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Conserved domains on  [gi|1928505583|ref|WP_194018608|]
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DNA repair protein RadA [Synechocystis salina]

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 ...
 1-480 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: 756.12  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583   1 MAKARTKFVCSACGADHAQWFGRCPKCHEYGTLQEEVVNAVSSGTNRRSlgaqksgsarvKTGQPQAALTFSQIRQENQG 80
Cdd:COG1066     1 MAKTKTVYVCQECGYESPKWLGRCPECGAWNTLVEEVVAKAKKGRAASG-----------AAGRASKPVPLSEVEAEEEP 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  81 RFPSGYGELDRVLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAEESGQQIKLRATRLGITqtvnasd 160
Cdd:COG1066    70 RISTGIGELDRVLGGGLVPGSVVLIGGEPGIGKSTLLLQVAARLAKKGGKVLYVSGEESASQIKLRAERLGLL------- 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 161 skmaeanlphDGNLFVLPETNLEDILRELEALQPQVAIIDSIQNLYFPALSSAPGSVSQVRECTGLLMQLAKRDHISLFI 240
Cdd:COG1066   143 ----------SDNLYLLAETDLEAILATIEELKPDLLVIDSIQTMYSEELESAPGSVSQVRECAAELIRLAKETGIAVFL 212

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 241 VGHVTKEGAIAGPKVLEHLVDTVLYFQGDRFASHRLLRSVKNRFGATQEIGIFEMVQSGLQEVLNPSQLFLGSREEFMSG 320
Cdd:COG1066   213 VGHVTKEGSIAGPRVLEHMVDTVLYFEGDRHSRYRILRAVKNRFGSTNEIGVFEMTEKGLREVSNPSELFLSERDEPVPG 292

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 321 TAITVACEGTRPLVVELQALVSPTSYASPRRSTTGVDYNRLLQVLAVLEKRLGVPLSKLDAYLSVAGGLEVEEPAVDLAM 400
Cdd:COG1066   293 SAVTVTMEGTRPLLVEVQALVSPSSFGNPRRTAVGLDSNRLAMLLAVLEKRAGLPLGDQDVYVNVVGGLKITEPAADLAV 372

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 401 AIALVASFRDRVVDPTMIILGEIGLGGQIRPISQLEIRLKEAAKLGFKKAIVPKGQT-GIESAGIKLIPVGKVFAAIAVA 479
Cdd:COG1066   373 ALAIASSFRDRPLPPDTVFFGEVGLTGEIRPVSRIEQRLKEAAKLGFKRAIVPKGNKkKLKPKGIEIIGVSTLEEALEAL 452


                  .
gi 1928505583 480 L 480
Cdd:COG1066   453 F 453
 
Name Accession Description Interval E-value
Sms COG1066
DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and ...
 1-480 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: 756.12  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583   1 MAKARTKFVCSACGADHAQWFGRCPKCHEYGTLQEEVVNAVSSGTNRRSlgaqksgsarvKTGQPQAALTFSQIRQENQG 80
Cdd:COG1066     1 MAKTKTVYVCQECGYESPKWLGRCPECGAWNTLVEEVVAKAKKGRAASG-----------AAGRASKPVPLSEVEAEEEP 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  81 RFPSGYGELDRVLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAEESGQQIKLRATRLGITqtvnasd 160
Cdd:COG1066    70 RISTGIGELDRVLGGGLVPGSVVLIGGEPGIGKSTLLLQVAARLAKKGGKVLYVSGEESASQIKLRAERLGLL------- 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 161 skmaeanlphDGNLFVLPETNLEDILRELEALQPQVAIIDSIQNLYFPALSSAPGSVSQVRECTGLLMQLAKRDHISLFI 240
Cdd:COG1066   143 ----------SDNLYLLAETDLEAILATIEELKPDLLVIDSIQTMYSEELESAPGSVSQVRECAAELIRLAKETGIAVFL 212

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 241 VGHVTKEGAIAGPKVLEHLVDTVLYFQGDRFASHRLLRSVKNRFGATQEIGIFEMVQSGLQEVLNPSQLFLGSREEFMSG 320
Cdd:COG1066   213 VGHVTKEGSIAGPRVLEHMVDTVLYFEGDRHSRYRILRAVKNRFGSTNEIGVFEMTEKGLREVSNPSELFLSERDEPVPG 292

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 321 TAITVACEGTRPLVVELQALVSPTSYASPRRSTTGVDYNRLLQVLAVLEKRLGVPLSKLDAYLSVAGGLEVEEPAVDLAM 400
Cdd:COG1066   293 SAVTVTMEGTRPLLVEVQALVSPSSFGNPRRTAVGLDSNRLAMLLAVLEKRAGLPLGDQDVYVNVVGGLKITEPAADLAV 372

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 401 AIALVASFRDRVVDPTMIILGEIGLGGQIRPISQLEIRLKEAAKLGFKKAIVPKGQT-GIESAGIKLIPVGKVFAAIAVA 479
Cdd:COG1066   373 ALAIASSFRDRPLPPDTVFFGEVGLTGEIRPVSRIEQRLKEAAKLGFKRAIVPKGNKkKLKPKGIEIIGVSTLEEALEAL 452


                  .
gi 1928505583 480 L 480
Cdd:COG1066   453 F 453
sms TIGR00416
DNA repair protein RadA; The gene protuct codes for a probable ATP-dependent protease involved ...
 1-476 0e+00

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: 751.25  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583   1 MAKARTKFVCSACGADHAQWFGRCPKCHEYGTLQEEVVNavssgtnrRSLGAQKSGSARVKTGQPQA--ALTFSQIRQEN 78
Cdd:TIGR00416   1 MAKAKSKFVCQHCGADSPKWQGKCPACHAWNTITEERLH--------RSLGAQKNRRNSGKAGIPQAqkSQTISAIELEE 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  79 QGRFPSGYGELDRVLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAEESGQQIKLRATRLGitqtvna 158
Cdd:TIGR00416  73 VPRFSSGFGELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVSGEESLQQIKMRAIRLG------- 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 159 sdskmaeanLPHDgNLFVLPETNLEDILRELEALQPQVAIIDSIQNLYFPALSSAPGSVSQVRECTGLLMQLAKRDHISL 238
Cdd:TIGR00416 146 ---------LPEP-NLYVLSETNWEQICANIEEENPQACVIDSIQTLYSPDISSAPGSVSQVRECTAELMRLAKTRGIAI 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 239 FIVGHVTKEGAIAGPKVLEHLVDTVLYFQGDRFASHRLLRSVKNRFGATQEIGIFEMVQSGLQEVLNPSQLFLGSREEFM 318
Cdd:TIGR00416 216 FIVGHVTKEGSIAGPKVLEHMVDTVLYFEGDRDSRFRILRSVKNRFGATNEIGIFEMTEQGLREVLNPSAIFLSRREEPM 295

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 319 SGTAITVACEGTRPLVVELQALVSPTSYASPRRSTTGVDYNRLLQVLAVLEKRLGVPLSKLDAYLSVAGGLEVEEPAVDL 398
Cdd:TIGR00416 296 SGSSITVTWEGTRPLLVEIQALVSPTSFANPRRVATGLDQNRLALLLAVLEKRLGLPLADQDVFLNVAGGVKVSEPAADL 375

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1928505583 399 AMAIALVASFRDRVVDPTMIILGEIGLGGQIRPISQLEIRLKEAAKLGFKKAIVPKGQT-GIESAGIKLIPVGKVFAAI 476
Cdd:TIGR00416 376 ALLIAIVSSFRDRPLDPDLVFLGEVGLAGEIRPVPSLEERLKEAAKLGFKRAIVPKANSpKTAPEGIKVIGVKKVGDAL 454
RadA_SMS_N cd01121
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a ...
 8-303 4.31e-162

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: 460.07  E-value: 4.31e-162
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583   8 FVCSACGADHAQWFGRCPKCHEYGTLQEEVVNAVSSGTNRRSlgaqksgsarvKTGQPQAALTFSQIRQENQGRFPSGYG 87
Cdd:cd01121     1 YVCQECGYESPKWLGRCPSCGEWNTFVEEVVSASSSASRRAS-----------ASPSPSKPLPLSDVEAEEEERISTGIG 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  88 ELDRVLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAEESGQQIKLRATRLGITqtvnasdskmaean 167
Cdd:cd01121    70 ELDRVLGGGLVPGSVVLIGGDPGIGKSTLLLQVAARLAQRGGKVLYVSGEESLSQIKLRAERLGLG-------------- 135

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 168 lphDGNLFVLPETNLEDILRELEALQPQVAIIDSIQNLYFPALSSAPGSVSQVRECTGLLMQLAKRDHISLFIVGHVTKE 247
Cdd:cd01121   136 ---SDNLYLLAETNLEAILAEIEELKPSLVVIDSIQTVYSPELTSSPGSVSQVRECAAELLRLAKETGIPVFLVGHVTKD 212

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1928505583 248 GAIAGPKVLEHLVDTVLYFQGDRFASHRLLRSVKNRFGATQEIGIFEMVQSGLQEV 303
Cdd:cd01121   213 GAIAGPKVLEHMVDTVLYFEGDRGSSYRILRSVKNRFGPTNEIGVFEMTENGLREV 268
ATPase pfam06745
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ...
 83-263 1.21e-14

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: 73.43  E-value: 1.21e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  83 PSGYGELDRVLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRL-PRILYVSAEESGQQIKLRATRLG--ITQTVNAS 159
Cdd:pfam06745   2 KTGIPGLDEILKGGFPEGRVVLITGGPGTGKTIFGLQFLYNGALKYgEPGVFVTLEEPPEDLRENARSFGwdLEKLEEEG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 160 DSKMAEANLPHDGNLFVLPETNLEDILRELE----ALQPQVAIIDSIQNLyfpALSSAPGSV-SQVREctgLLMQLAKRD 234
Cdd:pfam06745  82 KLAIIDASTSGIGIAEVEDRFDLEELIERLReairEIGAKRVVIDSITTL---FYLLKPAVArEILRR---LKRVLKGLG 155

                         170       180
                  ....*....|....*....|....*....
gi 1928505583 235 HISLFIVGHVTKEGAIAGPKVLEHLVDTV 263
Cdd:pfam06745 156 VTAIFTSEKPSGEGGIGGYGVEEFIVDGV 184
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 81-239 1.10e-11

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 66.83  E-value: 1.10e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  81 RFPSGYGELDRVLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAEESGQQIKLRATRLGItqtvnasD 160
Cdd:PRK09302  254 RISSGVPDLDEMLGGGFFRGSIILVSGATGTGKTLLASKFAEAACRRGERCLLFAFEESRAQLIRNARSWGI-------D 326

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 161 SKMAEAnlphDGNLFVL---PE-TNLED----ILRELEALQPQVAIIDSIQNLYfpalssAPGSVSQVRECTGLLMQLAK 232
Cdd:PRK09302  327 LEKMEE----KGLLKIIcarPEsYGLEDhliiIKREIEEFKPSRVAIDPLSALA------RGGSLNEFRQFVIRLTDYLK 396


                  ....*..
gi 1928505583 233 RDHISLF 239
Cdd:PRK09302  397 SEEITGL 403
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 99-266 9.43e-09

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: 54.30  E-value: 9.43e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583   99 PGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAEESGQQIKLRATRLGITQTVNASDSKMAeanlphdgnlfvlp 178
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELR-------------- 66

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  179 etnLEDILRELEALQPQVAIIDSIQNLyfpaLSSAPGSVSQVRECTGLLMQLAKRDHISLFIVGHVTKegaIAGPKVLEH 258
Cdd:smart00382  67 ---LRLALALARKLKPDVLILDEITSL----LDAEQEALLLLLEELRLLLLLKSEKNLTVILTTNDEK---DLGPALLRR 136


                   ....*...
gi 1928505583  259 LVDTVLYF 266
Cdd:smart00382 137 RFDRRIVL 144
 
Name Accession Description Interval E-value
Sms COG1066
DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and ...
 1-480 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: 756.12  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583   1 MAKARTKFVCSACGADHAQWFGRCPKCHEYGTLQEEVVNAVSSGTNRRSlgaqksgsarvKTGQPQAALTFSQIRQENQG 80
Cdd:COG1066     1 MAKTKTVYVCQECGYESPKWLGRCPECGAWNTLVEEVVAKAKKGRAASG-----------AAGRASKPVPLSEVEAEEEP 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  81 RFPSGYGELDRVLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAEESGQQIKLRATRLGITqtvnasd 160
Cdd:COG1066    70 RISTGIGELDRVLGGGLVPGSVVLIGGEPGIGKSTLLLQVAARLAKKGGKVLYVSGEESASQIKLRAERLGLL------- 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 161 skmaeanlphDGNLFVLPETNLEDILRELEALQPQVAIIDSIQNLYFPALSSAPGSVSQVRECTGLLMQLAKRDHISLFI 240
Cdd:COG1066   143 ----------SDNLYLLAETDLEAILATIEELKPDLLVIDSIQTMYSEELESAPGSVSQVRECAAELIRLAKETGIAVFL 212

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 241 VGHVTKEGAIAGPKVLEHLVDTVLYFQGDRFASHRLLRSVKNRFGATQEIGIFEMVQSGLQEVLNPSQLFLGSREEFMSG 320
Cdd:COG1066   213 VGHVTKEGSIAGPRVLEHMVDTVLYFEGDRHSRYRILRAVKNRFGSTNEIGVFEMTEKGLREVSNPSELFLSERDEPVPG 292

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 321 TAITVACEGTRPLVVELQALVSPTSYASPRRSTTGVDYNRLLQVLAVLEKRLGVPLSKLDAYLSVAGGLEVEEPAVDLAM 400
Cdd:COG1066   293 SAVTVTMEGTRPLLVEVQALVSPSSFGNPRRTAVGLDSNRLAMLLAVLEKRAGLPLGDQDVYVNVVGGLKITEPAADLAV 372

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 401 AIALVASFRDRVVDPTMIILGEIGLGGQIRPISQLEIRLKEAAKLGFKKAIVPKGQT-GIESAGIKLIPVGKVFAAIAVA 479
Cdd:COG1066   373 ALAIASSFRDRPLPPDTVFFGEVGLTGEIRPVSRIEQRLKEAAKLGFKRAIVPKGNKkKLKPKGIEIIGVSTLEEALEAL 452


                  .
gi 1928505583 480 L 480
Cdd:COG1066   453 F 453
sms TIGR00416
DNA repair protein RadA; The gene protuct codes for a probable ATP-dependent protease involved ...
 1-476 0e+00

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: 751.25  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583   1 MAKARTKFVCSACGADHAQWFGRCPKCHEYGTLQEEVVNavssgtnrRSLGAQKSGSARVKTGQPQA--ALTFSQIRQEN 78
Cdd:TIGR00416   1 MAKAKSKFVCQHCGADSPKWQGKCPACHAWNTITEERLH--------RSLGAQKNRRNSGKAGIPQAqkSQTISAIELEE 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  79 QGRFPSGYGELDRVLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAEESGQQIKLRATRLGitqtvna 158
Cdd:TIGR00416  73 VPRFSSGFGELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVSGEESLQQIKMRAIRLG------- 145

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 159 sdskmaeanLPHDgNLFVLPETNLEDILRELEALQPQVAIIDSIQNLYFPALSSAPGSVSQVRECTGLLMQLAKRDHISL 238
Cdd:TIGR00416 146 ---------LPEP-NLYVLSETNWEQICANIEEENPQACVIDSIQTLYSPDISSAPGSVSQVRECTAELMRLAKTRGIAI 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 239 FIVGHVTKEGAIAGPKVLEHLVDTVLYFQGDRFASHRLLRSVKNRFGATQEIGIFEMVQSGLQEVLNPSQLFLGSREEFM 318
Cdd:TIGR00416 216 FIVGHVTKEGSIAGPKVLEHMVDTVLYFEGDRDSRFRILRSVKNRFGATNEIGIFEMTEQGLREVLNPSAIFLSRREEPM 295

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 319 SGTAITVACEGTRPLVVELQALVSPTSYASPRRSTTGVDYNRLLQVLAVLEKRLGVPLSKLDAYLSVAGGLEVEEPAVDL 398
Cdd:TIGR00416 296 SGSSITVTWEGTRPLLVEIQALVSPTSFANPRRVATGLDQNRLALLLAVLEKRLGLPLADQDVFLNVAGGVKVSEPAADL 375

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1928505583 399 AMAIALVASFRDRVVDPTMIILGEIGLGGQIRPISQLEIRLKEAAKLGFKKAIVPKGQT-GIESAGIKLIPVGKVFAAI 476
Cdd:TIGR00416 376 ALLIAIVSSFRDRPLDPDLVFLGEVGLAGEIRPVPSLEERLKEAAKLGFKRAIVPKANSpKTAPEGIKVIGVKKVGDAL 454
RadA_SMS_N cd01121
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a ...
 8-303 4.31e-162

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: 460.07  E-value: 4.31e-162
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583   8 FVCSACGADHAQWFGRCPKCHEYGTLQEEVVNAVSSGTNRRSlgaqksgsarvKTGQPQAALTFSQIRQENQGRFPSGYG 87
Cdd:cd01121     1 YVCQECGYESPKWLGRCPSCGEWNTFVEEVVSASSSASRRAS-----------ASPSPSKPLPLSDVEAEEEERISTGIG 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  88 ELDRVLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAEESGQQIKLRATRLGITqtvnasdskmaean 167
Cdd:cd01121    70 ELDRVLGGGLVPGSVVLIGGDPGIGKSTLLLQVAARLAQRGGKVLYVSGEESLSQIKLRAERLGLG-------------- 135

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 168 lphDGNLFVLPETNLEDILRELEALQPQVAIIDSIQNLYFPALSSAPGSVSQVRECTGLLMQLAKRDHISLFIVGHVTKE 247
Cdd:cd01121   136 ---SDNLYLLAETNLEAILAEIEELKPSLVVIDSIQTVYSPELTSSPGSVSQVRECAAELLRLAKETGIPVFLVGHVTKD 212

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1928505583 248 GAIAGPKVLEHLVDTVLYFQGDRFASHRLLRSVKNRFGATQEIGIFEMVQSGLQEV 303
Cdd:cd01121   213 GAIAGPKVLEHMVDTVLYFEGDRGSSYRILRSVKNRFGPTNEIGVFEMTENGLREV 268
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
81-283 1.16e-23

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 98.83  E-value: 1.16e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  81 RFPSGYGELDRVLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAEESGQQIKLRATRLGItqtvnaSD 160
Cdd:COG0467     1 RVPTGIPGLDELLGGGLPRGSSTLLSGPPGTGKTTLALQFLAEGLRRGEKGLYVSFEESPEQLLRRAESLGL------DL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 161 SKMAEanlphDGNLFVL----------PETNLEDILRELEALQPQVAIIDSIQNLYfpalSSAPGSVSQVRECTGLLMQL 230
Cdd:COG0467    75 EEYIE-----SGLLRIIdlspeelgldLEELLARLREAVEEFGAKRVVIDSLSGLL----LALPDPERLREFLHRLLRYL 145

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1928505583 231 AKRDHISLFIVGHVTKEGAIAGPkVLEHLVDTVLYFQGDRFAS--HRLLRSVKNR 283
Cdd:COG0467   146 KKRGVTTLLTSETGGLEDEATEG-GLSYLADGVILLRYVELGGelRRALSVLKMR 199
KaiC-like cd01124
Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. ...
 83-285 9.58e-22

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: 93.48  E-value: 9.58e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  83 PSGYGELDRVLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAEESGQQIKLRATRLGITQTVNASDSK 162
Cdd:cd01124     2 KTGIPGLDELLGGGIPKGSVTLLTGGPGTGKTLFGLQFLYAGAKNGEPGLFFTFEESPERLLRNAKSFGWDFDEMEDEGK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 163 MAEANLPHDGNLFVLPETNLEDILRELEALQPQVAIIDSIQNLYfpalSSAPGSVSQVRECTGLLMQLAKRDHISLFIVG 242
Cdd:cd01124    82 LIIVDAPPTEAGRFSLDELLSRILSIIKSFKAKRVVIDSLSGLR----RAKEDQMRARRIVIALLNELRAAGVTTIFTSE 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1928505583 243 -HVTKEGAIAGPKVLEHLVDTV--LYFQGDRFASHRLLRSVKNRFG 285
Cdd:cd01124   158 mRSFLSSESAGGGDVSFIVDGVilLRYVEIEGELRRTIRVLKMRGT 203
RepA COG3598
RecA-family ATPase [Replication, recombination and repair];
96-351 3.41e-17

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


Pssm-ID: 442817 [Multi-domain]  Cd Length: 313  Bit Score: 82.26  E-value: 3.41e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  96 GIVP-GALILIGGDPGIGKSTLLLQVAFQLATRLP---------RILYVSAEESGQQIKLRATRLGITQTVNASDSkmae 165
Cdd:COG3598     8 GLLPeGGVTLLAGPPGTGKSFLALQLAAAVAAGGPwlgrrvppgKVLYLAAEDDRGELRRRLKALGADLGLPFADL---- 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 166 anlphDGNLFVLPETN-------LEDILRELEALQPQVAIIDSIQNLYFPALSSApgsvSQVRECTGLLMQLAKRDHISL 238
Cdd:COG3598    84 -----DGRLRLLSLAGdlddtddLEALERAIEEEGPDLVVIDPLARVFGGDENDA----EEMRAFLNPLDRLAERTGAAV 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 239 FIVGHVTKEGA-------IAGPKVLEHLVDTVLYFQGDRFASHRLLRSVKNRFGATQEigiFEMVQSGLQEVLNPSQLFL 311
Cdd:COG3598   155 LLVHHTGKGGAgkdsgdrARGSSALRGAARSVLVLSREKGEDLRVLTRAKSNYGPEIA---LRWDNGGRLALEEVAALTA 231

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 1928505583 312 GSREEFMSGTAITVACEGTRPLVVELQALVSPTSYASPRR 351
Cdd:COG3598   232 GAGEVELKELVGGVARTGTDSELEEGLLEVPLAEAESAGE 271
ATPase pfam06745
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ...
 83-263 1.21e-14

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: 73.43  E-value: 1.21e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  83 PSGYGELDRVLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRL-PRILYVSAEESGQQIKLRATRLG--ITQTVNAS 159
Cdd:pfam06745   2 KTGIPGLDEILKGGFPEGRVVLITGGPGTGKTIFGLQFLYNGALKYgEPGVFVTLEEPPEDLRENARSFGwdLEKLEEEG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 160 DSKMAEANLPHDGNLFVLPETNLEDILRELE----ALQPQVAIIDSIQNLyfpALSSAPGSV-SQVREctgLLMQLAKRD 234
Cdd:pfam06745  82 KLAIIDASTSGIGIAEVEDRFDLEELIERLReairEIGAKRVVIDSITTL---FYLLKPAVArEILRR---LKRVLKGLG 155

                         170       180
                  ....*....|....*....|....*....
gi 1928505583 235 HISLFIVGHVTKEGAIAGPKVLEHLVDTV 263
Cdd:pfam06745 156 VTAIFTSEKPSGEGGIGGYGVEEFIVDGV 184
AAA_25 pfam13481
AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.
 92-249 9.94e-13

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: 67.02  E-value: 9.94e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  92 VLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRLP-----------RILYVSAEESGQQIKLRATRLGITQTVNAS- 159
Cdd:pfam13481  25 LIKGLLPAGGLGLLAGAPGTGKTTLALDLAAAVATGKPwlggprvpeqgKVLYVSAEGPADELRRRLRAAGADLDLPARl 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 160 --DSKMAEANLPHDGNLFVLPETNLEDILRELEAL-QPQVAIIDSIQNLYFPALSSApgsvSQVRECTGLLMQLAKRDHI 236
Cdd:pfam13481 105 lfLSLVESLPLFFLDRGGPLLDADVDALEAALEEVeDPDLVVIDPLARALGGDENSN----SDVGRLVKALDRLARRTGA 180

                         170
                  ....*....|...
gi 1928505583 237 SLFIVGHVTKEGA 249
Cdd:pfam13481 181 TVLLVHHVGKDGA 193
KaiC-like_N cd19488
N-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 84-239 9.48e-12

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: 64.68  E-value: 9.48e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  84 SGYGELDRVLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAEESGQQIKLRATRLGIT-QTVNASDSK 162
Cdd:cd19488     3 TGIPGLDDILRGGLPPRRLYLVEGAPGTGKTTLALQFLLEGAANGETGLYITLSETEQELRAVALSHGWSlDGIHIFELS 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 163 MAEANLPHDGNLFVLPETNLE------DILRELEALQPQVAIIDSIQNLYFpalsSAPGSVSQVRECTGLLMQLAKRDHI 236
Cdd:cd19488    83 PSESALDAAQQYTILHPSELElsettrLIFERVERLKPSRVVIDSLSELRL----LAQDSLRYRRQILALKQFFAGRNTT 158


                  ...
gi 1928505583 237 SLF 239
Cdd:cd19488   159 VLL 161
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 81-239 1.10e-11

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 66.83  E-value: 1.10e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  81 RFPSGYGELDRVLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAEESGQQIKLRATRLGItqtvnasD 160
Cdd:PRK09302  254 RISSGVPDLDEMLGGGFFRGSIILVSGATGTGKTLLASKFAEAACRRGERCLLFAFEESRAQLIRNARSWGI-------D 326

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 161 SKMAEAnlphDGNLFVL---PE-TNLED----ILRELEALQPQVAIIDSIQNLYfpalssAPGSVSQVRECTGLLMQLAK 232
Cdd:PRK09302  327 LEKMEE----KGLLKIIcarPEsYGLEDhliiIKREIEEFKPSRVAIDPLSALA------RGGSLNEFRQFVIRLTDYLK 396


                  ....*..
gi 1928505583 233 RDHISLF 239
Cdd:PRK09302  397 SEEITGL 403
Rubredoxin_2 pfam18073
Rubredoxin metal binding domain; This is the C-terminal rubredoxin metal binding domain found ...
 8-35 1.69e-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: 1.69e-11
                          10        20
                  ....*....|....*....|....*...
gi 1928505583   8 FVCSACGADHAQWFGRCPKCHEYGTLQE 35
Cdd:pfam18073   1 YRCSQCGFESPQWFGRCPSCGSWGTLVE 28
KaiC_C cd19484
C-terminal domain of Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most ...
 83-239 2.46e-11

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: 63.12  E-value: 2.46e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  83 PSGYGELDRVL-GGGIVPGALILIGGDPGIGKStlLLQVAFQLAT--RLPRILYVSAEESGQQIKLRATRLGI--TQTVN 157
Cdd:cd19484     2 STGIPRLDAMLgGGGFFRGSSILVSGATGTGKT--LLAASFADAAcrRGERCLYFAFEESPAQLIRNAKSIGIdlEQMER 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 158 ASDSKMaEANLPhdgnlfvlPETNLED----ILRELEALQPQVAIIDSIQNLyfpalsSAPGSVSQVRECTGLLMQLAKR 233
Cdd:cd19484    80 KGLLKI-ICARP--------ELYGLEDhliiIKSEINEFKPSRVIVDPLSAL------ARGGSLNEVKEFVIRLIDYLKS 144


                  ....*.
gi 1928505583 234 DHISLF 239
Cdd:cd19484   145 QEITGL 150
KaiC-like_C cd19487
C-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 83-301 2.65e-10

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: 60.39  E-value: 2.65e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  83 PSGYGELDRVLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAEESGQQIKLRATRLGITQtvnasdSK 162
Cdd:cd19487     2 SSGVPELDELLGGGLERGTSTLLIGPAGVGKSTLALQFAKAAAARGERSVLFSFDESIGTLFERSEALGIDL------RA 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 163 MAEanlphDGNLFV-------LPETNLEDILR-ELEALQPQVAIIDSIqNLYfpaLSSAPGSVSQVRECTGLLMQLAKRD 234
Cdd:cd19487    76 MVE-----KGLLSIeqidpaeLSPGEFAQRVRtSVEQEDARVVVIDSL-NGY---LNAMPDERFLILQMHELLSYLNNQG 146

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1928505583 235 HISLFIVG-HVTKEGAIAGPKVLEHLVDTVLYFqgdRFASH--RLLRS---VKNRFGATQE-IGIFEMVQSGLQ 301
Cdd:cd19487   147 VTTLLIVAqHGLLGGDMGTPVDISYLADTVVLL---RYFEAegEVRKAisvLKKRTGDHERtIREFRITRSGLK 217
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 99-266 9.43e-09

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: 54.30  E-value: 9.43e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583   99 PGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAEESGQQIKLRATRLGITQTVNASDSKMAeanlphdgnlfvlp 178
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELR-------------- 66

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  179 etnLEDILRELEALQPQVAIIDSIQNLyfpaLSSAPGSVSQVRECTGLLMQLAKRDHISLFIVGHVTKegaIAGPKVLEH 258
Cdd:smart00382  67 ---LRLALALARKLKPDVLILDEITSL----LDAEQEALLLLLEELRLLLLLKSEKNLTVILTTNDEK---DLGPALLRR 136


                   ....*...
gi 1928505583  259 LVDTVLYF 266
Cdd:smart00382 137 RFDRRIVL 144
DnaB_C cd00984
C-terminal domain of DnaB helicase; DnaB helicase C-terminal domain. The hexameric helicase ...
 83-205 3.14e-08

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: 54.83  E-value: 3.14e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  83 PSGYGELDRVLGGgIVPGALILIGGDPGIGKSTLLLQVAFQLATRLP-RILYVSAEESGQQI--------------KLRA 147
Cdd:cd00984     3 PTGFTDLDKLTGG-LQPGDLIIIAARPSMGKTAFALNIAENIALDEGlPVLFFSLEMSAEQLaerllssesgvslsKLRT 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1928505583 148 TRLGITQ--TVNASDSKMAEANLPHDGNlfvlPETNLEDI---LRELEALQPQVA--IIDSIQNL 205
Cdd:cd00984    82 GRLDDEDweRLTAAMGELSELPLYIDDT----PGLTVDEIrakARRLKREHGGLGliVIDYLQLI 142
ChlI pfam13541
Subunit ChlI of Mg-chelatase;
392-455 5.28e-08

Subunit ChlI of Mg-chelatase;


Pssm-ID: 433293 [Multi-domain]  Cd Length: 121  Bit Score: 51.30  E-value: 5.28e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1928505583 392 EEPAVDLAMAIALVASFRDRVVDPTMIILGEIGLGGQIRPISQLEIRLKEAAKLGFKKAIVPKG 455
Cdd:pfam13541  57 EGSSFDLPIAIGILAAQGQIPVLEETIFLGELSLDGSLRPVRGALPIALAARKHGFRGLIVPKE 120
PRK06067 PRK06067
flagellar accessory protein FlaH; Validated
 83-201 7.51e-08

flagellar accessory protein FlaH; Validated


Pssm-ID: 180381  Cd Length: 234  Bit Score: 53.05  E-value: 7.51e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  83 PSGYGELDRVLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAEES--GQQIKLRATRLGITQTVNASD 160
Cdd:PRK06067    8 STGNEELDRKLGGGIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITTENTskSYLKQMESVKIDISDFFLWGY 87

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1928505583 161 SKMAEANLPHDGNLFVLPETNLEDILRELEALQPQVAIIDS 201
Cdd:PRK06067   88 LRIFPLNTEGFEWNSTLANKLLELIIEFIKSKREDVIIIDS 128
FlaH COG2874
Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];
81-202 9.35e-08

Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];


Pssm-ID: 442121  Cd Length: 230  Bit Score: 52.91  E-value: 9.35e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  81 RFPSGYGELDRVLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSaeesgqqiklraTRLGITQTVNasd 160
Cdd:COG2874     2 IISTGNDELDKRLGGGIPLGSLVLIEGENGTGKSVLSQQFAYGALENGLSVTYIS------------TELTTKEFIK--- 66

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1928505583 161 sKMAEANL---PH--DGNLFVLP---------ETNLEDILREL------EALQPQVAIIDSI 202
Cdd:COG2874    67 -QMKSLSYdisDYllRGRLLFLPvhplgfewnSKQRKDLLKRLmkyiasNLWEADVIIIDSL 127
radB PRK09361
DNA repair and recombination protein RadB; Provisional
 81-303 4.56e-07

DNA repair and recombination protein RadB; Provisional


Pssm-ID: 236482 [Multi-domain]  Cd Length: 225  Bit Score: 50.63  E-value: 4.56e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  81 RFPSGYGELDRVLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAEesgqqiKLRATRLgitqtvnasd 160
Cdd:PRK09361    4 RLPTGCKMLDELLGGGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE------GLSPERF---------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 161 SKMAEANLPHDGNLFVLPE-TNLED---ILRELEALQPQVA---IIDSIQNLYFPALSSAPGSVSQVRECT---GLLMQL 230
Cdd:PRK09361   68 KQIAGEDFEELLSNIIIFEpSSFEEqseAIRKAEKLAKENVgliVLDSATSLYRLELEDEEDNSKLNRELGrqlTHLLKL 147

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1928505583 231 AKRDHISLFIVGHV---TKEGAI--AGPKVLEHLVDTVLYFqgDRFA-SHRLLRSVKNRFGATQEIGIFEMVQSGLQEV 303
Cdd:PRK09361  148 ARKHDLAVVITNQVysdIDSDGLrpLGGHTLEHWSKTILRL--EKFRnGKRRATLEKHRSRPEGESAEFRITDRGIEII 224
archRadB cd01394
archaeal RadB; The archaeal protein RadB shares similarity RadA, the archaeal functional ...
 83-281 6.89e-07

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: 50.01  E-value: 6.89e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  83 PSGYGELDRVLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAE----ESGQQIklratrlgitqtvnA 158
Cdd:cd01394     2 STGSKSLDSLLGGGVERGTITQIYGPPGSGKTNICLQLAVEAAKQGKKVVYIDTEglspERFQQI--------------A 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 159 SDSKMAEANlphdgNLFVLPETNLED---ILRELEAL----QPQVAIIDSIQNLYFPALSSAPGSVSQVRECTGLLMQLA 231
Cdd:cd01394    68 GERFESIAS-----NIIVFEPYSFDEqgvAIQEAEKLlksdKVDLVVVDSATALYRLELGDDSEANRELSRQMSKLLSIA 142

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1928505583 232 KRDHISLFIVGHV---TKEGAIA--GPKVLEHLVDTVLYFQ----GDRFASHRLLRSVK 281
Cdd:cd01394   143 RKYDIPVVITNQVysdIDDDRLKpvGGTLLEHWSKAIIRLEksppGLRRATLEKHRSRP 201
DnaB_C pfam03796
DnaB-like helicase C terminal domain; The hexameric helicase DnaB unwinds the DNA duplex at ...
 83-150 6.13e-06

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: 47.80  E-value: 6.13e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1928505583  83 PSGYGELDRVLGGgIVPGALILIGGDPGIGKSTLLLQVAFQLATRLPR-ILYVSAEESGQQIklrATRL 150
Cdd:pfam03796   3 PTGFTDLDRLTGG-LQPGDLIIIAARPSMGKTAFALNIARNAAVKHKKpVAIFSLEMSAEQL---VMRL 67
RepA_RSF1010_like cd01125
Hexameric Replicative Helicase RepA of plasmid RSF1010 and related proteins; This family ...
 100-249 1.46e-05

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: 46.22  E-value: 1.46e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 100 GALILIGGDPGIGKSTLLLQVAFQLATRLP----------RILYVSAEESGQQIKLRATRLGitQTVNASDSKMAE---- 165
Cdd:cd01125     1 GTLGMLVGPPGSGKSFLALDLAVAVATGRDwlgerrvkqgRVVYLAAEDPRDGLRRRLKAIG--AHLGDEDAALAEnlvi 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 166 ANLPHDGNLFVLPETNLEDILRELEalQPQVAIIDSIQNLYFPALSSAPGSVSQVrectgllmqLAKRDHI------SLF 239
Cdd:cd01125    79 ENLRGKPVSIDAEAPELERIIEELE--GVRLIIIDTLARVLHGGDENDAADMGAF---------VAGLDRIaretgaAVL 147

                         170
                  ....*....|
gi 1928505583 240 IVGHVTKEGA 249
Cdd:cd01125   148 LVHHTGKDAA 157
DnaB COG0305
Replicative DNA helicase [Replication, recombination and repair];
70-150 1.55e-05

Replicative DNA helicase [Replication, recombination and repair];


Pssm-ID: 440074 [Multi-domain]  Cd Length: 429  Bit Score: 47.38  E-value: 1.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  70 TFSQI--RQENQGRF---PSGYGELDRVLGGgIVPGALILIGGDPGIGKSTLLLQVAFQLATR--LPrILYVSAEESGQQ 142
Cdd:COG0305   157 ALERIeeLYKNGGGItgvPTGFTDLDKLTGG-LQPGDLIILAARPSMGKTAFALNIARNAAIKegKP-VAIFSLEMSAEQ 234


                  ....*...
gi 1928505583 143 IklrATRL 150
Cdd:COG0305   235 L---VMRL 239
RecA-like_superfamily cd01120
RecA-like_NTPases; RecA-like NTPases. This superfamily includes the NTP binding domain of F1 ...
 103-247 4.17e-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: 42.88  E-value: 4.17e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 103 ILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAeesgqqiklratrlgitqtvnasdskmaeanlphdgnlfvlPETNL 182
Cdd:cd01120     1 ILITGPPGSGKTTLLLQFAEQALLSDEPVIFISF-----------------------------------------LDTIL 39

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1928505583 183 EDILRELEALQPQVAIIDSIQNLYFPalsSAPGSVSQVRECTGLLMQLAKRDHISLFIVGHVTKE 247
Cdd:cd01120    40 EAIEDLIEEKKLDIIIIDSLSSLARA---SQGDRSSELLEDLAKLLRAARNTGITVIATIHSDKF 101
PRK08533 PRK08533
flagellar accessory protein FlaH; Reviewed
 88-208 9.37e-05

flagellar accessory protein FlaH; Reviewed


Pssm-ID: 181459  Cd Length: 230  Bit Score: 43.90  E-value: 9.37e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  88 ELDRVLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSaeesgqqiklraTRLGITQTVNASDS-KMAEA 166
Cdd:PRK08533   12 ELHKRLGGGIPAGSLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVS------------TQLTTTEFIKQMMSlGYDIN 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1928505583 167 NLPHDGNLFVLP-----------ETNLEDILRELEALQPQVAIIDSIQNLYFP 208
Cdd:PRK08533   80 KKLISGKLLYIPvypllsgnsekRKFLKKLMNTRRFYEKDVIIIDSLSSLISN 132
Rad51D cd19489
RAD51D recombinase; RAD51D recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 94-250 9.70e-05

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: 43.39  E-value: 9.70e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  94 GGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRLP-RILYV------SAEESGQQIKLRAtrlGITQTVNASDSKMAEA 166
Cdd:cd19489     1 GGGLRTGEITELVGESSSGKTQLCLTAAANVASRSGqNVLYIdtkssfSARRLAQILKSRA---QDAEEIDKALQRIRVV 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 167 NLPHDGNLFVLPETNLEDILRELE--ALQPQVAIIDSIQNLYFPALSSapgsvSQVRECTGLLMQ-------LAKRDHIS 237
Cdd:cd19489    78 RVFDPYELLDLLEELRNTLSQQQEnlYSRLKLVIIDSLSALISPLLGG-----SKHSEGHALLASlarllkkLAAEYQIA 152

                         170
                  ....*....|...
gi 1928505583 238 LFIVGHVTKEGAI 250
Cdd:cd19489   153 VLVTNLTVRGGDG 165
XRCC3 cd19491
XRCC3 recombinase; XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells ...
 89-130 1.28e-04

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: 43.82  E-value: 1.28e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1928505583  89 LDRVLGGGIVPGALILIGGDPGIGKSTLLLQVAfqLATRLPR 130
Cdd:cd19491     1 LDELLGGGIPVGGITEIAGESGAGKTQLCLQLA--LTVQLPR 40
Rad51B cd19493
RAD51B recombinase; RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 90-233 1.58e-04

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: 43.08  E-value: 1.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  90 DRVLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRLP------RILYVSAEESGQQIKLRA---TRLGITQTVNASD 160
Cdd:cd19493     1 DTALAGGLPLGAITEITGASGSGKTQFALTLASSAAMPARkggldgGVLYIDTESKFSAERLAEiaeARFPEAFSGFMEE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 161 SKMAEANLphdGNLFVLPETNLEDILRELEALQPQVA-------IIDSIQNLYFPALSSAPGSVSQVRECTGLLMQLAKR 233
Cdd:cd19493    81 NERAEEML---KRVAVVRVTTLAQLLERLPNLEEHILssgvrlvVIDSIAALVRREFGGSDGEVTERHNALAREASSLKR 157
Lon_C pfam05362
Lon protease (S16) C-terminal proteolytic domain; The Lon serine proteases must hydrolyse ATP ...
 394-482 1.59e-04

Lon protease (S16) C-terminal proteolytic domain; The Lon serine proteases must hydrolyse ATP to degrade protein substrates. In Escherichia coli, these proteases are involved in turnover of intracellular proteins, including abnormal proteins following heat-shock. The active site for protease activity resides in a C-terminal domain. The Lon proteases are classified as family S16 in Merops.


Pssm-ID: 428442 [Multi-domain]  Cd Length: 205  Bit Score: 43.00  E-value: 1.59e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 394 PAVDLAMAIALVASFRDRVVDPTMIILGEIGLGGQIRPISQLEIRLKEAAKLGFKKAIVPK-GQTGIES------AGIKL 466
Cdd:pfam05362 110 PSAGVTMATALVSALTGIPVRKDVAMTGEITLRGRVLPIGGLKEKLLAAHRAGIKTVIIPKeNEKDLEDipenvrEGLEI 189

                          90
                  ....*....|....*.
gi 1928505583 467 IPVGKVFAAIAVALPA 482
Cdd:pfam05362 190 IPVEHVDEVLKHALVG 205
PRK07773 PRK07773
replicative DNA helicase; Validated
 83-146 2.40e-04

replicative DNA helicase; Validated


Pssm-ID: 236093 [Multi-domain]  Cd Length: 886  Bit Score: 43.97  E-value: 2.40e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1928505583  83 PSGYGELDRvLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATR--LPRILYvSAEESGQQIKLR 146
Cdd:PRK07773  201 PTGFTELDA-MTNGLHPGQLIIVAARPSMGKTTFGLDFARNCAIRhrLAVAIF-SLEMSKEQLVMR 264
YifB COG0606
Predicted Mg-chelatase, contains ChlI-like and ATPase domains, YifB family [Posttranslational ...
 397-469 3.04e-04

Predicted Mg-chelatase, contains ChlI-like and ATPase domains, YifB family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440371 [Multi-domain]  Cd Length: 502  Bit Score: 43.11  E-value: 3.04e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1928505583 397 DLAMAIA-LVAS--FRDRVVDPTMIIlGEIGLGGQIRPISQLEIRLKEAAKLGFKKAIVPKGQtGIESA---GIKLIPV 469
Cdd:COG0606    81 DLPIALGiLAASgqIPAEALEDYVFL-GELSLDGSLRPVRGVLPAALAAREAGIRRLIVPAAN-AAEAAlvpGIEVYGA 157
COG3899 COG3899
Predicted ATPase [General function prediction only];
89-205 5.87e-04

Predicted ATPase [General function prediction only];


Pssm-ID: 443106 [Multi-domain]  Cd Length: 1244  Bit Score: 42.54  E-value: 5.87e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583   89 LDRVLGGGivpGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAEESGQQIKLRATRLGITQTVNASDSKMAE--- 165
Cdd:COG3899    303 LERARAGR---GELVLVSGEAGIGKSRLVRELARRARARGGRVLRGKCDQLERGVPYAPLAQALRALLGQLPEDELAawr 379

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1928505583  166 ----ANLPHDGNLF--VLPETNLEDILRELEALQPQVAIIDSIQNL 205
Cdd:COG3899    380 arllAALGANGRLLadLLPELELQPAPPELDPEEARNRLFRALLRL 425
RecA-like cd01393
RecA family; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 100-231 6.14e-04

RecA family; RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs RadA and RadB.


Pssm-ID: 410881 [Multi-domain]  Cd Length: 185  Bit Score: 40.80  E-value: 6.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 100 GALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAEESgqqikLRATRL-GITQTVNASDSKMAEAnlphDGNLFVLP 178
Cdd:cd01393     1 GKITEIYGPPGSGKTQLALQLAANALLLGGGVVWIDTEGA-----FPPSRLvQILEASPSSELELAEA----LSRLLYFR 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1928505583 179 ETNLEDILRELEALQPQVA--------IIDSIQNLYFPALSSAPGSVSQVRECTGLLMQLA 231
Cdd:cd01393    72 PPDTLAHLLALDSLPESLFpppntslvVVDSVSALFRKAFPRGGDGDSSSSLRARLLSQLA 132
circ_KaiC TIGR02655
circadian clock protein KaiC; Members of this family are the circadian clock protein KaiC, ...
 65-205 1.17e-03

circadian clock protein KaiC; Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. [Cellular processes, Other]


Pssm-ID: 131703 [Multi-domain]  Cd Length: 484  Bit Score: 41.47  E-value: 1.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  65 PQAALTFSQiRQENQgRFPSGYGELDRVLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAEESGQQIK 144
Cdd:TIGR02655 230 PLGAMRLTQ-RSSNV-RVSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVSKFLENACANKERAILFAYEESRAQLL 307

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1928505583 145 LRATRLGItqtvnasDSKMAEanlpHDGNLFVL---PE-TNLEDILR----ELEALQPQVAIIDSIQNL 205
Cdd:TIGR02655 308 RNAYSWGI-------DFEEME----QQGLLKIIcayPEsAGLEDHLQiiksEIADFKPARIAIDSLSAL 365
PRK10787 PRK10787
DNA-binding ATP-dependent protease La; Provisional
 394-453 6.02e-03

DNA-binding ATP-dependent protease La; Provisional


Pssm-ID: 182730 [Multi-domain]  Cd Length: 784  Bit Score: 39.15  E-value: 6.02e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 394 PAVDLAMAIALVASFRDRVVDPTMIILGEIGLGGQIRPISQLEIRLKEAAKLGFKKAIVP 453
Cdd:PRK10787  678 PSAGIAMCTALVSCLTGNPVRADVAMTGEITLRGQVLPIGGLKEKLLAAHRGGIKTVLIP 737
KaiC-N cd19485
N-terminal domain of Circadian Clock Protein Kaic; KaiC is a circadian clock protein, most ...
 83-283 6.43e-03

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: 38.12  E-value: 6.43e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  83 PSGYGELDRVLGGGIVPGALILIGGDPGIGKSTLLLQ-VAFQLATRLPRILYVSAEESGQQIKLRATRLGITqtvnaSDS 161
Cdd:cd19485     2 PTGIEGFDDITHGGLPKGRPTLICGTAGTGKTLFAAQfLVNGIKEFGEPGVFVTFEESPEDIIKNMASFGWD-----LPK 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 162 KMAEANL------PHDGNLFVLPETNLEDILRELEALQPQVA----IIDSIQNLyFPALSSApgsvSQVRECTGLLMQLA 231
Cdd:cd19485    77 LVAEGKLlildasPEPSEEEVTGEYDLEALLIRIEYAIRKIGakrvSLDSLEAV-FSGLSDS----AVVRAELLRLFAWL 151

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1928505583 232 KRDHISLFIVGHVTKEGAIAGPKVLEHLVDTVLYF----QGDRfaSHRLLRSVKNR 283
Cdd:cd19485   152 KQKGVTAIMTGERGEDGPLTRYGVEEYVSDCVVILrnvlEGER--RRRTLEILKYR 205
COG4544 COG4544
Uncharacterized conserved protein [Function unknown];
72-125 7.01e-03

Uncharacterized conserved protein [Function unknown];


Pssm-ID: 443609 [Multi-domain]  Cd Length: 230  Bit Score: 37.99  E-value: 7.01e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1928505583  72 SQIRQENQGRFPSGYGELDRVL-GGGIVPGALI-LIGGDPGIGKSTLLLQVAFQLA 125
Cdd:COG4544    19 EGLAAAARAVLPTGFAALDAALpGGGLPRGALHeILGPAPGIGELGLLLPLLARLA 74
RecA-like_Gp4D_helicase cd19483
RecA-like domain of Escherichia coli bacteriophage T7 Gp4D helicase; This family includes the ...
 103-295 7.05e-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: 38.32  E-value: 7.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 103 ILIGGDPGIGKSTLLLQVAFQLATRLP-RILYVSAEES-------------GQQIKLRATRLGITQTvnasDSKMAEANL 168
Cdd:cd19483     1 VTIGAGSGIGKSTIVRELAYHLITEHGeKVGIISLEESveetakglagkhlGKPEPLELPRDDITEE----EEDDAFDNE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583 169 PHDGNLFVLPE---TNLEDILRELE----ALQPQVAIIDSIQnlyfpALSSAPGSVSQVRE---CTGLLMQLAKRDHISL 238
Cdd:cd19483    77 LGSGRFFLYDHfgsLDWDNLKEKIRymvkVLGCKVIVLDHLT-----ILVSGLDSSDERKEldeIMTELAALVKELGVTI 151

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1928505583 239 FIVGHVTK--------EGA------IAGPKVLEHLVDTVLYFQGDRFASH------RLLRSVKNR-FGATQEIGIFEM 295
Cdd:cd19483   152 ILVSHLRRpgggkgheEGGevsesdLRGSSAIAQLSDYVIGLERNKQADDpverntTRVRVLKNRfTGETGIAGTLYY 229
Pgk2 COG2074
2-phosphoglycerate kinase/Mevalonate-3-phosphate 5-kinase [Carbohydrate transport and ...
 103-128 7.76e-03

2-phosphoglycerate kinase/Mevalonate-3-phosphate 5-kinase [Carbohydrate transport and metabolism, Lipid transport and metabolism];


Pssm-ID: 441677  Cd Length: 207  Bit Score: 38.01  E-value: 7.76e-03
                          10        20
                  ....*....|....*....|....*.
gi 1928505583 103 ILIGGDPGIGKSTLllqvAFQLATRL 128
Cdd:COG2074     9 ILIGGASGVGKSTI----AAELARRL 30
PRK05973 PRK05973
replicative DNA helicase; Provisional
 97-201 8.18e-03

replicative DNA helicase; Provisional


Pssm-ID: 168322 [Multi-domain]  Cd Length: 237  Bit Score: 38.09  E-value: 8.18e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1928505583  97 IVPGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAEESGQQIKLRATRLGITQ-------TVNASDS-------- 161
Cdd:PRK05973   61 LKPGDLVLLGARPGHGKTLLGLELAVEAMKSGRTGVFFTLEYTEQDVRDRLRALGADRaqfadlfEFDTSDAicadyiia 140

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1928505583 162 KMAEANlphDGNLFVLPETNLEDILRELEALQPQVAIIDS 201
Cdd:PRK05973  141 RLASAP---RGTLVVIDYLQLLDQRREKPDLSVQVRALKS 177
FlaH cd19475
flagellar accessory protein FlaH; Flagellar accessory protein FlaH is part of the motor of the ...
 88-152 8.59e-03

flagellar accessory protein FlaH; Flagellar accessory protein FlaH is part of the motor of the archaellum membrane-anchored archaeal motility structure, together with FlaX and FlaI. FlaH forms a hexameric ring, and binds ATP which is essential for its interaction with FlaI and for archaellum assembly.


Pssm-ID: 410883  Cd Length: 220  Bit Score: 37.97  E-value: 8.59e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1928505583  88 ELDRVLGGGIVPGALILIGGDPGIGKSTLLLQVAFQLATRLPRILYVSAEESGQQIKLRATRLGI 152
Cdd:cd19475     7 DLDKRLGGGIPYPSSIMIEGEESTGKSVLSQRLVYGFLQNDYSGYYISTQQTTKEFLKQMKSLKY 71
 
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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