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Conserved domains on  [gi|647314601|ref|WP_025752660|]
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MULTISPECIES: toprim domain-containing protein [Bacillaceae]

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
TOPRIM_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 6-84 6.79e-16

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: 66.90  E-value: 6.79e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647314601   6 IEKVIIVEGKSDKKRIQDIIREpIEIICTNGTISLSKLDEIIDcTFNKEVYILVDSDDSGNKLRKQFKREL----PEAEH 81
Cdd:cd01027    1 IGEVIIVEGKNDTESLKKLGIE-AEIIETNGSIINKETIELIK-KAYRGVIILTDPDRKGEKIRKKLSEYLsgpvPEIKR 78


                 ...
gi 647314601  82 LYI 84
Cdd:cd01027   79 AFL 81
 
Name Accession Description Interval E-value
TOPRIM_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 6-84 6.79e-16

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: 66.90  E-value: 6.79e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647314601   6 IEKVIIVEGKSDKKRIQDIIREpIEIICTNGTISLSKLDEIIDcTFNKEVYILVDSDDSGNKLRKQFKREL----PEAEH 81
Cdd:cd01027    1 IGEVIIVEGKNDTESLKKLGIE-AEIIETNGSIINKETIELIK-KAYRGVIILTDPDRKGEKIRKKLSEYLsgpvPEIKR 78


                 ...
gi 647314601  82 LYI 84
Cdd:cd01027   79 AFL 81
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 4-86 3.01e-12

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


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 59.65  E-value: 3.01e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647314601   4 IEIEKVIIVEGKSDKKRIQDIIRepIEIICTNGT-ISLSKLDEIIDCTFNKEVYILVDSDDSGNKLRKQFKRELPEAEHL 82
Cdd:COG1658    5 SKIKEVIVVEGKDDTAALKRAVD--ADIIETNGSaISEETLELIKVAAEKRGVIILTDPDRAGERIRKRISEHLPGAKHA 82


                 ....
gi 647314601  83 YIDK 86
Cdd:COG1658   83 FIDR 86
5S_RNA_mat_M5 TIGR00334
ribonuclease M5; This family of orthologous proteins shows a weak but significant similarity ...
 5-89 1.54e-10

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: 55.22  E-value: 1.54e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647314601    5 EIEKVIIVEGKSDKKRIQDIIrePIEIICTNGT-ISLSKLDEIIDCTFNKEVYILVDSDDSGNKLRKQFKRELPEAEHLY 83
Cdd:TIGR00334   1 KIKEIIVVEGKDDQARIKQAF--DVDVIETNGSaLKDETINLIKKAQKKQGVIILTDPDFPGEKIRKKIEQHLPGYENCF 78


                  ....*.
gi 647314601   84 IDKMYR 89
Cdd:TIGR00334  79 IPKHLA 84
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
7-79 1.92e-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: 1.92e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 647314601     7 EKVIIVEGKSDKKRIQDIIREPIEIICTNGTI-SLSKLDEIIDCTFNKEVYILVDSDDSGNKLRKQFKRELPEA 79
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALGGHLlSKEQIKLLKKLAKKAEVILATDPDREGEAIAWELAELLKPA 74
 
Name Accession Description Interval E-value
TOPRIM_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 6-84 6.79e-16

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: 66.90  E-value: 6.79e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647314601   6 IEKVIIVEGKSDKKRIQDIIREpIEIICTNGTISLSKLDEIIDcTFNKEVYILVDSDDSGNKLRKQFKREL----PEAEH 81
Cdd:cd01027    1 IGEVIIVEGKNDTESLKKLGIE-AEIIETNGSIINKETIELIK-KAYRGVIILTDPDRKGEKIRKKLSEYLsgpvPEIKR 78


                 ...
gi 647314601  82 LYI 84
Cdd:cd01027   79 AFL 81
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 4-86 3.01e-12

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


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 59.65  E-value: 3.01e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647314601   4 IEIEKVIIVEGKSDKKRIQDIIRepIEIICTNGT-ISLSKLDEIIDCTFNKEVYILVDSDDSGNKLRKQFKRELPEAEHL 82
Cdd:COG1658    5 SKIKEVIVVEGKDDTAALKRAVD--ADIIETNGSaISEETLELIKVAAEKRGVIILTDPDRAGERIRKRISEHLPGAKHA 82


                 ....
gi 647314601  83 YIDK 86
Cdd:COG1658   83 FIDR 86
5S_RNA_mat_M5 TIGR00334
ribonuclease M5; This family of orthologous proteins shows a weak but significant similarity ...
 5-89 1.54e-10

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: 55.22  E-value: 1.54e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647314601    5 EIEKVIIVEGKSDKKRIQDIIrePIEIICTNGT-ISLSKLDEIIDCTFNKEVYILVDSDDSGNKLRKQFKRELPEAEHLY 83
Cdd:TIGR00334   1 KIKEIIVVEGKDDQARIKQAF--DVDVIETNGSaLKDETINLIKKAQKKQGVIILTDPDFPGEKIRKKIEQHLPGYENCF 78


                  ....*.
gi 647314601   84 IDKMYR 89
Cdd:TIGR00334  79 IPKHLA 84
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
7-79 1.92e-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: 1.92e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 647314601     7 EKVIIVEGKSDKKRIQDIIREPIEIICTNGTI-SLSKLDEIIDCTFNKEVYILVDSDDSGNKLRKQFKRELPEA 79
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALGGHLlSKEQIKLLKKLAKKAEVILATDPDREGEAIAWELAELLKPA 74
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 8-70 1.72e-05

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: 40.10  E-value: 1.72e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 647314601   8 KVIIVEGKSDKKRIQDIIREPIEIICTNGTISLSKLDEIIDC-TFNKEVYILVDSDDSGNKLRK 70
Cdd:cd00188    2 KLIIVEGPSDALALAQAGGYGGAVVALGGHALNKTRELLKRLlGEAKEVIIATDADREGEAIAL 65
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 8-67 2.42e-04

Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM domains [Replication, recombination and repair];


Pssm-ID: 442812 [Multi-domain]  Cd Length: 359  Bit Score: 38.83  E-value: 2.42e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 647314601   8 KVIIVEGKSD--------KKRIQDIIREPIEIICTNGTISLSKLDEIIDCtFNKEVYILVDSDDSGNK 67
Cdd:COG3593  282 KVILVEGDTEvillpalaRKLGKDLDEEGISIIPVGGKSNLKPLAKLLKA-LGIPVAVLTDGDEAGKA 348
 
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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