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Conserved domains on  [gi|1859887238|ref|WP_175384540|]
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ribonuclease M5 [Streptococcus pyogenes]

Protein Classification

toprim domain-containing protein( domain architecture ID 10004131)

toprim (topoisomerase-primase) domain-containing protein similar to Bacillus subtilis protein YusF

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 9-196 9.83e-68

5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure and biogenesis];


:

Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 204.87  E-value: 9.83e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859887238   9 TEKINIQEVLVVEGKDDTANLRRFYEVDTYETRGSAITEEDLERINRLNDLRGVIVLTDPDYNGERIRKLIMAAVPTARH 88
Cdd:COG1658     2 TDRSKIKEVIVVEGKDDTAALKRAVDADIIETNGSAISEETLELIKVAAEKRGVIILTDPDRAGERIRKRISEHLPGAKH 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859887238  89 AFLNRNEAvpssKSKGRSLGVEHARFEDLQKALAHVtQQYDDESYFDIRQTDLIHLGLLMASDSRKRREYLGEKLRIGYA 168
Cdd:COG1658    82 AFIDREKA----RKKKGIIGVEHASPEAIRRALSKV-RTEKEEEEEEFSLEDLLDAGLLGGGGAKKRRERLGEELGIGYG 156

                         170       180
                  ....*....|....*....|....*...
gi 1859887238 169 NGKQLLKRLELFGITLAEVEEVMETYEE 196
Cdd:COG1658   157 NGKQLLKRLNMFGITREEFEEALEEIEE 184
 
Name Accession Description Interval E-value
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 9-196 9.83e-68

5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 204.87  E-value: 9.83e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859887238   9 TEKINIQEVLVVEGKDDTANLRRFYEVDTYETRGSAITEEDLERINRLNDLRGVIVLTDPDYNGERIRKLIMAAVPTARH 88
Cdd:COG1658     2 TDRSKIKEVIVVEGKDDTAALKRAVDADIIETNGSAISEETLELIKVAAEKRGVIILTDPDRAGERIRKRISEHLPGAKH 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859887238  89 AFLNRNEAvpssKSKGRSLGVEHARFEDLQKALAHVtQQYDDESYFDIRQTDLIHLGLLMASDSRKRREYLGEKLRIGYA 168
Cdd:COG1658    82 AFIDREKA----RKKKGIIGVEHASPEAIRRALSKV-RTEKEEEEEEFSLEDLLDAGLLGGGGAKKRRERLGEELGIGYG 156

                         170       180
                  ....*....|....*....|....*...
gi 1859887238 169 NGKQLLKRLELFGITLAEVEEVMETYEE 196
Cdd:COG1658   157 NGKQLLKRLNMFGITREEFEEALEEIEE 184
5S_RNA_mat_M5 TIGR00334
ribonuclease M5; This family of orthologous proteins shows a weak but significant similarity ...
 14-187 3.48e-41

ribonuclease M5; This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases. [Transcription, RNA processing]


Pssm-ID: 273019 [Multi-domain]  Cd Length: 174  Bit Score: 137.26  E-value: 3.48e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859887238  14 IQEVLVVEGKDDTANLRRFYEVDTYETRGSAITEEDLERINRLNDLRGVIVLTDPDYNGERIRKLIMAAVPTARHAFLNR 93
Cdd:TIGR00334   2 IKEIIVVEGKDDQARIKQAFDVDVIETNGSALKDETINLIKKAQKKQGVIILTDPDFPGEKIRKKIEQHLPGYENCFIPK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859887238  94 NEAVPSSKskgrSLGVEHARFEDLQKALAHVTQQYDDESYfDIRQTDLIHLGLLmASDSRKRREYLGEKLRIGYANGKQL 173
Cdd:TIGR00334  82 HLAKPNKK----KIGVEEASVEAIIAALENVHEETKAQQS-DISWEDLLELGLI-GPASKCKRLRLCNLLKLGYFNHKQL 155

                         170
                  ....*....|....
gi 1859887238 174 LKRLELFGITLAEV 187
Cdd:TIGR00334 156 FKRLNLFQIKKSDV 169
DUF4093 pfam13331
Domain of unknown function (DUF4093); This domain lies at the C-terminus of primase proteins ...
 107-191 8.03e-32

Domain of unknown function (DUF4093); This domain lies at the C-terminus of primase proteins carrying the TOPRIM, pfam01751, domain. The exact function of the domain is not known.


Pssm-ID: 433122  Cd Length: 85  Bit Score: 110.25  E-value: 8.03e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859887238 107 LGVEHARFEDLQKALAHVTQQYDDESYFDIRQTDLIHLGLLMASDSRKRREYLGEKLRIGYANGKQLLKRLELFGITLAE 186
Cdd:pfam13331   1 LGVEHASPEAIREALAKAGTETEEKNNESITKADLLELGLIGGPDSKERREKLGKKLGIGYLNAKQLLKRLNMFGITREE 80


                  ....*
gi 1859887238 187 VEEVM 191
Cdd:pfam13331  81 FEEAL 85
TOPRIM_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 14-91 1.38e-19

TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea. RNase M5 catalyzes the maturation of 5S rRNA in low G+C Gram-positive bacteria. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173777  Cd Length: 81  Bit Score: 78.84  E-value: 1.38e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859887238  14 IQEVLVVEGKDDTANLRRFY-EVDTYETRGSAITEEDLERINRLNdlRGVIVLTDPDYNGERIRKLIMAA----VPTARH 88
Cdd:cd01027     1 IGEVIIVEGKNDTESLKKLGiEAEIIETNGSIINKETIELIKKAY--RGVIILTDPDRKGEKIRKKLSEYlsgpVPEIKR 78


                  ...
gi 1859887238  89 AFL 91
Cdd:cd01027    79 AFL 81
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
16-77 2.78e-05

topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 40.71  E-value: 2.78e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1859887238   16 EVLVVEGKDDTANLRRF--YEVDTYETRGSAITEEDLERINRLNDLRGVIVLTDPDYNGERIRK 77
Cdd:smart00493   2 VLIIVEGPADAIALEKAggKRGNVVALGGHLLSKEQIKLLKKLAKKAEVILATDPDREGEAIAW 65
 
Name Accession Description Interval E-value
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 9-196 9.83e-68

5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 204.87  E-value: 9.83e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859887238   9 TEKINIQEVLVVEGKDDTANLRRFYEVDTYETRGSAITEEDLERINRLNDLRGVIVLTDPDYNGERIRKLIMAAVPTARH 88
Cdd:COG1658     2 TDRSKIKEVIVVEGKDDTAALKRAVDADIIETNGSAISEETLELIKVAAEKRGVIILTDPDRAGERIRKRISEHLPGAKH 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859887238  89 AFLNRNEAvpssKSKGRSLGVEHARFEDLQKALAHVtQQYDDESYFDIRQTDLIHLGLLMASDSRKRREYLGEKLRIGYA 168
Cdd:COG1658    82 AFIDREKA----RKKKGIIGVEHASPEAIRRALSKV-RTEKEEEEEEFSLEDLLDAGLLGGGGAKKRRERLGEELGIGYG 156

                         170       180
                  ....*....|....*....|....*...
gi 1859887238 169 NGKQLLKRLELFGITLAEVEEVMETYEE 196
Cdd:COG1658   157 NGKQLLKRLNMFGITREEFEEALEEIEE 184
5S_RNA_mat_M5 TIGR00334
ribonuclease M5; This family of orthologous proteins shows a weak but significant similarity ...
 14-187 3.48e-41

ribonuclease M5; This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases. [Transcription, RNA processing]


Pssm-ID: 273019 [Multi-domain]  Cd Length: 174  Bit Score: 137.26  E-value: 3.48e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859887238  14 IQEVLVVEGKDDTANLRRFYEVDTYETRGSAITEEDLERINRLNDLRGVIVLTDPDYNGERIRKLIMAAVPTARHAFLNR 93
Cdd:TIGR00334   2 IKEIIVVEGKDDQARIKQAFDVDVIETNGSALKDETINLIKKAQKKQGVIILTDPDFPGEKIRKKIEQHLPGYENCFIPK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859887238  94 NEAVPSSKskgrSLGVEHARFEDLQKALAHVTQQYDDESYfDIRQTDLIHLGLLmASDSRKRREYLGEKLRIGYANGKQL 173
Cdd:TIGR00334  82 HLAKPNKK----KIGVEEASVEAIIAALENVHEETKAQQS-DISWEDLLELGLI-GPASKCKRLRLCNLLKLGYFNHKQL 155

                         170
                  ....*....|....
gi 1859887238 174 LKRLELFGITLAEV 187
Cdd:TIGR00334 156 FKRLNLFQIKKSDV 169
DUF4093 pfam13331
Domain of unknown function (DUF4093); This domain lies at the C-terminus of primase proteins ...
 107-191 8.03e-32

Domain of unknown function (DUF4093); This domain lies at the C-terminus of primase proteins carrying the TOPRIM, pfam01751, domain. The exact function of the domain is not known.


Pssm-ID: 433122  Cd Length: 85  Bit Score: 110.25  E-value: 8.03e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859887238 107 LGVEHARFEDLQKALAHVTQQYDDESYFDIRQTDLIHLGLLMASDSRKRREYLGEKLRIGYANGKQLLKRLELFGITLAE 186
Cdd:pfam13331   1 LGVEHASPEAIREALAKAGTETEEKNNESITKADLLELGLIGGPDSKERREKLGKKLGIGYLNAKQLLKRLNMFGITREE 80


                  ....*
gi 1859887238 187 VEEVM 191
Cdd:pfam13331  81 FEEAL 85
TOPRIM_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 14-91 1.38e-19

TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea. RNase M5 catalyzes the maturation of 5S rRNA in low G+C Gram-positive bacteria. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173777  Cd Length: 81  Bit Score: 78.84  E-value: 1.38e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859887238  14 IQEVLVVEGKDDTANLRRFY-EVDTYETRGSAITEEDLERINRLNdlRGVIVLTDPDYNGERIRKLIMAA----VPTARH 88
Cdd:cd01027     1 IGEVIIVEGKNDTESLKKLGiEAEIIETNGSIINKETIELIKKAY--RGVIILTDPDRKGEKIRKKLSEYlsgpVPEIKR 78


                  ...
gi 1859887238  89 AFL 91
Cdd:cd01027    79 AFL 81
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
16-77 2.78e-05

topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 40.71  E-value: 2.78e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1859887238   16 EVLVVEGKDDTANLRRF--YEVDTYETRGSAITEEDLERINRLNDLRGVIVLTDPDYNGERIRK 77
Cdd:smart00493   2 VLIIVEGPADAIALEKAggKRGNVVALGGHLLSKEQIKLLKKLAKKAEVILATDPDREGEAIAW 65
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 16-90 3.97e-05

Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.


Pssm-ID: 396354 [Multi-domain]  Cd Length: 93  Bit Score: 40.80  E-value: 3.97e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1859887238  16 EVLVVEGKDDTANLRRFYEVDTYE---TRGSAITEEDLERINRLNDLR-------GVIVLTDPDYNGERIRKLIMAAVPT 85
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGFQAvvaVLGHLLSLEKGPKKKALKALKelalkakEVILATDPDREGEAIALKLLELKEL 80


                  ....*
gi 1859887238  86 ARHAF 90
Cdd:pfam01751  81 LENAG 85
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 16-79 2.59e-04

Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173773 [Multi-domain]  Cd Length: 83  Bit Score: 38.18  E-value: 2.59e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1859887238  16 EVLVVEGKDDTANLRR--FYEVDTYETRGSAI--TEEDLERINRLNDlrGVIVLTDPDYNGERIRKLI 79
Cdd:cd00188     2 KLIIVEGPSDALALAQagGYGGAVVALGGHALnkTRELLKRLLGEAK--EVIIATDADREGEAIALRL 67
 
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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