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Conserved domains on  [gi|2210531360|ref|WP_241964786|]
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primase-helicase zinc-binding domain-containing protein [Salmonella enterica]

Protein Classification

TOPRIM and DUF927 domain-containing protein( domain architecture ID 11468652)

TOPRIM (topoisomerase-primase) and DUF927 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
COG4643 COG4643
Uncharacterized domain associated with phage/plasmid primase [Mobilome: prophages, transposons] ...
 3-303 5.58e-97

Uncharacterized domain associated with phage/plasmid primase [Mobilome: prophages, transposons];


:

Pssm-ID: 443681 [Multi-domain]  Cd Length: 435  Bit Score: 294.07  E-value: 5.58e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2210531360   3 TQSVSTISGAAIGRWPYILSALGIKVPSAghHGACPaCGGKDRFRLDDKAGR--GTWFCNQCGH--GDGLDLVRLVTGRK 78
Cdd:COG4643     2 STNVKEVKAAARGRWPDILAALGLDPPAL--HGPCP-CGGKDRFRFDDKRGRksGWYVCNQCGPpaGDGLDLLMKVFGWD 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2210531360  79 IKEAA-GMVSEALAL---------PEIQEKPALPARKKAAGKEAGAERYTRLRQQSC---NGEPVYLTNKGLHGYSLPLL 145
Cdd:COG4643    79 FKEAAlGLDAKGRELtpeeraaarARAAAARAAREAEREARQAAAARRAAALWAEARpatPGDHPYLARKGLAAHGLRFH 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2210531360 146 SQPLnlagitFSSGSLLLPLTDISGNITGGQLINPDGDKSLLPGSQLSGAFIALTDiPAETPEQVIITEGFATALTVSLL 225
Cdd:COG4643   159 PALL------LPGGALLVPLTDADGELVTLQRIYLDGEKRFLKGGRKKGAFIRIGP-LPPPGGTLLIAEGYATALSVHEA 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2210531360 226 TEGWIVAAVAATNLLKVTEQIRKRWPETRIILAGDNDLAdGKENTGRIQAEKAAKAVDGWVTLPP--VRHKADWDDYRQE 303
Cdd:COG4643   232 TGLPVVAALDAGNLLPVAQALRERYPVAELIIAADNDRN-TDGNPGQAAAEEAARAVGGLVALPPfpPKKGTDFNDLHQA 310
 
Name Accession Description Interval E-value
COG4643 COG4643
Uncharacterized domain associated with phage/plasmid primase [Mobilome: prophages, transposons] ...
 3-303 5.58e-97

Uncharacterized domain associated with phage/plasmid primase [Mobilome: prophages, transposons];


Pssm-ID: 443681 [Multi-domain]  Cd Length: 435  Bit Score: 294.07  E-value: 5.58e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2210531360   3 TQSVSTISGAAIGRWPYILSALGIKVPSAghHGACPaCGGKDRFRLDDKAGR--GTWFCNQCGH--GDGLDLVRLVTGRK 78
Cdd:COG4643     2 STNVKEVKAAARGRWPDILAALGLDPPAL--HGPCP-CGGKDRFRFDDKRGRksGWYVCNQCGPpaGDGLDLLMKVFGWD 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2210531360  79 IKEAA-GMVSEALAL---------PEIQEKPALPARKKAAGKEAGAERYTRLRQQSC---NGEPVYLTNKGLHGYSLPLL 145
Cdd:COG4643    79 FKEAAlGLDAKGRELtpeeraaarARAAAARAAREAEREARQAAAARRAAALWAEARpatPGDHPYLARKGLAAHGLRFH 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2210531360 146 SQPLnlagitFSSGSLLLPLTDISGNITGGQLINPDGDKSLLPGSQLSGAFIALTDiPAETPEQVIITEGFATALTVSLL 225
Cdd:COG4643   159 PALL------LPGGALLVPLTDADGELVTLQRIYLDGEKRFLKGGRKKGAFIRIGP-LPPPGGTLLIAEGYATALSVHEA 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2210531360 226 TEGWIVAAVAATNLLKVTEQIRKRWPETRIILAGDNDLAdGKENTGRIQAEKAAKAVDGWVTLPP--VRHKADWDDYRQE 303
Cdd:COG4643   232 TGLPVVAALDAGNLLPVAQALRERYPVAELIIAADNDRN-TDGNPGQAAAEEAARAVGGLVALPPfpPKKGTDFNDLHQA 310
Prim_Zn_Ribbon smart00778
Zinc-binding domain of primase-helicase; This region represents the zinc binding domain. It is ...
 32-68 3.49e-19

Zinc-binding domain of primase-helicase; This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.


Pssm-ID: 129016 [Multi-domain]  Cd Length: 37  Bit Score: 79.30  E-value: 3.49e-19
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 2210531360   32 GHHGACPACGGKDRFRLDDKAGRGTWFCNQCGHGDGL 68
Cdd:smart00778   1 GRHGPCPNCGGSDRFRFDDKDGRGTWFCSVCGAGDGI 37
Prim_Zn_Ribbon pfam08273
Zinc-binding domain of primase-helicase;
32-68 9.71e-19

Zinc-binding domain of primase-helicase;


Pssm-ID: 400529  Cd Length: 37  Bit Score: 78.18  E-value: 9.71e-19
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2210531360  32 GHHGACPACGGKDRFRLDDKAGRGTWFCNQCGHGDGL 68
Cdd:pfam08273   1 GYHGPCPVCGGRDRFRFDDKDGRGTWFCRVCGAGDGL 37
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 208-290 8.88e-09

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: 51.89  E-value: 8.88e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2210531360 208 EQVIITEGFATALTVSLLTegwIVAAVAA--TNLLKvtEQIRKRWPETR-IILAGDNDLAdGKEntGRIQAEKAAKAVDG 284
Cdd:cd01029     1 DEVIIVEGYMDVLALHQAG---IKNVVAAlgTANTE--EQLRLLKRFARtVILAFDNDEA-GKK--AAARALELLLALGG 72


                  ....*.
gi 2210531360 285 WVTLPP 290
Cdd:cd01029    73 RVRVPP 78
 
Name Accession Description Interval E-value
COG4643 COG4643
Uncharacterized domain associated with phage/plasmid primase [Mobilome: prophages, transposons] ...
 3-303 5.58e-97

Uncharacterized domain associated with phage/plasmid primase [Mobilome: prophages, transposons];


Pssm-ID: 443681 [Multi-domain]  Cd Length: 435  Bit Score: 294.07  E-value: 5.58e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2210531360   3 TQSVSTISGAAIGRWPYILSALGIKVPSAghHGACPaCGGKDRFRLDDKAGR--GTWFCNQCGH--GDGLDLVRLVTGRK 78
Cdd:COG4643     2 STNVKEVKAAARGRWPDILAALGLDPPAL--HGPCP-CGGKDRFRFDDKRGRksGWYVCNQCGPpaGDGLDLLMKVFGWD 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2210531360  79 IKEAA-GMVSEALAL---------PEIQEKPALPARKKAAGKEAGAERYTRLRQQSC---NGEPVYLTNKGLHGYSLPLL 145
Cdd:COG4643    79 FKEAAlGLDAKGRELtpeeraaarARAAAARAAREAEREARQAAAARRAAALWAEARpatPGDHPYLARKGLAAHGLRFH 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2210531360 146 SQPLnlagitFSSGSLLLPLTDISGNITGGQLINPDGDKSLLPGSQLSGAFIALTDiPAETPEQVIITEGFATALTVSLL 225
Cdd:COG4643   159 PALL------LPGGALLVPLTDADGELVTLQRIYLDGEKRFLKGGRKKGAFIRIGP-LPPPGGTLLIAEGYATALSVHEA 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2210531360 226 TEGWIVAAVAATNLLKVTEQIRKRWPETRIILAGDNDLAdGKENTGRIQAEKAAKAVDGWVTLPP--VRHKADWDDYRQE 303
Cdd:COG4643   232 TGLPVVAALDAGNLLPVAQALRERYPVAELIIAADNDRN-TDGNPGQAAAEEAARAVGGLVALPPfpPKKGTDFNDLHQA 310
Prim_Zn_Ribbon smart00778
Zinc-binding domain of primase-helicase; This region represents the zinc binding domain. It is ...
 32-68 3.49e-19

Zinc-binding domain of primase-helicase; This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.


Pssm-ID: 129016 [Multi-domain]  Cd Length: 37  Bit Score: 79.30  E-value: 3.49e-19
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 2210531360   32 GHHGACPACGGKDRFRLDDKAGRGTWFCNQCGHGDGL 68
Cdd:smart00778   1 GRHGPCPNCGGSDRFRFDDKDGRGTWFCSVCGAGDGI 37
Prim_Zn_Ribbon pfam08273
Zinc-binding domain of primase-helicase;
32-68 9.71e-19

Zinc-binding domain of primase-helicase;


Pssm-ID: 400529  Cd Length: 37  Bit Score: 78.18  E-value: 9.71e-19
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2210531360  32 GHHGACPACGGKDRFRLDDKAGRGTWFCNQCGHGDGL 68
Cdd:pfam08273   1 GYHGPCPVCGGRDRFRFDDKDGRGTWFCRVCGAGDGL 37
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 208-290 8.88e-09

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: 51.89  E-value: 8.88e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2210531360 208 EQVIITEGFATALTVSLLTegwIVAAVAA--TNLLKvtEQIRKRWPETR-IILAGDNDLAdGKEntGRIQAEKAAKAVDG 284
Cdd:cd01029     1 DEVIIVEGYMDVLALHQAG---IKNVVAAlgTANTE--EQLRLLKRFARtVILAFDNDEA-GKK--AAARALELLLALGG 72


                  ....*.
gi 2210531360 285 WVTLPP 290
Cdd:cd01029    73 RVRVPP 78
Toprim_3 pfam13362
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ...
 210-303 2.80e-08

Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic acid manipulation.


Pssm-ID: 433146 [Multi-domain]  Cd Length: 97  Bit Score: 50.86  E-value: 2.80e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2210531360 210 VIITEGFATALTVS---LLTEGWIVAAVAATNLLKVTeqirkrWPE--TRIILAGDNDladgKENTGRIQAEKAAKAV-- 282
Cdd:pfam13362   2 LIIGEGIETALSLTqrlNPPGTPVIALLSAANLKAVA------WPErvKRVYIAADND----AANDGQAAAEKLAERLea 71

                          90       100
                  ....*....|....*....|...
gi 2210531360 283 DGW--VTLPPvRHKADWDDYRQE 303
Cdd:pfam13362  72 AGIeaVLLEP-EAGEDWNDDLQQ 93
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
208-264 3.49e-04

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 38.78  E-value: 3.49e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2210531360  208 EQVIITEGFATALTV--SLLTEGWIVAAVAATNLLKVTEQIRKRWPETRIILAGDNDLA 264
Cdd:smart00493   1 KVLIIVEGPADAIALekAGGKRGNVVALGGHLLSKEQIKLLKKLAKKAEVILATDPDRE 59
zf-RRN7 pfam11781
Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7; This is the zinc-finger at the start of ...
 32-64 5.68e-04

Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7; This is the zinc-finger at the start of transcription-binding factor that associates strongly with both Rrn6 and Rrn7 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter.


Pssm-ID: 463348  Cd Length: 32  Bit Score: 36.80  E-value: 5.68e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2210531360  32 GHHGACPACGGkDRFRLDDkagrGTWFCNQCGH 64
Cdd:pfam11781   2 EKGPPCGVCGC-RLFYLDD----GFYYCRRCHT 29
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 209-289 1.90e-03

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: 36.64  E-value: 1.90e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2210531360 209 QVIITEGFATALTVS-LLTEGWIVAAVAATNLLKVTEQIRKRWPET-RIILAGDNDLAdGKENTGRIqaEKAAKAVDGWV 286
Cdd:cd00188     2 KLIIVEGPSDALALAqAGGYGGAVVALGGHALNKTRELLKRLLGEAkEVIIATDADRE-GEAIALRL--LELLKSLGKKV 78


                  ...
gi 2210531360 287 TLP 289
Cdd:cd00188    79 RRL 81
Zn_Tnp_IS1595 pfam12760
Transposase zinc-ribbon domain; This zinc binding domain is found in a range of transposase ...
 32-64 3.77e-03

Transposase zinc-ribbon domain; This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It is likely a zinc-binding beta ribbon domain that could bind the DNA.


Pssm-ID: 432764  Cd Length: 46  Bit Score: 34.96  E-value: 3.77e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2210531360  32 GHHGACPACGGKDRFRLddkAGRGTWFCNQCGH 64
Cdd:pfam12760  16 PNGFVCPHCGSRRAYRI---STRGLFQCKACRH 45
 
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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