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Conserved domains on  [gi|857274647|gb|AKO59857|]
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putative bifunctional DNA primase/polymerase [Brucella phage 1066_19]

Protein Classification

Prim_Pol and PriCT_2 domain-containing protein( domain architecture ID 10141356)

protein containing domains Prim_Pol, PriCT_2, and DUF3987

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PriCT_2 pfam08707
Primase C terminal 2 (PriCT-2); This alpha helical domain is found at the C terminal of ...
 207-278 6.34e-23

Primase C terminal 2 (PriCT-2); This alpha helical domain is found at the C terminal of primases.


:

Pssm-ID: 430165 [Multi-domain]  Cd Length: 76  Bit Score: 92.79  E-value: 6.34e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 857274647  207 DMLSHI--DCYDEYSDWIKIGMAIHDATHGNG--VALWDEWSRRSSKYNPEAIDARWHSFgKSSNPVTIGTLIKMA 278
Cdd:pfam08707   2 EALSALppDIADDYDEWLRVGMALKNEFGEAGegLDLWDEWSRQSSKYKDGECEKKWRSF-KGGGGITIGTLFHLA 76
Prim_Pol cd04859
Prim_Pol: Primase-polymerase (primpol) domain of the type found in bifunctional replicases ...
 38-181 1.63e-22

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: 94.39  E-value: 1.63e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857274647  38 GKHPVASNWQNTPQWDD-DQIENMSMmvDSMGRGYGVLC--SNLLVIDVDAKNGGLASYAALLEKFPDIASAgLIVETGS 114
Cdd:cd04859   10 SKRPLIKGWPKDAATTDpEQIEAWWR--DGPDANIGLRTgpSGLVVIDIDVKHDGAAALAALAELGKLPPLT-LTVRTGS 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 857274647 115 GGgsKHLYFSLPADVKTVQTHKDYK-GIDFK-HTGFVVGPGSPHKSGRNYNVlsGSVDDIDHAPSALVE 181
Cdd:cd04859   87 GG--RHLYFRVPDGVPVKSVKGKGGpGIDIRgGGGYVVAPPSVHPGGGYYVW--KSTVDPAPAPEWLLD 151
DUF3987 super family cl20483
Protein of unknown function (DUF3987); A family of uncharacterized proteins found by ...
 538-688 3.14e-05

Protein of unknown function (DUF3987); A family of uncharacterized proteins found by clustering human gut metagenomic sequences.


The actual alignment was detected with superfamily member pfam13148:

Pssm-ID: 432994  Cd Length: 365  Bit Score: 46.87  E-value: 3.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857274647  538 PFLSLIGFTTPTQLSRMMVIDNA-ESGFLGRTVMCVEP------DINPYPNPGFTKEDMPYGMKmKILALSGVDSSEEFD 610
Cdd:pfam13148 196 PRLSLLLMIQPSVLRDFLAGPGFrGDGLLARFLFAYPPstagwrDVDPPPIPDEVLEAYHARFR-ELLAEPLAEFLEGEL 274

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857274647  611 RIErrgPLKLvdiEPEAKELIERCINWTvdYNQSKIEMGLEPFSGLYRRVCEKAIKIALIL------GIPDGLITVEHVK 684
Cdd:pfam13148 275 EPT---TLRL---SPEAKELFNEFFNEI--ESRLRPGGDLEDIRDWASKLAGNVARIAGLLhlaredGGWARPISAETMD 346


                  ....
gi 857274647  685 WAMA 688
Cdd:pfam13148 347 AAIA 350
 
Name Accession Description Interval E-value
PriCT_2 pfam08707
Primase C terminal 2 (PriCT-2); This alpha helical domain is found at the C terminal of ...
 207-278 6.34e-23

Primase C terminal 2 (PriCT-2); This alpha helical domain is found at the C terminal of primases.


Pssm-ID: 430165 [Multi-domain]  Cd Length: 76  Bit Score: 92.79  E-value: 6.34e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 857274647  207 DMLSHI--DCYDEYSDWIKIGMAIHDATHGNG--VALWDEWSRRSSKYNPEAIDARWHSFgKSSNPVTIGTLIKMA 278
Cdd:pfam08707   2 EALSALppDIADDYDEWLRVGMALKNEFGEAGegLDLWDEWSRQSSKYKDGECEKKWRSF-KGGGGITIGTLFHLA 76
Prim_Pol cd04859
Prim_Pol: Primase-polymerase (primpol) domain of the type found in bifunctional replicases ...
 38-181 1.63e-22

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: 94.39  E-value: 1.63e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857274647  38 GKHPVASNWQNTPQWDD-DQIENMSMmvDSMGRGYGVLC--SNLLVIDVDAKNGGLASYAALLEKFPDIASAgLIVETGS 114
Cdd:cd04859   10 SKRPLIKGWPKDAATTDpEQIEAWWR--DGPDANIGLRTgpSGLVVIDIDVKHDGAAALAALAELGKLPPLT-LTVRTGS 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 857274647 115 GGgsKHLYFSLPADVKTVQTHKDYK-GIDFK-HTGFVVGPGSPHKSGRNYNVlsGSVDDIDHAPSALVE 181
Cdd:cd04859   87 GG--RHLYFRVPDGVPVKSVKGKGGpGIDIRgGGGYVVAPPSVHPGGGYYVW--KSTVDPAPAPEWLLD 151
Prim-Pol pfam09250
Bifunctional DNA primase/polymerase, N-terminal; Members of this family adopt a structure ...
 38-176 2.94e-21

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: 90.91  E-value: 2.94e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857274647   38 GKHPVASNWQNTPQWDDDQIENMSMmvDSMGRGYGVLC--SNLLVIDVDAKNGGLASYAAL----LEKFPDIasagLIVE 111
Cdd:pfam09250  18 GKHPLGPGWQKRATTDPEQIRAWWS--RHPNANIGLATgpSGLVVLDVDGPEAGADALARLeregGELLPVT----VTVT 91

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 857274647  112 TGSGGGSKHLYFSLPADVKTVQTHKDYK-GIDFK-HTGFVVGPGSPHkSGRNYNVLSGsVDDIDHAP 176
Cdd:pfam09250  92 TGSTGGGRHLYFRAPGGLALRNTAGKLAgGLDLRgDGGYVVAPPSVH-TGGAYRWLNG-PRPPAELP 156
Prim-Pol smart00943
Bifunctional DNA primase/polymerase, N-terminal; Members of this family adopt a structure ...
 38-168 4.63e-18

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: 81.62  E-value: 4.63e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857274647    38 GKHPVASNWQNTPQWDDDQIENMSMMVdsMGRGYGVLC--SNLLVIDVDAKNGGLAsYAALLEKfpDIASAGLIVETGSG 115
Cdd:smart00943  18 GKRPLICAGWKDATTDPEEIRAWWKKW--PGANIGLATgpSGLVVLDIDVKAGLEA-LAALAEL--GLLPATPTVRTPSG 92

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 857274647   116 GgsKHLYFSLPADVKTVQTHKDYK-GIDFK-HTGFVVGPGSPHKSGRNYNVLSGS 168
Cdd:smart00943  93 G--RHLYFRVPDGPKLPPNPGFLKpGLDIRgDGGYVVAPPSVHDTGRPYRWVRDP 145
DUF3987 pfam13148
Protein of unknown function (DUF3987); A family of uncharacterized proteins found by ...
 538-688 3.14e-05

Protein of unknown function (DUF3987); A family of uncharacterized proteins found by clustering human gut metagenomic sequences.


Pssm-ID: 432994  Cd Length: 365  Bit Score: 46.87  E-value: 3.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857274647  538 PFLSLIGFTTPTQLSRMMVIDNA-ESGFLGRTVMCVEP------DINPYPNPGFTKEDMPYGMKmKILALSGVDSSEEFD 610
Cdd:pfam13148 196 PRLSLLLMIQPSVLRDFLAGPGFrGDGLLARFLFAYPPstagwrDVDPPPIPDEVLEAYHARFR-ELLAEPLAEFLEGEL 274

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857274647  611 RIErrgPLKLvdiEPEAKELIERCINWTvdYNQSKIEMGLEPFSGLYRRVCEKAIKIALIL------GIPDGLITVEHVK 684
Cdd:pfam13148 275 EPT---TLRL---SPEAKELFNEFFNEI--ESRLRPGGDLEDIRDWASKLAGNVARIAGLLhlaredGGWARPISAETMD 346


                  ....
gi 857274647  685 WAMA 688
Cdd:pfam13148 347 AAIA 350
 
Name Accession Description Interval E-value
PriCT_2 pfam08707
Primase C terminal 2 (PriCT-2); This alpha helical domain is found at the C terminal of ...
 207-278 6.34e-23

Primase C terminal 2 (PriCT-2); This alpha helical domain is found at the C terminal of primases.


Pssm-ID: 430165 [Multi-domain]  Cd Length: 76  Bit Score: 92.79  E-value: 6.34e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 857274647  207 DMLSHI--DCYDEYSDWIKIGMAIHDATHGNG--VALWDEWSRRSSKYNPEAIDARWHSFgKSSNPVTIGTLIKMA 278
Cdd:pfam08707   2 EALSALppDIADDYDEWLRVGMALKNEFGEAGegLDLWDEWSRQSSKYKDGECEKKWRSF-KGGGGITIGTLFHLA 76
Prim_Pol cd04859
Prim_Pol: Primase-polymerase (primpol) domain of the type found in bifunctional replicases ...
 38-181 1.63e-22

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: 94.39  E-value: 1.63e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857274647  38 GKHPVASNWQNTPQWDD-DQIENMSMmvDSMGRGYGVLC--SNLLVIDVDAKNGGLASYAALLEKFPDIASAgLIVETGS 114
Cdd:cd04859   10 SKRPLIKGWPKDAATTDpEQIEAWWR--DGPDANIGLRTgpSGLVVIDIDVKHDGAAALAALAELGKLPPLT-LTVRTGS 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 857274647 115 GGgsKHLYFSLPADVKTVQTHKDYK-GIDFK-HTGFVVGPGSPHKSGRNYNVlsGSVDDIDHAPSALVE 181
Cdd:cd04859   87 GG--RHLYFRVPDGVPVKSVKGKGGpGIDIRgGGGYVVAPPSVHPGGGYYVW--KSTVDPAPAPEWLLD 151
Prim-Pol pfam09250
Bifunctional DNA primase/polymerase, N-terminal; Members of this family adopt a structure ...
 38-176 2.94e-21

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: 90.91  E-value: 2.94e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857274647   38 GKHPVASNWQNTPQWDDDQIENMSMmvDSMGRGYGVLC--SNLLVIDVDAKNGGLASYAAL----LEKFPDIasagLIVE 111
Cdd:pfam09250  18 GKHPLGPGWQKRATTDPEQIRAWWS--RHPNANIGLATgpSGLVVLDVDGPEAGADALARLeregGELLPVT----VTVT 91

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 857274647  112 TGSGGGSKHLYFSLPADVKTVQTHKDYK-GIDFK-HTGFVVGPGSPHkSGRNYNVLSGsVDDIDHAP 176
Cdd:pfam09250  92 TGSTGGGRHLYFRAPGGLALRNTAGKLAgGLDLRgDGGYVVAPPSVH-TGGAYRWLNG-PRPPAELP 156
Prim-Pol smart00943
Bifunctional DNA primase/polymerase, N-terminal; Members of this family adopt a structure ...
 38-168 4.63e-18

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: 81.62  E-value: 4.63e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857274647    38 GKHPVASNWQNTPQWDDDQIENMSMMVdsMGRGYGVLC--SNLLVIDVDAKNGGLAsYAALLEKfpDIASAGLIVETGSG 115
Cdd:smart00943  18 GKRPLICAGWKDATTDPEEIRAWWKKW--PGANIGLATgpSGLVVLDIDVKAGLEA-LAALAEL--GLLPATPTVRTPSG 92

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 857274647   116 GgsKHLYFSLPADVKTVQTHKDYK-GIDFK-HTGFVVGPGSPHKSGRNYNVLSGS 168
Cdd:smart00943  93 G--RHLYFRVPDGPKLPPNPGFLKpGLDIRgDGGYVVAPPSVHDTGRPYRWVRDP 145
AE_Prim_S_like cd00525
AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and ...
 38-156 9.65e-06

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: 45.82  E-value: 9.65e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857274647  38 GKHPVASNWQNTPQWDDDQIEnmsMMVDSMG-RGYGVLC--------SNLLVIDVDAKNG----GLASYAALLEKFPD-I 103
Cdd:cd00525   10 GKGPFQRHWPFGATTDDAEIL---AWLANLPpGNIGLSLgrydklwkPDLLVFDLDPDDYdcweDVKEAALLLRELLDeD 86

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 857274647 104 ASAGLIVETGSGGgsKHLYFSlpaDVktvqthkDYKGIDFKHTgfVVGPGSPH 156
Cdd:cd00525   87 GLNTLVVTSGSRG--LHVYVR---LI-------DIRVNARGRL--LVAPPSVH 125
DUF3987 pfam13148
Protein of unknown function (DUF3987); A family of uncharacterized proteins found by ...
 538-688 3.14e-05

Protein of unknown function (DUF3987); A family of uncharacterized proteins found by clustering human gut metagenomic sequences.


Pssm-ID: 432994  Cd Length: 365  Bit Score: 46.87  E-value: 3.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857274647  538 PFLSLIGFTTPTQLSRMMVIDNA-ESGFLGRTVMCVEP------DINPYPNPGFTKEDMPYGMKmKILALSGVDSSEEFD 610
Cdd:pfam13148 196 PRLSLLLMIQPSVLRDFLAGPGFrGDGLLARFLFAYPPstagwrDVDPPPIPDEVLEAYHARFR-ELLAEPLAEFLEGEL 274

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 857274647  611 RIErrgPLKLvdiEPEAKELIERCINWTvdYNQSKIEMGLEPFSGLYRRVCEKAIKIALIL------GIPDGLITVEHVK 684
Cdd:pfam13148 275 EPT---TLRL---SPEAKELFNEFFNEI--ESRLRPGGDLEDIRDWASKLAGNVARIAGLLhlaredGGWARPISAETMD 346


                  ....
gi 857274647  685 WAMA 688
Cdd:pfam13148 347 AAIA 350
 
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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