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Conserved domains on  [gi|2128760785|ref|WP_227954172|]
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DnaB-like helicase C-terminal domain-containing protein [Staphylococcus epidermidis]

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 8.65e-92

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: 279.45  E-value: 8.65e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 245 VMVTSGSGMGKSTFVRQQALAWGKRMGKRVGLAMLEESVEDTIQDMMGLNNKVRLRQSDEVKKAIAEDgrFDEWYDELFG 324
Cdd:cd19483     1 VTIGAGSGIGKSTIVRELAYHLITEHGEKVGIISLEESVEETAKGLAGKHLGKPEPLELPRDDITEEE--EDDAFDNELG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 325 DDTFHLYDSFAEAEADRLLAKLAYMRTGLGCDVIVLDHISIVVSASEESDERKMIDRLMTKLKGFAKSTGVVLVVICHLK 404
Cdd:cd19483    79 SGRFFLYDHFGSLDWDNLKEKIRYMVKVLGCKVIVLDHLTILVSGLDSSDERKELDEIMTELAALVKELGVTIILVSHLR 158

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2128760785 405 NPEKGKPHEEGRAVSITDLRGSGALRQLSDTIIALERNQQGDMP---NLVLVRLLKCRFTGDTGIAGYMEYNR 474
Cdd:cd19483   159 RPGGGKGHEEGGEVSESDLRGSSAIAQLSDYVIGLERNKQADDPverNTTRVRVLKNRFTGETGIAGTLYYDE 231
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
88-162 5.44e-12

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


:

Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 61.12  E-value: 5.44e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2128760785   88 KKIVVTEGEIDALTVMELQDCKYPVVSLGhGASAAKKTCAANYEYFDQFEqIILMFDMDDAGRKAVEEAAQVLPA 162
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALG-GHLLSKEQIKLLKKLAKKAE-VILATDPDREGEAIAWELAELLKP 73
 
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 8.65e-92

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: 279.45  E-value: 8.65e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 245 VMVTSGSGMGKSTFVRQQALAWGKRMGKRVGLAMLEESVEDTIQDMMGLNNKVRLRQSDEVKKAIAEDgrFDEWYDELFG 324
Cdd:cd19483     1 VTIGAGSGIGKSTIVRELAYHLITEHGEKVGIISLEESVEETAKGLAGKHLGKPEPLELPRDDITEEE--EDDAFDNELG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 325 DDTFHLYDSFAEAEADRLLAKLAYMRTGLGCDVIVLDHISIVVSASEESDERKMIDRLMTKLKGFAKSTGVVLVVICHLK 404
Cdd:cd19483    79 SGRFFLYDHFGSLDWDNLKEKIRYMVKVLGCKVIVLDHLTILVSGLDSSDERKELDEIMTELAALVKELGVTIILVSHLR 158

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2128760785 405 NPEKGKPHEEGRAVSITDLRGSGALRQLSDTIIALERNQQGDMP---NLVLVRLLKCRFTGDTGIAGYMEYNR 474
Cdd:cd19483   159 RPGGGKGHEEGGEVSESDLRGSSAIAQLSDYVIGLERNKQADDPverNTTRVRVLKNRFTGETGIAGTLYYDE 231
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
88-162 5.44e-12

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 61.12  E-value: 5.44e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2128760785   88 KKIVVTEGEIDALTVMELQDCKYPVVSLGhGASAAKKTCAANYEYFDQFEqIILMFDMDDAGRKAVEEAAQVLPA 162
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALG-GHLLSKEQIKLLKKLAKKAE-VILATDPDREGEAIAWELAELLKP 73
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
228-459 1.19e-11

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 64.17  E-value: 1.19e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 228 GCQGLnDRTL--GARGGEVVMVTSGSGMGKSTFVrQQALAWGKRMGKRVGLAMLEESVEDTIQDMMGLNnkvrlrqsdev 305
Cdd:COG0467     5 GIPGL-DELLggGLPRGSSTLLSGPPGTGKTTLA-LQFLAEGLRRGEKGLYVSFEESPEQLLRRAESLG----------- 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 306 kkaiaedgrFDewYDELFGDDTFHLYDSFAE---AEADRLLAKLAYMRTGLGCDVIVLDHISIVVSASEESDERKmidRL 382
Cdd:COG0467    72 ---------LD--LEEYIESGLLRIIDLSPEelgLDLEELLARLREAVEEFGAKRVVIDSLSGLLLALPDPERLR---EF 137

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2128760785 383 MTKLKGFAKSTGVVLVVICHLKnpekgkpheegravSITDLRGSGALRQLSDTIIALERNQQGDMPNLVLvRLLKCR 459
Cdd:COG0467   138 LHRLLRYLKKRGVTTLLTSETG--------------GLEDEATEGGLSYLADGVILLRYVELGGELRRAL-SVLKMR 199
Toprim_2 pfam13155
Toprim-like; This is a family or Toprim-like proteins.
 91-177 4.27e-11

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


Pssm-ID: 463793 [Multi-domain]  Cd Length: 88  Bit Score: 59.11  E-value: 4.27e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785  91 VVTEGEIDALTVMEL-QDCKYPVVSLGHGASAAKKtcaanyEYFDQF-EQIILMFDMDDAGRKAVEEAAQVLPAGKVRVA 168
Cdd:pfam13155   1 VVFEGYIDALSLAQAgIKNVLYVATLGTALTEAQI------KLLKRYpKEVILAFDNDEAGRKAAKRLAELLKEAGVDVK 74

                          90
                  ....*....|..
gi 2128760785 169 VL---PCKDANE 177
Cdd:pfam13155  75 IRllpDGKDWNE 86
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 88-171 2.23e-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: 53.81  E-value: 2.23e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785  88 KKIVVTEGEIDALTVMELqDCKYPVVSLGhgasaakktcAANYEY-----FDQFEQIILMFDMDDAGRKAVEEAAQVLPA 162
Cdd:cd01029     1 DEVIIVEGYMDVLALHQA-GIKNVVAALG----------TANTEEqlrllKRFARTVILAFDNDEAGKKAAARALELLLA 69


                  ....*....
gi 2128760785 163 GKVRVAVLP 171
Cdd:cd01029    70 LGGRVRVPP 78
PRK05636 PRK05636
replicative DNA helicase; Provisional
 228-441 6.18e-09

replicative DNA helicase; Provisional


Pssm-ID: 180177 [Multi-domain]  Cd Length: 505  Bit Score: 58.31  E-value: 6.18e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 228 GCQGLNDRTLGARGGEVVMVTSGSGMGKST----FVRQQALawgkRMGKRVGLAMLEESVEDTIQDMMGLNNKVRL---- 299
Cdd:PRK05636  251 GFKDLDDLTNGLRGGQMIIVAARPGVGKSTlaldFMRSASI----KHNKASVIFSLEMSKSEIVMRLLSAEAEVRLsdmr 326

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 300 --RQSDEVKKAIAEdgRFDEWYDE-LFGDDTFHLYDSFAEAEADRLLAKlaymrtgLGCDVIVLDHISIVVSASEESDER 376
Cdd:PRK05636  327 ggKMDEDAWEKLVQ--RLGKIAQApIFIDDSANLTMMEIRSKARRLKQK-------HDLKLIVVDYLQLMSSGKRVESRQ 397

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2128760785 377 KMIDRLMTKLKGFAKSTGVVLVVICHLKnpeKGKPHEEGRAVSITDLRGSGALRQLSDTIIALER 441
Cdd:PRK05636  398 QEVSEFSRQLKLLAKELDVPLIAISQLN---RGPESRTDKRPQLADLRESGSLEQDADMVMLLYR 459
AAA_25 pfam13481
AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.
 242-403 7.61e-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: 43.52  E-value: 7.61e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 242 GEVVMVTSGSGMGKSTFVRQQALA-------WGKRMGKRVGLAML---EESvEDTIQDmmglnnkvRLRqsdEVKKAIAE 311
Cdd:pfam13481  33 GGLGLLAGAPGTGKTTLALDLAAAvatgkpwLGGPRVPEQGKVLYvsaEGP-ADELRR--------RLR---AAGADLDL 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 312 DGRFDEWYDELFGDDTFHLYDSFAEAEADRLLAKLAYMRTGLgcDVIVLDHISIVVSASEESDERkmIDRLMTKLKGFAK 391
Cdd:pfam13481 101 PARLLFLSLVESLPLFFLDRGGPLLDADVDALEAALEEVEDP--DLVVIDPLARALGGDENSNSD--VGRLVKALDRLAR 176

                         170
                  ....*....|..
gi 2128760785 392 STGVVLVVICHL 403
Cdd:pfam13481 177 RTGATVLLVHHV 188
DnaG COG0358
DNA primase (bacterial type) [Replication, recombination and repair];
137-171 2.68e-04

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


Pssm-ID: 440127 [Multi-domain]  Cd Length: 465  Bit Score: 43.59  E-value: 2.68e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2128760785 137 EQIILMFDMDDAGRKAVEEAAQVL--PAGKVRVAVLP 171
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 ...
 245-474 8.65e-92

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: 279.45  E-value: 8.65e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 245 VMVTSGSGMGKSTFVRQQALAWGKRMGKRVGLAMLEESVEDTIQDMMGLNNKVRLRQSDEVKKAIAEDgrFDEWYDELFG 324
Cdd:cd19483     1 VTIGAGSGIGKSTIVRELAYHLITEHGEKVGIISLEESVEETAKGLAGKHLGKPEPLELPRDDITEEE--EDDAFDNELG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 325 DDTFHLYDSFAEAEADRLLAKLAYMRTGLGCDVIVLDHISIVVSASEESDERKMIDRLMTKLKGFAKSTGVVLVVICHLK 404
Cdd:cd19483    79 SGRFFLYDHFGSLDWDNLKEKIRYMVKVLGCKVIVLDHLTILVSGLDSSDERKELDEIMTELAALVKELGVTIILVSHLR 158

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2128760785 405 NPEKGKPHEEGRAVSITDLRGSGALRQLSDTIIALERNQQGDMP---NLVLVRLLKCRFTGDTGIAGYMEYNR 474
Cdd:cd19483   159 RPGGGKGHEEGGEVSESDLRGSSAIAQLSDYVIGLERNKQADDPverNTTRVRVLKNRFTGETGIAGTLYYDE 231
DnaB_C cd00984
C-terminal domain of DnaB helicase; DnaB helicase C-terminal domain. The hexameric helicase ...
 228-480 6.70e-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: 74.47  E-value: 6.70e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 228 GCQGLNDRTLGARGGEVVMVTSGSGMGKSTFVRQQALAWGKRMGKRVGLAMLEESVEDTIQDMMGLNNKV---RLR---Q 301
Cdd:cd00984     5 GFTDLDKLTGGLQPGDLIIIAARPSMGKTAFALNIAENIALDEGLPVLFFSLEMSAEQLAERLLSSESGVslsKLRtgrL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 302 SDEVKKAIAED-GRFDEWYdeLFGDDTFHLYDSFAEAEADRLLaklaymRTGLGCDVIVLDHISIVvSASEESDERK--- 377
Cdd:cd00984    85 DDEDWERLTAAmGELSELP--LYIDDTPGLTVDEIRAKARRLK------REHGGLGLIVIDYLQLI-RGSKRAENRQqev 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 378 -MIDRlmtKLKGFAKSTGVVLVVICHL-KNPEKGkpheEGRAVSITDLRGSGALRQLSDTIIALER----NQQGDMPNLV 451
Cdd:cd00984   156 aEISR---SLKALAKELNVPVIALSQLnRGVESR----TDKRPMLSDLRESGSIEQDADVVIFLYRdeyyDKDSEDKGIA 228

                         250       260
                  ....*....|....*....|....*....
gi 2128760785 452 LVRLLKCRFtGDTGIAgYMEYNRETGWLE 480
Cdd:cd00984   229 EIIIAKNRN-GPTGTV-YLAFNPEYTRFT 255
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
88-162 5.44e-12

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 61.12  E-value: 5.44e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2128760785   88 KKIVVTEGEIDALTVMELQDCKYPVVSLGhGASAAKKTCAANYEYFDQFEqIILMFDMDDAGRKAVEEAAQVLPA 162
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALG-GHLLSKEQIKLLKKLAKKAE-VILATDPDREGEAIAWELAELLKP 73
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
228-459 1.19e-11

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 64.17  E-value: 1.19e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 228 GCQGLnDRTL--GARGGEVVMVTSGSGMGKSTFVrQQALAWGKRMGKRVGLAMLEESVEDTIQDMMGLNnkvrlrqsdev 305
Cdd:COG0467     5 GIPGL-DELLggGLPRGSSTLLSGPPGTGKTTLA-LQFLAEGLRRGEKGLYVSFEESPEQLLRRAESLG----------- 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 306 kkaiaedgrFDewYDELFGDDTFHLYDSFAE---AEADRLLAKLAYMRTGLGCDVIVLDHISIVVSASEESDERKmidRL 382
Cdd:COG0467    72 ---------LD--LEEYIESGLLRIIDLSPEelgLDLEELLARLREAVEEFGAKRVVIDSLSGLLLALPDPERLR---EF 137

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2128760785 383 MTKLKGFAKSTGVVLVVICHLKnpekgkpheegravSITDLRGSGALRQLSDTIIALERNQQGDMPNLVLvRLLKCR 459
Cdd:COG0467   138 LHRLLRYLKKRGVTTLLTSETG--------------GLEDEATEGGLSYLADGVILLRYVELGGELRRAL-SVLKMR 199
Twinkle_C cd01122
C-terminal domain of Twinkle; Twinkle ( T7 gp4-like protein with intramitochondrial nucleoid ...
 207-477 1.23e-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: 64.95  E-value: 1.23e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 207 SLKDRVKEAMT-SEDAVGLLFDGCQGLNDRTLGARGGEVVMVTSGSGMGKSTFVRQQAL---------AWGKrmgkrvgl 276
Cdd:cd01122     7 DLRELVYEELLnSEQVAGVQWKRFPSLNKLLKGHRRGELTIFTGPTGSGKTTFLSEYSLdlcmqgvntLWGS-------- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 277 amLEESVEDTIQDMMGLNNKVRLRQSDEvkkaiaedgRFDEWYDElFGDDTFHLYDSFAEAEADRLLAKLAYMRTGLGCD 356
Cdd:cd01122    79 --FEIKNVRLAKTMLTQFAGKNLEDNLR---------EFDEWADK-FELLPMYFMKFHGSTDIDEVLDAMEHAVYVYDIQ 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 357 VIVLDHISIVVSASEESDERKMI-DRLMTKLKGFAKSTGVVLVVICHlknPEKgkpHEEGRAVSITDLRGSGALRQLSDT 435
Cdd:cd01122   147 HIVIDNLQFMMGTQASGSDRFELqDLIIGKFRRFATNNNVHITLVIH---PRK---EDDDNELTTSSIFGSAKATQEADN 220

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|..
gi 2128760785 436 IIALERNQQGDMPNLVLVRLLKCRFTGDTGIAgYMEYNRETG 477
Cdd:cd01122   221 VLILQDKRLISGEGKKFLQIKKNRFDGDLGVI-PLEFNKNSL 261
Toprim_2 pfam13155
Toprim-like; This is a family or Toprim-like proteins.
 91-177 4.27e-11

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


Pssm-ID: 463793 [Multi-domain]  Cd Length: 88  Bit Score: 59.11  E-value: 4.27e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785  91 VVTEGEIDALTVMEL-QDCKYPVVSLGHGASAAKKtcaanyEYFDQF-EQIILMFDMDDAGRKAVEEAAQVLPAGKVRVA 168
Cdd:pfam13155   1 VVFEGYIDALSLAQAgIKNVLYVATLGTALTEAQI------KLLKRYpKEVILAFDNDEAGRKAAKRLAELLKEAGVDVK 74

                          90
                  ....*....|..
gi 2128760785 169 VL---PCKDANE 177
Cdd:pfam13155  75 IRllpDGKDWNE 86
RecA-like_superfamily cd01120
RecA-like_NTPases; RecA-like NTPases. This superfamily includes the NTP binding domain of F1 ...
 245-430 3.56e-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: 3.56e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 245 VMVTSGSGMGKSTFVRQQALAWGKrMGKRVGLAMLeesvedtiqdmmglnnkvrlrqsdevkkaiaedgrfdewydelfg 324
Cdd:cd01120     1 ILITGPPGSGKTTLLLQFAEQALL-SDEPVIFISF--------------------------------------------- 34

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 325 ddtfhlydsfaeaeADRLLAKLAYMRTGLGCDVIVLDHISIVVSASEEsDERKMIDRLMTKLKGFAKSTGVVLVVICHLK 404
Cdd:cd01120    35 --------------LDTILEAIEDLIEEKKLDIIIIDSLSSLARASQG-DRSSELLEDLAKLLRAARNTGITVIATIHSD 99

                         170       180
                  ....*....|....*....|....*.
gi 2128760785 405 NPekgkphEEGRAVSITDLRGSGALR 430
Cdd:cd01120   100 KF------DIDRGGSSNDERLLKSLR 119
TOPRIM_primases cd01029
TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 88-171 2.23e-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: 53.81  E-value: 2.23e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785  88 KKIVVTEGEIDALTVMELqDCKYPVVSLGhgasaakktcAANYEY-----FDQFEQIILMFDMDDAGRKAVEEAAQVLPA 162
Cdd:cd01029     1 DEVIIVEGYMDVLALHQA-GIKNVVAALG----------TANTEEqlrllKRFARTVILAFDNDEAGKKAAARALELLLA 69


                  ....*....
gi 2128760785 163 GKVRVAVLP 171
Cdd:cd01029    70 LGGRVRVPP 78
PRK05636 PRK05636
replicative DNA helicase; Provisional
 228-441 6.18e-09

replicative DNA helicase; Provisional


Pssm-ID: 180177 [Multi-domain]  Cd Length: 505  Bit Score: 58.31  E-value: 6.18e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 228 GCQGLNDRTLGARGGEVVMVTSGSGMGKST----FVRQQALawgkRMGKRVGLAMLEESVEDTIQDMMGLNNKVRL---- 299
Cdd:PRK05636  251 GFKDLDDLTNGLRGGQMIIVAARPGVGKSTlaldFMRSASI----KHNKASVIFSLEMSKSEIVMRLLSAEAEVRLsdmr 326

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 300 --RQSDEVKKAIAEdgRFDEWYDE-LFGDDTFHLYDSFAEAEADRLLAKlaymrtgLGCDVIVLDHISIVVSASEESDER 376
Cdd:PRK05636  327 ggKMDEDAWEKLVQ--RLGKIAQApIFIDDSANLTMMEIRSKARRLKQK-------HDLKLIVVDYLQLMSSGKRVESRQ 397

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2128760785 377 KMIDRLMTKLKGFAKSTGVVLVVICHLKnpeKGKPHEEGRAVSITDLRGSGALRQLSDTIIALER 441
Cdd:PRK05636  398 QEVSEFSRQLKLLAKELDVPLIAISQLN---RGPESRTDKRPQLADLRESGSLEQDADMVMLLYR 459
KaiC-like cd01124
Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. ...
 242-470 3.21e-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: 54.19  E-value: 3.21e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 242 GEVVMVTSGSGMGKSTFVrQQALAWGKRMGKRVGLAMLEESVEDTIQDMMGLNNKVRlrqsdevkkAIAEDGRFDewyde 321
Cdd:cd01124    19 GSVTLLTGGPGTGKTLFG-LQFLYAGAKNGEPGLFFTFEESPERLLRNAKSFGWDFD---------EMEDEGKLI----- 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 322 lFGDDTFHLYDSFaeaEADRLLAKLAYMRTGLGCDVIVLDHISIVvsaSEESDERKMIDRLMTKLKGFAKSTGVVLVVIc 401
Cdd:cd01124    84 -IVDAPPTEAGRF---SLDELLSRILSIIKSFKAKRVVIDSLSGL---RRAKEDQMRARRIVIALLNELRAAGVTTIFT- 155

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 402 hlknpekgkphEEGRAVSITDLRGSGALRQLSDTIIALeRNQQGDMPNLVLVRLLKCRFTG-DTGIAGYM 470
Cdd:cd01124   156 -----------SEMRSFLSSESAGGGDVSFIVDGVILL-RYVEIEGELRRTIRVLKMRGTGhDTGTHPFE 213
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 89-162 1.15e-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: 49.66  E-value: 1.15e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785  89 KIVVTEGEIDALTVMELQDCKY--PVVSLGHGASAAKKTCAANYEYFDQF----EQIILMFDMDDAGRKAVEEAAQVLPA 162
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGFqaVVAVLGHLLSLEKGPKKKALKALKELalkaKEVILATDPDREGEAIALKLLELKEL 80
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 88-170 4.66e-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: 47.42  E-value: 4.66e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785  88 KKIVVTEGEIDALTVMELQDCKYPVVSL-GHGASAAKKTCAANyeyFDQFEQIILMFDMDDAGRKAVEEAAQVLPAGKVR 166
Cdd:cd00188     1 KKLIIVEGPSDALALAQAGGYGGAVVALgGHALNKTRELLKRL---LGEAKEVIIATDADREGEAIALRLLELLKSLGKK 77


                  ....
gi 2128760785 167 VAVL 170
Cdd:cd00188    78 VRRL 81
PRK08840 PRK08840
replicative DNA helicase; Provisional
 181-443 1.05e-06

replicative DNA helicase; Provisional


Pssm-ID: 181562 [Multi-domain]  Cd Length: 464  Bit Score: 51.14  E-value: 1.05e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 181 MGEDK--AILEQVWNANpwvpDGVVSALSLKDRVKEAM-----TSEDAVGLLFDGCQGLNDRTLGARGGEVVMVTSGSGM 253
Cdd:PRK08840  153 MAESKvfAIAEARTSEN----EGPQNVDSILEKTLERIellykTPQDGVTGVDTGFTDLNKKTAGLQGSDLIIVAARPSM 228

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 254 GKSTFVRQQALAWGKRMGKRVGLAMLEESVEDTIQDMMGL-----NNKVRLRQSDEVKKA-IAEDGRFDEWYDELFGDDT 327
Cdd:PRK08840  229 GKTTFAMNLCENAAMDQDKPVLIFSLEMPAEQLMMRMLASlsrvdQTKIRTGQLDDEDWArISSTMGILMEKKNMYIDDS 308

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 328 FHLYDSFAEAEADRLlaklayMRTGLGCDVIVLDHISIVVSASEESDERKMIDRLMTKLKGFAKSTGVVLVVICHLKNPE 407
Cdd:PRK08840  309 SGLTPTEVRSRARRI------AREHGGLSMIMVDYLQLMRVPALSDNRTLEIAEISRSLKALAKELNVPVVALSQLNRSL 382

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 2128760785 408 KGKphEEGRAVSiTDLRGSGALRQLSDTIIALERNQ 443
Cdd:PRK08840  383 EQR--ADKRPVN-SDLRESGSIEQDADLIMFIYRDE 415
TOPRIM_DnaG_primases cd03364
TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase ...
 88-170 1.60e-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: 45.97  E-value: 1.60e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785  88 KKIVVTEGEIDALTVMELQDcKYPVVSLGhgasaakktcAANYEyfDQFE-------QIILMFDMDDAGRKAVEEAAQVL 160
Cdd:cd03364     1 KKVILVEGYMDVIALHQAGI-KNVVASLG----------TALTE--EQAEllkrlakEVILAFDGDEAGQKAALRALELL 67

                          90
                  ....*....|..
gi 2128760785 161 -PAGK-VRVAVL 170
Cdd:cd03364    68 lKLGLnVRVLTL 79
PRK07004 PRK07004
replicative DNA helicase; Provisional
 228-443 5.08e-05

replicative DNA helicase; Provisional


Pssm-ID: 235907 [Multi-domain]  Cd Length: 460  Bit Score: 45.67  E-value: 5.08e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 228 GCQGLNDRTLGARGGEVVMVTSGSGMGKSTFvrqqALAWGKRMGKRVGLAMLEESVE--DTIQDMMGLNNKVRLRQSD-E 304
Cdd:PRK07004  199 GFVDLDRMTSGMHGGELIIVAGRPSMGKTAF----SMNIGEYVAVEYGLPVAVFSMEmpGTQLAMRMLGSVGRLDQHRmR 274

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 305 VKKAIAED--------GRFDEwyDELFGDDTFHLYDSFAEAEADRLLAKLAYMrtGLgcdvIVLDHISIVVSASEESDER 376
Cdd:PRK07004  275 TGRLTDEDwpklthavQKMSE--AQLFIDETGGLNPMELRSRARRLARQCGKL--GL----IIIDYLQLMSGSSQGENRA 346

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2128760785 377 KMIDRLMTKLKGFAKSTGVVLVVICHLKNPEKGKPHEegRAVsITDLRGSGALRQLSDTIIALERNQ 443
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.
 242-403 7.61e-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: 43.52  E-value: 7.61e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 242 GEVVMVTSGSGMGKSTFVRQQALA-------WGKRMGKRVGLAML---EESvEDTIQDmmglnnkvRLRqsdEVKKAIAE 311
Cdd:pfam13481  33 GGLGLLAGAPGTGKTTLALDLAAAvatgkpwLGGPRVPEQGKVLYvsaEGP-ADELRR--------RLR---AAGADLDL 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 312 DGRFDEWYDELFGDDTFHLYDSFAEAEADRLLAKLAYMRTGLgcDVIVLDHISIVVSASEESDERkmIDRLMTKLKGFAK 391
Cdd:pfam13481 101 PARLLFLSLVESLPLFFLDRGGPLLDADVDALEAALEEVEDP--DLVVIDPLARALGGDENSNSD--VGRLVKALDRLAR 176

                         170
                  ....*....|..
gi 2128760785 392 STGVVLVVICHL 403
Cdd:pfam13481 177 RTGATVLLVHHV 188
DnaG COG0358
DNA primase (bacterial type) [Replication, recombination and repair];
137-171 2.68e-04

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


Pssm-ID: 440127 [Multi-domain]  Cd Length: 465  Bit Score: 43.59  E-value: 2.68e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2128760785 137 EQIILMFDMDDAGRKAVEEAAQVL--PAGKVRVAVLP 171
Cdd:COG0358   300 DEVILCFDGDAAGQKAALRALELLlkDGLQVRVLFLP 336
PRK08760 PRK08760
replicative DNA helicase; Provisional
 231-442 2.78e-04

replicative DNA helicase; Provisional


Pssm-ID: 181547 [Multi-domain]  Cd Length: 476  Bit Score: 43.37  E-value: 2.78e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 231 GLND---RTLGARGGEVVMVTSGSGMGKSTFVRQQALAWGKRMGKRVGLAMLEESVEDTIQDMMGLNNKV---RLR---- 300
Cdd:PRK08760  215 GYNDfdaMTAGLQPTDLIILAARPAMGKTTFALNIAEYAAIKSKKGVAVFSMEMSASQLAMRLISSNGRInaqRLRtgal 294

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 301 QSDEVKKAIAEDGRFDEwyDELFGDDTFHLYDSFAEAEADRLLAKlaymrTGLGcdVIVLDHISIVVSASEESDERKMID 380
Cdd:PRK08760  295 EDEDWARVTGAIKMLKE--TKIFIDDTPGVSPEVLRSKCRRLKRE-----HDLG--LIVIDYLQLMSVPGNSENRATEIS 365

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2128760785 381 RLMTKLKGFAKSTGVVLVVICHLKNPEKGKphEEGRAVsITDLRGSGALRQLSDTIIALERN 442
Cdd:PRK08760  366 EISRSLKGLAKELNVPVIALSQLNRSLETR--TDKRPV-MADLRESGAIEQDADMIVFIYRD 424
PRK06904 PRK06904
replicative DNA helicase; Validated
 199-443 5.36e-04

replicative DNA helicase; Validated


Pssm-ID: 136106 [Multi-domain]  Cd Length: 472  Bit Score: 42.29  E-value: 5.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 199 PDGVVSAL-SLKDRVK--EAMTSEDAVGLLFDGCQGLNDRTLGARGGEVVMVTSGSGMGKSTFVRQQALAWGKRMGKRVG 275
Cdd:PRK06904  175 PQNVINLLeNTIDKIEnlAATPTNNGVTGVTTGFTDLDKKTAGLQPSDLIIVAARPSMGKTTFAMNLCENAAMASEKPVL 254

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 276 LAMLEESVEDTIQDMMGlnnkvRLRQSDEVKKAIAEDGRFDEW------------YDELFGDDTFHLYDSFAEAEADRLl 343
Cdd:PRK06904  255 VFSLEMPAEQIMMRMLA-----SLSRVDQTKIRTGQNLDQQDWakisstvgmfkqKPNLYIDDSSGLTPTELRSRARRV- 328

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 344 aklaYMRTGlGCDVIVLDHISIVVSASEESDERKMIDRLMTKLKGFAKSTGVVLVVICHLKNPEKGKphEEGRAVSiTDL 423
Cdd:PRK06904  329 ----YRENG-GLSLIMVDYLQLMRAPGFEDNRTLEIAEISRSLKALAKELKVPVVALSQLNRTLENR--GDKRPVN-SDL 400

                         250       260
                  ....*....|....*....|
gi 2128760785 424 RGSGALRQLSDTIIALERNQ 443
Cdd:PRK06904  401 RESGSIEQDADLIMFIYRDE 420
RepA_RSF1010_like cd01125
Hexameric Replicative Helicase RepA of plasmid RSF1010 and related proteins; This family ...
 242-446 6.95e-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: 41.21  E-value: 6.95e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 242 GEVVMVTSGSGMGKSTFVRQQALAwgkrmgkrvgLAmleesvedTIQDMMGLNNKVRLR--------QSDEVKKAIAEDG 313
Cdd:cd01125     1 GTLGMLVGPPGSGKSFLALDLAVA----------VA--------TGRDWLGERRVKQGRvvylaaedPRDGLRRRLKAIG 62

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 314 RFDEWYDELFGDDTFHLYDSFAEAEADRLLAKLAY-MRTGLGCDVIVLDHISIVVSASEESDERKMiDRLMTKLKGFAKS 392
Cdd:cd01125    63 AHLGDEDAALAENLVIENLRGKPVSIDAEAPELERiIEELEGVRLIIIDTLARVLHGGDENDAADM-GAFVAGLDRIARE 141

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2128760785 393 TGVVLVVICHlknpeKGKpheEGRAVSITDLRGSGALRQLSDTIIALERNQQGD 446
Cdd:cd01125   142 TGAAVLLVHH-----TGK---DAAGDSQQAARGSSALRGAADAEINLSKMDATE 187
PRK07773 PRK07773
replicative DNA helicase; Validated
 205-439 1.57e-03

replicative DNA helicase; Validated


Pssm-ID: 236093 [Multi-domain]  Cd Length: 886  Bit Score: 41.27  E-value: 1.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 205 ALSLKDRVKEAMTSEDAV---GLLFDGCQG----LNDRTLGARGGEVVMVTSGSGMGKSTFVRQQALAWGKRMGKRVGLA 277
Cdd:PRK07773  173 FVALEDLLQPTFDEIDAIassGGLARGVPTgfteLDAMTNGLHPGQLIIVAARPSMGKTTFGLDFARNCAIRHRLAVAIF 252

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 278 MLEESVEDTIQDMMGLNNKV--------RLRQSDEVKKAIAEdGRFDEWydELFGDDTFHLYDSFAEAEADRLLAKlayM 349
Cdd:PRK07773  253 SLEMSKEQLVMRLLSAEAKIklsdmrsgRMSDDDWTRLARAM-GEISEA--PIFIDDTPNLTVMEIRAKARRLRQE---A 326

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 350 RTGLgcdvIVLDHISIVVSASEESDERKMIDRLMTKLKGFAKSTGVVLVVICHL-KNPEK---GKPHeegravsITDLRG 425
Cdd:PRK07773  327 NLGL----IVVDYLQLMTSGKKYENRQQEVSEISRHLKLLAKELEVPVVALSQLsRGVEQrtdKRPM-------LSDLRE 395

                         250
                  ....*....|....
gi 2128760785 426 SGALRqlSDTIIAL 439
Cdd:PRK07773  396 SGCLT--GDTLILR 407
DnaB_C pfam03796
DnaB-like helicase C terminal domain; The hexameric helicase DnaB unwinds the DNA duplex at ...
 232-441 5.59e-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: 38.55  E-value: 5.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 232 LNDRTLGARGGEVVMVTSGSGMGKSTFVRQQALAWGKRMGKRVGLAMLEESVEDTIQDMMGLNNKV---RLR----QSDE 304
Cdd:pfam03796   9 LDRLTGGLQPGDLIIIAARPSMGKTAFALNIARNAAVKHKKPVAIFSLEMSAEQLVMRLLASEAGVdsqKLRtgqlTDED 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 305 VKKAIAEDGRFDEWydELFGDDTFHLydSFAE--AEADRLLAKLaymrtglGCDVIVLDHISIVvSASEESDERK----M 378
Cdd:pfam03796  89 WEKLAKAAGRLSEA--PLYIDDTPGL--SIAEirAKARRLKREH-------GLGLIVIDYLQLM-SGGSRGENRQqeisE 156

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2128760785 379 IDRlmtKLKGFAKSTGVVLVVICHL-KNPEKGKPHeegRAVsITDLRGSGALRQLSDTIIALER 441
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 ...
 242-388 8.98e-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: 38.00  E-value: 8.98e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2128760785 242 GEVVMVTSGSGMGKSTFVRQQALAWGKRMGKRVGLAMLEESVEDTIQDM--MGLNnkvrlrqsdevkkaiaedgrFDEWY 319
Cdd:pfam06745  19 GRVVLITGGPGTGKTIFGLQFLYNGALKYGEPGVFVTLEEPPEDLRENArsFGWD--------------------LEKLE 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2128760785 320 DE--LFGDDTFHLYDSFAEAE----ADRLLAKLAYMRTGLGCDVIVLDHISIVVSASEESDERKMIDRLMTKLKG 388
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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