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Conserved domains on  [gi|1278360562|gb|PIY99998|]
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MAG: cell division control protein Cdc6 [Candidatus Huberarchaeum crystalense]

Protein Classification

Cdc6/Cdc18 family protein( domain architecture ID 11444962)

Cdc6/Cdc18 family protein contains an N-terminal AAA+ ATPase domain and a C-terminal winged-helix (WH) domain, similar to human cell division control protein 6 homolog that is involved in the initiation of DNA replication

CATH:  3.40.50.300
Gene Ontology:  GO:0006270|GO:0051301|GO:0005524
PubMed:  20130679|22908236|18208389|16828312|18466635|15037233
SCOP:  3000034|4000283

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CDC6 COG1474
Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];
15-390 8.70e-130

Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];


:

Pssm-ID: 441083 [Multi-domain]  Cd Length: 389  Bit Score: 378.42  E-value: 8.70e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562  15 NQKSKIFKNKKILSLDYIPEQILHRQKQIEEITKILSPIFREEPTSNIFIYGKPGTGKTTTINYIIKEIKyfldkQENKN 94
Cdd:COG1474     7 LWDESIFRDREVLSPDYVPDRLPHREEEIEELASALRPALRGERPSNVLIYGPTGTGKTAVAKYVLEELE-----EEAEE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562  95 LQQKIKIIYLNCKEghvSDTEYRLISTTCS--YFGKQIPA-GLSIKNIYDEFFRVVDYQKANIILVLDEIDNIVSKNSDD 171
Cdd:COG1474    82 RGVDVRVVYVNCRQ---ASTRYRVLSRILEelGSGEDIPStGLSTDELFDRLYEALDERDGVLVVVLDEIDYLVDDEGDD 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 172 FLYNL--ARKRFKNINLTLIGISNNINFIELLDPRIKSALNQEEFIFPPYNAEELLDILKQRSDNAFEKSVVSEGVLEKV 249
Cdd:COG1474   159 LLYQLlrANEELEGARVGVIGISNDLEFLENLDPRVKSSLGEEEIVFPPYDADELRDILEDRAELAFYDGVLSDEVIPLI 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 250 AGIIAQQNGDMRRAINLLRVVGELAERNNLNKLSLELVEEAEKKLEENIMLEMIYSQPLHSKIILYSVLQNTIKTKTTTT 329
Cdd:COG1474   239 AALAAQEHGDARKAIDLLRVAGEIAEREGSDRVTEEHVREAREKIERDRLLEVLRGLPTHEKLVLLAIAELLKDGEDPVR 318

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1278360562 330 G-KVYEQYEQLCKTTKQKPLTSRRVTDFVVELDMLGLISTNIASYGRYGRTRELSINYPKQI 390
Cdd:COG1474   319 TgEVYEAYEELCEELGVDPLSYRRVRDYLSELEMLGLIEAEVSSKGRRGRTREISLSVDPEV 380
 
Name Accession Description Interval E-value
CDC6 COG1474
Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];
15-390 8.70e-130

Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];


Pssm-ID: 441083 [Multi-domain]  Cd Length: 389  Bit Score: 378.42  E-value: 8.70e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562  15 NQKSKIFKNKKILSLDYIPEQILHRQKQIEEITKILSPIFREEPTSNIFIYGKPGTGKTTTINYIIKEIKyfldkQENKN 94
Cdd:COG1474     7 LWDESIFRDREVLSPDYVPDRLPHREEEIEELASALRPALRGERPSNVLIYGPTGTGKTAVAKYVLEELE-----EEAEE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562  95 LQQKIKIIYLNCKEghvSDTEYRLISTTCS--YFGKQIPA-GLSIKNIYDEFFRVVDYQKANIILVLDEIDNIVSKNSDD 171
Cdd:COG1474    82 RGVDVRVVYVNCRQ---ASTRYRVLSRILEelGSGEDIPStGLSTDELFDRLYEALDERDGVLVVVLDEIDYLVDDEGDD 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 172 FLYNL--ARKRFKNINLTLIGISNNINFIELLDPRIKSALNQEEFIFPPYNAEELLDILKQRSDNAFEKSVVSEGVLEKV 249
Cdd:COG1474   159 LLYQLlrANEELEGARVGVIGISNDLEFLENLDPRVKSSLGEEEIVFPPYDADELRDILEDRAELAFYDGVLSDEVIPLI 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 250 AGIIAQQNGDMRRAINLLRVVGELAERNNLNKLSLELVEEAEKKLEENIMLEMIYSQPLHSKIILYSVLQNTIKTKTTTT 329
Cdd:COG1474   239 AALAAQEHGDARKAIDLLRVAGEIAEREGSDRVTEEHVREAREKIERDRLLEVLRGLPTHEKLVLLAIAELLKDGEDPVR 318

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1278360562 330 G-KVYEQYEQLCKTTKQKPLTSRRVTDFVVELDMLGLISTNIASYGRYGRTRELSINYPKQI 390
Cdd:COG1474   319 TgEVYEAYEELCEELGVDPLSYRRVRDYLSELEMLGLIEAEVSSKGRRGRTREISLSVDPEV 380
TIGR02928 TIGR02928
orc1/cdc6 family replication initiation protein; Members of this protein family are found ...
 20-383 7.81e-118

orc1/cdc6 family replication initiation protein; Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274354 [Multi-domain]  Cd Length: 365  Bit Score: 347.31  E-value: 7.81e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562  20 IFKNKKILSLDYIPEQILHRQKQIEEITKILSPIFREEPTSNIFIYGKPGTGKTTTINYIIKEIKYfldkqENKNLQQKI 99
Cdd:TIGR02928   1 IFRNRDLLEPDYVPDRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEE-----AAEDRDVRV 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 100 KIIYLNCkegHVSDTEYRLISTTC---SYFGKQIPA-GLSIKNIYDEFFRVVDYQKANIILVLDEIDNIVSKNsDDFLYN 175
Cdd:TIGR02928  76 VTVYVNC---QILDTLYQVLVELAnqlRGSGEEVPTtGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGDD-DDLLYQ 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 176 LARKRFK----NINLTLIGISNNINFIELLDPRIKSALNQEEFIFPPYNAEELLDILKQRSDNAFEKSVVSEGVLEKVAG 251
Cdd:TIGR02928 152 LSRARSNgdldNAKVGVIGISNDLKFRENLDPRVKSSLCEEEIIFPPYDAEELRDILENRAEKAFYDGVLDDGVIPLCAA 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 252 IIAQQNGDMRRAINLLRVVGELAERNNLNKLSLELVEEAEKKLEENIMLEMIYSQPLHSKIILYSVLQ-NTIKTKTTTTG 330
Cdd:TIGR02928 232 LAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIEKDRLLELIRGLPTHSKLVLLAIANlAANDEDPFRTG 311

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1278360562 331 KVYEQYEQLCKTTKQKPLTSRRVTDFVVELDMLGLISTNIASYGRYGRTRELS 383
Cdd:TIGR02928 312 EVYEVYKEVCEDIGVDPLTQRRISDLLNELDMLGLVEAEERNKGRGGRTREYS 364
cdc6 PRK00411
ORC1-type DNA replication protein;
5-387 2.10e-104

ORC1-type DNA replication protein;


Pssm-ID: 234751 [Multi-domain]  Cd Length: 394  Bit Score: 314.09  E-value: 2.10e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562   5 NIQEILQSIVNQKSKIFKNKKILSLDYIPEQILHRQKQIEEITKILSPIFREEPTSNIFIYGKPGTGKTTTINYIIKEIK 84
Cdd:PRK00411    1 SLDDIFEDLLMWDETIFKDEEVLEPDYVPENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562  85 yfldkqenkNLQQKIKIIYLNCkegHVSDTEYRLISTTC-SYFGKQIPA-GLSIKNIYDEFFRVVDYQKANIILVLDEID 162
Cdd:PRK00411   81 ---------EIAVKVVYVYINC---QIDRTRYAIFSEIArQLFGHPPPSsGLSFDELFDKIAEYLDERDRVLIVALDDIN 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 163 NIVSKNSDDFLYNLAR--KRFKNINLTLIGISNNINFIELLDPRIKSALNQEEFIFPPYNAEELLDILKQRSDNAFEKSV 240
Cdd:PRK00411  149 YLFEKEGNDVLYSLLRahEEYPGARIGVIGISSDLTFLYILDPRVKSVFRPEEIYFPPYTADEIFDILKDRVEEGFYPGV 228

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 241 VSEGVLEKVAGIIAQQNGDMRRAINLLRVVGELAERNNLNKLSLELVEEAEKKLEENIMLEMIYSQPLHSKIILYS-VLQ 319
Cdd:PRK00411  229 VDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIVHLSEVLRTLPLHEKLLLRAiVRL 308

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1278360562 320 NTIKTKTTTTGKVYEQYEQLCKTTKQKPLTSRRVTDFVVELDMLGLISTNIASYGRYGRTRELSINYP 387
Cdd:PRK00411  309 LKKGGDEVTTGEVYEEYKELCEELGYEPRTHTRFYEYINKLDMLGIINTRYSGKGGRGRTRLISLSYD 376
Cdc6_C cd08768
Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), ...
 307-390 2.14e-19

Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding; This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases the specificity of the ORC-origins interaction. Further studies suggest that hydrolysis of Cdc6-bound ATP promotes the association of the replication licensing factor Cdt1 with origins through an interaction with Orc6 and this in turn promotes the loading of MCM2-7 helicase onto chromatin. The MCM2-7 complex promotes the unwinding of DNA origins, and the binding of additional factors to initiate the DNA replication. S-Cdk (S-phase cyclin and cyclin-dependent kinase complex) prevents rereplication by causing the Cdc6 protein to dissociate from ORC and prevents the Cdc6 and MCM proteins from reassembling at any origin. By phosphorylating Cdc6, S-Cdk also triggers Cdc6's ubiquitination. The Cdc6 protein is composed of three domains, an N-terminal AAA+ domain with Walker A and B, and Sensor-1 and -2 motifs. The central region contains a conserved nucleotide binding/ATPase domain and is a member of the ATPase superfamily. The C-terminal domain (Cdc6_C) is a conserved winged-helix domain that possibly mediates protein-protein interactions or direct DNA interactions. Cdc6 is conserved in eukaryotes, and related genes are found in Archaea. The winged helix fold structure of Cdc6_C is similar to the structures of other eukaryotic replication initiators without apparent sequence similarity.


Pssm-ID: 176573 [Multi-domain]  Cd Length: 87  Bit Score: 82.28  E-value: 2.14e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 307 PLHSKIILYSV--LQNTIKTKTTTTGKVYEQYEQLCKTTKQKPLTSRRVTDFVVELDMLGLISTNIASYGRYGRTRELSI 384
Cdd:cd08768     1 PLHQKLVLLALllLFKRGGEEEATTGEVYEVYEELCEEIGVDPLTQRRISDLLSELEMLGLLETEVSSKGRRGRTRKISL 80


                  ....*.
gi 1278360562 385 NYPKQI 390
Cdd:cd08768    81 NVDPDD 86
Cdc6_C smart01074
CDC6, C terminal; The C terminal domain of CDC6 assumes a winged helix fold, with a five ...
 332-388 2.07e-15

CDC6, C terminal; The C terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity.


Pssm-ID: 215013 [Multi-domain]  Cd Length: 84  Bit Score: 70.74  E-value: 2.07e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1278360562  332 VYEQYEQLCKTTKQKPLTSRRVTDFVVELDMLGLISTNIASYGRYGRTRELSINYPK 388
Cdd:smart01074  21 VYEVYKELCKELGVDPLTYTRIYDLLNELEMLGIIELRVSNRGRRGRTREISLNVDP 77
Cdc6_C pfam09079
CDC6, C terminal winged helix domain; The C terminal domain of CDC6 assumes a winged helix ...
 332-387 1.97e-13

CDC6, C terminal winged helix domain; The C terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localization factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity.


Pssm-ID: 462672  Cd Length: 84  Bit Score: 65.31  E-value: 1.97e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1278360562 332 VYEQYEQLCKTTKQKPLTSRRVTDFVVELDMLGLISTNIASYGRY-GRTRELSINYP 387
Cdd:pfam09079  21 VYEVYKKLCEKLGVDPLTQRRVSDLLSELEMLGILEAEVSSRGRRgGRTRKIRLNVD 77
 
Name Accession Description Interval E-value
CDC6 COG1474
Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];
15-390 8.70e-130

Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];


Pssm-ID: 441083 [Multi-domain]  Cd Length: 389  Bit Score: 378.42  E-value: 8.70e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562  15 NQKSKIFKNKKILSLDYIPEQILHRQKQIEEITKILSPIFREEPTSNIFIYGKPGTGKTTTINYIIKEIKyfldkQENKN 94
Cdd:COG1474     7 LWDESIFRDREVLSPDYVPDRLPHREEEIEELASALRPALRGERPSNVLIYGPTGTGKTAVAKYVLEELE-----EEAEE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562  95 LQQKIKIIYLNCKEghvSDTEYRLISTTCS--YFGKQIPA-GLSIKNIYDEFFRVVDYQKANIILVLDEIDNIVSKNSDD 171
Cdd:COG1474    82 RGVDVRVVYVNCRQ---ASTRYRVLSRILEelGSGEDIPStGLSTDELFDRLYEALDERDGVLVVVLDEIDYLVDDEGDD 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 172 FLYNL--ARKRFKNINLTLIGISNNINFIELLDPRIKSALNQEEFIFPPYNAEELLDILKQRSDNAFEKSVVSEGVLEKV 249
Cdd:COG1474   159 LLYQLlrANEELEGARVGVIGISNDLEFLENLDPRVKSSLGEEEIVFPPYDADELRDILEDRAELAFYDGVLSDEVIPLI 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 250 AGIIAQQNGDMRRAINLLRVVGELAERNNLNKLSLELVEEAEKKLEENIMLEMIYSQPLHSKIILYSVLQNTIKTKTTTT 329
Cdd:COG1474   239 AALAAQEHGDARKAIDLLRVAGEIAEREGSDRVTEEHVREAREKIERDRLLEVLRGLPTHEKLVLLAIAELLKDGEDPVR 318

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1278360562 330 G-KVYEQYEQLCKTTKQKPLTSRRVTDFVVELDMLGLISTNIASYGRYGRTRELSINYPKQI 390
Cdd:COG1474   319 TgEVYEAYEELCEELGVDPLSYRRVRDYLSELEMLGLIEAEVSSKGRRGRTREISLSVDPEV 380
TIGR02928 TIGR02928
orc1/cdc6 family replication initiation protein; Members of this protein family are found ...
 20-383 7.81e-118

orc1/cdc6 family replication initiation protein; Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274354 [Multi-domain]  Cd Length: 365  Bit Score: 347.31  E-value: 7.81e-118
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562  20 IFKNKKILSLDYIPEQILHRQKQIEEITKILSPIFREEPTSNIFIYGKPGTGKTTTINYIIKEIKYfldkqENKNLQQKI 99
Cdd:TIGR02928   1 IFRNRDLLEPDYVPDRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEE-----AAEDRDVRV 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 100 KIIYLNCkegHVSDTEYRLISTTC---SYFGKQIPA-GLSIKNIYDEFFRVVDYQKANIILVLDEIDNIVSKNsDDFLYN 175
Cdd:TIGR02928  76 VTVYVNC---QILDTLYQVLVELAnqlRGSGEEVPTtGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGDD-DDLLYQ 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 176 LARKRFK----NINLTLIGISNNINFIELLDPRIKSALNQEEFIFPPYNAEELLDILKQRSDNAFEKSVVSEGVLEKVAG 251
Cdd:TIGR02928 152 LSRARSNgdldNAKVGVIGISNDLKFRENLDPRVKSSLCEEEIIFPPYDAEELRDILENRAEKAFYDGVLDDGVIPLCAA 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 252 IIAQQNGDMRRAINLLRVVGELAERNNLNKLSLELVEEAEKKLEENIMLEMIYSQPLHSKIILYSVLQ-NTIKTKTTTTG 330
Cdd:TIGR02928 232 LAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIEKDRLLELIRGLPTHSKLVLLAIANlAANDEDPFRTG 311

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1278360562 331 KVYEQYEQLCKTTKQKPLTSRRVTDFVVELDMLGLISTNIASYGRYGRTRELS 383
Cdd:TIGR02928 312 EVYEVYKEVCEDIGVDPLTQRRISDLLNELDMLGLVEAEERNKGRGGRTREYS 364
cdc6 PRK00411
ORC1-type DNA replication protein;
5-387 2.10e-104

ORC1-type DNA replication protein;


Pssm-ID: 234751 [Multi-domain]  Cd Length: 394  Bit Score: 314.09  E-value: 2.10e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562   5 NIQEILQSIVNQKSKIFKNKKILSLDYIPEQILHRQKQIEEITKILSPIFREEPTSNIFIYGKPGTGKTTTINYIIKEIK 84
Cdd:PRK00411    1 SLDDIFEDLLMWDETIFKDEEVLEPDYVPENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562  85 yfldkqenkNLQQKIKIIYLNCkegHVSDTEYRLISTTC-SYFGKQIPA-GLSIKNIYDEFFRVVDYQKANIILVLDEID 162
Cdd:PRK00411   81 ---------EIAVKVVYVYINC---QIDRTRYAIFSEIArQLFGHPPPSsGLSFDELFDKIAEYLDERDRVLIVALDDIN 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 163 NIVSKNSDDFLYNLAR--KRFKNINLTLIGISNNINFIELLDPRIKSALNQEEFIFPPYNAEELLDILKQRSDNAFEKSV 240
Cdd:PRK00411  149 YLFEKEGNDVLYSLLRahEEYPGARIGVIGISSDLTFLYILDPRVKSVFRPEEIYFPPYTADEIFDILKDRVEEGFYPGV 228

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 241 VSEGVLEKVAGIIAQQNGDMRRAINLLRVVGELAERNNLNKLSLELVEEAEKKLEENIMLEMIYSQPLHSKIILYS-VLQ 319
Cdd:PRK00411  229 VDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEIVHLSEVLRTLPLHEKLLLRAiVRL 308

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1278360562 320 NTIKTKTTTTGKVYEQYEQLCKTTKQKPLTSRRVTDFVVELDMLGLISTNIASYGRYGRTRELSINYP 387
Cdd:PRK00411  309 LKKGGDEVTTGEVYEEYKELCEELGYEPRTHTRFYEYINKLDMLGIINTRYSGKGGRGRTRLISLSYD 376
Cdc6_C cd08768
Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), ...
 307-390 2.14e-19

Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding; This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases the specificity of the ORC-origins interaction. Further studies suggest that hydrolysis of Cdc6-bound ATP promotes the association of the replication licensing factor Cdt1 with origins through an interaction with Orc6 and this in turn promotes the loading of MCM2-7 helicase onto chromatin. The MCM2-7 complex promotes the unwinding of DNA origins, and the binding of additional factors to initiate the DNA replication. S-Cdk (S-phase cyclin and cyclin-dependent kinase complex) prevents rereplication by causing the Cdc6 protein to dissociate from ORC and prevents the Cdc6 and MCM proteins from reassembling at any origin. By phosphorylating Cdc6, S-Cdk also triggers Cdc6's ubiquitination. The Cdc6 protein is composed of three domains, an N-terminal AAA+ domain with Walker A and B, and Sensor-1 and -2 motifs. The central region contains a conserved nucleotide binding/ATPase domain and is a member of the ATPase superfamily. The C-terminal domain (Cdc6_C) is a conserved winged-helix domain that possibly mediates protein-protein interactions or direct DNA interactions. Cdc6 is conserved in eukaryotes, and related genes are found in Archaea. The winged helix fold structure of Cdc6_C is similar to the structures of other eukaryotic replication initiators without apparent sequence similarity.


Pssm-ID: 176573 [Multi-domain]  Cd Length: 87  Bit Score: 82.28  E-value: 2.14e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 307 PLHSKIILYSV--LQNTIKTKTTTTGKVYEQYEQLCKTTKQKPLTSRRVTDFVVELDMLGLISTNIASYGRYGRTRELSI 384
Cdd:cd08768     1 PLHQKLVLLALllLFKRGGEEEATTGEVYEVYEELCEEIGVDPLTQRRISDLLSELEMLGLLETEVSSKGRRGRTRKISL 80


                  ....*.
gi 1278360562 385 NYPKQI 390
Cdd:cd08768    81 NVDPDD 86
PTZ00112 PTZ00112
origin recognition complex 1 protein; Provisional
 22-268 1.34e-17

origin recognition complex 1 protein; Provisional


Pssm-ID: 240274 [Multi-domain]  Cd Length: 1164  Bit Score: 85.04  E-value: 1.34e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562   22 KNKKILSLDYIPEQILHRQKQIEEITKILSPIFREEPTSNI-FIYGKPGTGKTTTINYIIKeikyFLDKQENKNLQQKIK 100
Cdd:PTZ00112   743 KAIRMMQLDVVPKYLPCREKEIKEVHGFLESGIKQSGSNQIlYISGMPGTGKTATVYSVIQ----LLQHKTKQKLLPSFN 818

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562  101 IIYLNCKEGHVSDTEYRLISTtcSYFGKQIPAGLSIKNIYDEFFRVVDYQKANI-ILVLDEIDNIVSKnSDDFLYNLARK 179
Cdd:PTZ00112   819 VFEINGMNVVHPNAAYQVLYK--QLFNKKPPNALNSFKILDRLFNQNKKDNRNVsILIIDEIDYLITK-TQKVLFTLFDW 895

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562  180 RFK-NINLTLIGISNNINFIELLDPRIKSALNQEEFIFPPYNAEELLDILKQRSDNAfeKSVVSEGVLEKVAGIIAQQNG 258
Cdd:PTZ00112   896 PTKiNSKLVLIAISNTMDLPERLIPRCRSRLAFGRLVFSPYKGDEIEKIIKERLENC--KEIIDHTAIQLCARKVANVSG 973

                          250
                   ....*....|
gi 1278360562  259 DMRRAINLLR 268
Cdd:PTZ00112   974 DIRKALQICR 983
Cdc6_C smart01074
CDC6, C terminal; The C terminal domain of CDC6 assumes a winged helix fold, with a five ...
 332-388 2.07e-15

CDC6, C terminal; The C terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity.


Pssm-ID: 215013 [Multi-domain]  Cd Length: 84  Bit Score: 70.74  E-value: 2.07e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1278360562  332 VYEQYEQLCKTTKQKPLTSRRVTDFVVELDMLGLISTNIASYGRYGRTRELSINYPK 388
Cdd:smart01074  21 VYEVYKELCKELGVDPLTYTRIYDLLNELEMLGIIELRVSNRGRRGRTREISLNVDP 77
Cdc6_C pfam09079
CDC6, C terminal winged helix domain; The C terminal domain of CDC6 assumes a winged helix ...
 332-387 1.97e-13

CDC6, C terminal winged helix domain; The C terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localization factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity.


Pssm-ID: 462672  Cd Length: 84  Bit Score: 65.31  E-value: 1.97e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1278360562 332 VYEQYEQLCKTTKQKPLTSRRVTDFVVELDMLGLISTNIASYGRY-GRTRELSINYP 387
Cdd:pfam09079  21 VYEVYKKLCEKLGVDPLTQRRVSDLLSELEMLGILEAEVSSRGRRgGRTRKIRLNVD 77
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 44-215 1.37e-09

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 56.39  E-value: 1.37e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562  44 EEITKILSPIFREEPTSNIFIYGKPGTGKTTTINYIIKEIKYfldkqenknlqQKIKIIYLNCKEghvsdteyrlisttc 123
Cdd:cd00009     4 EEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFR-----------PGAPFLYLNASD--------------- 57

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 124 syFGKQIPAGLSIKNIYDEFFRVVDYQKANIILVLDEIDNI---VSKNSDDFLYNLARKRFKNINLTLIGISNNINFIEl 200
Cdd:cd00009    58 --LLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSLsrgAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGD- 134

                         170
                  ....*....|....*
gi 1278360562 201 LDPRIKSALNQEEFI 215
Cdd:cd00009   135 LDRALYDRLDIRIVI 149
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 41-290 4.06e-08

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 54.92  E-value: 4.06e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562  41 KQIEEITKILS--PIFREE----PTSNIFIYGKPGTGKTTTINYIIKEIkyfldkqeNKNLqqkIKIiylnckegHVSDt 114
Cdd:COG0464   167 EELRELVALPLkrPELREEyglpPPRGLLLYGPPGTGKTLLARALAGEL--------GLPL---IEV--------DLSD- 226

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 115 eyrLISttcSYFGKqipaglSIKNIyDEFFRVVDyQKANIILVLDEIDNIVSKNSDD-----------FLYNLARKRFkn 183
Cdd:COG0464   227 ---LVS---KYVGE------TEKNL-REVFDKAR-GLAPCVLFIDEADALAGKRGEVgdgvgrrvvntLLTEMEELRS-- 290

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 184 iNLTLIGISNninFIELLDP----RIksalnQEEFIFPPYNAEELLDILKQRsdnaFEKSVVSEGV-LEKVAGIIAQQNG 258
Cdd:COG0464   291 -DVVVIAATN---RPDLLDPallrRF-----DEIIFFPLPDAEERLEIFRIH----LRKRPLDEDVdLEELAEATEGLSG 357

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1278360562 259 -DMRraiNLLRVVGELAERNNLNKLSLELVEEA 290
Cdd:COG0464   358 aDIR---NVVRRAALQALRLGREPVTTEDLLEA 387
AAA_22 pfam13401
AAA domain;
55-190 7.60e-08

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 50.80  E-value: 7.60e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562  55 REEPTSNIFIYGKPGTGKTTTINYIIkeikyfldkqeNKNLQQKIKIIYLNCKEGhvsDTEYRLISTTCSYFGKQIPAGL 134
Cdd:pfam13401   1 IRFGAGILVLTGESGTGKTTLLRRLL-----------EQLPEVRDSVVFVDLPSG---TSPKDLLRALLRALGLPLSGRL 66

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1278360562 135 SIKNIYDEFFRVVDYQKANIILVLDEIDNIvSKNSDDFLYNLARKRFKNINLTLIG 190
Cdd:pfam13401  67 SKEELLAALQQLLLALAVAVVLIIDEAQHL-SLEALEELRDLLNLSSKLLQLILVG 121
COG2842 COG2842
Bacteriophage DNA transposition protein, AAA+ family ATPase [Mobilome: prophages, transposons]; ...
 55-296 2.53e-07

Bacteriophage DNA transposition protein, AAA+ family ATPase [Mobilome: prophages, transposons];


Pssm-ID: 442090 [Multi-domain]  Cd Length: 254  Bit Score: 51.49  E-value: 2.53e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562  55 REEPTSNIfIYGKPGTGKTTTINYiikeikYfldKQENKNlqqkikIIYLnckEGHVSDTEYRLISTTCSYFGKQIPAGl 134
Cdd:COG2842    47 RALPGIGV-VYGESGVGKTTAARE------Y---ANRNPN------VIYV---TASPSWTSKELLEELAEELGIPAPPG- 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 135 sikNIYDEFFRVVDYQKANI-ILVLDEIDNIVSKNSDDF--LYNLArkrfkNINLTLIG---ISNNINFIELLDPRIKSA 208
Cdd:COG2842   107 ---TIADLRDRILERLAGTGrLLIIDEADHLKPKALEELrdIHDET-----GVGVVLIGmerLPAKLKRYEQLYSRIGFW 178

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 209 LNqeefiFPPYNAEELLDILKQRSDnafeksVVSEGVLEKvagIIAQQNGDMRRAINLLRVVGELAERNNLNKLSLELVE 288
Cdd:COG2842   179 VE-----FKPLSLEDVRALAEAWGE------LTDPDLLEL---LHRITRGNLRRLDRTLRLAARAAKRNGLTKITLDHVR 244


                  ....*...
gi 1278360562 289 EAEKKLEE 296
Cdd:COG2842   245 AAALMLGE 252
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 61-198 1.17e-06

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 47.75  E-value: 1.17e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562   61 NIFIYGKPGTGKTTTINYIIKEIKyfldkqenknlQQKIKIIYLNCKEGHVSDTEYRListtCSYFGKQIPAGLSIKNIY 140
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELG-----------PPGGGVIYIDGEDILEEVLDQLL----LIIVGGKKASGSGELRLR 68

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1278360562  141 DeFFRVVDYQKANIILvLDEIDNIVSKNSDDFLYNLARKRFKNI-----NLTLIGISNNINFI 198
Cdd:smart00382  69 L-ALALARKLKPDVLI-LDEITSLLDAEQEALLLLLEELRLLLLlksekNLTVILTTNDEKDL 129
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
34-296 2.45e-06

Predicted ATPase, AAA+ superfamily [General function prediction only];


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 48.34  E-value: 2.45e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562  34 EQILHRQKQIEEITKilspiFREEPTSNIFIYGKPGTGKTTTINYIIKEIkyfldkqenknlqqKIKIIYLNCKEghvsd 113
Cdd:COG1223    15 KLIIKELRRRENLRK-----FGLWPPRKILFYGPPGTGKTMLAEALAGEL--------------KLPLLTVRLDS----- 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 114 teyrLISttcSYFGKqipAGLSIKNIYDeffrvvdyqKANI---ILVLDEIDNIVSKNSDDflyNLAR--KRFKNINLTL 188
Cdd:COG1223    71 ----LIG---SYLGE---TARNLRKLFD---------FARRapcVIFFDEFDAIAKDRGDQ---NDVGevKRVVNALLQE 128

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 189 I-GISNNI------NFIELLDPRIKSALnQEEFIFPPYNAEELLDILKQRSdNAFEKSVvsegvlEKVAGIIAQQNGDM- 260
Cdd:COG1223   129 LdGLPSGSvviaatNHPELLDSALWRRF-DEVIEFPLPDKEERKEILELNL-KKFPLPF------ELDLKKLAKKLEGLs 200

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 1278360562 261 -RRAINLLRVVGELAERNNLNKLSLELVEEAEKKLEE 296
Cdd:COG1223   201 gADIEKVLKTALKKAILEDREKVTKEDLEEALKQRKE 237
TIP49 COG1224
DNA helicase TIP49, TBP-interacting protein [Transcription];
218-293 3.38e-05

DNA helicase TIP49, TBP-interacting protein [Transcription];


Pssm-ID: 440837 [Multi-domain]  Cd Length: 452  Bit Score: 45.73  E-value: 3.38e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1278360562 218 PYNAEELLDILKQRSDNafEKSVVSEGVLEKVAGIIAQQNgdMRRAINLLRVVGELAERNNLNKLSLELVEEAEKK 293
Cdd:COG1224   361 PYTEDEIREIIKIRAEE--EDIELSDDALEELTKIGVERS--LRYAVQLLEPAYIIAKRRGRSKVTVEDVEEASKL 432
HLD_clamp_RarA cd18139
helical lid domain of recombination factor protein RarA; Recombination factor RarA ...
 219-290 3.99e-05

helical lid domain of recombination factor protein RarA; Recombination factor RarA (Replication associated recombination gene/protein A, also known as MgsA (Maintenance of genome stability A) or Mgs1 in yeast and WRNIP1 in mammals) is a member of the clamp-loader clade of the AAA+ superfamily. It functions as a tetramer. RarA co-localize with the replication fork throughout the cell cycle and may play a role in the rescue of stalled replication forks.


Pssm-ID: 350841 [Multi-domain]  Cd Length: 75  Bit Score: 41.46  E-value: 3.99e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1278360562 219 YNAEELLDILKQR---SDNAFEKSV-VSEGVLEKvagIIAQQNGDMRRAINLLRVVGELAERNNLNKLSLELVEEA 290
Cdd:cd18139     1 LSEEDLEKLLKRAledKERGGDRKVtIDDEALEL---LAEAADGDARSALNLLELAVLSAEEDGGIVITLEDLEEV 73
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 62-219 5.61e-05

ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.


Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 42.58  E-value: 5.61e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562  62 IFIYGKPGTGKTTTINYIIKEIkyfldkqenknlqqKIKIIYLNCKEghvsdteyrLISTTcsyfgkqipAGLSIKNIyD 141
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKEL--------------GAPFIEISGSE---------LVSKY---------VGESEKRL-R 47

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 142 EFFRVVdYQKANIILVLDEIDNIVSKNSD----------DFLYN-LARKRFKNINLTLIGISNNinfIELLDPRIKSALn 210
Cdd:pfam00004  48 ELFEAA-KKLAPCVIFIDEIDALAGSRGSggdsesrrvvNQLLTeLDGFTSSNSKVIVIAATNR---PDKLDPALLGRF- 122


                  ....*....
gi 1278360562 211 qEEFIFPPY 219
Cdd:pfam00004 123 -DRIIEFPL 130
AAA_16 pfam13191
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 39-83 4.00e-04

AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily.


Pssm-ID: 433025 [Multi-domain]  Cd Length: 167  Bit Score: 40.95  E-value: 4.00e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1278360562  39 RQKQIEEITKILSPIFREEPtSNIFIYGKPGTGKTTTINYIIKEI 83
Cdd:pfam13191   5 REEELEQLLDALDRVRSGRP-PSVLLTGEAGTGKTTLLRELLRAL 48
COG1672 COG1672
Predicted ATPase, archaeal AAA+ ATPase superfamily [General function prediction only];
39-204 7.79e-04

Predicted ATPase, archaeal AAA+ ATPase superfamily [General function prediction only];


Pssm-ID: 441278 [Multi-domain]  Cd Length: 324  Bit Score: 41.05  E-value: 7.79e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562  39 RQKQIEEITKILspifREEPTSNIFIYGKPGTGKTTTINYIIKEIKYfldkqenknlqqkikiIYLNCKEGHVSDTEYRL 118
Cdd:COG1672     5 REEELEELEKLY----ESDGGELVVVYGRRRVGKTSLIKEFLKEKPA----------------IYFDAREESERESLRDF 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 119 ISTtcsyFGKQIPAGLSIKNI--YDEFFRVVD--YQKANIILVLDEIDNIVSKNsDDFLYNLAR---KRFKNINLTLIGI 191
Cdd:COG1672    65 SEA----LAEALGDPLSKKEFesWEEAFEYLAelAEGKRLVIVIDEFQYLVKLD-PSLLSILQYlwdELLSDSNVSLILC 139

                         170
                  ....*....|....*
gi 1278360562 192 SNNINFIE--LLDPR 204
Cdd:COG1672   140 GSSIGMMEelLLDYK 154
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 39-290 1.30e-03

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 40.84  E-value: 1.30e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562  39 RQKQIEEI---TKILSP--IFRE-----EPTSNIFiYGKPGTGKTTTINYIIKEIKYfldkqenknlqqkiKIIYLNCKE 108
Cdd:PRK13342    7 RPKTLDEVvgqEHLLGPgkPLRRmieagRLSSMIL-WGPPGTGKTTLARIIAGATDA--------------PFEALSAVT 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 109 GHVSDteyrlisttcsyfgkqipaglsIKNIYDEFFRVVDYQKaNIILVLDEIDNIvSKNSDDFLYNLARKRfkniNLTL 188
Cdd:PRK13342   72 SGVKD----------------------LREVIEEARQRRSAGR-RTILFIDEIHRF-NKAQQDALLPHVEDG----TITL 123

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 189 IGISN-NINFiELLDP-----RIksalnqeeFIFPPYNAEELLDILKQ-RSDNAFEKSVVSEGVLEKvagIIAQQNGDMR 261
Cdd:PRK13342  124 IGATTeNPSF-EVNPAllsraQV--------FELKPLSEEDIEQLLKRaLEDKERGLVELDDEALDA---LARLANGDAR 191

                         250       260
                  ....*....|....*....|....*....
gi 1278360562 262 RAINLLrvvgELAERNNlNKLSLELVEEA 290
Cdd:PRK13342  192 RALNLL----ELAALGV-DSITLELLEEA 215
recD TIGR01447
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ...
 63-102 1.79e-03

exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273631 [Multi-domain]  Cd Length: 582  Bit Score: 40.51  E-value: 1.79e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1278360562  63 FIYGKPGTGKTTTINYIIKeikyFLDKQENKNLQQKIKII 102
Cdd:TIGR01447 163 LITGGPGTGKTTTVARLLL----ALVKQSPKQGKLRIALA 198
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 214-290 1.96e-03

Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, recombination and repair];


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 40.04  E-value: 1.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 214 FIFPPYNAEELLDILKQ------RSDNAFEKSVvSEGVLEKvagIIAQQNGDMRRAINLLRVVGELAERNNLNKLSLELV 287
Cdd:COG2256   159 FVLKPLSEEDLEQLLERaladdeRGLGGYKLEL-DDEALEA---LARLADGDARRALNALELAVLSAPPDGVIEITLELV 234


                  ...
gi 1278360562 288 EEA 290
Cdd:COG2256   235 EEA 237
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
 62-83 2.80e-03

RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses.


Pssm-ID: 459992  Cd Length: 102  Bit Score: 37.20  E-value: 2.80e-03
                          10        20
                  ....*....|....*....|..
gi 1278360562  62 IFIYGKPGTGKTTTINYIIKEI 83
Cdd:pfam00910   1 IWLYGPPGCGKSTLAKYLARAL 22
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 6-81 3.15e-03

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 39.57  E-value: 3.15e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562   6 IQEILQSIVNQKSKIFKNKKILSLDY-----IPEQILHRQKQI---EEITKILSPIFREEPTS----------------- 60
Cdd:COG0507    62 IEAALAALVESGPLVLDGRRYLTRLLeaeqrLARRLRRLARPAldeADVEAALAALEPRAGITlsdeqreavalalttrr 141

                          90       100
                  ....*....|....*....|.
gi 1278360562  61 NIFIYGKPGTGKTTTINYIIK 81
Cdd:COG0507   142 VSVLTGGAGTGKTTTLRALLA 162
rad24 TIGR00602
checkpoint protein rad24; All proteins in this family for which functions are known are ...
 31-268 3.17e-03

checkpoint protein rad24; All proteins in this family for which functions are known are involved in DNA damage tolerance (likely cell cycle checkpoints).This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129690 [Multi-domain]  Cd Length: 637  Bit Score: 39.55  E-value: 3.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562  31 YIPE---QILHRQKQIEEITKILSPIFRE-EPTSNIFIYGKPGTGKTTTINYIIKEIKYfldkqenkNLQQKIKIIYLNC 106
Cdd:TIGR00602  78 YKPEtqhELAVHKKKIEEVETWLKAQVLEnAPKRILLITGPSGCGKSTTIKILSKELGI--------QVQEWSNPTLPDF 149

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 107 KEGHVSDTEYRlisttcsyfGKQIPAGLSIKNIYDEF---------FRVVDYQKANIILVLDEIDNIVSKNSdDFLYNLA 177
Cdd:TIGR00602 150 QKNDHKVTLSL---------ESCFSNFQSQIEVFSEFllratnklqMLGDDLMTDKKIILVEDLPNQFYRDT-RALHEIL 219

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278360562 178 RKRFKNINL---------TLIGISN---------NINFIELL-DPRIKSAlnQEEFIFPPYNAEELLDILKQRSDNAFEK 238
Cdd:TIGR00602 220 RWKYVSIGRcplvfiiteSLEGDNNqrrllfpaeTIMNKEILeEPRVSNI--SFNPIAPTIMKKFLNRIVTIEAKKNGEK 297

                         250       260       270
                  ....*....|....*....|....*....|
gi 1278360562 239 SVVSEGVLekVAGIIAQQNGDMRRAINLLR 268
Cdd:TIGR00602 298 IKVPKKTS--VELLCQGCSGDIRSAINSLQ 325
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 62-84 9.04e-03

DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350691 [Multi-domain]  Cd Length: 155  Bit Score: 36.76  E-value: 9.04e-03
                          10        20
                  ....*....|....*....|...
gi 1278360562  62 IFIYGKPGTGKTTTINYIIKEIK 84
Cdd:cd17933    15 SVLTGGAGTGKTTTLKALLAALE 37
 
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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