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Conserved domains on  [gi|226524704|ref|NP_415345|]
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putative pyruvate formate-lyase activating enzyme YbiY [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

glycyl-radical enzyme activating protein( domain architecture ID 11494368)

glycyl-radical enzyme activating protein similar to Clostridioides difficile 4-hydroxyphenylacetate decarboxylase activating enzyme that catalyzes the activation of 4-hydroxyphenylacetate decarboxylase under anaerobic conditions by generation of an organic free radical on a glycine residue, via a homolytic cleavage of S-adenosyl-L-methionine (SAM)

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PFLE_PFLC TIGR02494
glycyl-radical enzyme activating protein; This subset of the radical-SAM family (pfam04055) ...
2-292 9.27e-145

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: 408.65  E-value: 9.27e-145
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704    2 IFNIQRYSTHDGPGIRTVVFLKGCSLGCRWCQNPESRARTQDLLYDARLCLeGCELCAKAAP----EVIERALNGLLIHR 77
Cdd:TIGR02494   1 IFNIQRYSVHDGPGIRTTVFLKGCPLRCKWCSNPESQRKSPELLFKENRCL-GCGKCVEVCPagtaRLSELADGRNRIII 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704   78 EKLTPEHLTALTDCCPTQALTVCGEVKSVEEIMTTVLRDKPFYDRSGGGLTLSGGEPFMQPEMAMALLQASHEAGIHTAV 157
Cdd:TIGR02494  80 RREKCTHCGKCTEACPSGALSIVGEEMTVEEVMRVVLRDSIFYRNSGGGVTLSGGEPLLQPEFALALLQACHERGIHTAV 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704  158 ETCLHVPWKYIAPSLPYIDLFLADLKHVADAPFKQWTDGNAARVLDNLKKLAAAGKKIIIRVPLIQGFNADETSVKAITD 237
Cdd:TIGR02494 160 ETSGFTPWETIEKVLPYVDLFLFDIKHLDDERHKEVTGVDNEPILENLEALAAAGKNVVIRIPVIPGFNDSEENIEAIAA 239
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 226524704  238 FAADELH-VGEIHFLPYHTLGINKYHLLNLPYDAPEKPLDAPELLDFAQQYACQKG 292
Cdd:TIGR02494 240 FLRKLEPgVDEIDLLPYHRLGENKYRQLGREYPDSEIPDPAEEQLLELKEIFESKG 295
 
Name Accession Description Interval E-value
PFLE_PFLC TIGR02494
glycyl-radical enzyme activating protein; This subset of the radical-SAM family (pfam04055) ...
2-292 9.27e-145

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: 408.65  E-value: 9.27e-145
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704    2 IFNIQRYSTHDGPGIRTVVFLKGCSLGCRWCQNPESRARTQDLLYDARLCLeGCELCAKAAP----EVIERALNGLLIHR 77
Cdd:TIGR02494   1 IFNIQRYSVHDGPGIRTTVFLKGCPLRCKWCSNPESQRKSPELLFKENRCL-GCGKCVEVCPagtaRLSELADGRNRIII 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704   78 EKLTPEHLTALTDCCPTQALTVCGEVKSVEEIMTTVLRDKPFYDRSGGGLTLSGGEPFMQPEMAMALLQASHEAGIHTAV 157
Cdd:TIGR02494  80 RREKCTHCGKCTEACPSGALSIVGEEMTVEEVMRVVLRDSIFYRNSGGGVTLSGGEPLLQPEFALALLQACHERGIHTAV 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704  158 ETCLHVPWKYIAPSLPYIDLFLADLKHVADAPFKQWTDGNAARVLDNLKKLAAAGKKIIIRVPLIQGFNADETSVKAITD 237
Cdd:TIGR02494 160 ETSGFTPWETIEKVLPYVDLFLFDIKHLDDERHKEVTGVDNEPILENLEALAAAGKNVVIRIPVIPGFNDSEENIEAIAA 239
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 226524704  238 FAADELH-VGEIHFLPYHTLGINKYHLLNLPYDAPEKPLDAPELLDFAQQYACQKG 292
Cdd:TIGR02494 240 FLRKLEPgVDEIDLLPYHRLGENKYRQLGREYPDSEIPDPAEEQLLELKEIFESKG 295
ind_deCO2_activ NF033719
indoleacetate decarboxylase activase;
1-272 5.32e-71

indoleacetate decarboxylase activase;


Pssm-ID: 411307 [Multi-domain]  Cd Length: 302  Bit Score: 221.67  E-value: 5.32e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704   1 MIFNIQRYSTHDGPGIRTVVFLKGCSLGCRWCQNPESRARTQDLLYDARLCLeGCELCAKAAP-------EVIERALNGL 73
Cdd:NF033719   2 TVFDIQSFSTHDGPGIRTNVFLKGCPLKCPWCANPEGQKGTPELLYTKMKCV-GCMFCVKVCPhkaitavTDPEENAKYI 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704  74 LIHREKLTPEHLTALTDCCPTQALTVCGEVKSVEEIMTTVLRDKPFYdRSGGGLTLSGGEPFMQPEMAMALLQASHEAGI 153
Cdd:NF033719  81 KIDRSKCDKCTTHECVNACFNEALSVAGELMTVDDVMKKIERDSVYY-RAKGGVTLSGGDPLLQPDFALELLKACKEEAI 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704 154 HTAVETCLHVPWKYIAPSLPYIDLFLADLKHVADAPFKQWTDGNAARVLDNLKKLAAAGKKIIIRVPLIQGFNADETSVK 233
Cdd:NF033719 160 NTAIETELCVPPENIERFIPYIDLFLTDIKIMDPEKHKRITGVSNDVILKNIRLIGERCKRILLRIPIIPGYNDDDENID 239
                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 226524704 234 AITDFAADElHVGEIHFLPYHTLGINKYHLLNLPYDAPE 272
Cdd:NF033719 240 GTAKFAAEN-HISTINILPYHKLGVSKYERLGSTYLLPD 277
PflA COG1180
Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, ...
1-293 3.19e-66

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


Pssm-ID: 440793 [Multi-domain]  Cd Length: 242  Bit Score: 207.34  E-value: 3.19e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704   1 MIFNIQRYSTHDGPG-IRTVVFLKGCSLGCRWCQNPESRARTQDllydarlclegcelcakaapevieralngllihrek 79
Cdd:COG1180    6 RIYGISPFSTVDGPGsIRLSVFTQGCNLRCPYCHNPEISQGRPD------------------------------------ 49
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704  80 ltpehltaltdccptqaltVCGEVKSVEEIMTTVLRDKPFYDRSGggltlsggEPFMQPEMAMALLQASHEAGIHTAVET 159
Cdd:COG1180   50 -------------------AAGRELSPEELVEEALKDRGFLDSCGgvtf-sggEPTLQPEFLLDLAKLAKELGLHTALDT 109
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704 160 CLHVPWKYIAPSLPYIDLFLADLKHVADAPFKQWTDGNAARVLDNLKKLAAAGKKIIIRVPLIQGFNADETSVKAITDFA 239
Cdd:COG1180  110 NGYIPEEALEELLPYLDAVNIDLKAFDDEFYRKLTGVSLEPVLENLELLAESGVHVEIRTLVIPGLNDSEEELEAIARFI 189
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 226524704 240 ADELHVGEIHFLPYHTLginkyhllnlpYDAPEKPLDAPELLDFAQQYACQKGL 293
Cdd:COG1180  190 AELGDVIPVHLLPFHPL-----------YKLEDVPPPSPETLERAREIAREYGL 232
HPDL_rSAM_activ NF033717
4-hydroxyphenylacetate decarboxylase activase; 4-hydroxyphenylacetate decarboxylase activase ...
1-293 1.88e-55

4-hydroxyphenylacetate decarboxylase activase; 4-hydroxyphenylacetate decarboxylase activase is a radical SAM enzyme, found in anaerobic bacteria where 4-hydroxyphenylacetate decarboxylase occurs and required to prepare the glycyl radical active site of the enzyme.


Pssm-ID: 468152 [Multi-domain]  Cd Length: 311  Bit Score: 181.80  E-value: 1.88e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704   1 MIFNIQRYSTHDGPGIRTVVFLKGCSLGCRWCQNPESRARTQDLLYDARLCL--EGCELCAKAAPE-VIERALNGLL-IH 76
Cdd:NF033717   5 LIFDIQSFSVHDGPGCRTLVFLSGCPLRCEWCANPESWEKKKHIMFAEGKCKwdKGCRRCRDACPHgAIRFNDDGKPkID 84
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704  77 REKLTPEHLTALTDCCPTQALTVCGEVKSVEEIMTTVLRDKPFYdRSGGGLTLSGGEPFMQPEMAMALLQASHEAGIHTA 156
Cdd:NF033717  85 WEICEDCTTFECVNVCPNDALKQCVKEYTVDELMKILKRDRNNW-GSDGGVTFSGGEPLMQHEFLLEVLKKCKELNIHTA 163
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704 157 VETCLHVPWKYIAPSLPYIDLFLADLKHVADAPFKQWTDGNAARVLDNLKKLAAAGKK--IIIRVPLIQGFNADETSVKA 234
Cdd:NF033717 164 IETSAFASEEVFLKVMKYIDFAFIDIKHMDREKHKEGTGVGNELILSNIEALANSNWQgrLVLRVPTIAGFNDSVENASK 243
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 226524704 235 ITDFaADELHVGEIHFLPYHTLGINKYHLLNLPYDAPEKPLDAPELLDFAQQYACQKGL 293
Cdd:NF033717 244 TADF-MNENGLYEINLLPFHRLGESKWEQLGKEYEYTNDGDTSPEKLEELQDIYLDNGI 301
PRK10076 PRK10076
pyruvate formate lyase II activase; Provisional
90-299 3.15e-23

pyruvate formate lyase II activase; Provisional


Pssm-ID: 182224 [Multi-domain]  Cd Length: 213  Bit Score: 94.83  E-value: 3.15e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704  90 DCCPTQALTVCGEVKSVEEIMTTVLRDKPFYDRSGGGLTLSGGEPFMQPEMAMALLQASHEAGIHTAVETCLHVPWKYIA 169
Cdd:PRK10076   5 DECPSGAFERIGRDITLDALEREVMKDDIFFRTSGGGVTLSGGEVLMQAEFATRFLQRLRLWGVSCAIETAGDAPASKLL 84
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704 170 PSLPYIDLFLADLKHVADAPFKQWTDGNAARVLDNLKKLAAAGKKIIIRVPLIQGFNADETSVKAITDFAAdELHVGEIH 249
Cdd:PRK10076  85 PLAKLCDEVLFDLKIMDATQARDVVKMNLPRVLENLRLLVSEGVNVIPRLPLIPGFTLSRENMQQALDVLI-PLGIKQIH 163
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 226524704 250 FLPYHTLGINKYHLLNLPYDAPEKPLDAPELLDFAQQYACQKGLTATLRG 299
Cdd:PRK10076 164 LLPFHQYGEPKYRLLGKTWSMKEVPAPSSADVATMREMAERAGFQVTVGG 213
Fer4_12 pfam13353
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
12-37 4.27e-05

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


Pssm-ID: 433138 [Multi-domain]  Cd Length: 137  Bit Score: 42.54  E-value: 4.27e-05
                          10        20
                  ....*....|....*....|....*.
gi 226524704   12 DGPGIRTVVFLKGCSLGCRWCQNPES 37
Cdd:pfam13353   2 NGPGVRCSLFVSGCNHHCKGCFNPET 27
 
Name Accession Description Interval E-value
PFLE_PFLC TIGR02494
glycyl-radical enzyme activating protein; This subset of the radical-SAM family (pfam04055) ...
2-292 9.27e-145

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: 408.65  E-value: 9.27e-145
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704    2 IFNIQRYSTHDGPGIRTVVFLKGCSLGCRWCQNPESRARTQDLLYDARLCLeGCELCAKAAP----EVIERALNGLLIHR 77
Cdd:TIGR02494   1 IFNIQRYSVHDGPGIRTTVFLKGCPLRCKWCSNPESQRKSPELLFKENRCL-GCGKCVEVCPagtaRLSELADGRNRIII 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704   78 EKLTPEHLTALTDCCPTQALTVCGEVKSVEEIMTTVLRDKPFYDRSGGGLTLSGGEPFMQPEMAMALLQASHEAGIHTAV 157
Cdd:TIGR02494  80 RREKCTHCGKCTEACPSGALSIVGEEMTVEEVMRVVLRDSIFYRNSGGGVTLSGGEPLLQPEFALALLQACHERGIHTAV 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704  158 ETCLHVPWKYIAPSLPYIDLFLADLKHVADAPFKQWTDGNAARVLDNLKKLAAAGKKIIIRVPLIQGFNADETSVKAITD 237
Cdd:TIGR02494 160 ETSGFTPWETIEKVLPYVDLFLFDIKHLDDERHKEVTGVDNEPILENLEALAAAGKNVVIRIPVIPGFNDSEENIEAIAA 239
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 226524704  238 FAADELH-VGEIHFLPYHTLGINKYHLLNLPYDAPEKPLDAPELLDFAQQYACQKG 292
Cdd:TIGR02494 240 FLRKLEPgVDEIDLLPYHRLGENKYRQLGREYPDSEIPDPAEEQLLELKEIFESKG 295
ind_deCO2_activ NF033719
indoleacetate decarboxylase activase;
1-272 5.32e-71

indoleacetate decarboxylase activase;


Pssm-ID: 411307 [Multi-domain]  Cd Length: 302  Bit Score: 221.67  E-value: 5.32e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704   1 MIFNIQRYSTHDGPGIRTVVFLKGCSLGCRWCQNPESRARTQDLLYDARLCLeGCELCAKAAP-------EVIERALNGL 73
Cdd:NF033719   2 TVFDIQSFSTHDGPGIRTNVFLKGCPLKCPWCANPEGQKGTPELLYTKMKCV-GCMFCVKVCPhkaitavTDPEENAKYI 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704  74 LIHREKLTPEHLTALTDCCPTQALTVCGEVKSVEEIMTTVLRDKPFYdRSGGGLTLSGGEPFMQPEMAMALLQASHEAGI 153
Cdd:NF033719  81 KIDRSKCDKCTTHECVNACFNEALSVAGELMTVDDVMKKIERDSVYY-RAKGGVTLSGGDPLLQPDFALELLKACKEEAI 159
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704 154 HTAVETCLHVPWKYIAPSLPYIDLFLADLKHVADAPFKQWTDGNAARVLDNLKKLAAAGKKIIIRVPLIQGFNADETSVK 233
Cdd:NF033719 160 NTAIETELCVPPENIERFIPYIDLFLTDIKIMDPEKHKRITGVSNDVILKNIRLIGERCKRILLRIPIIPGYNDDDENID 239
                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 226524704 234 AITDFAADElHVGEIHFLPYHTLGINKYHLLNLPYDAPE 272
Cdd:NF033719 240 GTAKFAAEN-HISTINILPYHKLGVSKYERLGSTYLLPD 277
cutC_activ_rSAM TIGR04395
choline TMA-lyase-activating enzyme; Members of this family are CutD, a radical enzyme that ...
2-280 7.58e-68

choline TMA-lyase-activating enzyme; Members of this family are CutD, a radical enzyme that serves as an activase for choline TMA-lyase, CutC. CutC is a glycyl radical enzyme related to pyruvate formate-lyase, and this enzyme, CutD, is related to pyruvate formate-lyase activase. [Energy metabolism, Amino acids and amines]


Pssm-ID: 275188 [Multi-domain]  Cd Length: 309  Bit Score: 213.81  E-value: 7.58e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704    2 IFNIQRYSTHDGPGIRTVVFLKGCSLGCRWCQNPESRARTQDLLYDARLCLEgCELCAKAAPEVIERALNGL---LIHRE 78
Cdd:TIGR04395   7 IFNIQKYNMYDGPGVRTLVFFKGCPLRCKWCSNPEGQERKFQVLFKKDICVD-CGACVAVCPVGIHKMLAEGgkhVIDRS 85
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704   79 KltpehltaltDC---------CPTQALTVCGEVKSVEEIMTTVLRDKPFYDRSGGGLTLSGGEPFMQPEMAMALLQASH 149
Cdd:TIGR04395  86 I----------DCigcrkceeaCPKHALAIMGEDKTISELLEIIEEDRPFYEMSGGGVTLGGGEVLAQPEAAANLLMACK 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704  150 EAGIHTAVETCLHVPWKYIAPSLPYIDLFLADLKHVADAPFKQWTDGNAARVLDNLKKLAAAGKKIIIRVPLIQGFNADE 229
Cdd:TIGR04395 156 QRGIHTAIETCGYAKPEVILKVAEFVDLFLFDIKHMDSERHYELTGVRNELILSNLQELLENGYNVKIRMPLLKGVNDGE 235
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 226524704  230 TSVKAITDFAADELHVGE---IHFLPYHTLGINKYHLLNLPYDAPEKP-LDAPEL 280
Cdd:TIGR04395 236 EEIDQVIRFLKPYKYYKNfkgVDLLPYHKMGVNKYAQLDMDYPIEGDPsLDDADL 290
PflA COG1180
Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, ...
1-293 3.19e-66

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


Pssm-ID: 440793 [Multi-domain]  Cd Length: 242  Bit Score: 207.34  E-value: 3.19e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704   1 MIFNIQRYSTHDGPG-IRTVVFLKGCSLGCRWCQNPESRARTQDllydarlclegcelcakaapevieralngllihrek 79
Cdd:COG1180    6 RIYGISPFSTVDGPGsIRLSVFTQGCNLRCPYCHNPEISQGRPD------------------------------------ 49
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704  80 ltpehltaltdccptqaltVCGEVKSVEEIMTTVLRDKPFYDRSGggltlsggEPFMQPEMAMALLQASHEAGIHTAVET 159
Cdd:COG1180   50 -------------------AAGRELSPEELVEEALKDRGFLDSCGgvtf-sggEPTLQPEFLLDLAKLAKELGLHTALDT 109
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704 160 CLHVPWKYIAPSLPYIDLFLADLKHVADAPFKQWTDGNAARVLDNLKKLAAAGKKIIIRVPLIQGFNADETSVKAITDFA 239
Cdd:COG1180  110 NGYIPEEALEELLPYLDAVNIDLKAFDDEFYRKLTGVSLEPVLENLELLAESGVHVEIRTLVIPGLNDSEEELEAIARFI 189
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 226524704 240 ADELHVGEIHFLPYHTLginkyhllnlpYDAPEKPLDAPELLDFAQQYACQKGL 293
Cdd:COG1180  190 AELGDVIPVHLLPFHPL-----------YKLEDVPPPSPETLERAREIAREYGL 232
HPDL_rSAM_activ NF033717
4-hydroxyphenylacetate decarboxylase activase; 4-hydroxyphenylacetate decarboxylase activase ...
1-293 1.88e-55

4-hydroxyphenylacetate decarboxylase activase; 4-hydroxyphenylacetate decarboxylase activase is a radical SAM enzyme, found in anaerobic bacteria where 4-hydroxyphenylacetate decarboxylase occurs and required to prepare the glycyl radical active site of the enzyme.


Pssm-ID: 468152 [Multi-domain]  Cd Length: 311  Bit Score: 181.80  E-value: 1.88e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704   1 MIFNIQRYSTHDGPGIRTVVFLKGCSLGCRWCQNPESRARTQDLLYDARLCL--EGCELCAKAAPE-VIERALNGLL-IH 76
Cdd:NF033717   5 LIFDIQSFSVHDGPGCRTLVFLSGCPLRCEWCANPESWEKKKHIMFAEGKCKwdKGCRRCRDACPHgAIRFNDDGKPkID 84
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704  77 REKLTPEHLTALTDCCPTQALTVCGEVKSVEEIMTTVLRDKPFYdRSGGGLTLSGGEPFMQPEMAMALLQASHEAGIHTA 156
Cdd:NF033717  85 WEICEDCTTFECVNVCPNDALKQCVKEYTVDELMKILKRDRNNW-GSDGGVTFSGGEPLMQHEFLLEVLKKCKELNIHTA 163
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704 157 VETCLHVPWKYIAPSLPYIDLFLADLKHVADAPFKQWTDGNAARVLDNLKKLAAAGKK--IIIRVPLIQGFNADETSVKA 234
Cdd:NF033717 164 IETSAFASEEVFLKVMKYIDFAFIDIKHMDREKHKEGTGVGNELILSNIEALANSNWQgrLVLRVPTIAGFNDSVENASK 243
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 226524704 235 ITDFaADELHVGEIHFLPYHTLGINKYHLLNLPYDAPEKPLDAPELLDFAQQYACQKGL 293
Cdd:NF033717 244 TADF-MNENGLYEINLLPFHRLGESKWEQLGKEYEYTNDGDTSPEKLEELQDIYLDNGI 301
PFLA TIGR02493
pyruvate formate-lyase 1-activating enzyme; An iron-sulfur protein with a radical-SAM domain ...
10-288 3.71e-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: 137.50  E-value: 3.71e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704   10 THDGPGIRTVVFLKGCSLGCRWCQNPESrartqdllydarlclegceLCAKAAPEVieralngllihrekltpehltalt 89
Cdd:TIGR02493  10 TVDGPGIRFVVFMQGCPLRCQYCHNPDT-------------------WDLKGGTEV------------------------ 46
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704   90 dccptqaltvcgevkSVEEIMTTVLRDKPFYDRSGGGLTLSGGEPFMQPEMAMALLQASHEAGIHTAVETCLHVPW--KY 167
Cdd:TIGR02493  47 ---------------TPEELIKEVGSYKDFFKASGGGVTFSGGEPLLQPEFLSELFKACKELGIHTCLDTSGFLGGctEA 111
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704  168 IAPSLPYIDLFLADLKHVADAPFKQWTDGNAARVLDNLKKLAAAGKKIIIRVPLIQGFNADETSVKAITDFAADELHVGE 247
Cdd:TIGR02493 112 ADELLEYTDLVLLDIKHFNPEKYKKLTGVSLQPTLDFAKYLAKRNKPIWIRYVLVPGYTDSEEDIEALAEFVKTLPNVER 191
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 226524704  248 IHFLPYHTLGINKYHLLNLPYDAPE-KPLDAPELLDFAQQYA 288
Cdd:TIGR02493 192 VEVLPYHQLGVYKWEALGIEYPLEGvKPPNKEQLERAAEIFK 233
PRK10076 PRK10076
pyruvate formate lyase II activase; Provisional
90-299 3.15e-23

pyruvate formate lyase II activase; Provisional


Pssm-ID: 182224 [Multi-domain]  Cd Length: 213  Bit Score: 94.83  E-value: 3.15e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704  90 DCCPTQALTVCGEVKSVEEIMTTVLRDKPFYDRSGGGLTLSGGEPFMQPEMAMALLQASHEAGIHTAVETCLHVPWKYIA 169
Cdd:PRK10076   5 DECPSGAFERIGRDITLDALEREVMKDDIFFRTSGGGVTLSGGEVLMQAEFATRFLQRLRLWGVSCAIETAGDAPASKLL 84
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704 170 PSLPYIDLFLADLKHVADAPFKQWTDGNAARVLDNLKKLAAAGKKIIIRVPLIQGFNADETSVKAITDFAAdELHVGEIH 249
Cdd:PRK10076  85 PLAKLCDEVLFDLKIMDATQARDVVKMNLPRVLENLRLLVSEGVNVIPRLPLIPGFTLSRENMQQALDVLI-PLGIKQIH 163
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 226524704 250 FLPYHTLGINKYHLLNLPYDAPEKPLDAPELLDFAQQYACQKGLTATLRG 299
Cdd:PRK10076 164 LLPFHQYGEPKYRLLGKTWSMKEVPAPSSADVATMREMAERAGFQVTVGG 213
pflA PRK11145
pyruvate formate lyase 1-activating protein;
2-269 1.56e-21

pyruvate formate lyase 1-activating protein;


Pssm-ID: 182994 [Multi-domain]  Cd Length: 246  Bit Score: 90.86  E-value: 1.56e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704   2 IFNIQRYSTHDGPGIRTVVFLKGCSLGCRWCQNPEsrarTQDLlydarlclegcelcakaapevieralnglliHREKlt 81
Cdd:PRK11145   7 IHSFESCGTVDGPGIRFITFFQGCLMRCLYCHNRD----TWDT-------------------------------HGGK-- 49
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704  82 pehltaltdccptqaltvcgEVkSVEEIMTTVLRDKPFYDRSGGGLTLSGGEPFMQPEMAMALLQASHEAGIHTAVETCL 161
Cdd:PRK11145  50 --------------------EV-TVEELMKEVVTYRHFMNASGGGVTASGGEAILQAEFVRDWFRACKKEGIHTCLDTNG 108
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704 162 HVPwKY---IAPSLPYIDLFLADLKHVADAPFKQWTDGNAARVLDNLKKLAAAGKKIIIRVPLIQGFNADETSVKAITDF 238
Cdd:PRK11145 109 FVR-RYdpvIDELLDVTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFARYLAKRNQKTWIRYVVVPGWTDDDDSAHRLGEF 187
                        250       260       270
                 ....*....|....*....|....*....|.
gi 226524704 239 AADELHVGEIHFLPYHTLGINKYHLLNLPYD 269
Cdd:PRK11145 188 IKDMGNIEKIELLPYHELGKHKWEAMGEEYK 218
activase_YjjW TIGR04041
glycine radical enzyme activase, YjjW family; Members of this family are radical SAM enzymes, ...
1-238 7.82e-15

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: 73.05  E-value: 7.82e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704    1 MIFNIQRYSTHDGPGIRTVVFLKGCSLGCRWCQNPEsrarTQdllydaRLClEGCELCAKAAPEVIERALNGlLIHREKL 80
Cdd:TIGR04041   3 LVNKIIPFSCVDGPGNRLAIFLQGCNFDCKYCHNPE----TI------NHC-DHCGDCVAGCPAGALSLVDG-KVVWDKE 70
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704   81 TPEHLTALTDCCPTQAlTVCGEVKSVEEIMTTVLRDKPFYDrsggGLTLSGGEPFMQPEMAMALLQASHEAGIhtaveTC 160
Cdd:TIGR04041  71 RCIGCDTCIKVCPHQS-SPKTKEYTVEELLDRIRKNMPFIR----GITVSGGECTLQLDFLTELFKAIKAAGL-----TC 140
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 226524704  161 L--------HVPWKYIapsLPYIDLFLADLKHVADAPFKQWTDGNAARVLDNLKKLAAAGKKIIIRVPLIQGFNADETSV 232
Cdd:TIGR04041 141 FidsngsldLTGWPKL---LPVLDGAMLDLKAWDSETHRWLTGRDNHRVLKNIRFLAELGKLYEVRLVHIPGLSDLEQEI 217

                  ....*.
gi 226524704  233 KAITDF 238
Cdd:TIGR04041 218 DGLARF 223
NrdG TIGR02491
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
2-37 8.67e-06

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: 45.03  E-value: 8.67e-06
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 226524704    2 IFNIQRYSTHDGPGIRTVVFLKGCSLGCRWCQNPES 37
Cdd:TIGR02491   2 YMNIKPDDIVNGEGIRVSLFVAGCKHHCEGCFNKET 37
Fer4_12 pfam13353
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
12-37 4.27e-05

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


Pssm-ID: 433138 [Multi-domain]  Cd Length: 137  Bit Score: 42.54  E-value: 4.27e-05
                          10        20
                  ....*....|....*....|....*.
gi 226524704   12 DGPGIRTVVFLKGCSLGCRWCQNPES 37
Cdd:pfam13353   2 NGPGVRCSLFVSGCNHHCKGCFNPET 27
Fer COG1141
Ferredoxin [Energy production and conversion];
47-99 7.41e-03

Ferredoxin [Energy production and conversion];


Pssm-ID: 440756 [Multi-domain]  Cd Length: 63  Bit Score: 34.47  E-value: 7.41e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 226524704  47 DARLClEGCELCAKAAPEVIERALNGLLIHREKLTPEHLTALT----DCCPTQALTV 99
Cdd:COG1141    6 DRDTC-IGCGLCVALAPEVFELDDDGKAVVLDEEVPEELEEDVreaaDACPVGAITV 61
 
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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