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Conserved domains on  [gi|446582667|ref|WP_000660013|]
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ribonuclease M5 [Streptococcus pneumoniae]

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 ...
 1-186 9.59e-64

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


:

Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 194.47  E-value: 9.59e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446582667   1 MKEKISQVIVVEGRDDTVNLKRYFDVETYETRGSAINDQDIERIQRLHQRHGVIVFTDPDFNGERIRRMIMTVIPTVQHA 80
Cdd:COG1658    3 DRSKIKEVIVVEGKDDTAALKRAVDADIIETNGSAISEETLELIKVAAEKRGVIILTDPDRAGERIRKRISEHLPGAKHA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446582667  81 FLKRDEAVPKSKtkgrSLGIEHASYEDLKTALAQVTEQFEhESQFDISRSDLIRLGFLAGADSRKRREYLGETLRIGYSN 160
Cdd:COG1658   83 FIDREKARKKKG----IIGVEHASPEAIRRALSKVRTEKE-EEEEEFSLEDLLDAGLLGGGGAKKRRERLGEELGIGYGN 157

                        170       180
                 ....*....|....*....|....*.
gi 446582667 161 GKQLLKRLELFGVTLAEVEEAMKSYE 186
Cdd:COG1658  158 GKQLLKRLNMFGITREEFEEALEEIE 183
 
Name Accession Description Interval E-value
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 1-186 9.59e-64

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


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 194.47  E-value: 9.59e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446582667   1 MKEKISQVIVVEGRDDTVNLKRYFDVETYETRGSAINDQDIERIQRLHQRHGVIVFTDPDFNGERIRRMIMTVIPTVQHA 80
Cdd:COG1658    3 DRSKIKEVIVVEGKDDTAALKRAVDADIIETNGSAISEETLELIKVAAEKRGVIILTDPDRAGERIRKRISEHLPGAKHA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446582667  81 FLKRDEAVPKSKtkgrSLGIEHASYEDLKTALAQVTEQFEhESQFDISRSDLIRLGFLAGADSRKRREYLGETLRIGYSN 160
Cdd:COG1658   83 FIDREKARKKKG----IIGVEHASPEAIRRALSKVRTEKE-EEEEEFSLEDLLDAGLLGGGGAKKRRERLGEELGIGYGN 157

                        170       180
                 ....*....|....*....|....*.
gi 446582667 161 GKQLLKRLELFGVTLAEVEEAMKSYE 186
Cdd:COG1658  158 GKQLLKRLNMFGITREEFEEALEEIE 183
5S_RNA_mat_M5 TIGR00334
ribonuclease M5; This family of orthologous proteins shows a weak but significant similarity ...
 4-183 1.03e-45

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: 148.43  E-value: 1.03e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446582667    4 KISQVIVVEGRDDTVNLKRYFDVETYETRGSAINDQDIERIQRLHQRHGVIVFTDPDFNGERIRRMIMTVIPTVQHAFLK 83
Cdd:TIGR00334   1 KIKEIIVVEGKDDQARIKQAFDVDVIETNGSALKDETINLIKKAQKKQGVIILTDPDFPGEKIRKKIEQHLPGYENCFIP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446582667   84 RDEAVPKSKtkgrSLGIEHASYEDLKTALAQVTEqFEHESQFDISRSDLIRLGfLAGADSRKRREYLGETLRIGYSNGKQ 163
Cdd:TIGR00334  81 KHLAKPNKK----KIGVEEASVEAIIAALENVHE-ETKAQQSDISWEDLLELG-LIGPASKCKRLRLCNLLKLGYFNHKQ 154

                         170       180
                  ....*....|....*....|
gi 446582667  164 LLKRLELFGVTLAEVEEAMK 183
Cdd:TIGR00334 155 LFKRLNLFQIKKSDVMSALK 174
DUF4093 pfam13331
Domain of unknown function (DUF4093); This domain lies at the C-terminus of primase proteins ...
 98-182 9.72e-35

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: 117.19  E-value: 9.72e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446582667   98 LGIEHASYEDLKTALAQVTEQFEHESQFDISRSDLIRLGFLAGADSRKRREYLGETLRIGYSNGKQLLKRLELFGVTLAE 177
Cdd:pfam13331   1 LGVEHASPEAIREALAKAGTETEEKNNESITKADLLELGLIGGPDSKERREKLGKKLGIGYLNAKQLLKRLNMFGITREE 80


                  ....*
gi 446582667  178 VEEAM 182
Cdd:pfam13331  81 FEEAL 85
TOPRIM_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 5-82 6.80e-21

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: 81.92  E-value: 6.80e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446582667   5 ISQVIVVEGRDDTVNLKRYFD-VETYETRGSAINDQDIERIQRLhqRHGVIVFTDPDFNGERIRRMIM----TVIPTVQH 79
Cdd:cd01027    1 IGEVIIVEGKNDTESLKKLGIeAEIIETNGSIINKETIELIKKA--YRGVIILTDPDRKGEKIRKKLSeylsGPVPEIKR 78


                 ...
gi 446582667  80 AFL 82
Cdd:cd01027   79 AFL 81
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
6-70 7.80e-07

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 44.94  E-value: 7.80e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446582667     6 SQVIVVEGRDDTVNLKRY--FDVETYETRGSAINDQDIERIQRLHQRHGVIVFTDPDFNGERIRRMI 70
Cdd:smart00493   1 KVLIIVEGPADAIALEKAggKRGNVVALGGHLLSKEQIKLLKKLAKKAEVILATDPDREGEAIAWEL 67
 
Name Accession Description Interval E-value
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 1-186 9.59e-64

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


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 194.47  E-value: 9.59e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446582667   1 MKEKISQVIVVEGRDDTVNLKRYFDVETYETRGSAINDQDIERIQRLHQRHGVIVFTDPDFNGERIRRMIMTVIPTVQHA 80
Cdd:COG1658    3 DRSKIKEVIVVEGKDDTAALKRAVDADIIETNGSAISEETLELIKVAAEKRGVIILTDPDRAGERIRKRISEHLPGAKHA 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446582667  81 FLKRDEAVPKSKtkgrSLGIEHASYEDLKTALAQVTEQFEhESQFDISRSDLIRLGFLAGADSRKRREYLGETLRIGYSN 160
Cdd:COG1658   83 FIDREKARKKKG----IIGVEHASPEAIRRALSKVRTEKE-EEEEEFSLEDLLDAGLLGGGGAKKRRERLGEELGIGYGN 157

                        170       180
                 ....*....|....*....|....*.
gi 446582667 161 GKQLLKRLELFGVTLAEVEEAMKSYE 186
Cdd:COG1658  158 GKQLLKRLNMFGITREEFEEALEEIE 183
5S_RNA_mat_M5 TIGR00334
ribonuclease M5; This family of orthologous proteins shows a weak but significant similarity ...
 4-183 1.03e-45

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: 148.43  E-value: 1.03e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446582667    4 KISQVIVVEGRDDTVNLKRYFDVETYETRGSAINDQDIERIQRLHQRHGVIVFTDPDFNGERIRRMIMTVIPTVQHAFLK 83
Cdd:TIGR00334   1 KIKEIIVVEGKDDQARIKQAFDVDVIETNGSALKDETINLIKKAQKKQGVIILTDPDFPGEKIRKKIEQHLPGYENCFIP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446582667   84 RDEAVPKSKtkgrSLGIEHASYEDLKTALAQVTEqFEHESQFDISRSDLIRLGfLAGADSRKRREYLGETLRIGYSNGKQ 163
Cdd:TIGR00334  81 KHLAKPNKK----KIGVEEASVEAIIAALENVHE-ETKAQQSDISWEDLLELG-LIGPASKCKRLRLCNLLKLGYFNHKQ 154

                         170       180
                  ....*....|....*....|
gi 446582667  164 LLKRLELFGVTLAEVEEAMK 183
Cdd:TIGR00334 155 LFKRLNLFQIKKSDVMSALK 174
DUF4093 pfam13331
Domain of unknown function (DUF4093); This domain lies at the C-terminus of primase proteins ...
 98-182 9.72e-35

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: 117.19  E-value: 9.72e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446582667   98 LGIEHASYEDLKTALAQVTEQFEHESQFDISRSDLIRLGFLAGADSRKRREYLGETLRIGYSNGKQLLKRLELFGVTLAE 177
Cdd:pfam13331   1 LGVEHASPEAIREALAKAGTETEEKNNESITKADLLELGLIGGPDSKERREKLGKKLGIGYLNAKQLLKRLNMFGITREE 80


                  ....*
gi 446582667  178 VEEAM 182
Cdd:pfam13331  81 FEEAL 85
TOPRIM_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 5-82 6.80e-21

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: 81.92  E-value: 6.80e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446582667   5 ISQVIVVEGRDDTVNLKRYFD-VETYETRGSAINDQDIERIQRLhqRHGVIVFTDPDFNGERIRRMIM----TVIPTVQH 79
Cdd:cd01027    1 IGEVIIVEGKNDTESLKKLGIeAEIIETNGSIINKETIELIKKA--YRGVIILTDPDRKGEKIRKKLSeylsGPVPEIKR 78


                 ...
gi 446582667  80 AFL 82
Cdd:cd01027   79 AFL 81
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
6-70 7.80e-07

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 44.94  E-value: 7.80e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446582667     6 SQVIVVEGRDDTVNLKRY--FDVETYETRGSAINDQDIERIQRLHQRHGVIVFTDPDFNGERIRRMI 70
Cdd:smart00493   1 KVLIIVEGPADAIALEKAggKRGNVVALGGHLLSKEQIKLLKKLAKKAEVILATDPDREGEAIAWEL 67
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 7-81 2.00e-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: 41.57  E-value: 2.00e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446582667    7 QVIVVEGRDDTVNLKRYFDVETYE---TRGSAINDQDIERI-------QRLHQRHGVIVFTDPDFNGERIRRMIMTVIPT 76
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGFQAvvaVLGHLLSLEKGPKKkalkalkELALKAKEVILATDPDREGEAIALKLLELKEL 80


                  ....*
gi 446582667   77 VQHAF 81
Cdd:pfam01751  81 LENAG 85
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 6-74 1.17e-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: 39.33  E-value: 1.17e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446582667   6 SQVIVVEGRDDTVNLKRY--FDVETYETRGSAINDQdIERIQRLHQRHG-VIVFTDPDFNGERIRRMIMTVI 74
Cdd:cd00188    1 KKLIIVEGPSDALALAQAggYGGAVVALGGHALNKT-RELLKRLLGEAKeVIIATDADREGEAIALRLLELL 71
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 6-71 2.57e-04

Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic acid manipulation.


Pssm-ID: 433387 [Multi-domain]  Cd Length: 85  Bit Score: 38.42  E-value: 2.57e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446582667    6 SQVIVVEGRDDTVNLKRYFDVETYETRGSAINDQDIERIQRLHQRHG-----VIVFTDPDFNGERIRRMIM 71
Cdd:pfam13662   1 SEIIVVEGYADVIALEKAGYKGAVAVLGGALSPLDGIGPEDLNIDSLggikeVILALDGDVAGEKTALYLA 71
 
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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