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Conserved domains on  [gi|543996882|ref|WP_021034925|]
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pyruvate formate lyase 1-activating protein [Haemophilus influenzae]

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: 502.63  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882   1 MSVLGRIHSFESCGTVDGPGIRFILFMQGCLMRCKYCHNRDTWDLEGGKEISVEDLMKEVVTYRHFMNATGGGVTASGGE 80
Cdd:PRK11145   1 MSVIGRIHSFESCGTVDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEELMKEVVTYRHFMNASGGGVTASGGE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882  81 AVLQAEFVRDWFRACKEEGINTCLDTNGFVRHYDHIIDELLDVTDLVLLDLKELNDQVHQNLIGVPNKRTLEFAKYLQKR 160
Cdd:PRK11145  81 AILQAEFVRDWFRACKKEGIHTCLDTNGFVRRYDPVIDELLDVTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFARYLAKR 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882 161 NQHTWIRYVVVPGYTDSDHDVHLLGQFIEGMTNIEKVELLPYHRLGAHKWKTLGLDYELEDVLPPTKESLEHIKIILEGY 240
Cdd:PRK11145 161 NQKTWIRYVVVPGWTDDDDSAHRLGEFIKDMGNIEKIELLPYHELGKHKWEAMGEEYKLDGVKPPSKETMERVKGILEQY 240


                 ....*.
gi 543996882 241 GHTVKF 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: 502.63  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882   1 MSVLGRIHSFESCGTVDGPGIRFILFMQGCLMRCKYCHNRDTWDLEGGKEISVEDLMKEVVTYRHFMNATGGGVTASGGE 80
Cdd:PRK11145   1 MSVIGRIHSFESCGTVDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEELMKEVVTYRHFMNASGGGVTASGGE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882  81 AVLQAEFVRDWFRACKEEGINTCLDTNGFVRHYDHIIDELLDVTDLVLLDLKELNDQVHQNLIGVPNKRTLEFAKYLQKR 160
Cdd:PRK11145  81 AILQAEFVRDWFRACKKEGIHTCLDTNGFVRRYDPVIDELLDVTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFARYLAKR 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882 161 NQHTWIRYVVVPGYTDSDHDVHLLGQFIEGMTNIEKVELLPYHRLGAHKWKTLGLDYELEDVLPPTKESLEHIKIILEGY 240
Cdd:PRK11145 161 NQKTWIRYVVVPGWTDDDDSAHRLGEFIKDMGNIEKIELLPYHELGKHKWEAMGEEYKLDGVKPPSKETMERVKGILEQY 240


                 ....*.
gi 543996882 241 GHTVKF 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 5.34e-133

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: 374.40  E-value: 5.34e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882    6 RIHSFESCGTVDGPGIRFILFMQGCLMRCKYCHNRDTWDLEGGKEISVEDLMKEVVTYRHFMNATGGGVTASGGEAVLQA 85
Cdd:TIGR02493   1 RIHSTESMGTVDGPGIRFVVFMQGCPLRCQYCHNPDTWDLKGGTEVTPEELIKEVGSYKDFFKASGGGVTFSGGEPLLQP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882   86 EFVRDWFRACKEEGINTCLDTNGFVRHYDHIIDELLDVTDLVLLDLKELNDQVHQNLIGVPNKRTLEFAKYLQKRNQHTW 165
Cdd:TIGR02493  81 EFLSELFKACKELGIHTCLDTSGFLGGCTEAADELLEYTDLVLLDIKHFNPEKYKKLTGVSLQPTLDFAKYLAKRNKPIW 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 543996882  166 IRYVVVPGYTDSDHDVHLLGQFIEGMTNIEKVELLPYHRLGAHKWKTLGLDYELEDVLPPTKESLEHIKIILEGY 240
Cdd:TIGR02493 161 IRYVLVPGYTDSEEDIEALAEFVKTLPNVERVEVLPYHQLGVYKWEALGIEYPLEGVKPPNKEQLERAAEIFKEY 235
PflA COG1180
Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, ...
 1-241 1.53e-84

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


Pssm-ID: 440793 [Multi-domain]  Cd Length: 242  Bit Score: 251.64  E-value: 1.53e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882   1 MSVLGRIHSFESCGTVDGPG-IRFILFMQGCLMRCKYCHNRDTWDLE---GGKEISVEDLMKEVVTYRHFMNaTGGGVTA 76
Cdd:COG1180    1 EEVRGRIYGISPFSTVDGPGsIRLSVFTQGCNLRCPYCHNPEISQGRpdaAGRELSPEELVEEALKDRGFLD-SCGGVTF 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882  77 SGGEAVLQAEFVRDWFRACKEEGINTCLDTNGFV---------RHYDHI-IDelldvtdlvlldLKELNDQVHQNLIGVP 146
Cdd:COG1180   80 SGGEPTLQPEFLLDLAKLAKELGLHTALDTNGYIpeealeellPYLDAVnID------------LKAFDDEFYRKLTGVS 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882 147 NKRTLEFAKYLQKRNQHTWIRYVVVPGYTDSDHDVHLLGQFIEGMTNIEKVELLPYHRlgahkwktlglDYELEDVLPPT 226
Cdd:COG1180  148 LEPVLENLELLAESGVHVEIRTLVIPGLNDSEEELEAIARFIAELGDVIPVHLLPFHP-----------LYKLEDVPPPS 216

                        250
                 ....*....|....*
gi 543996882 227 KESLEHIKIILEGYG 241
Cdd:COG1180  217 PETLERAREIAREYG 231
Fer4_12 pfam13353
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
 16-119 7.58e-20

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: 82.60  E-value: 7.58e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882   16 VDGPGIRFILFMQGCLMRCKYCHNRDTWDLEGGKEISVEdLMKEVVTYrhFMNATGGGVTASGGEAVLQAEFVRDWFRAC 95
Cdd:pfam13353   1 VNGPGVRCSLFVSGCNHHCKGCFNPETWDFKYGKPFTEE-LEDEIIED--LAKPYIQGLTLSGGEPLLNAEALLELVKRV 77

                          90       100
                  ....*....|....*....|....*
gi 543996882   96 KEEGIN-TCLDTNGFVrhYDHIIDE 119
Cdd:pfam13353  78 REECPEkDIWLWTGYT--FEELQSK 100
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 24-203 8.17e-06

Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin.


Pssm-ID: 100105 [Multi-domain]  Cd Length: 204  Bit Score: 45.40  E-value: 8.17e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882  24 ILFMQGCLMRCKYCHNRDTWDLEGGKEISVEDlMKEVVTYRHFMNATGggVTASGGEAVLQAEFVRDWFRACKE-EGINT 102
Cdd:cd01335    1 LELTRGCNLNCGFCSNPASKGRGPESPPEIEE-ILDIVLEAKERGVEV--VILTGGEPLLYPELAELLRRLKKElPGFEI 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882 103 CLDTNGFVRHYDHIIDELLDVTDLVLLDLKELNDQVHQNLIGVPN--KRTLEFAKYLQKRNQHTWIRYVVVPGYTDS-DH 179
Cdd:cd01335   78 SIETNGTLLTEELLKELKELGLDGVGVSLDSGDEEVADKIRGSGEsfKERLEALKELREAGLGLSTTLLVGLGDEDEeDD 157

                        170       180
                 ....*....|....*....|....
gi 543996882 180 DVHLLgqFIEGMTNIEKVELLPYH 203
Cdd:cd01335  158 LEELE--LLAEFRSPDRVSLFRLL 179
viperin_w_prok NF038283
viperin family antiviral radical SAM protein; Homologs of a viral defense radical SAM enzyme ...
 30-109 9.72e-05

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: 42.54  E-value: 9.72e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882  30 CLMRCKYC--HNRDTWDLEGGKEISVEDLMKEVVTYRHFMNATGGGVTASGGEAVLQAEFVRDWFRACKEEGINTCLDTN 107
Cdd:NF038283  12 CNYRCKYCfaKWNDVKSPRHHDKGHLEKLLEELAEFFKLLSYGFVRINFAGGEPLLYPDRLLDLIKLAKELGFKTSIITN 91


                 ..
gi 543996882 108 GF 109
Cdd:NF038283  92 GS 93
 
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: 502.63  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882   1 MSVLGRIHSFESCGTVDGPGIRFILFMQGCLMRCKYCHNRDTWDLEGGKEISVEDLMKEVVTYRHFMNATGGGVTASGGE 80
Cdd:PRK11145   1 MSVIGRIHSFESCGTVDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEELMKEVVTYRHFMNASGGGVTASGGE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882  81 AVLQAEFVRDWFRACKEEGINTCLDTNGFVRHYDHIIDELLDVTDLVLLDLKELNDQVHQNLIGVPNKRTLEFAKYLQKR 160
Cdd:PRK11145  81 AILQAEFVRDWFRACKKEGIHTCLDTNGFVRRYDPVIDELLDVTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFARYLAKR 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882 161 NQHTWIRYVVVPGYTDSDHDVHLLGQFIEGMTNIEKVELLPYHRLGAHKWKTLGLDYELEDVLPPTKESLEHIKIILEGY 240
Cdd:PRK11145 161 NQKTWIRYVVVPGWTDDDDSAHRLGEFIKDMGNIEKIELLPYHELGKHKWEAMGEEYKLDGVKPPSKETMERVKGILEQY 240


                 ....*.
gi 543996882 241 GHTVKF 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 5.34e-133

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: 374.40  E-value: 5.34e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882    6 RIHSFESCGTVDGPGIRFILFMQGCLMRCKYCHNRDTWDLEGGKEISVEDLMKEVVTYRHFMNATGGGVTASGGEAVLQA 85
Cdd:TIGR02493   1 RIHSTESMGTVDGPGIRFVVFMQGCPLRCQYCHNPDTWDLKGGTEVTPEELIKEVGSYKDFFKASGGGVTFSGGEPLLQP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882   86 EFVRDWFRACKEEGINTCLDTNGFVRHYDHIIDELLDVTDLVLLDLKELNDQVHQNLIGVPNKRTLEFAKYLQKRNQHTW 165
Cdd:TIGR02493  81 EFLSELFKACKELGIHTCLDTSGFLGGCTEAADELLEYTDLVLLDIKHFNPEKYKKLTGVSLQPTLDFAKYLAKRNKPIW 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 543996882  166 IRYVVVPGYTDSDHDVHLLGQFIEGMTNIEKVELLPYHRLGAHKWKTLGLDYELEDVLPPTKESLEHIKIILEGY 240
Cdd:TIGR02493 161 IRYVLVPGYTDSEEDIEALAEFVKTLPNVERVEVLPYHQLGVYKWEALGIEYPLEGVKPPNKEQLERAAEIFKEY 235
PflA COG1180
Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, ...
 1-241 1.53e-84

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


Pssm-ID: 440793 [Multi-domain]  Cd Length: 242  Bit Score: 251.64  E-value: 1.53e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882   1 MSVLGRIHSFESCGTVDGPG-IRFILFMQGCLMRCKYCHNRDTWDLE---GGKEISVEDLMKEVVTYRHFMNaTGGGVTA 76
Cdd:COG1180    1 EEVRGRIYGISPFSTVDGPGsIRLSVFTQGCNLRCPYCHNPEISQGRpdaAGRELSPEELVEEALKDRGFLD-SCGGVTF 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882  77 SGGEAVLQAEFVRDWFRACKEEGINTCLDTNGFV---------RHYDHI-IDelldvtdlvlldLKELNDQVHQNLIGVP 146
Cdd:COG1180   80 SGGEPTLQPEFLLDLAKLAKELGLHTALDTNGYIpeealeellPYLDAVnID------------LKAFDDEFYRKLTGVS 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882 147 NKRTLEFAKYLQKRNQHTWIRYVVVPGYTDSDHDVHLLGQFIEGMTNIEKVELLPYHRlgahkwktlglDYELEDVLPPT 226
Cdd:COG1180  148 LEPVLENLELLAESGVHVEIRTLVIPGLNDSEEELEAIARFIAELGDVIPVHLLPFHP-----------LYKLEDVPPPS 216

                        250
                 ....*....|....*
gi 543996882 227 KESLEHIKIILEGYG 241
Cdd:COG1180  217 PETLERAREIAREYG 231
PFLE_PFLC TIGR02494
glycyl-radical enzyme activating protein; This subset of the radical-SAM family (pfam04055) ...
 17-241 9.78e-47

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: 157.11  E-value: 9.78e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882   17 DGPGIRFILFMQGCLMRCKYCHNRDTWD--------------------------------LEG----------------- 47
Cdd:TIGR02494  11 DGPGIRTTVFLKGCPLRCKWCSNPESQRkspellfkenrclgcgkcvevcpagtarlselADGrnriiirrekcthcgkc 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882   48 ------------GKEISVEDLMKEVVTYRHFMNATGGGVTASGGEAVLQAEFVRDWFRACKEEGINTCLDTNGFVRhyDH 115
Cdd:TIGR02494  91 teacpsgalsivGEEMTVEEVMRVVLRDSIFYRNSGGGVTLSGGEPLLQPEFALALLQACHERGIHTAVETSGFTP--WE 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882  116 IIDELLDVTDLVLLDLKELNDQVHQNLIGVPNKRTLEFAKYLQKRNQHTWIRYVVVPGYTDSDHDVHLLGQFIEGMTN-I 194
Cdd:TIGR02494 169 TIEKVLPYVDLFLFDIKHLDDERHKEVTGVDNEPILENLEALAAAGKNVVIRIPVIPGFNDSEENIEAIAAFLRKLEPgV 248

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*..
gi 543996882  195 EKVELLPYHRLGAHKWKTLGLDYELEDVLPPTKESLEHIKIILEGYG 241
Cdd:TIGR02494 249 DEIDLLPYHRLGENKYRQLGREYPDSEIPDPAEEQLLELKEIFESKG 295
activase_YjjW TIGR04041
glycine radical enzyme activase, YjjW family; Members of this family are radical SAM enzymes, ...
 6-241 4.58e-32

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: 118.12  E-value: 4.58e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882    6 RIHSFeSCgtVDGPGIRFILFMQGCLMRCKYCHNRDTWD------------------LEGGK------------------ 49
Cdd:TIGR04041   6 KIIPF-SC--VDGPGNRLAIFLQGCNFDCKYCHNPETINhcdhcgdcvagcpagalsLVDGKvvwdkercigcdtcikvc 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882   50 ---------EISVEDLMKEVVTYRHFMNatggGVTASGGEAVLQAEFVRDWFRACKEEGInTCL-DTNGFV--RHYDHI- 116
Cdd:TIGR04041  83 phqsspktkEYTVEELLDRIRKNMPFIR----GITVSGGECTLQLDFLTELFKAIKAAGL-TCFiDSNGSLdlTGWPKLl 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882  117 -------IDelldvtdlvlldLKELNDQVHQNLIGVPNKRTLEFAKYLQKRNQHTWIRYVVVPGYTDSDHDVHLLGQFIE 189
Cdd:TIGR04041 158 pvldgamLD------------LKAWDSETHRWLTGRDNHRVLKNIRFLAELGKLYEVRLVHIPGLSDLEQEIDGLARFLG 225

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 543996882  190 GMTNIEKVELLPYHRLGAHKwktlgldyELEDVLPPTKESLEHIKIILEGYG 241
Cdd:TIGR04041 226 DLPSDTRIKLIAFRHHGVRG--------EALEWPSPTDEQMEELAEALIKRG 269
Fer4_12 pfam13353
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
 16-119 7.58e-20

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: 82.60  E-value: 7.58e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882   16 VDGPGIRFILFMQGCLMRCKYCHNRDTWDLEGGKEISVEdLMKEVVTYrhFMNATGGGVTASGGEAVLQAEFVRDWFRAC 95
Cdd:pfam13353   1 VNGPGVRCSLFVSGCNHHCKGCFNPETWDFKYGKPFTEE-LEDEIIED--LAKPYIQGLTLSGGEPLLNAEALLELVKRV 77

                          90       100
                  ....*....|....*....|....*
gi 543996882   96 KEEGIN-TCLDTNGFVrhYDHIIDE 119
Cdd:pfam13353  78 REECPEkDIWLWTGYT--FEELQSK 100
PRK10076 PRK10076
pyruvate formate lyase II activase; Provisional
 48-245 3.07e-18

pyruvate formate lyase II activase; Provisional


Pssm-ID: 182224 [Multi-domain]  Cd Length: 213  Bit Score: 80.20  E-value: 3.07e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882  48 GKEISVEDLMKEVVTYRHFMNATGGGVTASGGEAVLQAEFVRDWFRACKEEGINTCLDTNGF---------VRHYDHIID 118
Cdd:PRK10076  16 GRDITLDALEREVMKDDIFFRTSGGGVTLSGGEVLMQAEFATRFLQRLRLWGVSCAIETAGDapaskllplAKLCDEVLF 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882 119 ElldvtdlvlldLKELNDQVHQNLIGVPNKRTLEFAKYLQKRNQHTWIRYVVVPGYTDSDHDVHLLGQFIEGMtNIEKVE 198
Cdd:PRK10076  96 D-----------LKIMDATQARDVVKMNLPRVLENLRLLVSEGVNVIPRLPLIPGFTLSRENMQQALDVLIPL-GIKQIH 163

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 543996882 199 LLPYHRLGAHKWKTLGLDYELEDVLPPTKESLEHIKIILEGYGHTVK 245
Cdd:PRK10076 164 LLPFHQYGEPKYRLLGKTWSMKEVPAPSSADVATMREMAERAGFQVT 210
NrdG2 TIGR02495
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
 6-108 1.49e-17

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: 77.79  E-value: 1.49e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882    6 RIHSFESCGTVDGPG-IRFILFMQGCLMRCKYCHNRDTWDLEGGKEISVEDLMKEVVTYRHFMNatggGVTASGGEAVLQ 84
Cdd:TIGR02495   1 RIAGLVPFSTVDYPGkLAFTIFLQGCNLKCPYCHNPLLIPRRGSGEIEVEELLEFLRRRRGLLD----GVVITGGEPTLQ 76

                          90       100
                  ....*....|....*....|....
gi 543996882   85 AEFVrDWFRACKEEGINTCLDTNG 108
Cdd:TIGR02495  77 AGLP-DFLREVRELGFEVKLDTNG 99
NrdG TIGR02491
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
 6-94 9.16e-16

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: 72.00  E-value: 9.16e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882    6 RIHSFESCGTVDGPGIRFILFMQGCLMRCKYCHNRDTWDLEGGKEISvEDLMKEVVtyRHFM-NATGGGVTASGGEAVLQ 84
Cdd:TIGR02491   1 NYMNIKPDDIVNGEGIRVSLFVAGCKHHCEGCFNKETWNFNGGKEFT-EALEKEII--RDLNdNPLIDGLTLSGGDPLYP 77

                          90
                  ....*....|....*.
gi 543996882   85 A------EFVRdWFRA 94
Cdd:TIGR02491  78 RnveeliELVK-KIKA 92
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 26-178 4.29e-13

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: 64.85  E-value: 4.29e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882   26 FMQGCLMRCKYCHNRDTWDLEGGKEISVEDLMKEVVTYRhfmNATGGGVTASGGEAVLQAEFVRDWFRACKE---EGINT 102
Cdd:pfam04055   1 ITRGCNLRCTYCAFPSIRARGKGRELSPEEILEEAKELK---RLGVEVVILGGGEPLLLPDLVELLERLLKLelaEGIRI 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 543996882  103 CLDTNGFVRHYDHIIDELLDVTDLVLLDLKELNDQVHQNLIGVPN-KRTLEFAKYLQKRNQH-TWIRYVVVPGYTDSD 178
Cdd:pfam04055  78 TLETNGTLLDEELLELLKEAGLDRVSIGLESGDDEVLKLINRGHTfEEVLEALELLREAGIPvVTDNIVGLPGETDED 155
QueE COG0602
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic ...
 21-110 9.05e-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: 56.68  E-value: 9.05e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882  21 IRFilfmQGCLMRCKYChnrDT---WDLEGGKEISVEDLMKEVVTYRHFMnatgggVTASGGEAVLQAEFvRDWFRACKE 97
Cdd:COG0602   25 VRL----AGCNLRCSWC---DTkyaWDGEGGKRMSAEEILEEVAALGARH------VVITGGEPLLQDDL-AELLEALKD 90

                         90
                 ....*....|...
gi 543996882  98 EGINTCLDTNGFV 110
Cdd:COG0602   91 AGYEVALETNGTL 103
nrdG PRK11121
anaerobic ribonucleoside-triphosphate reductase-activating protein;
8-49 3.01e-06

anaerobic ribonucleoside-triphosphate reductase-activating protein;


Pssm-ID: 236853  Cd Length: 154  Bit Score: 45.75  E-value: 3.01e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 543996882   8 HSFESCGTVDGPGIRFILFMQGCLMRCKYCHNRDTWDLEGGK 49
Cdd:PRK11121   4 HQYYPVDVVNGPGTRCTLFVSGCVHQCPGCYNKSTWRLNSGH 45
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 24-203 8.17e-06

Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin.


Pssm-ID: 100105 [Multi-domain]  Cd Length: 204  Bit Score: 45.40  E-value: 8.17e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882  24 ILFMQGCLMRCKYCHNRDTWDLEGGKEISVEDlMKEVVTYRHFMNATGggVTASGGEAVLQAEFVRDWFRACKE-EGINT 102
Cdd:cd01335    1 LELTRGCNLNCGFCSNPASKGRGPESPPEIEE-ILDIVLEAKERGVEV--VILTGGEPLLYPELAELLRRLKKElPGFEI 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882 103 CLDTNGFVRHYDHIIDELLDVTDLVLLDLKELNDQVHQNLIGVPN--KRTLEFAKYLQKRNQHTWIRYVVVPGYTDS-DH 179
Cdd:cd01335   78 SIETNGTLLTEELLKELKELGLDGVGVSLDSGDEEVADKIRGSGEsfKERLEALKELREAGLGLSTTLLVGLGDEDEeDD 157

                        170       180
                 ....*....|....*....|....
gi 543996882 180 DVHLLgqFIEGMTNIEKVELLPYH 203
Cdd:cd01335  158 LEELE--LLAEFRSPDRVSLFRLL 179
Tyw1 COG0731
Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily [Translation, ribosomal ...
 30-244 1.00e-05

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: 45.18  E-value: 1.00e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882  30 CLMRCKYCHNRDTWDL--EGGKEISVEDLMKEVVTYRHFMNATGGG---VTASG-GEAVLQAEFVR--DWFRACKeeGIN 101
Cdd:COG0731   34 CNFDCVYCQRGRTTDLtrERREFDDPEEILEELIEFLRKLPEEAREpdhITFSGsGEPTLYPNLGEliEEIKKLR--GIK 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882 102 TCLDTNGFVRHYDHIIDELLDVtdlvlldlkelnDQVHQ----------NLIGVPNKRtLEFAKYL-------QKRNQHT 164
Cdd:COG0731  112 TALLTNGSLLHRPEVREELLKA------------DQVYPsldaadeetfRKINRPHPG-LSWERIIeglelfrKLYKGRT 178

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882 165 WIRYVVVPGYTDSDHDVHLLGQFIEGmTNIEKVELLPYHRLGAhkwktlgldyeLEDVLPPTKESLEHIKIILEGYGHTV 244
Cdd:COG0731  179 VIETMLVKGINDSEEELEAYAELIKR-INPDFVELKTYMRPPA-----------LSRVNMPSHEELEEFAERLAELGYEV 246
Fer4_14 pfam13394
4Fe-4S single cluster domain;
25-80 2.53e-05

4Fe-4S single cluster domain;


Pssm-ID: 433171 [Multi-domain]  Cd Length: 115  Bit Score: 42.35  E-value: 2.53e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 543996882   25 LFMQGCLMRCKYCHNRDTWDLEGGkEISVEDLMKEVVTYRHFMNATGGGVTASGGE 80
Cdd:pfam13394   1 LFVSGCNHSCPGCDNKETWKFNYG-EPFTEELEDQIIADLKDSYIKRQGLVLTGGE 55
viperin_w_prok NF038283
viperin family antiviral radical SAM protein; Homologs of a viral defense radical SAM enzyme ...
 30-109 9.72e-05

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: 42.54  E-value: 9.72e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882  30 CLMRCKYC--HNRDTWDLEGGKEISVEDLMKEVVTYRHFMNATGGGVTASGGEAVLQAEFVRDWFRACKEEGINTCLDTN 107
Cdd:NF038283  12 CNYRCKYCfaKWNDVKSPRHHDKGHLEKLLEELAEFFKLLSYGFVRINFAGGEPLLYPDRLLDLIKLAKELGFKTSIITN 91


                 ..
gi 543996882 108 GF 109
Cdd:NF038283  92 GS 93
SkfB COG0535
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
 30-169 2.11e-04

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: 40.66  E-value: 2.11e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882  30 CLMRCKYCHNRdtWDLEGGKEISVEDLMKEVVTYRHFMNATgggVTASGGEAVLQAEFvRDWFRACKEEGINTCLDTNGf 109
Cdd:COG0535   10 CNLRCKHCYAD--AGPKRPGELSTEEAKRILDELAELGVKV---VGLTGGEPLLRPDL-FELVEYAKELGIRVNLSTNG- 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 543996882 110 vrhydHIIDElldvtdlvlLDLKELND---------------QVHQNLIGVPN--KRTLEFAKYLQKRNQHTWIRYV 169
Cdd:COG0535   83 -----TLLTE---------ELAERLAEagldhvtisldgvdpETHDKIRGVPGafDKVLEAIKLLKEAGIPVGINTV 145
RNR_activ_nrdG3 TIGR02826
anaerobic ribonucleoside-triphosphate reductase activating protein; Members of this family ...
 25-106 9.49e-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: 35.79  E-value: 9.49e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543996882   25 LFMQGCLMRCKYCHNRDTWDLEGGKEISVEDLMKEVVTYRHFMNAtgggVTASGGEAvlQAEFVRDWFRACKEE-GINTC 103
Cdd:TIGR02826  20 FYISGCPLGCPGCHSPELWHEDEGTPLTPEVLAQLLDKYRSLITC----VLFLGGEW--EPEALLSLLKYVKEHaGLKVC 93


                  ...
gi 543996882  104 LDT 106
Cdd:TIGR02826  94 LYT 96
 
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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