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Conserved domains on  [gi|485464616|ref|NP_001264871|]
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DNA repair protein RAD51 homolog 4 isoform 5 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rad51D cd19489
RAD51D recombinase; RAD51D recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 94-245 1.13e-54

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: 175.52  E-value: 1.13e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  94 DAGLYTGEVTEIVGGPGSGKTQVCLCVAANVAHSLQQNVLYVDSNGGMTASRLLQLLQARTQDEEKQASALQRIQVVRSF 173
Cdd:cd19489    1 GGGLRTGEITELVGESSSGKTQLCLTAAANVASRSGQNVLYIDTKSSFSARRLAQILKSRAQDAEEIDKALQRIRVVRVF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616 174 DIFRMLDMLQDLRGTIAQQ-------------------------------------------------------VTNHLT 198
Cdd:cd19489   81 DPYELLDLLEELRNTLSQQqenlysrlklviidslsalispllggskhseghallaslarllkklaaeyqiavlVTNLTV 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 485464616 199 RDWDGRRF---KPALGRSWSFVPSTRILLDVTEGAGTlGSSQRTVCLTKS 245
Cdd:cd19489  161 RGGDGGQQgstKPALGEYWESVPSTRLLLSRDENDPE-ESGVCTATLLKS 209
radA super family cl35256
DNA repair and recombination protein RadA; Validated
 10-173 8.99e-18

DNA repair and recombination protein RadA; Validated


The actual alignment was detected with superfamily member PRK04301:

Pssm-ID: 235273 [Multi-domain]  Cd Length: 317  Bit Score: 81.46  E-value: 8.99e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  10 PGLTEETVQLLRGRKIKTVADLAAADLEEVAQKCGLSYKA----LVALRRVL-LAQFSAfplnGADLYEELKtSTAILST 84
Cdd:PRK04301  12 PGVGPATAEKLREAGYDTVEAIAVASPKELSEAAGIGESTaakiIEAAREAAdIGGFET----ALEVLERRK-NVGKITT 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  85 GIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCVAANV-----AHSLQQNVLYVDSNGGMTASRLLQLLQARTQDEEK 159
Cdd:PRK04301  87 GSKELDELLGGGIETQSITEFYGEFGSGKTQICHQLAVNVqlpeeKGGLEGKAVYIDTEGTFRPERIEQMAEALGLDPDE 166

                        170
                 ....*....|....
gi 485464616 160 qasALQRIQVVRSF 173
Cdd:PRK04301 167 ---VLDNIHVARAY 177
 
Name Accession Description Interval E-value
Rad51D cd19489
RAD51D recombinase; RAD51D recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 94-245 1.13e-54

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: 175.52  E-value: 1.13e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  94 DAGLYTGEVTEIVGGPGSGKTQVCLCVAANVAHSLQQNVLYVDSNGGMTASRLLQLLQARTQDEEKQASALQRIQVVRSF 173
Cdd:cd19489    1 GGGLRTGEITELVGESSSGKTQLCLTAAANVASRSGQNVLYIDTKSSFSARRLAQILKSRAQDAEEIDKALQRIRVVRVF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616 174 DIFRMLDMLQDLRGTIAQQ-------------------------------------------------------VTNHLT 198
Cdd:cd19489   81 DPYELLDLLEELRNTLSQQqenlysrlklviidslsalispllggskhseghallaslarllkklaaeyqiavlVTNLTV 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 485464616 199 RDWDGRRF---KPALGRSWSFVPSTRILLDVTEGAGTlGSSQRTVCLTKS 245
Cdd:cd19489  161 RGGDGGQQgstKPALGEYWESVPSTRLLLSRDENDPE-ESGVCTATLLKS 209
recomb_radA TIGR02236
DNA repair and recombination protein RadA; This family consists exclusively of archaeal RadA ...
 10-204 1.94e-19

DNA repair and recombination protein RadA; This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 131290 [Multi-domain]  Cd Length: 310  Bit Score: 85.95  E-value: 1.94e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616   10 PGLTEETVQLLRGRKIKTVADLAAADLEEVAQKCGLS----YKALVALRRvlLAQFSAFPlNGADLYEELKTSTAIlSTG 85
Cdd:TIGR02236   5 PGVGPATAEKLREAGYDTFEAIAVASPKELSEIAGISegtaAKIIQAARK--AADLGGFE-TADDVLERRKTIGKI-TTG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616   86 IGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCVAANVAH-----SLQQNVLYVDSNGGMTASRLLQLLQARTQDEEKq 160
Cdd:TIGR02236  81 SKELDELLGGGIETQAITEVFGEFGSGKTQICHQLAVNVQLpeekgGLGGKAVYIDTENTFRPERIMQMAEARGLDPDE- 159

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 485464616  161 asALQRIQVVRSFDI-FRML------DMLQDLRGTIA----QQVTNHLTRDWDGR 204
Cdd:TIGR02236 160 --VLKNIYVARAYNSnHQMLlvekaeDLIKELNNPVKllivDSLTSHFRAEYVGR 212
radA PRK04301
DNA repair and recombination protein RadA; Validated
 10-173 8.99e-18

DNA repair and recombination protein RadA; Validated


Pssm-ID: 235273 [Multi-domain]  Cd Length: 317  Bit Score: 81.46  E-value: 8.99e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  10 PGLTEETVQLLRGRKIKTVADLAAADLEEVAQKCGLSYKA----LVALRRVL-LAQFSAfplnGADLYEELKtSTAILST 84
Cdd:PRK04301  12 PGVGPATAEKLREAGYDTVEAIAVASPKELSEAAGIGESTaakiIEAAREAAdIGGFET----ALEVLERRK-NVGKITT 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  85 GIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCVAANV-----AHSLQQNVLYVDSNGGMTASRLLQLLQARTQDEEK 159
Cdd:PRK04301  87 GSKELDELLGGGIETQSITEFYGEFGSGKTQICHQLAVNVqlpeeKGGLEGKAVYIDTEGTFRPERIEQMAEALGLDPDE 166

                        170
                 ....*....|....
gi 485464616 160 qasALQRIQVVRSF 173
Cdd:PRK04301 167 ---VLDNIHVARAY 177
radB PRK09361
DNA repair and recombination protein RadB; Provisional
 82-175 1.50e-12

DNA repair and recombination protein RadB; Provisional


Pssm-ID: 236482 [Multi-domain]  Cd Length: 225  Bit Score: 65.27  E-value: 1.50e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  82 LSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCVAANVAhSLQQNVLYVDSNgGMTASRLLQLLqartqdEEKQA 161
Cdd:PRK09361   5 LPTGCKMLDELLGGGFERGTITQIYGPPGSGKTNICLQLAVEAA-KNGKKVIYIDTE-GLSPERFKQIA------GEDFE 76

                         90
                 ....*....|....
gi 485464616 162 SALQRIQVVRSFDI 175
Cdd:PRK09361  77 ELLSNIIIFEPSSF 90
Rad51 pfam08423
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ...
 82-204 4.55e-11

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: 61.55  E-value: 4.55e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616   82 LSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVC--LCVAANVAHSL---QQNVLYVDSNGGMTASRLLQLLQARTQD 156
Cdd:pfam08423  19 ITTGSKELDKLLGGGIETGSITEIFGEFRTGKTQLChtLCVTCQLPLEMgggEGKALYIDTEGTFRPERLVAIAERYGLD 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 485464616  157 EEkqaSALQRIQVVRSFDIFRMLDMLQDLRGTIAQQ---------VTNHLTRDWDGR 204
Cdd:pfam08423  99 PE---DVLDNVAYARAYNSEHQMQLLQQAAAMMSESrfallivdsATALYRTDFSGR 152
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
82-135 2.14e-06

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 47.60  E-value: 2.14e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 485464616  82 LSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCVAANVAHSlQQNVLYV 135
Cdd:COG0467    2 VPTGIPGLDELLGGGLPRGSSTLLSGPPGTGKTTLALQFLAEGLRR-GEKGLYV 54
HhH-GPD pfam00730
HhH-GPD superfamily base excision DNA repair protein; This family contains a diverse range of ...
 20-92 6.16e-03

HhH-GPD superfamily base excision DNA repair protein; This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases. The methyl-CPG binding protein MBD4 also contains a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family.


Pssm-ID: 425841 [Multi-domain]  Cd Length: 141  Bit Score: 36.11  E-value: 6.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616   20 LRGRKIKTVADLAAADLEEVAQ---KCGLS-YKA--LVALRRVLLAQF-SAFPLNGADLYEELK-----TSTAILSTGIG 87
Cdd:pfam00730  21 LFEKFFPTPEDLADADEEELRElirGLGFYrRKAkyLKELARILVEGYgGEVPLDEEELEALLKgvgrwTAEAVLIFALG 100


                  ....*
gi 485464616   88 SLDKL 92
Cdd:pfam00730 101 RPDPL 105
 
Name Accession Description Interval E-value
Rad51D cd19489
RAD51D recombinase; RAD51D recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 94-245 1.13e-54

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: 175.52  E-value: 1.13e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  94 DAGLYTGEVTEIVGGPGSGKTQVCLCVAANVAHSLQQNVLYVDSNGGMTASRLLQLLQARTQDEEKQASALQRIQVVRSF 173
Cdd:cd19489    1 GGGLRTGEITELVGESSSGKTQLCLTAAANVASRSGQNVLYIDTKSSFSARRLAQILKSRAQDAEEIDKALQRIRVVRVF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616 174 DIFRMLDMLQDLRGTIAQQ-------------------------------------------------------VTNHLT 198
Cdd:cd19489   81 DPYELLDLLEELRNTLSQQqenlysrlklviidslsalispllggskhseghallaslarllkklaaeyqiavlVTNLTV 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 485464616 199 RDWDGRRF---KPALGRSWSFVPSTRILLDVTEGAGTlGSSQRTVCLTKS 245
Cdd:cd19489  161 RGGDGGQQgstKPALGEYWESVPSTRLLLSRDENDPE-ESGVCTATLLKS 209
RecA-like cd01393
RecA family; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 100-225 1.95e-23

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: 93.96  E-value: 1.95e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616 100 GEVTEIVGGPGSGKTQVCLCVAANVAHsLQQNVLYVDSNGGMTASRLLQLLQARTQDEEKQASALQRIQVVRSFD----- 174
Cdd:cd01393    1 GKITEIYGPPGSGKTQLALQLAANALL-LGGGVVWIDTEGAFPPSRLVQILEASPSSELELAEALSRLLYFRPPDtlahl 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616 175 --------------------------IFR-------MLDMLQDLRGTIAQQ-----------------VTNHLTRDWDGR 204
Cdd:cd01393   80 laldslpeslfpppntslvvvdsvsaLFRkafprggDGDSSSSLRARLLSQlaralqklaaqfnlavvVTNQVTTKIRGG 159

                        170       180
                 ....*....|....*....|....*
gi 485464616 205 ----RFKPALGRSWSFVPSTRILLD 225
Cdd:cd01393  160 sgasLVPPALGNTWEHSVSTRLLLY 184
recomb_radA TIGR02236
DNA repair and recombination protein RadA; This family consists exclusively of archaeal RadA ...
 10-204 1.94e-19

DNA repair and recombination protein RadA; This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 131290 [Multi-domain]  Cd Length: 310  Bit Score: 85.95  E-value: 1.94e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616   10 PGLTEETVQLLRGRKIKTVADLAAADLEEVAQKCGLS----YKALVALRRvlLAQFSAFPlNGADLYEELKTSTAIlSTG 85
Cdd:TIGR02236   5 PGVGPATAEKLREAGYDTFEAIAVASPKELSEIAGISegtaAKIIQAARK--AADLGGFE-TADDVLERRKTIGKI-TTG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616   86 IGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCVAANVAH-----SLQQNVLYVDSNGGMTASRLLQLLQARTQDEEKq 160
Cdd:TIGR02236  81 SKELDELLGGGIETQAITEVFGEFGSGKTQICHQLAVNVQLpeekgGLGGKAVYIDTENTFRPERIMQMAEARGLDPDE- 159

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 485464616  161 asALQRIQVVRSFDI-FRML------DMLQDLRGTIA----QQVTNHLTRDWDGR 204
Cdd:TIGR02236 160 --VLKNIYVARAYNSnHQMLlvekaeDLIKELNNPVKllivDSLTSHFRAEYVGR 212
Rad51C cd19492
RAD51C recombinase; RAD51C recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 100-246 4.86e-19

RAD51C recombinase; RAD51C 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. RAD51C, together with the other RAD51 paralogs, RAD51B, RAD51D, XRCC3, and XRCC2, helps recruit RAD51 to the break site. Additionally, RAD51C acts as a mediator in the early steps of DNA damage signaling.


Pssm-ID: 410900 [Multi-domain]  Cd Length: 172  Bit Score: 81.89  E-value: 4.86e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616 100 GEVTEIVGGPGSGKTQVCLCVAANV-----AHSLQQNVLYVDSNGG-------------MTAsrLLQLLQARTQDEEKqa 161
Cdd:cd19492    1 GKITEICGVPGVGKTQLCMQLAVNVqipkcFGGLAGEAIYIDTEGSfnihyfrvhdyveLLA--LINSLPKFLEDHPK-- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616 162 salQRIQVVRSFDI-FRM------------LDMLQDLRgTIAQQ------VTNHLT---RDWDGRRFKPALGRSWSFVPS 219
Cdd:cd19492   77 ---VKLIVVDSIAFpFRHdfddlaqrtrllNGLAQLLH-SLARQhnlavvLTNQVTtkiSEDGQSQLVPALGESWSHACT 152

                        170       180
                 ....*....|....*....|....*..
gi 485464616 220 TRILLdvtegagTLGSSQRTVCLTKSP 246
Cdd:cd19492  153 TRLFL-------TWDEKQRFAHLYKSP 172
radA PRK04301
DNA repair and recombination protein RadA; Validated
 10-173 8.99e-18

DNA repair and recombination protein RadA; Validated


Pssm-ID: 235273 [Multi-domain]  Cd Length: 317  Bit Score: 81.46  E-value: 8.99e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  10 PGLTEETVQLLRGRKIKTVADLAAADLEEVAQKCGLSYKA----LVALRRVL-LAQFSAfplnGADLYEELKtSTAILST 84
Cdd:PRK04301  12 PGVGPATAEKLREAGYDTVEAIAVASPKELSEAAGIGESTaakiIEAAREAAdIGGFET----ALEVLERRK-NVGKITT 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  85 GIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCVAANV-----AHSLQQNVLYVDSNGGMTASRLLQLLQARTQDEEK 159
Cdd:PRK04301  87 GSKELDELLGGGIETQSITEFYGEFGSGKTQICHQLAVNVqlpeeKGGLEGKAVYIDTEGTFRPERIEQMAEALGLDPDE 166

                        170
                 ....*....|....
gi 485464616 160 qasALQRIQVVRSF 173
Cdd:PRK04301 167 ---VLDNIHVARAY 177
Rad51B cd19493
RAD51B recombinase; RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 90-191 1.65e-13

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: 68.12  E-value: 1.65e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  90 DKLLDAGLYTGEVTEIVGGPGSGKTQVCLCVAANVA-----HSLQQNVLYVDSNGGMTASRLLQLLQART--------QD 156
Cdd:cd19493    1 DTALAGGLPLGAITEITGASGSGKTQFALTLASSAAmparkGGLDGGVLYIDTESKFSAERLAEIAEARFpeafsgfmEE 80

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 485464616 157 EEKQASALQRIQVVRSFDIFRMLDMLQDLRGTIAQ 191
Cdd:cd19493   81 NERAEEMLKRVAVVRVTTLAQLLERLPNLEEHILS 115
archRadB cd01394
archaeal RadB; The archaeal protein RadB shares similarity RadA, the archaeal functional ...
 82-174 2.46e-13

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: 67.34  E-value: 2.46e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  82 LSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCVAANVAhSLQQNVLYVDSNgGMTASRLLQLLQARTQdeekqa 161
Cdd:cd01394    1 LSTGSKSLDSLLGGGVERGTITQIYGPPGSGKTNICLQLAVEAA-KQGKKVVYIDTE-GLSPERFQQIAGERFE------ 72

                         90
                 ....*....|....*
gi 485464616 162 SALQRIQV--VRSFD 174
Cdd:cd01394   73 SIASNIIVfePYSFD 87
archRadA cd19515
archaeal recombinase Rad51/RadA; This group includes the archaeal protein RadA which is a ...
 82-204 8.45e-13

archaeal recombinase Rad51/RadA; This group includes the archaeal protein RadA which is a homolog of Rad51. RAD51 recombinase plays an essential role in DNA repair by homologous recombination (HR)


Pssm-ID: 410923 [Multi-domain]  Cd Length: 233  Bit Score: 66.23  E-value: 8.45e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  82 LSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCVAANVA-----HSLQQNVLYVDSNGGMTASRLLQLLQARTQD 156
Cdd:cd19515    1 ISTGSKELDKLLGGGIETQAITEVFGEFGSGKTQLCHQLAVNVQlppeeGGLNGKAVYIDTENTFRPERIMQMAKALGLD 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 485464616 157 EEKqasALQRIQVVRSF----------DIFRMLDMLQDLRGTIAQQVTNHLTRDWDGR 204
Cdd:cd19515   81 PDE---VLDNIYVARAYnsnhqmllveKAEDLIKEGNNIKLLIVDSLTSHFRAEYVGR 135
radB PRK09361
DNA repair and recombination protein RadB; Provisional
 82-175 1.50e-12

DNA repair and recombination protein RadB; Provisional


Pssm-ID: 236482 [Multi-domain]  Cd Length: 225  Bit Score: 65.27  E-value: 1.50e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  82 LSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCVAANVAhSLQQNVLYVDSNgGMTASRLLQLLqartqdEEKQA 161
Cdd:PRK09361   5 LPTGCKMLDELLGGGFERGTITQIYGPPGSGKTNICLQLAVEAA-KNGKKVIYIDTE-GLSPERFKQIA------GEDFE 76

                         90
                 ....*....|....
gi 485464616 162 SALQRIQVVRSFDI 175
Cdd:PRK09361  77 ELLSNIIIFEPSSF 90
PLN03186 PLN03186
DNA repair protein RAD51 homolog; Provisional
 11-149 1.21e-11

DNA repair protein RAD51 homolog; Provisional


Pssm-ID: 178728 [Multi-domain]  Cd Length: 342  Bit Score: 63.98  E-value: 1.21e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  11 GLTEETVQLLRGRKIKTVADLAAADLEEVAQKCGLS-YKALvalrRVLLAQFSAFPL---NGADLYEElKTSTAILSTGI 86
Cdd:PLN03186  35 GIAALDIKKLKDAGIHTVESLAYAPKKDLLQIKGISeAKVE----KILEAASKLVPLgftTASQLHAQ-RQEIIQITTGS 109

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  87 GSLDKLLDAGLYTGEVTEIVGGPGSGKTQVC--LCVAANVahSLQQ-----NVLYVDSNGGMTASRLLQL 149
Cdd:PLN03186 110 RELDKILEGGIETGSITEIYGEFRTGKTQLChtLCVTCQL--PLDQgggegKAMYIDTEGTFRPQRLIQI 177
Rad51 pfam08423
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ...
 82-204 4.55e-11

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: 61.55  E-value: 4.55e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616   82 LSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVC--LCVAANVAHSL---QQNVLYVDSNGGMTASRLLQLLQARTQD 156
Cdd:pfam08423  19 ITTGSKELDKLLGGGIETGSITEIFGEFRTGKTQLChtLCVTCQLPLEMgggEGKALYIDTEGTFRPERLVAIAERYGLD 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 485464616  157 EEkqaSALQRIQVVRSFDIFRMLDMLQDLRGTIAQQ---------VTNHLTRDWDGR 204
Cdd:pfam08423  99 PE---DVLDNVAYARAYNSEHQMQLLQQAAAMMSESrfallivdsATALYRTDFSGR 152
Rad51_DMC1_archRadA cd01123
recombinase Rad51, DMC1, and archaeal RadA; This group of recombinases includes the eukaryotic ...
 82-204 7.18e-10

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: 57.93  E-value: 7.18e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  82 LSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVC--LCVAANVAHS---LQQNVLYVDSNGGMTASRLLQLLQARTQD 156
Cdd:cd01123    1 ITTGSKELDKLLGGGIETGSITEMFGEFRTGKTQLChtLAVTCQLPIDrggGEGKAIYIDTEGTFRPERLRAIAQRFGLD 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 485464616 157 EEkqaSALQRIQVVRSFD-------IFRMLDMLQDLRGT--IAQQVTNHLTRDWDGR 204
Cdd:cd01123   81 PD---DVLDNVAYARAFNsdhqtqlLDQAAAMMVESRFKllIVDSATALYRTDYSGR 134
XRCC3 cd19491
XRCC3 recombinase; XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells ...
 89-246 1.10e-09

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: 57.30  E-value: 1.10e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  89 LDKLLDAGLYTGEVTEIVGGPGSGKTQVC--LCVAANVAHS---LQQNVLYVDSNGGMTASRLLQLLQAR---------- 153
Cdd:cd19491    1 LDELLGGGIPVGGITEIAGESGAGKTQLClqLALTVQLPRElggLGGGAVYICTESSFPSKRLQQLASSLpkryhlekak 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616 154 ---------------TQDE--EKQASAL---QRIQVV----------------------RSFDIFRMLDMLQDLRGT--- 188
Cdd:cd19491   81 nfldnifvehvadleTLEHclNYQLPALlerGPIRLVvidsiaalfrsefdtsrsdlveRAKYLRRLADHLKRLADKynl 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616 189 ---IAQQVT---------------------NHLTRDWDGRRFKPALGRSWSFVPSTRILLDVTEGAGTLGSSQ----RTV 240
Cdd:cd19491  161 avvVVNQVTdrfdsssdasglgvldylsqfSSFSGGVSGNRKVPALGLTWANLVNTRLMLSRTPKRITDSSAAsisvRRL 240


                 ....*.
gi 485464616 241 CLTKSP 246
Cdd:cd19491  241 EVVFSP 246
PTZ00035 PTZ00035
Rad51 protein; Provisional
 11-191 1.18e-09

Rad51 protein; Provisional


Pssm-ID: 185407 [Multi-domain]  Cd Length: 337  Bit Score: 58.09  E-value: 1.18e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  11 GLTEETVQLLRGRKIKTVADLAAADLEEVAQKCGLSY----KALVALRRVLLAQFsafpLNGADLYEeLKTSTAILSTGI 86
Cdd:PTZ00035  30 GINAADIKKLKEAGICTVESVAYATKKDLCNIKGISEakveKIKEAASKLVPMGF----ISATEYLE-ARKNIIRITTGS 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  87 GSLDKLLDAGLYTGEVTEIVGGPGSGKTQVC--LCVAANVAHSLQQN---VLYVDSNGGMTASRLLQLLQARTQDEEkqa 161
Cdd:PTZ00035 105 TQLDKLLGGGIETGSITELFGEFRTGKTQLChtLCVTCQLPIEQGGGegkVLYIDTEGTFRPERIVQIAERFGLDPE--- 181

                        170       180       190
                 ....*....|....*....|....*....|
gi 485464616 162 SALQRIQVVRSFDIFRMLDMLQDLRGTIAQ 191
Cdd:PTZ00035 182 DVLDNIAYARAYNHEHQMQLLSQAAAKMAE 211
Rad51 cd19513
RAD51D recombinase; RAD51 recombinase plays an essential role in DNA repair by homologous ...
 82-204 3.27e-08

RAD51D recombinase; RAD51 recombinase plays an essential 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. RAD51 is recruited to the break site with the help of its paralogs, RAD51D, RAD51B, RAD51C, XRCC3, and XRCC2, where it forms long helical polymers which wrap around the ssDNA tail at the break which leads to pairing and strand invasion.


Pssm-ID: 410921 [Multi-domain]  Cd Length: 235  Bit Score: 53.09  E-value: 3.27e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  82 LSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVC--LCVAANVAHSL---QQNVLYVDSNGGMTASRLLQLLQARTQD 156
Cdd:cd19513    1 ITTGSKELDKLLGGGIETGSITELFGEFRTGKTQLChtLAVTCQLPIDQgggEGKALYIDTEGTFRPERLLAIAERYGLN 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 485464616 157 EEkqaSALQRIQVVRSFDIFRMLDMLQDLRGTIAQQ---------VTNHLTRDWDGR 204
Cdd:cd19513   81 GE---DVLDNVAYARAYNTDHQMQLLIQASAMMAESryallivdsATALYRTDYSGR 134
recomb_RAD51 TIGR02239
DNA repair protein RAD51; This eukaryotic sequence family consists of RAD51, a protein ...
 11-191 3.53e-08

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: 53.58  E-value: 3.53e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616   11 GLTEETVQLLRGRKIKTVADLAAADLEEVAQKCGLS-YKAlvalRRVLLAQFSAFPLN--GADLYEELKTSTAILSTGIG 87
Cdd:TIGR02239   8 GITAADIKKLQEAGLHTVESVAYAPKKQLLEIKGISeAKA----DKILAEAAKLVPMGftTATEFHQRRQEVIQLTTGSK 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616   88 SLDKLLDAGLYTGEVTEIVGGPGSGKTQVC--LCVAANVAHSL---QQNVLYVDSNGGMTASRLLQLLQARTQDEEKqas 162
Cdd:TIGR02239  84 ELDKLLGGGIETGSITEIFGEFRTGKTQLChtLAVTCQLPIDQgggEGKALYIDTEGTFRPERLLAIAERYGLNPED--- 160

                         170       180
                  ....*....|....*....|....*....
gi 485464616  163 ALQRIQVVRSFDIFRMLDMLQDLRGTIAQ 191
Cdd:TIGR02239 161 VLDNVAYARAYNTDHQLQLLQQAAAMMSE 189
XRCC2 cd19490
XRCC2 recombinase; XRCC2 (X-ray repair complementing defective repair in Chinese hamster cells ...
 100-195 6.43e-08

XRCC2 recombinase; XRCC2 (X-ray repair complementing defective repair in Chinese hamster cells 2) 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. XRCC2, together with the other RAD51 paralogs, RAD51B, RAD51C, RAD51D, and XRCC3, helps recruit RAD51 to the break site.


Pssm-ID: 410898 [Multi-domain]  Cd Length: 226  Bit Score: 51.96  E-value: 6.43e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616 100 GEVTEIVGGPGSGKTQVCLCVAAN----------VAHSLQQNVLYVDSNGGMTASRLLQLLQAR--------------TQ 155
Cdd:cd19490    1 GDVIEITGPSGSGKTELLYHLAARcilpsswggvPLGGLEAAVVFIDTDGRFDILRLRSILEARiraaiqaanssddeED 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 485464616 156 DEEKQASALQRIQVVRSFDIFRMLDMLQDLRGTIAQQVTN 195
Cdd:cd19490   81 VEEIARECLQRLHIFRCHSSLQLLATLLSLENYLLSLSAN 120
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
82-135 2.14e-06

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 47.60  E-value: 2.14e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 485464616  82 LSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCVAANVAHSlQQNVLYV 135
Cdd:COG0467    2 VPTGIPGLDELLGGGLPRGSSTLLSGPPGTGKTTLALQFLAEGLRR-GEKGLYV 54
DMC1 cd19514
homologous-pairing protein DMC1; DMC1 has a central role in homologous recombination in ...
 82-183 3.32e-06

homologous-pairing protein DMC1; DMC1 has a central role in homologous recombination in meiosis. It assembles at the sites of programmed DNA double-strand breaks and carries out a search for allelic DNA sequences located on homologous chromatids. It forms octameric rings.


Pssm-ID: 410922 [Multi-domain]  Cd Length: 236  Bit Score: 46.97  E-value: 3.32e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  82 LSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVC--LCVAANVAHSL---QQNVLYVDSNGGMTASRLLQLLQARTQD 156
Cdd:cd19514    1 ISTGSTELDKLLGGGIESMSITEVFGEFRTGKTQLShtLCVTAQLPGSMgggGGKVAYIDTEGTFRPDRIRPIAERFGVD 80

                         90       100
                 ....*....|....*....|....*..
gi 485464616 157 eekQASALQRIQVVRSFDIFRMLDMLQ 183
Cdd:cd19514   81 ---HDAVLDNILYARAYTSEHQMELLD 104
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
83-124 1.20e-05

RecA/RadA recombinase [Replication, recombination and repair];


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 45.93  E-value: 1.20e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 485464616  83 STGIGSLDKLL-DAGLYTGEVTEIVGGPGSGKTQVCLCVAANV 124
Cdd:COG0468   45 STGSLALDIALgVGGLPRGRIVEIYGPESSGKTTLALHAIAEA 87
ATPase pfam06745
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ...
 82-135 1.48e-05

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: 44.93  E-value: 1.48e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 485464616   82 LSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCVAANVAHSLQQNVLYV 135
Cdd:pfam06745   1 VKTGIPGLDEILKGGFPEGRVVLITGGPGTGKTIFGLQFLYNGALKYGEPGVFV 54
RadA_SMS_N cd01121
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a ...
 82-135 2.79e-05

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: 44.44  E-value: 2.79e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 485464616  82 LSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCVAANVAhSLQQNVLYV 135
Cdd:cd01121   64 ISTGIGELDRVLGGGLVPGSVVLIGGDPGIGKSTLLLQVAARLA-QRGGKVLYV 116
recomb_DMC1 TIGR02238
meiotic recombinase Dmc1; This model describes DMC1, a subfamily of a larger family of DNA ...
 82-173 4.50e-05

meiotic recombinase Dmc1; This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.


Pssm-ID: 131292 [Multi-domain]  Cd Length: 313  Bit Score: 44.00  E-value: 4.50e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616   82 LSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVC--LCVAANVAHSL---QQNVLYVDSNGGMTASRLLQLLQARTQD 156
Cdd:TIGR02238  78 ITTGSQALDGILGGGIESMSITEVFGEFRCGKTQLShtLCVTAQLPREMgggNGKVAYIDTEGTFRPDRIRAIAERFGVD 157

                          90
                  ....*....|....*..
gi 485464616  157 EEkqaSALQRIQVVRSF 173
Cdd:TIGR02238 158 PD---AVLDNILYARAY 171
KaiC-like cd01124
Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. ...
 82-135 4.64e-05

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: 43.41  E-value: 4.64e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 485464616  82 LSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCVAANVAhSLQQNVLYV 135
Cdd:cd01124    1 VKTGIPGLDELLGGGIPKGSVTLLTGGPGTGKTLFGLQFLYAGA-KNGEPGLFF 53
PLN03187 PLN03187
meiotic recombination protein DMC1 homolog; Provisional
 68-204 5.38e-05

meiotic recombination protein DMC1 homolog; Provisional


Pssm-ID: 215620 [Multi-domain]  Cd Length: 344  Bit Score: 44.00  E-value: 5.38e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  68 GADLYEELKTSTAIlSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVC--LCVAANVAHSLQ---QNVLYVDSNGGMT 142
Cdd:PLN03187  95 GSDALLKRKSVVRI-TTGSQALDELLGGGIETRCITEAFGEFRSGKTQLAhtLCVTTQLPTEMGggnGKVAYIDTEGTFR 173

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 485464616 143 ASRLLQL---------------LQARTQDEEKQASALQRIQVVRSFDIFRMLdmlqdlrgtIAQQVTNHLTRDWDGR 204
Cdd:PLN03187 174 PDRIVPIaerfgmdadavldniIYARAYTYEHQYNLLLGLAAKMAEEPFRLL---------IVDSVIALFRVDFTGR 241
DnaB_C pfam03796
DnaB-like helicase C terminal domain; The hexameric helicase DnaB unwinds the DNA duplex at ...
 82-135 9.45e-04

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: 39.71  E-value: 9.45e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 485464616   82 LSTGIGSLDKLLdAGLYTGEVTeIVGG-PGSGKTQVCLCVAANVAHSLQQNVLYV 135
Cdd:pfam03796   2 LPTGFTDLDRLT-GGLQPGDLI-IIAArPSMGKTAFALNIARNAAVKHKKPVAIF 54
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 61-114 1.14e-03

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 39.86  E-value: 1.14e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 485464616  61 FSAFPLNGADLyeELKTSTAILSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKT 114
Cdd:PRK09302 236 ISVLPLTAMRL--TQRSSNERISSGVPDLDEMLGGGFFRGSIILVSGATGTGKT 287
AAA_25 pfam13481
AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.
 100-197 6.07e-03

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: 36.98  E-value: 6.07e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616  100 GEVTEIVGGPGSGKTQVCLCVAANVA----------HSLQQNVLYVDSNGG--MTASRLLQLLQARTQDEekqasalqRI 167
Cdd:pfam13481  33 GGLGLLAGAPGTGKTTLALDLAAAVAtgkpwlggprVPEQGKVLYVSAEGPadELRRRLRAAGADLDLPA--------RL 104

                          90       100       110
                  ....*....|....*....|....*....|
gi 485464616  168 QVVRSFDIFRMLDMlqDLRGTIAQQVTNHL 197
Cdd:pfam13481 105 LFLSLVESLPLFFL--DRGGPLLDADVDAL 132
HhH-GPD pfam00730
HhH-GPD superfamily base excision DNA repair protein; This family contains a diverse range of ...
 20-92 6.16e-03

HhH-GPD superfamily base excision DNA repair protein; This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases. The methyl-CPG binding protein MBD4 also contains a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family.


Pssm-ID: 425841 [Multi-domain]  Cd Length: 141  Bit Score: 36.11  E-value: 6.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485464616   20 LRGRKIKTVADLAAADLEEVAQ---KCGLS-YKA--LVALRRVLLAQF-SAFPLNGADLYEELK-----TSTAILSTGIG 87
Cdd:pfam00730  21 LFEKFFPTPEDLADADEEELRElirGLGFYrRKAkyLKELARILVEGYgGEVPLDEEELEALLKgvgrwTAEAVLIFALG 100


                  ....*
gi 485464616   88 SLDKL 92
Cdd:pfam00730 101 RPDPL 105
 
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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