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Conserved domains on  [gi|374279604|gb|AEZ04009|]
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recombinase A, partial [Rhizobium binae]

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

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List of domain hits

 Name Accession Description Interval E-value
recA super family cl35814
recombinase A; Provisional
 1-153 2.26e-118

recombinase A; Provisional


The actual alignment was detected with superfamily member PRK09354:

Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 337.54  E-value: 2.26e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604   1 FGKGSIMKLGSNEnVIEIETISTGSLGLDIALGVGGLPKGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEHAL 80
Cdd:PRK09354  22 FGKGSIMRLGDDA-AMDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHAL 100

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 374279604  81 DPVYARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGDSLPGLQARLMS 153
Cdd:PRK09354 101 DPVYAKKLGVDIDNLLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMS 173
 
Name Accession Description Interval E-value
recA PRK09354
recombinase A; Provisional
 1-153 2.26e-118

recombinase A; Provisional


Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 337.54  E-value: 2.26e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604   1 FGKGSIMKLGSNEnVIEIETISTGSLGLDIALGVGGLPKGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEHAL 80
Cdd:PRK09354  22 FGKGSIMRLGDDA-AMDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHAL 100

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 374279604  81 DPVYARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGDSLPGLQARLMS 153
Cdd:PRK09354 101 DPVYAKKLGVDIDNLLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMS 173
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
1-153 1.35e-113

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 325.59  E-value: 1.35e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604   1 FGKGSIMKLGSNENViEIETISTGSLGLDIALGVGGLPKGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEHAL 80
Cdd:COG0468   25 FGKGSIMRLGDKARQ-DVEVISTGSLALDIALGVGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGIAAFIDAEHAL 103

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 374279604  81 DPVYARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGDSLPGLQARLMS 153
Cdd:COG0468  104 DPEYAKKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMS 176
RecA pfam00154
recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA ...
 1-153 1.79e-106

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: 304.32  E-value: 1.79e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604    1 FGKGSIMKLGSNENViEIETISTGSLGLDIALGVGGLPKGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEHAL 80
Cdd:pfam00154  14 FGKGSIMKLGDEKKL-DVETISTGSLALDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHAL 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 374279604   81 DPVYARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGDSLPGLQARLMS 153
Cdd:pfam00154  93 DPVYAKKLGVDIDNLLVSQPDTGEQALEIADMLVRSGAIDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMS 165
tigrfam_recA TIGR02012
protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization ...
 1-153 2.50e-105

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: 303.52  E-value: 2.50e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604    1 FGKGSIMKLGsNENVIEIETISTGSLGLDIALGVGGLPKGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEHAL 80
Cdd:TIGR02012  17 FGKGSIMRLG-EKTVMDVETISTGSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHAL 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 374279604   81 DPVYARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGDSLPGLQARLMS 153
Cdd:TIGR02012  96 DPVYARKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVDIIVVDSVAALVPKAEIEGEMGDSHVGLQARLMS 168
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 17-153 1.23e-97

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: 280.60  E-value: 1.23e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  17 EIETISTGSLGLDIALGVGGLPKGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEHALDPVYARKLGVDLQNLL 96
Cdd:cd00983    1 DVEVIPTGSLSLDIALGIGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKLGGTAAFIDAEHALDPEYAKKLGVDIDNLL 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 374279604  97 ISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGDSLPGLQARLMS 153
Cdd:cd00983   81 VSQPDTGEQALEIADTLIRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMS 137
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 39-140 5.67e-09

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 51.61  E-value: 5.67e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604    39 KGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISqpDTGEQALEITDTLVRSGA 118
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS--GSGELRLRLALALARKLK 78

                           90       100
                   ....*....|....*....|..
gi 374279604   119 VDVLVVDSVAALTPRAEIEGEM 140
Cdd:smart00382  79 PDVLILDEITSLLDAEQEALLL 100
 
Name Accession Description Interval E-value
recA PRK09354
recombinase A; Provisional
 1-153 2.26e-118

recombinase A; Provisional


Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 337.54  E-value: 2.26e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604   1 FGKGSIMKLGSNEnVIEIETISTGSLGLDIALGVGGLPKGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEHAL 80
Cdd:PRK09354  22 FGKGSIMRLGDDA-AMDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHAL 100

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 374279604  81 DPVYARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGDSLPGLQARLMS 153
Cdd:PRK09354 101 DPVYAKKLGVDIDNLLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMS 173
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
1-153 1.35e-113

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 325.59  E-value: 1.35e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604   1 FGKGSIMKLGSNENViEIETISTGSLGLDIALGVGGLPKGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEHAL 80
Cdd:COG0468   25 FGKGSIMRLGDKARQ-DVEVISTGSLALDIALGVGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGIAAFIDAEHAL 103

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 374279604  81 DPVYARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGDSLPGLQARLMS 153
Cdd:COG0468  104 DPEYAKKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMS 176
RecA pfam00154
recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA ...
 1-153 1.79e-106

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: 304.32  E-value: 1.79e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604    1 FGKGSIMKLGSNENViEIETISTGSLGLDIALGVGGLPKGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEHAL 80
Cdd:pfam00154  14 FGKGSIMKLGDEKKL-DVETISTGSLALDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHAL 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 374279604   81 DPVYARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGDSLPGLQARLMS 153
Cdd:pfam00154  93 DPVYAKKLGVDIDNLLVSQPDTGEQALEIADMLVRSGAIDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMS 165
tigrfam_recA TIGR02012
protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization ...
 1-153 2.50e-105

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: 303.52  E-value: 2.50e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604    1 FGKGSIMKLGsNENVIEIETISTGSLGLDIALGVGGLPKGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEHAL 80
Cdd:TIGR02012  17 FGKGSIMRLG-EKTVMDVETISTGSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHAL 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 374279604   81 DPVYARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGDSLPGLQARLMS 153
Cdd:TIGR02012  96 DPVYARKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVDIIVVDSVAALVPKAEIEGEMGDSHVGLQARLMS 168
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 17-153 1.23e-97

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: 280.60  E-value: 1.23e-97
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  17 EIETISTGSLGLDIALGVGGLPKGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEHALDPVYARKLGVDLQNLL 96
Cdd:cd00983    1 DVEVIPTGSLSLDIALGIGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKLGGTAAFIDAEHALDPEYAKKLGVDIDNLL 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 374279604  97 ISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGDSLPGLQARLMS 153
Cdd:cd00983   81 VSQPDTGEQALEIADTLIRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMS 137
recA PRK09519
intein-containing recombinase RecA;
1-153 1.75e-71

intein-containing recombinase RecA;


Pssm-ID: 77219 [Multi-domain]  Cd Length: 790  Bit Score: 228.82  E-value: 1.75e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604   1 FGKGSIMKLGsNENVIEIETISTGSLGLDIALGVGGLPKGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEHAL 80
Cdd:PRK09519  22 YGKGSVMRLG-DEARQPISVIPTGSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHAL 100

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 374279604  81 DPVYARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGDSLPGLQARLMS 153
Cdd:PRK09519 101 DPDYAKKLGVDTDSLLVSQPDTGEQALEIADMLIRSGALDIVVIDSVAALVPRAELEGEMGDSHVGLQARLMS 173
RecA-like cd01393
RecA family; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 40-153 3.37e-34

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: 117.84  E-value: 3.37e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  40 GRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEHALDPVYAR-----------KLGVDLQNLLISQPDTGEQALE 108
Cdd:cd01393    1 GKITEIYGPPGSGKTQLALQLAANALLLGGGVVWIDTEGAFPPSRLVqileaspsselELAEALSRLLYFRPPDTLAHLL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 374279604 109 ITDTLVRSGA----VDVLVVDSVAALTPRAEIEGEMGDSLPGLQARLMS 153
Cdd:cd01393   81 ALDSLPESLFpppnTSLVVVDSVSALFRKAFPRGGDGDSSSSLRARLLS 129
archRadB cd01394
archaeal RadB; The archaeal protein RadB shares similarity RadA, the archaeal functional ...
 21-143 8.76e-18

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: 76.20  E-value: 8.76e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  21 ISTGSLGLDIALGvGGLPKGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEhALDP-----VYARKLGVDLQNL 95
Cdd:cd01394    1 LSTGSKSLDSLLG-GGVERGTITQIYGPPGSGKTNICLQLAVEAAKQGKKVVYIDTE-GLSPerfqqIAGERFESIASNI 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 374279604  96 LISQP-DTGEQALEITDT--LVRSGAVDVLVVDSVAALTpRAEiegEMGDS 143
Cdd:cd01394   79 IVFEPySFDEQGVAIQEAekLLKSDKVDLVVVDSATALY-RLE---LGDDS 125
radB PRK09361
DNA repair and recombination protein RadB; Provisional
 17-139 4.41e-13

DNA repair and recombination protein RadB; Provisional


Pssm-ID: 236482 [Multi-domain]  Cd Length: 225  Bit Score: 64.11  E-value: 4.41e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  17 EIETISTGSLGLDIALGvGGLPKGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEhALDPVYARKLGVD----- 91
Cdd:PRK09361   1 MDERLPTGCKMLDELLG-GGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE-GLSPERFKQIAGEdfeel 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 374279604  92 LQNLLISQP-DTGEQALEITDT--LVRSGaVDVLVVDSVAALTpRAEIEGE 139
Cdd:PRK09361  79 LSNIIIFEPsSFEEQSEAIRKAekLAKEN-VGLIVLDSATSLY-RLELEDE 127
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
21-130 4.86e-13

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 63.78  E-value: 4.86e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  21 ISTGSLGLDIALGvGGLPKGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEHALDPV--YARKLGVDLQ----- 93
Cdd:COG0467    2 VPTGIPGLDELLG-GGLPRGSSTLLSGPPGTGKTTLALQFLAEGLRRGEKGLYVSFEESPEQLlrRAESLGLDLEeyies 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 374279604  94 -NLLISQPDTGEQALEITDTL------VRSGAVDVLVVDSVAAL 130
Cdd:COG0467   81 gLLRIIDLSPEELGLDLEELLarlreaVEEFGAKRVVIDSLSGL 124
COG4544 COG4544
Uncharacterized conserved protein [Function unknown];
20-134 8.11e-13

Uncharacterized conserved protein [Function unknown];


Pssm-ID: 443609 [Multi-domain]  Cd Length: 230  Bit Score: 63.41  E-value: 8.11e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  20 TISTGSLGLDIALGVGGLPKGRIIEIYGPE-SSGKTTLALQTIAESQKKGGICAFVDAEHALDPVYARKLGVDLQNLLIS 98
Cdd:COG4544   28 VLPTGFAALDAALPGGGLPRGALHEILGPApGIGELGLLLPLLARLAQAGGPVLWIAPPYDLYAPGLAAAGLDPERLLLV 107

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 374279604  99 QPDTGEQALEITDTLVRSGAVDVLVVDsVAALTPRA 134
Cdd:COG4544  108 RARRPADALWAAEEALRSGACGAVVAW-LERLDLTA 142
recomb_radB TIGR02237
DNA repair and recombination protein RadB; This family consists exclusively of archaeal RadB ...
 28-151 3.21e-12

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: 61.28  E-value: 3.21e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604   28 LDIALGvGGLPKGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEhALDPVYARKLGVD-----LQNLLISQP-- 100
Cdd:TIGR02237   1 IDELLG-GGVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTE-GLSPERFKQIAEDrperaLSNFIVFEVfd 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 374279604  101 -DTGEQALEITDTLVRSGAVDVLVVDSVAALTpRAEIEGEMGDSLPGLQARL 151
Cdd:TIGR02237  79 fDEQGVAIQKTSKFIDRDSASLVVVDSFTALY-RLELSDDRISRNRELARQL 129
KaiC-like cd01124
Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. ...
 21-130 4.09e-10

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: 55.73  E-value: 4.09e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  21 ISTGSLGLDIALGvGGLPKGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEHALDPVY--ARKLGVDL-----Q 93
Cdd:cd01124    1 VKTGIPGLDELLG-GGIPKGSVTLLTGGPGTGKTLFGLQFLYAGAKNGEPGLFFTFEESPERLLrnAKSFGWDFdemedE 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 374279604  94 NLLI--SQPDTGEQALEITDTL------VRSGAVDVLVVDSVAAL 130
Cdd:cd01124   80 GKLIivDAPPTEAGRFSLDELLsrilsiIKSFKAKRVVIDSLSGL 124
Rad51B cd19493
RAD51B recombinase; RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 29-142 3.32e-09

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: 53.48  E-value: 3.32e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  29 DIALGvGGLPKGRIIEIYGPESSGKT----TLALQTIAESQKKG--GICAFVDAEHAL------------DPVYARK--- 87
Cdd:cd19493    1 DTALA-GGLPLGAITEITGASGSGKTqfalTLASSAAMPARKGGldGGVLYIDTESKFsaerlaeiaearFPEAFSGfme 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 374279604  88 ----LGVDLQNLLISQPDTGEQALEITDTL---VRSGAVDVLVVDSVAALTpRAEIEGEMGD 142
Cdd:cd19493   80 enerAEEMLKRVAVVRVTTLAQLLERLPNLeehILSSGVRLVVIDSIAALV-RREFGGSDGE 140
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 39-140 5.67e-09

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 51.61  E-value: 5.67e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604    39 KGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISqpDTGEQALEITDTLVRSGA 118
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS--GSGELRLRLALALARKLK 78

                           90       100
                   ....*....|....*....|..
gi 374279604   119 VDVLVVDSVAALTPRAEIEGEM 140
Cdd:smart00382  79 PDVLILDEITSLLDAEQEALLL 100
Rad51 pfam08423
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ...
 17-138 1.71e-08

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: 51.53  E-value: 1.71e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604   17 EIETISTGSLGLDIALGvGGLPKGRIIEIYGPESSGKT----TLAL--QTIAESQKKGGICAFVDAEHALDPV----YAR 86
Cdd:pfam08423  15 ELIQITTGSKELDKLLG-GGIETGSITEIFGEFRTGKTqlchTLCVtcQLPLEMGGGEGKALYIDTEGTFRPErlvaIAE 93

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 374279604   87 KLGVDLQNLLISQP-------DTGEQALEITDTLVRSGAVDVLVVDSVAALTpRAEIEG 138
Cdd:pfam08423  94 RYGLDPEDVLDNVAyaraynsEHQMQLLQQAAAMMSESRFALLIVDSATALY-RTDFSG 151
KaiC-like_N cd19488
N-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 21-132 3.06e-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: 50.81  E-value: 3.06e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  21 ISTGSLGLDIALGvGGLPKGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFV---DAEHALDPVyARKLGVDLQNLLI 97
Cdd:cd19488    1 ISTGIPGLDDILR-GGLPPRRLYLVEGAPGTGKTTLALQFLLEGAANGETGLYItlsETEQELRAV-ALSHGWSLDGIHI 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 374279604  98 ---SQPDTGEQALEITDTL----VRSGAVDVLVVDSVAALTP 132
Cdd:cd19488   79 felSPSESALDAAQQYTILhpseLELSETTRLIFERVERLKP 120
DMC1 cd19514
homologous-pairing protein DMC1; DMC1 has a central role in homologous recombination in ...
 21-130 3.10e-08

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: 50.82  E-value: 3.10e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  21 ISTGSLGLDIALGvGGLPKGRIIEIYGPESSGKTTLA------LQTIAESQKKGGICAFVDAEHALDP----VYARKLGV 90
Cdd:cd19514    1 ISTGSTELDKLLG-GGIESMSITEVFGEFRTGKTQLShtlcvtAQLPGSMGGGGGKVAYIDTEGTFRPdrirPIAERFGV 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 374279604  91 D----LQNLLISQPDTGEQALEITDTL----VRSGAVDVLVVDSVAAL 130
Cdd:cd19514   80 DhdavLDNILYARAYTSEHQMELLDYVaakfHEEAVFRLLIIDSIMAL 127
ATPase pfam06745
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ...
 21-131 6.10e-08

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


Pssm-ID: 429095 [Multi-domain]  Cd Length: 231  Bit Score: 49.94  E-value: 6.10e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604   21 ISTGSLGLDIALGvGGLPKGRIIEIYGPESSGKTTLALQTIAESQKKGGI-CAFVDA-EHALDPVY-ARKLGVDLQNLL- 96
Cdd:pfam06745   1 VKTGIPGLDEILK-GGFPEGRVVLITGGPGTGKTIFGLQFLYNGALKYGEpGVFVTLeEPPEDLREnARSFGWDLEKLEe 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 374279604   97 --------ISQPDTGEQALEITDTL----------VRSGAVDVLVVDSVAALT 131
Cdd:pfam06745  80 egklaiidASTSGIGIAEVEDRFDLeelierlreaIREIGAKRVVIDSITTLF 132
Rad51_DMC1_archRadA cd01123
recombinase Rad51, DMC1, and archaeal RadA; This group of recombinases includes the eukaryotic ...
 21-130 2.19e-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: 48.30  E-value: 2.19e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  21 ISTGSLGLDIALGvGGLPKGRIIEIYGPESSGKT----TLAL--QTIAESQKKGGICAFVDAEHALDPV----YARKLGV 90
Cdd:cd01123    1 ITTGSKELDKLLG-GGIETGSITEMFGEFRTGKTqlchTLAVtcQLPIDRGGGEGKAIYIDTEGTFRPErlraIAQRFGL 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 374279604  91 D----LQNLLISQPDTGEQALEITD---TLVRSGAVDVLVVDSVAAL 130
Cdd:cd01123   80 DpddvLDNVAYARAFNSDHQTQLLDqaaAMMVESRFKLLIVDSATAL 126
radA PRK04301
DNA repair and recombination protein RadA; Validated
 17-138 9.33e-07

DNA repair and recombination protein RadA; Validated


Pssm-ID: 235273 [Multi-domain]  Cd Length: 317  Bit Score: 46.79  E-value: 9.33e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  17 EIETISTGSLGLDIALGvGGLPKGRIIEIYGPESSGKTTLALQTIAESQ---KKGGI---CAFVDAE------------- 77
Cdd:PRK04301  80 NVGKITTGSKELDELLG-GGIETQSITEFYGEFGSGKTQICHQLAVNVQlpeEKGGLegkAVYIDTEgtfrperieqmae 158

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  78 -HALDP-------VYARKLGVDLQNLLIsqpdtgEQALEitdtLVRSG-AVDVLVVDSVAALTpRAEIEG 138
Cdd:PRK04301 159 aLGLDPdevldniHVARAYNSDHQMLLA------EKAEE----LIKEGeNIKLVIVDSLTAHF-RAEYVG 217
RadA_SMS_N cd01121
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a ...
 16-127 1.35e-06

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: 46.37  E-value: 1.35e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  16 IEIETISTGSLGLDIALGvGGLPKGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEHALDPV--YARKLGVDLQ 93
Cdd:cd01121   59 EEEERISTGIGELDRVLG-GGLVPGSVVLIGGDPGIGKSTLLLQVAARLAQRGGKVLYVSGEESLSQIklRAERLGLGSD 137

                         90       100       110
                 ....*....|....*....|....*....|....
gi 374279604  94 NLLIsqpdTGEQALEITDTLVRSGAVDVLVVDSV 127
Cdd:cd01121  138 NLYL----LAETNLEAILAEIEELKPSLVVIDSI 167
archRadA cd19515
archaeal recombinase Rad51/RadA; This group includes the archaeal protein RadA which is a ...
 21-138 1.72e-06

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: 45.82  E-value: 1.72e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  21 ISTGSLGLDIALGvGGLPKGRIIEIYGPESSGKTTLALQTIAESQK---KGGI---CAFVDAEHALDP----VYARKLGV 90
Cdd:cd19515    1 ISTGSKELDKLLG-GGIETQAITEVFGEFGSGKTQLCHQLAVNVQLppeEGGLngkAVYIDTENTFRPerimQMAKALGL 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 374279604  91 D----LQNLLISQP-DTGEQAL---EITDTLVRSGAVDVLVVDSVAALTpRAEIEG 138
Cdd:cd19515   80 DpdevLDNIYVARAyNSNHQMLlveKAEDLIKEGNNIKLLIVDSLTSHF-RAEYVG 134
PLN03187 PLN03187
meiotic recombination protein DMC1 homolog; Provisional
 21-130 1.87e-06

meiotic recombination protein DMC1 homolog; Provisional


Pssm-ID: 215620 [Multi-domain]  Cd Length: 344  Bit Score: 45.92  E-value: 1.87e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  21 ISTGSLGLDIALGvGGLPKGRIIEIYGPESSGKT----TLALQTIAESQKKGGI--CAFVDAEHALDP----VYARKLGV 90
Cdd:PLN03187 108 ITTGSQALDELLG-GGIETRCITEAFGEFRSGKTqlahTLCVTTQLPTEMGGGNgkVAYIDTEGTFRPdrivPIAERFGM 186

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 374279604  91 D----LQNLLISQPDTGEQaleITDTLVRSGA------VDVLVVDSVAAL 130
Cdd:PLN03187 187 DadavLDNIIYARAYTYEH---QYNLLLGLAAkmaeepFRLLIVDSVIAL 233
recomb_DMC1 TIGR02238
meiotic recombinase Dmc1; This model describes DMC1, a subfamily of a larger family of DNA ...
 21-130 3.02e-06

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: 45.54  E-value: 3.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604   21 ISTGSLGLDIALGvGGLPKGRIIEIYGPESSGKTTLA------LQTIAESQKKGGICAFVDAEHALDP----VYARKLGV 90
Cdd:TIGR02238  78 ITTGSQALDGILG-GGIESMSITEVFGEFRCGKTQLShtlcvtAQLPREMGGGNGKVAYIDTEGTFRPdrirAIAERFGV 156

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 374279604   91 D----LQNLLISQPDTGEQALEITDTLVRSGAVD---VLVVDSVAAL 130
Cdd:TIGR02238 157 DpdavLDNILYARAYTSEHQMELLDYLAAKFSEEpfrLLIVDSIMAL 203
PTZ00035 PTZ00035
Rad51 protein; Provisional
 17-130 8.89e-06

Rad51 protein; Provisional


Pssm-ID: 185407 [Multi-domain]  Cd Length: 337  Bit Score: 44.22  E-value: 8.89e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  17 EIETISTGSLGLDIALGvGGLPKGRIIEIYGPESSGKT----TLAL--QTIAESQKKGGICAFVDAEHALDP----VYAR 86
Cdd:PTZ00035  96 NIIRITTGSTQLDKLLG-GGIETGSITELFGEFRTGKTqlchTLCVtcQLPIEQGGGEGKVLYIDTEGTFRPerivQIAE 174

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 374279604  87 KLGVD----LQNLLISQPDTGEQALEItdtLVRSGAVDV------LVVDSVAAL 130
Cdd:PTZ00035 175 RFGLDpedvLDNIAYARAYNHEHQMQL---LSQAAAKMAeerfalLIVDSATAL 225
XRCC3 cd19491
XRCC3 recombinase; XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells ...
 28-130 1.88e-05

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


Pssm-ID: 410899 [Multi-domain]  Cd Length: 250  Bit Score: 43.05  E-value: 1.88e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  28 LDIALGvGGLPKGRIIEIYGPESSGKTTLALQ---TIAESQKKGGI---CAFVDAEHAL-------------DPVYARKL 88
Cdd:cd19491    1 LDELLG-GGIPVGGITEIAGESGAGKTQLCLQlalTVQLPRELGGLgggAVYICTESSFpskrlqqlasslpKRYHLEKA 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 374279604  89 GVDLQNLLISQPDTGEQALEITDT----LVRSGAVDVLVVDSVAAL 130
Cdd:cd19491   80 KNFLDNIFVEHVADLETLEHCLNYqlpaLLERGPIRLVVIDSIAAL 125
recomb_RAD51 TIGR02239
DNA repair protein RAD51; This eukaryotic sequence family consists of RAD51, a protein ...
 17-130 2.13e-05

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: 42.79  E-value: 2.13e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604   17 EIETISTGSLGLDIALGvGGLPKGRIIEIYGPESSGKT----TLALQ-TIAESQKKG-GICAFVDAE------------- 77
Cdd:TIGR02239  74 EVIQLTTGSKELDKLLG-GGIETGSITEIFGEFRTGKTqlchTLAVTcQLPIDQGGGeGKALYIDTEgtfrperllaiae 152

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 374279604   78 -------HALDPV-YARKLGVDLQNLLISQpdtgeqaleiTDTLVRSGAVDVLVVDSVAAL 130
Cdd:TIGR02239 153 ryglnpeDVLDNVaYARAYNTDHQLQLLQQ----------AAAMMSESRFALLIVDSATAL 203
PLN03186 PLN03186
DNA repair protein RAD51 homolog; Provisional
 17-138 2.95e-05

DNA repair protein RAD51 homolog; Provisional


Pssm-ID: 178728 [Multi-domain]  Cd Length: 342  Bit Score: 42.41  E-value: 2.95e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  17 EIETISTGSLGLDIALGvGGLPKGRIIEIYGPESSGKT----TLAL--QTIAESQKKGGICAFVDAEHALDP----VYAR 86
Cdd:PLN03186 101 EIIQITTGSRELDKILE-GGIETGSITEIYGEFRTGKTqlchTLCVtcQLPLDQGGGEGKAMYIDTEGTFRPqrliQIAE 179

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 374279604  87 KLGVD----LQNLLISQPDTGEQALEItdtLVRSGA------VDVLVVDSVAALTpRAEIEG 138
Cdd:PLN03186 180 RFGLNgadvLENVAYARAYNTDHQSEL---LLEAASmmaetrFALMIVDSATALY-RTEFSG 237
KaiC_C cd19484
C-terminal domain of Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most ...
 21-131 7.36e-05

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: 41.16  E-value: 7.36e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  21 ISTGSLGLDIALGVGGLPKGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEHALDPVY--ARKLGVDLQNLLIS 98
Cdd:cd19484    1 ISTGIPRLDAMLGGGGFFRGSSILVSGATGTGKTLLAASFADAACRRGERCLYFAFEESPAQLIrnAKSIGIDLEQMERK 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 374279604  99 Q---------PDTG-EQALEITDTLVRSGAVDVLVVDSVAALT 131
Cdd:cd19484   81 GllkiicarpELYGlEDHLIIIKSEINEFKPSRVIVDPLSALA 123
Rad51 cd19513
RAD51D recombinase; RAD51 recombinase plays an essential role in DNA repair by homologous ...
 21-130 1.17e-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: 1.17e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  21 ISTGSLGLDIALGvGGLPKGRIIEIYGPESSGKT----TLAL--QTIAESQKKGGICAFVDAE----------------- 77
Cdd:cd19513    1 ITTGSKELDKLLG-GGIETGSITELFGEFRTGKTqlchTLAVtcQLPIDQGGGEGKALYIDTEgtfrperllaiaerygl 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 374279604  78 ---HALDPV-YARKLGVDLQNLLISQpdtgeqaleiTDTLVRSGAVDVLVVDSVAAL 130
Cdd:cd19513   80 ngeDVLDNVaYARAYNTDHQMQLLIQ----------ASAMMAESRYALLIVDSATAL 126
PRK10851 PRK10851
sulfate/thiosulfate ABC transporter ATP-binding protein CysA;
16-94 1.69e-04

sulfate/thiosulfate ABC transporter ATP-binding protein CysA;


Pssm-ID: 182778 [Multi-domain]  Cd Length: 353  Bit Score: 40.45  E-value: 1.69e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  16 IEIETIS-----TGSLGlDIALGVgglPKGRIIEIYGPESSGKTTLaLQTIA--ESQKKGGICaF----VDAEHALDpvy 84
Cdd:PRK10851   3 IEIANIKksfgrTQVLN-DISLDI---PSGQMVALLGPSGSGKTTL-LRIIAglEHQTSGHIR-FhgtdVSRLHARD--- 73

                         90
                 ....*....|
gi 374279604  85 aRKLGVDLQN 94
Cdd:PRK10851  74 -RKVGFVFQH 82
AAA_24 pfam13479
AAA domain; This AAA domain is found in a wide variety of presumed phage proteins.
 39-127 1.88e-04

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


Pssm-ID: 433243  Cd Length: 199  Bit Score: 40.00  E-value: 1.88e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604   39 KGRIIEIYGPESSGKTTLALQTiaesqkkgGICAFVDAEHALDPVYARKLgvDLQNLLISQPDTGEQALEITDTLVRSga 118
Cdd:pfam13479   1 KKLKILIYGPSGIGKTTFAKTL--------PKPLFLDTEKGSKALDGDRF--PDIVIRDSWQDFLDAIDELTAAELAD-- 68


                  ....*....
gi 374279604  119 VDVLVVDSV 127
Cdd:pfam13479  69 YKTIVIDTV 77
KaiC-like_C cd19487
C-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 21-128 2.02e-04

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: 39.98  E-value: 2.02e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  21 ISTGSLGLDIALGvGGLPKGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEHALDPVYAR--KLGVDLQ----- 93
Cdd:cd19487    1 VSSGVPELDELLG-GGLERGTSTLLIGPAGVGKSTLALQFAKAAAARGERSVLFSFDESIGTLFERseALGIDLRamvek 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 374279604  94 -NLLISQPDT-----GEQALEITDTLVRSGAvDVLVVDSVA 128
Cdd:cd19487   80 gLLSIEQIDPaelspGEFAQRVRTSVEQEDA-RVVVIDSLN 119
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 17-73 2.16e-04

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 40.25  E-value: 2.16e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 374279604  17 EIETISTGSLGLDIALGvGGLPKGRIIEIYGPESSGKTTLALQTIAEsqkkgGICAF 73
Cdd:PRK09302   9 GIEKLPTGIEGFDDITH-GGLPKGRPTLVSGTAGTGKTLFALQFLVN-----GIKRF 59
FlaH COG2874
Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];
19-59 2.37e-04

Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];


Pssm-ID: 442121  Cd Length: 230  Bit Score: 39.82  E-value: 2.37e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 374279604  19 ETISTGSLGLDIALGvGGLPKGRIIEIYGPESSGKTTLALQ 59
Cdd:COG2874    1 EIISTGNDELDKRLG-GGIPLGSLVLIEGENGTGKSVLSQQ 40
ATPase_2 pfam01637
ATPase domain predominantly from Archaea; This family contain a conserved P-loop motif that is ...
 42-76 2.58e-04

ATPase domain predominantly from Archaea; This family contain a conserved P-loop motif that is involved in binding ATP. There are eukaryote members as well as archaeal members in this family.


Pssm-ID: 376582 [Multi-domain]  Cd Length: 222  Bit Score: 39.61  E-value: 2.58e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 374279604   42 IIEIYGPESSGKTTLALQTIAESQKKGGICAFVDA 76
Cdd:pfam01637  22 IYVIYGPEGCGKTALLRESIENLLDLGYYVIYYDP 56
Rad51D cd19489
RAD51D recombinase; RAD51D recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 35-65 3.34e-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: 3.34e-04
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 374279604  35 GGLPKGRIIEIYGPESSGKT----TLALQTIAESQ 65
Cdd:cd19489    2 GGLRTGEITELVGESSSGKTqlclTAAANVASRSG 36
XRCC2 cd19490
XRCC2 recombinase; XRCC2 (X-ray repair complementing defective repair in Chinese hamster cells ...
 40-62 3.63e-04

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: 39.25  E-value: 3.63e-04
                         10        20
                 ....*....|....*....|...
gi 374279604  40 GRIIEIYGPESSGKTTLALQTIA 62
Cdd:cd19490    1 GDVIEITGPSGSGKTELLYHLAA 23
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 19-131 5.53e-04

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 39.09  E-value: 5.53e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  19 ETISTGSLGLDIALGvGGLPKGRIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEHALDPVY--ARKLGVDLQN-- 94
Cdd:PRK09302 253 ERISSGVPDLDEMLG-GGFFRGSIILVSGATGTGKTLLASKFAEAACRRGERCLLFAFEESRAQLIrnARSWGIDLEKme 331

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 374279604  95 ----LLI--SQPD-TG-EQALEITDTLVRSGAVDVLVVDSVAALT 131
Cdd:PRK09302 332 ekglLKIicARPEsYGlEDHLIIIKREIEEFKPSRVAIDPLSALA 376
PRK06067 PRK06067
flagellar accessory protein FlaH; Validated
 17-137 6.07e-04

flagellar accessory protein FlaH; Validated


Pssm-ID: 180381  Cd Length: 234  Bit Score: 38.41  E-value: 6.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  17 EIETISTGSLGLDIALGvGGLPKGRIIEIYGPESSGKTTLALQTI--------------AESQKKGGICAFVDAEHALDP 82
Cdd:PRK06067   3 KKEIISTGNEELDRKLG-GGIPFPSLILIEGDHGTGKSVLSQQFVygalkqgkkvyvitTENTSKSYLKQMESVKIDISD 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 374279604  83 VYAR-KLGVDLQNLLISQ--PDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIE 137
Cdd:PRK06067  82 FFLWgYLRIFPLNTEGFEwnSTLANKLLELIIEFIKSKREDVIIIDSLTIFATYAEED 139
RepA COG3598
RecA-family ATPase [Replication, recombination and repair];
37-141 1.12e-03

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


Pssm-ID: 442817 [Multi-domain]  Cd Length: 313  Bit Score: 37.96  E-value: 1.12e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604  37 LPKGRIIEIYGPESSGKTTLALQ---TIAESQK------KGGICAFVDAE----------HALDPVYARKLGVDLQNLLI 97
Cdd:COG3598   10 LPEGGVTLLAGPPGTGKSFLALQlaaAVAAGGPwlgrrvPPGKVLYLAAEddrgelrrrlKALGADLGLPFADLDGRLRL 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 374279604  98 SQPDTGEQALEITDTL---VRSGAVDVLVVDSVAALTPRAEIE-GEMG 141
Cdd:COG3598   90 LSLAGDLDDTDDLEALeraIEEEGPDLVVIDPLARVFGGDENDaEEMR 137
ABC_UvrA_I cd03270
ATP-binding cassette domain I of the excision repair protein UvrA; Nucleotide excision repair ...
 37-67 8.28e-03

ATP-binding cassette domain I of the excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.


Pssm-ID: 213237 [Multi-domain]  Cd Length: 226  Bit Score: 35.31  E-value: 8.28e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 374279604  37 LPKGRIIEIYGPESSGKTTLALQTI-AESQKK 67
Cdd:cd03270   18 IPRNKLVVITGVSGSGKSSLAFDTIyAEGQRR 49
AAA_22 pfam13401
AAA domain;
41-134 8.35e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 34.62  E-value: 8.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 374279604   41 RIIEIYGPESSGKTTLALQTIAESQKKGGICAFVDAEHALDPV-YARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAV 119
Cdd:pfam13401   6 GILVLTGESGTGKTTLLRRLLEQLPEVRDSVVFVDLPSGTSPKdLLRALLRALGLPLSGRLSKEELLAALQQLLLALAVA 85

                          90
                  ....*....|....*
gi 374279604  120 DVLVVDSVAALTPRA 134
Cdd:pfam13401  86 VVLIIDEAQHLSLEA 100
NadR3 COG3172
Nicotinamide riboside kinase [Coenzyme transport and metabolism]; Nicotinamide riboside kinase ...
 41-59 9.87e-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: 34.80  E-value: 9.87e-03
                         10
                 ....*....|....*....
gi 374279604  41 RIIEIYGPESSGKTTLALQ 59
Cdd:COG3172    9 KKIVLLGAESTGKTTLARA 27
 
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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