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Conserved domains on  [gi|1524746639|gb|AZF91795|]
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replication protein [Streptococcus phage CHPC1067]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Prim_Pol cd04859
Prim_Pol: Primase-polymerase (primpol) domain of the type found in bifunctional replicases ...
 15-165 5.24e-34

Prim_Pol: Primase-polymerase (primpol) domain of the type found in bifunctional replicases from archaeal plasmids, including ORF904 protein of the crenarchaeal plasmid pRN1 from Sulfolobus islandicus (pRN1 primpol). These primpol domains belong to the archaeal/eukaryal primase (AEP) superfamily. This group includes archaeal plasmids and bacteriophage AEPs. The ORF904 protein is a multifunctional protein having ATPase, primase and DNA polymerase activity, and may play a role in the replication of the archaeal plasmid. The pRN1 primpol domain exhibits DNA polymerase and primase activities; a cluster of active site residues (three acidic residues, and a histidine) is required for both these activities. For pRN1 primpol, the primase activity prefers dNTPs to rNTPs; incorporation of dNTPs requires rNTP as cofactor. The pRN1 primpol contains an unusual zinc-binding stem, which is not conserved in other members of this group.


:

Pssm-ID: 240129  Cd Length: 152  Bit Score: 120.59  E-value: 5.24e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1524746639  15 YSVIPISKNGKTPLISFADKPPMT--ENDIRRVWRDNPDANIALKTDT--FFVIDVDMHGDVDGLTNLRnWEHARLIPKT 90
Cdd:cd04859     1 FAVIPLDPGSKRPLIKGWPKDAATtdPEQIEAWWRDGPDANIGLRTGPsgLVVIDIDVKHDGAAALAAL-AELGKLPPLT 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1524746639  91 LQAITPSGGRHIYLKKDPNHPISQNIGM-IEGVDIKAHvNNYILVPPSNNSKGYYEWDtvhsPKDGSITEAPLALI 165
Cdd:cd04859    80 LTVRTGSGGRHLYFRVPDGVPVKSVKGKgGPGIDIRGG-GGYVVAPPSVHPGGGYYVW----KSTVDPAPAPEWLL 150
PriCT_1 smart00942
Primase C terminal 1 (PriCT-1); This alpha helical domain is found at the C terminal of ...
 202-264 5.86e-15

Primase C terminal 1 (PriCT-1); This alpha helical domain is found at the C terminal of primases.


:

Pssm-ID: 214926  Cd Length: 66  Bit Score: 67.74  E-value: 5.86e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1524746639  202 LGFGDKGGRNNALAEFVGGLLLRG-VDPEITYHLAKMANN-NTQEPLGNKEFERTFKSMLDKEIR 264
Cdd:smart00942   2 LGGVDEGNRNNTLFRLAGRLLRRGyVDEEEAYALLLAANSaNCNPPLPERELEKTAESAYRRESR 66
 
Name Accession Description Interval E-value
Prim_Pol cd04859
Prim_Pol: Primase-polymerase (primpol) domain of the type found in bifunctional replicases ...
 15-165 5.24e-34

Prim_Pol: Primase-polymerase (primpol) domain of the type found in bifunctional replicases from archaeal plasmids, including ORF904 protein of the crenarchaeal plasmid pRN1 from Sulfolobus islandicus (pRN1 primpol). These primpol domains belong to the archaeal/eukaryal primase (AEP) superfamily. This group includes archaeal plasmids and bacteriophage AEPs. The ORF904 protein is a multifunctional protein having ATPase, primase and DNA polymerase activity, and may play a role in the replication of the archaeal plasmid. The pRN1 primpol domain exhibits DNA polymerase and primase activities; a cluster of active site residues (three acidic residues, and a histidine) is required for both these activities. For pRN1 primpol, the primase activity prefers dNTPs to rNTPs; incorporation of dNTPs requires rNTP as cofactor. The pRN1 primpol contains an unusual zinc-binding stem, which is not conserved in other members of this group.


Pssm-ID: 240129  Cd Length: 152  Bit Score: 120.59  E-value: 5.24e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1524746639  15 YSVIPISKNGKTPLISFADKPPMT--ENDIRRVWRDNPDANIALKTDT--FFVIDVDMHGDVDGLTNLRnWEHARLIPKT 90
Cdd:cd04859     1 FAVIPLDPGSKRPLIKGWPKDAATtdPEQIEAWWRDGPDANIGLRTGPsgLVVIDIDVKHDGAAALAAL-AELGKLPPLT 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1524746639  91 LQAITPSGGRHIYLKKDPNHPISQNIGM-IEGVDIKAHvNNYILVPPSNNSKGYYEWDtvhsPKDGSITEAPLALI 165
Cdd:cd04859    80 LTVRTGSGGRHLYFRVPDGVPVKSVKGKgGPGIDIRGG-GGYVVAPPSVHPGGGYYVW----KSTVDPAPAPEWLL 150
Prim-Pol smart00943
Bifunctional DNA primase/polymerase, N-terminal; Members of this family adopt a structure ...
 7-159 5.75e-32

Bifunctional DNA primase/polymerase, N-terminal; Members of this family adopt a structure consisting of a core of antiparallel beta sheets. They are found in various bacterial hypothetical proteins, and have been shown to harbour both primase and polymerase activities.


Pssm-ID: 214927  Cd Length: 154  Bit Score: 115.13  E-value: 5.75e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1524746639    7 AINYQRMGYSVIPISKNGKTPLI-SFADKPPMTENDIRRVWRDNPDANIALKTDT--FFVIDVDMHGDVDGLtnlRNWEH 83
Cdd:smart00943   1 ALRYAARGWPVIPLPPGGKRPLIcAGWKDATTDPEEIRAWWKKWPGANIGLATGPsgLVVLDIDVKAGLEAL---AALAE 77

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1524746639   84 ARLIPKTLQAITPSGGRHIYLKKDPNHPISQNIGMI-EGVDIKAHvNNYILVPPSNNSKGY-YEWDTVHSPKDGSITE 159
Cdd:smart00943  78 LGLLPATPTVRTPSGGRHLYFRVPDGPKLPPNPGFLkPGLDIRGD-GGYVVAPPSVHDTGRpYRWVRDPTPASPPIPP 154
Prim-Pol pfam09250
Bifunctional DNA primase/polymerase, N-terminal; Members of this family adopt a structure ...
 7-161 1.93e-27

Bifunctional DNA primase/polymerase, N-terminal; Members of this family adopt a structure consisting of a core of antiparallel beta sheets. They are found in various bacterial hypothetical proteins, and have been shown to harbour both primase and polymerase activities.


Pssm-ID: 430484  Cd Length: 158  Bit Score: 103.62  E-value: 1.93e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1524746639   7 AINYQRMGYSVIPISKNGKTPLISFADKPPMTEND-IRRVWRDNPDANIALKTDT--FFVIDVDMHGD-VDGLTNLRNwE 82
Cdd:pfam09250   1 ALAYAERGWPVFPLPPGGKHPLGPGWQKRATTDPEqIRAWWSRHPNANIGLATGPsgLVVLDVDGPEAgADALARLER-E 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1524746639  83 HARLIPKTLQAITPS--GGRHIYLKKDPNHPISQNIGMI-EGVDIKAHvNNYILVPPSNNSKGYYEWdtVHSPKDgsITE 159
Cdd:pfam09250  80 GGELLPVTVTVTTGStgGGRHLYFRAPGGLALRNTAGKLaGGLDLRGD-GGYVVAPPSVHTGGAYRW--LNGPRP--PAE 154


                  ..
gi 1524746639 160 AP 161
Cdd:pfam09250 155 LP 156
PriCT_1 smart00942
Primase C terminal 1 (PriCT-1); This alpha helical domain is found at the C terminal of ...
 202-264 5.86e-15

Primase C terminal 1 (PriCT-1); This alpha helical domain is found at the C terminal of primases.


Pssm-ID: 214926  Cd Length: 66  Bit Score: 67.74  E-value: 5.86e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1524746639  202 LGFGDKGGRNNALAEFVGGLLLRG-VDPEITYHLAKMANN-NTQEPLGNKEFERTFKSMLDKEIR 264
Cdd:smart00942   2 LGGVDEGNRNNTLFRLAGRLLRRGyVDEEEAYALLLAANSaNCNPPLPERELEKTAESAYRRESR 66
PriCT_1 pfam08708
Primase C terminal 1 (PriCT-1); This alpha helical domain is found at the C terminal of ...
 201-264 3.93e-11

Primase C terminal 1 (PriCT-1); This alpha helical domain is found at the C terminal of primases.


Pssm-ID: 430166  Cd Length: 64  Bit Score: 57.31  E-value: 3.93e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1524746639 201 LLGFGDKGGRNNALAEFVGGLLLRGVDPEITYHLAKMANNNTQEPLGNKEFERTFKSMLDKEIR 264
Cdd:pfam08708   1 TLGPVASGGRNNALFRLAGALARRGIDRESVLALLHALNSNLEPPLDESEVEKTVKSVYRYVYA 64
 
Name Accession Description Interval E-value
Prim_Pol cd04859
Prim_Pol: Primase-polymerase (primpol) domain of the type found in bifunctional replicases ...
 15-165 5.24e-34

Prim_Pol: Primase-polymerase (primpol) domain of the type found in bifunctional replicases from archaeal plasmids, including ORF904 protein of the crenarchaeal plasmid pRN1 from Sulfolobus islandicus (pRN1 primpol). These primpol domains belong to the archaeal/eukaryal primase (AEP) superfamily. This group includes archaeal plasmids and bacteriophage AEPs. The ORF904 protein is a multifunctional protein having ATPase, primase and DNA polymerase activity, and may play a role in the replication of the archaeal plasmid. The pRN1 primpol domain exhibits DNA polymerase and primase activities; a cluster of active site residues (three acidic residues, and a histidine) is required for both these activities. For pRN1 primpol, the primase activity prefers dNTPs to rNTPs; incorporation of dNTPs requires rNTP as cofactor. The pRN1 primpol contains an unusual zinc-binding stem, which is not conserved in other members of this group.


Pssm-ID: 240129  Cd Length: 152  Bit Score: 120.59  E-value: 5.24e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1524746639  15 YSVIPISKNGKTPLISFADKPPMT--ENDIRRVWRDNPDANIALKTDT--FFVIDVDMHGDVDGLTNLRnWEHARLIPKT 90
Cdd:cd04859     1 FAVIPLDPGSKRPLIKGWPKDAATtdPEQIEAWWRDGPDANIGLRTGPsgLVVIDIDVKHDGAAALAAL-AELGKLPPLT 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1524746639  91 LQAITPSGGRHIYLKKDPNHPISQNIGM-IEGVDIKAHvNNYILVPPSNNSKGYYEWDtvhsPKDGSITEAPLALI 165
Cdd:cd04859    80 LTVRTGSGGRHLYFRVPDGVPVKSVKGKgGPGIDIRGG-GGYVVAPPSVHPGGGYYVW----KSTVDPAPAPEWLL 150
Prim-Pol smart00943
Bifunctional DNA primase/polymerase, N-terminal; Members of this family adopt a structure ...
 7-159 5.75e-32

Bifunctional DNA primase/polymerase, N-terminal; Members of this family adopt a structure consisting of a core of antiparallel beta sheets. They are found in various bacterial hypothetical proteins, and have been shown to harbour both primase and polymerase activities.


Pssm-ID: 214927  Cd Length: 154  Bit Score: 115.13  E-value: 5.75e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1524746639    7 AINYQRMGYSVIPISKNGKTPLI-SFADKPPMTENDIRRVWRDNPDANIALKTDT--FFVIDVDMHGDVDGLtnlRNWEH 83
Cdd:smart00943   1 ALRYAARGWPVIPLPPGGKRPLIcAGWKDATTDPEEIRAWWKKWPGANIGLATGPsgLVVLDIDVKAGLEAL---AALAE 77

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1524746639   84 ARLIPKTLQAITPSGGRHIYLKKDPNHPISQNIGMI-EGVDIKAHvNNYILVPPSNNSKGY-YEWDTVHSPKDGSITE 159
Cdd:smart00943  78 LGLLPATPTVRTPSGGRHLYFRVPDGPKLPPNPGFLkPGLDIRGD-GGYVVAPPSVHDTGRpYRWVRDPTPASPPIPP 154
Prim-Pol pfam09250
Bifunctional DNA primase/polymerase, N-terminal; Members of this family adopt a structure ...
 7-161 1.93e-27

Bifunctional DNA primase/polymerase, N-terminal; Members of this family adopt a structure consisting of a core of antiparallel beta sheets. They are found in various bacterial hypothetical proteins, and have been shown to harbour both primase and polymerase activities.


Pssm-ID: 430484  Cd Length: 158  Bit Score: 103.62  E-value: 1.93e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1524746639   7 AINYQRMGYSVIPISKNGKTPLISFADKPPMTEND-IRRVWRDNPDANIALKTDT--FFVIDVDMHGD-VDGLTNLRNwE 82
Cdd:pfam09250   1 ALAYAERGWPVFPLPPGGKHPLGPGWQKRATTDPEqIRAWWSRHPNANIGLATGPsgLVVLDVDGPEAgADALARLER-E 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1524746639  83 HARLIPKTLQAITPS--GGRHIYLKKDPNHPISQNIGMI-EGVDIKAHvNNYILVPPSNNSKGYYEWdtVHSPKDgsITE 159
Cdd:pfam09250  80 GGELLPVTVTVTTGStgGGRHLYFRAPGGLALRNTAGKLaGGLDLRGD-GGYVVAPPSVHTGGAYRW--LNGPRP--PAE 154


                  ..
gi 1524746639 160 AP 161
Cdd:pfam09250 155 LP 156
PriCT_1 smart00942
Primase C terminal 1 (PriCT-1); This alpha helical domain is found at the C terminal of ...
 202-264 5.86e-15

Primase C terminal 1 (PriCT-1); This alpha helical domain is found at the C terminal of primases.


Pssm-ID: 214926  Cd Length: 66  Bit Score: 67.74  E-value: 5.86e-15
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1524746639  202 LGFGDKGGRNNALAEFVGGLLLRG-VDPEITYHLAKMANN-NTQEPLGNKEFERTFKSMLDKEIR 264
Cdd:smart00942   2 LGGVDEGNRNNTLFRLAGRLLRRGyVDEEEAYALLLAANSaNCNPPLPERELEKTAESAYRRESR 66
PriCT_1 pfam08708
Primase C terminal 1 (PriCT-1); This alpha helical domain is found at the C terminal of ...
 201-264 3.93e-11

Primase C terminal 1 (PriCT-1); This alpha helical domain is found at the C terminal of primases.


Pssm-ID: 430166  Cd Length: 64  Bit Score: 57.31  E-value: 3.93e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1524746639 201 LLGFGDKGGRNNALAEFVGGLLLRGVDPEITYHLAKMANNNTQEPLGNKEFERTFKSMLDKEIR 264
Cdd:pfam08708   1 TLGPVASGGRNNALFRLAGALARRGIDRESVLALLHALNSNLEPPLDESEVEKTVKSVYRYVYA 64
AE_Prim_S_like cd00525
AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and ...
 15-137 2.54e-10

AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In eukaryotes, this small catalytically active primase subunit (p50) and a larger primase subunit (p60), referred to jointly as the core primase, associate with the B subunit and the DNA polymerase alpha subunit in a complex, called Pol alpha-pri. In addition to its catalytic role in replication, eukaryotic DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. Pfu41 and Pfu46 comprise the primase complex of the archaea Pyrococcus furiosus; these proteins have sequence identity to the eukaryotic p50 and p60 primase proteins respectively. Pfu41 preferentially uses dNTPs as substrate. Pfu46 regulates the primase activity of Pfu41. Also found in this group is the primase-polymerase (primpol) domain of replicases from archaeal plasmids including the ORF904 protein of pRN1 from Sulfolobus islandicus (pRN1 primpol). The pRN1 primpol domain exhibits DNA polymerase and primase activities; a cluster of active site residues (three acidic residues, and a histidine) is required for both these activities. The pRN1 primpol primase activity prefers dNTPs to rNTPs; however incorporation of dNTPs requires rNTP as cofactor. This group also includes the Pol domain of bacterial LigD proteins such Mycobacterium tuberculosis (Mt)LigD. MtLigD contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. LigD Pol plays a role in non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB) in vivo, perhaps by filling in short 5'-overhangs with ribonucleotides; the filled in termini would be sealed by the associated LigD ligase domain. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro.


Pssm-ID: 238291 [Multi-domain]  Cd Length: 136  Bit Score: 56.99  E-value: 2.54e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1524746639  15 YSVIPISKNGKTPLISFADKPPM-TENDIRRVWRDNPDANIALKTDT--------FFVIDVDMHgDVDGLTNLRNWEH-- 83
Cdd:cd00525     1 RPVSPIRPPGKGPFQRHWPFGATtDDAEILAWLANLPPGNIGLSLGRydklwkpdLLVFDLDPD-DYDCWEDVKEAALll 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1524746639  84 ----ARLIPKTLQAITPSGGRHIYLKKdpnhpisqnigmiegVDIKAH-VNNYILVPPS 137
Cdd:cd00525    80 rellDEDGLNTLVVTSGSRGLHVYVRL---------------IDIRVNaRGRLLVAPPS 123
 
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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