NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1802384813|gb|KAF1276455|]
View 

hypothetical protein BUE72_11205 [Bacillus amyloliquefaciens]

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_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 28-105 2.21e-20

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: 79.22  E-value: 2.21e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802384813  28 EKVIIVEGKSDKIKVREVLIEpAEIVCTNGTIGQTELEDLADRlFDRDVYILTDADDSGEKLRKQLKREL----PEARHI 103
Cdd:cd01027     2 GEVIIVEGKNDTESLKKLGIE-AEIIETNGSIINKETIELIKK-AYRGVIILTDPDRKGEKIRKKLSEYLsgpvPEIKRA 79


                  ..
gi 1802384813 104 YI 105
Cdd:cd01027    80 FL 81
 
Name Accession Description Interval E-value
TOPRIM_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 28-105 2.21e-20

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: 79.22  E-value: 2.21e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802384813  28 EKVIIVEGKSDKIKVREVLIEpAEIVCTNGTIGQTELEDLADRlFDRDVYILTDADDSGEKLRKQLKREL----PEARHI 103
Cdd:cd01027     2 GEVIIVEGKNDTESLKKLGIE-AEIIETNGSIINKETIELIKK-AYRGVIILTDPDRKGEKIRKKLSEYLsgpvPEIKRA 79


                  ..
gi 1802384813 104 YI 105
Cdd:cd01027    80 FL 81
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 30-107 2.16e-17

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


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 74.29  E-value: 2.16e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1802384813  30 VIIVEGKSDKIKVREvLIEpAEIVCTNGT-IGQTELEDLADRLFDRDVYILTDADDSGEKLRKQLKRELPEARHIYIDR 107
Cdd:COG1658    10 VIVVEGKDDTAALKR-AVD-ADIIETNGSaISEETLELIKVAAEKRGVIILTDPDRAGERIRKRISEHLPGAKHAFIDR 86
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
28-100 5.49e-11

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 54.96  E-value: 5.49e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1802384813   28 EKVIIVEGKSDKIKVREVLIEPAEIVCTNGTIGQTELEDLADRLFDRD-VYILTDADDSGEKLRKQLKRELPEA 100
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALGGHLLSKEQIKLLKKLAKKAeVILATDPDREGEAIAWELAELLKPA 74
5S_RNA_mat_M5 TIGR00334
ribonuclease M5; This family of orthologous proteins shows a weak but significant similarity ...
 30-110 9.51e-09

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: 51.36  E-value: 9.51e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802384813  30 VIIVEGKSDKIKVREVLiePAEIVCTNGTIGQTELEDLADRLFD-RDVYILTDADDSGEKLRKQLKRELPEARHIYIDRT 108
Cdd:TIGR00334   5 IIVVEGKDDQARIKQAF--DVDVIETNGSALKDETINLIKKAQKkQGVIILTDPDFPGEKIRKKIEQHLPGYENCFIPKH 82


                  ..
gi 1802384813 109 YR 110
Cdd:TIGR00334  83 LA 84
PRK04017 PRK04017
hypothetical protein; Provisional
 24-97 4.71e-06

hypothetical protein; Provisional


Pssm-ID: 179711  Cd Length: 132  Bit Score: 43.02  E-value: 4.71e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1802384813  24 YNGDEKVIIVEGKSDKIKVREVLIEPAEIVCTNGTIgqTELEDLAdRLFDRDVYILTDADDSGEKLRKQLKREL 97
Cdd:PRK04017   19 FSEAGAPIIVEGKRDVESLRKLGVEGEIIKVSRTPL--AEIAELI-ASRGKEVIILTDFDRKGEELAKKLSEYL 89
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 29-102 2.60e-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: 40.42  E-value: 2.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802384813  29 KVIIVEGKSDKIKVREVL-IEPAEIVCTNGTI-------GQTELEDLADRLFDRD-VYILTDADDSGEKLRKQLKRELPE 99
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALgGGFQAVVAVLGHLlslekgpKKKALKALKELALKAKeVILATDPDREGEAIALKLLELKEL 80


                  ...
gi 1802384813 100 ARH 102
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 ...
 28-105 2.21e-20

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: 79.22  E-value: 2.21e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802384813  28 EKVIIVEGKSDKIKVREVLIEpAEIVCTNGTIGQTELEDLADRlFDRDVYILTDADDSGEKLRKQLKREL----PEARHI 103
Cdd:cd01027     2 GEVIIVEGKNDTESLKKLGIE-AEIIETNGSIINKETIELIKK-AYRGVIILTDPDRKGEKIRKKLSEYLsgpvPEIKRA 79


                  ..
gi 1802384813 104 YI 105
Cdd:cd01027    80 FL 81
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 30-107 2.16e-17

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


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 74.29  E-value: 2.16e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1802384813  30 VIIVEGKSDKIKVREvLIEpAEIVCTNGT-IGQTELEDLADRLFDRDVYILTDADDSGEKLRKQLKRELPEARHIYIDR 107
Cdd:COG1658    10 VIVVEGKDDTAALKR-AVD-ADIIETNGSaISEETLELIKVAAEKRGVIILTDPDRAGERIRKRISEHLPGAKHAFIDR 86
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
28-100 5.49e-11

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 54.96  E-value: 5.49e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1802384813   28 EKVIIVEGKSDKIKVREVLIEPAEIVCTNGTIGQTELEDLADRLFDRD-VYILTDADDSGEKLRKQLKRELPEA 100
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALGGHLLSKEQIKLLKKLAKKAeVILATDPDREGEAIAWELAELLKPA 74
5S_RNA_mat_M5 TIGR00334
ribonuclease M5; This family of orthologous proteins shows a weak but significant similarity ...
 30-110 9.51e-09

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: 51.36  E-value: 9.51e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802384813  30 VIIVEGKSDKIKVREVLiePAEIVCTNGTIGQTELEDLADRLFD-RDVYILTDADDSGEKLRKQLKRELPEARHIYIDRT 108
Cdd:TIGR00334   5 IIVVEGKDDQARIKQAF--DVDVIETNGSALKDETINLIKKAQKkQGVIILTDPDFPGEKIRKKIEQHLPGYENCFIPKH 82


                  ..
gi 1802384813 109 YR 110
Cdd:TIGR00334  83 LA 84
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 29-101 7.21e-08

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: 47.04  E-value: 7.21e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1802384813  29 KVIIVEGKSDKIKVREVLIEPAEIVCTNGTIGQTELEDLADRL-FDRDVYILTDADDSGEKLRKQLKRELPEAR 101
Cdd:cd00188     2 KLIIVEGPSDALALAQAGGYGGAVVALGGHALNKTRELLKRLLgEAKEVIIATDADREGEAIALRLLELLKSLG 75
PRK04017 PRK04017
hypothetical protein; Provisional
 24-97 4.71e-06

hypothetical protein; Provisional


Pssm-ID: 179711  Cd Length: 132  Bit Score: 43.02  E-value: 4.71e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1802384813  24 YNGDEKVIIVEGKSDKIKVREVLIEPAEIVCTNGTIgqTELEDLAdRLFDRDVYILTDADDSGEKLRKQLKREL 97
Cdd:PRK04017   19 FSEAGAPIIVEGKRDVESLRKLGVEGEIIKVSRTPL--AEIAELI-ASRGKEVIILTDFDRKGEELAKKLSEYL 89
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 29-102 2.60e-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: 40.42  E-value: 2.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802384813  29 KVIIVEGKSDKIKVREVL-IEPAEIVCTNGTI-------GQTELEDLADRLFDRD-VYILTDADDSGEKLRKQLKRELPE 99
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALgGGFQAVVAVLGHLlslekgpKKKALKALKELALKAKeVILATDPDREGEAIALKLLELKEL 80


                  ...
gi 1802384813 100 ARH 102
Cdd:pfam01751  81 LEN 83
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 28-105 1.08e-03

TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM 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. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. The prototypical bacterial primase. Escherichia coli DnaG is a single subunit enzyme.


Pssm-ID: 173779 [Multi-domain]  Cd Length: 79  Bit Score: 35.71  E-value: 1.08e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1802384813  28 EKVIIVEGKSDKIKVREVLIEPAeiVCTNGTiGQTELEDLADRLFDRDVYILTDADDSGEK-LRKQLKRELPEARHIYI 105
Cdd:cd01029     1 DEVIIVEGYMDVLALHQAGIKNV--VAALGT-ANTEEQLRLLKRFARTVILAFDNDEAGKKaAARALELLLALGGRVRV 76
Toprim_2 pfam13155
Toprim-like; This is a family or Toprim-like proteins.
 31-111 9.38e-03

Toprim-like; This is a family or Toprim-like proteins.


Pssm-ID: 463793 [Multi-domain]  Cd Length: 88  Bit Score: 33.30  E-value: 9.38e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802384813  31 IIVEGKSDKIKVREVLIEPAEIVCTNGTIGQTELEDLADRlFDRDVYILTDADDSGEKLRKQLKRELPEARHIYIDRTYR 110
Cdd:pfam13155   1 VVFEGYIDALSLAQAGIKNVLYVATLGTALTEAQIKLLKR-YPKEVILAFDNDEAGRKAAKRLAELLKEAGVDVKIRLLP 79


                  .
gi 1802384813 111 Q 111
Cdd:pfam13155  80 D 80
 
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