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Conserved domains on  [gi|1070102214|ref|YP_009286646|]
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DNA primase/helicase [Citrobacter phage SH1]

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 ...
 307-536 2.16e-91

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: 280.23  E-value: 2.16e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 307 VMVTSGSGMGKSTFVRQQALAWGKRMGKRVGLAMLEESVEDTIQDMMGLNNKVRLRQSDEVKKAIAEDgrFDEWYDELFG 386
Cdd:cd19483     1 VTIGAGSGIGKSTIVRELAYHLITEHGEKVGIISLEESVEETAKGLAGKHLGKPEPLELPRDDITEEE--EDDAFDNELG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 387 DDTFHLYDSFAEAEADRLLAKLAYMRTGLGCDVIVLDHISIVVSASEESDERKMIDRLMTKLKGFAKSTGVVLVVICHLK 466
Cdd:cd19483    79 SGRFFLYDHFGSLDWDNLKEKIRYMVKVLGCKVIVLDHLTILVSGLDSSDERKELDEIMTELAALVKELGVTIILVSHLR 158

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1070102214 467 NPEKGKPHEEGRAVSITDLRGSGALRQLSDTIIALERNQQGDMP---NLVLVRLLKCRFTGDTGIAGYMEYNR 536
Cdd:cd19483   159 RPGGGKGHEEGGEVSESDLRGSSAIAQLSDYVIGLERNKQADDPverNTTRVRVLKNRFTGETGIAGTLYYDE 231
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
150-224 3.17e-12

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


:

Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 61.89  E-value: 3.17e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1070102214  150 KKIVVTEGEIDALTVMELQDCKYPVVSLGhGASAAKKTCAANYEYFDQFEqIILMFDMDDAGRKAVEEAAQVLPA 224
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALG-GHLLSKEQIKLLKKLAKKAE-VILATDPDREGEAIAWELAELLKP 73
zf-CHC2 super family cl21601
CHC2 zinc finger; This domain is principally involved in DNA binding in DNA primases.
 10-39 5.54e-07

CHC2 zinc finger; This domain is principally involved in DNA binding in DNA primases.


The actual alignment was detected with superfamily member smart00778:

Pssm-ID: 451328 [Multi-domain]  Cd Length: 37  Bit Score: 46.17  E-value: 5.54e-07
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1070102214   10 LFHAPCENCGSSDGNSvYSD----GHEWCFVCEH 39
Cdd:smart00778   1 GRHGPCPNCGGSDRFR-FDDkdgrGTWFCSVCGA 33
 
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 ...
 307-536 2.16e-91

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: 280.23  E-value: 2.16e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 307 VMVTSGSGMGKSTFVRQQALAWGKRMGKRVGLAMLEESVEDTIQDMMGLNNKVRLRQSDEVKKAIAEDgrFDEWYDELFG 386
Cdd:cd19483     1 VTIGAGSGIGKSTIVRELAYHLITEHGEKVGIISLEESVEETAKGLAGKHLGKPEPLELPRDDITEEE--EDDAFDNELG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 387 DDTFHLYDSFAEAEADRLLAKLAYMRTGLGCDVIVLDHISIVVSASEESDERKMIDRLMTKLKGFAKSTGVVLVVICHLK 466
Cdd:cd19483    79 SGRFFLYDHFGSLDWDNLKEKIRYMVKVLGCKVIVLDHLTILVSGLDSSDERKELDEIMTELAALVKELGVTIILVSHLR 158

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1070102214 467 NPEKGKPHEEGRAVSITDLRGSGALRQLSDTIIALERNQQGDMP---NLVLVRLLKCRFTGDTGIAGYMEYNR 536
Cdd:cd19483   159 RPGGGKGHEEGGEVSESDLRGSSAIAQLSDYVIGLERNKQADDPverNTTRVRVLKNRFTGETGIAGTLYYDE 231
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
150-224 3.17e-12

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 61.89  E-value: 3.17e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1070102214  150 KKIVVTEGEIDALTVMELQDCKYPVVSLGhGASAAKKTCAANYEYFDQFEqIILMFDMDDAGRKAVEEAAQVLPA 224
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALG-GHLLSKEQIKLLKKLAKKAE-VILATDPDREGEAIAWELAELLKP 73
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
290-521 7.01e-12

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 65.32  E-value: 7.01e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 290 GCQGLnDRTL--GARGGEVVMVTSGSGMGKSTFVrQQALAWGKRMGKRVGLAMLEESVEDTIQDMMGLNnkvrlrqsdev 367
Cdd:COG0467     5 GIPGL-DELLggGLPRGSSTLLSGPPGTGKTTLA-LQFLAEGLRRGEKGLYVSFEESPEQLLRRAESLG----------- 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 368 kkaiaedgrFDewYDELFGDDTFHLYDSFAE---AEADRLLAKLAYMRTGLGCDVIVLDHISIVVSASEESDERKmidRL 444
Cdd:COG0467    72 ---------LD--LEEYIESGLLRIIDLSPEelgLDLEELLARLREAVEEFGAKRVVIDSLSGLLLALPDPERLR---EF 137

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1070102214 445 MTKLKGFAKSTGVVLVVICHLKnpekgkpheegravSITDLRGSGALRQLSDTIIALERNQQGDMPNLVLvRLLKCR 521
Cdd:COG0467   138 LHRLLRYLKKRGVTTLLTSETG--------------GLEDEATEGGLSYLADGVILLRYVELGGELRRAL-SVLKMR 199
Toprim_2 pfam13155
Toprim-like; This is a family or Toprim-like proteins.
 153-239 2.91e-11

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


Pssm-ID: 463793 [Multi-domain]  Cd Length: 88  Bit Score: 59.88  E-value: 2.91e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 153 VVTEGEIDALTVMEL-QDCKYPVVSLGHGASAAKKtcaanyEYFDQF-EQIILMFDMDDAGRKAVEEAAQVLPAGKVRVA 230
Cdd:pfam13155   1 VVFEGYIDALSLAQAgIKNVLYVATLGTALTEAQI------KLLKRYpKEVILAFDNDEAGRKAAKRLAELLKEAGVDVK 74

                          90
                  ....*....|..
gi 1070102214 231 VL---PCKDANE 239
Cdd:pfam13155  75 IRllpDGKDWNE 86
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 150-233 1.29e-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: 54.97  E-value: 1.29e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 150 KKIVVTEGEIDALTVMELqDCKYPVVSLGhgasaakktcAANYEY-----FDQFEQIILMFDMDDAGRKAVEEAAQVLPA 224
Cdd:cd01029     1 DEVIIVEGYMDVLALHQA-GIKNVVAALG----------TANTEEqlrllKRFARTVILAFDNDEAGKKAAARALELLLA 69


                  ....*....
gi 1070102214 225 GKVRVAVLP 233
Cdd:cd01029    70 LGGRVRVPP 78
PRK05636 PRK05636
replicative DNA helicase; Provisional
 290-503 4.75e-09

replicative DNA helicase; Provisional


Pssm-ID: 180177 [Multi-domain]  Cd Length: 505  Bit Score: 58.70  E-value: 4.75e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 290 GCQGLNDRTLGARGGEVVMVTSGSGMGKST----FVRQQALawgkRMGKRVGLAMLEESVEDTIQDMMGLNNKVRL---- 361
Cdd:PRK05636  251 GFKDLDDLTNGLRGGQMIIVAARPGVGKSTlaldFMRSASI----KHNKASVIFSLEMSKSEIVMRLLSAEAEVRLsdmr 326

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 362 --RQSDEVKKAIAEdgRFDEWYDE-LFGDDTFHLYDSFAEAEADRLLAKlaymrtgLGCDVIVLDHISIVVSASEESDER 438
Cdd:PRK05636  327 ggKMDEDAWEKLVQ--RLGKIAQApIFIDDSANLTMMEIRSKARRLKQK-------HDLKLIVVDYLQLMSSGKRVESRQ 397

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1070102214 439 KMIDRLMTKLKGFAKSTGVVLVVICHLKnpeKGKPHEEGRAVSITDLRGSGALRQLSDTIIALER 503
Cdd:PRK05636  398 QEVSEFSRQLKLLAKELDVPLIAISQLN---RGPESRTDKRPQLADLRESGSLEQDADMVMLLYR 459
Prim_Zn_Ribbon smart00778
Zinc-binding domain of primase-helicase; This region represents the zinc binding domain. It is ...
 10-39 5.54e-07

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: 46.17  E-value: 5.54e-07
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1070102214   10 LFHAPCENCGSSDGNSvYSD----GHEWCFVCEH 39
Cdd:smart00778   1 GRHGPCPNCGGSDRFR-FDDkdgrGTWFCSVCGA 33
AAA_25 pfam13481
AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.
 304-465 6.59e-05

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: 43.91  E-value: 6.59e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 304 GEVVMVTSGSGMGKSTFVRQQALA-------WGKRMGKRVGLAML---EESvEDTIQDmmglnnkvRLRqsdEVKKAIAE 373
Cdd:pfam13481  33 GGLGLLAGAPGTGKTTLALDLAAAvatgkpwLGGPRVPEQGKVLYvsaEGP-ADELRR--------RLR---AAGADLDL 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 374 DGRFDEWYDELFGDDTFHLYDSFAEAEADRLLAKLAYMRTGLgcDVIVLDHISIVVSASEESDERkmIDRLMTKLKGFAK 453
Cdd:pfam13481 101 PARLLFLSLVESLPLFFLDRGGPLLDADVDALEAALEEVEDP--DLVVIDPLARALGGDENSNSD--VGRLVKALDRLAR 176

                         170
                  ....*....|..
gi 1070102214 454 STGVVLVVICHL 465
Cdd:pfam13481 177 RTGATVLLVHHV 188
DnaG COG0358
DNA primase (bacterial type) [Replication, recombination and repair];
199-233 2.89e-04

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


Pssm-ID: 440127 [Multi-domain]  Cd Length: 465  Bit Score: 43.59  E-value: 2.89e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1070102214 199 EQIILMFDMDDAGRKAVEEAAQVL--PAGKVRVAVLP 233
Cdd:COG0358   300 DEVILCFDGDAAGQKAALRALELLlkDGLQVRVLFLP 336
 
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 ...
 307-536 2.16e-91

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: 280.23  E-value: 2.16e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 307 VMVTSGSGMGKSTFVRQQALAWGKRMGKRVGLAMLEESVEDTIQDMMGLNNKVRLRQSDEVKKAIAEDgrFDEWYDELFG 386
Cdd:cd19483     1 VTIGAGSGIGKSTIVRELAYHLITEHGEKVGIISLEESVEETAKGLAGKHLGKPEPLELPRDDITEEE--EDDAFDNELG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 387 DDTFHLYDSFAEAEADRLLAKLAYMRTGLGCDVIVLDHISIVVSASEESDERKMIDRLMTKLKGFAKSTGVVLVVICHLK 466
Cdd:cd19483    79 SGRFFLYDHFGSLDWDNLKEKIRYMVKVLGCKVIVLDHLTILVSGLDSSDERKELDEIMTELAALVKELGVTIILVSHLR 158

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1070102214 467 NPEKGKPHEEGRAVSITDLRGSGALRQLSDTIIALERNQQGDMP---NLVLVRLLKCRFTGDTGIAGYMEYNR 536
Cdd:cd19483   159 RPGGGKGHEEGGEVSESDLRGSSAIAQLSDYVIGLERNKQADDPverNTTRVRVLKNRFTGETGIAGTLYYDE 231
DnaB_C cd00984
C-terminal domain of DnaB helicase; DnaB helicase C-terminal domain. The hexameric helicase ...
 290-542 3.99e-15

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: 75.24  E-value: 3.99e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 290 GCQGLNDRTLGARGGEVVMVTSGSGMGKSTFVRQQALAWGKRMGKRVGLAMLEESVEDTIQDMMGLNNKV---RLR---Q 363
Cdd:cd00984     5 GFTDLDKLTGGLQPGDLIIIAARPSMGKTAFALNIAENIALDEGLPVLFFSLEMSAEQLAERLLSSESGVslsKLRtgrL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 364 SDEVKKAIAED-GRFDEWYdeLFGDDTFHLYDSFAEAEADRLLaklaymRTGLGCDVIVLDHISIVvSASEESDERK--- 439
Cdd:cd00984    85 DDEDWERLTAAmGELSELP--LYIDDTPGLTVDEIRAKARRLK------REHGGLGLIVIDYLQLI-RGSKRAENRQqev 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 440 -MIDRlmtKLKGFAKSTGVVLVVICHL-KNPEKGkpheEGRAVSITDLRGSGALRQLSDTIIALER----NQQGDMPNLV 513
Cdd:cd00984   156 aEISR---SLKALAKELNVPVIALSQLnRGVESR----TDKRPMLSDLRESGSIEQDADVVIFLYRdeyyDKDSEDKGIA 228

                         250       260
                  ....*....|....*....|....*....
gi 1070102214 514 LVRLLKCRFtGDTGIAgYMEYNRETGWLE 542
Cdd:cd00984   229 EIIIAKNRN-GPTGTV-YLAFNPEYTRFT 255
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
150-224 3.17e-12

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 61.89  E-value: 3.17e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1070102214  150 KKIVVTEGEIDALTVMELQDCKYPVVSLGhGASAAKKTCAANYEYFDQFEqIILMFDMDDAGRKAVEEAAQVLPA 224
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALG-GHLLSKEQIKLLKKLAKKAE-VILATDPDREGEAIAWELAELLKP 73
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
290-521 7.01e-12

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 65.32  E-value: 7.01e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 290 GCQGLnDRTL--GARGGEVVMVTSGSGMGKSTFVrQQALAWGKRMGKRVGLAMLEESVEDTIQDMMGLNnkvrlrqsdev 367
Cdd:COG0467     5 GIPGL-DELLggGLPRGSSTLLSGPPGTGKTTLA-LQFLAEGLRRGEKGLYVSFEESPEQLLRRAESLG----------- 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 368 kkaiaedgrFDewYDELFGDDTFHLYDSFAE---AEADRLLAKLAYMRTGLGCDVIVLDHISIVVSASEESDERKmidRL 444
Cdd:COG0467    72 ---------LD--LEEYIESGLLRIIDLSPEelgLDLEELLARLREAVEEFGAKRVVIDSLSGLLLALPDPERLR---EF 137

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1070102214 445 MTKLKGFAKSTGVVLVVICHLKnpekgkpheegravSITDLRGSGALRQLSDTIIALERNQQGDMPNLVLvRLLKCR 521
Cdd:COG0467   138 LHRLLRYLKKRGVTTLLTSETG--------------GLEDEATEGGLSYLADGVILLRYVELGGELRRAL-SVLKMR 199
Twinkle_C cd01122
C-terminal domain of Twinkle; Twinkle ( T7 gp4-like protein with intramitochondrial nucleoid ...
 269-539 1.05e-11

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: 65.34  E-value: 1.05e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 269 SLKDRVKEAMT-SEDAVGLLFDGCQGLNDRTLGARGGEVVMVTSGSGMGKSTFVRQQAL---------AWGKrmgkrvgl 338
Cdd:cd01122     7 DLRELVYEELLnSEQVAGVQWKRFPSLNKLLKGHRRGELTIFTGPTGSGKTTFLSEYSLdlcmqgvntLWGS-------- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 339 amLEESVEDTIQDMMGLNNKVRLRQSDEvkkaiaedgRFDEWYDElFGDDTFHLYDSFAEAEADRLLAKLAYMRTGLGCD 418
Cdd:cd01122    79 --FEIKNVRLAKTMLTQFAGKNLEDNLR---------EFDEWADK-FELLPMYFMKFHGSTDIDEVLDAMEHAVYVYDIQ 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 419 VIVLDHISIVVSASEESDERKMI-DRLMTKLKGFAKSTGVVLVVICHlknPEKgkpHEEGRAVSITDLRGSGALRQLSDT 497
Cdd:cd01122   147 HIVIDNLQFMMGTQASGSDRFELqDLIIGKFRRFATNNNVHITLVIH---PRK---EDDDNELTTSSIFGSAKATQEADN 220

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 1070102214 498 IIALERNQQGDMPNLVLVRLLKCRFTGDTGIAgYMEYNRETG 539
Cdd:cd01122   221 VLILQDKRLISGEGKKFLQIKKNRFDGDLGVI-PLEFNKNSL 261
Toprim_2 pfam13155
Toprim-like; This is a family or Toprim-like proteins.
 153-239 2.91e-11

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


Pssm-ID: 463793 [Multi-domain]  Cd Length: 88  Bit Score: 59.88  E-value: 2.91e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 153 VVTEGEIDALTVMEL-QDCKYPVVSLGHGASAAKKtcaanyEYFDQF-EQIILMFDMDDAGRKAVEEAAQVLPAGKVRVA 230
Cdd:pfam13155   1 VVFEGYIDALSLAQAgIKNVLYVATLGTALTEAQI------KLLKRYpKEVILAFDNDEAGRKAAKRLAELLKEAGVDVK 74

                          90
                  ....*....|..
gi 1070102214 231 VL---PCKDANE 239
Cdd:pfam13155  75 IRllpDGKDWNE 86
RecA-like_superfamily cd01120
RecA-like_NTPases; RecA-like NTPases. This superfamily includes the NTP binding domain of F1 ...
 307-492 4.05e-10

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: 57.51  E-value: 4.05e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 307 VMVTSGSGMGKSTFVRQQALAWGKrMGKRVGLAMLeesvedtiqdmmglnnkvrlrqsdevkkaiaedgrfdewydelfg 386
Cdd:cd01120     1 ILITGPPGSGKTTLLLQFAEQALL-SDEPVIFISF--------------------------------------------- 34

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 387 ddtfhlydsfaeaeADRLLAKLAYMRTGLGCDVIVLDHISIVVSASEEsDERKMIDRLMTKLKGFAKSTGVVLVVICHLK 466
Cdd:cd01120    35 --------------LDTILEAIEDLIEEKKLDIIIIDSLSSLARASQG-DRSSELLEDLAKLLRAARNTGITVIATIHSD 99

                         170       180
                  ....*....|....*....|....*.
gi 1070102214 467 NPekgkphEEGRAVSITDLRGSGALR 492
Cdd:cd01120   100 KF------DIDRGGSSNDERLLKSLR 119
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 150-233 1.29e-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: 54.97  E-value: 1.29e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 150 KKIVVTEGEIDALTVMELqDCKYPVVSLGhgasaakktcAANYEY-----FDQFEQIILMFDMDDAGRKAVEEAAQVLPA 224
Cdd:cd01029     1 DEVIIVEGYMDVLALHQA-GIKNVVAALG----------TANTEEqlrllKRFARTVILAFDNDEAGKKAAARALELLLA 69


                  ....*....
gi 1070102214 225 GKVRVAVLP 233
Cdd:cd01029    70 LGGRVRVPP 78
PRK05636 PRK05636
replicative DNA helicase; Provisional
 290-503 4.75e-09

replicative DNA helicase; Provisional


Pssm-ID: 180177 [Multi-domain]  Cd Length: 505  Bit Score: 58.70  E-value: 4.75e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 290 GCQGLNDRTLGARGGEVVMVTSGSGMGKST----FVRQQALawgkRMGKRVGLAMLEESVEDTIQDMMGLNNKVRL---- 361
Cdd:PRK05636  251 GFKDLDDLTNGLRGGQMIIVAARPGVGKSTlaldFMRSASI----KHNKASVIFSLEMSKSEIVMRLLSAEAEVRLsdmr 326

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 362 --RQSDEVKKAIAEdgRFDEWYDE-LFGDDTFHLYDSFAEAEADRLLAKlaymrtgLGCDVIVLDHISIVVSASEESDER 438
Cdd:PRK05636  327 ggKMDEDAWEKLVQ--RLGKIAQApIFIDDSANLTMMEIRSKARRLKQK-------HDLKLIVVDYLQLMSSGKRVESRQ 397

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1070102214 439 KMIDRLMTKLKGFAKSTGVVLVVICHLKnpeKGKPHEEGRAVSITDLRGSGALRQLSDTIIALER 503
Cdd:PRK05636  398 QEVSEFSRQLKLLAKELDVPLIAISQLN---RGPESRTDKRPQLADLRESGSLEQDADMVMLLYR 459
KaiC-like cd01124
Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. ...
 304-532 2.29e-08

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: 54.96  E-value: 2.29e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 304 GEVVMVTSGSGMGKSTFVrQQALAWGKRMGKRVGLAMLEESVEDTIQDMMGLNNKVRlrqsdevkkAIAEDGRFDewyde 383
Cdd:cd01124    19 GSVTLLTGGPGTGKTLFG-LQFLYAGAKNGEPGLFFTFEESPERLLRNAKSFGWDFD---------EMEDEGKLI----- 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 384 lFGDDTFHLYDSFaeaEADRLLAKLAYMRTGLGCDVIVLDHISIVvsaSEESDERKMIDRLMTKLKGFAKSTGVVLVVIc 463
Cdd:cd01124    84 -IVDAPPTEAGRF---SLDELLSRILSIIKSFKAKRVVIDSLSGL---RRAKEDQMRARRIVIALLNELRAAGVTTIFT- 155

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 464 hlknpekgkphEEGRAVSITDLRGSGALRQLSDTIIALeRNQQGDMPNLVLVRLLKCRFTG-DTGIAGYM 532
Cdd:cd01124   156 -----------SEMRSFLSSESAGGGDVSFIVDGVILL-RYVEIEGELRRTIRVLKMRGTGhDTGTHPFE 213
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 151-224 7.52e-08

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: 50.05  E-value: 7.52e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 151 KIVVTEGEIDALTVMELQDCKY--PVVSLGHGASAAKKTCAANYEYFDQF----EQIILMFDMDDAGRKAVEEAAQVLPA 224
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGFqaVVAVLGHLLSLEKGPKKKALKALKELalkaKEVILATDPDREGEAIALKLLELKEL 80
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 150-232 3.23e-07

Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173773 [Multi-domain]  Cd Length: 83  Bit Score: 48.19  E-value: 3.23e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 150 KKIVVTEGEIDALTVMELQDCKYPVVSL-GHGASAAKKTCAANyeyFDQFEQIILMFDMDDAGRKAVEEAAQVLPAGKVR 228
Cdd:cd00188     1 KKLIIVEGPSDALALAQAGGYGGAVVALgGHALNKTRELLKRL---LGEAKEVIIATDADREGEAIALRLLELLKSLGKK 77


                  ....
gi 1070102214 229 VAVL 232
Cdd:cd00188    78 VRRL 81
Prim_Zn_Ribbon smart00778
Zinc-binding domain of primase-helicase; This region represents the zinc binding domain. It is ...
 10-39 5.54e-07

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: 46.17  E-value: 5.54e-07
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1070102214   10 LFHAPCENCGSSDGNSvYSD----GHEWCFVCEH 39
Cdd:smart00778   1 GRHGPCPNCGGSDRFR-FDDkdgrGTWFCSVCGA 33
PRK08840 PRK08840
replicative DNA helicase; Provisional
 243-505 8.74e-07

replicative DNA helicase; Provisional


Pssm-ID: 181562 [Multi-domain]  Cd Length: 464  Bit Score: 51.53  E-value: 8.74e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 243 MGEDK--AILEQVWNANpwvpDGVVSALSLKDRVKEAM-----TSEDAVGLLFDGCQGLNDRTLGARGGEVVMVTSGSGM 315
Cdd:PRK08840  153 MAESKvfAIAEARTSEN----EGPQNVDSILEKTLERIellykTPQDGVTGVDTGFTDLNKKTAGLQGSDLIIVAARPSM 228

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 316 GKSTFVRQQALAWGKRMGKRVGLAMLEESVEDTIQDMMGL-----NNKVRLRQSDEVKKA-IAEDGRFDEWYDELFGDDT 389
Cdd:PRK08840  229 GKTTFAMNLCENAAMDQDKPVLIFSLEMPAEQLMMRMLASlsrvdQTKIRTGQLDDEDWArISSTMGILMEKKNMYIDDS 308

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 390 FHLYDSFAEAEADRLlaklayMRTGLGCDVIVLDHISIVVSASEESDERKMIDRLMTKLKGFAKSTGVVLVVICHLKNPE 469
Cdd:PRK08840  309 SGLTPTEVRSRARRI------AREHGGLSMIMVDYLQLMRVPALSDNRTLEIAEISRSLKALAKELNVPVVALSQLNRSL 382

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 1070102214 470 KGKphEEGRAVSiTDLRGSGALRQLSDTIIALERNQ 505
Cdd:PRK08840  383 EQR--ADKRPVN-SDLRESGSIEQDADLIMFIYRDE 415
TOPRIM_DnaG_primases cd03364
TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase ...
 150-232 1.00e-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: 46.74  E-value: 1.00e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 150 KKIVVTEGEIDALTVMELQDcKYPVVSLGhgasaakktcAANYEyfDQFE-------QIILMFDMDDAGRKAVEEAAQVL 222
Cdd:cd03364     1 KKVILVEGYMDVIALHQAGI-KNVVASLG----------TALTE--EQAEllkrlakEVILAFDGDEAGQKAALRALELL 67

                          90
                  ....*....|..
gi 1070102214 223 -PAGK-VRVAVL 232
Cdd:cd03364    68 lKLGLnVRVLTL 79
PRK07004 PRK07004
replicative DNA helicase; Provisional
 290-505 5.91e-05

replicative DNA helicase; Provisional


Pssm-ID: 235907 [Multi-domain]  Cd Length: 460  Bit Score: 45.67  E-value: 5.91e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 290 GCQGLNDRTLGARGGEVVMVTSGSGMGKSTFvrqqALAWGKRMGKRVGLAMLEESVE--DTIQDMMGLNNKVRLRQSD-E 366
Cdd:PRK07004  199 GFVDLDRMTSGMHGGELIIVAGRPSMGKTAF----SMNIGEYVAVEYGLPVAVFSMEmpGTQLAMRMLGSVGRLDQHRmR 274

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 367 VKKAIAED--------GRFDEwyDELFGDDTFHLYDSFAEAEADRLLAKLAYMrtGLgcdvIVLDHISIVVSASEESDER 438
Cdd:PRK07004  275 TGRLTDEDwpklthavQKMSE--AQLFIDETGGLNPMELRSRARRLARQCGKL--GL----IIIDYLQLMSGSSQGENRA 346

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1070102214 439 KMIDRLMTKLKGFAKSTGVVLVVICHLKNPEKGKPHEegRAVsITDLRGSGALRQLSDTIIALERNQ 505
Cdd:PRK07004  347 TEISEISRSLKSLAKELDVPVIALSQLNRGLEQRPNK--RPV-MSDLRESGAIEQDADVILFIYRDE 410
AAA_25 pfam13481
AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.
 304-465 6.59e-05

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: 43.91  E-value: 6.59e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 304 GEVVMVTSGSGMGKSTFVRQQALA-------WGKRMGKRVGLAML---EESvEDTIQDmmglnnkvRLRqsdEVKKAIAE 373
Cdd:pfam13481  33 GGLGLLAGAPGTGKTTLALDLAAAvatgkpwLGGPRVPEQGKVLYvsaEGP-ADELRR--------RLR---AAGADLDL 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 374 DGRFDEWYDELFGDDTFHLYDSFAEAEADRLLAKLAYMRTGLgcDVIVLDHISIVVSASEESDERkmIDRLMTKLKGFAK 453
Cdd:pfam13481 101 PARLLFLSLVESLPLFFLDRGGPLLDADVDALEAALEEVEDP--DLVVIDPLARALGGDENSNSD--VGRLVKALDRLAR 176

                         170
                  ....*....|..
gi 1070102214 454 STGVVLVVICHL 465
Cdd:pfam13481 177 RTGATVLLVHHV 188
PRK08760 PRK08760
replicative DNA helicase; Provisional
 293-504 2.71e-04

replicative DNA helicase; Provisional


Pssm-ID: 181547 [Multi-domain]  Cd Length: 476  Bit Score: 43.75  E-value: 2.71e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 293 GLND---RTLGARGGEVVMVTSGSGMGKSTFVRQQALAWGKRMGKRVGLAMLEESVEDTIQDMMGLNNKV---RLR---- 362
Cdd:PRK08760  215 GYNDfdaMTAGLQPTDLIILAARPAMGKTTFALNIAEYAAIKSKKGVAVFSMEMSASQLAMRLISSNGRInaqRLRtgal 294

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 363 QSDEVKKAIAEDGRFDEwyDELFGDDTFHLYDSFAEAEADRLLAKlaymrTGLGcdVIVLDHISIVVSASEESDERKMID 442
Cdd:PRK08760  295 EDEDWARVTGAIKMLKE--TKIFIDDTPGVSPEVLRSKCRRLKRE-----HDLG--LIVIDYLQLMSVPGNSENRATEIS 365

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1070102214 443 RLMTKLKGFAKSTGVVLVVICHLKNPEKGKphEEGRAVsITDLRGSGALRQLSDTIIALERN 504
Cdd:PRK08760  366 EISRSLKGLAKELNVPVIALSQLNRSLETR--TDKRPV-MADLRESGAIEQDADMIVFIYRD 424
DnaG COG0358
DNA primase (bacterial type) [Replication, recombination and repair];
199-233 2.89e-04

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


Pssm-ID: 440127 [Multi-domain]  Cd Length: 465  Bit Score: 43.59  E-value: 2.89e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1070102214 199 EQIILMFDMDDAGRKAVEEAAQVL--PAGKVRVAVLP 233
Cdd:COG0358   300 DEVILCFDGDAAGQKAALRALELLlkDGLQVRVLFLP 336
RepA_RSF1010_like cd01125
Hexameric Replicative Helicase RepA of plasmid RSF1010 and related proteins; This family ...
 304-508 6.04e-04

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: 41.60  E-value: 6.04e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 304 GEVVMVTSGSGMGKSTFVRQQALAwgkrmgkrvgLAmleesvedTIQDMMGLNNKVRLR--------QSDEVKKAIAEDG 375
Cdd:cd01125     1 GTLGMLVGPPGSGKSFLALDLAVA----------VA--------TGRDWLGERRVKQGRvvylaaedPRDGLRRRLKAIG 62

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 376 RFDEWYDELFGDDTFHLYDSFAEAEADRLLAKLAY-MRTGLGCDVIVLDHISIVVSASEESDERKMiDRLMTKLKGFAKS 454
Cdd:cd01125    63 AHLGDEDAALAENLVIENLRGKPVSIDAEAPELERiIEELEGVRLIIIDTLARVLHGGDENDAADM-GAFVAGLDRIARE 141

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1070102214 455 TGVVLVVICHlknpeKGKpheEGRAVSITDLRGSGALRQLSDTIIALERNQQGD 508
Cdd:cd01125   142 TGAAVLLVHH-----TGK---DAAGDSQQAARGSSALRGAADAEINLSKMDATE 187
PRK06904 PRK06904
replicative DNA helicase; Validated
 261-505 6.30e-04

replicative DNA helicase; Validated


Pssm-ID: 136106 [Multi-domain]  Cd Length: 472  Bit Score: 42.29  E-value: 6.30e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 261 PDGVVSAL-SLKDRVK--EAMTSEDAVGLLFDGCQGLNDRTLGARGGEVVMVTSGSGMGKSTFVRQQALAWGKRMGKRVG 337
Cdd:PRK06904  175 PQNVINLLeNTIDKIEnlAATPTNNGVTGVTTGFTDLDKKTAGLQPSDLIIVAARPSMGKTTFAMNLCENAAMASEKPVL 254

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 338 LAMLEESVEDTIQDMMGlnnkvRLRQSDEVKKAIAEDGRFDEW------------YDELFGDDTFHLYDSFAEAEADRLl 405
Cdd:PRK06904  255 VFSLEMPAEQIMMRMLA-----SLSRVDQTKIRTGQNLDQQDWakisstvgmfkqKPNLYIDDSSGLTPTELRSRARRV- 328

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 406 aklaYMRTGlGCDVIVLDHISIVVSASEESDERKMIDRLMTKLKGFAKSTGVVLVVICHLKNPEKGKphEEGRAVSiTDL 485
Cdd:PRK06904  329 ----YRENG-GLSLIMVDYLQLMRAPGFEDNRTLEIAEISRSLKALAKELKVPVVALSQLNRTLENR--GDKRPVN-SDL 400

                         250       260
                  ....*....|....*....|
gi 1070102214 486 RGSGALRQLSDTIIALERNQ 505
Cdd:PRK06904  401 RESGSIEQDADLIMFIYRDE 420
PRK07773 PRK07773
replicative DNA helicase; Validated
 267-501 1.40e-03

replicative DNA helicase; Validated


Pssm-ID: 236093 [Multi-domain]  Cd Length: 886  Bit Score: 41.66  E-value: 1.40e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 267 ALSLKDRVKEAMTSEDAV---GLLFDGCQG----LNDRTLGARGGEVVMVTSGSGMGKSTFVRQQALAWGKRMGKRVGLA 339
Cdd:PRK07773  173 FVALEDLLQPTFDEIDAIassGGLARGVPTgfteLDAMTNGLHPGQLIIVAARPSMGKTTFGLDFARNCAIRHRLAVAIF 252

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 340 MLEESVEDTIQDMMGLNNKV--------RLRQSDEVKKAIAEdGRFDEWydELFGDDTFHLYDSFAEAEADRLLAKlayM 411
Cdd:PRK07773  253 SLEMSKEQLVMRLLSAEAKIklsdmrsgRMSDDDWTRLARAM-GEISEA--PIFIDDTPNLTVMEIRAKARRLRQE---A 326

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 412 RTGLgcdvIVLDHISIVVSASEESDERKMIDRLMTKLKGFAKSTGVVLVVICHL-KNPEK---GKPHeegravsITDLRG 487
Cdd:PRK07773  327 NLGL----IVVDYLQLMTSGKKYENRQQEVSEISRHLKLLAKELEVPVVALSQLsRGVEQrtdKRPM-------LSDLRE 395

                         250
                  ....*....|....
gi 1070102214 488 SGALRqlSDTIIAL 501
Cdd:PRK07773  396 SGCLT--GDTLILR 407
DnaB_C pfam03796
DnaB-like helicase C terminal domain; The hexameric helicase DnaB unwinds the DNA duplex at ...
 294-503 3.90e-03

DnaB-like helicase C terminal domain; The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli 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: 427509 [Multi-domain]  Cd Length: 254  Bit Score: 39.32  E-value: 3.90e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 294 LNDRTLGARGGEVVMVTSGSGMGKSTFVRQQALAWGKRMGKRVGLAMLEESVEDTIQDMMGLNNKV---RLR----QSDE 366
Cdd:pfam03796   9 LDRLTGGLQPGDLIIIAARPSMGKTAFALNIARNAAVKHKKPVAIFSLEMSAEQLVMRLLASEAGVdsqKLRtgqlTDED 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 367 VKKAIAEDGRFDEWydELFGDDTFHLydSFAE--AEADRLlaklayMRTGlGCDVIVLDHISIVvSASEESDERK----M 440
Cdd:pfam03796  89 WEKLAKAAGRLSEA--PLYIDDTPGL--SIAEirAKARRL------KREH-GLGLIVIDYLQLM-SGGSRGENRQqeisE 156

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1070102214 441 IDRlmtKLKGFAKSTGVVLVVICHL-KNPEKGKPHeegRAVsITDLRGSGALRQLSDTIIALER 503
Cdd:pfam03796 157 ISR---SLKALAKELNVPVIALSQLsRAVEQRTDK---RPQ-LSDLRESGAIEQDADVVMFLYR 213
ATPase pfam06745
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ...
 304-450 7.44e-03

KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and eukaryotes. More than one copy is sometimes found in each protein. This family includes KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria.


Pssm-ID: 429095 [Multi-domain]  Cd Length: 231  Bit Score: 38.38  E-value: 7.44e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1070102214 304 GEVVMVTSGSGMGKSTFVRQQALAWGKRMGKRVGLAMLEESVEDTIQDM--MGLNnkvrlrqsdevkkaiaedgrFDEWY 381
Cdd:pfam06745  19 GRVVLITGGPGTGKTIFGLQFLYNGALKYGEPGVFVTLEEPPEDLRENArsFGWD--------------------LEKLE 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1070102214 382 DE--LFGDDTFHLYDSFAEAE----ADRLLAKLAYMRTGLGCDVIVLDHISIVVSASEESDERKMIDRLMTKLKG 450
Cdd:pfam06745  79 EEgkLAIIDASTSGIGIAEVEdrfdLEELIERLREAIREIGAKRVVIDSITTLFYLLKPAVAREILRRLKRVLKG 153
 
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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