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Conserved domains on  [gi|937554937|gb|ALI57890|]
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recombinase A, partial [Rhizobium sp. RAFAB_9]

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
 1-128 1.16e-103

recombinase A; Provisional


The actual alignment was detected with superfamily member PRK09354:

Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 299.02  E-value: 1.16e-103
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   1 GSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQPDTG 80
Cdd:PRK09354  44 GSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQPDTG 123

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 937554937  81 EQALEITDTLVRSGAIDVLVVDSVAALTPRAEIEGEMGDSLPGLQARL 128
Cdd:PRK09354 124 EQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARL 171
 
Name Accession Description Interval E-value
recA PRK09354
recombinase A; Provisional
 1-128 1.16e-103

recombinase A; Provisional


Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 299.02  E-value: 1.16e-103
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   1 GSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQPDTG 80
Cdd:PRK09354  44 GSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQPDTG 123

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 937554937  81 EQALEITDTLVRSGAIDVLVVDSVAALTPRAEIEGEMGDSLPGLQARL 128
Cdd:PRK09354 124 EQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARL 171
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
1-128 6.97e-100

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 289.38  E-value: 6.97e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   1 GSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQPDTG 80
Cdd:COG0468   47 GSLALDIALGVGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGIAAFIDAEHALDPEYAKKLGVDIDNLLVSQPDTG 126

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 937554937  81 EQALEITDTLVRSGAIDVLVVDSVAALTPRAEIEGEMGDSLPGLQARL 128
Cdd:COG0468  127 EQALEIAETLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARL 174
RecA pfam00154
recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA ...
 1-128 1.71e-93

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: 270.04  E-value: 1.71e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937    1 GSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQPDTG 80
Cdd:pfam00154  36 GSLALDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQPDTG 115

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 937554937   81 EQALEITDTLVRSGAIDVLVVDSVAALTPRAEIEGEMGDSLPGLQARL 128
Cdd:pfam00154 116 EQALEIADMLVRSGAIDLIVVDSVAALVPKAEIEGEMGDSHVGLQARL 163
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 1-128 9.08e-93

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: 267.11  E-value: 9.08e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   1 GSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQPDTG 80
Cdd:cd00983    8 GSLSLDIALGIGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKLGGTAAFIDAEHALDPEYAKKLGVDIDNLLVSQPDTG 87

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 937554937  81 EQALEITDTLVRSGAIDVLVVDSVAALTPRAEIEGEMGDSLPGLQARL 128
Cdd:cd00983   88 EQALEIADTLIRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARL 135
tigrfam_recA TIGR02012
protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization ...
 1-128 4.10e-92

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: 268.85  E-value: 4.10e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937    1 GSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQPDTG 80
Cdd:TIGR02012  39 GSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYARKLGVDIDNLLVSQPDTG 118

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 937554937   81 EQALEITDTLVRSGAIDVLVVDSVAALTPRAEIEGEMGDSLPGLQARL 128
Cdd:TIGR02012 119 EQALEIAETLVRSGAVDIIVVDSVAALVPKAEIEGEMGDSHVGLQARL 166
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 16-117 5.29e-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: 51.22  E-value: 5.29e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937    16 KGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISqpDTGEQALEITDTLVRSGA 95
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS--GSGELRLRLALALARKLK 78

                           90       100
                   ....*....|....*....|..
gi 937554937    96 IDVLVVDSVAALTPRAEIEGEM 117
Cdd:smart00382  79 PDVLILDEITSLLDAEQEALLL 100
 
Name Accession Description Interval E-value
recA PRK09354
recombinase A; Provisional
 1-128 1.16e-103

recombinase A; Provisional


Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 299.02  E-value: 1.16e-103
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   1 GSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQPDTG 80
Cdd:PRK09354  44 GSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQPDTG 123

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 937554937  81 EQALEITDTLVRSGAIDVLVVDSVAALTPRAEIEGEMGDSLPGLQARL 128
Cdd:PRK09354 124 EQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARL 171
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
1-128 6.97e-100

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 289.38  E-value: 6.97e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   1 GSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQPDTG 80
Cdd:COG0468   47 GSLALDIALGVGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGIAAFIDAEHALDPEYAKKLGVDIDNLLVSQPDTG 126

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 937554937  81 EQALEITDTLVRSGAIDVLVVDSVAALTPRAEIEGEMGDSLPGLQARL 128
Cdd:COG0468  127 EQALEIAETLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARL 174
RecA pfam00154
recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA ...
 1-128 1.71e-93

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: 270.04  E-value: 1.71e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937    1 GSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQPDTG 80
Cdd:pfam00154  36 GSLALDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQPDTG 115

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 937554937   81 EQALEITDTLVRSGAIDVLVVDSVAALTPRAEIEGEMGDSLPGLQARL 128
Cdd:pfam00154 116 EQALEIADMLVRSGAIDLIVVDSVAALVPKAEIEGEMGDSHVGLQARL 163
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 1-128 9.08e-93

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: 267.11  E-value: 9.08e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   1 GSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQPDTG 80
Cdd:cd00983    8 GSLSLDIALGIGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKLGGTAAFIDAEHALDPEYAKKLGVDIDNLLVSQPDTG 87

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 937554937  81 EQALEITDTLVRSGAIDVLVVDSVAALTPRAEIEGEMGDSLPGLQARL 128
Cdd:cd00983   88 EQALEIADTLIRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARL 135
tigrfam_recA TIGR02012
protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization ...
 1-128 4.10e-92

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: 268.85  E-value: 4.10e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937    1 GSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQPDTG 80
Cdd:TIGR02012  39 GSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYARKLGVDIDNLLVSQPDTG 118

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 937554937   81 EQALEITDTLVRSGAIDVLVVDSVAALTPRAEIEGEMGDSLPGLQARL 128
Cdd:TIGR02012 119 EQALEIAETLVRSGAVDIIVVDSVAALVPKAEIEGEMGDSHVGLQARL 166
recA PRK09519
intein-containing recombinase RecA;
1-128 4.89e-65

intein-containing recombinase RecA;


Pssm-ID: 77219 [Multi-domain]  Cd Length: 790  Bit Score: 210.33  E-value: 4.89e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   1 GSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQPDTG 80
Cdd:PRK09519  44 GSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDYAKKLGVDTDSLLVSQPDTG 123

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 937554937  81 EQALEITDTLVRSGAIDVLVVDSVAALTPRAEIEGEMGDSLPGLQARL 128
Cdd:PRK09519 124 EQALEIADMLIRSGALDIVVIDSVAALVPRAELEGEMGDSHVGLQARL 171
RecA-like cd01393
RecA family; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 17-128 4.44e-33

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: 113.99  E-value: 4.44e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937  17 GRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYAR-----------KLGVDLQNLLISQPDTGEQALE 85
Cdd:cd01393    1 GKITEIYGPPGSGKTQLALQLAANALLLGGGVVWIDTEGAFPPSRLVqileaspsselELAEALSRLLYFRPPDTLAHLL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 937554937  86 ITDTLVRSGA----IDVLVVDSVAALTPRAEIEGEMGDSLPGLQARL 128
Cdd:cd01393   81 ALDSLPESLFpppnTSLVVVDSVSALFRKAFPRGGDGDSSSSLRARL 127
archRadB cd01394
archaeal RadB; The archaeal protein RadB shares similarity RadA, the archaeal functional ...
 1-120 1.10e-16

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: 72.73  E-value: 1.10e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   1 GSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEhALDP-----VYARKLGVDLQNLLIS 75
Cdd:cd01394    4 GSKSLDSLLG-GGVERGTITQIYGPPGSGKTNICLQLAVEAAKQGKKVVYIDTE-GLSPerfqqIAGERFESIASNIIVF 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 937554937  76 QP-DTGEQALEITDT--LVRSGAIDVLVVDSVAALTpRAEiegEMGDS 120
Cdd:cd01394   82 EPySFDEQGVAIQEAekLLKSDKVDLVVVDSATALY-RLE---LGDDS 125
recomb_radB TIGR02237
DNA repair and recombination protein RadB; This family consists exclusively of archaeal RadB ...
 5-128 3.09e-13

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


Pssm-ID: 274047 [Multi-domain]  Cd Length: 209  Bit Score: 63.20  E-value: 3.09e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937    5 LDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEhALDPVYARKLGVD-----LQNLLISQP-- 77
Cdd:TIGR02237   1 IDELLG-GGVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTE-GLSPERFKQIAEDrperaLSNFIVFEVfd 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 937554937   78 -DTGEQALEITDTLVRSGAIDVLVVDSVAALTpRAEIEGEMGDSLPGLQARL 128
Cdd:TIGR02237  79 fDEQGVAIQKTSKFIDRDSASLVVVDSFTALY-RLELSDDRISRNRELARQL 129
radB PRK09361
DNA repair and recombination protein RadB; Provisional
 1-116 4.36e-12

DNA repair and recombination protein RadB; Provisional


Pssm-ID: 236482 [Multi-domain]  Cd Length: 225  Bit Score: 60.26  E-value: 4.36e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   1 GSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEhALDPVYARKLGVD-----LQNLLIS 75
Cdd:PRK09361   8 GCKMLDELLG-GGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE-GLSPERFKQIAGEdfeelLSNIIIF 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 937554937  76 QP-DTGEQALEITDT--LVRSGaIDVLVVDSVAALTpRAEIEGE 116
Cdd:PRK09361  86 EPsSFEEQSEAIRKAekLAKEN-VGLIVLDSATSLY-RLELEDE 127
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
5-107 2.77e-11

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 58.39  E-value: 2.77e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   5 LDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPV--YARKLGVDLQ------NLLISQ 76
Cdd:COG0467    9 LDELLG-GGLPRGSSTLLSGPPGTGKTTLALQFLAEGLRRGEKGLYVSFEESPEQLlrRAESLGLDLEeyiesgLLRIID 87

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 937554937  77 PDTGEQALEITDTL------VRSGAIDVLVVDSVAAL 107
Cdd:COG0467   88 LSPEELGLDLEELLarlreaVEEFGAKRVVIDSLSGL 124
COG4544 COG4544
Uncharacterized conserved protein [Function unknown];
1-111 1.17e-10

Uncharacterized conserved protein [Function unknown];


Pssm-ID: 443609 [Multi-domain]  Cd Length: 230  Bit Score: 56.48  E-value: 1.17e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   1 GSLSLDIALGIGGLPKGRIIEIYGPE-SSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISQPDT 79
Cdd:COG4544   32 GFAALDAALPGGGLPRGALHEILGPApGIGELGLLLPLLARLAQAGGPVLWIAPPYDLYAPGLAAAGLDPERLLLVRARR 111

                         90       100       110
                 ....*....|....*....|....*....|..
gi 937554937  80 GEQALEITDTLVRSGAIDVLVVDsVAALTPRA 111
Cdd:COG4544  112 PADALWAAEEALRSGACGAVVAW-LERLDLTA 142
Rad51B cd19493
RAD51B recombinase; RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 6-119 2.05e-09

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


Pssm-ID: 410901 [Multi-domain]  Cd Length: 222  Bit Score: 53.09  E-value: 2.05e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   6 DIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEA---QKKGG---ICAFVDAEHAL------------DPVYARK--- 64
Cdd:cd19493    1 DTALA-GGLPLGAITEITGASGSGKTQFALTLASSAampARKGGldgGVLYIDTESKFsaerlaeiaearFPEAFSGfme 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 937554937  65 ----LGVDLQNLLISQPDTGEQALEITDTL---VRSGAIDVLVVDSVAALTpRAEIEGEMGD 119
Cdd:cd19493   80 enerAEEMLKRVAVVRVTTLAQLLERLPNLeehILSSGVRLVVIDSIAALV-RREFGGSDGE 140
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 16-117 5.29e-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: 51.22  E-value: 5.29e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937    16 KGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYARKLGVDLQNLLISqpDTGEQALEITDTLVRSGA 95
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS--GSGELRLRLALALARKLK 78

                           90       100
                   ....*....|....*....|..
gi 937554937    96 IDVLVVDSVAALTPRAEIEGEM 117
Cdd:smart00382  79 PDVLILDEITSLLDAEQEALLL 100
KaiC-like cd01124
Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. ...
 5-107 1.72e-08

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: 50.73  E-value: 1.72e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   5 LDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVY--ARKLGVDL-----QNLLI--S 75
Cdd:cd01124    8 LDELLG-GGIPKGSVTLLTGGPGTGKTLFGLQFLYAGAKNGEPGLFFTFEESPERLLrnAKSFGWDFdemedEGKLIivD 86

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 937554937  76 QPDTGEQALEITDTL------VRSGAIDVLVVDSVAAL 107
Cdd:cd01124   87 APPTEAGRFSLDELLsrilsiIKSFKAKRVVIDSLSGL 124
ATPase pfam06745
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ...
 12-108 1.17e-07

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


Pssm-ID: 429095 [Multi-domain]  Cd Length: 231  Bit Score: 48.40  E-value: 1.17e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   12 GGLPKGRIIEIYGPESSGKTTLALQ-TIAEAQKKGGICAFVDA-EHALDPVY-ARKLGVDLQNLL---------ISQPDT 79
Cdd:pfam06745  14 GGFPEGRVVLITGGPGTGKTIFGLQfLYNGALKYGEPGVFVTLeEPPEDLREnARSFGWDLEKLEeegklaiidASTSGI 93

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 937554937   80 GEQALEITDTL----------VRSGAIDVLVVDSVAALT 108
Cdd:pfam06745  94 GIAEVEDRFDLeelierlreaIREIGAKRVVIDSITTLF 132
Rad51 pfam08423
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ...
 1-115 3.85e-07

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


Pssm-ID: 462471 [Multi-domain]  Cd Length: 255  Bit Score: 46.91  E-value: 3.85e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937    1 GSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQ---KKGGI---CAFVDAEHALDPV----YARKLGVDLQ 70
Cdd:pfam08423  22 GSKELDKLLG-GGIETGSITEIFGEFRTGKTQLCHTLCVTCQlplEMGGGegkALYIDTEGTFRPErlvaIAERYGLDPE 100

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 937554937   71 NLLISQP-------DTGEQALEITDTLVRSGAIDVLVVDSVAALTpRAEIEG 115
Cdd:pfam08423 101 DVLDNVAyaraynsEHQMQLLQQAAAMMSESRFALLIVDSATALY-RTDFSG 151
DMC1 cd19514
homologous-pairing protein DMC1; DMC1 has a central role in homologous recombination in ...
 1-107 1.21e-06

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: 45.43  E-value: 1.21e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   1 GSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQ------KKGGICAFVDAEHALDP----VYARKLGVD-- 68
Cdd:cd19514    4 GSTELDKLLG-GGIESMSITEVFGEFRTGKTQLSHTLCVTAQlpgsmgGGGGKVAYIDTEGTFRPdrirPIAERFGVDhd 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 937554937  69 --LQNLLISQPDTGEQALEITDTL----VRSGAIDVLVVDSVAAL 107
Cdd:cd19514   83 avLDNILYARAYTSEHQMELLDYVaakfHEEAVFRLLIIDSIMAL 127
XRCC3 cd19491
XRCC3 recombinase; XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells ...
 5-107 4.28e-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: 44.20  E-value: 4.28e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   5 LDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQ------KKGGICAFVDAEHAL-------------DPVYARKL 65
Cdd:cd19491    1 LDELLG-GGIPVGGITEIAGESGAGKTQLCLQLALTVQlprelgGLGGGAVYICTESSFpskrlqqlasslpKRYHLEKA 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 937554937  66 GVDLQNLLISQPDTGEQALEITDT----LVRSGAIDVLVVDSVAAL 107
Cdd:cd19491   80 KNFLDNIFVEHVADLETLEHCLNYqlpaLLERGPIRLVVIDSIAAL 125
Rad51_DMC1_archRadA cd01123
recombinase Rad51, DMC1, and archaeal RadA; This group of recombinases includes the eukaryotic ...
 1-107 8.24e-06

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: 43.29  E-value: 8.24e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   1 GSLSLDIALGiGGLPKGRIIEIYGPESSGKT----TLAL--QTIAEAQKKGGICAFVDAEHALDPV----YARKLGVD-- 68
Cdd:cd01123    4 GSKELDKLLG-GGIETGSITEMFGEFRTGKTqlchTLAVtcQLPIDRGGGEGKAIYIDTEGTFRPErlraIAQRFGLDpd 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 937554937  69 --LQNLLISQPDTGEQALEITD---TLVRSGAIDVLVVDSVAAL 107
Cdd:cd01123   83 dvLDNVAYARAFNSDHQTQLLDqaaAMMVESRFKLLIVDSATAL 126
RadA_SMS_N cd01121
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a ...
 5-104 9.13e-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: 43.29  E-value: 9.13e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   5 LDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPV--YARKLGVDLQNLLIsqpdTGEQ 82
Cdd:cd01121   71 LDRVLG-GGLVPGSVVLIGGDPGIGKSTLLLQVAARLAQRGGKVLYVSGEESLSQIklRAERLGLGSDNLYL----LAET 145

                         90       100
                 ....*....|....*....|..
gi 937554937  83 ALEITDTLVRSGAIDVLVVDSV 104
Cdd:cd01121  146 NLEAILAEIEELKPSLVVIDSI 167
AAA_24 pfam13479
AAA domain; This AAA domain is found in a wide variety of presumed phage proteins.
 16-104 1.16e-05

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


Pssm-ID: 433243  Cd Length: 199  Bit Score: 42.70  E-value: 1.16e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   16 KGRIIEIYGPESSGKTTLAlqtiAEAQKKggicAFVDAEHALDPVYARKLgvDLQNLLISQPDTGEQALEITDTLVRSga 95
Cdd:pfam13479   1 KKLKILIYGPSGIGKTTFA----KTLPKP----LFLDTEKGSKALDGDRF--PDIVIRDSWQDFLDAIDELTAAELAD-- 68


                  ....*....
gi 937554937   96 IDVLVVDSV 104
Cdd:pfam13479  69 YKTIVIDTV 77
KaiC-like_N cd19488
N-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 5-109 1.89e-05

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: 42.34  E-value: 1.89e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   5 LDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFV---DAEHALDPVyARKLGVDLQNLLI---SQPD 78
Cdd:cd19488    8 LDDILR-GGLPPRRLYLVEGAPGTGKTTLALQFLLEGAANGETGLYItlsETEQELRAV-ALSHGWSLDGIHIfelSPSE 85

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 937554937  79 TGEQALEITDTL----VRSGAIDVLVVDSVAALTP 109
Cdd:cd19488   86 SALDAAQQYTILhpseLELSETTRLIFERVERLKP 120
PLN03187 PLN03187
meiotic recombination protein DMC1 homolog; Provisional
 1-107 2.66e-05

meiotic recombination protein DMC1 homolog; Provisional


Pssm-ID: 215620 [Multi-domain]  Cd Length: 344  Bit Score: 42.07  E-value: 2.66e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   1 GSLSLDIALGiGGLPKGRIIEIYGPESSGKT----TLALQTIAEAQKKGGI--CAFVDAEHALDP----VYARKLGVD-- 68
Cdd:PLN03187 111 GSQALDELLG-GGIETRCITEAFGEFRSGKTqlahTLCVTTQLPTEMGGGNgkVAYIDTEGTFRPdrivPIAERFGMDad 189

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 937554937  69 --LQNLLISQPDTGEQaleITDTLVRSGA------IDVLVVDSVAAL 107
Cdd:PLN03187 190 avLDNIIYARAYTYEH---QYNLLLGLAAkmaeepFRLLIVDSVIAL 233
radA PRK04301
DNA repair and recombination protein RadA; Validated
 1-115 3.20e-05

DNA repair and recombination protein RadA; Validated


Pssm-ID: 235273 [Multi-domain]  Cd Length: 317  Bit Score: 41.79  E-value: 3.20e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   1 GSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQ---KKGGI---CAFVDAE--------------HALDP- 59
Cdd:PRK04301  87 GSKELDELLG-GGIETQSITEFYGEFGSGKTQICHQLAVNVQlpeEKGGLegkAVYIDTEgtfrperieqmaeaLGLDPd 165

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 937554937  60 ------VYARKLGVDLQNLLIsqpdtgEQALEitdtLVRSG-AIDVLVVDSVAALTpRAEIEG 115
Cdd:PRK04301 166 evldniHVARAYNSDHQMLLA------EKAEE----LIKEGeNIKLVIVDSLTAHF-RAEYVG 217
archRadA cd19515
archaeal recombinase Rad51/RadA; This group includes the archaeal protein RadA which is a ...
 1-115 3.84e-05

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


Pssm-ID: 410923 [Multi-domain]  Cd Length: 233  Bit Score: 41.19  E-value: 3.84e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   1 GSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQK---KGGI---CAFVDAEHALDP----VYARKLGVD-- 68
Cdd:cd19515    4 GSKELDKLLG-GGIETQAITEVFGEFGSGKTQLCHQLAVNVQLppeEGGLngkAVYIDTENTFRPerimQMAKALGLDpd 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 937554937  69 --LQNLLISQP-DTGEQAL---EITDTLVRSGAIDVLVVDSVAALTpRAEIEG 115
Cdd:cd19515   83 evLDNIYVARAyNSNHQMLlveKAEDLIKEGNNIKLLIVDSLTSHF-RAEYVG 134
recomb_DMC1 TIGR02238
meiotic recombinase Dmc1; This model describes DMC1, a subfamily of a larger family of DNA ...
 1-107 5.14e-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: 41.30  E-value: 5.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937    1 GSLSLDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQ------KKGGICAFVDAEHALDP----VYARKLGVD-- 68
Cdd:TIGR02238  81 GSQALDGILG-GGIESMSITEVFGEFRCGKTQLSHTLCVTAQlpremgGGNGKVAYIDTEGTFRPdrirAIAERFGVDpd 159

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 937554937   69 --LQNLLISQPDTGEQALEITDTL---VRSGAIDVLVVDSVAAL 107
Cdd:TIGR02238 160 avLDNILYARAYTSEHQMELLDYLaakFSEEPFRLLIVDSIMAL 203
KaiC-like_C cd19487
C-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 5-105 1.90e-04

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


Pssm-ID: 410895 [Multi-domain]  Cd Length: 219  Bit Score: 39.20  E-value: 1.90e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   5 LDIALGiGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVYAR--KLGVDLQ------NLLISQ 76
Cdd:cd19487    8 LDELLG-GGLERGTSTLLIGPAGVGKSTLALQFAKAAAARGERSVLFSFDESIGTLFERseALGIDLRamvekgLLSIEQ 86

                         90       100       110
                 ....*....|....*....|....*....|....
gi 937554937  77 PDT-----GEQALEITDTLVRSGAiDVLVVDSVA 105
Cdd:cd19487   87 IDPaelspGEFAQRVRTSVEQEDA-RVVVIDSLN 119
Rad51D cd19489
RAD51D recombinase; RAD51D recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 12-41 2.65e-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: 38.77  E-value: 2.65e-04
                         10        20        30
                 ....*....|....*....|....*....|
gi 937554937  12 GGLPKGRIIEIYGPESSGKTTLALQTIAEA 41
Cdd:cd19489    2 GGLRTGEITELVGESSSGKTQLCLTAAANV 31
XRCC2 cd19490
XRCC2 recombinase; XRCC2 (X-ray repair complementing defective repair in Chinese hamster cells ...
 17-39 3.18e-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: 38.48  E-value: 3.18e-04
                         10        20
                 ....*....|....*....|...
gi 937554937  17 GRIIEIYGPESSGKTTLALQTIA 39
Cdd:cd19490    1 GDVIEITGPSGSGKTELLYHLAA 23
PTZ00035 PTZ00035
Rad51 protein; Provisional
 1-107 3.76e-04

Rad51 protein; Provisional


Pssm-ID: 185407 [Multi-domain]  Cd Length: 337  Bit Score: 38.83  E-value: 3.76e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   1 GSLSLDIALGiGGLPKGRIIEIYGPESSGKT----TLAL--QTIAEAQKKGGICAFVDAEHALDP----VYARKLGVD-- 68
Cdd:PTZ00035 103 GSTQLDKLLG-GGIETGSITELFGEFRTGKTqlchTLCVtcQLPIEQGGGEGKVLYIDTEGTFRPerivQIAERFGLDpe 181

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 937554937  69 --LQNLLISQPDTGEQALEItdtLVRSGAIDV------LVVDSVAAL 107
Cdd:PTZ00035 182 dvLDNIAYARAYNHEHQMQL---LSQAAAKMAeerfalLIVDSATAL 225
PRK10851 PRK10851
sulfate/thiosulfate ABC transporter ATP-binding protein CysA;
6-71 4.18e-04

sulfate/thiosulfate ABC transporter ATP-binding protein CysA;


Pssm-ID: 182778 [Multi-domain]  Cd Length: 353  Bit Score: 38.53  E-value: 4.18e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 937554937   6 DIALGIgglPKGRIIEIYGPESSGKTTLaLQTIA--EAQKKGGICaF----VDAEHALDpvyaRKLGVDLQN 71
Cdd:PRK10851  20 DISLDI---PSGQMVALLGPSGSGKTTL-LRIIAglEHQTSGHIR-FhgtdVSRLHARD----RKVGFVFQH 82
ATPase_2 pfam01637
ATPase domain predominantly from Archaea; This family contain a conserved P-loop motif that is ...
 19-53 4.20e-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: 4.20e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 937554937   19 IIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDA 53
Cdd:pfam01637  22 IYVIYGPEGCGKTALLRESIENLLDLGYYVIYYDP 56
PLN03186 PLN03186
DNA repair protein RAD51 homolog; Provisional
 1-115 1.27e-03

DNA repair protein RAD51 homolog; Provisional


Pssm-ID: 178728 [Multi-domain]  Cd Length: 342  Bit Score: 37.02  E-value: 1.27e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   1 GSLSLDIALGiGGLPKGRIIEIYGPESSGKT----TLALQTIAEAQKKG--GICAFVDAEHALDP----VYARKLGVD-- 68
Cdd:PLN03186 108 GSRELDKILE-GGIETGSITEIYGEFRTGKTqlchTLCVTCQLPLDQGGgeGKAMYIDTEGTFRPqrliQIAERFGLNga 186

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 937554937  69 --LQNLLISQPDTGEQALEItdtLVRSGAI------DVLVVDSVAALTpRAEIEG 115
Cdd:PLN03186 187 dvLENVAYARAYNTDHQSEL---LLEAASMmaetrfALMIVDSATALY-RTEFSG 237
recomb_RAD51 TIGR02239
DNA repair protein RAD51; This eukaryotic sequence family consists of RAD51, a protein ...
 1-107 1.95e-03

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: 36.63  E-value: 1.95e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937    1 GSLSLDIALGiGGLPKGRIIEIYGPESSGKT----TLALQTIAEAQKKG--GICAFVDAE-------------------- 54
Cdd:TIGR02239  81 GSKELDKLLG-GGIETGSITEIFGEFRTGKTqlchTLAVTCQLPIDQGGgeGKALYIDTEgtfrperllaiaeryglnpe 159

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 937554937   55 HALDPV-YARKLGVDLQNLLISQpdtgeqaleiTDTLVRSGAIDVLVVDSVAAL 107
Cdd:TIGR02239 160 DVLDNVaYARAYNTDHQLQLLQQ----------AAAMMSESRFALLIVDSATAL 203
KaiC_C cd19484
C-terminal domain of Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most ...
 1-108 2.09e-03

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


Pssm-ID: 410892 [Multi-domain]  Cd Length: 218  Bit Score: 36.15  E-value: 2.09e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   1 GSLSLDIALGIGGLPKGRIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPVY--ARKLGVDLQNLLISQ-- 76
Cdd:cd19484    4 GIPRLDAMLGGGGFFRGSSILVSGATGTGKTLLAASFADAACRRGERCLYFAFEESPAQLIrnAKSIGIDLEQMERKGll 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 937554937  77 -------PDTG-EQALEITDTLVRSGAIDVLVVDSVAALT 108
Cdd:cd19484   84 kiicarpELYGlEDHLIIIKSEINEFKPSRVIVDPLSALA 123
AAA_22 pfam13401
AAA domain;
18-111 2.22e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 35.40  E-value: 2.22e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   18 RIIEIYGPESSGKTTLALQTIAEAQKKGGICAFVDAEHALDPV-YARKLGVDLQNLLISQPDTGEQALEITDTLVRSGAI 96
Cdd:pfam13401   6 GILVLTGESGTGKTTLLRRLLEQLPEVRDSVVFVDLPSGTSPKdLLRALLRALGLPLSGRLSKEELLAALQQLLLALAVA 85

                          90
                  ....*....|....*
gi 937554937   97 DVLVVDSVAALTPRA 111
Cdd:pfam13401  86 VVLIIDEAQHLSLEA 100
RepA COG3598
RecA-family ATPase [Replication, recombination and repair];
14-118 3.47e-03

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


Pssm-ID: 442817 [Multi-domain]  Cd Length: 313  Bit Score: 36.03  E-value: 3.47e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937  14 LPKGRIIEIYGPESSGKTTLALQ---TIAEAQK------KGGICAFVDAE----------HALDPVYARKLGVDLQNLLI 74
Cdd:COG3598   10 LPEGGVTLLAGPPGTGKSFLALQlaaAVAAGGPwlgrrvPPGKVLYLAAEddrgelrrrlKALGADLGLPFADLDGRLRL 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 937554937  75 SQPDTGEQALEITDTL---VRSGAIDVLVVDSVAALTPRAEIE-GEMG 118
Cdd:COG3598   90 LSLAGDLDDTDDLEALeraIEEEGPDLVVIDPLARVFGGDENDaEEMR 137
Rad51 cd19513
RAD51D recombinase; RAD51 recombinase plays an essential role in DNA repair by homologous ...
 1-107 3.86e-03

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: 35.76  E-value: 3.86e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937   1 GSLSLDIALGiGGLPKGRIIEIYGPESSGKT----TLAL--QTIAEAQKKGGICAFVDAEHALDPV----YARKLGVD-- 68
Cdd:cd19513    4 GSKELDKLLG-GGIETGSITELFGEFRTGKTqlchTLAVtcQLPIDQGGGEGKALYIDTEGTFRPErllaIAERYGLNge 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 937554937  69 --LQNLLISQPDTGEQALEItdtLVRSGAI------DVLVVDSVAAL 107
Cdd:cd19513   83 dvLDNVAYARAYNTDHQMQL---LIQASAMmaesryALLIVDSATAL 126
ABC_UvrA_I cd03270
ATP-binding cassette domain I of the excision repair protein UvrA; Nucleotide excision repair ...
 14-44 3.95e-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: 3.95e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 937554937  14 LPKGRIIEIYGPESSGKTTLALQTI-AEAQKK 44
Cdd:cd03270   18 IPRNKLVVITGVSGSGKSSLAFDTIyAEGQRR 49
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 12-50 6.05e-03

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 35.24  E-value: 6.05e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 937554937  12 GGLPKGRIIEIYGPESSGKTTLALQTIAEaqkkgGICAF 50
Cdd:PRK09302  26 GGLPKGRPTLVSGTAGTGKTLFALQFLVN-----GIKRF 59
FlaH COG2874
Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];
5-36 6.30e-03

Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];


Pssm-ID: 442121  Cd Length: 230  Bit Score: 34.81  E-value: 6.30e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 937554937   5 LDIALGiGGLPKGRIIEIYGPESSGKTTLALQ 36
Cdd:COG2874   10 LDKRLG-GGIPLGSLVLIEGENGTGKSVLSQQ 40
uvra TIGR00630
excinuclease ABC, A subunit; This family is a member of the ABC transporter superfamily of ...
 14-44 8.28e-03

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


Pssm-ID: 273184 [Multi-domain]  Cd Length: 925  Bit Score: 34.99  E-value: 8.28e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 937554937   14 LPKGRIIEIYGPESSGKTTLALQTI-AEAQKK 44
Cdd:TIGR00630  19 IPRDKLVVITGLSGSGKSSLAFDTIyAEGQRR 50
COG1373 COG1373
Predicted ATPase, AAA+ superfamily [General function prediction only];
14-73 9.09e-03

Predicted ATPase, AAA+ superfamily [General function prediction only];


Pssm-ID: 440984 [Multi-domain]  Cd Length: 405  Bit Score: 34.53  E-value: 9.09e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 937554937  14 LPKGRIIEIYGPESSGKTTLALQTIAEAQKkggiCAFVDAEhalDPVYARKLGVDLQNLL 73
Cdd:COG1373   17 LDNRKAVVITGPRQVGKTTLLKQLAKELEN----ILYINLD---DPRLRALAEEDPDDLL 69
NadR3 COG3172
Nicotinamide riboside kinase [Coenzyme transport and metabolism]; Nicotinamide riboside kinase ...
 18-36 9.39e-03

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


Pssm-ID: 442405 [Multi-domain]  Cd Length: 178  Bit Score: 34.41  E-value: 9.39e-03
                         10
                 ....*....|....*....
gi 937554937  18 RIIEIYGPESSGKTTLALQ 36
Cdd:COG3172    9 KKIVLLGAESTGKTTLARA 27
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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