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Conserved domains on  [gi|502958642|ref|WP_013193618|]
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toprim domain-containing protein [Methanohalobium evestigatum]

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
 13-144 1.33e-57

hypothetical protein; Provisional


:

Pssm-ID: 179711  Cd Length: 132  Bit Score: 176.30  E-value: 1.33e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502958642  13 EYRKHLEQIEQILDVLFQHSEEGDILVVEGKRDICSLEKLGIDGDIETVSNKSLLDFSENVAYTGKSVVILTDWDRRGEI 92
Cdd:PRK04017   1 MYRENYERFEEIIEELKEFSEAGAPIIVEGKRDVESLRKLGVEGEIIKVSRTPLAEIAELIASRGKEVIILTDFDRKGEE 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 502958642  93 LASKLSEYLQTLDTDYDIEIREQLKSLVKKEIKDIESLYTYVVKLRSITGST 144
Cdd:PRK04017  81 LAKKLSEYLQGYGIKVDTEIRRELFSIVKKDIKDIESLYSYVEKLRLIVGPP 132
 
Name Accession Description Interval E-value
PRK04017 PRK04017
hypothetical protein; Provisional
 13-144 1.33e-57

hypothetical protein; Provisional


Pssm-ID: 179711  Cd Length: 132  Bit Score: 176.30  E-value: 1.33e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502958642  13 EYRKHLEQIEQILDVLFQHSEEGDILVVEGKRDICSLEKLGIDGDIETVSNKSLLDFSENVAYTGKSVVILTDWDRRGEI 92
Cdd:PRK04017   1 MYRENYERFEEIIEELKEFSEAGAPIIVEGKRDVESLRKLGVEGEIIKVSRTPLAEIAELIASRGKEVIILTDFDRKGEE 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 502958642  93 LASKLSEYLQTLDTDYDIEIREQLKSLVKKEIKDIESLYTYVVKLRSITGST 144
Cdd:PRK04017  81 LAKKLSEYLQGYGIKVDTEIRRELFSIVKKDIKDIESLYSYVEKLRLIVGPP 132
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 31-131 2.63e-20

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


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 82.38  E-value: 2.63e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502958642  31 HSEEGDILVVEGKRDICSLEKLgIDGDIETVSNKSLLDFSEN---VAYTGKSVVILTDWDRRGEILASKLSEYLQTLdtd 107
Cdd:COG1658    4 RSKIKEVIVVEGKDDTAALKRA-VDADIIETNGSAISEETLElikVAAEKRGVIILTDPDRAGERIRKRISEHLPGA--- 79

                         90       100
                 ....*....|....*....|....*
gi 502958642 108 YDIEI-REQLKSlvKKEIKDIESLY 131
Cdd:COG1658   80 KHAFIdREKARK--KKGIIGVEHAS 102
TOPRIM_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 37-105 3.34e-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: 63.82  E-value: 3.34e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502958642  37 ILVVEGKRDICSLEKLGIDGD-IETVSNKSLLDFSENVAYTGKSVVILTDWDRRGEILASKLSEYLQTLD 105
Cdd:cd01027    4 VIIVEGKNDTESLKKLGIEAEiIETNGSIINKETIELIKKAYRGVIILTDPDRKGEKIRKKLSEYLSGPV 73
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
37-102 8.85e-07

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 44.17  E-value: 8.85e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502958642    37 ILVVEGKRDICSLEKLGIDGDIETVSNKSLLD---FSENVAYT-GKSVVILTDWDRRGEILASKLSEYLQ 102
Cdd:smart00493   3 LIIVEGPADAIALEKAGGKRGNVVALGGHLLSkeqIKLLKKLAkKAEVILATDPDREGEAIAWELAELLK 72
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 37-107 1.83e-05

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: 41.12  E-value: 1.83e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 502958642   37 ILVVEGKRDICSLEKLGID-------GDIETVSNKSLLDFSENVAYTGKSVVILTDWDRRGEILASKLSEYLQTLDTD 107
Cdd:pfam13662   3 IIVVEGYADVIALEKAGYKgavavlgGALSPLDGIGPEDLNIDSLGGIKEVILALDGDVAGEKTALYLAEALLEEGVK 80
 
Name Accession Description Interval E-value
PRK04017 PRK04017
hypothetical protein; Provisional
 13-144 1.33e-57

hypothetical protein; Provisional


Pssm-ID: 179711  Cd Length: 132  Bit Score: 176.30  E-value: 1.33e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502958642  13 EYRKHLEQIEQILDVLFQHSEEGDILVVEGKRDICSLEKLGIDGDIETVSNKSLLDFSENVAYTGKSVVILTDWDRRGEI 92
Cdd:PRK04017   1 MYRENYERFEEIIEELKEFSEAGAPIIVEGKRDVESLRKLGVEGEIIKVSRTPLAEIAELIASRGKEVIILTDFDRKGEE 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 502958642  93 LASKLSEYLQTLDTDYDIEIREQLKSLVKKEIKDIESLYTYVVKLRSITGST 144
Cdd:PRK04017  81 LAKKLSEYLQGYGIKVDTEIRRELFSIVKKDIKDIESLYSYVEKLRLIVGPP 132
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 31-131 2.63e-20

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


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 82.38  E-value: 2.63e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502958642  31 HSEEGDILVVEGKRDICSLEKLgIDGDIETVSNKSLLDFSEN---VAYTGKSVVILTDWDRRGEILASKLSEYLQTLdtd 107
Cdd:COG1658    4 RSKIKEVIVVEGKDDTAALKRA-VDADIIETNGSAISEETLElikVAAEKRGVIILTDPDRAGERIRKRISEHLPGA--- 79

                         90       100
                 ....*....|....*....|....*
gi 502958642 108 YDIEI-REQLKSlvKKEIKDIESLY 131
Cdd:COG1658   80 KHAFIdREKARK--KKGIIGVEHAS 102
PRK14719 PRK14719
bifunctional RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional
 15-150 7.60e-16

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


Pssm-ID: 237801 [Multi-domain]  Cd Length: 360  Bit Score: 73.43  E-value: 7.60e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502958642  15 RKHLEQIEQILDVLFQHSEEGDILVVEGKRDICSLEKLGIDGDIETVSNKSLLDFSENVAYTGKS-VVILTDWDRRGEIL 93
Cdd:PRK14719   4 QESLEKLLLIIDDLKLLAEKGIPILVEGPNDILSLKNLKINANFITVSNTPVFQIADDLIAENISeVILLTDFDRAGRVY 83

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 502958642  94 ASKLSEYLQTLDTDYDIEIREQLKSLVKKEIKDIESLYTYVVKLRSItgsTSDFADI 150
Cdd:PRK14719  84 AKNIMEEFQSRGIKVNNLIRKEIIKYSRGDLKDIESLYPYISRRINI---NSDLSDI 137
TOPRIM_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 37-105 3.34e-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: 63.82  E-value: 3.34e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502958642  37 ILVVEGKRDICSLEKLGIDGD-IETVSNKSLLDFSENVAYTGKSVVILTDWDRRGEILASKLSEYLQTLD 105
Cdd:cd01027    4 VIIVEGKNDTESLKKLGIEAEiIETNGSIINKETIELIKKAYRGVIILTDPDRKGEKIRKKLSEYLSGPV 73
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
37-102 8.85e-07

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 44.17  E-value: 8.85e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502958642    37 ILVVEGKRDICSLEKLGIDGDIETVSNKSLLD---FSENVAYT-GKSVVILTDWDRRGEILASKLSEYLQ 102
Cdd:smart00493   3 LIIVEGPADAIALEKAGGKRGNVVALGGHLLSkeqIKLLKKLAkKAEVILATDPDREGEAIAWELAELLK 72
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 37-107 1.83e-05

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: 41.12  E-value: 1.83e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 502958642   37 ILVVEGKRDICSLEKLGID-------GDIETVSNKSLLDFSENVAYTGKSVVILTDWDRRGEILASKLSEYLQTLDTD 107
Cdd:pfam13662   3 IIVVEGYADVIALEKAGYKgavavlgGALSPLDGIGPEDLNIDSLGGIKEVILALDGDVAGEKTALYLAEALLEEGVK 80
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 37-102 2.72e-04

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: 37.79  E-value: 2.72e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502958642  37 ILVVEGKRDICSLEKLGIDGDIETVS----NKSLLDFSENVAYTGKSVVILTDWDRRGEILASKLSEYLQ 102
Cdd:cd00188    3 LIIVEGPSDALALAQAGGYGGAVVALgghaLNKTRELLKRLLGEAKEVIIATDADREGEAIALRLLELLK 72
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 37-104 7.36e-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: 36.95  E-value: 7.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502958642   37 ILVVEGKRDICSLEKLGIDGDIE-TVSNKSLLDFSENVAYT-----------GKSVVILTDWDRRGEILASKLSEYLQTL 104
Cdd:pfam01751   2 LIIVEGPSDAIALEKALGGGFQAvVAVLGHLLSLEKGPKKKalkalkelalkAKEVILATDPDREGEAIALKLLELKELL 81
 
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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