NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|446563524|ref|WP_000640870|]
View 

MULTISPECIES: toprim domain-containing protein [Bacillus]

Protein Classification

toprim domain-containing protein( domain architecture ID 10004131)

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

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
TOPRIM super family cl00718
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 4-82 4.74e-14

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.


The actual alignment was detected with superfamily member cd01027:

Pssm-ID: 469888  Cd Length: 81  Bit Score: 61.89  E-value: 4.74e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446563524   4 VEKVIIVEGTSDRRKIESIIREpVEIVCTNGTIGLSKMDELVDQFfDKEVYVLVDADDAGEKLRKQFRKEF----PQAEH 79
Cdd:cd01027    1 IGEVIIVEGKNDTESLKKLGIE-AEIIETNGSIINKETIELIKKA-YRGVIILTDPDRKGEKIRKKLSEYLsgpvPEIKR 78


                 ...
gi 446563524  80 IYI 82
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 ...
 4-82 4.74e-14

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: 61.89  E-value: 4.74e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446563524   4 VEKVIIVEGTSDRRKIESIIREpVEIVCTNGTIGLSKMDELVDQFfDKEVYVLVDADDAGEKLRKQFRKEF----PQAEH 79
Cdd:cd01027    1 IGEVIIVEGKNDTESLKKLGIE-AEIIETNGSIINKETIELIKKA-YRGVIILTDPDRKGEKIRKKLSEYLsgpvPEIKR 78


                 ...
gi 446563524  80 IYI 82
Cdd:cd01027   79 AFL 81
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 7-84 5.70e-11

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


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 56.19  E-value: 5.70e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446563524   7 VIIVEGTSDRRKIESIIRepVEIVCTNGtiglSKMDELVDQFF-----DKEVYVLVDADDAGEKLRKQFRKEFPQAEHIY 81
Cdd:COG1658   10 VIVVEGKDDTAALKRAVD--ADIIETNG----SAISEETLELIkvaaeKRGVIILTDPDRAGERIRKRISEHLPGAKHAF 83


                 ...
gi 446563524  82 IDR 84
Cdd:COG1658   84 IDR 86
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
5-77 1.47e-07

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 45.33  E-value: 1.47e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446563524     5 EKVIIVEGTSDRRKIESIIREPVEIVCTNGTIG-LSKMDELVDQFFDKEVYVLVDADDAGEKLRKQFRKEFPQA 77
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALGGHLLsKEQIKLLKKLAKKAEVILATDPDREGEAIAWELAELLKPA 74
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 6-79 6.27e-04

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: 36.18  E-value: 6.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446563524    6 KVIIVEGTSDRRKIESII-REPVEIVCTNGTI------GLSKMDELVDQFF--DKEVYVLVDADDAGEKLRKQFRKEFPQ 76
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALgGGFQAVVAVLGHLlslekgPKKKALKALKELAlkAKEVILATDPDREGEAIALKLLELKEL 80


                  ...
gi 446563524   77 AEH 79
Cdd:pfam01751  81 LEN 83
 
Name Accession Description Interval E-value
TOPRIM_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 4-82 4.74e-14

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: 61.89  E-value: 4.74e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446563524   4 VEKVIIVEGTSDRRKIESIIREpVEIVCTNGTIGLSKMDELVDQFfDKEVYVLVDADDAGEKLRKQFRKEF----PQAEH 79
Cdd:cd01027    1 IGEVIIVEGKNDTESLKKLGIE-AEIIETNGSIINKETIELIKKA-YRGVIILTDPDRKGEKIRKKLSEYLsgpvPEIKR 78


                 ...
gi 446563524  80 IYI 82
Cdd:cd01027   79 AFL 81
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 7-84 5.70e-11

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


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 56.19  E-value: 5.70e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446563524   7 VIIVEGTSDRRKIESIIRepVEIVCTNGtiglSKMDELVDQFF-----DKEVYVLVDADDAGEKLRKQFRKEFPQAEHIY 81
Cdd:COG1658   10 VIVVEGKDDTAALKRAVD--ADIIETNG----SAISEETLELIkvaaeKRGVIILTDPDRAGERIRKRISEHLPGAKHAF 83


                 ...
gi 446563524  82 IDR 84
Cdd:COG1658   84 IDR 86
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
5-77 1.47e-07

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 45.33  E-value: 1.47e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446563524     5 EKVIIVEGTSDRRKIESIIREPVEIVCTNGTIG-LSKMDELVDQFFDKEVYVLVDADDAGEKLRKQFRKEFPQA 77
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALGGHLLsKEQIKLLKKLAKKAEVILATDPDREGEAIAWELAELLKPA 74
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 6-68 3.16e-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: 42.03  E-value: 3.16e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446563524   6 KVIIVEGTSDRRKIESIIREPVEIVCTNGTIgLSKMDELVDQFFD--KEVYVLVDADDAGEKLRK 68
Cdd:cd00188    2 KLIIVEGPSDALALAQAGGYGGAVVALGGHA-LNKTRELLKRLLGeaKEVIIATDADREGEAIAL 65
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 1-65 1.98e-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: 1.98e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446563524   1 MIYVEKVIIVEGTSD--------RRKIESIIREPVEIVCTNGTIGLSKMDELVdQFFDKEVYVLVDADDAGEK 65
Cdd:COG3593  277 LLFARKVILVEGDTEvillpalaRKLGKDLDEEGISIIPVGGKSNLKPLAKLL-KALGIPVAVLTDGDEAGKA 348
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 6-79 6.27e-04

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: 36.18  E-value: 6.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446563524    6 KVIIVEGTSDRRKIESII-REPVEIVCTNGTI------GLSKMDELVDQFF--DKEVYVLVDADDAGEKLRKQFRKEFPQ 76
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALgGGFQAVVAVLGHLlslekgPKKKALKALKELAlkAKEVILATDPDREGEAIALKLLELKEL 80


                  ...
gi 446563524   77 AEH 79
Cdd:pfam01751  81 LEN 83
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH