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Conserved domains on  [gi|1842033247|ref|YP_009820166|]
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DNA primase/helicase [Escherichia phage NC-A]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RecA-like_Gp4D_helicase cd19483
RecA-like domain of Escherichia coli bacteriophage T7 Gp4D helicase; This family includes the ...
 245-474 2.73e-95

RecA-like domain of Escherichia coli bacteriophage T7 Gp4D helicase; This family includes the RecA-like domain of the Gp4D fragment of the Gene4 helicase-primase (Gp4) from bacteriophage T7. Gp4D (residues 241-566) is the minimal fragment of the Gp4 that forms hexameric rings, it contains the helicase domain and the linker connecting the helicase and primase domains. Helicases are ring-shaped oligomeric enzymes that unwind DNA at the replication fork; they couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands. This family belongs to the RecA-like NTPase superfamily which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


:

Pssm-ID: 410891 [Multi-domain]  Cd Length: 231  Bit Score: 288.31  E-value: 2.73e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 245 IMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEESVEETAEDLIGLHNRVRlrQSDSLKREIIENGKFDQWFDELFG 324
Cdd:cd19483     1 VTIGAGSGIGKSTIVRELAYHLITEHGEKVGIISLEESVEETAKGLAGKHLGKP--EPLELPRDDITEEEEDDAFDNELG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 325 NDSFHLYDSFAEAETDRLLAKLAYMRSGLGCDVIILDHISIVVSASGESDERKMIDNLMTKLKGFAKSTGVVLVVICHLK 404
Cdd:cd19483    79 SGRFFLYDHFGSLDWDNLKEKIRYMVKVLGCKVIVLDHLTILVSGLDSSDERKELDEIMTELAALVKELGVTIILVSHLR 158

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1842033247 405 NPEKGRAHEEGRPVSITDLRGSGALRQLSDTIIALERNQQGDNP---NLVLVRILKCRFTGDTGVAGFMEYNK 474
Cdd:cd19483   159 RPGGGKGHEEGGEVSESDLRGSSAIAQLSDYVIGLERNKQADDPverNTTRVRVLKNRFTGETGIAGTLYYDE 231
Toprim_2 super family cl48160
Toprim-like; This is a family or Toprim-like proteins.
 91-177 1.16e-11

Toprim-like; This is a family or Toprim-like proteins.


The actual alignment was detected with superfamily member pfam13155:

Pssm-ID: 463793 [Multi-domain]  Cd Length: 88  Bit Score: 60.65  E-value: 1.16e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247  91 VVTEGEIDMLTVMEL-QDCKYPVVSLGHGASAAKKtcaanyEYFDQF-EQIILMFDMDEAGRKAVEEAAQVLPAGKVRVA 168
Cdd:pfam13155   1 VVFEGYIDALSLAQAgIKNVLYVATLGTALTEAQI------KLLKRYpKEVILAFDNDEAGRKAAKRLAELLKEAGVDVK 74

                          90
                  ....*....|..
gi 1842033247 169 VL---PCKDANE 177
Cdd:pfam13155  75 IRllpDGKDWNE 86
 
Name Accession Description Interval E-value
RecA-like_Gp4D_helicase cd19483
RecA-like domain of Escherichia coli bacteriophage T7 Gp4D helicase; This family includes the ...
 245-474 2.73e-95

RecA-like domain of Escherichia coli bacteriophage T7 Gp4D helicase; This family includes the RecA-like domain of the Gp4D fragment of the Gene4 helicase-primase (Gp4) from bacteriophage T7. Gp4D (residues 241-566) is the minimal fragment of the Gp4 that forms hexameric rings, it contains the helicase domain and the linker connecting the helicase and primase domains. Helicases are ring-shaped oligomeric enzymes that unwind DNA at the replication fork; they couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands. This family belongs to the RecA-like NTPase superfamily which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410891 [Multi-domain]  Cd Length: 231  Bit Score: 288.31  E-value: 2.73e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 245 IMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEESVEETAEDLIGLHNRVRlrQSDSLKREIIENGKFDQWFDELFG 324
Cdd:cd19483     1 VTIGAGSGIGKSTIVRELAYHLITEHGEKVGIISLEESVEETAKGLAGKHLGKP--EPLELPRDDITEEEEDDAFDNELG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 325 NDSFHLYDSFAEAETDRLLAKLAYMRSGLGCDVIILDHISIVVSASGESDERKMIDNLMTKLKGFAKSTGVVLVVICHLK 404
Cdd:cd19483    79 SGRFFLYDHFGSLDWDNLKEKIRYMVKVLGCKVIVLDHLTILVSGLDSSDERKELDEIMTELAALVKELGVTIILVSHLR 158

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1842033247 405 NPEKGRAHEEGRPVSITDLRGSGALRQLSDTIIALERNQQGDNP---NLVLVRILKCRFTGDTGVAGFMEYNK 474
Cdd:cd19483   159 RPGGGKGHEEGGEVSESDLRGSSAIAQLSDYVIGLERNKQADDPverNTTRVRVLKNRFTGETGIAGTLYYDE 231
Toprim_2 pfam13155
Toprim-like; This is a family or Toprim-like proteins.
 91-177 1.16e-11

Toprim-like; This is a family or Toprim-like proteins.


Pssm-ID: 463793 [Multi-domain]  Cd Length: 88  Bit Score: 60.65  E-value: 1.16e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247  91 VVTEGEIDMLTVMEL-QDCKYPVVSLGHGASAAKKtcaanyEYFDQF-EQIILMFDMDEAGRKAVEEAAQVLPAGKVRVA 168
Cdd:pfam13155   1 VVFEGYIDALSLAQAgIKNVLYVATLGTALTEAQI------KLLKRYpKEVILAFDNDEAGRKAAKRLAELLKEAGVDVK 74

                          90
                  ....*....|..
gi 1842033247 169 VL---PCKDANE 177
Cdd:pfam13155  75 IRllpDGKDWNE 86
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
88-162 1.88e-11

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 59.58  E-value: 1.88e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1842033247   88 KKIVVTEGEIDMLTVMELQDCKYPVVSLGhGASAAKKTCAANYEYFDQFEqIILMFDMDEAGRKAVEEAAQVLPA 162
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALG-GHLLSKEQIKLLKKLAKKAE-VILATDPDREGEAIAWELAELLKP 73
PRK08840 PRK08840
replicative DNA helicase; Provisional
 193-443 2.26e-10

replicative DNA helicase; Provisional


Pssm-ID: 181562 [Multi-domain]  Cd Length: 464  Bit Score: 62.70  E-value: 2.26e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 193 NAGPWIPDGVVSalSLRERIR-EHLSSEESVGLLFSGCTGINDKTLGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMG 271
Cdd:PRK08840  169 NEGPQNVDSILE--KTLERIElLYKTPQDGVTGVDTGFTDLNKKTAGLQGSDLIIVAARPSMGKTTFAMNLCENAAMDQD 246

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 272 KKVGLAMLEESVEETAEDLIGLHNRVrlrqsDSLKreiIENGKFDqwfDE-----------LFGNDSFHLYDSFAEAETD 340
Cdd:PRK08840  247 KPVLIFSLEMPAEQLMMRMLASLSRV-----DQTK---IRTGQLD---DEdwarisstmgiLMEKKNMYIDDSSGLTPTE 315

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 341 -RLLAKLAYMRSGlGCDVIILDHISIvVSASGESDERKM-IDNLMTKLKGFAKSTGVVLVVICHLKNPEKGRAheEGRPV 418
Cdd:PRK08840  316 vRSRARRIAREHG-GLSMIMVDYLQL-MRVPALSDNRTLeIAEISRSLKALAKELNVPVVALSQLNRSLEQRA--DKRPV 391

                         250       260
                  ....*....|....*....|....*
gi 1842033247 419 SiTDLRGSGALRQLSDTIIALERNQ 443
Cdd:PRK08840  392 N-SDLRESGSIEQDADLIMFIYRDE 415
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
230-459 4.28e-10

RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 59.54  E-value: 4.28e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 230 TGIN--DKTL--GARGGEVIMVTSGSGMGKSTFVrQQALQWGTAMGKKVGLAMLEESVEetaedliglhnrvrlrqsdSL 305
Cdd:COG0467     4 TGIPglDELLggGLPRGSSTLLSGPPGTGKTTLA-LQFLAEGLRRGEKGLYVSFEESPE-------------------QL 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 306 KREIIENGkFDqwFDELFGNDSFHLYDSFAEAET---DRLLAKLAYMRSGLGCDVIILDHISIVVSAsgeSDERKMIDNL 382
Cdd:COG0467    64 LRRAESLG-LD--LEEYIESGLLRIIDLSPEELGldlEELLARLREAVEEFGAKRVVIDSLSGLLLA---LPDPERLREF 137

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1842033247 383 MTKLKGFAKSTGVVLVVIChlknpEKGRAHEEgrpvsitdlRGSGALRQLSDTIIALERNQQGDNPNLVLvRILKCR 459
Cdd:COG0467   138 LHRLLRYLKKRGVTTLLTS-----ETGGLEDE---------ATEGGLSYLADGVILLRYVELGGELRRAL-SVLKMR 199
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 88-171 4.55e-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: 53.04  E-value: 4.55e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247  88 KKIVVTEGEIDMLTVMELqDCKYPVVSLGhgasaakktcAANYEY-----FDQFEQIILMFDMDEAGRKAVEEAAQVLPA 162
Cdd:cd01029     1 DEVIIVEGYMDVLALHQA-GIKNVVAALG----------TANTEEqlrllKRFARTVILAFDNDEAGKKAAARALELLLA 69


                  ....*....
gi 1842033247 163 GKVRVAVLP 171
Cdd:cd01029    70 LGGRVRVPP 78
DnaG COG0358
DNA primase (bacterial type) [Replication, recombination and repair];
15-184 1.56e-05

DNA primase (bacterial type) [Replication, recombination and repair];


Pssm-ID: 440127 [Multi-domain]  Cd Length: 465  Bit Score: 47.44  E-value: 1.56e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247  15 YSALTARGISKETCQKAGYWIAKVDGVMYqvaDY---------RDQNGNIV--SQKVRDKDK----N------FkttgsH 73
Cdd:COG0358   167 LKHLKKKGFSEEELVEAGLVIEREDGGYY---DRfrgrimfpiRDLRGRVIgfGGRVLDDGEpkylNspetplF-----H 238

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247  74 KSDALFGKHL----WNGGKKIVVTEGEIDmltVMELQ--DCKYPVVSLG------HgASAAKKTCaanyeyfdqfEQIIL 141
Cdd:COG0358   239 KGRVLYGLDLarkaIRKEDRVIVVEGYMD---VIALHqaGIKNAVATLGtalteeH-IKLLKRYT----------DEVIL 304

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1842033247 142 MFDMDEAGRKAVEEAAQVL--PAGKVRVAVLPckdanechlNGHD 184
Cdd:COG0358   305 CFDGDAAGQKAALRALELLlkDGLQVRVLFLP---------DGED 340
AAA_25 pfam13481
AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.
 242-403 3.34e-03

AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.


Pssm-ID: 463892 [Multi-domain]  Cd Length: 193  Bit Score: 38.90  E-value: 3.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 242 GEVIMVTSGSGMGKSTFVrqqaLQWGTAMGKKVGLAMLEESVEE------TAED-LIGLHNRVR--LRQSDSLKREIIEN 312
Cdd:pfam13481  33 GGLGLLAGAPGTGKTTLA----LDLAAAVATGKPWLGGPRVPEQgkvlyvSAEGpADELRRRLRaaGADLDLPARLLFLS 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 313 GKFDQwfdELFGNDSFHlydSFAEAETDRLLAKLAYMRsglGCDVIILDHISIVVSAS--GESDERKMIDnlmtKLKGFA 390
Cdd:pfam13481 109 LVESL---PLFFLDRGG---PLLDADVDALEAALEEVE---DPDLVVIDPLARALGGDenSNSDVGRLVK----ALDRLA 175

                         170
                  ....*....|...
gi 1842033247 391 KSTGVVLVVICHL 403
Cdd:pfam13481 176 RRTGATVLLVHHV 188
 
Name Accession Description Interval E-value
RecA-like_Gp4D_helicase cd19483
RecA-like domain of Escherichia coli bacteriophage T7 Gp4D helicase; This family includes the ...
 245-474 2.73e-95

RecA-like domain of Escherichia coli bacteriophage T7 Gp4D helicase; This family includes the RecA-like domain of the Gp4D fragment of the Gene4 helicase-primase (Gp4) from bacteriophage T7. Gp4D (residues 241-566) is the minimal fragment of the Gp4 that forms hexameric rings, it contains the helicase domain and the linker connecting the helicase and primase domains. Helicases are ring-shaped oligomeric enzymes that unwind DNA at the replication fork; they couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands. This family belongs to the RecA-like NTPase superfamily which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410891 [Multi-domain]  Cd Length: 231  Bit Score: 288.31  E-value: 2.73e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 245 IMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEESVEETAEDLIGLHNRVRlrQSDSLKREIIENGKFDQWFDELFG 324
Cdd:cd19483     1 VTIGAGSGIGKSTIVRELAYHLITEHGEKVGIISLEESVEETAKGLAGKHLGKP--EPLELPRDDITEEEEDDAFDNELG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 325 NDSFHLYDSFAEAETDRLLAKLAYMRSGLGCDVIILDHISIVVSASGESDERKMIDNLMTKLKGFAKSTGVVLVVICHLK 404
Cdd:cd19483    79 SGRFFLYDHFGSLDWDNLKEKIRYMVKVLGCKVIVLDHLTILVSGLDSSDERKELDEIMTELAALVKELGVTIILVSHLR 158

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1842033247 405 NPEKGRAHEEGRPVSITDLRGSGALRQLSDTIIALERNQQGDNP---NLVLVRILKCRFTGDTGVAGFMEYNK 474
Cdd:cd19483   159 RPGGGKGHEEGGEVSESDLRGSSAIAQLSDYVIGLERNKQADDPverNTTRVRVLKNRFTGETGIAGTLYYDE 231
DnaB_C cd00984
C-terminal domain of DnaB helicase; DnaB helicase C-terminal domain. The hexameric helicase ...
 225-480 4.91e-16

C-terminal domain of DnaB helicase; DnaB helicase C-terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.


Pssm-ID: 410864 [Multi-domain]  Cd Length: 256  Bit Score: 77.94  E-value: 4.91e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 225 LFSGCTGINDKTLGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEESVEETAEDLIGLHNRVrlrqsdS 304
Cdd:cd00984     2 LPTGFTDLDKLTGGLQPGDLIIIAARPSMGKTAFALNIAENIALDEGLPVLFFSLEMSAEQLAERLLSSESGV------S 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 305 LKReiIENGK--FDQW------FDELfGNDSFHLYDSFA------EAETDRLLaklaymRSGLGCDVIILDHISIVvSAS 370
Cdd:cd00984    76 LSK--LRTGRldDEDWerltaaMGEL-SELPLYIDDTPGltvdeiRAKARRLK------REHGGLGLIVIDYLQLI-RGS 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 371 GESDERKM-IDNLMTKLKGFAKSTGVVLVVICHL-KNPEKgraHEEGRPVsITDLRGSGALRQLSDTIIALER----NQQ 444
Cdd:cd00984   146 KRAENRQQeVAEISRSLKALAKELNVPVIALSQLnRGVES---RTDKRPM-LSDLRESGSIEQDADVVIFLYRdeyyDKD 221

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 1842033247 445 GDNPNLVLVRILKCRFtGDTGVAgFMEYNKETGWLE 480
Cdd:cd00984   222 SEDKGIAEIIIAKNRN-GPTGTV-YLAFNPEYTRFT 255
Twinkle_C cd01122
C-terminal domain of Twinkle; Twinkle ( T7 gp4-like protein with intramitochondrial nucleoid ...
 207-477 4.93e-14

C-terminal domain of Twinkle; Twinkle ( T7 gp4-like protein with intramitochondrial nucleoid localization, also known as C10orf2, PEO1, SCA8, ATXN8, IOSCA, PEOA3 or SANDO) is a homohexameric DNA helicases which unwinds short stretches of double-stranded DNA in the 5' to 3' direction and, along with mitochondrial single-stranded DNA binding protein and mtDNA polymerase gamma, is thought to play a key role in mtDNA replication. Mutations in the human gene cause infantile onset spinocerebellar ataxia (IOSCA) and progressive external ophthalmoplegia (PEO) and are also associated with several mitochondrial depletion syndromes. This group also contains viral GP4-like and related bacterial helicases.


Pssm-ID: 410867  Cd Length: 266  Bit Score: 72.27  E-value: 4.93e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 207 SLRERIREHLS-SEESVGLLFSGCTGINDKTLGARGGEVIMVTSGSGMGKSTFVRQQALQ---------WGTAMGKKVGL 276
Cdd:cd01122     7 DLRELVYEELLnSEQVAGVQWKRFPSLNKLLKGHRRGELTIFTGPTGSGKTTFLSEYSLDlcmqgvntlWGSFEIKNVRL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 277 AmleesveetaedliglhnRVRLRQsDSLKREIIENGKFDQWFDElFGNDSFHLYDSFAEAETDRLLAKLAYMRSGLGCD 356
Cdd:cd01122    87 A------------------KTMLTQ-FAGKNLEDNLREFDEWADK-FELLPMYFMKFHGSTDIDEVLDAMEHAVYVYDIQ 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 357 VIILDHISIVVSASGESDERKMI-DNLMTKLKGFAKSTGVVLVVICHLknpekgRAHEEGRPVSITDLRGSGALRQLSDT 435
Cdd:cd01122   147 HIVIDNLQFMMGTQASGSDRFELqDLIIGKFRRFATNNNVHITLVIHP------RKEDDDNELTTSSIFGSAKATQEADN 220

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 1842033247 436 IIALERNQQGDNPNLVLVRILKCRFTGDTGVAGfMEYNKETG 477
Cdd:cd01122   221 VLILQDKRLISGEGKKFLQIKKNRFDGDLGVIP-LEFNKNSL 261
RecA-like_superfamily cd01120
RecA-like_NTPases; RecA-like NTPases. This superfamily includes the NTP binding domain of F1 ...
 245-430 7.98e-12

RecA-like_NTPases; RecA-like NTPases. This superfamily includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410865 [Multi-domain]  Cd Length: 119  Bit Score: 62.14  E-value: 7.98e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 245 IMVTSGSGMGKSTFVRQQALQWgTAMGKKVGLAMLEESVEETAEDLIGLHnrvrlrqsdslkreiiengkfdqwfdelfg 324
Cdd:cd01120     1 ILITGPPGSGKTTLLLQFAEQA-LLSDEPVIFISFLDTILEAIEDLIEEK------------------------------ 49

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 325 ndsfhlydsfaeaetdrllaklaymrsglGCDVIILDHISIVVSASgESDERKMIDNLMTKLKGFAKSTGVVLVVICHLK 404
Cdd:cd01120    50 -----------------------------KLDIIIIDSLSSLARAS-QGDRSSELLEDLAKLLRAARNTGITVIATIHSD 99

                         170       180
                  ....*....|....*....|....*.
gi 1842033247 405 NPekgrahEEGRPVSITDLRGSGALR 430
Cdd:cd01120   100 KF------DIDRGGSSNDERLLKSLR 119
Toprim_2 pfam13155
Toprim-like; This is a family or Toprim-like proteins.
 91-177 1.16e-11

Toprim-like; This is a family or Toprim-like proteins.


Pssm-ID: 463793 [Multi-domain]  Cd Length: 88  Bit Score: 60.65  E-value: 1.16e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247  91 VVTEGEIDMLTVMEL-QDCKYPVVSLGHGASAAKKtcaanyEYFDQF-EQIILMFDMDEAGRKAVEEAAQVLPAGKVRVA 168
Cdd:pfam13155   1 VVFEGYIDALSLAQAgIKNVLYVATLGTALTEAQI------KLLKRYpKEVILAFDNDEAGRKAAKRLAELLKEAGVDVK 74

                          90
                  ....*....|..
gi 1842033247 169 VL---PCKDANE 177
Cdd:pfam13155  75 IRllpDGKDWNE 86
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
88-162 1.88e-11

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 59.58  E-value: 1.88e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1842033247   88 KKIVVTEGEIDMLTVMELQDCKYPVVSLGhGASAAKKTCAANYEYFDQFEqIILMFDMDEAGRKAVEEAAQVLPA 162
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALG-GHLLSKEQIKLLKKLAKKAE-VILATDPDREGEAIAWELAELLKP 73
PRK08840 PRK08840
replicative DNA helicase; Provisional
 193-443 2.26e-10

replicative DNA helicase; Provisional


Pssm-ID: 181562 [Multi-domain]  Cd Length: 464  Bit Score: 62.70  E-value: 2.26e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 193 NAGPWIPDGVVSalSLRERIR-EHLSSEESVGLLFSGCTGINDKTLGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMG 271
Cdd:PRK08840  169 NEGPQNVDSILE--KTLERIElLYKTPQDGVTGVDTGFTDLNKKTAGLQGSDLIIVAARPSMGKTTFAMNLCENAAMDQD 246

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 272 KKVGLAMLEESVEETAEDLIGLHNRVrlrqsDSLKreiIENGKFDqwfDE-----------LFGNDSFHLYDSFAEAETD 340
Cdd:PRK08840  247 KPVLIFSLEMPAEQLMMRMLASLSRV-----DQTK---IRTGQLD---DEdwarisstmgiLMEKKNMYIDDSSGLTPTE 315

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 341 -RLLAKLAYMRSGlGCDVIILDHISIvVSASGESDERKM-IDNLMTKLKGFAKSTGVVLVVICHLKNPEKGRAheEGRPV 418
Cdd:PRK08840  316 vRSRARRIAREHG-GLSMIMVDYLQL-MRVPALSDNRTLeIAEISRSLKALAKELNVPVVALSQLNRSLEQRA--DKRPV 391

                         250       260
                  ....*....|....*....|....*
gi 1842033247 419 SiTDLRGSGALRQLSDTIIALERNQ 443
Cdd:PRK08840  392 N-SDLRESGSIEQDADLIMFIYRDE 415
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
230-459 4.28e-10

RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 59.54  E-value: 4.28e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 230 TGIN--DKTL--GARGGEVIMVTSGSGMGKSTFVrQQALQWGTAMGKKVGLAMLEESVEetaedliglhnrvrlrqsdSL 305
Cdd:COG0467     4 TGIPglDELLggGLPRGSSTLLSGPPGTGKTTLA-LQFLAEGLRRGEKGLYVSFEESPE-------------------QL 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 306 KREIIENGkFDqwFDELFGNDSFHLYDSFAEAET---DRLLAKLAYMRSGLGCDVIILDHISIVVSAsgeSDERKMIDNL 382
Cdd:COG0467    64 LRRAESLG-LD--LEEYIESGLLRIIDLSPEELGldlEELLARLREAVEEFGAKRVVIDSLSGLLLA---LPDPERLREF 137

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1842033247 383 MTKLKGFAKSTGVVLVVIChlknpEKGRAHEEgrpvsitdlRGSGALRQLSDTIIALERNQQGDNPNLVLvRILKCR 459
Cdd:COG0467   138 LHRLLRYLKKRGVTTLLTS-----ETGGLEDE---------ATEGGLSYLADGVILLRYVELGGELRRAL-SVLKMR 199
KaiC-like cd01124
Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. ...
 230-470 1.92e-09

Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. KaiC, an autokinase, autophosphatase, and ATPase, is part of the core oscillator, composed of three proteins: KaiA, KaiB, and KaiC. The circadian oscillation is regulated via KaiC phosphorylation.


Pssm-ID: 410869 [Multi-domain]  Cd Length: 222  Bit Score: 57.66  E-value: 1.92e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 230 TGIN--DKTLGarGG----EVIMVTSGSGMGKSTFVrQQALQWGTAMGKKVGLAmleeSVEETAEDLIglhnrvrlRQSD 303
Cdd:cd01124     3 TGIPglDELLG--GGipkgSVTLLTGGPGTGKTLFG-LQFLYAGAKNGEPGLFF----TFEESPERLL--------RNAK 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 304 SL---KREIIENGKFDQwfdelfgndSFHLYDSFAEAETDRLLAKLAYMRSGLGCDVIILDHISIVVSAsgeSDERKMID 380
Cdd:cd01124    68 SFgwdFDEMEDEGKLII---------VDAPPTEAGRFSLDELLSRILSIIKSFKAKRVVIDSLSGLRRA---KEDQMRAR 135

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 381 NLMTKLKGFAKSTGVVLVVIchlknpekgrahEEGRPVSITDLRGSGALRQLSDTIIALeRNQQGDNPNLVLVRILKCRF 460
Cdd:cd01124   136 RIVIALLNELRAAGVTTIFT------------SEMRSFLSSESAGGGDVSFIVDGVILL-RYVEIEGELRRTIRVLKMRG 202

                         250
                  ....*....|.
gi 1842033247 461 TG-DTGVAGFM 470
Cdd:cd01124   203 TGhDTGTHPFE 213
PRK06904 PRK06904
replicative DNA helicase; Validated
 227-459 2.16e-09

replicative DNA helicase; Validated


Pssm-ID: 136106 [Multi-domain]  Cd Length: 472  Bit Score: 59.62  E-value: 2.16e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 227 SGCTGINDKTLGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEESVEETAEDLIGLHNRV---RLRQSD 303
Cdd:PRK06904  206 TGFTDLDKKTAGLQPSDLIIVAARPSMGKTTFAMNLCENAAMASEKPVLVFSLEMPAEQIMMRMLASLSRVdqtKIRTGQ 285

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 304 SLKReiIENGKFDQWFDELFGNDSFHLYDSFAEAETD-RLLAKLAYMRSGlGCDVIILDHISIvVSASGESDERKM-IDN 381
Cdd:PRK06904  286 NLDQ--QDWAKISSTVGMFKQKPNLYIDDSSGLTPTElRSRARRVYRENG-GLSLIMVDYLQL-MRAPGFEDNRTLeIAE 361

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 382 LMTKLKGFAKSTGVVLVVICHLKNPEKGRAheEGRPVSiTDLRGSGALRQLSDTIIALERNQ-----QGDNPNLVLVRIL 456
Cdd:PRK06904  362 ISRSLKALAKELKVPVVALSQLNRTLENRG--DKRPVN-SDLRESGSIEQDADLIMFIYRDEvynetTEDNKGVAEIIIG 438


                  ...
gi 1842033247 457 KCR 459
Cdd:PRK06904  439 KQR 441
PRK05636 PRK05636
replicative DNA helicase; Provisional
 227-448 3.98e-09

replicative DNA helicase; Provisional


Pssm-ID: 180177 [Multi-domain]  Cd Length: 505  Bit Score: 58.70  E-value: 3.98e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 227 SGCTGINDKTLGARGGEVIMVTSGSGMGKST----FVRQQALQwgtaMGKKVGLAMLEESVEETAEDLIGLHNRVRLRQS 302
Cdd:PRK05636  250 TGFKDLDDLTNGLRGGQMIIVAARPGVGKSTlaldFMRSASIK----HNKASVIFSLEMSKSEIVMRLLSAEAEVRLSDM 325

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 303 DSLKREIIENGKFDQWFDE-----LFGNDSFHLYDSFAEAETDRLLAKlaymrsgLGCDVIILDHISIVVSASGESDERK 377
Cdd:PRK05636  326 RGGKMDEDAWEKLVQRLGKiaqapIFIDDSANLTMMEIRSKARRLKQK-------HDLKLIVVDYLQLMSSGKRVESRQQ 398

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1842033247 378 MIDNLMTKLKGFAKSTGVVLVVICHL-KNPEkgrAHEEGRPvSITDLRGSGALRQLSDTIIALER--NQQGDNP 448
Cdd:PRK05636  399 EVSEFSRQLKLLAKELDVPLIAISQLnRGPE---SRTDKRP-QLADLRESGSLEQDADMVMLLYRpdSQDKDDE 468
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 88-171 4.55e-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: 53.04  E-value: 4.55e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247  88 KKIVVTEGEIDMLTVMELqDCKYPVVSLGhgasaakktcAANYEY-----FDQFEQIILMFDMDEAGRKAVEEAAQVLPA 162
Cdd:cd01029     1 DEVIIVEGYMDVLALHQA-GIKNVVAALG----------TANTEEqlrllKRFARTVILAFDNDEAGKKAAARALELLLA 69


                  ....*....
gi 1842033247 163 GKVRVAVLP 171
Cdd:cd01029    70 LGGRVRVPP 78
PRK08760 PRK08760
replicative DNA helicase; Provisional
 210-442 1.52e-08

replicative DNA helicase; Provisional


Pssm-ID: 181547 [Multi-domain]  Cd Length: 476  Bit Score: 56.85  E-value: 1.52e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 210 ERIREHLSSEESVGLLFSGCTGINDKTLGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEESVEETAED 289
Cdd:PRK08760  197 EELRNRFENGGNITGLPTGYNDFDAMTAGLQPTDLIILAARPAMGKTTFALNIAEYAAIKSKKGVAVFSMEMSASQLAMR 276

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 290 LIGLHNRVRLRQSDSLKREIIENGKFDQWFDELFGNDSFhlYDSFAEAETDRLLAKLAYMRSGLGCDVIILDHISIVvSA 369
Cdd:PRK08760  277 LISSNGRINAQRLRTGALEDEDWARVTGAIKMLKETKIF--IDDTPGVSPEVLRSKCRRLKREHDLGLIVIDYLQLM-SV 353

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1842033247 370 SGESDERKM-IDNLMTKLKGFAKSTGVVLVVICHLKNPEKGRAheEGRPVsITDLRGSGALRQLSDTIIALERN 442
Cdd:PRK08760  354 PGNSENRATeISEISRSLKGLAKELNVPVIALSQLNRSLETRT--DKRPV-MADLRESGAIEQDADMIVFIYRD 424
PRK07004 PRK07004
replicative DNA helicase; Provisional
 210-449 8.87e-08

replicative DNA helicase; Provisional


Pssm-ID: 235907 [Multi-domain]  Cd Length: 460  Bit Score: 54.53  E-value: 8.87e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 210 ERIRE--HLSSEESVGLLFSGCTGINDKTLGARGGEVIMVTSGSGMGKSTFvrqqALQWGTAMGKKVGLAMLEESVEETA 287
Cdd:PRK07004  179 ERIDTlyHTANPSDVTGTPTGFVDLDRMTSGMHGGELIIVAGRPSMGKTAF----SMNIGEYVAVEYGLPVAVFSMEMPG 254

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 288 EDL-------IGLHNRVRLRQSDSLKRE------IIENGKFDQWF-DELFGNDSFHLydsfaEAETDRLlaklAYMRSGL 353
Cdd:PRK07004  255 TQLamrmlgsVGRLDQHRMRTGRLTDEDwpklthAVQKMSEAQLFiDETGGLNPMEL-----RSRARRL----ARQCGKL 325

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 354 GcdVIILDHISIVVSASGESDERKMIDNLMTKLKGFAKSTGVVLVVICHLKNPEKGRAHEegRPVsITDLRGSGALRQLS 433
Cdd:PRK07004  326 G--LIIIDYLQLMSGSSQGENRATEISEISRSLKSLAKELDVPVIALSQLNRGLEQRPNK--RPV-MSDLRESGAIEQDA 400

                         250
                  ....*....|....*...
gi 1842033247 434 DTIIALERNQ--QGDNPN 449
Cdd:PRK07004  401 DVILFIYRDEvyNPDSPD 418
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 89-162 2.97e-07

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: 48.51  E-value: 2.97e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247  89 KIVVTEGEIDMLTVMELQDCKY--PVVSLGHGASAAKKTCAANYEYFDQF----EQIILMFDMDEAGRKAVEEAAQVLPA 162
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGFqaVVAVLGHLLSLEKGPKKKALKALKELalkaKEVILATDPDREGEAIALKLLELKEL 80
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 88-170 1.71e-06

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: 45.88  E-value: 1.71e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247  88 KKIVVTEGEIDMLTVMELQDCKYPVVSL-GHGASAAKKTCAANyeyFDQFEQIILMFDMDEAGRKAVEEAAQVLPAGKVR 166
Cdd:cd00188     1 KKLIIVEGPSDALALAQAGGYGGAVVALgGHALNKTRELLKRL---LGEAKEVIIATDADREGEAIALRLLELLKSLGKK 77


                  ....
gi 1842033247 167 VAVL 170
Cdd:cd00188    78 VRRL 81
TOPRIM_DnaG_primases cd03364
TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase ...
 88-170 5.69e-06

TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. 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. E. coli DnaG is a single subunit enzyme.


Pssm-ID: 173784 [Multi-domain]  Cd Length: 79  Bit Score: 44.43  E-value: 5.69e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247  88 KKIVVTEGEIDMLTVMELQDcKYPVVSLGhgasaakktcAANYEyfDQFE-------QIILMFDMDEAGRKAVEEAAQVL 160
Cdd:cd03364     1 KKVILVEGYMDVIALHQAGI-KNVVASLG----------TALTE--EQAEllkrlakEVILAFDGDEAGQKAALRALELL 67

                          90
                  ....*....|..
gi 1842033247 161 -PAGK-VRVAVL 170
Cdd:cd03364    68 lKLGLnVRVLTL 79
DnaG COG0358
DNA primase (bacterial type) [Replication, recombination and repair];
15-184 1.56e-05

DNA primase (bacterial type) [Replication, recombination and repair];


Pssm-ID: 440127 [Multi-domain]  Cd Length: 465  Bit Score: 47.44  E-value: 1.56e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247  15 YSALTARGISKETCQKAGYWIAKVDGVMYqvaDY---------RDQNGNIV--SQKVRDKDK----N------FkttgsH 73
Cdd:COG0358   167 LKHLKKKGFSEEELVEAGLVIEREDGGYY---DRfrgrimfpiRDLRGRVIgfGGRVLDDGEpkylNspetplF-----H 238

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247  74 KSDALFGKHL----WNGGKKIVVTEGEIDmltVMELQ--DCKYPVVSLG------HgASAAKKTCaanyeyfdqfEQIIL 141
Cdd:COG0358   239 KGRVLYGLDLarkaIRKEDRVIVVEGYMD---VIALHqaGIKNAVATLGtalteeH-IKLLKRYT----------DEVIL 304

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1842033247 142 MFDMDEAGRKAVEEAAQVL--PAGKVRVAVLPckdanechlNGHD 184
Cdd:COG0358   305 CFDGDAAGQKAALRALELLlkDGLQVRVLFLP---------DGED 340
RepA_RSF1010_like cd01125
Hexameric Replicative Helicase RepA of plasmid RSF1010 and related proteins; This family ...
 242-460 9.39e-05

Hexameric Replicative Helicase RepA of plasmid RSF1010 and related proteins; This family includes the homo-hexameric replicative helicase RepA encoded by plasmid RSF1010. RSF1010 is found in most Gram-negative bacteria and some Gram-positive bacteria . The RepA protein of Plasmid RSF1010 is a 5'-3' DNA helicase which can utilize ATP, dATP, GTP and dGTP (and CTP and dCTP to a lesser extent).


Pssm-ID: 410870  Cd Length: 238  Bit Score: 43.91  E-value: 9.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 242 GEVIMVTSGSGMGKSTFvrqqALQWGTAMGkkvglamleesveeTAEDLIGLHNRVRLR--------QSDSLKREIIENG 313
Cdd:cd01125     1 GTLGMLVGPPGSGKSFL----ALDLAVAVA--------------TGRDWLGERRVKQGRvvylaaedPRDGLRRRLKAIG 62

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 314 KFDQWFDELFGNDSFHLYDSFAEAETDRLLAKLAY-MRSGLGCDVIILDHISIVVSASGESDERKMiDNLMTKLKGFAKS 392
Cdd:cd01125    63 AHLGDEDAALAENLVIENLRGKPVSIDAEAPELERiIEELEGVRLIIIDTLARVLHGGDENDAADM-GAFVAGLDRIARE 141

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1842033247 393 TGVVLVVICHLKnpeKGRAHEegrpvSITDLRGSGALRQLSDTIIALERNQQGDNPNLVLVRILKCRF 460
Cdd:cd01125   142 TGAAVLLVHHTG---KDAAGD-----SQQAARGSSALRGAADAEINLSKMDATEAEKVGLDKDLRRRF 201
PRK08506 PRK08506
replicative DNA helicase; Provisional
 227-442 2.52e-04

replicative DNA helicase; Provisional


Pssm-ID: 236278 [Multi-domain]  Cd Length: 472  Bit Score: 43.46  E-value: 2.52e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 227 SGCTGINDKTLGARGGEVIMVTSGSGMGKSTFVRQQALqwgTAMGKKVGLAMLeeSVEETAEDL----------IGLHNR 296
Cdd:PRK08506  177 TGFVELNKMTKGFNKGDLIIIAARPSMGKTTLCLNMAL---KALNQDKGVAFF--SLEMPAEQLmlrmlsaktsIPLQNL 251

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 297 VRLRQSDslkreiiengkfDQW------FDE-----LFGNDSfhlydSFAEAETDRL-LAKLAYMRSGLGCDVIilDHIS 364
Cdd:PRK08506  252 RTGDLDD------------DEWerlsdaCDElskkkLFVYDS-----GYVNIHQVRAqLRKLKSQHPEIGLAVI--DYLQ 312

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1842033247 365 IVVSASGESDERKMIDNLMTKLKGFAKSTGVVLVVICHLKNPEKGRAHEegRPVsITDLRGSGALRQLSDTIIALERN 442
Cdd:PRK08506  313 LMSGSGNFKDRHLQISEISRGLKLLARELDIPIIALSQLNRSLESRADK--RPM-LSDLRESGAIEQDADIILFVYRD 387
DnaB COG0305
Replicative DNA helicase [Replication, recombination and repair];
210-474 7.13e-04

Replicative DNA helicase [Replication, recombination and repair];


Pssm-ID: 440074 [Multi-domain]  Cd Length: 429  Bit Score: 41.99  E-value: 7.13e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 210 ERIREHLSSEESVGLLFSGCTGINDKTLGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLEESVEETAED 289
Cdd:COG0305   159 ERIEELYKNGGGITGVPTGFTDLDKLTGGLQPGDLIILAARPSMGKTAFALNIARNAAIKEGKPVAIFSLEMSAEQLVMR 238

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 290 LIGLHNRVrlrqsdSLKReiIENGKFDQW-FDEL------FGNDSFHLYDSfAEAETDRLLAKLAYMRSGLGCDVIILDH 362
Cdd:COG0305   239 LLSSEARI------DSSK--LRTGKLSDEdWERLssaageLSEAPIYIDDT-PGLTIAEIRAKARRLKREHGLGLIVIDY 309

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 363 ISIVvSASGESDERKM-IDNLMTKLKGFAKSTGVVLVVICHLKnpekgRAHEE---GRPVsITDLRGSGALRQLSDTIIA 438
Cdd:COG0305   310 LQLM-SGSGRSENRQQeISEISRSLKALAKELNVPVIALSQLS-----RAVEQrtdKRPQ-LSDLRESGSIEQDADVVMF 382

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 1842033247 439 LER----NQQGDNPNLVLVRILKCRF--TGDTGVAGFMEYNK 474
Cdd:COG0305   383 LYRdeyyNPDSEDKGIAEIIIAKQRNgpTGTVKLAFDGEYTR 424
AAA_25 pfam13481
AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.
 242-403 3.34e-03

AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.


Pssm-ID: 463892 [Multi-domain]  Cd Length: 193  Bit Score: 38.90  E-value: 3.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 242 GEVIMVTSGSGMGKSTFVrqqaLQWGTAMGKKVGLAMLEESVEE------TAED-LIGLHNRVR--LRQSDSLKREIIEN 312
Cdd:pfam13481  33 GGLGLLAGAPGTGKTTLA----LDLAAAVATGKPWLGGPRVPEQgkvlyvSAEGpADELRRRLRaaGADLDLPARLLFLS 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1842033247 313 GKFDQwfdELFGNDSFHlydSFAEAETDRLLAKLAYMRsglGCDVIILDHISIVVSAS--GESDERKMIDnlmtKLKGFA 390
Cdd:pfam13481 109 LVESL---PLFFLDRGG---PLLDADVDALEAALEEVE---DPDLVVIDPLARALGGDenSNSDVGRLVK----ALDRLA 175

                         170
                  ....*....|...
gi 1842033247 391 KSTGVVLVVICHL 403
Cdd:pfam13481 176 RRTGATVLLVHHV 188
 
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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