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Conserved domains on  [gi|340548422|gb|AEK52378|]
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recombinase A, partial [Aeromonas sp. Ae74(2011)]

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
 1-187 7.39e-155

recombinase A; Provisional


The actual alignment was detected with superfamily member PRK09354:

Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 431.52  E-value: 7.39e-155
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422   1 QFGKGSIMRLGDSKTMDIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEHAL 80
Cdd:PRK09354  21 QFGKGSIMRLGDDAAMDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHAL 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  81 DPIYAAKLGVNVDDLLISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLT 160
Cdd:PRK09354 101 DPVYAKKLGVDIDNLLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLT 180

                        170       180
                 ....*....|....*....|....*..
gi 340548422 161 ANIKNANCLCIFINQIRMKIGVMFGSP 187
Cdd:PRK09354 181 GNISKSNTTVIFINQIREKIGVMFGNP 207
 
Name Accession Description Interval E-value
recA PRK09354
recombinase A; Provisional
 1-187 7.39e-155

recombinase A; Provisional


Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 431.52  E-value: 7.39e-155
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422   1 QFGKGSIMRLGDSKTMDIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEHAL 80
Cdd:PRK09354  21 QFGKGSIMRLGDDAAMDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHAL 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  81 DPIYAAKLGVNVDDLLISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLT 160
Cdd:PRK09354 101 DPVYAKKLGVDIDNLLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLT 180

                        170       180
                 ....*....|....*....|....*..
gi 340548422 161 ANIKNANCLCIFINQIRMKIGVMFGSP 187
Cdd:PRK09354 181 GNISKSNTTVIFINQIREKIGVMFGNP 207
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
1-187 1.34e-151

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 423.04  E-value: 1.34e-151
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422   1 QFGKGSIMRLGDSKTMDIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEHAL 80
Cdd:COG0468   24 QFGKGSIMRLGDKARQDVEVISTGSLALDIALGVGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGIAAFIDAEHAL 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  81 DPIYAAKLGVNVDDLLISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLT 160
Cdd:COG0468  104 DPEYAKKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLT 183

                        170       180
                 ....*....|....*....|....*..
gi 340548422 161 ANIKNANCLCIFINQIRMKIGVMFGSP 187
Cdd:COG0468  184 GAISKSNTTVIFINQLREKIGVMFGNP 210
RecA pfam00154
recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA ...
 1-187 2.68e-136

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: 380.98  E-value: 2.68e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422    1 QFGKGSIMRLGDSKTMDIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEHAL 80
Cdd:pfam00154  13 QFGKGSIMKLGDEKKLDVETISTGSLALDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHAL 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422   81 DPIYAAKLGVNVDDLLISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLT 160
Cdd:pfam00154  93 DPVYAKKLGVDIDNLLVSQPDTGEQALEIADMLVRSGAIDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLT 172

                         170       180
                  ....*....|....*....|....*..
gi 340548422  161 ANIKNANCLCIFINQIRMKIGVMFGSP 187
Cdd:pfam00154 173 GSISKSNTTVIFINQIREKIGVMFGNP 199
tigrfam_recA TIGR02012
protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization ...
 1-187 4.26e-136

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: 382.87  E-value: 4.26e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422    1 QFGKGSIMRLGDSKTMDIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEHAL 80
Cdd:TIGR02012  16 QFGKGSIMRLGEKTVMDVETISTGSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHAL 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422   81 DPIYAAKLGVNVDDLLISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLT 160
Cdd:TIGR02012  96 DPVYARKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVDIIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLT 175

                         170       180
                  ....*....|....*....|....*..
gi 340548422  161 ANIKNANCLCIFINQIRMKIGVMFGSP 187
Cdd:TIGR02012 176 GALSKSNTTAIFINQIREKIGVMFGNP 202
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 17-187 1.32e-123

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: 348.01  E-value: 1.32e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  17 DIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEHALDPIYAAKLGVNVDDLL 96
Cdd:cd00983    1 DVEVIPTGSLSLDIALGIGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKLGGTAAFIDAEHALDPEYAKKLGVDIDNLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  97 ISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLTANIKNANCLCIFINQI 176
Cdd:cd00983   81 VSQPDTGEQALEIADTLIRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGSLSKSKTTVIFINQL 160

                        170
                 ....*....|.
gi 340548422 177 RMKIGVMFGSP 187
Cdd:cd00983  161 REKIGVMFGNP 171
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 40-181 6.45e-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: 52.38  E-value: 6.45e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422    40 GRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEHALDPIYAAKLGVNVDDLLISqpDTGEQALEICDMLVRSNAV 119
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS--GSGELRLRLALALARKLKP 79

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 340548422   120 DVIIVDSVAALTPKaeiegemgdshVGLQARLMSQALRKLTANIKNANCLCIFINQIRMKIG 181
Cdd:smart00382  80 DVLILDEITSLLDA-----------EQEALLLLLEELRLLLLLKSEKNLTVILTTNDEKDLG 130
 
Name Accession Description Interval E-value
recA PRK09354
recombinase A; Provisional
 1-187 7.39e-155

recombinase A; Provisional


Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 431.52  E-value: 7.39e-155
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422   1 QFGKGSIMRLGDSKTMDIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEHAL 80
Cdd:PRK09354  21 QFGKGSIMRLGDDAAMDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHAL 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  81 DPIYAAKLGVNVDDLLISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLT 160
Cdd:PRK09354 101 DPVYAKKLGVDIDNLLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLT 180

                        170       180
                 ....*....|....*....|....*..
gi 340548422 161 ANIKNANCLCIFINQIRMKIGVMFGSP 187
Cdd:PRK09354 181 GNISKSNTTVIFINQIREKIGVMFGNP 207
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
1-187 1.34e-151

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 423.04  E-value: 1.34e-151
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422   1 QFGKGSIMRLGDSKTMDIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEHAL 80
Cdd:COG0468   24 QFGKGSIMRLGDKARQDVEVISTGSLALDIALGVGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGIAAFIDAEHAL 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  81 DPIYAAKLGVNVDDLLISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLT 160
Cdd:COG0468  104 DPEYAKKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLT 183

                        170       180
                 ....*....|....*....|....*..
gi 340548422 161 ANIKNANCLCIFINQIRMKIGVMFGSP 187
Cdd:COG0468  184 GAISKSNTTVIFINQLREKIGVMFGNP 210
RecA pfam00154
recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA ...
 1-187 2.68e-136

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: 380.98  E-value: 2.68e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422    1 QFGKGSIMRLGDSKTMDIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEHAL 80
Cdd:pfam00154  13 QFGKGSIMKLGDEKKLDVETISTGSLALDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHAL 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422   81 DPIYAAKLGVNVDDLLISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLT 160
Cdd:pfam00154  93 DPVYAKKLGVDIDNLLVSQPDTGEQALEIADMLVRSGAIDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLT 172

                         170       180
                  ....*....|....*....|....*..
gi 340548422  161 ANIKNANCLCIFINQIRMKIGVMFGSP 187
Cdd:pfam00154 173 GSISKSNTTVIFINQIREKIGVMFGNP 199
tigrfam_recA TIGR02012
protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization ...
 1-187 4.26e-136

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: 382.87  E-value: 4.26e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422    1 QFGKGSIMRLGDSKTMDIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEHAL 80
Cdd:TIGR02012  16 QFGKGSIMRLGEKTVMDVETISTGSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHAL 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422   81 DPIYAAKLGVNVDDLLISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLT 160
Cdd:TIGR02012  96 DPVYARKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVDIIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLT 175

                         170       180
                  ....*....|....*....|....*..
gi 340548422  161 ANIKNANCLCIFINQIRMKIGVMFGSP 187
Cdd:TIGR02012 176 GALSKSNTTAIFINQIREKIGVMFGNP 202
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 17-187 1.32e-123

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: 348.01  E-value: 1.32e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  17 DIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEHALDPIYAAKLGVNVDDLL 96
Cdd:cd00983    1 DVEVIPTGSLSLDIALGIGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKLGGTAAFIDAEHALDPEYAKKLGVDIDNLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  97 ISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLTANIKNANCLCIFINQI 176
Cdd:cd00983   81 VSQPDTGEQALEIADTLIRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGSLSKSKTTVIFINQL 160

                        170
                 ....*....|.
gi 340548422 177 RMKIGVMFGSP 187
Cdd:cd00983  161 REKIGVMFGNP 171
recA PRK09519
intein-containing recombinase RecA;
2-187 1.29e-90

intein-containing recombinase RecA;


Pssm-ID: 77219 [Multi-domain]  Cd Length: 790  Bit Score: 280.83  E-value: 1.29e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422   2 FGKGSIMRLGDSKTMDIEAISTGSLSLDVALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEHALD 81
Cdd:PRK09519  22 YGKGSVMRLGDEARQPISVIPTGSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALD 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  82 PIYAAKLGVNVDDLLISQPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLTA 161
Cdd:PRK09519 102 PDYAKKLGVDTDSLLVSQPDTGEQALEIADMLIRSGALDIVVIDSVAALVPRAELEGEMGDSHVGLQARLMSQALRKMTG 181

                        170       180
                 ....*....|....*....|....*.
gi 340548422 162 NIKNANCLCIFINQIRMKIGVMFGSP 187
Cdd:PRK09519 182 ALNNSGTTAIFINQLRDKIGVMFGSP 207
RecA-like cd01393
RecA family; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 40-186 2.33e-46

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: 150.20  E-value: 2.33e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  40 GRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEHALDPIYA-----------AKLGVNVDDLLISQPDTGEQALE 108
Cdd:cd01393    1 GKITEIYGPPGSGKTQLALQLAANALLLGGGVVWIDTEGAFPPSRLvqileaspsseLELAEALSRLLYFRPPDTLAHLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422 109 ICDMLVRSNA----VDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQALRKLTANIKNANCLCIFINQIRMKIGVMF 184
Cdd:cd01393   81 ALDSLPESLFpppnTSLVVVDSVSALFRKAFPRGGDGDSSSSLRARLLSQLARALQKLAAQFNLAVVVTNQVTTKIRGGS 160


                 ..
gi 340548422 185 GS 186
Cdd:cd01393  161 GA 162
archRadB cd01394
archaeal RadB; The archaeal protein RadB shares similarity RadA, the archaeal functional ...
 21-181 9.47e-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: 77.35  E-value: 9.47e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  21 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEhALDP-----IYAAKLGVNVDDL 95
Cdd:cd01394    1 LSTGSKSLDSLLG-GGVERGTITQIYGPPGSGKTNICLQLAVEAAKQGKKVVYIDTE-GLSPerfqqIAGERFESIASNI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  96 LISQP-DTGEQALEICDM--LVRSNAVDVIIVDSVAALTpKAEiegEMGDShvGLQARLMSQaLRKLTANIKNANCLCIF 172
Cdd:cd01394   79 IVFEPySFDEQGVAIQEAekLLKSDKVDLVVVDSATALY-RLE---LGDDS--EANRELSRQ-MSKLLSIARKYDIPVVI 151


                 ....*....
gi 340548422 173 INQIRMKIG 181
Cdd:cd01394  152 TNQVYSDID 160
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
21-178 3.47e-15

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 70.71  E-value: 3.47e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  21 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEHALDPI--YAAKLGVNVDDLL-- 96
Cdd:COG0467    2 VPTGIPGLDELLG-GGLPRGSSTLLSGPPGTGKTTLALQFLAEGLRRGEKGLYVSFEESPEQLlrRAESLGLDLEEYIes 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  97 ----ISQPDTGEQALEICDML------VRSNAVDVIIVDSVAALtpkaeiEGEMGDShvglqaRLMSQALRKLTANIKNA 166
Cdd:COG0467   81 gllrIIDLSPEELGLDLEELLarlreaVEEFGAKRVVIDSLSGL------LLALPDP------ERLREFLHRLLRYLKKR 148

                        170
                 ....*....|..
gi 340548422 167 NCLCIFINQIRM 178
Cdd:COG0467  149 GVTTLLTSETGG 160
recomb_radB TIGR02237
DNA repair and recombination protein RadB; This family consists exclusively of archaeal RadB ...
 28-181 4.54e-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: 64.74  E-value: 4.54e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422   28 LDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEhALDP-----IYAAKLGVNVDDLLISQP-D 101
Cdd:TIGR02237   1 IDELLG-GGVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTE-GLSPerfkqIAEDRPERALSNFIVFEVfD 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  102 TGEQALEICDM--LVRSNAVDVIIVDSVAALTpKAEIEGEMGDSHVGLQARLmsQALRKLTANIKNAnclCIFINQIRMK 179
Cdd:TIGR02237  79 FDEQGVAIQKTskFIDRDSASLVVVDSFTALY-RLELSDDRISRNRELARQL--TLLLSLARKKNLA---VVITNQVYTD 152


                  ..
gi 340548422  180 IG 181
Cdd:TIGR02237 153 VN 154
COG4544 COG4544
Uncharacterized conserved protein [Function unknown];
20-134 9.65e-13

Uncharacterized conserved protein [Function unknown];


Pssm-ID: 443609 [Multi-domain]  Cd Length: 230  Bit Score: 64.18  E-value: 9.65e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  20 AISTGSLSLDVALGIGGLPCGRIVEIYGPE-SSGKTTLTLQVIAEAQKKGKTCAFVDAEHALdpiYA---AKLGVNVDDL 95
Cdd:COG4544   28 VLPTGFAALDAALPGGGLPRGALHEILGPApGIGELGLLLPLLARLAQAGGPVLWIAPPYDL---YApglAAAGLDPERL 104

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 340548422  96 LISQPDTGEQALEICDMLVRSNAVDVIIVDsVAALTPKA 134
Cdd:COG4544  105 LLVRARRPADALWAAEEALRSGACGAVVAW-LERLDLTA 142
radB PRK09361
DNA repair and recombination protein RadB; Provisional
 18-130 1.28e-11

DNA repair and recombination protein RadB; Provisional


Pssm-ID: 236482 [Multi-domain]  Cd Length: 225  Bit Score: 61.03  E-value: 1.28e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  18 IEAISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEhALDPIYAAKL-GVNVDDLL 96
Cdd:PRK09361   2 DERLPTGCKMLDELLG-GGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE-GLSPERFKQIaGEDFEELL 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 340548422  97 ----ISQP-DTGEQALEICDM--LVRSNaVDVIIVDSVAAL 130
Cdd:PRK09361  80 sniiIFEPsSFEEQSEAIRKAekLAKEN-VGLIVLDSATSL 119
radA PRK04301
DNA repair and recombination protein RadA; Validated
 16-187 2.95e-10

DNA repair and recombination protein RadA; Validated


Pssm-ID: 235273 [Multi-domain]  Cd Length: 317  Bit Score: 57.97  E-value: 2.95e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  16 MDIEAISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQK------KGKTCAFVDAE------------ 77
Cdd:PRK04301  79 KNVGKITTGSKELDELLG-GGIETQSITEFYGEFGSGKTQICHQLAVNVQLpeekggLEGKAVYIDTEgtfrperieqma 157

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  78 --------HALDPIYAAKlGVNVDD--LLIsqpdtgEQALEICDmlvRSNAVDVIIVDSVAALTpKAEiegemgdsHVGL 147
Cdd:PRK04301 158 ealgldpdEVLDNIHVAR-AYNSDHqmLLA------EKAEELIK---EGENIKLVIVDSLTAHF-RAE--------YVGR 218

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 340548422 148 ------QARLMSQ--ALRKLtANIKnaNCLCIFINQIRMKIGVMFGSP 187
Cdd:PRK04301 219 gnlaerQQKLNKHlhDLLRL-ADLY--NAAVVVTNQVMARPDAFFGDP 263
Rad51B cd19493
RAD51B recombinase; RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 29-181 1.63e-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: 55.02  E-value: 1.63e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  29 DVALGiGGLPCGRIVEIYGPESSGKT----TLTLQVIAEAQKKGKT--CAFVDAEHALDP-----IYAAKLGVN------ 91
Cdd:cd19493    1 DTALA-GGLPLGAITEITGASGSGKTqfalTLASSAAMPARKGGLDggVLYIDTESKFSAerlaeIAEARFPEAfsgfme 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  92 --------VDDLLISQPDTGEQALEICDML---VRSNAVDVIIVDSVAALTPKaeiegEMGDSHVGLQARlmSQALRKLT 160
Cdd:cd19493   80 eneraeemLKRVAVVRVTTLAQLLERLPNLeehILSSGVRLVVIDSIAALVRR-----EFGGSDGEVTER--HNALAREA 152

                        170       180
                 ....*....|....*....|....*
gi 340548422 161 ANIKN-ANCLCIFI---NQIRMKIG 181
Cdd:cd19493  153 SSLKRlAEEFRIAVlvtNQATTHFG 177
KaiC-like cd01124
Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. ...
 21-177 6.16e-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: 53.42  E-value: 6.16e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  21 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEHALDPIY--AAKLGVNVD----- 93
Cdd:cd01124    1 VKTGIPGLDELLG-GGIPKGSVTLLTGGPGTGKTLFGLQFLYAGAKNGEPGLFFTFEESPERLLrnAKSFGWDFDemede 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  94 -DLLISQPDTGEQALEICDML-------VRSNAVDVIIVDSVAALTPKAEiegemgdshvglQARLMSQALRKLTANIKN 165
Cdd:cd01124   80 gKLIIVDAPPTEAGRFSLDELlsrilsiIKSFKAKRVVIDSLSGLRRAKE------------DQMRARRIVIALLNELRA 147

                        170
                 ....*....|..
gi 340548422 166 ANCLCIFINQIR 177
Cdd:cd01124  148 AGVTTIFTSEMR 159
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 40-181 6.45e-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: 52.38  E-value: 6.45e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422    40 GRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEHALDPIYAAKLGVNVDDLLISqpDTGEQALEICDMLVRSNAV 119
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS--GSGELRLRLALALARKLKP 79

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 340548422   120 DVIIVDSVAALTPKaeiegemgdshVGLQARLMSQALRKLTANIKNANCLCIFINQIRMKIG 181
Cdd:smart00382  80 DVLILDEITSLLDA-----------EQEALLLLLEELRLLLLLKSEKNLTVILTTNDEKDLG 130
Rad51 pfam08423
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ...
 21-130 8.66e-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: 53.46  E-value: 8.66e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422   21 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTL--TLQVIAEAQK-----KGKtCAFVDAEHALDPI----YAAKLG 89
Cdd:pfam08423  19 ITTGSKELDKLLG-GGIETGSITEIFGEFRTGKTQLchTLCVTCQLPLemgggEGK-ALYIDTEGTFRPErlvaIAERYG 96

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 340548422   90 VNVDDLLISQP-------DTGEQALEICDMLVRSNAVDVIIVDSVAAL 130
Cdd:pfam08423  97 LDPEDVLDNVAyaraynsEHQMQLLQQAAAMMSESRFALLIVDSATAL 144
ATPase pfam06745
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ...
 21-178 1.87e-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: 52.25  E-value: 1.87e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422   21 ISTGSLSLDvALGIGGLPCGRIVEIYGPESSGKTTLTLQVIAE-AQKKGKTCAFVDA-EHALDPIYAAK-LGVNVDDLL- 96
Cdd:pfam06745   1 VKTGIPGLD-EILKGGFPEGRVVLITGGPGTGKTIFGLQFLYNgALKYGEPGVFVTLeEPPEDLRENARsFGWDLEKLEe 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422   97 --------ISQPDTGEQALEICDML----------VRSNAVDVIIVDSVAALtpkAEIEGEMgdshvglQARlmsQALRK 158
Cdd:pfam06745  80 egklaiidASTSGIGIAEVEDRFDLeelierlreaIREIGAKRVVIDSITTL---FYLLKPA-------VAR---EILRR 146

                         170       180
                  ....*....|....*....|
gi 340548422  159 LTANIKNANCLCIFINQIRM 178
Cdd:pfam06745 147 LKRVLKGLGVTAIFTSEKPS 166
DMC1 cd19514
homologous-pairing protein DMC1; DMC1 has a central role in homologous recombination in ...
 21-130 3.24e-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: 51.59  E-value: 3.24e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  21 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTL--TLQVIAEAQKK-----GKTCaFVDAEHALDP----IYAAKLG 89
Cdd:cd19514    1 ISTGSTELDKLLG-GGIESMSITEVFGEFRTGKTQLshTLCVTAQLPGSmggggGKVA-YIDTEGTFRPdrirPIAERFG 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 340548422  90 VN----VDDLLISQPDTGEQALEICDMLVRSNAVD----VIIVDSVAAL 130
Cdd:cd19514   79 VDhdavLDNILYARAYTSEHQMELLDYVAAKFHEEavfrLLIIDSIMAL 127
RadA_SMS_N cd01121
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a ...
 8-127 6.43e-08

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: 50.99  E-value: 6.43e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422   8 MRLGDSKTMDIEAISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEHALDPI--YA 85
Cdd:cd01121   51 LPLSDVEAEEEERISTGIGELDRVLG-GGLVPGSVVLIGGDPGIGKSTLLLQVAARLAQRGGKVLYVSGEESLSQIklRA 129

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 340548422  86 AKLGVNVDDLLIsqpdTGEQALE-ICDMLVRSNAvDVIIVDSV 127
Cdd:cd01121  130 ERLGLGSDNLYL----LAETNLEaILAEIEELKP-SLVVIDSI 167
archRadA cd19515
archaeal recombinase Rad51/RadA; This group includes the archaeal protein RadA which is a ...
 21-187 6.96e-08

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: 50.44  E-value: 6.96e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  21 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKK------GKTCAFVDAEHALDP----IYAAKLGV 90
Cdd:cd19515    1 ISTGSKELDKLLG-GGIETQAITEVFGEFGSGKTQLCHQLAVNVQLPpeegglNGKAVYIDTENTFRPerimQMAKALGL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  91 NVDDLL-----ISQPDTGEQAL---EICDMLVRSNAVDVIIVDSVAALTpKAEI--EGEMGDSHVGLqARLMSQALRklT 160
Cdd:cd19515   80 DPDEVLdniyvARAYNSNHQMLlveKAEDLIKEGNNIKLLIVDSLTSHF-RAEYvgRGTLAERQQKL-NKHLHDLHR--L 155

                        170       180
                 ....*....|....*....|....*...
gi 340548422 161 ANIKNAnclCIFI-NQIRMKIGVMFGSP 187
Cdd:cd19515  156 ADLYNI---AVLVtNQVMAKPDAFFGDP 180
PLN03186 PLN03186
DNA repair protein RAD51 homolog; Provisional
 17-160 1.54e-07

DNA repair protein RAD51 homolog; Provisional


Pssm-ID: 178728 [Multi-domain]  Cd Length: 342  Bit Score: 50.12  E-value: 1.54e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  17 DIEAISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTL--TLQV-----IAEAQKKGKtCAFVDAEHALDP----IYA 85
Cdd:PLN03186 101 EIIQITTGSRELDKILE-GGIETGSITEIYGEFRTGKTQLchTLCVtcqlpLDQGGGEGK-AMYIDTEGTFRPqrliQIA 178

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  86 AKLGVNVDDLL-----ISQPDTGEQA---LEICDMLVRSNaVDVIIVDSVAALTpKAEIEGEmGDshvgLQAR--LMSQA 155
Cdd:PLN03186 179 ERFGLNGADVLenvayARAYNTDHQSellLEAASMMAETR-FALMIVDSATALY-RTEFSGR-GE----LSARqmHLGKF 251


                 ....*
gi 340548422 156 LRKLT 160
Cdd:PLN03186 252 LRSLQ 256
XRCC3 cd19491
XRCC3 recombinase; XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells ...
 28-176 2.31e-07

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


Pssm-ID: 410899 [Multi-domain]  Cd Length: 250  Bit Score: 49.21  E-value: 2.31e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  28 LDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQ------KKGKTCAFVDAEHAL----------------DPIYA 85
Cdd:cd19491    1 LDELLG-GGIPVGGITEIAGESGAGKTQLCLQLALTVQlprelgGLGGGAVYICTESSFpskrlqqlasslpkryHLEKA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  86 AKLGVNVddLLISQPDTgeQALEICDM-----LVRSNAVDVIIVDSVAALtpkAEIEGEMGDSHVGLQARLMSQALRKLT 160
Cdd:cd19491   80 KNFLDNI--FVEHVADL--ETLEHCLNyqlpaLLERGPIRLVVIDSIAAL---FRSEFDTSRSDLVERAKYLRRLADHLK 152

                        170
                 ....*....|....*.
gi 340548422 161 ANIKNANCLCIFINQI 176
Cdd:cd19491  153 RLADKYNLAVVVVNQV 168
Rad51_DMC1_archRadA cd01123
recombinase Rad51, DMC1, and archaeal RadA; This group of recombinases includes the eukaryotic ...
 21-130 2.53e-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: 49.07  E-value: 2.53e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  21 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTL--TLQV-----IAEAQKKGKtCAFVDAEHALDPI----YAAKLG 89
Cdd:cd01123    1 ITTGSKELDKLLG-GGIETGSITEMFGEFRTGKTQLchTLAVtcqlpIDRGGGEGK-AIYIDTEGTFRPErlraIAQRFG 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 340548422  90 VNVDDLL----ISQPDTGEQALEICD----MLVRSnAVDVIIVDSVAAL 130
Cdd:cd01123   79 LDPDDVLdnvaYARAFNSDHQTQLLDqaaaMMVES-RFKLLIVDSATAL 126
KaiC-like_N cd19488
N-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 21-113 7.93e-07

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: 47.34  E-value: 7.93e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  21 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEHALDPIY--AAKLGVNVDDLLI- 97
Cdd:cd19488    1 ISTGIPGLDDILR-GGLPPRRLYLVEGAPGTGKTTLALQFLLEGAANGETGLYITLSETEQELRavALSHGWSLDGIHIf 79

                         90
                 ....*....|....*...
gi 340548422  98 --SQPDTGEQALEICDML 113
Cdd:cd19488   80 elSPSESALDAAQQYTIL 97
FlaH COG2874
Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];
21-131 2.84e-06

Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];


Pssm-ID: 442121  Cd Length: 230  Bit Score: 45.98  E-value: 2.84e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  21 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEHA----LDPIYAakLGVNVDDLL 96
Cdd:COG2874    3 ISTGNDELDKRLG-GGIPLGSLVLIEGENGTGKSVLSQQFAYGALENGLSVTYISTELTtkefIKQMKS--LSYDISDYL 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 340548422  97 IS--------QPDTGE----QALEICDMLVRSNA-----VDVIIVDSVAALT 131
Cdd:COG2874   80 LRgrllflpvHPLGFEwnskQRKDLLKRLMKYIAsnlweADVIIIDSLSALL 131
Rad51 cd19513
RAD51D recombinase; RAD51 recombinase plays an essential role in DNA repair by homologous ...
 21-130 1.50e-05

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: 43.85  E-value: 1.50e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  21 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTL--TLQV-----IAEAQKKGKtCAFVDAEHALDP----IYAAKLG 89
Cdd:cd19513    1 ITTGSKELDKLLG-GGIETGSITELFGEFRTGKTQLchTLAVtcqlpIDQGGGEGK-ALYIDTEGTFRPerllAIAERYG 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 340548422  90 VNVDDLL-----ISQPDTGEQA---LEICDMLVRSNaVDVIIVDSVAAL 130
Cdd:cd19513   79 LNGEDVLdnvayARAYNTDHQMqllIQASAMMAESR-YALLIVDSATAL 126
recomb_DMC1 TIGR02238
meiotic recombinase Dmc1; This model describes DMC1, a subfamily of a larger family of DNA ...
 21-130 2.61e-05

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


Pssm-ID: 131292 [Multi-domain]  Cd Length: 313  Bit Score: 43.61  E-value: 2.61e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422   21 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTL--TLQVIAEAQKKGK----TCAFVDAEHALDP----IYAAKLGV 90
Cdd:TIGR02238  78 ITTGSQALDGILG-GGIESMSITEVFGEFRCGKTQLshTLCVTAQLPREMGggngKVAYIDTEGTFRPdrirAIAERFGV 156

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 340548422   91 N----VDDLLISQPDTGEQALEICDMLVRSNAVD---VIIVDSVAAL 130
Cdd:TIGR02238 157 DpdavLDNILYARAYTSEHQMELLDYLAAKFSEEpfrLLIVDSIMAL 203
PRK06067 PRK06067
flagellar accessory protein FlaH; Validated
 17-137 3.13e-05

flagellar accessory protein FlaH; Validated


Pssm-ID: 180381  Cd Length: 234  Bit Score: 43.04  E-value: 3.13e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  17 DIEAISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEHALDPiYAAK---LGVNVD 93
Cdd:PRK06067   3 KKEIISTGNEELDRKLG-GGIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITTENTSKS-YLKQmesVKIDIS 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 340548422  94 DLLIS---------------QPDTGEQALEICDMLVRSNAVDVIIVDSVAALTPKAEIE 137
Cdd:PRK06067  81 DFFLWgylrifplntegfewNSTLANKLLELIIEFIKSKREDVIIIDSLTIFATYAEED 139
PTZ00035 PTZ00035
Rad51 protein; Provisional
 21-130 4.02e-05

Rad51 protein; Provisional


Pssm-ID: 185407 [Multi-domain]  Cd Length: 337  Bit Score: 43.06  E-value: 4.02e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  21 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTL--TLQVIAE-----AQKKGKtCAFVDAEHALDP-----IyAAKL 88
Cdd:PTZ00035 100 ITTGSTQLDKLLG-GGIETGSITELFGEFRTGKTQLchTLCVTCQlpieqGGGEGK-VLYIDTEGTFRPerivqI-AERF 176

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 340548422  89 GVN----VDDLLISQPDTGEQALE----ICDMLVRSNAVdVIIVDSVAAL 130
Cdd:PTZ00035 177 GLDpedvLDNIAYARAYNHEHQMQllsqAAAKMAEERFA-LLIVDSATAL 225
recomb_RAD51 TIGR02239
DNA repair protein RAD51; This eukaryotic sequence family consists of RAD51, a protein ...
 17-130 6.15e-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: 42.40  E-value: 6.15e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422   17 DIEAISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTL--TLQV-----IAEAQKKGKtCAFVDAEHALDPI----YA 85
Cdd:TIGR02239  74 EVIQLTTGSKELDKLLG-GGIETGSITEIFGEFRTGKTQLchTLAVtcqlpIDQGGGEGK-ALYIDTEGTFRPErllaIA 151

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 340548422   86 AKLGVNVDDLLIS-------QPDTGEQALEICDMLVRSNAVDVIIVDSVAAL 130
Cdd:TIGR02239 152 ERYGLNPEDVLDNvayarayNTDHQLQLLQQAAAMMSESRFALLIVDSATAL 203
Rad51D cd19489
RAD51D recombinase; RAD51D recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 35-64 9.00e-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: 41.47  E-value: 9.00e-05
                         10        20        30
                 ....*....|....*....|....*....|
gi 340548422  35 GGLPCGRIVEIYGPESSGKTTLTLQVIAEA 64
Cdd:cd19489    2 GGLRTGEITELVGESSSGKTQLCLTAAANV 31
XRCC2 cd19490
XRCC2 recombinase; XRCC2 (X-ray repair complementing defective repair in Chinese hamster cells ...
 40-181 1.72e-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: 40.79  E-value: 1.72e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  40 GRIVEIYGPESSGKTTLTLQVIA---------EAQKKGKTCA--FVDAEHALDP-----IYAAKLGVNVDDLLISQPDTG 103
Cdd:cd19490    1 GDVIEITGPSGSGKTELLYHLAArcilpsswgGVPLGGLEAAvvFIDTDGRFDIlrlrsILEARIRAAIQAANSSDDEED 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422 104 -EQALEIC-----------------------DMLVRSNA---VDVIIVDSVAALTPKAEIEGEMGDSHVGLQARLMSQAL 156
Cdd:cd19490   81 vEEIAREClqrlhifrchsslqllatllsleNYLLSLSAnpeLGLLLIDSISAFYWQDRFSAELARAAPLLQEAALRAIL 160

                        170       180
                 ....*....|....*....|....*
gi 340548422 157 RKLTANIKNANCLCIFINQIRMKIG 181
Cdd:cd19490  161 RELRRLRRRFQLVVIATKQALFPGK 185
ATPase_2 pfam01637
ATPase domain predominantly from Archaea; This family contain a conserved P-loop motif that is ...
 42-76 3.50e-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: 40.00  E-value: 3.50e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 340548422   42 IVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDA 76
Cdd:pfam01637  22 IYVIYGPEGCGKTALLRESIENLLDLGYYVIYYDP 56
PLN03187 PLN03187
meiotic recombination protein DMC1 homolog; Provisional
 17-130 7.44e-04

meiotic recombination protein DMC1 homolog; Provisional


Pssm-ID: 215620 [Multi-domain]  Cd Length: 344  Bit Score: 39.38  E-value: 7.44e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  17 DIEAISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTL--TLQVIAE-AQKKGKTC---AFVDAEHALDP----IYAA 86
Cdd:PLN03187 104 SVVRITTGSQALDELLG-GGIETRCITEAFGEFRSGKTQLahTLCVTTQlPTEMGGGNgkvAYIDTEGTFRPdrivPIAE 182

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 340548422  87 KLGVN----VDDLLISQPDTGEQ---ALEICDMLVRSNAVDVIIVDSVAAL 130
Cdd:PLN03187 183 RFGMDadavLDNIIYARAYTYEHqynLLLGLAAKMAEEPFRLLIVDSVIAL 233
KaiC-like_C cd19487
C-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 21-72 1.83e-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: 37.66  E-value: 1.83e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 340548422  21 ISTGSLSLDVALGiGGLPCGRIVEIYGPESSGKTTLTLQVIAEAQKKGKTCA 72
Cdd:cd19487    1 VSSGVPELDELLG-GGLERGTSTLLIGPAGVGKSTLALQFAKAAAARGERSV 51
AAA_24 pfam13479
AAA domain; This AAA domain is found in a wide variety of presumed phage proteins.
 41-127 2.11e-03

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


Pssm-ID: 433243  Cd Length: 199  Bit Score: 37.31  E-value: 2.11e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422   41 RIVeIYGPESSGKTTLtlqvIAEAQKKgktcAFVDAEHALDPIYAAKLGVnvddllISQPDTGEQALEICDMLVRSNAV- 119
Cdd:pfam13479   4 KIL-IYGPSGIGKTTF----AKTLPKP----LFLDTEKGSKALDGDRFPD------IVIRDSWQDFLDAIDELTAAELAd 68


                  ....*....
gi 340548422  120 -DVIIVDSV 127
Cdd:pfam13479  69 yKTIVIDTV 77
RepA COG3598
RecA-family ATPase [Replication, recombination and repair];
37-159 2.41e-03

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


Pssm-ID: 442817 [Multi-domain]  Cd Length: 313  Bit Score: 37.57  E-value: 2.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422  37 LPCGRIVEIYGPESSGKTTLTLQV---IAEAQK------KGKTCAFVDAEHALDPI------YAAKLGVNVDDL-----L 96
Cdd:COG3598   10 LPEGGVTLLAGPPGTGKSFLALQLaaaVAAGGPwlgrrvPPGKVLYLAAEDDRGELrrrlkaLGADLGLPFADLdgrlrL 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 340548422  97 IS-----QPDTGEQALEicdMLVRSNAVDVIIVDSVAALTPkaeiegemGDSHVGLQARLMSQALRKL 159
Cdd:COG3598   90 LSlagdlDDTDDLEALE---RAIEEEGPDLVVIDPLARVFG--------GDENDAEEMRAFLNPLDRL 146
Grc3 COG1341
Polynucleotide 5'-kinase, involved in rRNA processing [Translation, ribosomal structure and ...
 34-76 2.80e-03

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


Pssm-ID: 440952  Cd Length: 353  Bit Score: 37.69  E-value: 2.80e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 340548422  34 IGGLPCGRIVeIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDA 76
Cdd:COG1341   30 ILSSGPGRIM-VLGPVDSGKSTLTTLLANKLLAEGLKVAIIDA 71
PRK10851 PRK10851
sulfate/thiosulfate ABC transporter ATP-binding protein CysA;
29-71 3.13e-03

sulfate/thiosulfate ABC transporter ATP-binding protein CysA;


Pssm-ID: 182778 [Multi-domain]  Cd Length: 353  Bit Score: 37.37  E-value: 3.13e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 340548422  29 DVALGIgglPCGRIVEIYGPESSGKTTLtLQVIA--EAQKKGKTC 71
Cdd:PRK10851  20 DISLDI---PSGQMVALLGPSGSGKTTL-LRIIAglEHQTSGHIR 60
AAA_22 pfam13401
AAA domain;
41-134 4.79e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 35.78  E-value: 4.79e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340548422   41 RIVEIYGPESSGKTTLTLQVIAEAQKKGKTCAFVDAEHALDPI-YAAKLGVNVDDLLISQPDTGEQALEICDMLVRSNAV 119
Cdd:pfam13401   6 GILVLTGESGTGKTTLLRRLLEQLPEVRDSVVFVDLPSGTSPKdLLRALLRALGLPLSGRLSKEELLAALQQLLLALAVA 85

                          90
                  ....*....|....*
gi 340548422  120 DVIIVDSVAALTPKA 134
Cdd:pfam13401  86 VVLIIDEAQHLSLEA 100
NadR3 COG3172
Nicotinamide riboside kinase [Coenzyme transport and metabolism]; Nicotinamide riboside kinase ...
 41-59 4.92e-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: 4.92e-03
                         10
                 ....*....|....*....
gi 340548422  41 RIVeIYGPESSGKTTLTLQ 59
Cdd:COG3172   10 KIV-LLGAESTGKTTLARA 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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