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Conserved domains on  [gi|506272057|ref|WP_015791832|]
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toprim domain-containing protein [Methanocaldococcus fervens]

Protein Classification

toprim domain-containing protein; DUF3991 and TOPRIM domain-containing protein( domain architecture ID 10012118)

toprim (topoisomerase-primase) domain-containing protein| DUF3991 and toprim (topoisomerase-primase) domain-containing protein may function as a bifunctional DNA primase/helicase

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK04017 PRK04017
hypothetical protein; Provisional
 2-128 2.98e-50

hypothetical protein; Provisional


:

Pssm-ID: 179711  Cd Length: 132  Bit Score: 155.89  E-value: 2.98e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506272057   2 RRDEYFEKLLEVIEELKIEAEE-KPIIVEGKRDVESLEKLGIEGTFIVISKTPVYLIAdELVRKGIKEVILLTDFDRRGR 80
Cdd:PRK04017   1 MYRENYERFEEIIEELKEFSEAgAPIIVEGKRDVESLRKLGVEGEIIKVSRTPLAEIA-ELIASRGKEVIILTDFDRKGE 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 506272057  81 LLAKAIVEEFRHRGIKVNTKLRHEIFIYTNSGIKDIESLFSYVNKRSF 128
Cdd:PRK04017  80 ELAKKLSEYLQGYGIKVDTEIRRELFSIVKKDIKDIESLYSYVEKLRL 127
 
Name Accession Description Interval E-value
PRK04017 PRK04017
hypothetical protein; Provisional
 2-128 2.98e-50

hypothetical protein; Provisional


Pssm-ID: 179711  Cd Length: 132  Bit Score: 155.89  E-value: 2.98e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506272057   2 RRDEYFEKLLEVIEELKIEAEE-KPIIVEGKRDVESLEKLGIEGTFIVISKTPVYLIAdELVRKGIKEVILLTDFDRRGR 80
Cdd:PRK04017   1 MYRENYERFEEIIEELKEFSEAgAPIIVEGKRDVESLRKLGVEGEIIKVSRTPLAEIA-ELIASRGKEVIILTDFDRKGE 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 506272057  81 LLAKAIVEEFRHRGIKVNTKLRHEIFIYTNSGIKDIESLFSYVNKRSF 128
Cdd:PRK04017  80 ELAKKLSEYLQGYGIKVDTEIRRELFSIVKKDIKDIESLYSYVEKLRL 127
TOPRIM_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 23-92 3.35e-15

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: 65.36  E-value: 3.35e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506272057  23 EKPIIVEGKRDVESLEKLGIEGTFIVISKTPVYLIADELVRKGIKEVILLTDFDRRGRLLAKAIVEEFRH 92
Cdd:cd01027    2 GEVIIVEGKNDTESLKKLGIEAEIIETNGSIINKETIELIKKAYRGVIILTDPDRKGEKIRKKLSEYLSG 71
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 22-119 2.54e-12

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


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 60.42  E-value: 2.54e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506272057  22 EEKPIIVEGKRDVESLEKLgIEGTFIVISKTPVYLIADELVRK--GIKEVILLTDFDRRGRLLAKAIVEEFR-HRGIKVN 98
Cdd:COG1658    7 IKEVIVVEGKDDTAALKRA-VDADIIETNGSAISEETLELIKVaaEKRGVIILTDPDRAGERIRKRISEHLPgAKHAFID 85

                         90       100
                 ....*....|....*....|.
gi 506272057  99 tklRHEIFIytNSGIKDIESL 119
Cdd:COG1658   86 ---REKARK--KKGIIGVEHA 101
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
26-94 1.16e-08

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 48.41  E-value: 1.16e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 506272057    26 IIVEGKRDVESLEKLGIEGTFIVISKTPVYL--IADELVRKGIK-EVILLTDFDRRGRLLAKAIVEEFRHRG 94
Cdd:smart00493   4 IIVEGPADAIALEKAGGKRGNVVALGGHLLSkeQIKLLKKLAKKaEVILATDPDREGEAIAWELAELLKPAG 75
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 26-97 4.84e-08

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: 46.89  E-value: 4.84e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 506272057   26 IIVEGKRDVESLEKLGIEGTFIV----ISKTPVYLIAD--ELVRKGIKEVILLTDFDRRGRLLAKAIVEEFRHRGIKV 97
Cdd:pfam13662   4 IVVEGYADVIALEKAGYKGAVAVlggaLSPLDGIGPEDlnIDSLGGIKEVILALDGDVAGEKTALYLAEALLEEGVKV 81
 
Name Accession Description Interval E-value
PRK04017 PRK04017
hypothetical protein; Provisional
 2-128 2.98e-50

hypothetical protein; Provisional


Pssm-ID: 179711  Cd Length: 132  Bit Score: 155.89  E-value: 2.98e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506272057   2 RRDEYFEKLLEVIEELKIEAEE-KPIIVEGKRDVESLEKLGIEGTFIVISKTPVYLIAdELVRKGIKEVILLTDFDRRGR 80
Cdd:PRK04017   1 MYRENYERFEEIIEELKEFSEAgAPIIVEGKRDVESLRKLGVEGEIIKVSRTPLAEIA-ELIASRGKEVIILTDFDRKGE 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 506272057  81 LLAKAIVEEFRHRGIKVNTKLRHEIFIYTNSGIKDIESLFSYVNKRSF 128
Cdd:PRK04017  80 ELAKKLSEYLQGYGIKVDTEIRRELFSIVKKDIKDIESLYSYVEKLRL 127
PRK14719 PRK14719
bifunctional RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional
 1-126 4.29e-40

bifunctional RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional


Pssm-ID: 237801 [Multi-domain]  Cd Length: 360  Bit Score: 136.99  E-value: 4.29e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506272057   1 MRRDEYFEKLLEVIEELKIEAEEK-PIIVEGKRDVESLEKLGIEGTFIVISKTPVYLIADELVRKGIKEVILLTDFDRRG 79
Cdd:PRK14719   1 MDKQESLEKLLLIIDDLKLLAEKGiPILVEGPNDILSLKNLKINANFITVSNTPVFQIADDLIAENISEVILLTDFDRAG 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 506272057  80 RLLAKAIVEEFRHRGIKVNTKLRHEIFIYTNSGIKDIESLFSYVNKR 126
Cdd:PRK14719  81 RVYAKNIMEEFQSRGIKVNNLIRKEIIKYSRGDLKDIESLYPYISRR 127
TOPRIM_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 23-92 3.35e-15

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: 65.36  E-value: 3.35e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506272057  23 EKPIIVEGKRDVESLEKLGIEGTFIVISKTPVYLIADELVRKGIKEVILLTDFDRRGRLLAKAIVEEFRH 92
Cdd:cd01027    2 GEVIIVEGKNDTESLKKLGIEAEIIETNGSIINKETIELIKKAYRGVIILTDPDRKGEKIRKKLSEYLSG 71
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 22-119 2.54e-12

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


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 60.42  E-value: 2.54e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506272057  22 EEKPIIVEGKRDVESLEKLgIEGTFIVISKTPVYLIADELVRK--GIKEVILLTDFDRRGRLLAKAIVEEFR-HRGIKVN 98
Cdd:COG1658    7 IKEVIVVEGKDDTAALKRA-VDADIIETNGSAISEETLELIKVaaEKRGVIILTDPDRAGERIRKRISEHLPgAKHAFID 85

                         90       100
                 ....*....|....*....|.
gi 506272057  99 tklRHEIFIytNSGIKDIESL 119
Cdd:COG1658   86 ---REKARK--KKGIIGVEHA 101
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
26-94 1.16e-08

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 48.41  E-value: 1.16e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 506272057    26 IIVEGKRDVESLEKLGIEGTFIVISKTPVYL--IADELVRKGIK-EVILLTDFDRRGRLLAKAIVEEFRHRG 94
Cdd:smart00493   4 IIVEGPADAIALEKAGGKRGNVVALGGHLLSkeQIKLLKKLAKKaEVILATDPDREGEAIAWELAELLKPAG 75
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 26-97 4.84e-08

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: 46.89  E-value: 4.84e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 506272057   26 IIVEGKRDVESLEKLGIEGTFIV----ISKTPVYLIAD--ELVRKGIKEVILLTDFDRRGRLLAKAIVEEFRHRGIKV 97
Cdd:pfam13662   4 IVVEGYADVIALEKAGYKGAVAVlggaLSPLDGIGPEDlnIDSLGGIKEVILALDGDVAGEKTALYLAEALLEEGVKV 81
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 26-97 9.22e-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: 46.27  E-value: 9.22e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 506272057  26 IIVEGKRDVESLEKLGIEGTFIVISK-TPVYLIADELVR--KGIKEVILLTDFDRRGRLLAKAIVEEFRHRGIKV 97
Cdd:cd00188    4 IIVEGPSDALALAQAGGYGGAVVALGgHALNKTRELLKRllGEAKEVIIATDADREGEAIALRLLELLKSLGKKV 78
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 26-91 1.45e-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: 40.80  E-value: 1.45e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 506272057   26 IIVEGKRDVESLEKLGIEGTFIVIS------------KTPVYLIADELVRKgIKEVILLTDFDRRGRLLAKAIVEEFR 91
Cdd:pfam01751   3 IIVEGPSDAIALEKALGGGFQAVVAvlghllslekgpKKKALKALKELALK-AKEVILATDPDREGEAIALKLLELKE 79
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 26-97 2.16e-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: 34.55  E-value: 2.16e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 506272057  26 IIVEGKRDVESLEKLGIEGTFIVISkTPVYLIADELVRKGIKEVILLTDFDRRGRLLAKAIVEEFRHRGIKV 97
Cdd:cd01029    4 IIVEGYMDVLALHQAGIKNVVAALG-TANTEEQLRLLKRFARTVILAFDNDEAGKKAAARALELLLALGGRV 74
 
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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