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Conserved domains on  [gi|516475829|ref|WP_017864273|]
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MULTISPECIES: ribonuclease M5 [Lactococcus]

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 ...
 1-204 9.11e-67

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


:

Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 202.95  E-value: 9.11e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516475829   1 MVEKQKINEVIVVEGRDDTANLKRYFDCETYETGGSSIDDRDLERLKRLEDKRGIIVFTDPDFQGERIRKIIMQAVPNAK 80
Cdd:COG1658    1 MTDRSKIKEVIVVEGKDDTAALKRAVDADIIETNGSAISEETLELIKVAAEKRGVIILTDPDRAGERIRKRISEHLPGAK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516475829  81 HAFLNRDEARPKgKGSLGVEHANFEALNQALAEVFGGEKVTDEfgsaktqglssdrssvskkevltELTQTDLMSFGLVM 160
Cdd:COG1658   81 HAFIDREKARKK-KGIIGVEHASPEAIRRALSKVRTEKEEEEE-----------------------EFSLEDLLDAGLLG 136

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 516475829 161 AADSRKRREFLCEQLRIGYANGKQIKKRLNMFKITKEQIENVMK 204
Cdd:COG1658  137 GGGAKKRRERLGEELGIGYGNGKQLLKRLNMFGITREEFEEALE 180
 
Name Accession Description Interval E-value
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 1-204 9.11e-67

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


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 202.95  E-value: 9.11e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516475829   1 MVEKQKINEVIVVEGRDDTANLKRYFDCETYETGGSSIDDRDLERLKRLEDKRGIIVFTDPDFQGERIRKIIMQAVPNAK 80
Cdd:COG1658    1 MTDRSKIKEVIVVEGKDDTAALKRAVDADIIETNGSAISEETLELIKVAAEKRGVIILTDPDRAGERIRKRISEHLPGAK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516475829  81 HAFLNRDEARPKgKGSLGVEHANFEALNQALAEVFGGEKVTDEfgsaktqglssdrssvskkevltELTQTDLMSFGLVM 160
Cdd:COG1658   81 HAFIDREKARKK-KGIIGVEHASPEAIRRALSKVRTEKEEEEE-----------------------EFSLEDLLDAGLLG 136

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 516475829 161 AADSRKRREFLCEQLRIGYANGKQIKKRLNMFKITKEQIENVMK 204
Cdd:COG1658  137 GGGAKKRRERLGEELGIGYGNGKQLLKRLNMFGITREEFEEALE 180
5S_RNA_mat_M5 TIGR00334
ribonuclease M5; This family of orthologous proteins shows a weak but significant similarity ...
 6-204 4.44e-46

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: 149.97  E-value: 4.44e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516475829    6 KINEVIVVEGRDDTANLKRYFDCETYETGGSSIDDRDLERLKRLEDKRGIIVFTDPDFQGERIRKIIMQAVPNAKHAFLN 85
Cdd:TIGR00334   1 KIKEIIVVEGKDDQARIKQAFDVDVIETNGSALKDETINLIKKAQKKQGVIILTDPDFPGEKIRKKIEQHLPGYENCFIP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516475829   86 RDEARPKGKGsLGVEHANFEALNQALAEVfggekvtDEFGSAKTQGLSSDrssvskkevlteltqtDLMSFGLVMAAdSR 165
Cdd:TIGR00334  81 KHLAKPNKKK-IGVEEASVEAIIAALENV-------HEETKAQQSDISWE----------------DLLELGLIGPA-SK 135

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 516475829  166 KRREFLCEQLRIGYANGKQIKKRLNMFKITKEQIENVMK 204
Cdd:TIGR00334 136 CKRLRLCNLLKLGYFNHKQLFKRLNLFQIKKSDVMSALK 174
DUF4093 pfam13331
Domain of unknown function (DUF4093); This domain lies at the C-terminus of primase proteins ...
 97-203 1.29e-26

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: 97.16  E-value: 1.29e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516475829   97 LGVEHANFEALNQALAEVFGGEKVTDEFgsaktqglssdrssvskkevltELTQTDLMSFGLVMAADSRKRREFLCEQLR 176
Cdd:pfam13331   1 LGVEHASPEAIREALAKAGTETEEKNNE----------------------SITKADLLELGLIGGPDSKERREKLGKKLG 58

                          90       100
                  ....*....|....*....|....*..
gi 516475829  177 IGYANGKQIKKRLNMFKITKEQIENVM 203
Cdd:pfam13331  59 IGYLNAKQLLKRLNMFGITREEFEEAL 85
TOPRIM_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 7-84 9.43e-23

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: 87.31  E-value: 9.43e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516475829   7 INEVIVVEGRDDTANLKRYFD-CETYETGGSSIDDRDLERLKRLedKRGIIVFTDPDFQGERIRKIIMQA----VPNAKH 81
Cdd:cd01027    1 IGEVIIVEGKNDTESLKKLGIeAEIIETNGSIINKETIELIKKA--YRGVIILTDPDRKGEKIRKKLSEYlsgpVPEIKR 78


                 ...
gi 516475829  82 AFL 84
Cdd:cd01027   79 AFL 81
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
8-80 1.86e-09

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 52.26  E-value: 1.86e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 516475829     8 NEVIVVEGRDDTANLKRYFDCETY--ETGGSSIDDRDLERLKRLEDKRGIIVFTDPDFQGERIRKIIMQAVPNAK 80
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNvvALGGHLLSKEQIKLLKKLAKKAEVILATDPDREGEAIAWELAELLKPAG 75
PRK04031 PRK04031
DNA primase; Provisional
 8-70 7.65e-03

DNA primase; Provisional


Pssm-ID: 235206  Cd Length: 408  Bit Score: 36.71  E-value: 7.65e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 516475829   8 NEVIVVEGRDDTANLKRYFDCETYETGGSSIDdrdlERLKRLEDKRGIIVFTDPDFQGERIRK 70
Cdd:PRK04031 170 DAIIVVEGRADVLNLLRYGIKNAIAVEGTNVP----ETIIELSKKKTVTAFLDGDRGGELILK 228
 
Name Accession Description Interval E-value
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 1-204 9.11e-67

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


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 202.95  E-value: 9.11e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516475829   1 MVEKQKINEVIVVEGRDDTANLKRYFDCETYETGGSSIDDRDLERLKRLEDKRGIIVFTDPDFQGERIRKIIMQAVPNAK 80
Cdd:COG1658    1 MTDRSKIKEVIVVEGKDDTAALKRAVDADIIETNGSAISEETLELIKVAAEKRGVIILTDPDRAGERIRKRISEHLPGAK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516475829  81 HAFLNRDEARPKgKGSLGVEHANFEALNQALAEVFGGEKVTDEfgsaktqglssdrssvskkevltELTQTDLMSFGLVM 160
Cdd:COG1658   81 HAFIDREKARKK-KGIIGVEHASPEAIRRALSKVRTEKEEEEE-----------------------EFSLEDLLDAGLLG 136

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 516475829 161 AADSRKRREFLCEQLRIGYANGKQIKKRLNMFKITKEQIENVMK 204
Cdd:COG1658  137 GGGAKKRRERLGEELGIGYGNGKQLLKRLNMFGITREEFEEALE 180
5S_RNA_mat_M5 TIGR00334
ribonuclease M5; This family of orthologous proteins shows a weak but significant similarity ...
 6-204 4.44e-46

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: 149.97  E-value: 4.44e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516475829    6 KINEVIVVEGRDDTANLKRYFDCETYETGGSSIDDRDLERLKRLEDKRGIIVFTDPDFQGERIRKIIMQAVPNAKHAFLN 85
Cdd:TIGR00334   1 KIKEIIVVEGKDDQARIKQAFDVDVIETNGSALKDETINLIKKAQKKQGVIILTDPDFPGEKIRKKIEQHLPGYENCFIP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516475829   86 RDEARPKGKGsLGVEHANFEALNQALAEVfggekvtDEFGSAKTQGLSSDrssvskkevlteltqtDLMSFGLVMAAdSR 165
Cdd:TIGR00334  81 KHLAKPNKKK-IGVEEASVEAIIAALENV-------HEETKAQQSDISWE----------------DLLELGLIGPA-SK 135

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 516475829  166 KRREFLCEQLRIGYANGKQIKKRLNMFKITKEQIENVMK 204
Cdd:TIGR00334 136 CKRLRLCNLLKLGYFNHKQLFKRLNLFQIKKSDVMSALK 174
DUF4093 pfam13331
Domain of unknown function (DUF4093); This domain lies at the C-terminus of primase proteins ...
 97-203 1.29e-26

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: 97.16  E-value: 1.29e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516475829   97 LGVEHANFEALNQALAEVFGGEKVTDEFgsaktqglssdrssvskkevltELTQTDLMSFGLVMAADSRKRREFLCEQLR 176
Cdd:pfam13331   1 LGVEHASPEAIREALAKAGTETEEKNNE----------------------SITKADLLELGLIGGPDSKERREKLGKKLG 58

                          90       100
                  ....*....|....*....|....*..
gi 516475829  177 IGYANGKQIKKRLNMFKITKEQIENVM 203
Cdd:pfam13331  59 IGYLNAKQLLKRLNMFGITREEFEEAL 85
TOPRIM_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 7-84 9.43e-23

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: 87.31  E-value: 9.43e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516475829   7 INEVIVVEGRDDTANLKRYFD-CETYETGGSSIDDRDLERLKRLedKRGIIVFTDPDFQGERIRKIIMQA----VPNAKH 81
Cdd:cd01027    1 IGEVIIVEGKNDTESLKKLGIeAEIIETNGSIINKETIELIKKA--YRGVIILTDPDRKGEKIRKKLSEYlsgpVPEIKR 78


                 ...
gi 516475829  82 AFL 84
Cdd:cd01027   79 AFL 81
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
8-80 1.86e-09

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 52.26  E-value: 1.86e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 516475829     8 NEVIVVEGRDDTANLKRYFDCETY--ETGGSSIDDRDLERLKRLEDKRGIIVFTDPDFQGERIRKIIMQAVPNAK 80
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNvvALGGHLLSKEQIKLLKKLAKKAEVILATDPDREGEAIAWELAELLKPAG 75
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 8-75 8.87e-06

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: 42.41  E-value: 8.87e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 516475829   8 NEVIVVEGRDDTANLKRY--FDCETYETGGSSIDDRD--LERLKRLEDKrgIIVFTDPDFQGERIRKIIMQA 75
Cdd:cd00188    1 KKLIIVEGPSDALALAQAggYGGAVVALGGHALNKTRelLKRLLGEAKE--VIIATDADREGEAIALRLLEL 70
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 9-83 1.12e-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: 42.34  E-value: 1.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516475829    9 EVIVVEGRDDTANLKRYFDCETYE---TGGSSIDDRD------LERLKRLEDK-RGIIVFTDPDFQGERIRKIIMQAVPN 78
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGFQAvvaVLGHLLSLEKgpkkkaLKALKELALKaKEVILATDPDREGEAIALKLLELKEL 80


                  ....*
gi 516475829   79 AKHAF 83
Cdd:pfam01751  81 LENAG 85
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 8-67 2.38e-03

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: 35.72  E-value: 2.38e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 516475829    8 NEVIVVEGRDDTANLKRYFDCETYETGGSSIDDRD---LERLKR--LEDKRGIIVFTDPDFQGER 67
Cdd:pfam13662   1 SEIIVVEGYADVIALEKAGYKGAVAVLGGALSPLDgigPEDLNIdsLGGIKEVILALDGDVAGEK 65
PRK04031 PRK04031
DNA primase; Provisional
 8-70 7.65e-03

DNA primase; Provisional


Pssm-ID: 235206  Cd Length: 408  Bit Score: 36.71  E-value: 7.65e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 516475829   8 NEVIVVEGRDDTANLKRYFDCETYETGGSSIDdrdlERLKRLEDKRGIIVFTDPDFQGERIRK 70
Cdd:PRK04031 170 DAIIVVEGRADVLNLLRYGIKNAIAVEGTNVP----ETIIELSKKKTVTAFLDGDRGGELILK 228
 
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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