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Conserved domains on  [gi|697870835|gb|AIT68905|]
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recombination protein A, partial [Bradyrhizobium sp. 5563D]

Protein Classification

recombinase RecA family protein( domain architecture ID 1000164)

recombinase RecA catalyzes an ATP-dependent DNA strand-exchange reaction, which is a critical step in the repair of DNA double-strand breaks by homologous recombination

CATH:  3.30.250.10|3.40.50.300
Gene Ontology:  GO:0005524|GO:0003697|GO:0006310|GO:0006281|GO:0140664|GO:0003684|GO:0016887
PubMed:  12045091|9187054

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
recA super family cl35814
recombinase A; Provisional
 1-170 3.43e-133

recombinase A; Provisional


The actual alignment was detected with superfamily member PRK09354:

Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 375.67  E-value: 3.43e-133
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835   1 FGKGSVMKLGKNDRsMDVEAISSGSLGLDIALGIGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHAL 80
Cdd:PRK09354  22 FGKGSIMRLGDDAA-MDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHAL 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  81 DPVYARKLGVNIDELLISQPDTGEQALEICDTLVRSGAVDVLVIDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLT 160
Cdd:PRK09354 101 DPVYAKKLGVDIDNLLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLT 180

                        170
                 ....*....|
gi 697870835 161 ASINKSNTMV 170
Cdd:PRK09354 181 GNISKSNTTV 190
 
Name Accession Description Interval E-value
recA PRK09354
recombinase A; Provisional
 1-170 3.43e-133

recombinase A; Provisional


Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 375.67  E-value: 3.43e-133
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835   1 FGKGSVMKLGKNDRsMDVEAISSGSLGLDIALGIGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHAL 80
Cdd:PRK09354  22 FGKGSIMRLGDDAA-MDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHAL 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  81 DPVYARKLGVNIDELLISQPDTGEQALEICDTLVRSGAVDVLVIDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLT 160
Cdd:PRK09354 101 DPVYAKKLGVDIDNLLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLT 180

                        170
                 ....*....|
gi 697870835 161 ASINKSNTMV 170
Cdd:PRK09354 181 GNISKSNTTV 190
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
1-170 1.62e-128

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 364.11  E-value: 1.62e-128
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835   1 FGKGSVMKLGKNDRsMDVEAISSGSLGLDIALGIGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHAL 80
Cdd:COG0468   25 FGKGSIMRLGDKAR-QDVEVISTGSLALDIALGVGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGIAAFIDAEHAL 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  81 DPVYARKLGVNIDELLISQPDTGEQALEICDTLVRSGAVDVLVIDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLT 160
Cdd:COG0468  104 DPEYAKKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLT 183

                        170
                 ....*....|
gi 697870835 161 ASINKSNTMV 170
Cdd:COG0468  184 GAISKSNTTV 193
RecA pfam00154
recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA ...
 1-170 3.77e-119

recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA repair systems. RecA protein catalyzes an ATP-dependent DNA strand-exchange reaction that is the central step in the repair of dsDNA breaks by homologous recombination.


Pssm-ID: 425488 [Multi-domain]  Cd Length: 262  Bit Score: 337.06  E-value: 3.77e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835    1 FGKGSVMKLGKNDRsMDVEAISSGSLGLDIALGIGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHAL 80
Cdd:pfam00154  14 FGKGSIMKLGDEKK-LDVETISTGSLALDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHAL 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835   81 DPVYARKLGVNIDELLISQPDTGEQALEICDTLVRSGAVDVLVIDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLT 160
Cdd:pfam00154  93 DPVYAKKLGVDIDNLLVSQPDTGEQALEIADMLVRSGAIDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLT 172

                         170
                  ....*....|
gi 697870835  161 ASINKSNTMV 170
Cdd:pfam00154 173 GSISKSNTTV 182
tigrfam_recA TIGR02012
protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization ...
 1-170 2.47e-117

protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 162659 [Multi-domain]  Cd Length: 321  Bit Score: 334.72  E-value: 2.47e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835    1 FGKGSVMKLGkNDRSMDVEAISSGSLGLDIALGIGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHAL 80
Cdd:TIGR02012  17 FGKGSIMRLG-EKTVMDVETISTGSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHAL 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835   81 DPVYARKLGVNIDELLISQPDTGEQALEICDTLVRSGAVDVLVIDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLT 160
Cdd:TIGR02012  96 DPVYARKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVDIIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLT 175

                         170
                  ....*....|
gi 697870835  161 ASINKSNTMV 170
Cdd:TIGR02012 176 GALSKSNTTA 185
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 17-170 1.26e-110

recombinase A; 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.


Pssm-ID: 410863 [Multi-domain]  Cd Length: 235  Bit Score: 314.49  E-value: 1.26e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  17 DVEAISSGSLGLDIALGIGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYARKLGVNIDELL 96
Cdd:cd00983    1 DVEVIPTGSLSLDIALGIGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKLGGTAAFIDAEHALDPEYAKKLGVDIDNLL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 697870835  97 ISQPDTGEQALEICDTLVRSGAVDVLVIDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLTASINKSNTMV 170
Cdd:cd00983   81 VSQPDTGEQALEIADTLIRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGSLSKSKTTV 154
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 39-168 4.18e-08

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: 49.68  E-value: 4.18e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835    39 KGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYARKLGVNIDELLISqpDTGEQALEICDTLVRSGA 118
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS--GSGELRLRLALALARKLK 78

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 697870835   119 VDVLVIDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLTASINKSNT 168
Cdd:smart00382  79 PDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVILTTNDEKD 128
 
Name Accession Description Interval E-value
recA PRK09354
recombinase A; Provisional
 1-170 3.43e-133

recombinase A; Provisional


Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 375.67  E-value: 3.43e-133
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835   1 FGKGSVMKLGKNDRsMDVEAISSGSLGLDIALGIGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHAL 80
Cdd:PRK09354  22 FGKGSIMRLGDDAA-MDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHAL 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  81 DPVYARKLGVNIDELLISQPDTGEQALEICDTLVRSGAVDVLVIDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLT 160
Cdd:PRK09354 101 DPVYAKKLGVDIDNLLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLT 180

                        170
                 ....*....|
gi 697870835 161 ASINKSNTMV 170
Cdd:PRK09354 181 GNISKSNTTV 190
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
1-170 1.62e-128

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 364.11  E-value: 1.62e-128
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835   1 FGKGSVMKLGKNDRsMDVEAISSGSLGLDIALGIGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHAL 80
Cdd:COG0468   25 FGKGSIMRLGDKAR-QDVEVISTGSLALDIALGVGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGIAAFIDAEHAL 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  81 DPVYARKLGVNIDELLISQPDTGEQALEICDTLVRSGAVDVLVIDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLT 160
Cdd:COG0468  104 DPEYAKKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLT 183

                        170
                 ....*....|
gi 697870835 161 ASINKSNTMV 170
Cdd:COG0468  184 GAISKSNTTV 193
RecA pfam00154
recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA ...
 1-170 3.77e-119

recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA repair systems. RecA protein catalyzes an ATP-dependent DNA strand-exchange reaction that is the central step in the repair of dsDNA breaks by homologous recombination.


Pssm-ID: 425488 [Multi-domain]  Cd Length: 262  Bit Score: 337.06  E-value: 3.77e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835    1 FGKGSVMKLGKNDRsMDVEAISSGSLGLDIALGIGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHAL 80
Cdd:pfam00154  14 FGKGSIMKLGDEKK-LDVETISTGSLALDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHAL 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835   81 DPVYARKLGVNIDELLISQPDTGEQALEICDTLVRSGAVDVLVIDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLT 160
Cdd:pfam00154  93 DPVYAKKLGVDIDNLLVSQPDTGEQALEIADMLVRSGAIDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLT 172

                         170
                  ....*....|
gi 697870835  161 ASINKSNTMV 170
Cdd:pfam00154 173 GSISKSNTTV 182
tigrfam_recA TIGR02012
protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization ...
 1-170 2.47e-117

protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 162659 [Multi-domain]  Cd Length: 321  Bit Score: 334.72  E-value: 2.47e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835    1 FGKGSVMKLGkNDRSMDVEAISSGSLGLDIALGIGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHAL 80
Cdd:TIGR02012  17 FGKGSIMRLG-EKTVMDVETISTGSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHAL 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835   81 DPVYARKLGVNIDELLISQPDTGEQALEICDTLVRSGAVDVLVIDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLT 160
Cdd:TIGR02012  96 DPVYARKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVDIIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLT 175

                         170
                  ....*....|
gi 697870835  161 ASINKSNTMV 170
Cdd:TIGR02012 176 GALSKSNTTA 185
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 17-170 1.26e-110

recombinase A; 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.


Pssm-ID: 410863 [Multi-domain]  Cd Length: 235  Bit Score: 314.49  E-value: 1.26e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  17 DVEAISSGSLGLDIALGIGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYARKLGVNIDELL 96
Cdd:cd00983    1 DVEVIPTGSLSLDIALGIGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKLGGTAAFIDAEHALDPEYAKKLGVDIDNLL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 697870835  97 ISQPDTGEQALEICDTLVRSGAVDVLVIDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLTASINKSNTMV 170
Cdd:cd00983   81 VSQPDTGEQALEIADTLIRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGSLSKSKTTV 154
recA PRK09519
intein-containing recombinase RecA;
1-168 2.78e-80

intein-containing recombinase RecA;


Pssm-ID: 77219 [Multi-domain]  Cd Length: 790  Bit Score: 253.09  E-value: 2.78e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835   1 FGKGSVMKLGKNDRSmDVEAISSGSLGLDIALGIGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHAL 80
Cdd:PRK09519  22 YGKGSVMRLGDEARQ-PISVIPTGSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHAL 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  81 DPVYARKLGVNIDELLISQPDTGEQALEICDTLVRSGAVDVLVIDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLT 160
Cdd:PRK09519 101 DPDYAKKLGVDTDSLLVSQPDTGEQALEIADMLIRSGALDIVVIDSVAALVPRAELEGEMGDSHVGLQARLMSQALRKMT 180


                 ....*...
gi 697870835 161 ASINKSNT 168
Cdd:PRK09519 181 GALNNSGT 188
RecA-like cd01393
RecA family; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 40-170 3.69e-36

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: 123.62  E-value: 3.69e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  40 GRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYAR-----------KLGVNIDELLISQPDTGEQALE 108
Cdd:cd01393    1 GKITEIYGPPGSGKTQLALQLAANALLLGGGVVWIDTEGAFPPSRLVqileaspsselELAEALSRLLYFRPPDTLAHLL 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 697870835 109 ICDTLVRSGA----VDVLVIDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLTASINKSNTMV 170
Cdd:cd01393   81 ALDSLPESLFpppnTSLVVVDSVSALFRKAFPRGGDGDSSSSLRARLLSQLARALQKLAAQFNLAV 146
archRadB cd01394
archaeal RadB; The archaeal protein RadB shares similarity RadA, the archaeal functional ...
 21-130 4.28e-14

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: 66.95  E-value: 4.28e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  21 ISSGSLGLDIALGiGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEhALDP-----VYARKLGVNIDEL 95
Cdd:cd01394    1 LSTGSKSLDSLLG-GGVERGTITQIYGPPGSGKTNICLQLAVEAAKQGKKVVYIDTE-GLSPerfqqIAGERFESIASNI 78

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 697870835  96 LISQP-DTGEQALEICDT--LVRSGAVDVLVIDSVAAL 130
Cdd:cd01394   79 IVFEPySFDEQGVAIQEAekLLKSDKVDLVVVDSATAL 116
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
21-130 2.36e-13

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 64.94  E-value: 2.36e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  21 ISSGSLGLDIALGiGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPV--YARKLGVNIDELL-- 96
Cdd:COG0467    2 VPTGIPGLDELLG-GGLPRGSSTLLSGPPGTGKTTLALQFLAEGLRRGEKGLYVSFEESPEQLlrRAESLGLDLEEYIes 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 697870835  97 ----ISQPDTGEQALEICDTL------VRSGAVDVLVIDSVAAL 130
Cdd:COG0467   81 gllrIIDLSPEELGLDLEELLarlreaVEEFGAKRVVIDSLSGL 124
KaiC-like cd01124
Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. ...
 21-130 3.99e-12

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: 61.90  E-value: 3.99e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  21 ISSGSLGLDIALGiGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVY--ARKLGVNIDE---- 94
Cdd:cd01124    1 VKTGIPGLDELLG-GGIPKGSVTLLTGGPGTGKTLFGLQFLYAGAKNGEPGLFFTFEESPERLLrnAKSFGWDFDEmede 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 697870835  95 --LLISQPDTGEQALEICDTL-------VRSGAVDVLVIDSVAAL 130
Cdd:cd01124   80 gkLIIVDAPPTEAGRFSLDELlsrilsiIKSFKAKRVVIDSLSGL 124
COG4544 COG4544
Uncharacterized conserved protein [Function unknown];
18-125 2.85e-11

Uncharacterized conserved protein [Function unknown];


Pssm-ID: 443609 [Multi-domain]  Cd Length: 230  Bit Score: 59.56  E-value: 2.85e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  18 VEAISSGSLGLDIALGIGGLPKGRVVEIYGPE-SSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYARKLGVNIDELL 96
Cdd:COG4544   26 RAVLPTGFAALDAALPGGGLPRGALHEILGPApGIGELGLLLPLLARLAQAGGPVLWIAPPYDLYAPGLAAAGLDPERLL 105

                         90       100
                 ....*....|....*....|....*....
gi 697870835  97 ISQPDTGEQALEICDTLVRSGAVDVLVID 125
Cdd:COG4544  106 LVRARRPADALWAAEEALRSGACGAVVAW 134
recomb_radB TIGR02237
DNA repair and recombination protein RadB; This family consists exclusively of archaeal RadB ...
 28-158 2.06e-10

DNA repair and recombination protein RadB; This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).


Pssm-ID: 274047 [Multi-domain]  Cd Length: 209  Bit Score: 57.04  E-value: 2.06e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835   28 LDIALGiGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEhALDPVYARKLGVNIDELLISQ------PD 101
Cdd:TIGR02237   1 IDELLG-GGVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTE-GLSPERFKQIAEDRPERALSNfivfevFD 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 697870835  102 TGEQALEICDT--LVRSGAVDVLVIDSVAALVpKAELEGEMGDALPGL--QARLMSQALRK 158
Cdd:TIGR02237  79 FDEQGVAIQKTskFIDRDSASLVVVDSFTALY-RLELSDDRISRNRELarQLTLLLSLARK 138
Rad51B cd19493
RAD51B recombinase; RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 29-144 5.44e-10

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: 55.79  E-value: 5.44e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  29 DIALGiGGLPKGRVVEIYGPESSGKTTLALHTVAE-------GQKKGGiCAFIDAEHALDP-------------VYARKL 88
Cdd:cd19493    1 DTALA-GGLPLGAITEITGASGSGKTQFALTLASSaamparkGGLDGG-VLYIDTESKFSAerlaeiaearfpeAFSGFM 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 697870835  89 GVNIDELLISQ------PDTGEQALEICDTL---VRSGAVDVLVIDSVAALVPKaELEGEMGDAL 144
Cdd:cd19493   79 EENERAEEMLKrvavvrVTTLAQLLERLPNLeehILSSGVRLVVIDSIAALVRR-EFGGSDGEVT 142
radB PRK09361
DNA repair and recombination protein RadB; Provisional
 19-139 1.11e-09

DNA repair and recombination protein RadB; Provisional


Pssm-ID: 236482 [Multi-domain]  Cd Length: 225  Bit Score: 55.25  E-value: 1.11e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  19 EAISSGSLGLDIALGiGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEhALDPVYARKL-GVNIDELL- 96
Cdd:PRK09361   3 ERLPTGCKMLDELLG-GGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE-GLSPERFKQIaGEDFEELLs 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 697870835  97 ---ISQP-DTGEQALEICDT--LVRSGaVDVLVIDSVAALVpKAELEGE 139
Cdd:PRK09361  81 niiIFEPsSFEEQSEAIRKAekLAKEN-VGLIVLDSATSLY-RLELEDE 127
KaiC-like_N cd19488
N-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 21-74 2.19e-08

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: 51.58  E-value: 2.19e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 697870835  21 ISSGSLGLDIALGiGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFI 74
Cdd:cd19488    1 ISTGIPGLDDILR-GGLPPRRLYLVEGAPGTGKTTLALQFLLEGAANGETGLYI 53
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 39-168 4.18e-08

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: 49.68  E-value: 4.18e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835    39 KGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYARKLGVNIDELLISqpDTGEQALEICDTLVRSGA 118
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS--GSGELRLRLALALARKLK 78

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 697870835   119 VDVLVIDSVAALVPKAELEGEMGDALPGLQARLMSQALRKLTASINKSNT 168
Cdd:smart00382  79 PDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVILTTNDEKD 128
Rad51 pfam08423
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ...
 21-130 1.15e-07

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: 49.61  E-value: 1.15e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835   21 ISSGSLGLDIALGiGGLPKGRVVEIYGPESSGKTTLAlHTVA-------EGQKKGGICAFIDAEHALDPV----YARKLG 89
Cdd:pfam08423  19 ITTGSKELDKLLG-GGIETGSITEIFGEFRTGKTQLC-HTLCvtcqlplEMGGGEGKALYIDTEGTFRPErlvaIAERYG 96

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 697870835   90 VNIDELLISQP-------DTGEQALEICDTLVRSGAVDVLVIDSVAAL 130
Cdd:pfam08423  97 LDPEDVLDNVAyaraynsEHQMQLLQQAAAMMSESRFALLIVDSATAL 144
ATPase pfam06745
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ...
 21-131 2.75e-07

KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and eukaryotes. More than one copy is sometimes found in each protein. This family includes KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria.


Pssm-ID: 429095 [Multi-domain]  Cd Length: 231  Bit Score: 48.40  E-value: 2.75e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835   21 ISSGSLGLDiALGIGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGI-CAFIDA-EHALDPVY-ARKLGVNIDELL- 96
Cdd:pfam06745   1 VKTGIPGLD-EILKGGFPEGRVVLITGGPGTGKTIFGLQFLYNGALKYGEpGVFVTLeEPPEDLREnARSFGWDLEKLEe 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 697870835   97 --------ISQPDTGEQALEICDTL----------VRSGAVDVLVIDSVAALV 131
Cdd:pfam06745  80 egklaiidASTSGIGIAEVEDRFDLeelierlreaIREIGAKRVVIDSITTLF 132
XRCC3 cd19491
XRCC3 recombinase; XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells ...
 28-159 3.62e-07

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


Pssm-ID: 410899 [Multi-domain]  Cd Length: 250  Bit Score: 48.44  E-value: 3.62e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  28 LDIALGiGGLPKGRVVEIYGPESSGKTTLALH-------TVAEGQKKGGiCAFIDAEHAL----------------DPVY 84
Cdd:cd19491    1 LDELLG-GGIPVGGITEIAGESGAGKTQLCLQlaltvqlPRELGGLGGG-AVYICTESSFpskrlqqlasslpkryHLEK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  85 ARKLGVNIdeLLISQPDTgeQALEICDT-----LVRSGAVDVLVIDSVAALVpKAELEGEMGDALpgLQARLMSQALRKL 159
Cdd:cd19491   79 AKNFLDNI--FVEHVADL--ETLEHCLNyqlpaLLERGPIRLVVIDSIAALF-RSEFDTSRSDLV--ERAKYLRRLADHL 151
Rad51_DMC1_archRadA cd01123
recombinase Rad51, DMC1, and archaeal RadA; This group of recombinases includes the eukaryotic ...
 21-130 4.29e-07

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: 47.91  E-value: 4.29e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  21 ISSGSLGLDIALGiGGLPKGRVVEIYGPESSGKTTLAlHTVA-------EGQKKGGICAFIDAEHALDPV----YARKLG 89
Cdd:cd01123    1 ITTGSKELDKLLG-GGIETGSITEMFGEFRTGKTQLC-HTLAvtcqlpiDRGGGEGKAIYIDTEGTFRPErlraIAQRFG 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 697870835  90 VNIDELL----ISQPDTGEQALEICD---TLVRSGAVDVLVIDSVAAL 130
Cdd:cd01123   79 LDPDDVLdnvaYARAFNSDHQTQLLDqaaAMMVESRFKLLIVDSATAL 126
XRCC2 cd19490
XRCC2 recombinase; XRCC2 (X-ray repair complementing defective repair in Chinese hamster cells ...
 40-162 3.99e-06

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: 45.03  E-value: 3.99e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  40 GRVVEIYGPESSGKTTLALHTVA--------EGQKKGG--ICA-FIDAEHALDPVyarKLgVNIDELLISQ--------- 99
Cdd:cd19490    1 GDVIEITGPSGSGKTELLYHLAArcilpsswGGVPLGGleAAVvFIDTDGRFDIL---RL-RSILEARIRAaiqaanssd 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835 100 -PDTGEQALEIC--------------------------DTLVRSGAVDVLVIDSVAALVPKAELEGEMGDALPGLQARLM 152
Cdd:cd19490   77 dEEDVEEIAREClqrlhifrchsslqllatllslenylLSLSANPELGLLLIDSISAFYWQDRFSAELARAAPLLQEAAL 156

                        170
                 ....*....|...
gi 697870835 153 ---SQALRKLTAS 162
Cdd:cd19490  157 raiLRELRRLRRR 169
KaiC-like_C cd19487
C-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 21-128 1.94e-05

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: 43.06  E-value: 1.94e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  21 ISSGSLGLDIALGiGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVYARKLGVNID------- 93
Cdd:cd19487    1 VSSGVPELDELLG-GGLERGTSTLLIGPAGVGKSTLALQFAKAAAARGERSVLFSFDESIGTLFERSEALGIDlramvek 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 697870835  94 -ELLISQPDTGE----QALEICDTLVRSGAVDVLVIDSVA 128
Cdd:cd19487   80 gLLSIEQIDPAElspgEFAQRVRTSVEQEDARVVVIDSLN 119
radA PRK04301
DNA repair and recombination protein RadA; Validated
 14-96 2.44e-05

DNA repair and recombination protein RadA; Validated


Pssm-ID: 235273 [Multi-domain]  Cd Length: 317  Bit Score: 43.33  E-value: 2.44e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  14 RSMDVEAISSGSLGLDIALGiGGLPKGRVVEIYGPESSGKTTLAlHTVAEG----QKKGGI---CAFIDAEHALDP---- 82
Cdd:PRK04301  77 RRKNVGKITTGSKELDELLG-GGIETQSITEFYGEFGSGKTQIC-HQLAVNvqlpEEKGGLegkAVYIDTEGTFRPerie 154

                         90
                 ....*....|....
gi 697870835  83 VYARKLGVNIDELL 96
Cdd:PRK04301 155 QMAEALGLDPDEVL 168
recomb_DMC1 TIGR02238
meiotic recombinase Dmc1; This model describes DMC1, a subfamily of a larger family of DNA ...
 18-130 2.62e-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: 43.23  E-value: 2.62e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835   18 VEAISSGSLGLDIALGiGGLPKGRVVEIYGPESSGKTTLAlHTVA-------EGQKKGGICAFIDAEHALDP----VYAR 86
Cdd:TIGR02238  75 VLKITTGSQALDGILG-GGIESMSITEVFGEFRCGKTQLS-HTLCvtaqlprEMGGGNGKVAYIDTEGTFRPdrirAIAE 152

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 697870835   87 KLGVN----IDELLISQPDTGEQALE---ICDTLVRSGAVDVLVIDSVAAL 130
Cdd:TIGR02238 153 RFGVDpdavLDNILYARAYTSEHQMElldYLAAKFSEEPFRLLIVDSIMAL 203
RepA COG3598
RecA-family ATPase [Replication, recombination and repair];
37-135 4.44e-05

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


Pssm-ID: 442817 [Multi-domain]  Cd Length: 313  Bit Score: 42.58  E-value: 4.44e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  37 LPKGRVVEIYGPESSGKTTLALH---TVAEGQK------KGGICAFIDAE----------HALDPVYARKLGVNIDELLI 97
Cdd:COG3598   10 LPEGGVTLLAGPPGTGKSFLALQlaaAVAAGGPwlgrrvPPGKVLYLAAEddrgelrrrlKALGADLGLPFADLDGRLRL 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 697870835  98 SQPDTGEQALEICDTL---VRSGAVDVLVIDSVAALVPKAE 135
Cdd:COG3598   90 LSLAGDLDDTDDLEALeraIEEEGPDLVVIDPLARVFGGDE 130
PLN03187 PLN03187
meiotic recombination protein DMC1 homolog; Provisional
 14-130 5.47e-05

meiotic recombination protein DMC1 homolog; Provisional


Pssm-ID: 215620 [Multi-domain]  Cd Length: 344  Bit Score: 42.07  E-value: 5.47e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  14 RSMDVEAISSGSLGLDIALGiGGLPKGRVVEIYGPESSGKTTLAlHTVAEG----QKKGGIC---AFIDAEHALDP---- 82
Cdd:PLN03187 101 KRKSVVRITTGSQALDELLG-GGIETRCITEAFGEFRSGKTQLA-HTLCVTtqlpTEMGGGNgkvAYIDTEGTFRPdriv 178

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 697870835  83 VYARKLGVN----IDELLISQPDTGEQ---ALEICDTLVRSGAVDVLVIDSVAAL 130
Cdd:PLN03187 179 PIAERFGMDadavLDNIIYARAYTYEHqynLLLGLAAKMAEEPFRLLIVDSVIAL 233
archRadA cd19515
archaeal recombinase Rad51/RadA; This group includes the archaeal protein RadA which is a ...
 21-130 5.74e-05

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: 41.97  E-value: 5.74e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  21 ISSGSLGLDIALGiGGLPKGRVVEIYGPESSGKTTLAlHTVAEG----QKKGGI---CAFIDAEHALDP----VYARKLG 89
Cdd:cd19515    1 ISTGSKELDKLLG-GGIETQAITEVFGEFGSGKTQLC-HQLAVNvqlpPEEGGLngkAVYIDTENTFRPerimQMAKALG 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 697870835  90 VNIDELL-----ISQPDTGEQAL---EICDTLVRSGAVDVLVIDSVAAL 130
Cdd:cd19515   79 LDPDEVLdniyvARAYNSNHQMLlveKAEDLIKEGNNIKLLIVDSLTSH 127
AAA_24 pfam13479
AAA domain; This AAA domain is found in a wide variety of presumed phage proteins.
 39-127 6.14e-05

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


Pssm-ID: 433243  Cd Length: 199  Bit Score: 41.54  E-value: 6.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835   39 KGRVVEIYGPESSGKTTLALHTvaegqkkgGICAFIDAEHALDPVYARKLGVnidellISQPDTGEQALEICDTLVRSGA 118
Cdd:pfam13479   1 KKLKILIYGPSGIGKTTFAKTL--------PKPLFLDTEKGSKALDGDRFPD------IVIRDSWQDFLDAIDELTAAEL 66

                          90
                  ....*....|.
gi 697870835  119 V--DVLVIDSV 127
Cdd:pfam13479  67 AdyKTIVIDTV 77
Rad51 cd19513
RAD51D recombinase; RAD51 recombinase plays an essential role in DNA repair by homologous ...
 21-96 1.41e-04

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: 40.76  E-value: 1.41e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  21 ISSGSLGLDIALGiGGLPKGRVVEIYGPESSGKTTLAlHTVA-------EGQKKGGICAFIDAEHALDPV----YARKLG 89
Cdd:cd19513    1 ITTGSKELDKLLG-GGIETGSITELFGEFRTGKTQLC-HTLAvtcqlpiDQGGGEGKALYIDTEGTFRPErllaIAERYG 78


                 ....*..
gi 697870835  90 VNIDELL 96
Cdd:cd19513   79 LNGEDVL 85
PLN03186 PLN03186
DNA repair protein RAD51 homolog; Provisional
 21-160 2.21e-04

DNA repair protein RAD51 homolog; Provisional


Pssm-ID: 178728 [Multi-domain]  Cd Length: 342  Bit Score: 40.49  E-value: 2.21e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  21 ISSGSLGLDIALGiGGLPKGRVVEIYGPESSGKTTLAlHTVA----------EGQKKggiCAFIDAEHALDP----VYAR 86
Cdd:PLN03186 105 ITTGSRELDKILE-GGIETGSITEIYGEFRTGKTQLC-HTLCvtcqlpldqgGGEGK---AMYIDTEGTFRPqrliQIAE 179

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  87 KLGVNIDELL----ISQPDTGEQALEIcdtLVRSGA------VDVLVIDSVAALVpKAELEGEmGDalpgLQAR--LMSQ 154
Cdd:PLN03186 180 RFGLNGADVLenvaYARAYNTDHQSEL---LLEAASmmaetrFALMIVDSATALY-RTEFSGR-GE----LSARqmHLGK 250


                 ....*.
gi 697870835 155 ALRKLT 160
Cdd:PLN03186 251 FLRSLQ 256
recomb_RAD51 TIGR02239
DNA repair protein RAD51; This eukaryotic sequence family consists of RAD51, a protein ...
 14-130 2.41e-04

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: 40.09  E-value: 2.41e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835   14 RSMDVEAISSGSLGLDIALGiGGLPKGRVVEIYGPESSGKTTLAlHTVA------EGQKKG-GICAFIDAEHALDPV--- 83
Cdd:TIGR02239  71 RRQEVIQLTTGSKELDKLLG-GGIETGSITEIFGEFRTGKTQLC-HTLAvtcqlpIDQGGGeGKALYIDTEGTFRPErll 148

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 697870835   84 -YARKLGVNIDELLIS-------QPDTGEQALEICDTLVRSGAVDVLVIDSVAAL 130
Cdd:TIGR02239 149 aIAERYGLNPEDVLDNvayarayNTDHQLQLLQQAAAMMSESRFALLIVDSATAL 203
Rad51D cd19489
RAD51D recombinase; RAD51D recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 35-65 4.86e-04

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: 39.16  E-value: 4.86e-04
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 697870835  35 GGLPKGRVVEIYGPESSGKT----TLALHTVAEGQ 65
Cdd:cd19489    2 GGLRTGEITELVGESSSGKTqlclTAAANVASRSG 36
KaiC_C cd19484
C-terminal domain of Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most ...
 21-130 8.25e-04

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: 38.46  E-value: 8.25e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  21 ISSGSLGLDIALGIGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVY--ARKLGVNIDELLIS 98
Cdd:cd19484    1 ISTGIPRLDAMLGGGGFFRGSSILVSGATGTGKTLLAASFADAACRRGERCLYFAFEESPAQLIrnAKSIGIDLEQMERK 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 697870835  99 Q---------PDTG-EQALEICDTLVRSGAVDVLVIDSVAAL 130
Cdd:cd19484   81 GllkiicarpELYGlEDHLIIIKSEINEFKPSRVIVDPLSAL 122
PTZ00035 PTZ00035
Rad51 protein; Provisional
 21-130 1.20e-03

Rad51 protein; Provisional


Pssm-ID: 185407 [Multi-domain]  Cd Length: 337  Bit Score: 38.06  E-value: 1.20e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  21 ISSGSLGLDIALGiGGLPKGRVVEIYGPESSGKTTLAlHTVA-------EGQKKGGICAFIDAEHALDP----VYARKLG 89
Cdd:PTZ00035 100 ITTGSTQLDKLLG-GGIETGSITELFGEFRTGKTQLC-HTLCvtcqlpiEQGGGEGKVLYIDTEGTFRPerivQIAERFG 177

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 697870835  90 VNIDELL----ISQPDTGEQALEIcdtLVRSGAVDV------LVIDSVAAL 130
Cdd:PTZ00035 178 LDPEDVLdniaYARAYNHEHQMQL---LSQAAAKMAeerfalLIVDSATAL 225
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 19-130 1.78e-03

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 37.94  E-value: 1.78e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835  19 EAISSGSLGLDIALGiGGLPKGRVVEIYGPESSGKTTLALHTVAEGQKKGGICAFIDAEHALDPVY--ARKLGVNIDE-- 94
Cdd:PRK09302 253 ERISSGVPDLDEMLG-GGFFRGSIILVSGATGTGKTLLASKFAEAACRRGERCLLFAFEESRAQLIrnARSWGIDLEKme 331

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 697870835  95 ----LLI--SQPD-TG-EQALEICDTLVRSGAVDVLVIDSVAAL 130
Cdd:PRK09302 332 ekglLKIicARPEsYGlEDHLIIIKREIEEFKPSRVAIDPLSAL 375
NadR3 COG3172
Nicotinamide riboside kinase [Coenzyme transport and metabolism]; Nicotinamide riboside kinase ...
 41-57 3.67e-03

Nicotinamide riboside kinase [Coenzyme transport and metabolism]; Nicotinamide riboside kinase is part of the Pathway/BioSystem: NAD biosynthesis


Pssm-ID: 442405 [Multi-domain]  Cd Length: 178  Bit Score: 36.34  E-value: 3.67e-03
                         10
                 ....*....|....*..
gi 697870835  41 RVVeIYGPESSGKTTLA 57
Cdd:COG3172   10 KIV-LLGAESTGKTTLA 25
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 14-64 3.72e-03

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 36.78  E-value: 3.72e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 697870835  14 RSMDVEAISSGSLGLDIALGiGGLPKGRVVEIYGPESSGKTTLALHTVAEG 64
Cdd:PRK09302   6 ASPGIEKLPTGIEGFDDITH-GGLPKGRPTLVSGTAGTGKTLFALQFLVNG 55
AAA_25 pfam13481
AAA domain; This AAA domain is found in a wide variety of presumed DNA repair proteins.
 37-132 8.22e-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: 35.43  E-value: 8.22e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 697870835   37 LPKGRVVEIYGPESSGKTTLALH---TVAEGQK--------KGGICAFIDAE--------------HALDPVyARKLGVN 91
Cdd:pfam13481  30 LPAGGLGLLAGAPGTGKTTLALDlaaAVATGKPwlggprvpEQGKVLYVSAEgpadelrrrlraagADLDLP-ARLLFLS 108

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 697870835   92 I-DELLISQPDTGEQAL-----EICDTLVRSGAVDVLVIDSVAALVP 132
Cdd:pfam13481 109 LvESLPLFFLDRGGPLLdadvdALEAALEEVEDPDLVVIDPLARALG 155
uvra TIGR00630
excinuclease ABC, A subunit; This family is a member of the ABC transporter superfamily of ...
 37-67 9.22e-03

excinuclease ABC, A subunit; This family is a member of the ABC transporter superfamily of proteins of which all members for which functions are known except the UvrA proteins are involved in the transport of material through membranes. UvrA orthologs are involved in the recognition of DNA damage as a step in nucleotide excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273184 [Multi-domain]  Cd Length: 925  Bit Score: 35.76  E-value: 9.22e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 697870835   37 LPKGRVVEIYGPESSGKTTLALHTV-AEGQKK 67
Cdd:TIGR00630  19 IPRDKLVVITGLSGSGKSSLAFDTIyAEGQRR 50
 
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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