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Conserved domains on  [gi|1268150279|ref|WP_098703656.1|]
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ribonuclease M5

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 ...
 1-182 6.20e-66

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


:

Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 199.87  E-value: 6.20e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1268150279   1 MKKKIKEVIVVEGKDDISAVKNAVDAEVFQVNGHAVRKnKSIEILKLAYENKGLIILTDPDYAGEEIRKYLCKHFPNAKN 80
Cdd:COG1658     3 DRSKIKEVIVVEGKDDTAALKRAVDADIIETNGSAISE-ETLELIKVAAEKRGVIILTDPDRAGERIRKRISEHLPGAKH 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1268150279  81 AYISRISGT-KDGDIGVENASPEDIITALEKARFSLDNSENIFNLDLMIDYNLIGKDNSADLRALLGAELGIGYSNGKQF 159
Cdd:COG1658    82 AFIDREKARkKKGIIGVEHASPEAIRRALSKVRTEKEEEEEEFSLEDLLDAGLLGGGGAKKRRERLGEELGIGYGNGKQL 161

                         170       180
                  ....*....|....*....|...
gi 1268150279 160 MAKLNRYGISLEEFKKAYEKINK 182
Cdd:COG1658   162 LKRLNMFGITREEFEEALEEIEE 184
 
Name Accession Description Interval E-value
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 1-182 6.20e-66

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


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 199.87  E-value: 6.20e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1268150279   1 MKKKIKEVIVVEGKDDISAVKNAVDAEVFQVNGHAVRKnKSIEILKLAYENKGLIILTDPDYAGEEIRKYLCKHFPNAKN 80
Cdd:COG1658     3 DRSKIKEVIVVEGKDDTAALKRAVDADIIETNGSAISE-ETLELIKVAAEKRGVIILTDPDRAGERIRKRISEHLPGAKH 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1268150279  81 AYISRISGT-KDGDIGVENASPEDIITALEKARFSLDNSENIFNLDLMIDYNLIGKDNSADLRALLGAELGIGYSNGKQF 159
Cdd:COG1658    82 AFIDREKARkKKGIIGVEHASPEAIRRALSKVRTEKEEEEEEFSLEDLLDAGLLGGGGAKKRRERLGEELGIGYGNGKQL 161

                         170       180
                  ....*....|....*....|...
gi 1268150279 160 MAKLNRYGISLEEFKKAYEKINK 182
Cdd:COG1658   162 LKRLNMFGITREEFEEALEEIEE 184
5S_RNA_mat_M5 TIGR00334
ribonuclease M5; This family of orthologous proteins shows a weak but significant similarity ...
 4-176 3.95e-34

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: 118.77  E-value: 3.95e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1268150279   4 KIKEVIVVEGKDDISAVKNAVDAEVFQVNGHAVrKNKSIEILKLAYENKGLIILTDPDYAGEEIRKYLCKHFPNAKNAYI 83
Cdd:TIGR00334   1 KIKEIIVVEGKDDQARIKQAFDVDVIETNGSAL-KDETINLIKKAQKKQGVIILTDPDFPGEKIRKKIEQHLPGYENCFI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1268150279  84 SRISGTKDG-DIGVENASPEDIITALEKARFSLDNSENIFNLDLMIDYNLIGkDNSADLRALLGAELGIGYSNGKQFMAK 162
Cdd:TIGR00334  80 PKHLAKPNKkKIGVEEASVEAIIAALENVHEETKAQQSDISWEDLLELGLIG-PASKCKRLRLCNLLKLGYFNHKQLFKR 158

                         170
                  ....*....|....
gi 1268150279 163 LNRYGISLEEFKKA 176
Cdd:TIGR00334 159 LNLFQIKKSDVMSA 172
DUF4093 pfam13331
Domain of unknown function (DUF4093); This domain lies at the C-terminus of primase proteins ...
 94-176 1.76e-28

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: 101.39  E-value: 1.76e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1268150279  94 IGVENASPEDIITALEKARFSL-DNSENIFNLDLMIDYNLIGKDNSADLRALLGAELGIGYSNGKQFMAKLNRYGISLEE 172
Cdd:pfam13331   1 LGVEHASPEAIREALAKAGTETeEKNNESITKADLLELGLIGGPDSKERREKLGKKLGIGYLNAKQLLKRLNMFGITREE 80


                  ....
gi 1268150279 173 FKKA 176
Cdd:pfam13331  81 FEEA 84
TOPRIM_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 5-83 3.80e-18

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: 74.60  E-value: 3.80e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1268150279   5 IKEVIVVEGKDDISAVKNAVD-AEVFQVNGHAVRKnKSIEILKLAYenKGLIILTDPDYAGEEIRKYLCKHF----PNAK 79
Cdd:cd01027     1 IGEVIIVEGKNDTESLKKLGIeAEIIETNGSIINK-ETIELIKKAY--RGVIILTDPDRKGEKIRKKLSEYLsgpvPEIK 77


                  ....
gi 1268150279  80 NAYI 83
Cdd:cd01027    78 RAFL 81
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
6-79 7.55e-08

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 47.64  E-value: 7.55e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1268150279    6 KEVIVVEGKDDISAVKNA--VDAEVFQVNGHAvRKNKSIEILKLAYENKGLIILTDPDYAGEEIRKYLCKHFPNAK 79
Cdd:smart00493   1 KVLIIVEGPADAIALEKAggKRGNVVALGGHL-LSKEQIKLLKKLAKKAEVILATDPDREGEAIAWELAELLKPAG 75
PRK04017 PRK04017
hypothetical protein; Provisional
 8-75 3.58e-03

hypothetical protein; Provisional


Pssm-ID: 179711  Cd Length: 132  Bit Score: 36.09  E-value: 3.58e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1268150279   8 VIVVEGKDDISAVKN-AVDAEVFQVNGHAVRKnksIEILkLAYENKGLIILTDPDYAGEEIRKYLCKHF 75
Cdd:PRK04017   25 PIIVEGKRDVESLRKlGVEGEIIKVSRTPLAE---IAEL-IASRGKEVIILTDFDRKGEELAKKLSEYL 89
 
Name Accession Description Interval E-value
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 1-182 6.20e-66

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


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 199.87  E-value: 6.20e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1268150279   1 MKKKIKEVIVVEGKDDISAVKNAVDAEVFQVNGHAVRKnKSIEILKLAYENKGLIILTDPDYAGEEIRKYLCKHFPNAKN 80
Cdd:COG1658     3 DRSKIKEVIVVEGKDDTAALKRAVDADIIETNGSAISE-ETLELIKVAAEKRGVIILTDPDRAGERIRKRISEHLPGAKH 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1268150279  81 AYISRISGT-KDGDIGVENASPEDIITALEKARFSLDNSENIFNLDLMIDYNLIGKDNSADLRALLGAELGIGYSNGKQF 159
Cdd:COG1658    82 AFIDREKARkKKGIIGVEHASPEAIRRALSKVRTEKEEEEEEFSLEDLLDAGLLGGGGAKKRRERLGEELGIGYGNGKQL 161

                         170       180
                  ....*....|....*....|...
gi 1268150279 160 MAKLNRYGISLEEFKKAYEKINK 182
Cdd:COG1658   162 LKRLNMFGITREEFEEALEEIEE 184
5S_RNA_mat_M5 TIGR00334
ribonuclease M5; This family of orthologous proteins shows a weak but significant similarity ...
 4-176 3.95e-34

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: 118.77  E-value: 3.95e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1268150279   4 KIKEVIVVEGKDDISAVKNAVDAEVFQVNGHAVrKNKSIEILKLAYENKGLIILTDPDYAGEEIRKYLCKHFPNAKNAYI 83
Cdd:TIGR00334   1 KIKEIIVVEGKDDQARIKQAFDVDVIETNGSAL-KDETINLIKKAQKKQGVIILTDPDFPGEKIRKKIEQHLPGYENCFI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1268150279  84 SRISGTKDG-DIGVENASPEDIITALEKARFSLDNSENIFNLDLMIDYNLIGkDNSADLRALLGAELGIGYSNGKQFMAK 162
Cdd:TIGR00334  80 PKHLAKPNKkKIGVEEASVEAIIAALENVHEETKAQQSDISWEDLLELGLIG-PASKCKRLRLCNLLKLGYFNHKQLFKR 158

                         170
                  ....*....|....
gi 1268150279 163 LNRYGISLEEFKKA 176
Cdd:TIGR00334 159 LNLFQIKKSDVMSA 172
DUF4093 pfam13331
Domain of unknown function (DUF4093); This domain lies at the C-terminus of primase proteins ...
 94-176 1.76e-28

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: 101.39  E-value: 1.76e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1268150279  94 IGVENASPEDIITALEKARFSL-DNSENIFNLDLMIDYNLIGKDNSADLRALLGAELGIGYSNGKQFMAKLNRYGISLEE 172
Cdd:pfam13331   1 LGVEHASPEAIREALAKAGTETeEKNNESITKADLLELGLIGGPDSKERREKLGKKLGIGYLNAKQLLKRLNMFGITREE 80


                  ....
gi 1268150279 173 FKKA 176
Cdd:pfam13331  81 FEEA 84
TOPRIM_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 5-83 3.80e-18

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: 74.60  E-value: 3.80e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1268150279   5 IKEVIVVEGKDDISAVKNAVD-AEVFQVNGHAVRKnKSIEILKLAYenKGLIILTDPDYAGEEIRKYLCKHF----PNAK 79
Cdd:cd01027     1 IGEVIIVEGKNDTESLKKLGIeAEIIETNGSIINK-ETIELIKKAY--RGVIILTDPDRKGEKIRKKLSEYLsgpvPEIK 77


                  ....
gi 1268150279  80 NAYI 83
Cdd:cd01027    78 RAFL 81
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
6-79 7.55e-08

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 47.64  E-value: 7.55e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1268150279    6 KEVIVVEGKDDISAVKNA--VDAEVFQVNGHAvRKNKSIEILKLAYENKGLIILTDPDYAGEEIRKYLCKHFPNAK 79
Cdd:smart00493   1 KVLIIVEGPADAIALEKAggKRGNVVALGGHL-LSKEQIKLLKKLAKKAEVILATDPDREGEAIAWELAELLKPAG 75
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 7-86 1.10e-07

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: 47.74  E-value: 1.10e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1268150279   7 EVIVVEGKDDISAVKNAVDAEVFQV---NGHAV------RKNKSIEILKLAYENKGLIILTDPDYAGEEIRKYLCKHFPN 77
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGFQAVvavLGHLLslekgpKKKALKALKELALKAKEVILATDPDREGEAIALKLLELKEL 80

                          90
                  ....*....|...
gi 1268150279  78 AKN----AYISRI 86
Cdd:pfam01751  81 LENaggrVEFSEL 93
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 6-79 7.20e-07

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: 45.11  E-value: 7.20e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1268150279   6 KEVIVVEGKDDISAVKNA--VDAEVFQVNGHAVRKNKSIeILKLAYENKGLIILTDPDYAGEEIRKYLCKHFPNAK 79
Cdd:cd00188     1 KKLIIVEGPSDALALAQAggYGGAVVALGGHALNKTREL-LKRLLGEAKEVIIATDADREGEAIALRLLELLKSLG 75
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 6-86 1.82e-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: 38.80  E-value: 1.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1268150279   6 KEVIVVEGKDDISAVKNAVDAEVFQVNGHAVRKNKSIEILKLAYENKG----LIILTDPDYAGEEIRKYLCKHFPNAKNA 81
Cdd:pfam13662   1 SEIIVVEGYADVIALEKAGYKGAVAVLGGALSPLDGIGPEDLNIDSLGgikeVILALDGDVAGEKTALYLAEALLEEGVK 80


                  ....*
gi 1268150279  82 yISRI 86
Cdd:pfam13662  81 -VSRL 84
PRK04017 PRK04017
hypothetical protein; Provisional
 8-75 3.58e-03

hypothetical protein; Provisional


Pssm-ID: 179711  Cd Length: 132  Bit Score: 36.09  E-value: 3.58e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1268150279   8 VIVVEGKDDISAVKN-AVDAEVFQVNGHAVRKnksIEILkLAYENKGLIILTDPDYAGEEIRKYLCKHF 75
Cdd:PRK04017   25 PIIVEGKRDVESLRKlGVEGEIIKVSRTPLAE---IAEL-IASRGKEVIILTDFDRKGEELAKKLSEYL 89
 
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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