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Conserved domains on  [gi|494730182|ref|WP_007466048|]
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DNA repair protein RadA [Micromonospora lupini]

Protein Classification

DNA repair protein RadA( domain architecture ID 11437487)

DNA repair protein RadA is responsible for the stabilization or processing of branched DNA molecules

EC:  3.6.4.-
Gene Ontology:  GO:0046872|GO:0005524|GO:0016887|GO:0003684|GO:0140664|GO:0006281

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Sms COG1066
DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and ...
 26-479 0e+00

DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and repair];


:

Pssm-ID: 440685 [Multi-domain]  Cd Length: 453  Bit Score: 649.42  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  26 PRPAYECDACGHQPPKWVGRCPECGEWGAVVESTVTGPTVAGRVVSSRLPSEPARPIATISAAPARAVPTGVSELDRVLG 105
Cdd:COG1066    4 TKTVYVCQECGYESPKWLGRCPECGAWNTLVEEVVAKAKKGRAASGAAGRASKPVPLSEVEAEEEPRISTGIGELDRVLG 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 106 GGLVPGAVVLLAGEPGVGKSTLLLDVAQQWAvGAGSPSLVVSGEESVSQVRLRAERMGTLHDKLYLAAESDLGSVLGHLD 185
Cdd:COG1066   84 GGLVPGSVVLIGGEPGIGKSTLLLQVAARLA-KKGGKVLYVSGEESASQIKLRAERLGLLSDNLYLLAETDLEAILATIE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 186 AVKPGLLVLDSVQTISTTGTEGVPGGVTQVRAVTAALVSVAKERGIATVLVGHVTKDGQVAGPRVLEHLVDVVLHFEGDK 265
Cdd:COG1066  163 ELKPDLLVIDSIQTMYSEELESAPGSVSQVRECAAELIRLAKETGIAVFLVGHVTKEGSIAGPRVLEHMVDTVLYFEGDR 242

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 266 HSSLRLVRGVKNRFGAADEVGCFEMHEGGISSLADPSGLFLTRYSEPVPGTCVTVAMEGRRALVTEVQALIGATVAGSPR 345
Cdd:COG1066  243 HSRYRILRAVKNRFGSTNEIGVFEMTEKGLREVSNPSELFLSERDEPVPGSAVTVTMEGTRPLLVEVQALVSPSSFGNPR 322

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 346 RTVSGLDSARLAMVLAVLQRRTeRLTLHDREVFAATVGGIRVVEPaadlavalavasgGLNLAIA-------------PH 412
Cdd:COG1066  323 RTAVGLDSNRLAMLLAVLEKRA-GLPLGDQDVYVNVVGGLKITEP-------------AADLAVAlaiassfrdrplpPD 388

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 494730182 413 LVAIGEVGLTGEVRRVGAVPRRLAEAARLGFKVALVPPGCGPastGAGPDGMRVTEVTDVRSALHHA 479
Cdd:COG1066  389 TVFFGEVGLTGEIRPVSRIEQRLKEAAKLGFKRAIVPKGNKK---KLKPKGIEIIGVSTLEEALEAL 452
 
Name Accession Description Interval E-value
Sms COG1066
DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and ...
 26-479 0e+00

DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and repair];


Pssm-ID: 440685 [Multi-domain]  Cd Length: 453  Bit Score: 649.42  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  26 PRPAYECDACGHQPPKWVGRCPECGEWGAVVESTVTGPTVAGRVVSSRLPSEPARPIATISAAPARAVPTGVSELDRVLG 105
Cdd:COG1066    4 TKTVYVCQECGYESPKWLGRCPECGAWNTLVEEVVAKAKKGRAASGAAGRASKPVPLSEVEAEEEPRISTGIGELDRVLG 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 106 GGLVPGAVVLLAGEPGVGKSTLLLDVAQQWAvGAGSPSLVVSGEESVSQVRLRAERMGTLHDKLYLAAESDLGSVLGHLD 185
Cdd:COG1066   84 GGLVPGSVVLIGGEPGIGKSTLLLQVAARLA-KKGGKVLYVSGEESASQIKLRAERLGLLSDNLYLLAETDLEAILATIE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 186 AVKPGLLVLDSVQTISTTGTEGVPGGVTQVRAVTAALVSVAKERGIATVLVGHVTKDGQVAGPRVLEHLVDVVLHFEGDK 265
Cdd:COG1066  163 ELKPDLLVIDSIQTMYSEELESAPGSVSQVRECAAELIRLAKETGIAVFLVGHVTKEGSIAGPRVLEHMVDTVLYFEGDR 242

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 266 HSSLRLVRGVKNRFGAADEVGCFEMHEGGISSLADPSGLFLTRYSEPVPGTCVTVAMEGRRALVTEVQALIGATVAGSPR 345
Cdd:COG1066  243 HSRYRILRAVKNRFGSTNEIGVFEMTEKGLREVSNPSELFLSERDEPVPGSAVTVTMEGTRPLLVEVQALVSPSSFGNPR 322

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 346 RTVSGLDSARLAMVLAVLQRRTeRLTLHDREVFAATVGGIRVVEPaadlavalavasgGLNLAIA-------------PH 412
Cdd:COG1066  323 RTAVGLDSNRLAMLLAVLEKRA-GLPLGDQDVYVNVVGGLKITEP-------------AADLAVAlaiassfrdrplpPD 388

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 494730182 413 LVAIGEVGLTGEVRRVGAVPRRLAEAARLGFKVALVPPGCGPastGAGPDGMRVTEVTDVRSALHHA 479
Cdd:COG1066  389 TVFFGEVGLTGEIRPVSRIEQRLKEAAKLGFKRAIVPKGNKK---KLKPKGIEIIGVSTLEEALEAL 452
sms TIGR00416
DNA repair protein RadA; The gene protuct codes for a probable ATP-dependent protease involved ...
 27-476 2.82e-145

DNA repair protein RadA; The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus (SP:P45266) and in Listeria monocytogenes (SP:Q48761) . for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273067 [Multi-domain]  Cd Length: 454  Bit Score: 423.83  E-value: 2.82e-145
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182   27 RPAYECDACGHQPPKWVGRCPECGEWGAVVESTVTGPTVAGRVVSSRL--PSEPARPIATISAAPARAVP---TGVSELD 101
Cdd:TIGR00416   5 KSKFVCQHCGADSPKWQGKCPACHAWNTITEERLHRSLGAQKNRRNSGkaGIPQAQKSQTISAIELEEVPrfsSGFGELD 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  102 RVLGGGLVPGAVVLLAGEPGVGKSTLLLDVAQQWAvGAGSPSLVVSGEESVSQVRLRAERMGTLHDKLYLAAESDLGSVL 181
Cdd:TIGR00416  85 RVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQLA-KNQMKVLYVSGEESLQQIKMRAIRLGLPEPNLYVLSETNWEQIC 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  182 GHLDAVKPGLLVLDSVQTISTTGTEGVPGGVTQVRAVTAALVSVAKERGIATVLVGHVTKDGQVAGPRVLEHLVDVVLHF 261
Cdd:TIGR00416 164 ANIEEENPQACVIDSIQTLYSPDISSAPGSVSQVRECTAELMRLAKTRGIAIFIVGHVTKEGSIAGPKVLEHMVDTVLYF 243

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  262 EGDKHSSLRLVRGVKNRFGAADEVGCFEMHEGGISSLADPSGLFLTRYSEPVPGTCVTVAMEGRRALVTEVQALIGATVA 341
Cdd:TIGR00416 244 EGDRDSRFRILRSVKNRFGATNEIGIFEMTEQGLREVLNPSAIFLSRREEPMSGSSITVTWEGTRPLLVEIQALVSPTSF 323

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  342 GSPRRTVSGLDSARLAMVLAVLQRRTErLTLHDREVFAATVGGIRVVEPAADLAVALAVASGGLNLAIAPHLVAIGEVGL 421
Cdd:TIGR00416 324 ANPRRVATGLDQNRLALLLAVLEKRLG-LPLADQDVFLNVAGGVKVSEPAADLALLIAIVSSFRDRPLDPDLVFLGEVGL 402

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 494730182  422 TGEVRRVGAVPRRLAEAARLGFKVALVPPGCGPastGAGPDGMRVTEVTDVRSAL 476
Cdd:TIGR00416 403 AGEIRPVPSLEERLKEAAKLGFKRAIVPKANSP---KTAPEGIKVIGVKKVGDAL 454
RadA_SMS_N cd01121
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a ...
 30-295 1.19e-140

bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a role in recombination and recombinational repair of DNA damaged by UV radiation, X-rays, and chemical agent and is responsible for the stabilization or processing of branched DNA molecules.


Pssm-ID: 410866 [Multi-domain]  Cd Length: 268  Bit Score: 404.61  E-value: 1.19e-140
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  30 YECDACGHQPPKWVGRCPECGEWGAVVESTVTGPTVAGRVVSSRLPSEPARPIATISAAPARAVPTGVSELDRVLGGGLV 109
Cdd:cd01121    1 YVCQECGYESPKWLGRCPSCGEWNTFVEEVVSASSSASRRASASPSPSKPLPLSDVEAEEEERISTGIGELDRVLGGGLV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 110 PGAVVLLAGEPGVGKSTLLLDVAQQWAvGAGSPSLVVSGEESVSQVRLRAERMGTLHDKLYLAAESDLGSVLGHLDAVKP 189
Cdd:cd01121   81 PGSVVLIGGDPGIGKSTLLLQVAARLA-QRGGKVLYVSGEESLSQIKLRAERLGLGSDNLYLLAETNLEAILAEIEELKP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 190 GLLVLDSVQTISTTGTEGVPGGVTQVRAVTAALVSVAKERGIATVLVGHVTKDGQVAGPRVLEHLVDVVLHFEGDKHSSL 269
Cdd:cd01121  160 SLVVIDSIQTVYSPELTSSPGSVSQVRECAAELLRLAKETGIPVFLVGHVTKDGAIAGPKVLEHMVDTVLYFEGDRGSSY 239

                        250       260
                 ....*....|....*....|....*.
gi 494730182 270 RLVRGVKNRFGAADEVGCFEMHEGGI 295
Cdd:cd01121  240 RILRSVKNRFGPTNEIGVFEMTENGL 265
ATPase pfam06745
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ...
 93-260 1.14e-16

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: 79.21  E-value: 1.14e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182   93 VPTGVSELDRVLGGGLVPGAVVLLAGEPGVGKSTLLLDVAQQWAVGAGSPSLVVSGEESVSQVRLRAERMGTLHDKLY-- 170
Cdd:pfam06745   1 VKTGIPGLDEILKGGFPEGRVVLITGGPGTGKTIFGLQFLYNGALKYGEPGVFVTLEEPPEDLRENARSFGWDLEKLEee 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  171 -----------------LAAESDLGSVLGHL----DAVKPGLLVLDSVQTISTTGTEGVpggvtqVRAVTAALVSVAKER 229
Cdd:pfam06745  81 gklaiidastsgigiaeVEDRFDLEELIERLreaiREIGAKRVVIDSITTLFYLLKPAV------AREILRRLKRVLKGL 154

                         170       180       190
                  ....*....|....*....|....*....|..
gi 494730182  230 GIATVLVGHVTKD-GQVAGPRVLEHLVDVVLH 260
Cdd:pfam06745 155 GVTAIFTSEKPSGeGGIGGYGVEEFIVDGVIR 186
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 110-262 7.73e-11

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: 60.08  E-value: 7.73e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182   110 PGAVVLLAGEPGVGKSTLLLDVAQQwAVGAGSPSLVVSGEESVSQVRLRAERMGTLHDKLYLAAESDLGSVLGHLDAVKP 189
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARE-LGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLKP 79

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 494730182   190 GLLVLDSVQTISTTGTEGVPggvtQVRAVTAALVSVAKERGIATVLVGHVTKDgqvAGPRVLEHLVDVVLHFE 262
Cdd:smart00382  80 DVLILDEITSLLDAEQEALL----LLLEELRLLLLLKSEKNLTVILTTNDEKD---LGPALLRRRFDRRIVLL 145
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 93-234 3.18e-09

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 59.12  E-value: 3.18e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  93 VPTGVSELDRVLGGGLVPGAVVLLAGEPGVGKSTLLLDVAQQwAVGAGSPSLVVSGEESVSQ-VR---------LRAERM 162
Cdd:PRK09302 255 ISSGVPDLDEMLGGGFFRGSIILVSGATGTGKTLLASKFAEA-ACRRGERCLLFAFEESRAQlIRnarswgidlEKMEEK 333

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 494730182 163 GTLHdklYLAAESDLGSVLGHL-------DAVKPGLLVLDSVQTISTTGTEGvpggvtQVRAVTAALVSVAKERGIATV 234
Cdd:PRK09302 334 GLLK---IICARPESYGLEDHLiiikreiEEFKPSRVAIDPLSALARGGSLN------EFRQFVIRLTDYLKSEEITGL 403
 
Name Accession Description Interval E-value
Sms COG1066
DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and ...
 26-479 0e+00

DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and repair];


Pssm-ID: 440685 [Multi-domain]  Cd Length: 453  Bit Score: 649.42  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  26 PRPAYECDACGHQPPKWVGRCPECGEWGAVVESTVTGPTVAGRVVSSRLPSEPARPIATISAAPARAVPTGVSELDRVLG 105
Cdd:COG1066    4 TKTVYVCQECGYESPKWLGRCPECGAWNTLVEEVVAKAKKGRAASGAAGRASKPVPLSEVEAEEEPRISTGIGELDRVLG 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 106 GGLVPGAVVLLAGEPGVGKSTLLLDVAQQWAvGAGSPSLVVSGEESVSQVRLRAERMGTLHDKLYLAAESDLGSVLGHLD 185
Cdd:COG1066   84 GGLVPGSVVLIGGEPGIGKSTLLLQVAARLA-KKGGKVLYVSGEESASQIKLRAERLGLLSDNLYLLAETDLEAILATIE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 186 AVKPGLLVLDSVQTISTTGTEGVPGGVTQVRAVTAALVSVAKERGIATVLVGHVTKDGQVAGPRVLEHLVDVVLHFEGDK 265
Cdd:COG1066  163 ELKPDLLVIDSIQTMYSEELESAPGSVSQVRECAAELIRLAKETGIAVFLVGHVTKEGSIAGPRVLEHMVDTVLYFEGDR 242

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 266 HSSLRLVRGVKNRFGAADEVGCFEMHEGGISSLADPSGLFLTRYSEPVPGTCVTVAMEGRRALVTEVQALIGATVAGSPR 345
Cdd:COG1066  243 HSRYRILRAVKNRFGSTNEIGVFEMTEKGLREVSNPSELFLSERDEPVPGSAVTVTMEGTRPLLVEVQALVSPSSFGNPR 322

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 346 RTVSGLDSARLAMVLAVLQRRTeRLTLHDREVFAATVGGIRVVEPaadlavalavasgGLNLAIA-------------PH 412
Cdd:COG1066  323 RTAVGLDSNRLAMLLAVLEKRA-GLPLGDQDVYVNVVGGLKITEP-------------AADLAVAlaiassfrdrplpPD 388

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 494730182 413 LVAIGEVGLTGEVRRVGAVPRRLAEAARLGFKVALVPPGCGPastGAGPDGMRVTEVTDVRSALHHA 479
Cdd:COG1066  389 TVFFGEVGLTGEIRPVSRIEQRLKEAAKLGFKRAIVPKGNKK---KLKPKGIEIIGVSTLEEALEAL 452
sms TIGR00416
DNA repair protein RadA; The gene protuct codes for a probable ATP-dependent protease involved ...
 27-476 2.82e-145

DNA repair protein RadA; The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus (SP:P45266) and in Listeria monocytogenes (SP:Q48761) . for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273067 [Multi-domain]  Cd Length: 454  Bit Score: 423.83  E-value: 2.82e-145
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182   27 RPAYECDACGHQPPKWVGRCPECGEWGAVVESTVTGPTVAGRVVSSRL--PSEPARPIATISAAPARAVP---TGVSELD 101
Cdd:TIGR00416   5 KSKFVCQHCGADSPKWQGKCPACHAWNTITEERLHRSLGAQKNRRNSGkaGIPQAQKSQTISAIELEEVPrfsSGFGELD 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  102 RVLGGGLVPGAVVLLAGEPGVGKSTLLLDVAQQWAvGAGSPSLVVSGEESVSQVRLRAERMGTLHDKLYLAAESDLGSVL 181
Cdd:TIGR00416  85 RVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQLA-KNQMKVLYVSGEESLQQIKMRAIRLGLPEPNLYVLSETNWEQIC 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  182 GHLDAVKPGLLVLDSVQTISTTGTEGVPGGVTQVRAVTAALVSVAKERGIATVLVGHVTKDGQVAGPRVLEHLVDVVLHF 261
Cdd:TIGR00416 164 ANIEEENPQACVIDSIQTLYSPDISSAPGSVSQVRECTAELMRLAKTRGIAIFIVGHVTKEGSIAGPKVLEHMVDTVLYF 243

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  262 EGDKHSSLRLVRGVKNRFGAADEVGCFEMHEGGISSLADPSGLFLTRYSEPVPGTCVTVAMEGRRALVTEVQALIGATVA 341
Cdd:TIGR00416 244 EGDRDSRFRILRSVKNRFGATNEIGIFEMTEQGLREVLNPSAIFLSRREEPMSGSSITVTWEGTRPLLVEIQALVSPTSF 323

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  342 GSPRRTVSGLDSARLAMVLAVLQRRTErLTLHDREVFAATVGGIRVVEPAADLAVALAVASGGLNLAIAPHLVAIGEVGL 421
Cdd:TIGR00416 324 ANPRRVATGLDQNRLALLLAVLEKRLG-LPLADQDVFLNVAGGVKVSEPAADLALLIAIVSSFRDRPLDPDLVFLGEVGL 402

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 494730182  422 TGEVRRVGAVPRRLAEAARLGFKVALVPPGCGPastGAGPDGMRVTEVTDVRSAL 476
Cdd:TIGR00416 403 AGEIRPVPSLEERLKEAAKLGFKRAIVPKANSP---KTAPEGIKVIGVKKVGDAL 454
RadA_SMS_N cd01121
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a ...
 30-295 1.19e-140

bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a role in recombination and recombinational repair of DNA damaged by UV radiation, X-rays, and chemical agent and is responsible for the stabilization or processing of branched DNA molecules.


Pssm-ID: 410866 [Multi-domain]  Cd Length: 268  Bit Score: 404.61  E-value: 1.19e-140
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  30 YECDACGHQPPKWVGRCPECGEWGAVVESTVTGPTVAGRVVSSRLPSEPARPIATISAAPARAVPTGVSELDRVLGGGLV 109
Cdd:cd01121    1 YVCQECGYESPKWLGRCPSCGEWNTFVEEVVSASSSASRRASASPSPSKPLPLSDVEAEEEERISTGIGELDRVLGGGLV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 110 PGAVVLLAGEPGVGKSTLLLDVAQQWAvGAGSPSLVVSGEESVSQVRLRAERMGTLHDKLYLAAESDLGSVLGHLDAVKP 189
Cdd:cd01121   81 PGSVVLIGGDPGIGKSTLLLQVAARLA-QRGGKVLYVSGEESLSQIKLRAERLGLGSDNLYLLAETNLEAILAEIEELKP 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 190 GLLVLDSVQTISTTGTEGVPGGVTQVRAVTAALVSVAKERGIATVLVGHVTKDGQVAGPRVLEHLVDVVLHFEGDKHSSL 269
Cdd:cd01121  160 SLVVIDSIQTVYSPELTSSPGSVSQVRECAAELLRLAKETGIPVFLVGHVTKDGAIAGPKVLEHMVDTVLYFEGDRGSSY 239

                        250       260
                 ....*....|....*....|....*.
gi 494730182 270 RLVRGVKNRFGAADEVGCFEMHEGGI 295
Cdd:cd01121  240 RILRSVKNRFGPTNEIGVFEMTENGL 265
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
93-295 4.34e-28

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 111.16  E-value: 4.34e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  93 VPTGVSELDRVLGGGLVPGAVVLLAGEPGVGKSTLLLDVAQQwAVGAGSPSLVVSGEESVSQVRLRAERMG--------- 163
Cdd:COG0467    2 VPTGIPGLDELLGGGLPRGSSTLLSGPPGTGKTTLALQFLAE-GLRRGEKGLYVSFEESPEQLLRRAESLGldleeyies 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 164 ---TLHDKLYLAAESDLGSVLGHL----DAVKPGLLVLDSVQTISTTGTEgvpggVTQVRAVTAALVSVAKERGIATVLV 236
Cdd:COG0467   81 gllRIIDLSPEELGLDLEELLARLreavEEFGAKRVVIDSLSGLLLALPD-----PERLREFLHRLLRYLKKRGVTTLLT 155

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 494730182 237 GHVTKDGQVAGPRVLEHLVDVVLHFEGDKHSSlRLVRG---VKNRFGAAD----EvgcFEMHEGGI 295
Cdd:COG0467  156 SETGGLEDEATEGGLSYLADGVILLRYVELGG-ELRRAlsvLKMRGSAHDrtirE---FEITDGGI 217
KaiC-like cd01124
Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. ...
 93-280 2.65e-19

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: 86.55  E-value: 2.65e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  93 VPTGVSELDRVLGGGLVPGAVVLLAGEPGVGKSTLlldvAQQWAVGA---GSPSLVVSGEESVSQVRLRAERMG----TL 165
Cdd:cd01124    1 VKTGIPGLDELLGGGIPKGSVTLLTGGPGTGKTLF----GLQFLYAGaknGEPGLFFTFEESPERLLRNAKSFGwdfdEM 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 166 HD--KLYLAAES----------DLGSVLGH-LDAVKPGLLVLDSVqtisTTGTEGVPGGVTQVRAVTaALVSVAKERGIA 232
Cdd:cd01124   77 EDegKLIIVDAPpteagrfsldELLSRILSiIKSFKAKRVVIDSL----SGLRRAKEDQMRARRIVI-ALLNELRAAGVT 151

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 494730182 233 TVLVG--HVTKDGQVAGPRVLEHLVD--VVLHFEGDKHSSLRLVRGVKNRFG 280
Cdd:cd01124  152 TIFTSemRSFLSSESAGGGDVSFIVDgvILLRYVEIEGELRRTIRVLKMRGT 203
ATPase pfam06745
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ...
 93-260 1.14e-16

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: 79.21  E-value: 1.14e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182   93 VPTGVSELDRVLGGGLVPGAVVLLAGEPGVGKSTLLLDVAQQWAVGAGSPSLVVSGEESVSQVRLRAERMGTLHDKLY-- 170
Cdd:pfam06745   1 VKTGIPGLDEILKGGFPEGRVVLITGGPGTGKTIFGLQFLYNGALKYGEPGVFVTLEEPPEDLRENARSFGWDLEKLEee 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  171 -----------------LAAESDLGSVLGHL----DAVKPGLLVLDSVQTISTTGTEGVpggvtqVRAVTAALVSVAKER 229
Cdd:pfam06745  81 gklaiidastsgigiaeVEDRFDLEELIERLreaiREIGAKRVVIDSITTLFYLLKPAV------AREILRRLKRVLKGL 154

                         170       180       190
                  ....*....|....*....|....*....|..
gi 494730182  230 GIATVLVGHVTKD-GQVAGPRVLEHLVDVVLH 260
Cdd:pfam06745 155 GVTAIFTSEKPSGeGGIGGYGVEEFIVDGVIR 186
RepA COG3598
RecA-family ATPase [Replication, recombination and repair];
107-384 2.57e-14

RecA-family ATPase [Replication, recombination and repair];


Pssm-ID: 442817 [Multi-domain]  Cd Length: 313  Bit Score: 73.78  E-value: 2.57e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 107 GLVP-GAVVLLAGEPGVGKSTLLLDVAQqwAVGAGSP----------SLVVSGEESVSQVRLRAERMGT--------LHD 167
Cdd:COG3598    8 GLLPeGGVTLLAGPPGTGKSFLALQLAA--AVAAGGPwlgrrvppgkVLYLAAEDDRGELRRRLKALGAdlglpfadLDG 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 168 KLYLAAE-------SDLGSVLGHLDAVKPGLLVLDSVQTiSTTGTEGVPggvTQVRAVTAALVSVAKERGIATVLVGHVT 240
Cdd:COG3598   86 RLRLLSLagdlddtDDLEALERAIEEEGPDLVVIDPLAR-VFGGDENDA---EEMRAFLNPLDRLAERTGAAVLLVHHTG 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 241 KDGQ-------VAGPRVLEHLVDVVLHFEGDKHSSLRLVRGVKNRFGAADEvgcFEMHEGGISSLADPSGLFLTRYSEPV 313
Cdd:COG3598  162 KGGAgkdsgdrARGSSALRGAARSVLVLSREKGEDLRVLTRAKSNYGPEIA---LRWDNGGRLALEEVAALTAGAGEVEL 238

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 494730182 314 PGTCVTVAMEGRRALVTEVQALIGATVAGSPRRTVSGLD----SARLAMVLAVLQRRTERLTLHDREVFAATVGG 384
Cdd:COG3598  239 KELVGGVARTGTDSELEEGLLEVPLAEAESAGEDAELAAkavaDEKDAARAVARLKAGGGKSKKVREGRLAAGRE 313
Rubredoxin_2 pfam18073
Rubredoxin metal binding domain; This is the C-terminal rubredoxin metal binding domain found ...
 30-57 1.49e-11

Rubredoxin metal binding domain; This is the C-terminal rubredoxin metal binding domain found in Interest in lipopolysaccharide (LPS) assembly protein B (LapB). Rubredoxin proteins form small non-heme iron binding sites that use four cysteine residues to coordinate a single metal ion in a tetrahedral environment. Rubredoxins are most commonly found in bacterial systems, but have also been found in eukaryotes. The key features of these rubredoxin-like domains are the extended loops or 'knuckles' and the tetracysteine mode of iron binding. Structural analysis of LapB from Escherichia coli show that the rubredoxin metal binding domain is intimately bound to the TPR motifs and that this association to the TPR motifs is essential to LPS regulation and growth in vivo. Other family members include RadA proteins which play a role in DNA damage repair. In E. coli, a protein known as RadA (or Sms) participates in the recombinational repair of radiation-damaged DNA in a process that uses an undamaged DNA strand in one DNA duplex to fill a DNA strand gap in a homologous sister DNA duplex. RadA carries a zinc finger at the N-terminal domain.


Pssm-ID: 436248 [Multi-domain]  Cd Length: 28  Bit Score: 58.71  E-value: 1.49e-11
                          10        20
                  ....*....|....*....|....*...
gi 494730182   30 YECDACGHQPPKWVGRCPECGEWGAVVE 57
Cdd:pfam18073   1 YRCSQCGFESPQWFGRCPSCGSWGTLVE 28
AAA_25 pfam13481
AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.
 85-244 7.14e-11

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: 61.24  E-value: 7.14e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182   85 ISAAPARAVPTGVSELDRVLGGGLVPGAVVLLAGEPGVGKSTLLLDVAQQWAVG----------AGSPSLVVSGEESVSQ 154
Cdd:pfam13481   7 LLDVLADGLAAPPPPRRWLIKGLLPAGGLGLLAGAPGTGKTTLALDLAAAVATGkpwlggprvpEQGKVLYVSAEGPADE 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  155 VRLRAERMGT---LHDKLYL-------------AAESDLGSVLGHLDAV-----KPGLLVLDSVQTIsttgTEGVPGGVT 213
Cdd:pfam13481  87 LRRRLRAAGAdldLPARLLFlslveslplffldRGGPLLDADVDALEAAleeveDPDLVVIDPLARA----LGGDENSNS 162

                         170       180       190
                  ....*....|....*....|....*....|.
gi 494730182  214 QVRAVTAALVSVAKERGIATVLVGHVTKDGQ 244
Cdd:pfam13481 163 DVGRLVKALDRLARRTGATVLLVHHVGKDGA 193
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 110-262 7.73e-11

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: 60.08  E-value: 7.73e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182   110 PGAVVLLAGEPGVGKSTLLLDVAQQwAVGAGSPSLVVSGEESVSQVRLRAERMGTLHDKLYLAAESDLGSVLGHLDAVKP 189
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARE-LGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLKP 79

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 494730182   190 GLLVLDSVQTISTTGTEGVPggvtQVRAVTAALVSVAKERGIATVLVGHVTKDgqvAGPRVLEHLVDVVLHFE 262
Cdd:smart00382  80 DVLILDEITSLLDAEQEALL----LLLEELRLLLLLKSEKNLTVILTTNDEKD---LGPALLRRRFDRRIVLL 145
KaiC-like_C cd19487
C-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 93-163 9.14e-11

C-terminal domain of KaiC family protein; uncharacterized subfamily; 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: 410895 [Multi-domain]  Cd Length: 219  Bit Score: 61.55  E-value: 9.14e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 494730182  93 VPTGVSELDRVLGGGLVPGAVVLLAGEPGVGKSTLLLDVAQQwAVGAGSPSLVVSGEESVSQVRLRAERMG 163
Cdd:cd19487    1 VSSGVPELDELLGGGLERGTSTLLIGPAGVGKSTLALQFAKA-AAARGERSVLFSFDESIGTLFERSEALG 70
KaiC_C cd19484
C-terminal domain of Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most ...
 93-243 8.52e-10

C-terminal domain of 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: 410892 [Multi-domain]  Cd Length: 218  Bit Score: 58.88  E-value: 8.52e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  93 VPTGVSELDRVL-GGGLVPGAVVLLAGEPGVGKSTLLLDVAQQwAVGAGSPSLVVSGEESVSQV-R---------LRAER 161
Cdd:cd19484    1 ISTGIPRLDAMLgGGGFFRGSSILVSGATGTGKTLLAASFADA-ACRRGERCLYFAFEESPAQLiRnaksigidlEQMER 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 162 MGTLHdklYLAAESDLGSVLGHL-------DAVKPGLLVLDSVQTISTTGTEgvpggvTQVRAVTAALVSVAKERGIaTV 234
Cdd:cd19484   80 KGLLK---IICARPELYGLEDHLiiikseiNEFKPSRVIVDPLSALARGGSL------NEVKEFVIRLIDYLKSQEI-TG 149


                 ....*....
gi 494730182 235 LVGHVTKDG 243
Cdd:cd19484  150 LFTNLTPDG 158
DnaB_C pfam03796
DnaB-like helicase C terminal domain; The hexameric helicase DnaB unwinds the DNA duplex at ...
 93-175 9.45e-10

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: 58.97  E-value: 9.45e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182   93 VPTGVSELDRVLGGgLVPGAVVLLAGEPGVGKSTLLLDVAQQWAVGAGSPSLVVSGEESVSQVrlrAERMgtlhdklyLA 172
Cdd:pfam03796   2 LPTGFTDLDRLTGG-LQPGDLIIIAARPSMGKTAFALNIARNAAVKHKKPVAIFSLEMSAEQL---VMRL--------LA 69


                  ...
gi 494730182  173 AES 175
Cdd:pfam03796  70 SEA 72
KaiC-like_N cd19488
N-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 95-196 1.46e-09

N-terminal domain of KaiC family protein; uncharacterized subfamily; 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: 410896 [Multi-domain]  Cd Length: 225  Bit Score: 58.13  E-value: 1.46e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  95 TGVSELDRVLGGGLVPGAVVLLAGEPGVGKSTLLLDVAQQwAVGAGSPSLVVSGEESVSQVRLRAERMG----------- 163
Cdd:cd19488    3 TGIPGLDDILRGGLPPRRLYLVEGAPGTGKTTLALQFLLE-GAANGETGLYITLSETEQELRAVALSHGwsldgihifel 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 494730182 164 ---------TLHDKLYLAAESDLGS----VLGHLDAVKPGLLVLDS 196
Cdd:cd19488   82 spsesaldaAQQYTILHPSELELSEttrlIFERVERLKPSRVVIDS 127
DnaB_C cd00984
C-terminal domain of DnaB helicase; DnaB helicase C-terminal domain. The hexameric helicase ...
 92-177 2.57e-09

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: 57.91  E-value: 2.57e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  92 AVPTGVSELDRVLGGgLVPGAVVLLAGEPGVGKSTLLLDVAQQWAVGAGSPSLVVSGEESVSQVrlrAERMgtlhdklyL 171
Cdd:cd00984    1 GLPTGFTDLDKLTGG-LQPGDLIIIAARPSMGKTAFALNIAENIALDEGLPVLFFSLEMSAEQL---AERL--------L 68


                 ....*.
gi 494730182 172 AAESDL 177
Cdd:cd00984   69 SSESGV 74
KaiC-N cd19485
N-terminal domain of Circadian Clock Protein Kaic; KaiC is a circadian clock protein, most ...
 93-298 2.76e-09

N-terminal domain of 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: 410893 [Multi-domain]  Cd Length: 226  Bit Score: 57.38  E-value: 2.76e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  93 VPTGVSELDRVLGGGLVPGAVVLLAGEPGVGKSTLLLDVAQQWAVGAGSPSLVVSGEESVSQVR-------------LRA 159
Cdd:cd19485    1 LPTGIEGFDDITHGGLPKGRPTLICGTAGTGKTLFAAQFLVNGIKEFGEPGVFVTFEESPEDIIknmasfgwdlpklVAE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 160 ERMGTLH-----DKLYLAAESDLGSVLGHL----DAVKPGLLVLDSVQTISTTGTEGvpggvTQVRAVTAALVSVAKERG 230
Cdd:cd19485   81 GKLLILDaspepSEEEVTGEYDLEALLIRIeyaiRKIGAKRVSLDSLEAVFSGLSDS-----AVVRAELLRLFAWLKQKG 155

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 494730182 231 IATVLVGHVTKDGQVAGPRVLEHLVD--VVLHFEGDKHSSLRLVRGVKNRfGAADEVG--CFEMHEGGISSL 298
Cdd:cd19485  156 VTAIMTGERGEDGPLTRYGVEEYVSDcvVILRNVLEGERRRRTLEILKYR-GSSHGKGeyPFTITENGISIL 226
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 93-234 3.18e-09

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 59.12  E-value: 3.18e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  93 VPTGVSELDRVLGGGLVPGAVVLLAGEPGVGKSTLLLDVAQQwAVGAGSPSLVVSGEESVSQ-VR---------LRAERM 162
Cdd:PRK09302 255 ISSGVPDLDEMLGGGFFRGSIILVSGATGTGKTLLASKFAEA-ACRRGERCLLFAFEESRAQlIRnarswgidlEKMEEK 333

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 494730182 163 GTLHdklYLAAESDLGSVLGHL-------DAVKPGLLVLDSVQTISTTGTEGvpggvtQVRAVTAALVSVAKERGIATV 234
Cdd:PRK09302 334 GLLK---IICARPESYGLEDHLiiikreiEEFKPSRVAIDPLSALARGGSLN------EFRQFVIRLTDYLKSEEITGL 403
DnaB COG0305
Replicative DNA helicase [Replication, recombination and repair];
93-175 6.89e-09

Replicative DNA helicase [Replication, recombination and repair];


Pssm-ID: 440074 [Multi-domain]  Cd Length: 429  Bit Score: 57.78  E-value: 6.89e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  93 VPTGVSELDRVLGGgLVPGAVVLLAGEPGVGKSTLLLDVAQQWAVGAGSPSLVVSGEESVSQVrlrAERMgtlhdklyLA 172
Cdd:COG0305  174 VPTGFTDLDKLTGG-LQPGDLIILAARPSMGKTAFALNIARNAAIKEGKPVAIFSLEMSAEQL---VMRL--------LS 241


                 ...
gi 494730182 173 AES 175
Cdd:COG0305  242 SEA 244
PRK07773 PRK07773
replicative DNA helicase; Validated
 90-158 3.74e-08

replicative DNA helicase; Validated


Pssm-ID: 236093 [Multi-domain]  Cd Length: 886  Bit Score: 55.91  E-value: 3.74e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 494730182  90 ARAVPTGVSELDRvLGGGLVPGAVVLLAGEPGVGKSTLLLDVAQQWAVGAGSPSLVVSGEESVSQVRLR 158
Cdd:PRK07773 197 ARGVPTGFTELDA-MTNGLHPGQLIIVAARPSMGKTTFGLDFARNCAIRHRLAVAIFSLEMSKEQLVMR 264
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 93-298 7.88e-08

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 54.50  E-value: 7.88e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  93 VPTGVSELDRVLGGGLVPGAVVLLAGEPGVGKsTLLldvAQQWAV-GA---GSPSLVVSGEESVSQVRLRAERMGTLHDK 168
Cdd:PRK09302  13 LPTGIEGFDDITHGGLPKGRPTLVSGTAGTGK-TLF---ALQFLVnGIkrfDEPGVFVTFEESPEDIIRNVASFGWDLQK 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 169 L------------------YLAAESDLGSV---LGHL-DAVKPGLLVLDSVQTI-STTGTEGVpggvtqVRAVTAALVSV 225
Cdd:PRK09302  89 LidegklfildaspdpseqEEAGEYDLEALfirIEYAiDKIGAKRVVLDSIEALfSGFSNEAV------VRRELRRLFAW 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 226 AKERGIATVLVGHVTKD-GQVAGPRVLEHLVDVVLH----FEGDKhsSLRLVRGVKNRfGAADEVG--CFEMHEGGISSL 298
Cdd:PRK09302 163 LKQKGVTAVITGERGDEyGPLTRYGVEEFVSDCVIIlrnrLEGEK--RTRTLRILKYR-GTTHGKNeyPFTITEDGISVL 239
archRadB cd01394
archaeal RadB; The archaeal protein RadB shares similarity RadA, the archaeal functional ...
 93-296 9.64e-08

archaeal RadB; The archaeal protein RadB shares similarity RadA, the archaeal functional homologue to the bacterial RecA. The precise function of RadB is unclear.


Pssm-ID: 410882 [Multi-domain]  Cd Length: 216  Bit Score: 52.70  E-value: 9.64e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  93 VPTGVSELDRVLGGGLVPGAVVLLAGEPGVGKSTLLLdvaqQWAVGAGSPSLVVS--GEESVSQVRLRA---ERMGTLHD 167
Cdd:cd01394    1 LSTGSKSLDSLLGGGVERGTITQIYGPPGSGKTNICL----QLAVEAAKQGKKVVyiDTEGLSPERFQQiagERFESIAS 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 168 KLYLAAESD-------LGSVLGHLDAVKPGLLVLDSVQTISTTGTEGVPGGVTQVRAVTAALVSVAKERGIATVLVGHV- 239
Cdd:cd01394   77 NIIVFEPYSfdeqgvaIQEAEKLLKSDKVDLVVVDSATALYRLELGDDSEANRELSRQMSKLLSIARKYDIPVVITNQVy 156

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 494730182 240 --TKDGQVA--GPRVLEHLVDVVLHFEgDKHSSLRLVRGVKNRFGAADEVGCFEMHEGGIS 296
Cdd:cd01394  157 sdIDDDRLKpvGGTLLEHWSKAIIRLE-KSPPGLRRATLEKHRSRPEGQSAGFRITDRGIR 216
RepA_RSF1010_like cd01125
Hexameric Replicative Helicase RepA of plasmid RSF1010 and related proteins; This family ...
 111-244 4.40e-07

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: 50.84  E-value: 4.40e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 111 GAVVLLAGEPGVGKSTLLLDVA----------QQWAVGAGsPSLVVSGEESVSQVRLRAERMGTLHDKLYLAAESDL--- 177
Cdd:cd01125    1 GTLGMLVGPPGSGKSFLALDLAvavatgrdwlGERRVKQG-RVVYLAAEDPRDGLRRRLKAIGAHLGDEDAALAENLvie 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 178 ---------GSVLGHLDAVK-----PGLLVLDSVQTISTTGTEGVPGgvtQVRAVTAALVSVAKERGIATVLVGHVTKDG 243
Cdd:cd01125   80 nlrgkpvsiDAEAPELERIIeelegVRLIIIDTLARVLHGGDENDAA---DMGAFVAGLDRIARETGAAVLLVHHTGKDA 156


                 .
gi 494730182 244 Q 244
Cdd:cd01125  157 A 157
PRK05636 PRK05636
replicative DNA helicase; Provisional
 90-158 1.03e-06

replicative DNA helicase; Provisional


Pssm-ID: 180177 [Multi-domain]  Cd Length: 505  Bit Score: 50.99  E-value: 1.03e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 494730182  90 ARAVPTGVSELDRvLGGGLVPGAVVLLAGEPGVGKSTLLLDVAQQWAVGAGSPSLVVSGEESVSQVRLR 158
Cdd:PRK05636 245 ATGIPTGFKDLDD-LTNGLRGGQMIIVAARPGVGKSTLALDFMRSASIKHNKASVIFSLEMSKSEIVMR 312
PRK07004 PRK07004
replicative DNA helicase; Provisional
 93-158 2.00e-06

replicative DNA helicase; Provisional


Pssm-ID: 235907 [Multi-domain]  Cd Length: 460  Bit Score: 49.91  E-value: 2.00e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 494730182  93 VPTGVSELDRvLGGGLVPGAVVLLAGEPGVGKSTLLLDVAQQWAVGAGSPSLVVSGEESVSQVRLR 158
Cdd:PRK07004 196 TPTGFVDLDR-MTSGMHGGELIIVAGRPSMGKTAFSMNIGEYVAVEYGLPVAVFSMEMPGTQLAMR 260
XRCC3 cd19491
XRCC3 recombinase; XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells ...
 100-240 3.46e-06

XRCC3 recombinase; XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells 3) recombinase, a RAD51 paralog, plays an important role in DNA repair by homologous recombination (HR). HR is an important error-free repair mechanism for chromosomal double-strand break (DSB) which otherwise leads to cell cycle arrest and death. XRCC3, together with the other RAD51 paralogs, RAD51B, RAD51C, RAD51D, and XRCC2, helps recruit RAD51 to the break site.


Pssm-ID: 410899 [Multi-domain]  Cd Length: 250  Bit Score: 48.44  E-value: 3.46e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 100 LDRVLGGGLVPGAVVLLAGEPGVGKSTLLLdvaqQWAV---------GAGSPSLVVSGEESVSQVRLRaERMGTLHDKLY 170
Cdd:cd19491    1 LDELLGGGIPVGGITEIAGESGAGKTQLCL----QLALtvqlprelgGLGGGAVYICTESSFPSKRLQ-QLASSLPKRYH 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 171 LAAESDLGSV--------LGHLDAV-----------KP-GLLVLDSVQTISTTGTEGVPGGVTQvRA-----VTAALVSV 225
Cdd:cd19491   76 LEKAKNFLDNifvehvadLETLEHClnyqlpallerGPiRLVVIDSIAALFRSEFDTSRSDLVE-RAkylrrLADHLKRL 154

                        170
                 ....*....|....*
gi 494730182 226 AKERGIATVLVGHVT 240
Cdd:cd19491  155 ADKYNLAVVVVNQVT 169
Rad51B cd19493
RAD51B recombinase; RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 101-240 4.17e-06

RAD51B recombinase; RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair by homologous recombination (HR). HR is an important error-free repair mechanism for chromosomal double-strand break (DSB) which otherwise leads to cell cycle arrest and death. RAD51B, together with the other RAD51 paralogs, RAD51C, RAD51D, XRCC3, and XRCC2, helps recruit RAD51 to the break site.


Pssm-ID: 410901 [Multi-domain]  Cd Length: 222  Bit Score: 47.70  E-value: 4.17e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 101 DRVLGGGLVPGAVVLLAGEPGVGKSTLLLDVAQQWAVGA---GSPSLVV--SGEESVSQVRLRA---------------- 159
Cdd:cd19493    1 DTALAGGLPLGAITEITGASGSGKTQFALTLASSAAMPArkgGLDGGVLyiDTESKFSAERLAEiaearfpeafsgfmee 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 160 -ERMGTLHDKLYLAAESDLGSVLGHLDAV-------KPGLLVLDSVQTISTTGTEGVPGGVTQ----VRAVTAALVSVAK 227
Cdd:cd19493   81 nERAEEMLKRVAVVRVTTLAQLLERLPNLeehilssGVRLVVIDSIAALVRREFGGSDGEVTErhnaLAREASSLKRLAE 160

                        170
                 ....*....|...
gi 494730182 228 ERGIATVLVGHVT 240
Cdd:cd19493  161 EFRIAVLVTNQAT 173
FlaH COG2874
Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];
93-139 1.19e-05

Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];


Pssm-ID: 442121  Cd Length: 230  Bit Score: 46.36  E-value: 1.19e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 494730182  93 VPTGVSELDRVLGGGLVPGAVVLLAGEPGVGKSTLlldvAQQWAVGA 139
Cdd:COG2874    3 ISTGNDELDKRLGGGIPLGSLVLIEGENGTGKSVL----SQQFAYGA 45
RecA-like_Gp4D_helicase cd19483
RecA-like domain of Escherichia coli bacteriophage T7 Gp4D helicase; This family includes the ...
 113-280 2.27e-05

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: 45.64  E-value: 2.27e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 113 VVLLAGEpGVGKSTLLLDVAQQWAVGAGSPSLVVSGEESVSQVRLR-----AERMGTLH--------DKLYLAAESDLGS 179
Cdd:cd19483    1 VTIGAGS-GIGKSTIVRELAYHLITEHGEKVGIISLEESVEETAKGlagkhLGKPEPLElprdditeEEEDDAFDNELGS 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 180 ----VLGHLDAVKPGLL----------------VLDSVQTISTTGTEGVpgGVTQVRAVTAALVSVAKERGIATVLVGHV 239
Cdd:cd19483   80 grffLYDHFGSLDWDNLkekirymvkvlgckviVLDHLTILVSGLDSSD--ERKELDEIMTELAALVKELGVTIILVSHL 157

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 494730182 240 TKDG--------------QVAGPRVLEHLVDVVLHFEGDKHSSLRLVRGV------KNRFG 280
Cdd:cd19483  158 RRPGggkgheeggevsesDLRGSSAIAQLSDYVIGLERNKQADDPVERNTtrvrvlKNRFT 218
PRK05973 PRK05973
replicative DNA helicase; Provisional
 108-239 2.64e-05

replicative DNA helicase; Provisional


Pssm-ID: 168322 [Multi-domain]  Cd Length: 237  Bit Score: 45.41  E-value: 2.64e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 108 LVPGAVVLLAGEPGVGKSTLLLDVAQQwAVGAGSPSLVVSGEESVSQVRLRAERMG---TLHDKLYLAAESDLGS---VL 181
Cdd:PRK05973  61 LKPGDLVLLGARPGHGKTLLGLELAVE-AMKSGRTGVFFTLEYTEQDVRDRLRALGadrAQFADLFEFDTSDAICadyII 139

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 494730182 182 GHLDAVKPG-LLVLDSVQTISTTGTEgvPGGVTQVRavtaALVSVAKERGIATVLVGHV 239
Cdd:PRK05973 140 ARLASAPRGtLVVIDYLQLLDQRREK--PDLSVQVR----ALKSFARERGLIIVFISQI 192
PRK05748 PRK05748
replicative DNA helicase; Provisional
 93-158 3.80e-05

replicative DNA helicase; Provisional


Pssm-ID: 180232 [Multi-domain]  Cd Length: 448  Bit Score: 46.10  E-value: 3.80e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 494730182  93 VPTGVSELDRVLGGgLVPGAVVLLAGEPGVGKSTLLLDVAQQWAVGAGSPSLVVSGEESVSQVRLR 158
Cdd:PRK05748 186 IPTGFTDLDKMTSG-LQPNDLIIVAARPSVGKTAFALNIAQNVATKTDKNVAIFSLEMGAESLVMR 250
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 114-201 3.95e-05

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: 43.67  E-value: 3.95e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 114 VLLAGEPGVGKSTLLLDVAQQwAVGAGSPSLVVSGEESVSQVRLRAERMGTLHDKLYLAAESDlgsvlghldavKPGLLV 193
Cdd:cd00009   22 LLLYGPPGTGKTTLARAIANE-LFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKA-----------KPGVLF 89


                 ....*...
gi 494730182 194 LDSVQTIS 201
Cdd:cd00009   90 IDEIDSLS 97
radB PRK09361
DNA repair and recombination protein RadB; Provisional
 91-132 4.89e-05

DNA repair and recombination protein RadB; Provisional


Pssm-ID: 236482 [Multi-domain]  Cd Length: 225  Bit Score: 44.47  E-value: 4.89e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 494730182  91 RAVPTGVSELDRVLGGGLVPGAVVLLAGEPGVGKSTLLLDVA 132
Cdd:PRK09361   3 ERLPTGCKMLDELLGGGFERGTITQIYGPPGSGKTNICLQLA 44
PRK04328 PRK04328
hypothetical protein; Provisional
 93-163 6.39e-05

hypothetical protein; Provisional


Pssm-ID: 235281  Cd Length: 249  Bit Score: 44.30  E-value: 6.39e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 494730182  93 VPTGVSELDRVLGGGLVPGAVVLLAGEPGVGKSTLlldvAQQW---AVGAGSPSLVVSGEESVSQVRLRAERMG 163
Cdd:PRK04328   5 VKTGIPGMDEILYGGIPERNVVLLSGGPGTGKSIF----SQQFlwnGLQMGEPGVYVALEEHPVQVRRNMRQFG 74
PRK06067 PRK06067
flagellar accessory protein FlaH; Validated
 93-163 7.29e-05

flagellar accessory protein FlaH; Validated


Pssm-ID: 180381  Cd Length: 234  Bit Score: 44.19  E-value: 7.29e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 494730182  93 VPTGVSELDRVLGGGLVPGAVVLLAGEPGVGKSTLLldvaQQWAVGA---GSPSLVVSGEESVSQVRLRAERMG 163
Cdd:PRK06067   7 ISTGNEELDRKLGGGIPFPSLILIEGDHGTGKSVLS----QQFVYGAlkqGKKVYVITTENTSKSYLKQMESVK 76
KaiC_arch cd19486
KaiC family protein; uncharacterized subfamily similar to Pyrococcus horikoshii PH0284; KaiC ...
 93-163 9.67e-05

KaiC family protein; uncharacterized subfamily similar to Pyrococcus horikoshii PH0284; 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: 410894  Cd Length: 230  Bit Score: 43.62  E-value: 9.67e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 494730182  93 VPTGVSELDRVLGGGLVPGAVVLLAGEPGVGKSTLlldvAQQW---AVGAGSPSLVVSGEESVSQVRLRAERMG 163
Cdd:cd19486    1 VKTGIPGMDEILHGGIPERNVVLLSGGPGTGKSIF----SQQFlwnGLKEGEPGVFVALEEHPVQVRRNMEQFG 70
HemYx COG3898
Uncharacterized protein HemY, contains HemY_N domain and TPR repeats (unrelated to HemY-type ...
 12-94 1.14e-03

Uncharacterized protein HemY, contains HemY_N domain and TPR repeats (unrelated to HemY-type protoporphyrinogen oxidase) [Function unknown];


Pssm-ID: 443105 [Multi-domain]  Cd Length: 468  Bit Score: 41.42  E-value: 1.14e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  12 GTAGAARG---RSATREPRPAYECDACGHQPPKWVGRCPECGEWGAVVESTVTGPTVAGRVVSSRLPSEPARPIATISAA 88
Cdd:COG3898  375 GDDGRVREwlaRALRAPRDPAWVCDACGTVSDDWAPVSPVCGRLDAFEWKTPPERLAAPPAEAEMLPLIVGLPAAEAEAA 454


                 ....*...
gi 494730182  89 --PARAVP 94
Cdd:COG3898  455 apPAEAVP 462
Rad51_DMC1_archRadA cd01123
recombinase Rad51, DMC1, and archaeal RadA; This group of recombinases includes the eukaryotic ...
 93-167 2.64e-03

recombinase Rad51, DMC1, and archaeal RadA; This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal protein RadA. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .


Pssm-ID: 410868 [Multi-domain]  Cd Length: 234  Bit Score: 39.44  E-value: 2.64e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182  93 VPTGVSELDRVLGGGLVPGAVVLLAGEPGVGKSTL--LLDVAQQWAVGAGSPS---LVVSGEESVSQVRLR--AERMGTL 165
Cdd:cd01123    1 ITTGSKELDKLLGGGIETGSITEMFGEFRTGKTQLchTLAVTCQLPIDRGGGEgkaIYIDTEGTFRPERLRaiAQRFGLD 80


                 ..
gi 494730182 166 HD 167
Cdd:cd01123   81 PD 82
RecA-like_superfamily cd01120
RecA-like_NTPases; RecA-like NTPases. This superfamily includes the NTP binding domain of F1 ...
 114-249 4.83e-03

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: 37.10  E-value: 4.83e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 114 VLLAGEPGVGKSTLLLDVAQQWAvGAGSPSLVVSGEESVsqvrLRAermgtlhdklylaaesdlgsVLGHLDAVKPGLLV 193
Cdd:cd01120    1 ILITGPPGSGKTTLLLQFAEQAL-LSDEPVIFISFLDTI----LEA--------------------IEDLIEEKKLDIII 55

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 494730182 194 LDSVQTISTTGTEGVPGgvtQVRAVTAALVSVAKERGIATVLVGHVTKDGQVAGPR 249
Cdd:cd01120   56 IDSLSSLARASQGDRSS---ELLEDLAKLLRAARNTGITVIATIHSDKFDIDRGGS 108
Rad51D cd19489
RAD51D recombinase; RAD51D recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 105-244 9.41e-03

RAD51D recombinase; RAD51D recombinase, a RAD51 paralog, plays an important role in DNA repair by homologous recombination (HR). HR is an important error-free repair mechanism for chromosomal double-strand break (DSB) which otherwise leads to cell cycle arrest and death. RAD51D, together with the other RAD51 paralogs, RAD51B, RAD51C, XRCC3, and XRCC2, helps recruit RAD51 to the break site.


Pssm-ID: 410897 [Multi-domain]  Cd Length: 209  Bit Score: 37.62  E-value: 9.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 105 GGGLVPGAVVLLAGEPGVGKSTLLLDVAQQWAVGAGSPSLVVSGEESVSQVRLR---------AERMGTLHDKLYLAAES 175
Cdd:cd19489    1 GGGLRTGEITELVGESSSGKTQLCLTAAANVASRSGQNVLYIDTKSSFSARRLAqilksraqdAEEIDKALQRIRVVRVF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494730182 176 DLGSVLGHLDAVK-------------PGLLVLDSV-QTIST-TGTEGVPGGVTQVRAVTAALVSVAKERGIATVLVGHVT 240
Cdd:cd19489   81 DPYELLDLLEELRntlsqqqenlysrLKLVIIDSLsALISPlLGGSKHSEGHALLASLARLLKKLAAEYQIAVLVTNLTV 160


                 ....
gi 494730182 241 KDGQ 244
Cdd:cd19489  161 RGGD 164
 
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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