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Conserved domains on  [gi|193090241|gb|ACF15292|]
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recombination protein A, partial [Rhizobium sp. CCBAU 65810]

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
 1-166 2.42e-126

recombinase A; Provisional


The actual alignment was detected with superfamily member PRK09354:

Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 358.34  E-value: 2.42e-126
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241   1 SVMKLGSnDSIVEIETVSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVY 80
Cdd:PRK09354  26 SIMRLGD-DAAMDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVY 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  81 ARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGDMGDSLPGLQARLFSQALRKLTASIS 160
Cdd:PRK09354 105 AKKLGVDIDNLLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGNIS 184


                 ....*.
gi 193090241 161 KSKTMV 166
Cdd:PRK09354 185 KSNTTV 190
 
Name Accession Description Interval E-value
recA PRK09354
recombinase A; Provisional
 1-166 2.42e-126

recombinase A; Provisional


Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 358.34  E-value: 2.42e-126
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241   1 SVMKLGSnDSIVEIETVSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVY 80
Cdd:PRK09354  26 SIMRLGD-DAAMDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVY 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  81 ARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGDMGDSLPGLQARLFSQALRKLTASIS 160
Cdd:PRK09354 105 AKKLGVDIDNLLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGNIS 184


                 ....*.
gi 193090241 161 KSKTMV 166
Cdd:PRK09354 185 KSNTTV 190
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
1-166 3.02e-121

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 345.23  E-value: 3.02e-121
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241   1 SVMKLGSnDSIVEIETVSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVY 80
Cdd:COG0468   29 SIMRLGD-KARQDVEVISTGSLALDIALGVGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGIAAFIDAEHALDPEY 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  81 ARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGDMGDSLPGLQARLFSQALRKLTASIS 160
Cdd:COG0468  108 AKKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGAIS 187


                 ....*.
gi 193090241 161 KSKTMV 166
Cdd:COG0468  188 KSNTTV 193
RecA pfam00154
recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA ...
 1-166 2.97e-113

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: 322.04  E-value: 2.97e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241    1 SVMKLGSNDsIVEIETVSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVY 80
Cdd:pfam00154  18 SIMKLGDEK-KLDVETISTGSLALDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVY 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241   81 ARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGDMGDSLPGLQARLFSQALRKLTASIS 160
Cdd:pfam00154  97 AKKLGVDIDNLLVSQPDTGEQALEIADMLVRSGAIDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGSIS 176


                  ....*.
gi 193090241  161 KSKTMV 166
Cdd:pfam00154 177 KSNTTV 182
tigrfam_recA TIGR02012
protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization ...
 1-166 6.12e-111

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: 318.16  E-value: 6.12e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241    1 SVMKLGsNDSIVEIETVSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVY 80
Cdd:TIGR02012  21 SIMRLG-EKTVMDVETISTGSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVY 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241   81 ARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGDMGDSLPGLQARLFSQALRKLTASIS 160
Cdd:TIGR02012 100 ARKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVDIIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGALS 179


                  ....*.
gi 193090241  161 KSKTMV 166
Cdd:TIGR02012 180 KSNTTA 185
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 13-166 9.27e-108

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: 306.79  E-value: 9.27e-108
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  13 EIETVSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLL 92
Cdd:cd00983    1 DVEVIPTGSLSLDIALGIGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKLGGTAAFIDAEHALDPEYAKKLGVDIDNLL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 193090241  93 ISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGDMGDSLPGLQARLFSQALRKLTASISKSKTMV 166
Cdd:cd00983   81 VSQPDTGEQALEIADTLIRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGSLSKSKTTV 154
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 35-130 7.34e-09

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


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 51.61  E-value: 7.34e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241    35 KGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISqpDTGEQALEITDTLVRSGA 114
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS--GSGELRLRLALALARKLK 78

                           90
                   ....*....|....*.
gi 193090241   115 VDVLVVDSVAALTPRA 130
Cdd:smart00382  79 PDVLILDEITSLLDAE 94
 
Name Accession Description Interval E-value
recA PRK09354
recombinase A; Provisional
 1-166 2.42e-126

recombinase A; Provisional


Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 358.34  E-value: 2.42e-126
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241   1 SVMKLGSnDSIVEIETVSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVY 80
Cdd:PRK09354  26 SIMRLGD-DAAMDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVY 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  81 ARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGDMGDSLPGLQARLFSQALRKLTASIS 160
Cdd:PRK09354 105 AKKLGVDIDNLLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGNIS 184


                 ....*.
gi 193090241 161 KSKTMV 166
Cdd:PRK09354 185 KSNTTV 190
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
1-166 3.02e-121

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 345.23  E-value: 3.02e-121
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241   1 SVMKLGSnDSIVEIETVSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVY 80
Cdd:COG0468   29 SIMRLGD-KARQDVEVISTGSLALDIALGVGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGIAAFIDAEHALDPEY 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  81 ARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGDMGDSLPGLQARLFSQALRKLTASIS 160
Cdd:COG0468  108 AKKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGAIS 187


                 ....*.
gi 193090241 161 KSKTMV 166
Cdd:COG0468  188 KSNTTV 193
RecA pfam00154
recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA ...
 1-166 2.97e-113

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: 322.04  E-value: 2.97e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241    1 SVMKLGSNDsIVEIETVSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVY 80
Cdd:pfam00154  18 SIMKLGDEK-KLDVETISTGSLALDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVY 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241   81 ARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGDMGDSLPGLQARLFSQALRKLTASIS 160
Cdd:pfam00154  97 AKKLGVDIDNLLVSQPDTGEQALEIADMLVRSGAIDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGSIS 176


                  ....*.
gi 193090241  161 KSKTMV 166
Cdd:pfam00154 177 KSNTTV 182
tigrfam_recA TIGR02012
protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization ...
 1-166 6.12e-111

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: 318.16  E-value: 6.12e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241    1 SVMKLGsNDSIVEIETVSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVY 80
Cdd:TIGR02012  21 SIMRLG-EKTVMDVETISTGSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVY 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241   81 ARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGDMGDSLPGLQARLFSQALRKLTASIS 160
Cdd:TIGR02012 100 ARKLGVDIDNLLVSQPDTGEQALEIAETLVRSGAVDIIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGALS 179


                  ....*.
gi 193090241  161 KSKTMV 166
Cdd:TIGR02012 180 KSNTTA 185
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 13-166 9.27e-108

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: 306.79  E-value: 9.27e-108
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  13 EIETVSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLL 92
Cdd:cd00983    1 DVEVIPTGSLSLDIALGIGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKLGGTAAFIDAEHALDPEYAKKLGVDIDNLL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 193090241  93 ISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGDMGDSLPGLQARLFSQALRKLTASISKSKTMV 166
Cdd:cd00983   81 VSQPDTGEQALEIADTLIRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGSLSKSKTTV 154
recA PRK09519
intein-containing recombinase RecA;
1-164 7.11e-74

intein-containing recombinase RecA;


Pssm-ID: 77219 [Multi-domain]  Cd Length: 790  Bit Score: 235.76  E-value: 7.11e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241   1 SVMKLGsNDSIVEIETVSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVY 80
Cdd:PRK09519  26 SVMRLG-DEARQPISVIPTGSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDY 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  81 ARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIEGDMGDSLPGLQARLFSQALRKLTASIS 160
Cdd:PRK09519 105 AKKLGVDTDSLLVSQPDTGEQALEIADMLIRSGALDIVVIDSVAALVPRAELEGEMGDSHVGLQARLMSQALRKMTGALN 184


                 ....
gi 193090241 161 KSKT 164
Cdd:PRK09519 185 NSGT 188
RecA-like cd01393
RecA family; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 36-156 9.14e-35

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: 120.15  E-value: 9.14e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  36 GRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYAR-----------KLGVDLQNLLISQPDTGEQALE 104
Cdd:cd01393    1 GKITEIYGPPGSGKTQLALQLAANALLLGGGVVWIDTEGAFPPSRLVqileaspsselELAEALSRLLYFRPPDTLAHLL 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 193090241 105 ITDTLVRSGA----VDVLVVDSVAALTPRAEIEGDMGDSLPGLQARLFSQALRKLT 156
Cdd:cd01393   81 ALDSLPESLFpppnTSLVVVDSVSALFRKAFPRGGDGDSSSSLRARLLSQLARALQ 136
archRadB cd01394
archaeal RadB; The archaeal protein RadB shares similarity RadA, the archaeal functional ...
 17-135 3.37e-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: 77.74  E-value: 3.37e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  17 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEhALDP-----VYARKLGVDLQNL 91
Cdd:cd01394    1 LSTGSKSLDSLLG-GGVERGTITQIYGPPGSGKTNICLQLAVEAAKQGKKVVYIDTE-GLSPerfqqIAGERFESIASNI 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 193090241  92 LISQP-DTGEQALEITDT--LVRSGAVDVLVVDSVAALTpRAEIEGD 135
Cdd:cd01394   79 IVFEPySFDEQGVAIQEAekLLKSDKVDLVVVDSATALY-RLELGDD 124
recomb_radB TIGR02237
DNA repair and recombination protein RadB; This family consists exclusively of archaeal RadB ...
 24-148 1.45e-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: 65.52  E-value: 1.45e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241   24 LDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEhALDPVYARKLGVD-----LQNLLISQP-- 96
Cdd:TIGR02237   1 IDELLG-GGVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTE-GLSPERFKQIAEDrperaLSNFIVFEVfd 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 193090241   97 -DTGEQALEITDTLVRSGAVDVLVVDSVAALTpRAEIEGDMGDSLPGLQARLF 148
Cdd:TIGR02237  79 fDEQGVAIQKTSKFIDRDSASLVVVDSFTALY-RLELSDDRISRNRELARQLT 130
COG4544 COG4544
Uncharacterized conserved protein [Function unknown];
16-130 1.72e-13

Uncharacterized conserved protein [Function unknown];


Pssm-ID: 443609 [Multi-domain]  Cd Length: 230  Bit Score: 65.34  E-value: 1.72e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  16 TVSTGSLSLDIALGIGGLPKGRIIEIYGPE-SSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLIS 94
Cdd:COG4544   28 VLPTGFAALDAALPGGGLPRGALHEILGPApGIGELGLLLPLLARLAQAGGPVLWIAPPYDLYAPGLAAAGLDPERLLLV 107

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 193090241  95 QPDTGEQALEITDTLVRSGAVDVLVVDsVAALTPRA 130
Cdd:COG4544  108 RARRPADALWAAEEALRSGACGAVVAW-LERLDLTA 142
radB PRK09361
DNA repair and recombination protein RadB; Provisional
 13-135 1.83e-13

DNA repair and recombination protein RadB; Provisional


Pssm-ID: 236482 [Multi-domain]  Cd Length: 225  Bit Score: 65.27  E-value: 1.83e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  13 EIETVSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEhALDPVYARKLGVD----- 87
Cdd:PRK09361   1 MDERLPTGCKMLDELLG-GGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE-GLSPERFKQIAGEdfeel 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 193090241  88 LQNLLISQP-DTGEQALEITDT--LVRSGaVDVLVVDSVAALTpRAEIEGD 135
Cdd:PRK09361  79 LSNIIIFEPsSFEEQSEAIRKAekLAKEN-VGLIVLDSATSLY-RLELEDE 127
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
17-126 1.07e-12

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 63.40  E-value: 1.07e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  17 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPV--YARKLGVDLQ----- 89
Cdd:COG0467    2 VPTGIPGLDELLG-GGLPRGSSTLLSGPPGTGKTTLALQFLAEGLRRGEKGLYVSFEESPEQLlrRAESLGLDLEeyies 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 193090241  90 -NLLISQPDTGEQALEITDTL------VRSGAVDVLVVDSVAAL 126
Cdd:COG0467   81 gLLRIIDLSPEELGLDLEELLarlreaVEEFGAKRVVIDSLSGL 124
KaiC-like cd01124
Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. ...
 17-126 1.08e-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: 54.96  E-value: 1.08e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  17 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVY--ARKLGVDL-----Q 89
Cdd:cd01124    1 VKTGIPGLDELLG-GGIPKGSVTLLTGGPGTGKTLFGLQFLYAGAKNGEPGLFFTFEESPERLLrnAKSFGWDFdemedE 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 193090241  90 NLLI--SQPDTGEQALEITDTL------VRSGAVDVLVVDSVAAL 126
Cdd:cd01124   80 GKLIivDAPPTEAGRFSLDELLsrilsiIKSFKAKRVVIDSLSGL 124
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 35-130 7.34e-09

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


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 51.61  E-value: 7.34e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241    35 KGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISqpDTGEQALEITDTLVRSGA 114
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS--GSGELRLRLALALARKLK 78

                           90
                   ....*....|....*.
gi 193090241   115 VDVLVVDSVAALTPRA 130
Cdd:smart00382  79 PDVLILDEITSLLDAE 94
Rad51 pfam08423
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ...
 13-134 1.78e-08

Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ATPase RecA protein.


Pssm-ID: 462471 [Multi-domain]  Cd Length: 255  Bit Score: 51.92  E-value: 1.78e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241   13 EIETVSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQ---KKGGI---CAFVDAEHALDPV----YAR 82
Cdd:pfam08423  15 ELIQITTGSKELDKLLG-GGIETGSITEIFGEFRTGKTQLCHTLCVTCQlplEMGGGegkALYIDTEGTFRPErlvaIAE 93

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 193090241   83 KLGVDLQNLLISQP-------DTGEQALEITDTLVRSGAVDVLVVDSVAALTpRAEIEG 134
Cdd:pfam08423  94 RYGLDPEDVLDNVAyaraynsEHQMQLLQQAAAMMSESRFALLIVDSATALY-RTDFSG 151
Rad51B cd19493
RAD51B recombinase; RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 25-138 1.99e-08

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: 51.55  E-value: 1.99e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  25 DIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEA---QKKGG---ICAFVDAEHAL------------DPVYARK--- 83
Cdd:cd19493    1 DTALA-GGLPLGAITEITGASGSGKTQFALTLASSAampARKGGldgGVLYIDTESKFsaerlaeiaearFPEAFSGfme 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 193090241  84 ----LGVDLQNLLISQPDTGEQALEITDTL---VRSGAVDVLVVDSVAALTpRAEIEGDMGD 138
Cdd:cd19493   80 enerAEEMLKRVAVVRVTTLAQLLERLPNLeehILSSGVRLVVIDSIAALV-RREFGGSDGE 140
ATPase pfam06745
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ...
 17-127 3.29e-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: 51.09  E-value: 3.29e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241   17 VSTGSLSLDiALGIGGLPKGRIIEIYGPESSGKTTLALQ-TIAEAQKKGGICAFVDA-EHALDPVY-ARKLGVDLQNLL- 92
Cdd:pfam06745   1 VKTGIPGLD-EILKGGFPEGRVVLITGGPGTGKTIFGLQfLYNGALKYGEPGVFVTLeEPPEDLREnARSFGWDLEKLEe 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 193090241   93 --------ISQPDTGEQALEITDTL----------VRSGAVDVLVVDSVAALT 127
Cdd:pfam06745  80 egklaiidASTSGIGIAEVEDRFDLeelierlreaIREIGAKRVVIDSITTLF 132
DMC1 cd19514
homologous-pairing protein DMC1; DMC1 has a central role in homologous recombination in ...
 17-126 4.24e-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: 50.82  E-value: 4.24e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  17 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQ------KKGGICAFVDAEHALDP----VYARKLGV 86
Cdd:cd19514    1 ISTGSTELDKLLG-GGIESMSITEVFGEFRTGKTQLSHTLCVTAQlpgsmgGGGGKVAYIDTEGTFRPdrirPIAERFGV 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 193090241  87 D----LQNLLISQPDTGEQALEITDTL----VRSGAVDVLVVDSVAAL 126
Cdd:cd19514   80 DhdavLDNILYARAYTSEHQMELLDYVaakfHEEAVFRLLIIDSIMAL 127
Rad51_DMC1_archRadA cd01123
recombinase Rad51, DMC1, and archaeal RadA; This group of recombinases includes the eukaryotic ...
 17-126 1.93e-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: 1.93e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  17 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKT----TLAL--QTIAEAQKKGGICAFVDAEHALDPV----YARKLGV 86
Cdd:cd01123    1 ITTGSKELDKLLG-GGIETGSITEMFGEFRTGKTqlchTLAVtcQLPIDRGGGEGKAIYIDTEGTFRPErlraIAQRFGL 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 193090241  87 D----LQNLLISQPDTGEQALEITD---TLVRSGAVDVLVVDSVAAL 126
Cdd:cd01123   80 DpddvLDNVAYARAFNSDHQTQLLDqaaAMMVESRFKLLIVDSATAL 126
radA PRK04301
DNA repair and recombination protein RadA; Validated
 13-134 8.03e-07

DNA repair and recombination protein RadA; Validated


Pssm-ID: 235273 [Multi-domain]  Cd Length: 317  Bit Score: 47.56  E-value: 8.03e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  13 EIETVSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQ---KKGGI---CAFVDAE------------- 73
Cdd:PRK04301  80 NVGKITTGSKELDELLG-GGIETQSITEFYGEFGSGKTQICHQLAVNVQlpeEKGGLegkAVYIDTEgtfrperieqmae 158

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  74 -HALDP-------VYARKLGVDLQNLLIsqpdtgEQALEitdtLVRSG-AVDVLVVDSVAALTpRAEIEG 134
Cdd:PRK04301 159 aLGLDPdevldniHVARAYNSDHQMLLA------EKAEE----LIKEGeNIKLVIVDSLTAHF-RAEYVG 217
KaiC-like_N cd19488
N-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 17-153 9.07e-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: 46.96  E-value: 9.07e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  17 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFV---DAEHALDPVyARKLGVDLQNLLI 93
Cdd:cd19488    1 ISTGIPGLDDILR-GGLPPRRLYLVEGAPGTGKTTLALQFLLEGAANGETGLYItlsETEQELRAV-ALSHGWSLDGIHI 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 193090241  94 ---SQPDTGEQALEITDTL----VRSGAVDVLVVDSVAALTP-RAEIegdmgDSLpgLQARLFSQ-ALR 153
Cdd:cd19488   79 felSPSESALDAAQQYTILhpseLELSETTRLIFERVERLKPsRVVI-----DSL--SELRLLAQdSLR 140
archRadA cd19515
archaeal recombinase Rad51/RadA; This group includes the archaeal protein RadA which is a ...
 17-134 1.68e-06

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


Pssm-ID: 410923 [Multi-domain]  Cd Length: 233  Bit Score: 46.20  E-value: 1.68e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  17 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQK---KGGI---CAFVDAEHALDP----VYARKLGV 86
Cdd:cd19515    1 ISTGSKELDKLLG-GGIETQAITEVFGEFGSGKTQLCHQLAVNVQLppeEGGLngkAVYIDTENTFRPerimQMAKALGL 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 193090241  87 D----LQNLLISQP-DTGEQAL---EITDTLVRSGAVDVLVVDSVAALTpRAEIEG 134
Cdd:cd19515   80 DpdevLDNIYVARAyNSNHQMLlveKAEDLIKEGNNIKLLIVDSLTSHF-RAEYVG 134
RadA_SMS_N cd01121
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a ...
 7-123 2.04e-06

bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a role in recombination and recombinational repair of DNA damaged by UV radiation, X-rays, and chemical agent and is responsible for the stabilization or processing of branched DNA molecules.


Pssm-ID: 410866 [Multi-domain]  Cd Length: 268  Bit Score: 45.99  E-value: 2.04e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241   7 SNDSIVEIETVSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPV--YARKL 84
Cdd:cd01121   54 SDVEAEEEERISTGIGELDRVLG-GGLVPGSVVLIGGDPGIGKSTLLLQVAARLAQRGGKVLYVSGEESLSQIklRAERL 132

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 193090241  85 GVDLQNLLIsqpdTGEQALEITDTLVRSGAVDVLVVDSV 123
Cdd:cd01121  133 GLGSDNLYL----LAETNLEAILAEIEELKPSLVVIDSI 167
recomb_DMC1 TIGR02238
meiotic recombinase Dmc1; This model describes DMC1, a subfamily of a larger family of DNA ...
 17-126 4.36e-06

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


Pssm-ID: 131292 [Multi-domain]  Cd Length: 313  Bit Score: 45.15  E-value: 4.36e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241   17 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQ------KKGGICAFVDAEHALDP----VYARKLGV 86
Cdd:TIGR02238  78 ITTGSQALDGILG-GGIESMSITEVFGEFRCGKTQLSHTLCVTAQlpremgGGNGKVAYIDTEGTFRPdrirAIAERFGV 156

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 193090241   87 D----LQNLLISQPDTGEQALEITDTLVRSGAVD---VLVVDSVAAL 126
Cdd:TIGR02238 157 DpdavLDNILYARAYTSEHQMELLDYLAAKFSEEpfrLLIVDSIMAL 203
PLN03187 PLN03187
meiotic recombination protein DMC1 homolog; Provisional
 17-126 6.21e-06

meiotic recombination protein DMC1 homolog; Provisional


Pssm-ID: 215620 [Multi-domain]  Cd Length: 344  Bit Score: 44.77  E-value: 6.21e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  17 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKT----TLALQTIAEAQKKGGI--CAFVDAEHALDP----VYARKLGV 86
Cdd:PLN03187 108 ITTGSQALDELLG-GGIETRCITEAFGEFRSGKTqlahTLCVTTQLPTEMGGGNgkVAYIDTEGTFRPdrivPIAERFGM 186

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 193090241  87 D----LQNLLISQPDTGEQaleITDTLVRSGA------VDVLVVDSVAAL 126
Cdd:PLN03187 187 DadavLDNIIYARAYTYEH---QYNLLLGLAAkmaeepFRLLIVDSVIAL 233
XRCC3 cd19491
XRCC3 recombinase; XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells ...
 24-155 7.48e-06

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: 44.59  E-value: 7.48e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  24 LDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQ------KKGGICAFVDAEHAL-------------DPVYARKL 84
Cdd:cd19491    1 LDELLG-GGIPVGGITEIAGESGAGKTQLCLQLALTVQlprelgGLGGGAVYICTESSFpskrlqqlasslpKRYHLEKA 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 193090241  85 GVDLQNLLISQPDTGEQALEITDT----LVRSGAVDVLVVDSVAALTpRAEIEGDMGDSLpgLQARLFSQALRKL 155
Cdd:cd19491   80 KNFLDNIFVEHVADLETLEHCLNYqlpaLLERGPIRLVVIDSIAALF-RSEFDTSRSDLV--ERAKYLRRLADHL 151
PTZ00035 PTZ00035
Rad51 protein; Provisional
 13-126 1.88e-05

Rad51 protein; Provisional


Pssm-ID: 185407 [Multi-domain]  Cd Length: 337  Bit Score: 43.45  E-value: 1.88e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  13 EIETVSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKT----TLAL--QTIAEAQKKGGICAFVDAEHALDP----VYAR 82
Cdd:PTZ00035  96 NIIRITTGSTQLDKLLG-GGIETGSITELFGEFRTGKTqlchTLCVtcQLPIEQGGGEGKVLYIDTEGTFRPerivQIAE 174

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 193090241  83 KLGVD----LQNLLISQPDTGEQALEItdtLVRSGAVDV------LVVDSVAAL 126
Cdd:PTZ00035 175 RFGLDpedvLDNIAYARAYNHEHQMQL---LSQAAAKMAeerfalLIVDSATAL 225
recomb_RAD51 TIGR02239
DNA repair protein RAD51; This eukaryotic sequence family consists of RAD51, a protein ...
 13-126 2.19e-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: 43.17  E-value: 2.19e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241   13 EIETVSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKT----TLALQTIAEAQKKG--GICAFVDAE------------- 73
Cdd:TIGR02239  74 EVIQLTTGSKELDKLLG-GGIETGSITEIFGEFRTGKTqlchTLAVTCQLPIDQGGgeGKALYIDTEgtfrperllaiae 152

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 193090241   74 -------HALDPV-YARKLGVDLQNLLISQpdtgeqaleiTDTLVRSGAVDVLVVDSVAAL 126
Cdd:TIGR02239 153 ryglnpeDVLDNVaYARAYNTDHQLQLLQQ----------AAAMMSESRFALLIVDSATAL 203
PLN03186 PLN03186
DNA repair protein RAD51 homolog; Provisional
 13-134 3.79e-05

DNA repair protein RAD51 homolog; Provisional


Pssm-ID: 178728 [Multi-domain]  Cd Length: 342  Bit Score: 42.41  E-value: 3.79e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  13 EIETVSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKT----TLALQTIAEAQKKG--GICAFVDAEHALDP----VYAR 82
Cdd:PLN03186 101 EIIQITTGSRELDKILE-GGIETGSITEIYGEFRTGKTqlchTLCVTCQLPLDQGGgeGKAMYIDTEGTFRPqrliQIAE 179

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 193090241  83 KLGVD----LQNLLISQPDTGEQALEItdtLVRSGA------VDVLVVDSVAALTpRAEIEG 134
Cdd:PLN03186 180 RFGLNgadvLENVAYARAYNTDHQSEL---LLEAASmmaetrFALMIVDSATALY-RTEFSG 237
KaiC-like_C cd19487
C-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 17-124 4.89e-05

C-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock protein, most studied in cyanobacteria. KaiC, an autokinase, autophosphatase, and ATPase, is part of the core oscillator, composed of three proteins: KaiA, KaiB, and KaiC. The circadian oscillation is regulated via KaiC phosphorylation.


Pssm-ID: 410895 [Multi-domain]  Cd Length: 219  Bit Score: 41.90  E-value: 4.89e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  17 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYAR--KLGVDLQ----- 89
Cdd:cd19487    1 VSSGVPELDELLG-GGLERGTSTLLIGPAGVGKSTLALQFAKAAAARGERSVLFSFDESIGTLFERseALGIDLRamvek 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 193090241  90 -NLLISQPDT-----GEQALEITDTLVRSGAvDVLVVDSVA 124
Cdd:cd19487   80 gLLSIEQIDPaelspGEFAQRVRTSVEQEDA-RVVVIDSLN 119
KaiC_C cd19484
C-terminal domain of Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most ...
 17-127 1.21e-04

C-terminal domain of Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. KaiC, an autokinase, autophosphatase, and ATPase, is part of the core oscillator, composed of three proteins: KaiA, KaiB, and KaiC. The circadian oscillation is regulated via KaiC phosphorylation.


Pssm-ID: 410892 [Multi-domain]  Cd Length: 218  Bit Score: 40.77  E-value: 1.21e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  17 VSTGSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVY--ARKLGVDLQNLLIS 94
Cdd:cd19484    1 ISTGIPRLDAMLGGGGFFRGSSILVSGATGTGKTLLAASFADAACRRGERCLYFAFEESPAQLIrnAKSIGIDLEQMERK 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 193090241  95 Q---------PDTG-EQALEITDTLVRSGAVDVLVVDSVAALT 127
Cdd:cd19484   81 GllkiicarpELYGlEDHLIIIKSEINEFKPSRVIVDPLSALA 123
RepA COG3598
RecA-family ATPase [Replication, recombination and repair];
33-155 1.28e-04

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


Pssm-ID: 442817 [Multi-domain]  Cd Length: 313  Bit Score: 41.04  E-value: 1.28e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  33 LPKGRIIEIYGPESSGKTTLALQ---TIAEAQK------KGGICAFVDAE----------HALDPVYARKLGVDLQNLLI 93
Cdd:COG3598   10 LPEGGVTLLAGPPGTGKSFLALQlaaAVAAGGPwlgrrvPPGKVLYLAAEddrgelrrrlKALGADLGLPFADLDGRLRL 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 193090241  94 SQPDTGEQALEITDTL---VRSGAVDVLVVDSVAALtpraeIEGDMGDSlpgLQARLFSQALRKL 155
Cdd:COG3598   90 LSLAGDLDDTDDLEALeraIEEEGPDLVVIDPLARV-----FGGDENDA---EEMRAFLNPLDRL 146
AAA_24 pfam13479
AAA domain; This AAA domain is found in a wide variety of presumed phage proteins.
 35-157 1.53e-04

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


Pssm-ID: 433243  Cd Length: 199  Bit Score: 40.39  E-value: 1.53e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241   35 KGRIIEIYGPESSGKTTLAlqtiAEAQKKggicAFVDAEHALDPVYARKLgvDLQNLLISQPDTGEQALEITDTLVRSga 114
Cdd:pfam13479   1 KKLKILIYGPSGIGKTTFA----KTLPKP----LFLDTEKGSKALDGDRF--PDIVIRDSWQDFLDAIDELTAAELAD-- 68

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 193090241  115 VDVLVVDSVAAL-----------TPRAEIEGDMGDSLP-GLQARLFSQALRKLTA 157
Cdd:pfam13479  69 YKTIVIDTVDWLerlclayickqNGKGSSIEDGGYGKGyGELGEEFRRLLDALQE 123
Rad51 cd19513
RAD51D recombinase; RAD51 recombinase plays an essential role in DNA repair by homologous ...
 17-126 1.64e-04

RAD51D recombinase; RAD51 recombinase plays an essential role in DNA repair by homologous recombination (HR). HR is an important error-free repair mechanism for chromosomal double-strand break (DSB) which otherwise leads to cell cycle arrest and death. RAD51 is recruited to the break site with the help of its paralogs, RAD51D, RAD51B, RAD51C, XRCC3, and XRCC2, where it forms long helical polymers which wrap around the ssDNA tail at the break which leads to pairing and strand invasion.


Pssm-ID: 410921 [Multi-domain]  Cd Length: 235  Bit Score: 40.38  E-value: 1.64e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  17 VSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKT----TLAL--QTIAEAQKKGGICAFVDAE----------------- 73
Cdd:cd19513    1 ITTGSKELDKLLG-GGIETGSITELFGEFRTGKTqlchTLAVtcQLPIDQGGGEGKALYIDTEgtfrperllaiaerygl 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 193090241  74 ---HALDPV-YARKLGVDLQNLLISQpdtgeqaleiTDTLVRSGAVDVLVVDSVAAL 126
Cdd:cd19513   80 ngeDVLDNVaYARAYNTDHQMQLLIQ----------ASAMMAESRYALLIVDSATAL 126
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 15-127 1.94e-04

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 40.63  E-value: 1.94e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  15 ETVSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVY--ARKLGVDLQN-- 90
Cdd:PRK09302 253 ERISSGVPDLDEMLG-GGFFRGSIILVSGATGTGKTLLASKFAEAACRRGERCLLFAFEESRAQLIrnARSWGIDLEKme 331

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 193090241  91 ----LLI--SQPD-TG-EQALEITDTLVRSGAVDVLVVDSVAALT 127
Cdd:PRK09302 332 ekglLKIicARPEsYGlEDHLIIIKREIEEFKPSRVAIDPLSALA 376
XRCC2 cd19490
XRCC2 recombinase; XRCC2 (X-ray repair complementing defective repair in Chinese hamster cells ...
 36-158 2.04e-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: 40.02  E-value: 2.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  36 GRIIEIYGPESSGKTTLALQTIAEA---QKKGGICA--------FVDAEHALDPVYARKL-------------------G 85
Cdd:cd19490    1 GDVIEITGPSGSGKTELLYHLAARCilpSSWGGVPLggleaavvFIDTDGRFDILRLRSIleariraaiqaanssddeeD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  86 VD------LQNLLISQPDTGEQ------ALEIT-DTLVRSGAVDVLVVDSVAALTPRAEIEGDMGDSLPGLQ---ARLFS 149
Cdd:cd19490   81 VEeiarecLQRLHIFRCHSSLQllatllSLENYlLSLSANPELGLLLIDSISAFYWQDRFSAELARAAPLLQeaaLRAIL 160


                 ....*....
gi 193090241 150 QALRKLTAS 158
Cdd:cd19490  161 RELRRLRRR 169
FlaH COG2874
Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];
15-55 4.97e-04

Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];


Pssm-ID: 442121  Cd Length: 230  Bit Score: 39.05  E-value: 4.97e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 193090241  15 ETVSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQ 55
Cdd:COG2874    1 EIISTGNDELDKRLG-GGIPLGSLVLIEGENGTGKSVLSQQ 40
ATPase_2 pfam01637
ATPase domain predominantly from Archaea; This family contain a conserved P-loop motif that is ...
 38-72 6.80e-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: 38.46  E-value: 6.80e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 193090241   38 IIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDA 72
Cdd:pfam01637  22 IYVIYGPEGCGKTALLRESIENLLDLGYYVIYYDP 56
PRK10851 PRK10851
sulfate/thiosulfate ABC transporter ATP-binding protein CysA;
12-90 7.81e-04

sulfate/thiosulfate ABC transporter ATP-binding protein CysA;


Pssm-ID: 182778 [Multi-domain]  Cd Length: 353  Bit Score: 38.91  E-value: 7.81e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  12 VEIETVS-----TGSLSlDIALGIgglPKGRIIEIYGPESSGKTTLaLQTIA--EAQKKGGICaF----VDAEHALDpvy 80
Cdd:PRK10851   3 IEIANIKksfgrTQVLN-DISLDI---PSGQMVALLGPSGSGKTTL-LRIIAglEHQTSGHIR-FhgtdVSRLHARD--- 73

                         90
                 ....*....|
gi 193090241  81 aRKLGVDLQN 90
Cdd:PRK10851  74 -RKVGFVFQH 82
Rad51D cd19489
RAD51D recombinase; RAD51D recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 31-60 8.20e-04

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


Pssm-ID: 410897 [Multi-domain]  Cd Length: 209  Bit Score: 38.39  E-value: 8.20e-04
                         10        20        30
                 ....*....|....*....|....*....|
gi 193090241  31 GGLPKGRIIEIYGPESSGKTTLALQTIAEA 60
Cdd:cd19489    2 GGLRTGEITELVGESSSGKTQLCLTAAANV 31
PRK06067 PRK06067
flagellar accessory protein FlaH; Validated
 13-133 2.09e-03

flagellar accessory protein FlaH; Validated


Pssm-ID: 180381  Cd Length: 234  Bit Score: 37.26  E-value: 2.09e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241  13 EIETVSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAE--------------HALDP 78
Cdd:PRK06067   3 KKEIISTGNEELDRKLG-GGIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITTEntsksylkqmesvkIDISD 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 193090241  79 VYAR-KLGVDLQNLLISQ--PDTGEQALEITDTLVRSGAVDVLVVDSVAALTPRAEIE 133
Cdd:PRK06067  82 FFLWgYLRIFPLNTEGFEwnSTLANKLLELIIEFIKSKREDVIIIDSLTIFATYAEED 139
AAA_22 pfam13401
AAA domain;
37-130 2.12e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 36.17  E-value: 2.12e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 193090241   37 RIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPV-YARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAV 115
Cdd:pfam13401   6 GILVLTGESGTGKTTLLRRLLEQLPEVRDSVVFVDLPSGTSPKdLLRALLRALGLPLSGRLSKEELLAALQQLLLALAVA 85

                          90
                  ....*....|....*
gi 193090241  116 DVLVVDSVAALTPRA 130
Cdd:pfam13401  86 VVLIIDEAQHLSLEA 100
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 13-69 4.47e-03

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 36.78  E-value: 4.47e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 193090241  13 EIETVSTGSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEaqkkgGICAF 69
Cdd:PRK09302   9 GIEKLPTGIEGFDDITH-GGLPKGRPTLVSGTAGTGKTLFALQFLVN-----GIKRF 59
ABC_UvrA_I cd03270
ATP-binding cassette domain I of the excision repair protein UvrA; Nucleotide excision repair ...
 33-63 6.56e-03

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


Pssm-ID: 213237 [Multi-domain]  Cd Length: 226  Bit Score: 35.70  E-value: 6.56e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 193090241  33 LPKGRIIEIYGPESSGKTTLALQTI-AEAQKK 63
Cdd:cd03270   18 IPRNKLVVITGVSGSGKSSLAFDTIyAEGQRR 49
PAXNEB pfam05625
PAXNEB protein; PAXNEB or PAX6 neighbour is found in several eukaryotic organizms. PAXNED is ...
 16-53 8.85e-03

PAXNEB protein; PAXNEB or PAX6 neighbour is found in several eukaryotic organizms. PAXNED is an RNA polymerase II Elongator protein subunit. It is part of the HAP subcomplex of Elongator, which is a six-subunit component of the RNA polymerase II holoenzyme. The HAP subcomplex is required for Elongator structural integrity and histone acetyltransferase activity. This protein family has a P-loop-like motif and adopts a RecA-ATPase-like fold, lacking the conserved sequence signature of ATPases.


Pssm-ID: 461696  Cd Length: 359  Bit Score: 35.65  E-value: 8.85e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 193090241   16 TVSTGSLSLDIALGiGGLPKGRIIEIygpESSGKTTLA 53
Cdd:pfam05625  18 TTSTGTPSLDKLLG-GGLPLGSSLLI---EEDGTTDFA 51
 
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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