NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2519633945|ref|WP_285155309|]
View 

anaerobic ribonucleoside-triphosphate reductase activating protein [Slackia exigua]

Protein Classification

4Fe-4S single cluster domain-containing protein( domain architecture ID 12135473)

4Fe-4S single cluster domain-containing protein binds iron-sulfur clusters

Gene Ontology:  GO:0051539
PubMed:  29601957

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Fer4_12 pfam13353
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
 12-155 2.75e-65

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: 196.62  E-value: 2.75e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2519633945  12 ANGEGVRTVLFVSGCRMRCPFCFNEEAWNFHAGNPFDAAVQDQIVESLRPLYVDGLSVLGGEPMepENQAGLVDFLERVR 91
Cdd:pfam13353   1 VNGPGVRCSLFVSGCNHHCKGCFNPETWDFKYGKPFTEELEDEIIEDLAKPYIQGLTLSGGEPL--LNAEALLELVKRVR 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2519633945  92 REFPDKTIWLYSGHTFENLTRGSghtecTDRIMATLDVLVDGPFVQAKKSMGLRFRGSSNQRVI 155
Cdd:pfam13353  79 EECPEKDIWLWTGYTFEELQSKD-----QLELLKLIDVLVDGKFEQSLKDPSLRFRGSSNQRII 137
 
Name Accession Description Interval E-value
Fer4_12 pfam13353
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
 12-155 2.75e-65

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: 196.62  E-value: 2.75e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2519633945  12 ANGEGVRTVLFVSGCRMRCPFCFNEEAWNFHAGNPFDAAVQDQIVESLRPLYVDGLSVLGGEPMepENQAGLVDFLERVR 91
Cdd:pfam13353   1 VNGPGVRCSLFVSGCNHHCKGCFNPETWDFKYGKPFTEELEDEIIEDLAKPYIQGLTLSGGEPL--LNAEALLELVKRVR 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2519633945  92 REFPDKTIWLYSGHTFENLTRGSghtecTDRIMATLDVLVDGPFVQAKKSMGLRFRGSSNQRVI 155
Cdd:pfam13353  79 EECPEKDIWLWTGYTFEELQSKD-----QLELLKLIDVLVDGKFEQSLKDPSLRFRGSSNQRII 137
NrdG TIGR02491
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
 3-158 1.07e-64

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: 195.65  E-value: 1.07e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2519633945   3 YSTIKYCDIANGEGVRTVLFVSGCRMRCPFCFNEEAWNFHAGNPFDAAVQDQIVESL-RPLYVDGLSVLGGEPMEPENQA 81
Cdd:TIGR02491   2 YMNIKPDDIVNGEGIRVSLFVAGCKHHCEGCFNKETWNFNGGKEFTEALEKEIIRDLnDNPLIDGLTLSGGDPLYPRNVE 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2519633945  82 GLVDFLERVRREFPDKTIWLYSGHTFENLTRGSGHTEctdrIMATLDVLVDGPFVQAKKSMGLRFRGSSNQRVIDVP 158
Cdd:TIGR02491  82 ELIELVKKIKAEFPEKDIWLWTGYTWEEILEDEKHLE----VLKYIDVLVDGKFELSKKDLKLKFRGSSNQRIIDLK 154
nrdG PRK11121
anaerobic ribonucleoside-triphosphate reductase-activating protein;
1-154 2.14e-49

anaerobic ribonucleoside-triphosphate reductase-activating protein;


Pssm-ID: 236853  Cd Length: 154  Bit Score: 157.08  E-value: 2.14e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2519633945   1 MHYSTIKYCDIANGEGVRTVLFVSGCRMRCPFCFNEEAWNFHAGNPFDAAVQDQIVESLRPLYV--DGLSVLGGEPMEPE 78
Cdd:PRK11121    1 MNYHQYYPVDVVNGPGTRCTLFVSGCVHQCPGCYNKSTWRLNSGHPFTKEMEDQIIADLNDTRIkrQGLSLSGGDPLHPQ 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2519633945  79 NQAGLVDFLERVRREFPDKTIWLYSGHTFENLtrgsghTECTDRIMATLDVLVDGPFVQAKKSMGLRFRGSSNQRV 154
Cdd:PRK11121   81 NVPDILKLVQRVKAECPGKDIWVWTGYKLDEL------NAAQRQVVDLIDVLVDGKFVQDLADPSLIWRGSSNQVI 150
PflA COG1180
Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, ...
 17-93 1.25e-08

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


Pssm-ID: 440793 [Multi-domain]  Cd Length: 242  Bit Score: 52.88  E-value: 1.25e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2519633945  17 VRTVLFVSGCRMRCPFCFNEEAWNFHAGNPFDAAVQDQIVE---SLRPLY--VDGLSVLGGEP-MEPEnqaGLVDFLERV 90
Cdd:COG1180    22 IRLSVFTQGCNLRCPYCHNPEISQGRPDAAGRELSPEELVEealKDRGFLdsCGGVTFSGGEPtLQPE---FLLDLAKLA 98


                  ...
gi 2519633945  91 RRE 93
Cdd:COG1180    99 KEL 101
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 20-112 1.65e-07

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


Pssm-ID: 100105 [Multi-domain]  Cd Length: 204  Bit Score: 49.25  E-value: 1.65e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2519633945  20 VLFVSGCRMRCPFCFNEEAWNFHAGNPFDAAVQDQIVESLRPLYVDGLSVLGGEPMEPEnqaGLVDFLERVRREFPDKTI 99
Cdd:cd01335     1 LELTRGCNLNCGFCSNPASKGRGPESPPEIEEILDIVLEAKERGVEVVILTGGEPLLYP---ELAELLRRLKKELPGFEI 77

                          90
                  ....*....|...
gi 2519633945 100 WLYSGHTFENLTR 112
Cdd:cd01335    78 SIETNGTLLTEEL 90
 
Name Accession Description Interval E-value
Fer4_12 pfam13353
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
 12-155 2.75e-65

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: 196.62  E-value: 2.75e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2519633945  12 ANGEGVRTVLFVSGCRMRCPFCFNEEAWNFHAGNPFDAAVQDQIVESLRPLYVDGLSVLGGEPMepENQAGLVDFLERVR 91
Cdd:pfam13353   1 VNGPGVRCSLFVSGCNHHCKGCFNPETWDFKYGKPFTEELEDEIIEDLAKPYIQGLTLSGGEPL--LNAEALLELVKRVR 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2519633945  92 REFPDKTIWLYSGHTFENLTRGSghtecTDRIMATLDVLVDGPFVQAKKSMGLRFRGSSNQRVI 155
Cdd:pfam13353  79 EECPEKDIWLWTGYTFEELQSKD-----QLELLKLIDVLVDGKFEQSLKDPSLRFRGSSNQRII 137
NrdG TIGR02491
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
 3-158 1.07e-64

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: 195.65  E-value: 1.07e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2519633945   3 YSTIKYCDIANGEGVRTVLFVSGCRMRCPFCFNEEAWNFHAGNPFDAAVQDQIVESL-RPLYVDGLSVLGGEPMEPENQA 81
Cdd:TIGR02491   2 YMNIKPDDIVNGEGIRVSLFVAGCKHHCEGCFNKETWNFNGGKEFTEALEKEIIRDLnDNPLIDGLTLSGGDPLYPRNVE 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2519633945  82 GLVDFLERVRREFPDKTIWLYSGHTFENLTRGSGHTEctdrIMATLDVLVDGPFVQAKKSMGLRFRGSSNQRVIDVP 158
Cdd:TIGR02491  82 ELIELVKKIKAEFPEKDIWLWTGYTWEEILEDEKHLE----VLKYIDVLVDGKFELSKKDLKLKFRGSSNQRIIDLK 154
nrdG PRK11121
anaerobic ribonucleoside-triphosphate reductase-activating protein;
1-154 2.14e-49

anaerobic ribonucleoside-triphosphate reductase-activating protein;


Pssm-ID: 236853  Cd Length: 154  Bit Score: 157.08  E-value: 2.14e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2519633945   1 MHYSTIKYCDIANGEGVRTVLFVSGCRMRCPFCFNEEAWNFHAGNPFDAAVQDQIVESLRPLYV--DGLSVLGGEPMEPE 78
Cdd:PRK11121    1 MNYHQYYPVDVVNGPGTRCTLFVSGCVHQCPGCYNKSTWRLNSGHPFTKEMEDQIIADLNDTRIkrQGLSLSGGDPLHPQ 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2519633945  79 NQAGLVDFLERVRREFPDKTIWLYSGHTFENLtrgsghTECTDRIMATLDVLVDGPFVQAKKSMGLRFRGSSNQRV 154
Cdd:PRK11121   81 NVPDILKLVQRVKAECPGKDIWVWTGYKLDEL------NAAQRQVVDLIDVLVDGKFVQDLADPSLIWRGSSNQVI 150
Fer4_14 pfam13394
4Fe-4S single cluster domain;
21-134 6.51e-38

4Fe-4S single cluster domain;


Pssm-ID: 433171 [Multi-domain]  Cd Length: 115  Bit Score: 126.32  E-value: 6.51e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2519633945  21 LFVSGCRMRCPFCFNEEAWNFHAGNPFDAAVQDQIVESLRPLYV--DGLSVLGGEPMEPENQAGLVDFLERVRREFPDKT 98
Cdd:pfam13394   1 LFVSGCNHSCPGCDNKETWKFNYGEPFTEELEDQIIADLKDSYIkrQGLVLTGGEPLHPWNLPVLLKLLKRVKEEYPSKD 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2519633945  99 IWLYSGHTFeNLTRGSGHTECTDRIMATLDVLVDGP 134
Cdd:pfam13394  81 IWLETGYTL-AIDFEYPDTEEQLFTLSVIDVLVDGK 115
PflA COG1180
Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, ...
 17-93 1.25e-08

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


Pssm-ID: 440793 [Multi-domain]  Cd Length: 242  Bit Score: 52.88  E-value: 1.25e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2519633945  17 VRTVLFVSGCRMRCPFCFNEEAWNFHAGNPFDAAVQDQIVE---SLRPLY--VDGLSVLGGEP-MEPEnqaGLVDFLERV 90
Cdd:COG1180    22 IRLSVFTQGCNLRCPYCHNPEISQGRPDAAGRELSPEELVEealKDRGFLdsCGGVTFSGGEPtLQPE---FLLDLAKLA 98


                  ...
gi 2519633945  91 RRE 93
Cdd:COG1180    99 KEL 101
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 20-112 1.65e-07

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


Pssm-ID: 100105 [Multi-domain]  Cd Length: 204  Bit Score: 49.25  E-value: 1.65e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2519633945  20 VLFVSGCRMRCPFCFNEEAWNFHAGNPFDAAVQDQIVESLRPLYVDGLSVLGGEPMEPEnqaGLVDFLERVRREFPDKTI 99
Cdd:cd01335     1 LELTRGCNLNCGFCSNPASKGRGPESPPEIEEILDIVLEAKERGVEVVILTGGEPLLYP---ELAELLRRLKKELPGFEI 77

                          90
                  ....*....|...
gi 2519633945 100 WLYSGHTFENLTR 112
Cdd:cd01335    78 SIETNGTLLTEEL 90
pflA PRK11145
pyruvate formate lyase 1-activating protein;
9-75 8.26e-07

pyruvate formate lyase 1-activating protein;


Pssm-ID: 182994 [Multi-domain]  Cd Length: 246  Bit Score: 47.71  E-value: 8.26e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2519633945   9 CDIANGEGVRTVLFVSGCRMRCPFCFNEEAWNFHAGNpfDAAVQDQIVE--SLRPlYVD----GLSVLGGEPM 75
Cdd:PRK11145   13 CGTVDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGGK--EVTVEELMKEvvTYRH-FMNasggGVTASGGEAI 82
NrdG2 TIGR02495
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
 20-91 1.11e-06

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: 46.59  E-value: 1.11e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2519633945  20 VLFVSGCRMRCPFCFNEE----------AWNFhagnpfdaaVQDQIVEslRPLYVDGLSVLGGEPMEpenQAGLVDFLER 89
Cdd:TIGR02495  20 TIFLQGCNLKCPYCHNPLliprrgsgeiEVEE---------LLEFLRR--RRGLLDGVVITGGEPTL---QAGLPDFLRE 85


                  ..
gi 2519633945  90 VR 91
Cdd:TIGR02495  86 VR 87
QueE COG0602
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic ...
 14-93 1.52e-06

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: 46.28  E-value: 1.52e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2519633945  14 GE----GVRTVlFV--SGCRMRCPFCFNEEAWNFHAGNPFDAavqDQIVESLRPLYVDGLSVLGGEPMEpenQAGLVDFL 87
Cdd:COG0602    13 GEgalaGRPAV-FVrlAGCNLRCSWCDTKYAWDGEGGKRMSA---EEILEEVAALGARHVVITGGEPLL---QDDLAELL 85


                  ....*.
gi 2519633945  88 ERVRRE 93
Cdd:COG0602    86 EALKDA 91
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 22-93 1.56e-04

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: 40.20  E-value: 1.56e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2519633945  22 FVSGCRMRCPFCFNEEAWNFHAGNPFDAAVQDQIVESLRPLYVDGLSVLGGEPMepeNQAGLVDFLERVRRE 93
Cdd:pfam04055   1 ITRGCNLRCTYCAFPSIRARGKGRELSPEEILEEAKELKRLGVEVVILGGGEPL---LLPDLVELLERLLKL 69
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH