLTEELLkeLKELGLDGVGVSLDSG---DEEVADKIRGSGEsfkERLEALKELREAGLGLSTTLLVGLGDED 153
                       170       180       190
                ....*....|....*....|....*....|..
gi 16128869 177 DDDSAhRLGEFTRDMGNVEKIELLPYHELGKH 208
Cdd:cd01335 154 EEDDL-EELELLAEFRSPDRVSLFRLLPEEGT 184
Tyw1 COG0731
Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily [Translation, ribosomal ...
30-244 2.06e-08

Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily [Translation, ribosomal structure and biogenesis]; Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440495 [Multi-domain]  Cd Length: 248  Bit Score: 53.27  E-value: 2.06e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869  30 CLMRCLYCH-NRDTWDTHGGKE-VTVEDLMKEVVTYRHFMNASGGG---VTASG-GEAILQAEFVR--DWFRacKKEGIH 101
Cdd:COG0731  34 CNFDCVYCQrGRTTDLTRERREfDDPEEILEELIEFLRKLPEEAREpdhITFSGsGEPTLYPNLGEliEEIK--KLRGIK 111
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869 102 TCLDTNGfVRRYDP-VIDELLEVtDLVMLDLKQMNDEIHQNLVGVsnHRTLEFAKYLAN-------KNVKVWIRYVVVPG 173
Cdd:COG0731 112 TALLTNG-SLLHRPeVREELLKA-DQVYPSLDAADEETFRKINRP--HPGLSWERIIEGlelfrklYKGRTVIETMLVKG 187
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 16128869 174 WSDDDDSAHRLGEFTRDmGNVEKIEL-----LPyhelgkhkwvamgeeyKLDGVKPPKKETMERVKGILEQYGHKV 244
Cdd:COG0731 188 INDSEEELEAYAELIKR-INPDFVELktymrPP----------------ALSRVNMPSHEELEEFAERLAELGYEV 246
SkfB COG0535
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
30-169 7.28e-07

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: 47.59  E-value: 7.28e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869  30 CLMRCLYCHNRdtWDTHGGKEVTVED---LMKEVVTYRHFMnasgggVTASGGEAILQAEFvRDWFRACKKEGIHTCLDT 106
Cdd:COG0535  10 CNLRCKHCYAD--AGPKRPGELSTEEakrILDELAELGVKV------VGLTGGEPLLRPDL-FELVEYAKELGIRVNLST 80
                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 16128869 107 NGfVRRYDPVIDELLEV-TDLVMLDLKQMNDEIHQNLVGVSNH--RTLEFAKYLANKNVKVWIRYV 169
Cdd:COG0535  81 NG-TLLTEELAERLAEAgLDHVTISLDGVDPETHDKIRGVPGAfdKVLEAIKLLKEAGIPVGINTV 145
RbsK COG0524
Sugar or nucleoside kinase, ribokinase family [Carbohydrate transport and metabolism]; Sugar ...
85-166 3.29e-04

Sugar or nucleoside kinase, ribokinase family [Carbohydrate transport and metabolism]; Sugar or nucleoside kinase, ribokinase family is part of the Pathway/BioSystem: Glycolysis


Pssm-ID: 440290 [Multi-domain]  Cd Length: 301  Bit Score: 41.02  E-value: 3.29e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869  85 AEFVRDWFRACKKEGIHTCLDTN---GFVRRYDPVIDELLEVTDLVMldlkqMNDEIHQNLVGVSNHRtlEFAKYLANKN 161
Cdd:COG0524 144 REALLAALEAARAAGVPVSLDPNyrpALWEPARELLRELLALVDILF-----PNEEEAELLTGETDPE--EAAAALLARG 216

                ....*
gi 16128869 162 VKVWI 166
Cdd:COG0524 217 VKLVV 221
Fer4_14 pfam13394
4Fe-4S single cluster domain;
26-80 6.60e-04

4Fe-4S single cluster domain;


Pssm-ID: 433171 [Multi-domain]  Cd Length: 115  Bit Score: 38.50  E-value: 6.60e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 16128869    26 FFQGCLMRCLYCHNRDTWDTHGGKEVTvEDLMKEVVTYRHFMNASGGGVTASGGE 80
Cdd:pfam13394   2 FVSGCNHSCPGCDNKETWKFNYGEPFT-EELEDQIIADLKDSYIKRQGLVLTGGE 55
viperin_w_prok NF038283
viperin family antiviral radical SAM protein; Homologs of a viral defense radical SAM enzyme ...
30-118 8.43e-04

viperin family antiviral radical SAM protein; Homologs of a viral defense radical SAM enzyme found in Homo sapiens, viperin (RSAD2), occur in prokaryotes with a strong bias toward placement in phage defense islands, encoded next to CRISPR system and restriction enzyme genes. Further investigation shows members indeed perform the anti-viral function of synthesizing modified ribonucleotides such as ddhCTP, ddh-guanosine triphosphate (ddhGTP) and ddh-uridine triphosphate (ddhUTP). Those non-standard ribonucleotides can interfere with viral replication machinery.


Pssm-ID: 468450 [Multi-domain]  Cd Length: 280  Bit Score: 39.84  E-value: 8.43e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128869   30 CLMRCLYC--HNRDTWDTHGGKEVTVEDLMKEVVTYRHFMNASGGGVTASGGEAILQAEFVRDWFRACKKEGIHTCLDTN 107
Cdd:NF038283  12 CNYRCKYCfaKWNDVKSPRHHDKGHLEKLLEELAEFFKLLSYGFVRINFAGGEPLLYPDRLLDLIKLAKELGFKTSIITN 91
                         90
                 ....*....|....*..
gi 16128869  108 G------FVRRYDPVID 118
Cdd:NF038283  92 GsllteeFLEELAPYLD 108
nrdG PRK11121
anaerobic ribonucleoside-triphosphate reductase-activating protein;
8-54 1.60e-03

anaerobic ribonucleoside-triphosphate reductase-activating protein;


Pssm-ID: 236853  Cd Length: 154  Bit Score: 38.05  E-value: 1.60e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 16128869    8 HSFESCGTVDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTVE 54
Cdd:PRK11121   4 HQYYPVDVVNGPGTRCTLFVSGCVHQCPGCYNKSTWRLNSGHPFTKE 50
 
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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