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Conserved domains on  [gi|425918277|gb|AFV66596|]
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recombinase A, partial [Aeromonas sp. REp-amp_128]

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
 1-173 1.59e-140

recombinase A; Provisional


The actual alignment was detected with superfamily member PRK09354:

Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 394.55  E-value: 1.59e-140
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277   1 SIMRLGDSKTMDIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEHALDPIYA 80
Cdd:PRK09354  26 SIMRLGDDAAMDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYA 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  81 AKLGVNVDDLLISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLTANIKN 160
Cdd:PRK09354 106 KKLGVDIDNLLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGNISK 185

                        170
                 ....*....|...
gi 425918277 161 ANCLCIFINQIRM 173
Cdd:PRK09354 186 SNTTVIFINQIRE 198
 
Name Accession Description Interval E-value
recA PRK09354
recombinase A; Provisional
 1-173 1.59e-140

recombinase A; Provisional


Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 394.55  E-value: 1.59e-140
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277   1 SIMRLGDSKTMDIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEHALDPIYA 80
Cdd:PRK09354  26 SIMRLGDDAAMDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYA 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  81 AKLGVNVDDLLISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLTANIKN 160
Cdd:PRK09354 106 KKLGVDIDNLLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGNISK 185

                        170
                 ....*....|...
gi 425918277 161 ANCLCIFINQIRM 173
Cdd:PRK09354 186 SNTTVIFINQIRE 198
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
1-173 1.12e-137

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 387.22  E-value: 1.12e-137
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277   1 SIMRLGDSKTMDIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEHALDPIYA 80
Cdd:COG0468   29 SIMRLGDKARQDVEVISTGSLALDIALGVGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGIAAFIDAEHALDPEYA 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  81 AKLGVNVDDLLISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLTANIKN 160
Cdd:COG0468  109 KKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGAISK 188

                        170
                 ....*....|...
gi 425918277 161 ANCLCIFINQIRM 173
Cdd:COG0468  189 SNTTVIFINQLRE 201
RecA pfam00154
recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA ...
 1-173 1.91e-123

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: 347.85  E-value: 1.91e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277    1 SIMRLGDSKTMDIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEHALDPIYA 80
Cdd:pfam00154  18 SIMKLGDEKKLDVETISTGSLALDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYA 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277   81 AKLGVNVDDLLISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLTANIKN 160
Cdd:pfam00154  98 KKLGVDIDNLLVSQPDTGEQALEIADMLVRSGAIDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGSISK 177

                         170
                  ....*....|...
gi 425918277  161 ANCLCIFINQIRM 173
Cdd:pfam00154 178 SNTTVIFINQIRE 190
tigrfam_recA TIGR02012
protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization ...
 1-173 4.69e-123

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: 349.36  E-value: 4.69e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277    1 SIMRLGDSKTMDIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEHALDPIYA 80
Cdd:TIGR02012  21 SIMRLGEKTVMDVETISTGSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYA 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277   81 AKLGVNVDDLLISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLTANIKN 160
Cdd:TIGR02012 101 RKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVDIIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGALSK 180

                         170
                  ....*....|...
gi 425918277  161 ANCLCIFINQIRM 173
Cdd:TIGR02012 181 SNTTAIFINQIRE 193
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 12-173 2.43e-116

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: 329.13  E-value: 2.43e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  12 DIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEHALDPIYAAKLGVNVDDLL 91
Cdd:cd00983    1 DVEVIPTGSLSLDIALGIGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKLGGTAAFIDAEHALDPEYAKKLGVDIDNLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  92 ISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLTANIKNANCLCIFINQI 171
Cdd:cd00983   81 VSQPDTGEQALEIADTLIRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGSLSKSKTTVIFINQL 160


                 ..
gi 425918277 172 RM 173
Cdd:cd00983  161 RE 162
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 35-173 1.83e-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: 50.83  E-value: 1.83e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277    35 GRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEHALDPIYAAKLGVNVDDLLISqpDTGEQALEICDMLVRSNAV 114
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS--GSGELRLRLALALARKLKP 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 425918277   115 DVIIVDSVAALTPKaeiegemgdshVGLQARLMSQALRKLTANIKNANCLCIFINQIRM 173
Cdd:smart00382  80 DVLILDEITSLLDA-----------EQEALLLLLEELRLLLLLKSEKNLTVILTTNDEK 127
 
Name Accession Description Interval E-value
recA PRK09354
recombinase A; Provisional
 1-173 1.59e-140

recombinase A; Provisional


Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 394.55  E-value: 1.59e-140
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277   1 SIMRLGDSKTMDIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEHALDPIYA 80
Cdd:PRK09354  26 SIMRLGDDAAMDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYA 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  81 AKLGVNVDDLLISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLTANIKN 160
Cdd:PRK09354 106 KKLGVDIDNLLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGNISK 185

                        170
                 ....*....|...
gi 425918277 161 ANCLCIFINQIRM 173
Cdd:PRK09354 186 SNTTVIFINQIRE 198
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
1-173 1.12e-137

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 387.22  E-value: 1.12e-137
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277   1 SIMRLGDSKTMDIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEHALDPIYA 80
Cdd:COG0468   29 SIMRLGDKARQDVEVISTGSLALDIALGVGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGIAAFIDAEHALDPEYA 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  81 AKLGVNVDDLLISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLTANIKN 160
Cdd:COG0468  109 KKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGAISK 188

                        170
                 ....*....|...
gi 425918277 161 ANCLCIFINQIRM 173
Cdd:COG0468  189 SNTTVIFINQLRE 201
RecA pfam00154
recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA ...
 1-173 1.91e-123

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: 347.85  E-value: 1.91e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277    1 SIMRLGDSKTMDIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEHALDPIYA 80
Cdd:pfam00154  18 SIMKLGDEKKLDVETISTGSLALDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYA 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277   81 AKLGVNVDDLLISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLTANIKN 160
Cdd:pfam00154  98 KKLGVDIDNLLVSQPDTGEQALEIADMLVRSGAIDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGSISK 177

                         170
                  ....*....|...
gi 425918277  161 ANCLCIFINQIRM 173
Cdd:pfam00154 178 SNTTVIFINQIRE 190
tigrfam_recA TIGR02012
protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization ...
 1-173 4.69e-123

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: 349.36  E-value: 4.69e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277    1 SIMRLGDSKTMDIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEHALDPIYA 80
Cdd:TIGR02012  21 SIMRLGEKTVMDVETISTGSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYA 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277   81 AKLGVNVDDLLISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLTANIKN 160
Cdd:TIGR02012 101 RKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVDIIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGALSK 180

                         170
                  ....*....|...
gi 425918277  161 ANCLCIFINQIRM 173
Cdd:TIGR02012 181 SNTTAIFINQIRE 193
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 12-173 2.43e-116

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: 329.13  E-value: 2.43e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  12 DIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEHALDPIYAAKLGVNVDDLL 91
Cdd:cd00983    1 DVEVIPTGSLSLDIALGIGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKLGGTAAFIDAEHALDPEYAKKLGVDIDNLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  92 ISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLTANIKNANCLCIFINQI 171
Cdd:cd00983   81 VSQPDTGEQALEIADTLIRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGSLSKSKTTVIFINQL 160


                 ..
gi 425918277 172 RM 173
Cdd:cd00983  161 RE 162
recA PRK09519
intein-containing recombinase RecA;
1-172 7.16e-82

intein-containing recombinase RecA;


Pssm-ID: 77219 [Multi-domain]  Cd Length: 790  Bit Score: 257.33  E-value: 7.16e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277   1 SIMRLGDSKTMDIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEHALDPIYA 80
Cdd:PRK09519  26 SVMRLGDEARQPISVIPTGSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDYA 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  81 AKLGVNVDDLLISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLTANIKN 160
Cdd:PRK09519 106 KKLGVDTDSLLVSQPDTGEQALEIADMLIRSGALDIVVIDSVAALVPRAELEGEMGDSHVGLQARLMSQALRKMTGALNN 185

                        170
                 ....*....|..
gi 425918277 161 ANCLCIFINQIR 172
Cdd:PRK09519 186 SGTTAIFINQLR 197
RecA-like cd01393
RecA family; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 35-173 1.15e-42

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: 140.57  E-value: 1.15e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  35 GRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEHALDPIYA-----------AKLGVNVDDLLISQPDTGEQALE 103
Cdd:cd01393    1 GKITEIYGPPGSGKTQLALQLAANALLLGGGVVWIDTEGAFPPSRLvqileaspsseLELAEALSRLLYFRPPDTLAHLL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 425918277 104 ICDMLVRSNA----VDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLTANIKNANCLCIFINQIRM 173
Cdd:cd01393   81 ALDSLPESLFpppnTSLVVVDSVSALFRKAFPRGGDGDSSSSLRARLLSQLARALQKLAAQFNLAVVVTNQVTT 154
archRadB cd01394
archaeal RadB; The archaeal protein RadB shares similarity RadA, the archaeal functional ...
 16-173 1.89e-17

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: 1.89e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  16 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEhALDP-----IYAAKLGVNVDDL 90
Cdd:cd01394    1 LSTGSKSLDSLLG-GGVERGTITQIYGPPGSGKTNICLQLAVEAAKQGKKVVYIDTE-GLSPerfqqIAGERFESIASNI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  91 LISQP-DTGEQALEICDM--LVRSNAVDVIIVDSVAALTpKAEiegEMGDShvGLQARLMSQaLRKLTANIKNANCLCIF 167
Cdd:cd01394   79 IVFEPySFDEQGVAIQEAekLLKSDKVDLVVVDSATALY-RLE---LGDDS--EANRELSRQ-MSKLLSIARKYDIPVVI 151


                 ....*.
gi 425918277 168 INQIRM 173
Cdd:cd01394  152 TNQVYS 157
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
16-173 7.01e-15

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 69.17  E-value: 7.01e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  16 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEHALDPI--YAAKLGVNVDDLL-- 91
Cdd:COG0467    2 VPTGIPGLDELLG-GGLPRGSSTLLSGPPGTGKTTLALQFLAEGLRRGEKGLYVSFEESPEQLlrRAESLGLDLEEYIes 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  92 ----ISQPDTGEQALEICDML------VRSNAVDVIIVDSVAALtpkaeiEGEMGDShvglqaRLMSQALRKLTANIKNA 161
Cdd:COG0467   81 gllrIIDLSPEELGLDLEELLarlreaVEEFGAKRVVIDSLSGL------LLALPDP------ERLREFLHRLLRYLKKR 148

                        170
                 ....*....|..
gi 425918277 162 NCLCIFINQIRM 173
Cdd:COG0467  149 GVTTLLTSETGG 160
recomb_radB TIGR02237
DNA repair and recombination protein RadB; This family consists exclusively of archaeal RadB ...
 23-172 5.70e-13

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: 63.97  E-value: 5.70e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277   23 LDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEhALDP-----IYAAKLGVNVDDLLISQP-D 96
Cdd:TIGR02237   1 IDELLG-GGVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTE-GLSPerfkqIAEDRPERALSNFIVFEVfD 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 425918277   97 TGEQALEICDM--LVRSNAVDVIIVDSVAALTpKAEIEGEMGDSHVGLQARLmsQALRKLTANIKNAnclCIFINQIR 172
Cdd:TIGR02237  79 FDEQGVAIQKTskFIDRDSASLVVVDSFTALY-RLELSDDRISRNRELARQL--TLLLSLARKKNLA---VVITNQVY 150
COG4544 COG4544
Uncharacterized conserved protein [Function unknown];
15-129 3.43e-12

Uncharacterized conserved protein [Function unknown];


Pssm-ID: 443609 [Multi-domain]  Cd Length: 230  Bit Score: 62.25  E-value: 3.43e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  15 AISTGSLSLDVALGIGGLPCGRIVEIYGPE-SSGKTTLTLQVIAEAQKKGKVCAFIDAEHALdpiYA---AKLGVNVDDL 90
Cdd:COG4544   28 VLPTGFAALDAALPGGGLPRGALHEILGPApGIGELGLLLPLLARLAQAGGPVLWIAPPYDL---YApglAAAGLDPERL 104

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 425918277  91 LISQPDTGEQALEICDMLVRSNAVDVIIVDsVAALTPKA 129
Cdd:COG4544  105 LLVRARRPADALWAAEEALRSGACGAVVAW-LERLDLTA 142
radB PRK09361
DNA repair and recombination protein RadB; Provisional
 13-125 2.38e-11

DNA repair and recombination protein RadB; Provisional


Pssm-ID: 236482 [Multi-domain]  Cd Length: 225  Bit Score: 59.88  E-value: 2.38e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  13 IEAISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEhALDPIYAAKL-GVNVDDLL 91
Cdd:PRK09361   2 DERLPTGCKMLDELLG-GGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE-GLSPERFKQIaGEDFEELL 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 425918277  92 ----ISQP-DTGEQALEICDM--LVRSNaVDVIIVDSVAAL 125
Cdd:PRK09361  80 sniiIFEPsSFEEQSEAIRKAekLAKEN-VGLIVLDSATSL 119
DMC1 cd19514
homologous-pairing protein DMC1; DMC1 has a central role in homologous recombination in ...
 16-125 8.35e-10

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: 55.83  E-value: 8.35e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  16 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTL--TLQVIAEAQKK-----GKVCaFIDAEHALDP----IYAAKLG 84
Cdd:cd19514    1 ISTGSTELDKLLG-GGIESMSITEVFGEFRTGKTQLshTLCVTAQLPGSmggggGKVA-YIDTEGTFRPdrirPIAERFG 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 425918277  85 VN----VDDLLISQPDTGEQALEICDMLVRSNAVD----VIIVDSVAAL 125
Cdd:cd19514   79 VDhdavLDNILYARAYTSEHQMELLDYVAAKFHEEavfrLLIIDSIMAL 127
Rad51B cd19493
RAD51B recombinase; RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 24-148 9.98e-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: 55.40  E-value: 9.98e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  24 DVALGiGGLPCGRIVEIYGPESSGKT----TLTLQVIAEAQKKGK--VCAFIDAEHALDP-----IYAAKLGVN------ 86
Cdd:cd19493    1 DTALA-GGLPLGAITEITGASGSGKTqfalTLASSAAMPARKGGLdgGVLYIDTESKFSAerlaeIAEARFPEAfsgfme 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 425918277  87 --------VDDLLISQPDTGEQALEICDML---VRSNAVDVIIVDSVAALTPKA--EIEGEMGDSHVGLqARLMS 148
Cdd:cd19493   80 eneraeemLKRVAVVRVTTLAQLLERLPNLeehILSSGVRLVVIDSIAALVRREfgGSDGEVTERHNAL-AREAS 153
Rad51 pfam08423
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ...
 16-125 1.32e-09

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: 55.39  E-value: 1.32e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277   16 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTL--TLQVIAEAQK-----KGKvCAFIDAEHALDPI----YAAKLG 84
Cdd:pfam08423  19 ITTGSKELDKLLG-GGIETGSITEIFGEFRTGKTQLchTLCVTCQLPLemgggEGK-ALYIDTEGTFRPErlvaIAERYG 96

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 425918277   85 VNVDDLLISQP-------DTGEQALEICDMLVRSNAVDVIIVDSVAAL 125
Cdd:pfam08423  97 LDPEDVLDNVAyaraynsEHQMQLLQQAAAMMSESRFALLIVDSATAL 144
KaiC-like cd01124
Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. ...
 16-172 6.70e-09

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: 53.04  E-value: 6.70e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  16 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEHALDPIY--AAKLGVNVD----- 88
Cdd:cd01124    1 VKTGIPGLDELLG-GGIPKGSVTLLTGGPGTGKTLFGLQFLYAGAKNGEPGLFFTFEESPERLLrnAKSFGWDFDemede 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  89 -DLLISQPDTGEQALEICDML-------VRSNAVDVIIVDSVAALTPKAEiegemgdshvglQARLMSQALRKLTANIKN 160
Cdd:cd01124   80 gKLIIVDAPPTEAGRFSLDELlsrilsiIKSFKAKRVVIDSLSGLRRAKE------------DQMRARRIVIALLNELRA 147

                        170
                 ....*....|..
gi 425918277 161 ANCLCIFINQIR 172
Cdd:cd01124  148 AGVTTIFTSEMR 159
radA PRK04301
DNA repair and recombination protein RadA; Validated
 11-124 1.25e-08

DNA repair and recombination protein RadA; Validated


Pssm-ID: 235273 [Multi-domain]  Cd Length: 317  Bit Score: 52.96  E-value: 1.25e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  11 MDIEAISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQK------KGKVCAFIDAE------------ 72
Cdd:PRK04301  79 KNVGKITTGSKELDELLG-GGIETQSITEFYGEFGSGKTQICHQLAVNVQLpeekggLEGKAVYIDTEgtfrperieqma 157

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 425918277  73 --------HALDPIYAAKlGVNVDD--LLIsqpdtgEQALEICDmlvRSNAVDVIIVDSVAA 124
Cdd:PRK04301 158 ealgldpdEVLDNIHVAR-AYNSDHqmLLA------EKAEELIK---EGENIKLVIVDSLTA 209
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 35-173 1.83e-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: 50.83  E-value: 1.83e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277    35 GRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEHALDPIYAAKLGVNVDDLLISqpDTGEQALEICDMLVRSNAV 114
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS--GSGELRLRLALALARKLKP 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 425918277   115 DVIIVDSVAALTPKaeiegemgdshVGLQARLMSQALRKLTANIKNANCLCIFINQIRM 173
Cdd:smart00382  80 DVLILDEITSLLDA-----------EQEALLLLLEELRLLLLLKSEKNLTVILTTNDEK 127
ATPase pfam06745
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ...
 16-173 1.91e-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: 51.86  E-value: 1.91e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277   16 ISTGSLSLDvALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAE-AQKKGKVCAFIDA-EHALDPIYAAK-LGVNVDDLL- 91
Cdd:pfam06745   1 VKTGIPGLD-EILKGGFPEGRVVLITGGPGTGKTIFGLQFLYNgALKYGEPGVFVTLeEPPEDLRENARsFGWDLEKLEe 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277   92 --------ISQPDTGEQALEICDML----------VRSNAVDVIIVDSVAALtpkAEIEGEMgdshvglQARlmsQALRK 153
Cdd:pfam06745  80 egklaiidASTSGIGIAEVEDRFDLeelierlreaIREIGAKRVVIDSITTL---FYLLKPA-------VAR---EILRR 146

                         170       180
                  ....*....|....*....|
gi 425918277  154 LTANIKNANCLCIFINQIRM 173
Cdd:pfam06745 147 LKRVLKGLGVTAIFTSEKPS 166
PLN03186 PLN03186
DNA repair protein RAD51 homolog; Provisional
 12-155 3.45e-08

DNA repair protein RAD51 homolog; Provisional


Pssm-ID: 178728 [Multi-domain]  Cd Length: 342  Bit Score: 51.66  E-value: 3.45e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  12 DIEAISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTL--TLQV-----IAEAQKKGKvCAFIDAEHALDP----IYA 80
Cdd:PLN03186 101 EIIQITTGSRELDKILE-GGIETGSITEIYGEFRTGKTQLchTLCVtcqlpLDQGGGEGK-AMYIDTEGTFRPqrliQIA 178

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  81 AKLGVNVDDLL-----ISQPDTGEQA---LEICDMLVRSNaVDVIIVDSVAALTpKAEIEGEmGDshvgLQAR--LMSQA 150
Cdd:PLN03186 179 ERFGLNGADVLenvayARAYNTDHQSellLEAASMMAETR-FALMIVDSATALY-RTEFSGR-GE----LSARqmHLGKF 251


                 ....*
gi 425918277 151 LRKLT 155
Cdd:PLN03186 252 LRSLQ 256
Rad51_DMC1_archRadA cd01123
recombinase Rad51, DMC1, and archaeal RadA; This group of recombinases includes the eukaryotic ...
 16-125 5.00e-08

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: 50.61  E-value: 5.00e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  16 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTL--TLQV-----IAEAQKKGKvCAFIDAEHALDPI----YAAKLG 84
Cdd:cd01123    1 ITTGSKELDKLLG-GGIETGSITEMFGEFRTGKTQLchTLAVtcqlpIDRGGGEGK-AIYIDTEGTFRPErlraIAQRFG 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 425918277  85 VNVDDLL----ISQPDTGEQALEICD----MLVRSnAVDVIIVDSVAAL 125
Cdd:cd01123   79 LDPDDVLdnvaYARAFNSDHQTQLLDqaaaMMVES-RFKLLIVDSATAL 126
XRCC3 cd19491
XRCC3 recombinase; XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells ...
 23-171 8.04e-08

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: 50.37  E-value: 8.04e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  23 LDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQ------KKGKVCAFIDAEHAL----------------DPIYA 80
Cdd:cd19491    1 LDELLG-GGIPVGGITEIAGESGAGKTQLCLQLALTVQlprelgGLGGGAVYICTESSFpskrlqqlasslpkryHLEKA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  81 AKLGVNVddLLISQPDTgeQALEICDM-----LVRSNAVDVIIVDSVAALtpkAEIEGEMGDSHVGLQARLMSQALRKLT 155
Cdd:cd19491   80 KNFLDNI--FVEHVADL--ETLEHCLNyqlpaLLERGPIRLVVIDSIAAL---FRSEFDTSRSDLVERAKYLRRLADHLK 152

                        170
                 ....*....|....*.
gi 425918277 156 ANIKNANCLCIFINQI 171
Cdd:cd19491  153 RLADKYNLAVVVVNQV 168
RadA_SMS_N cd01121
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a ...
 3-122 2.96e-07

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: 48.68  E-value: 2.96e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277   3 MRLGDSKTMDIEAISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAE-AQKKGKVcAFIDAEHALDPI--Y 79
Cdd:cd01121   51 LPLSDVEAEEEERISTGIGELDRVLG-GGLVPGSVVLIGGDPGIGKSTLLLQVAARlAQRGGKV-LYVSGEESLSQIklR 128

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 425918277  80 AAKLGVNVDDLLIsqpdTGEQALE-ICDMLVRSNAvDVIIVDSV 122
Cdd:cd01121  129 AERLGLGSDNLYL----LAETNLEaILAEIEELKP-SLVVIDSI 167
archRadA cd19515
archaeal recombinase Rad51/RadA; This group includes the archaeal protein RadA which is a ...
 16-125 7.93e-07

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: 47.36  E-value: 7.93e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  16 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQK-------KGKVcAFIDAEHALDP----IYAAKLG 84
Cdd:cd19515    1 ISTGSKELDKLLG-GGIETQAITEVFGEFGSGKTQLCHQLAVNVQLppeegglNGKA-VYIDTENTFRPerimQMAKALG 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 425918277  85 VNVDDLL-----ISQPDTGEQAL---EICDMLVRSNAVDVIIVDSVAAL 125
Cdd:cd19515   79 LDPDEVLdniyvARAYNSNHQMLlveKAEDLIKEGNNIKLLIVDSLTSH 127
recomb_DMC1 TIGR02238
meiotic recombinase Dmc1; This model describes DMC1, a subfamily of a larger family of DNA ...
 16-125 1.07e-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: 47.08  E-value: 1.07e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277   16 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTL--TLQVIAEAQKK-----GKVCaFIDAEHALDP----IYAAKLG 84
Cdd:TIGR02238  78 ITTGSQALDGILG-GGIESMSITEVFGEFRCGKTQLshTLCVTAQLPREmgggnGKVA-YIDTEGTFRPdrirAIAERFG 155

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 425918277   85 VN----VDDLLISQPDTGEQALEICDMLVRSNAVD---VIIVDSVAAL 125
Cdd:TIGR02238 156 VDpdavLDNILYARAYTSEHQMELLDYLAAKFSEEpfrLLIVDSIMAL 203
KaiC-like_N cd19488
N-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 16-108 2.36e-06

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: 45.80  E-value: 2.36e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  16 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEHALDPIY--AAKLGVNVDDLLI- 92
Cdd:cd19488    1 ISTGIPGLDDILR-GGLPPRRLYLVEGAPGTGKTTLALQFLLEGAANGETGLYITLSETEQELRavALSHGWSLDGIHIf 79

                         90
                 ....*....|....*...
gi 425918277  93 --SQPDTGEQALEICDML 108
Cdd:cd19488   80 elSPSESALDAAQQYTIL 97
Rad51 cd19513
RAD51D recombinase; RAD51 recombinase plays an essential role in DNA repair by homologous ...
 16-125 2.47e-06

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: 45.77  E-value: 2.47e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  16 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTL--TLQV-----IAEAQKKGKvCAFIDAEHALDP----IYAAKLG 84
Cdd:cd19513    1 ITTGSKELDKLLG-GGIETGSITELFGEFRTGKTQLchTLAVtcqlpIDQGGGEGK-ALYIDTEGTFRPerllAIAERYG 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 425918277  85 VNVDDLL-----ISQPDTGEQA---LEICDMLVRSNaVDVIIVDSVAAL 125
Cdd:cd19513   79 LNGEDVLdnvayARAYNTDHQMqllIQASAMMAESR-YALLIVDSATAL 126
PTZ00035 PTZ00035
Rad51 protein; Provisional
 16-125 3.92e-06

Rad51 protein; Provisional


Pssm-ID: 185407 [Multi-domain]  Cd Length: 337  Bit Score: 45.76  E-value: 3.92e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  16 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTL--TLQVIAE-----AQKKGKVCaFIDAEHALDP-----IyAAKL 83
Cdd:PTZ00035 100 ITTGSTQLDKLLG-GGIETGSITELFGEFRTGKTQLchTLCVTCQlpieqGGGEGKVL-YIDTEGTFRPerivqI-AERF 176

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 425918277  84 GVN----VDDLLISQPDTGEQALE----ICDMLVRSNAVdVIIVDSVAAL 125
Cdd:PTZ00035 177 GLDpedvLDNIAYARAYNHEHQMQllsqAAAKMAEERFA-LLIVDSATAL 225
FlaH COG2874
Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];
16-126 1.09e-05

Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];


Pssm-ID: 442121  Cd Length: 230  Bit Score: 44.05  E-value: 1.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  16 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEHA----LDPIYAakLGVNVDDLL 91
Cdd:COG2874    3 ISTGNDELDKRLG-GGIPLGSLVLIEGENGTGKSVLSQQFAYGALENGLSVTYISTELTtkefIKQMKS--LSYDISDYL 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 425918277  92 IS--------QPDTGE----QALEICDMLVRSNA-----VDVIIVDSVAALT 126
Cdd:COG2874   80 LRgrllflpvHPLGFEwnskQRKDLLKRLMKYIAsnlweADVIIIDSLSALL 131
recomb_RAD51 TIGR02239
DNA repair protein RAD51; This eukaryotic sequence family consists of RAD51, a protein ...
 12-125 1.38e-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: 43.95  E-value: 1.38e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277   12 DIEAISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTL--TLQV-----IAEAQKKGKvCAFIDAEHALDPI----YA 80
Cdd:TIGR02239  74 EVIQLTTGSKELDKLLG-GGIETGSITEIFGEFRTGKTQLchTLAVtcqlpIDQGGGEGK-ALYIDTEGTFRPErllaIA 151

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 425918277   81 AKLGVNVDDLLIS-------QPDTGEQALEICDMLVRSNAVDVIIVDSVAAL 125
Cdd:TIGR02239 152 ERYGLNPEDVLDNvayarayNTDHQLQLLQQAAAMMSESRFALLIVDSATAL 203
PLN03187 PLN03187
meiotic recombination protein DMC1 homolog; Provisional
 12-125 4.39e-05

meiotic recombination protein DMC1 homolog; Provisional


Pssm-ID: 215620 [Multi-domain]  Cd Length: 344  Bit Score: 42.46  E-value: 4.39e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  12 DIEAISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTL--TLQV-----IAEAQKKGKVcAFIDAEHALDP----IYA 80
Cdd:PLN03187 104 SVVRITTGSQALDELLG-GGIETRCITEAFGEFRSGKTQLahTLCVttqlpTEMGGGNGKV-AYIDTEGTFRPdrivPIA 181

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 425918277  81 AKLGVN----VDDLLISQPDTGEQ---ALEICDMLVRSNAVDVIIVDSVAAL 125
Cdd:PLN03187 182 ERFGMDadavLDNIIYARAYTYEHqynLLLGLAAKMAEEPFRLLIVDSVIAL 233
PRK06067 PRK06067
flagellar accessory protein FlaH; Validated
 12-132 9.49e-05

flagellar accessory protein FlaH; Validated


Pssm-ID: 180381  Cd Length: 234  Bit Score: 41.11  E-value: 9.49e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  12 DIEAISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEHALDPiYAAK---LGVNVD 88
Cdd:PRK06067   3 KKEIISTGNEELDRKLG-GGIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITTENTSKS-YLKQmesVKIDIS 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 425918277  89 DLLIS---------------QPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIE 132
Cdd:PRK06067  81 DFFLWgylrifplntegfewNSTLANKLLELIIEFIKSKREDVIIIDSLTIFATYAEED 139
XRCC2 cd19490
XRCC2 recombinase; XRCC2 (X-ray repair complementing defective repair in Chinese hamster cells ...
 35-173 9.74e-05

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: 41.18  E-value: 9.74e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  35 GRIVEIYGPESSGKTTLTLQVIAEA-----------QKKGKVCAFIDAEHALDP-----IYAAKLGVNVDDLLISQPDTG 98
Cdd:cd19490    1 GDVIEITGPSGSGKTELLYHLAARCilpsswggvplGGLEAAVVFIDTDGRFDIlrlrsILEARIRAAIQAANSSDDEED 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  99 -EQALEIC-----------------------DMLVRSNA---VDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQAL 151
Cdd:cd19490   81 vEEIAREClqrlhifrchsslqllatllsleNYLLSLSAnpeLGLLLIDSISAFYWQDRFSAELARAAPLLQEAALRAIL 160

                        170       180
                 ....*....|....*....|..
gi 425918277 152 RKLTANIKNANCLCIFINQIRM 173
Cdd:cd19490  161 RELRRLRRRFQLVVIATKQALF 182
Rad51D cd19489
RAD51D recombinase; RAD51D recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 30-59 9.79e-05

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


Pssm-ID: 410897 [Multi-domain]  Cd Length: 209  Bit Score: 41.08  E-value: 9.79e-05
                         10        20        30
                 ....*....|....*....|....*....|
gi 425918277  30 GGLPCGRIVEIYGPESSGKTTLTLQVIAEA 59
Cdd:cd19489    2 GGLRTGEITELVGESSSGKTQLCLTAAANV 31
ATPase_2 pfam01637
ATPase domain predominantly from Archaea; This family contain a conserved P-loop motif that is ...
 37-71 3.47e-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: 3.47e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 425918277   37 IVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDA 71
Cdd:pfam01637  22 IYVIYGPEGCGKTALLRESIENLLDLGYYVIYYDP 56
AAA_24 pfam13479
AAA domain; This AAA domain is found in a wide variety of presumed phage proteins.
 36-122 5.35e-04

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


Pssm-ID: 433243  Cd Length: 199  Bit Score: 38.85  E-value: 5.35e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277   36 RIVeIYGPESSGKTTLtlqvIAEAQKKgkvcAFIDAEHALDPIYAAKLGVnvddllISQPDTGEQALEICDMLVRSNAV- 114
Cdd:pfam13479   4 KIL-IYGPSGIGKTTF----AKTLPKP----LFLDTEKGSKALDGDRFPD------IVIRDSWQDFLDAIDELTAAELAd 68


                  ....*....
gi 425918277  115 -DVIIVDSV 122
Cdd:pfam13479  69 yKTIVIDTV 77
RepA COG3598
RecA-family ATPase [Replication, recombination and repair];
32-154 7.37e-04

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


Pssm-ID: 442817 [Multi-domain]  Cd Length: 313  Bit Score: 39.11  E-value: 7.37e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  32 LPCGRIVEIYGPESSGKTTLTLQV---IAEAQ-------KKGKVcAFIDAEHALDPI------YAAKLGVNVDDL----- 90
Cdd:COG3598   10 LPEGGVTLLAGPPGTGKSFLALQLaaaVAAGGpwlgrrvPPGKV-LYLAAEDDRGELrrrlkaLGADLGLPFADLdgrlr 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 425918277  91 LIS-----QPDTGEQALEicdMLVRSNAVDVIIVDSVAALTPkaeiegemGDSHVGLQARLMSQALRKL 154
Cdd:COG3598   89 LLSlagdlDDTDDLEALE---RAIEEEGPDLVVIDPLARVFG--------GDENDAEEMRAFLNPLDRL 146
PRK10851 PRK10851
sulfate/thiosulfate ABC transporter ATP-binding protein CysA;
24-66 1.12e-03

sulfate/thiosulfate ABC transporter ATP-binding protein CysA;


Pssm-ID: 182778 [Multi-domain]  Cd Length: 353  Bit Score: 38.53  E-value: 1.12e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 425918277  24 DVALGIgglPCGRIVEIYGPESSGKTTLtLQVIA--EAQKKGKVC 66
Cdd:PRK10851  20 DISLDI---PSGQMVALLGPSGSGKTTL-LRIIAglEHQTSGHIR 60
Grc3 COG1341
Polynucleotide 5'-kinase, involved in rRNA processing [Translation, ribosomal structure and ...
 29-71 1.40e-03

Polynucleotide 5'-kinase, involved in rRNA processing [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440952  Cd Length: 353  Bit Score: 38.08  E-value: 1.40e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 425918277  29 IGGLPCGRIVeIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDA 71
Cdd:COG1341   30 ILSSGPGRIM-VLGPVDSGKSTLTTLLANKLLAEGLKVAIIDA 71
KaiC-like_C cd19487
C-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 16-67 2.50e-03

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: 36.89  E-value: 2.50e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 425918277  16 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCA 67
Cdd:cd19487    1 VSSGVPELDELLG-GGLERGTSTLLIGPAGVGKSTLALQFAKAAAARGERSV 51
NadR3 COG3172
Nicotinamide riboside kinase [Coenzyme transport and metabolism]; Nicotinamide riboside kinase ...
 36-54 4.17e-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: 4.17e-03
                         10
                 ....*....|....*....
gi 425918277  36 RIVeIYGPESSGKTTLTLQ 54
Cdd:COG3172   10 KIV-LLGAESTGKTTLARA 27
KaiC_C cd19484
C-terminal domain of Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most ...
 16-126 6.85e-03

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: 35.77  E-value: 6.85e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  16 ISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKVCAFIDAEHALDPIY--AAKLGVNVDDLLIS 93
Cdd:cd19484    1 ISTGIPRLDAMLGGGGFFRGSSILVSGATGTGKTLLAASFADAACRRGERCLYFAFEESPAQLIrnAKSIGIDLEQMERK 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 425918277  94 Q---------PDTG-EQALEICDMLVRSNAVDVIIVDSVAALT 126
Cdd:cd19484   81 GllkiicarpELYGlEDHLIIIKSEINEFKPSRVIVDPLSALA 123
Tdk COG1435
Thymidine kinase [Nucleotide transport and metabolism]; Thymidine kinase is part of the ...
 35-120 8.04e-03

Thymidine kinase [Nucleotide transport and metabolism]; Thymidine kinase is part of the Pathway/BioSystem: Pyrimidine salvage


Pssm-ID: 441044  Cd Length: 192  Bit Score: 35.46  E-value: 8.04e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 425918277  35 GRIVEIYGPESSGKTTLTLQVI--AEAQKKgKVCAFIdaeHALDPIYAAK-----LGVNVDDLLISQPDtgeqalEICDM 107
Cdd:COG1435    4 GKLEFIYGPMFSGKSEELLRRAhnYEEAGQ-KVLLFK---PAIDDRYGEGkivsrIGLSREAIPVDDDT------DILEL 73

                         90
                 ....*....|...
gi 425918277 108 LVRSNAVDVIIVD 120
Cdd:COG1435   74 VREGPDVDVVLID 86
 
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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