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Conserved domains on  [gi|805339807|gb|AKB20832|]
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Small primase-like proteins (Toprim domain) [Methanosarcina sp. WH1]

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
 6-137 7.85e-59

hypothetical protein; Provisional


:

Pssm-ID: 179711  Cd Length: 132  Bit Score: 178.62  E-value: 7.85e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805339807   6 IYRKRLERIEGLLSELSEHSERGAVIIVEGKRDILSMKRLGIEGNFELATRHPLFNFSERIAKLGCEVIILTDWDRRGDL 85
Cdd:PRK04017   1 MYRENYERFEEIIEELKEFSEAGAPIIVEGKRDVESLRKLGVEGEIIKVSRTPLAEIAELIASRGKEVIILTDFDRKGEE 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 805339807  86 LAVKLSEYFGNFGIKPELQIRKKLKLITQKEIKDVESLYTYVSKLRSKTGSS 137
Cdd:PRK04017  81 LAKKLSEYLQGYGIKVDTEIRRELFSIVKKDIKDIESLYSYVEKLRLIVGPP 132
 
Name Accession Description Interval E-value
PRK04017 PRK04017
hypothetical protein; Provisional
 6-137 7.85e-59

hypothetical protein; Provisional


Pssm-ID: 179711  Cd Length: 132  Bit Score: 178.62  E-value: 7.85e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805339807   6 IYRKRLERIEGLLSELSEHSERGAVIIVEGKRDILSMKRLGIEGNFELATRHPLFNFSERIAKLGCEVIILTDWDRRGDL 85
Cdd:PRK04017   1 MYRENYERFEEIIEELKEFSEAGAPIIVEGKRDVESLRKLGVEGEIIKVSRTPLAEIAELIASRGKEVIILTDFDRKGEE 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 805339807  86 LAVKLSEYFGNFGIKPELQIRKKLKLITQKEIKDVESLYTYVSKLRSKTGSS 137
Cdd:PRK04017  81 LAKKLSEYLQGYGIKVDTEIRRELFSIVKKDIKDIESLYSYVEKLRLIVGPP 132
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 22-143 1.00e-17

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


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 75.06  E-value: 1.00e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805339807  22 SEHSERGAVIIVEGKRDILSMKRLgIEGNFELATRHPLFNFSE---RIAKLGCEVIILTDWDRRGDLLAVKLSEYFGN-F 97
Cdd:COG1658    2 TDRSKIKEVIVVEGKDDTAALKRA-VDADIIETNGSAISEETLeliKVAAEKRGVIILTDPDRAGERIRKRISEHLPGaK 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 805339807  98 GIKPelqirKKLKLITQKEIKDVESLY-TYVSKLRSKTGSSLDPEYE 143
Cdd:COG1658   81 HAFI-----DREKARKKKGIIGVEHASpEAIRRALSKVRTEKEEEEE 122
TOPRIM_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 28-96 6.69e-17

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: 70.36  E-value: 6.69e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 805339807  28 GAVIIVEGKRDILSMKRLGIEGNFeLATRHPLFN--FSERIAKLGCEVIILTDWDRRGDLLAVKLSEYFGN 96
Cdd:cd01027    2 GEVIIVEGKNDTESLKKLGIEAEI-IETNGSIINkeTIELIKKAYRGVIILTDPDRKGEKIRKKLSEYLSG 71
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
29-98 1.39e-09

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 51.11  E-value: 1.39e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 805339807    29 AVIIVEGKRDILSMKRLGIEGNFELATRHPLFNFS--ERIAKL--GCEVIILTDWDRRGDLLAVKLSEYFGNFG 98
Cdd:smart00493   2 VLIIVEGPADAIALEKAGGKRGNVVALGGHLLSKEqiKLLKKLakKAEVILATDPDREGEAIAWELAELLKPAG 75
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 29-95 6.37e-06

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: 41.96  E-value: 6.37e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 805339807   29 AVIIVEGKRDILSMKRLGIEGNFE-LATRHPLFNFSER-----------IAKLGCEVIILTDWDRRGDLLAVKLSEYFG 95
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGFQAvVAVLGHLLSLEKGpkkkalkalkeLALKAKEVILATDPDREGEAIALKLLELKE 79
 
Name Accession Description Interval E-value
PRK04017 PRK04017
hypothetical protein; Provisional
 6-137 7.85e-59

hypothetical protein; Provisional


Pssm-ID: 179711  Cd Length: 132  Bit Score: 178.62  E-value: 7.85e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805339807   6 IYRKRLERIEGLLSELSEHSERGAVIIVEGKRDILSMKRLGIEGNFELATRHPLFNFSERIAKLGCEVIILTDWDRRGDL 85
Cdd:PRK04017   1 MYRENYERFEEIIEELKEFSEAGAPIIVEGKRDVESLRKLGVEGEIIKVSRTPLAEIAELIASRGKEVIILTDFDRKGEE 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 805339807  86 LAVKLSEYFGNFGIKPELQIRKKLKLITQKEIKDVESLYTYVSKLRSKTGSS 137
Cdd:PRK04017  81 LAKKLSEYLQGYGIKVDTEIRRELFSIVKKDIKDIESLYSYVEKLRLIVGPP 132
PRK14719 PRK14719
bifunctional RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional
 8-129 7.16e-22

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


Pssm-ID: 237801 [Multi-domain]  Cd Length: 360  Bit Score: 89.23  E-value: 7.16e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805339807   8 RKRLERIEGLLSELSEHSERGAVIIVEGKRDILSMKRLGIEGNFELATRHPLFNFSERIAKLGC-EVIILTDWDRRGDLL 86
Cdd:PRK14719   4 QESLEKLLLIIDDLKLLAEKGIPILVEGPNDILSLKNLKINANFITVSNTPVFQIADDLIAENIsEVILLTDFDRAGRVY 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 805339807  87 AVKLSEYFGNFGIKPELQIRKKLKLITQKEIKDVESLYTYVSK 129
Cdd:PRK14719  84 AKNIMEEFQSRGIKVNNLIRKEIIKYSRGDLKDIESLYPYISR 126
RnmV COG1658
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ...
 22-143 1.00e-17

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


Pssm-ID: 441264 [Multi-domain]  Cd Length: 184  Bit Score: 75.06  E-value: 1.00e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805339807  22 SEHSERGAVIIVEGKRDILSMKRLgIEGNFELATRHPLFNFSE---RIAKLGCEVIILTDWDRRGDLLAVKLSEYFGN-F 97
Cdd:COG1658    2 TDRSKIKEVIVVEGKDDTAALKRA-VDADIIETNGSAISEETLeliKVAAEKRGVIILTDPDRAGERIRKRISEHLPGaK 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 805339807  98 GIKPelqirKKLKLITQKEIKDVESLY-TYVSKLRSKTGSSLDPEYE 143
Cdd:COG1658   81 HAFI-----DREKARKKKGIIGVEHASpEAIRRALSKVRTEKEEEEE 122
TOPRIM_RNase_M5_like cd01027
TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase ...
 28-96 6.69e-17

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: 70.36  E-value: 6.69e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 805339807  28 GAVIIVEGKRDILSMKRLGIEGNFeLATRHPLFN--FSERIAKLGCEVIILTDWDRRGDLLAVKLSEYFGN 96
Cdd:cd01027    2 GEVIIVEGKNDTESLKKLGIEAEI-IETNGSIINkeTIELIKKAYRGVIILTDPDRKGEKIRKKLSEYLSG 71
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
29-98 1.39e-09

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 51.11  E-value: 1.39e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 805339807    29 AVIIVEGKRDILSMKRLGIEGNFELATRHPLFNFS--ERIAKL--GCEVIILTDWDRRGDLLAVKLSEYFGNFG 98
Cdd:smart00493   2 VLIIVEGPADAIALEKAGGKRGNVVALGGHLLSKEqiKLLKKLakKAEVILATDPDREGEAIAWELAELLKPAG 75
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 30-100 2.14e-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: 48.58  E-value: 2.14e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 805339807  30 VIIVEGKRDILSMKRLGIEGNFELATR----HPLFNFSERIAKLGCEVIILTDWDRRGDLLAVKLSEYFGNFGIK 100
Cdd:cd00188    3 LIIVEGPSDALALAQAGGYGGAVVALGghalNKTRELLKRLLGEAKEVIIATDADREGEAIALRLLELLKSLGKK 77
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 29-95 6.37e-06

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: 41.96  E-value: 6.37e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 805339807   29 AVIIVEGKRDILSMKRLGIEGNFE-LATRHPLFNFSER-----------IAKLGCEVIILTDWDRRGDLLAVKLSEYFG 95
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGFQAvVAVLGHLLSLEKGpkkkalkalkeLALKAKEVILATDPDREGEAIALKLLELKE 79
Toprim_4 pfam13662
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 28-100 7.08e-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: 39.19  E-value: 7.08e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 805339807   28 GAVIIVEGKRDILSMKRLGIEGNF-----ELATRH---PLfNFSERIAKLGCEVIILTDWDRRGDLLAVKLSEYFGNFGI 99
Cdd:pfam13662   1 SEIIVVEGYADVIALEKAGYKGAVavlggALSPLDgigPE-DLNIDSLGGIKEVILALDGDVAGEKTALYLAEALLEEGV 79


                  .
gi 805339807  100 K 100
Cdd:pfam13662  80 K 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.
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