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Conserved domains on  [gi|497916711|ref|WP_010230867|]
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DNA repair protein RadA [Chlamydia muridarum]

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 ...
 5-454 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: 674.84  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711   5 KIKTQWACSECGSYSPKWLGQCPGCFQWNTLVEEIHSSKLKTS---SYPLSSTTPVPLNTVKFQEEIRISTRSKGWNRLL 81
Cdd:COG1066    3 KTKTVYVCQECGYESPKWLGRCPECGAWNTLVEEVVAKAKKGRaasGAAGRASKPVPLSEVEAEEEPRISTGIGELDRVL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  82 GGGTVCGSLTLLGGEPGIGKSTLLLQISSQFAEQGYKVLYVCGEESVSQTSLRAQRLQISSSNIFLFPETNLEDIKQQIS 161
Cdd:COG1066   83 GGGLVPGSVVLIGGEPGIGKSTLLLQVAARLAKKGGKVLYVSGEESASQIKLRAERLGLLSDNLYLLAETDLEAILATIE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711 162 DLAPDiliidsiqiiF----------SPSLSSAPGSVAQVRETTAELMHIAKQKQITTFIIGHVTKSGEIAGPRILEHLV 231
Cdd:COG1066  163 ELKPD----------LlvidsiqtmySEELESAPGSVSQVRECAAELIRLAKETGIAVFLVGHVTKEGSIAGPRVLEHMV 232

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711 232 DTVLYFEGNAHTNYRMIRSVKNRFGPTNELLILSMQTDGLHEVENPSGFFLQEKVVETTGSTIIPIVEGSETLLVEVQAL 311
Cdd:COG1066  233 DTVLYFEGDRHSRYRILRAVKNRFGSTNEIGVFEMTEKGLREVSNPSELFLSERDEPVPGSAVTVTMEGTRPLLVEVQAL 312

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711 312 VSSSPFSNPVRKTSGFDPNRFSLLLAVLEKRANVKLYTSDVFLSIAGGLKITQPSADLGAVLSVVSSLYNRYLPKNYTYT 391
Cdd:COG1066  313 VSPSSFGNPRRTAVGLDSNRLAMLLAVLEKRAGLPLGDQDVYVNVVGGLKITEPAADLAVALAIASSFRDRPLPPDTVFF 392

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 497916711 392 GEIGLGGEIRHVTHIEHRIKESIIMGFKGIVMPSGQIKGLPKEyldQIDIIGVKTIKDAVRLL 454
Cdd:COG1066  393 GEVGLTGEIRPVSRIEQRLKEAAKLGFKRAIVPKGNKKKLKPK---GIEIIGVSTLEEALEAL 452
 
Name Accession Description Interval E-value
Sms COG1066
DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and ...
 5-454 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: 674.84  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711   5 KIKTQWACSECGSYSPKWLGQCPGCFQWNTLVEEIHSSKLKTS---SYPLSSTTPVPLNTVKFQEEIRISTRSKGWNRLL 81
Cdd:COG1066    3 KTKTVYVCQECGYESPKWLGRCPECGAWNTLVEEVVAKAKKGRaasGAAGRASKPVPLSEVEAEEEPRISTGIGELDRVL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  82 GGGTVCGSLTLLGGEPGIGKSTLLLQISSQFAEQGYKVLYVCGEESVSQTSLRAQRLQISSSNIFLFPETNLEDIKQQIS 161
Cdd:COG1066   83 GGGLVPGSVVLIGGEPGIGKSTLLLQVAARLAKKGGKVLYVSGEESASQIKLRAERLGLLSDNLYLLAETDLEAILATIE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711 162 DLAPDiliidsiqiiF----------SPSLSSAPGSVAQVRETTAELMHIAKQKQITTFIIGHVTKSGEIAGPRILEHLV 231
Cdd:COG1066  163 ELKPD----------LlvidsiqtmySEELESAPGSVSQVRECAAELIRLAKETGIAVFLVGHVTKEGSIAGPRVLEHMV 232

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711 232 DTVLYFEGNAHTNYRMIRSVKNRFGPTNELLILSMQTDGLHEVENPSGFFLQEKVVETTGSTIIPIVEGSETLLVEVQAL 311
Cdd:COG1066  233 DTVLYFEGDRHSRYRILRAVKNRFGSTNEIGVFEMTEKGLREVSNPSELFLSERDEPVPGSAVTVTMEGTRPLLVEVQAL 312

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711 312 VSSSPFSNPVRKTSGFDPNRFSLLLAVLEKRANVKLYTSDVFLSIAGGLKITQPSADLGAVLSVVSSLYNRYLPKNYTYT 391
Cdd:COG1066  313 VSPSSFGNPRRTAVGLDSNRLAMLLAVLEKRAGLPLGDQDVYVNVVGGLKITEPAADLAVALAIASSFRDRPLPPDTVFF 392

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 497916711 392 GEIGLGGEIRHVTHIEHRIKESIIMGFKGIVMPSGQIKGLPKEyldQIDIIGVKTIKDAVRLL 454
Cdd:COG1066  393 GEVGLTGEIRPVSRIEQRLKEAAKLGFKRAIVPKGNKKKLKPK---GIEIIGVSTLEEALEAL 452
sms TIGR00416
DNA repair protein RadA; The gene protuct codes for a probable ATP-dependent protease involved ...
 5-451 3.48e-173

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: 493.55  E-value: 3.48e-173
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711    5 KIKTQWACSECGSYSPKWLGQCPGCFQWNTLVEEIHSSKLKTSSYPLSS--------TTPVPLNTVKFQEEIRISTRSKG 76
Cdd:TIGR00416   3 KAKSKFVCQHCGADSPKWQGKCPACHAWNTITEERLHRSLGAQKNRRNSgkagipqaQKSQTISAIELEEVPRFSSGFGE 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711   77 WNRLLGGGTVCGSLTLLGGEPGIGKSTLLLQISSQFAEQGYKVLYVCGEESVSQTSLRAQRLQISSSNIFLFPETNLEDI 156
Cdd:TIGR00416  83 LDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVSGEESLQQIKMRAIRLGLPEPNLYVLSETNWEQI 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  157 KQQISDLAPDILIIDSIQIIFSPSLSSAPGSVAQVRETTAELMHIAKQKQITTFIIGHVTKSGEIAGPRILEHLVDTVLY 236
Cdd:TIGR00416 163 CANIEEENPQACVIDSIQTLYSPDISSAPGSVSQVRECTAELMRLAKTRGIAIFIVGHVTKEGSIAGPKVLEHMVDTVLY 242

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  237 FEGNAHTNYRMIRSVKNRFGPTNELLILSMQTDGLHEVENPSGFFLQEKVVETTGSTIIPIVEGSETLLVEVQALVSSSP 316
Cdd:TIGR00416 243 FEGDRDSRFRILRSVKNRFGATNEIGIFEMTEQGLREVLNPSAIFLSRREEPMSGSSITVTWEGTRPLLVEIQALVSPTS 322

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  317 FSNPVRKTSGFDPNRFSLLLAVLEKRANVKLYTSDVFLSIAGGLKITQPSADLGAVLSVVSSLYNRYLPKNYTYTGEIGL 396
Cdd:TIGR00416 323 FANPRRVATGLDQNRLALLLAVLEKRLGLPLADQDVFLNVAGGVKVSEPAADLALLIAIVSSFRDRPLDPDLVFLGEVGL 402

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 497916711  397 GGEIRHVTHIEHRIKESIIMGFKGIVMPSGQIKGLPKEyldQIDIIGVKTIKDAV 451
Cdd:TIGR00416 403 AGEIRPVPSLEERLKEAAKLGFKRAIVPKANSPKTAPE---GIKVIGVKKVGDAL 454
RadA_SMS_N cd01121
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a ...
 10-274 1.10e-138

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: 398.44  E-value: 1.10e-138
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  10 WACSECGSYSPKWLGQCPGCFQWNTLVEEIHSSKLKTSSYP---LSSTTPVPLNTVKFQEEIRISTRSKGWNRLLGGGTV 86
Cdd:cd01121    1 YVCQECGYESPKWLGRCPSCGEWNTFVEEVVSASSSASRRAsasPSPSKPLPLSDVEAEEEERISTGIGELDRVLGGGLV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  87 CGSLTLLGGEPGIGKSTLLLQISSQFAEQGYKVLYVCGEESVSQTSLRAQRLQISSSNIFLFPETNLEDIKQQISDLAPD 166
Cdd:cd01121   81 PGSVVLIGGDPGIGKSTLLLQVAARLAQRGGKVLYVSGEESLSQIKLRAERLGLGSDNLYLLAETNLEAILAEIEELKPS 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711 167 ILIIDSIQIIFSPSLSSAPGSVAQVRETTAELMHIAKQKQITTFIIGHVTKSGEIAGPRILEHLVDTVLYFEGNAHTNYR 246
Cdd:cd01121  161 LVVIDSIQTVYSPELTSSPGSVSQVRECAAELLRLAKETGIPVFLVGHVTKDGAIAGPKVLEHMVDTVLYFEGDRGSSYR 240

                        250       260
                 ....*....|....*....|....*...
gi 497916711 247 MIRSVKNRFGPTNELLILSMQTDGLHEV 274
Cdd:cd01121  241 ILRSVKNRFGPTNEIGVFEMTENGLREV 268
Rubredoxin_2 pfam18073
Rubredoxin metal binding domain; This is the C-terminal rubredoxin metal binding domain found ...
 10-37 6.96e-10

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: 53.70  E-value: 6.96e-10
                          10        20
                  ....*....|....*....|....*...
gi 497916711   10 WACSECGSYSPKWLGQCPGCFQWNTLVE 37
Cdd:pfam18073   1 YRCSQCGFESPQWFGRCPSCGSWGTLVE 28
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 67-210 2.12e-09

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 59.51  E-value: 2.12e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  67 EIRISTRSKGWNRLLGGGTVCGSLTLLGGEPGIGKSTLllqiSSQFAE----QGYKVLYVCGEESVSQTS---------- 132
Cdd:PRK09302 252 NERISSGVPDLDEMLGGGFFRGSIILVSGATGTGKTLL----ASKFAEaacrRGERCLLFAFEESRAQLIrnarswgidl 327

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711 133 ---LRAQRLQISSSniflFPE-TNLED----IKQQISDLAPDILIIDsiqiifspSLSS--APGSVAQVRETTAELMHIA 202
Cdd:PRK09302 328 ekmEEKGLLKIICA----RPEsYGLEDhliiIKREIEEFKPSRVAID--------PLSAlaRGGSLNEFRQFVIRLTDYL 395


                 ....*...
gi 497916711 203 KQKQITTF 210
Cdd:PRK09302 396 KSEEITGL 403
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 88-238 1.58e-07

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: 50.45  E-value: 1.58e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711    88 GSLTLLGGEPGIGKSTLLLQISSQFAEQGYKVLYVCGEESVSQTSLRAQRLQISSSNIFLFPETNLEDIKQQISDLAP-- 165
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLKPdv 81

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 497916711   166 ---DiliidsiqiifSPSLSSAPGSVAQVRETTAELMHIAKQKQITTFIIGHVTKSGEIaGPRILEHLVDTVLYFE 238
Cdd:smart00382  82 lilD-----------EITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVILTTNDEKDL-GPALLRRRFDRRIVLL 145
 
Name Accession Description Interval E-value
Sms COG1066
DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and ...
 5-454 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: 674.84  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711   5 KIKTQWACSECGSYSPKWLGQCPGCFQWNTLVEEIHSSKLKTS---SYPLSSTTPVPLNTVKFQEEIRISTRSKGWNRLL 81
Cdd:COG1066    3 KTKTVYVCQECGYESPKWLGRCPECGAWNTLVEEVVAKAKKGRaasGAAGRASKPVPLSEVEAEEEPRISTGIGELDRVL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  82 GGGTVCGSLTLLGGEPGIGKSTLLLQISSQFAEQGYKVLYVCGEESVSQTSLRAQRLQISSSNIFLFPETNLEDIKQQIS 161
Cdd:COG1066   83 GGGLVPGSVVLIGGEPGIGKSTLLLQVAARLAKKGGKVLYVSGEESASQIKLRAERLGLLSDNLYLLAETDLEAILATIE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711 162 DLAPDiliidsiqiiF----------SPSLSSAPGSVAQVRETTAELMHIAKQKQITTFIIGHVTKSGEIAGPRILEHLV 231
Cdd:COG1066  163 ELKPD----------LlvidsiqtmySEELESAPGSVSQVRECAAELIRLAKETGIAVFLVGHVTKEGSIAGPRVLEHMV 232

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711 232 DTVLYFEGNAHTNYRMIRSVKNRFGPTNELLILSMQTDGLHEVENPSGFFLQEKVVETTGSTIIPIVEGSETLLVEVQAL 311
Cdd:COG1066  233 DTVLYFEGDRHSRYRILRAVKNRFGSTNEIGVFEMTEKGLREVSNPSELFLSERDEPVPGSAVTVTMEGTRPLLVEVQAL 312

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711 312 VSSSPFSNPVRKTSGFDPNRFSLLLAVLEKRANVKLYTSDVFLSIAGGLKITQPSADLGAVLSVVSSLYNRYLPKNYTYT 391
Cdd:COG1066  313 VSPSSFGNPRRTAVGLDSNRLAMLLAVLEKRAGLPLGDQDVYVNVVGGLKITEPAADLAVALAIASSFRDRPLPPDTVFF 392

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 497916711 392 GEIGLGGEIRHVTHIEHRIKESIIMGFKGIVMPSGQIKGLPKEyldQIDIIGVKTIKDAVRLL 454
Cdd:COG1066  393 GEVGLTGEIRPVSRIEQRLKEAAKLGFKRAIVPKGNKKKLKPK---GIEIIGVSTLEEALEAL 452
sms TIGR00416
DNA repair protein RadA; The gene protuct codes for a probable ATP-dependent protease involved ...
 5-451 3.48e-173

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: 493.55  E-value: 3.48e-173
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711    5 KIKTQWACSECGSYSPKWLGQCPGCFQWNTLVEEIHSSKLKTSSYPLSS--------TTPVPLNTVKFQEEIRISTRSKG 76
Cdd:TIGR00416   3 KAKSKFVCQHCGADSPKWQGKCPACHAWNTITEERLHRSLGAQKNRRNSgkagipqaQKSQTISAIELEEVPRFSSGFGE 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711   77 WNRLLGGGTVCGSLTLLGGEPGIGKSTLLLQISSQFAEQGYKVLYVCGEESVSQTSLRAQRLQISSSNIFLFPETNLEDI 156
Cdd:TIGR00416  83 LDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVSGEESLQQIKMRAIRLGLPEPNLYVLSETNWEQI 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  157 KQQISDLAPDILIIDSIQIIFSPSLSSAPGSVAQVRETTAELMHIAKQKQITTFIIGHVTKSGEIAGPRILEHLVDTVLY 236
Cdd:TIGR00416 163 CANIEEENPQACVIDSIQTLYSPDISSAPGSVSQVRECTAELMRLAKTRGIAIFIVGHVTKEGSIAGPKVLEHMVDTVLY 242

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  237 FEGNAHTNYRMIRSVKNRFGPTNELLILSMQTDGLHEVENPSGFFLQEKVVETTGSTIIPIVEGSETLLVEVQALVSSSP 316
Cdd:TIGR00416 243 FEGDRDSRFRILRSVKNRFGATNEIGIFEMTEQGLREVLNPSAIFLSRREEPMSGSSITVTWEGTRPLLVEIQALVSPTS 322

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  317 FSNPVRKTSGFDPNRFSLLLAVLEKRANVKLYTSDVFLSIAGGLKITQPSADLGAVLSVVSSLYNRYLPKNYTYTGEIGL 396
Cdd:TIGR00416 323 FANPRRVATGLDQNRLALLLAVLEKRLGLPLADQDVFLNVAGGVKVSEPAADLALLIAIVSSFRDRPLDPDLVFLGEVGL 402

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 497916711  397 GGEIRHVTHIEHRIKESIIMGFKGIVMPSGQIKGLPKEyldQIDIIGVKTIKDAV 451
Cdd:TIGR00416 403 AGEIRPVPSLEERLKEAAKLGFKRAIVPKANSPKTAPE---GIKVIGVKKVGDAL 454
RadA_SMS_N cd01121
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a ...
 10-274 1.10e-138

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: 398.44  E-value: 1.10e-138
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  10 WACSECGSYSPKWLGQCPGCFQWNTLVEEIHSSKLKTSSYP---LSSTTPVPLNTVKFQEEIRISTRSKGWNRLLGGGTV 86
Cdd:cd01121    1 YVCQECGYESPKWLGRCPSCGEWNTFVEEVVSASSSASRRAsasPSPSKPLPLSDVEAEEEERISTGIGELDRVLGGGLV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  87 CGSLTLLGGEPGIGKSTLLLQISSQFAEQGYKVLYVCGEESVSQTSLRAQRLQISSSNIFLFPETNLEDIKQQISDLAPD 166
Cdd:cd01121   81 PGSVVLIGGDPGIGKSTLLLQVAARLAQRGGKVLYVSGEESLSQIKLRAERLGLGSDNLYLLAETNLEAILAEIEELKPS 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711 167 ILIIDSIQIIFSPSLSSAPGSVAQVRETTAELMHIAKQKQITTFIIGHVTKSGEIAGPRILEHLVDTVLYFEGNAHTNYR 246
Cdd:cd01121  161 LVVIDSIQTVYSPELTSSPGSVSQVRECAAELLRLAKETGIPVFLVGHVTKDGAIAGPKVLEHMVDTVLYFEGDRGSSYR 240

                        250       260
                 ....*....|....*....|....*...
gi 497916711 247 MIRSVKNRFGPTNELLILSMQTDGLHEV 274
Cdd:cd01121  241 ILRSVKNRFGPTNEIGVFEMTENGLREV 268
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
69-254 2.26e-18

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 83.43  E-value: 2.26e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  69 RISTRSKGWNRLLGGGTVCGSLTLLGGEPGIGKSTLLLQISSQFAEQGYKVLYVCGEESVSQTSLRAQRL------QISS 142
Cdd:COG0467    1 RVPTGIPGLDELLGGGLPRGSSTLLSGPPGTGKTTLALQFLAEGLRRGEKGLYVSFEESPEQLLRRAESLgldleeYIES 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711 143 SNIF---LFPE---TNLEDIKQQISDLAPDiliidsiqiiFSP------SLS---SAPGSVAQVRETTAELMHIAKQKQI 207
Cdd:COG0467   81 GLLRiidLSPEelgLDLEELLARLREAVEE----------FGAkrvvidSLSgllLALPDPERLREFLHRLLRYLKKRGV 150

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 497916711 208 TTFIIGHVTKSGEIAGPRILEHLVDTVL---YFEGNAHTNyRMIRSVKNR 254
Cdd:COG0467  151 TTLLTSETGGLEDEATEGGLSYLADGVIllrYVELGGELR-RALSVLKMR 199
KaiC-like cd01124
Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. ...
 70-257 2.10e-14

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: 72.30  E-value: 2.10e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  70 ISTRSKGWNRLLGGGTVCGSLTLLGGEPGIGKSTLLLQISSQFAEQGYKVLYVCGEESVSQtsLRAQ------------- 136
Cdd:cd01124    1 VKTGIPGLDELLGGGIPKGSVTLLTGGPGTGKTLFGLQFLYAGAKNGEPGLFFTFEESPER--LLRNaksfgwdfdemed 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711 137 --RLQISSSNIFLFPETNLEDIKQQISDLAPDILIIDSIQIIFSPSLSSAPGSVAQVRETTAeLMHIAKQKQITTFIIG- 213
Cdd:cd01124   79 egKLIIVDAPPTEAGRFSLDELLSRILSIIKSFKAKRVVIDSLSGLRRAKEDQMRARRIVIA-LLNELRAAGVTTIFTSe 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 497916711 214 -HVTKSGEIAGPRILEHLVDTV--LYFEGNAHTNYRMIRSVKNRFGP 257
Cdd:cd01124  158 mRSFLSSESAGGGDVSFIVDGVilLRYVEIEGELRRTIRVLKMRGTG 204
RepA COG3598
RecA-family ATPase [Replication, recombination and repair];
88-275 5.57e-10

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


Pssm-ID: 442817 [Multi-domain]  Cd Length: 313  Bit Score: 60.30  E-value: 5.57e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  88 GSLTLLGGEPGIGKSTLLLQISSQFA----------EQGyKVLYVCGEESVSQTSLRAQRL--------QISSSNIFLFP 149
Cdd:COG3598   13 GGVTLLAGPPGTGKSFLALQLAAAVAaggpwlgrrvPPG-KVLYLAAEDDRGELRRRLKALgadlglpfADLDGRLRLLS 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711 150 ETN-------LEDIKQQISDLAP-----DiliidsiqiifspSLSSAPG----SVAQVRETTAELMHIAKQKQITTFIIG 213
Cdd:COG3598   92 LAGdlddtddLEALERAIEEEGPdlvviD-------------PLARVFGgdenDAEEMRAFLNPLDRLAERTGAAVLLVH 158

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 497916711 214 HVTKSGE-------IAGPRILEHLVDTVLYFEGNAHTNYRMIRSVKNRFGPTNELLILSMQTDGLHEVE 275
Cdd:COG3598  159 HTGKGGAgkdsgdrARGSSALRGAARSVLVLSREKGEDLRVLTRAKSNYGPEIALRWDNGGRLALEEVA 227
Rubredoxin_2 pfam18073
Rubredoxin metal binding domain; This is the C-terminal rubredoxin metal binding domain found ...
 10-37 6.96e-10

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: 53.70  E-value: 6.96e-10
                          10        20
                  ....*....|....*....|....*...
gi 497916711   10 WACSECGSYSPKWLGQCPGCFQWNTLVE 37
Cdd:pfam18073   1 YRCSQCGFESPQWFGRCPSCGSWGTLVE 28
archRadB cd01394
archaeal RadB; The archaeal protein RadB shares similarity RadA, the archaeal functional ...
 70-164 1.56e-09

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: 57.71  E-value: 1.56e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  70 ISTRSKGWNRLLGGGTVCGSLTLLGGEPGIGKSTLLLQISSQFAEQGYKVLYVCGEesvsqtSLRAQRL-QIS------- 141
Cdd:cd01394    1 LSTGSKSLDSLLGGGVERGTITQIYGPPGSGKTNICLQLAVEAAKQGKKVVYIDTE------GLSPERFqQIAgerfesi 74

                         90       100
                 ....*....|....*....|...
gi 497916711 142 SSNIFLFPETNLEDIKQQISDLA 164
Cdd:cd01394   75 ASNIIVFEPYSFDEQGVAIQEAE 97
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 67-210 2.12e-09

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 59.51  E-value: 2.12e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  67 EIRISTRSKGWNRLLGGGTVCGSLTLLGGEPGIGKSTLllqiSSQFAE----QGYKVLYVCGEESVSQTS---------- 132
Cdd:PRK09302 252 NERISSGVPDLDEMLGGGFFRGSIILVSGATGTGKTLL----ASKFAEaacrRGERCLLFAFEESRAQLIrnarswgidl 327

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711 133 ---LRAQRLQISSSniflFPE-TNLED----IKQQISDLAPDILIIDsiqiifspSLSS--APGSVAQVRETTAELMHIA 202
Cdd:PRK09302 328 ekmEEKGLLKIICA----RPEsYGLEDhliiIKREIEEFKPSRVAID--------PLSAlaRGGSLNEFRQFVIRLTDYL 395


                 ....*...
gi 497916711 203 KQKQITTF 210
Cdd:PRK09302 396 KSEEITGL 403
radB PRK09361
DNA repair and recombination protein RadB; Provisional
 69-165 2.76e-08

DNA repair and recombination protein RadB; Provisional


Pssm-ID: 236482 [Multi-domain]  Cd Length: 225  Bit Score: 54.10  E-value: 2.76e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  69 RISTRSKGWNRLLGGGTVCGSLTLLGGEPGIGKSTLLLQISSQFAEQGYKVLYVCGEesvsqtSLRAQRL-QIS------ 141
Cdd:PRK09361   4 RLPTGCKMLDELLGGGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE------GLSPERFkQIAgedfee 77

                         90       100
                 ....*....|....*....|....*
gi 497916711 142 -SSNIFLFPETNLEDIKQQISDLAP 165
Cdd:PRK09361  78 lLSNIIIFEPSSFEEQSEAIRKAEK 102
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 88-238 1.58e-07

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: 50.45  E-value: 1.58e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711    88 GSLTLLGGEPGIGKSTLLLQISSQFAEQGYKVLYVCGEESVSQTSLRAQRLQISSSNIFLFPETNLEDIKQQISDLAP-- 165
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLKPdv 81

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 497916711   166 ---DiliidsiqiifSPSLSSAPGSVAQVRETTAELMHIAKQKQITTFIIGHVTKSGEIaGPRILEHLVDTVLYFE 238
Cdd:smart00382  82 lilD-----------EITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVILTTNDEKDL-GPALLRRRFDRRIVLL 145
KaiC-like_N cd19488
N-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 70-165 4.23e-07

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: 50.81  E-value: 4.23e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  70 ISTRSKGWNRLLGGGTVCGSLTLLGGEPGIGKSTLLLQISSQFAEQGYKVLYVCGEESVSQTSLRAQRLQISSSNIFLF- 148
Cdd:cd19488    1 ISTGIPGLDDILRGGLPPRRLYLVEGAPGTGKTTLALQFLLEGAANGETGLYITLSETEQELRAVALSHGWSLDGIHIFe 80

                         90
                 ....*....|....*....
gi 497916711 149 --PETNLEDIKQQISDLAP 165
Cdd:cd19488   81 lsPSESALDAAQQYTILHP 99
ATPase pfam06745
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ...
 70-254 7.59e-07

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: 49.94  E-value: 7.59e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711   70 ISTRSKGWNRLLGGGTVCGSLTLLGGEPGIGKSTLLLQ-ISSQFAEQGYKVLYVCGEESVSQTSLRAQRLQIsssniflf 148
Cdd:pfam06745   1 VKTGIPGLDEILKGGFPEGRVVLITGGPGTGKTIFGLQfLYNGALKYGEPGVFVTLEEPPEDLRENARSFGW-------- 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  149 petNLEDIKQQ----ISDLAPDILIIDSIQIIFSP----------------------SLSSAPGS--VAQVRETTAELMH 200
Cdd:pfam06745  73 ---DLEKLEEEgklaIIDASTSGIGIAEVEDRFDLeelierlreaireigakrvvidSITTLFYLlkPAVAREILRRLKR 149

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 497916711  201 IAKQKQITTFIIGHVTKS-GEIAGPRILEHLVDTV--LYFEGNAHTNYRMIRSVKNR 254
Cdd:pfam06745 150 VLKGLGVTAIFTSEKPSGeGGIGGYGVEEFIVDGVirLDLKEIEEERVRTIEIVKMR 206
KaiC_C cd19484
C-terminal domain of Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most ...
 70-210 8.84e-07

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: 49.63  E-value: 8.84e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  70 ISTRSKGWNRLL-GGGTVCGSLTLLGGEPGIGKSTLllqiSSQFAE----QGYKVLYVCGEESVSQTS------------ 132
Cdd:cd19484    1 ISTGIPRLDAMLgGGGFFRGSSILVSGATGTGKTLL----AASFADaacrRGERCLYFAFEESPAQLIrnaksigidleq 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711 133 -LRAQRLQISSSniflFPET-NLED----IKQQISDLAPDILIIDsiqiifspSLS--SAPGSVAQVRETTAELMHIAKQ 204
Cdd:cd19484   77 mERKGLLKIICA----RPELyGLEDhliiIKSEINEFKPSRVIVD--------PLSalARGGSLNEVKEFVIRLIDYLKS 144


                 ....*.
gi 497916711 205 KQITTF 210
Cdd:cd19484  145 QEITGL 150
KaiC-like_C cd19487
C-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 70-271 1.19e-06

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: 49.22  E-value: 1.19e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  70 ISTRSKGWNRLLGGGTVCGSLTLLGGEPGIGKSTLLLQISSQFAEQGYKVLYVCGEESVSQTSLRAQRLQIsssNIFLFP 149
Cdd:cd19487    1 VSSGVPELDELLGGGLERGTSTLLIGPAGVGKSTLALQFAKAAAARGERSVLFSFDESIGTLFERSEALGI---DLRAMV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711 150 ETNLEDIKQQI-SDLAP------------DILIIDSIQIIFSPSLSSAPGSVAQVREtTAELMHIAKQKQITTFIIG--H 214
Cdd:cd19487   78 EKGLLSIEQIDpAELSPgefaqrvrtsveQEDARVVVIDSLNGYLNAMPDERFLILQ-MHELLSYLNNQGVTTLLIVaqH 156

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 497916711 215 VTKSGEIAGPRILEHLVDTVL---YFEGNAHTNyRMIRSVKNRFGPtNELLI--LSMQTDGL 271
Cdd:cd19487  157 GLLGGDMGTPVDISYLADTVVllrYFEAEGEVR-KAISVLKKRTGD-HERTIreFRITRSGL 216
AAA_25 pfam13481
AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.
 88-220 1.24e-05

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


Pssm-ID: 463892 [Multi-domain]  Cd Length: 193  Bit Score: 45.83  E-value: 1.24e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711   88 GSLTLLGGEPGIGKSTLLLQIS-----------SQFAEQGYKVLYVCGEESVSQTSLRAQR-------------LQISSS 143
Cdd:pfam13481  33 GGLGLLAGAPGTGKTTLALDLAaavatgkpwlgGPRVPEQGKVLYVSAEGPADELRRRLRAagadldlparllfLSLVES 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  144 NIFLFPETNLEDIKQQISDLAPDILIIDSIQI----IFSPSLSSAPGSVAQVRETTAELMHIAKQKQITTFIIGHVTKSG 219
Cdd:pfam13481 113 LPLFFLDRGGPLLDADVDALEAALEEVEDPDLvvidPLARALGGDENSNSDVGRLVKALDRLARRTGATVLLVHHVGKDG 192


                  .
gi 497916711  220 E 220
Cdd:pfam13481 193 A 193
XRCC3 cd19491
XRCC3 recombinase; XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells ...
 79-139 1.32e-05

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: 46.52  E-value: 1.32e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 497916711  79 RLLGGGTVCGSLTLLGGEPGIGKSTLLLQIS--SQFAEQ----GYKVLYVCGEESVSqtslrAQRLQ 139
Cdd:cd19491    3 ELLGGGIPVGGITEIAGESGAGKTQLCLQLAltVQLPRElgglGGGAVYICTESSFP-----SKRLQ 64
RecA-like_superfamily cd01120
RecA-like_NTPases; RecA-like NTPases. This superfamily includes the NTP binding domain of F1 ...
 91-226 5.87e-05

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: 42.49  E-value: 5.87e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  91 TLLGGEPGIGKSTLLLQISSQFAEQGYKVLYvcgeesvsqtslraqrlqisssniFLFPETNLEDIKQQISDLAPDILII 170
Cdd:cd01120    1 ILITGPPGSGKTTLLLQFAEQALLSDEPVIF------------------------ISFLDTILEAIEDLIEEKKLDIIII 56

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 497916711 171 DSIQIIFSPSLssaPGSVAQVRETTAELMHIAKQKQITTFIIGHVTKSGEIAGPRI 226
Cdd:cd01120   57 DSLSSLARASQ---GDRSSELLEDLAKLLRAARNTGITVIATIHSDKFDIDRGGSS 109
FlaH COG2874
Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];
78-128 6.00e-05

Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];


Pssm-ID: 442121  Cd Length: 230  Bit Score: 44.44  E-value: 6.00e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 497916711  78 NRLLGGGTVCGSLTLLGGEPGIGKSTLLLQISSQFAEQGYKVLYVCGEESV 128
Cdd:COG2874   11 DKRLGGGIPLGSLVLIEGENGTGKSVLSQQFAYGALENGLSVTYISTELTT 61
PRK06067 PRK06067
flagellar accessory protein FlaH; Validated
 70-157 6.76e-04

flagellar accessory protein FlaH; Validated


Pssm-ID: 180381  Cd Length: 234  Bit Score: 41.11  E-value: 6.76e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  70 ISTRSKGWNRLLGGGTVCGSLTLLGGEPGIGKSTLLLQISSQFAEQGYKVLYVCGEESVSQTSLRAQRLQISSSNIFL-- 147
Cdd:PRK06067   7 ISTGNEELDRKLGGGIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITTENTSKSYLKQMESVKIDISDFFLwg 86

                         90
                 ....*....|....
gi 497916711 148 ----FPeTNLEDIK 157
Cdd:PRK06067  87 ylriFP-LNTEGFE 99
Rad51 pfam08423
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ...
 51-138 1.35e-03

Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ATPase RecA protein.


Pssm-ID: 462471 [Multi-domain]  Cd Length: 255  Bit Score: 40.36  E-value: 1.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711   51 LSSTTPVPLNTvKFQEEIRISTRSKGWNRLLGGGTVCGSLTLLGGEPGIGKStlllQISSQFA-------EQG---YKVL 120
Cdd:pfam08423   1 MGFTTATELHQ-RRSELIQITTGSKELDKLLGGGIETGSITEIFGEFRTGKT----QLCHTLCvtcqlplEMGggeGKAL 75

                          90
                  ....*....|....*...
gi 497916711  121 YVCGEesvsqTSLRAQRL 138
Cdd:pfam08423  76 YIDTE-----GTFRPERL 88
COG3899 COG3899
Predicted ATPase [General function prediction only];
77-135 1.45e-03

Predicted ATPase [General function prediction only];


Pssm-ID: 443106 [Multi-domain]  Cd Length: 1244  Bit Score: 41.38  E-value: 1.45e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 497916711   77 WNRLLGGGtvcGSLTLLGGEPGIGKSTLLLQISSQFAEQGYKVLYVCGEESVSQTSLRA 135
Cdd:COG3899   303 LERARAGR---GELVLVSGEAGIGKSRLVRELARRARARGGRVLRGKCDQLERGVPYAP 358
radA PRK04301
DNA repair and recombination protein RadA; Validated
 69-113 1.83e-03

DNA repair and recombination protein RadA; Validated


Pssm-ID: 235273 [Multi-domain]  Cd Length: 317  Bit Score: 40.25  E-value: 1.83e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 497916711  69 RISTRSKGWNRLLGGGTVCGSLTLLGGEPGIGKStlllQISSQFA 113
Cdd:PRK04301  83 KITTGSKELDELLGGGIETQSITEFYGEFGSGKT----QICHQLA 123
Rad51_DMC1_archRadA cd01123
recombinase Rad51, DMC1, and archaeal RadA; This group of recombinases includes the eukaryotic ...
 70-145 2.04e-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: 39.82  E-value: 2.04e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  70 ISTRSKGWNRLLGGGTVCGSLTLLGGEPGIGKSTL--LLQISSQF-AEQGY---KVLYVCGEESVSQTSLR--AQRLQIS 141
Cdd:cd01123    1 ITTGSKELDKLLGGGIETGSITEMFGEFRTGKTQLchTLAVTCQLpIDRGGgegKAIYIDTEGTFRPERLRaiAQRFGLD 80


                 ....
gi 497916711 142 SSNI 145
Cdd:cd01123   81 PDDV 84
AAA_16 pfam13191
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 87-166 2.85e-03

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: 38.64  E-value: 2.85e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711   87 CGSLTLLGGEPGIGKSTLLLQISSQFAEQGYKVLYVCGEESVS---------QTSLRAQRLQISSSNIFLFPETNLEDIK 157
Cdd:pfam13191  23 RPPSVLLTGEAGTGKTTLLRELLRALERDGGYFLRGKCDENLPyspllealtREGLLRQLLDELESSLLEAWRAALLEAL 102


                  ....*....
gi 497916711  158 QQISDLAPD 166
Cdd:pfam13191 103 APVPELPGD 111
Twinkle_C cd01122
C-terminal domain of Twinkle; Twinkle ( T7 gp4-like protein with intramitochondrial nucleoid ...
 78-125 4.33e-03

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


Pssm-ID: 410867  Cd Length: 266  Bit Score: 38.76  E-value: 4.33e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 497916711  78 NRLLGGGTVcGSLTLLGGEPGIGKSTLLLQISSQFAEQGYKVLYVCGE 125
Cdd:cd01122   34 NKLLKGHRR-GELTIFTGPTGSGKTTFLSEYSLDLCMQGVNTLWGSFE 80
Rad51B cd19493
RAD51B recombinase; RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 78-152 4.46e-03

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: 38.45  E-value: 4.46e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  78 NRLLGGGTVCGSLTLLGGEPGIGKSTLLLQISSQFA------EQGYKVLYVCGEESVSqtslrAQRLQIssSNIFLFPET 151
Cdd:cd19493    1 DTALAGGLPLGAITEITGASGSGKTQFALTLASSAAmparkgGLDGGVLYIDTESKFS-----AERLAE--IAEARFPEA 73


                 .
gi 497916711 152 N 152
Cdd:cd19493   74 F 74
RecA-like_Gp4D_helicase cd19483
RecA-like domain of Escherichia coli bacteriophage T7 Gp4D helicase; This family includes the ...
 91-256 4.51e-03

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: 38.71  E-value: 4.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711  91 TLLGGEPGIGKSTLLLQISSQFA-EQGYKVLYVCGEESVSQTSLR--------------------AQRLQ------ISSS 143
Cdd:cd19483    1 VTIGAGSGIGKSTIVRELAYHLItEHGEKVGIISLEESVEETAKGlagkhlgkpeplelprdditEEEEDdafdneLGSG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711 144 NIFL---FPETNLEDIKQQISDLAP---------DILIIdsiqiiFSPSLSSAPGSVAQVrETTAELMHIAKQKQITTFI 211
Cdd:cd19483   81 RFFLydhFGSLDWDNLKEKIRYMVKvlgckvivlDHLTI------LVSGLDSSDERKELD-EIMTELAALVKELGVTIIL 153

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 497916711 212 IGHVTKSG--------------EIAGPRILEHLVDTVLYFEGNAHT------NYRMIRSVKNRFG 256
Cdd:cd19483  154 VSHLRRPGggkgheeggevsesDLRGSSAIAQLSDYVIGLERNKQAddpverNTTRVRVLKNRFT 218
PTZ00035 PTZ00035
Rad51 protein; Provisional
 65-122 7.90e-03

Rad51 protein; Provisional


Pssm-ID: 185407 [Multi-domain]  Cd Length: 337  Bit Score: 38.44  E-value: 7.90e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 497916711  65 QEEIRISTRSKGWNRLLGGGTVCGSLTLLGGEPGIGKSTL--LLQISSQFA-EQGY---KVLYV 122
Cdd:PTZ00035  95 KNIIRITTGSTQLDKLLGGGIETGSITELFGEFRTGKTQLchTLCVTCQLPiEQGGgegKVLYI 158
SIMIBI cd01983
SIMIBI (signal recognition particle, MinD and BioD)-class NTPases; SIMIBI (after signal ...
 92-122 8.20e-03

SIMIBI (signal recognition particle, MinD and BioD)-class NTPases; SIMIBI (after signal recognition particle, MinD, and BioD), consists of signal recognition particle (SRP) GTPases, the assemblage of MinD-like ATPases, which are involved in protein localization, chromosome partitioning, and membrane transport, and a group of metabolic enzymes with kinase or related phosphate transferase activity. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.


Pssm-ID: 349751 [Multi-domain]  Cd Length: 107  Bit Score: 35.87  E-value: 8.20e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 497916711  92 LLGGEPGIGKSTLLLQISSQFAEQGYKVLYV 122
Cdd:cd01983    5 VTGGKGGVGKTTLAAALAVALAAKGYKVLLI 35
recomb_RAD51 TIGR02239
DNA repair protein RAD51; This eukaryotic sequence family consists of RAD51, a protein ...
 50-156 8.34e-03

DNA repair protein RAD51; This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).


Pssm-ID: 274048 [Multi-domain]  Cd Length: 316  Bit Score: 38.17  E-value: 8.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 497916711   50 PLSSTTPVPLNtVKFQEEIRISTRSKGWNRLLGGGTVCGSLTLLGGEPGIGKSTL--LLQISSQFA-EQG---YKVLYVC 123
Cdd:TIGR02239  59 PMGFTTATEFH-QRRQEVIQLTTGSKELDKLLGGGIETGSITEIFGEFRTGKTQLchTLAVTCQLPiDQGggeGKALYID 137

                          90       100       110
                  ....*....|....*....|....*....|...
gi 497916711  124 GEesvsqTSLRAQRLQISSSNIFLFPETNLEDI 156
Cdd:TIGR02239 138 TE-----GTFRPERLLAIAERYGLNPEDVLDNV 165
 
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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