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Conserved domains on  [gi|1025728149|gb|ANC57762|]
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recombinase A, partial [Mesorhizobium sp. NWXJ42]

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
 1-130 2.75e-103

recombinase A; Provisional


The actual alignment was detected with superfamily member PRK09354:

Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 298.25  E-value: 2.75e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   1 EKIVEIETVPTGSLGLDIALGVGGLPRGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEHALDPVYARKLGVDL 80
Cdd:PRK09354   33 DAAMDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDI 112

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1025728149  81 ENLLISQPDTGEQALEICDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGD 130
Cdd:PRK09354  113 DNLLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGD 162
 
Name Accession Description Interval E-value
recA PRK09354
recombinase A; Provisional
 1-130 2.75e-103

recombinase A; Provisional


Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 298.25  E-value: 2.75e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   1 EKIVEIETVPTGSLGLDIALGVGGLPRGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEHALDPVYARKLGVDL 80
Cdd:PRK09354   33 DAAMDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDI 112

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1025728149  81 ENLLISQPDTGEQALEICDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGD 130
Cdd:PRK09354  113 DNLLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGD 162
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
1-130 1.55e-100

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 291.30  E-value: 1.55e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   1 EKIVEIETVPTGSLGLDIALGVGGLPRGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEHALDPVYARKLGVDL 80
Cdd:COG0468    36 KARQDVEVISTGSLALDIALGVGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGIAAFIDAEHALDPEYAKKLGVDI 115

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1025728149  81 ENLLISQPDTGEQALEICDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGD 130
Cdd:COG0468   116 DNLLVSQPDTGEQALEIAETLVRSGAVDLIVVDSVAALVPKAEIEGEMGD 165
RecA pfam00154
recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA ...
 1-130 1.15e-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: 270.81  E-value: 1.15e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   1 EKIVEIETVPTGSLGLDIALGVGGLPRGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEHALDPVYARKLGVDL 80
Cdd:pfam00154  25 EKKLDVETISTGSLALDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDI 104

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1025728149  81 ENLLISQPDTGEQALEICDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGD 130
Cdd:pfam00154 105 DNLLVSQPDTGEQALEIADMLVRSGAIDLIVVDSVAALVPKAEIEGEMGD 154
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 5-130 9.55e-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: 267.50  E-value: 9.55e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   5 EIETVPTGSLGLDIALGVGGLPRGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEHALDPVYARKLGVDLENLL 84
Cdd:cd00983     1 DVEVIPTGSLSLDIALGIGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKLGGTAAFIDAEHALDPEYAKKLGVDIDNLL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1025728149  85 ISQPDTGEQALEICDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGD 130
Cdd:cd00983    81 VSQPDTGEQALEIADTLIRSGAVDLIVVDSVAALVPKAEIEGEMGD 126
tigrfam_recA TIGR02012
protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization ...
 1-130 1.51e-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: 270.01  E-value: 1.51e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   1 EKIVEIETVPTGSLGLDIALGVGGLPRGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEHALDPVYARKLGVDL 80
Cdd:TIGR02012  28 KTVMDVETISTGSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYARKLGVDI 107

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1025728149  81 ENLLISQPDTGEQALEICDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGD 130
Cdd:TIGR02012 108 DNLLVSQPDTGEQALEIAETLVRSGAVDIIVVDSVAALVPKAEIEGEMGD 157
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 27-128 1.16e-07

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: 47.37  E-value: 1.16e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   27 RGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEHALDPVYARKLGVDLENLLISqpDTGEQALEICDTLVRSGA 106
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS--GSGELRLRLALALARKLK 78

                           90       100
                   ....*....|....*....|..
gi 1025728149  107 VDVLVVDSVAALTPRAEIEGEM 128
Cdd:smart00382  79 PDVLILDEITSLLDAEQEALLL 100
 
Name Accession Description Interval E-value
recA PRK09354
recombinase A; Provisional
 1-130 2.75e-103

recombinase A; Provisional


Pssm-ID: 236476 [Multi-domain]  Cd Length: 349  Bit Score: 298.25  E-value: 2.75e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   1 EKIVEIETVPTGSLGLDIALGVGGLPRGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEHALDPVYARKLGVDL 80
Cdd:PRK09354   33 DAAMDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDI 112

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1025728149  81 ENLLISQPDTGEQALEICDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGD 130
Cdd:PRK09354  113 DNLLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGD 162
RecA COG0468
RecA/RadA recombinase [Replication, recombination and repair];
1-130 1.55e-100

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


Pssm-ID: 440236 [Multi-domain]  Cd Length: 351  Bit Score: 291.30  E-value: 1.55e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   1 EKIVEIETVPTGSLGLDIALGVGGLPRGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEHALDPVYARKLGVDL 80
Cdd:COG0468    36 KARQDVEVISTGSLALDIALGVGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGIAAFIDAEHALDPEYAKKLGVDI 115

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1025728149  81 ENLLISQPDTGEQALEICDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGD 130
Cdd:COG0468   116 DNLLVSQPDTGEQALEIAETLVRSGAVDLIVVDSVAALVPKAEIEGEMGD 165
RecA pfam00154
recA bacterial DNA recombination protein; RecA is a DNA-dependent ATPase and functions in DNA ...
 1-130 1.15e-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: 270.81  E-value: 1.15e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   1 EKIVEIETVPTGSLGLDIALGVGGLPRGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEHALDPVYARKLGVDL 80
Cdd:pfam00154  25 EKKLDVETISTGSLALDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDI 104

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1025728149  81 ENLLISQPDTGEQALEICDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGD 130
Cdd:pfam00154 105 DNLLVSQPDTGEQALEIADMLVRSGAIDLIVVDSVAALVPKAEIEGEMGD 154
RecA cd00983
recombinase A; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 5-130 9.55e-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: 267.50  E-value: 9.55e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   5 EIETVPTGSLGLDIALGVGGLPRGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEHALDPVYARKLGVDLENLL 84
Cdd:cd00983     1 DVEVIPTGSLSLDIALGIGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKLGGTAAFIDAEHALDPEYAKKLGVDIDNLL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1025728149  85 ISQPDTGEQALEICDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGD 130
Cdd:cd00983    81 VSQPDTGEQALEIADTLIRSGAVDLIVVDSVAALVPKAEIEGEMGD 126
tigrfam_recA TIGR02012
protein RecA; This model describes orthologs of the recA protein. RecA promotes hybridization ...
 1-130 1.51e-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: 270.01  E-value: 1.51e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   1 EKIVEIETVPTGSLGLDIALGVGGLPRGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEHALDPVYARKLGVDL 80
Cdd:TIGR02012  28 KTVMDVETISTGSLALDLALGVGGLPKGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYARKLGVDI 107

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1025728149  81 ENLLISQPDTGEQALEICDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGD 130
Cdd:TIGR02012 108 DNLLVSQPDTGEQALEIAETLVRSGAVDIIVVDSVAALVPKAEIEGEMGD 157
recA PRK09519
intein-containing recombinase RecA;
6-130 3.01e-65

intein-containing recombinase RecA;


Pssm-ID: 77219 [Multi-domain]  Cd Length: 790  Bit Score: 211.10  E-value: 3.01e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   6 IETVPTGSLGLDIALGVGGLPRGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEHALDPVYARKLGVDLENLLI 85
Cdd:PRK09519   38 ISVIPTGSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDYAKKLGVDTDSLLV 117

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1025728149  86 SQPDTGEQALEICDTLVRSGAVDVLVVDSVAALTPRAEIEGEMGD 130
Cdd:PRK09519  118 SQPDTGEQALEIADMLIRSGALDIVVIDSVAALVPRAELEGEMGD 162
RecA-like cd01393
RecA family; RecA is a bacterial enzyme which has roles in homologous recombination, DNA ...
 28-130 1.03e-31

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: 110.91  E-value: 1.03e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149  28 GRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEHALDPVYAR-----------KLGVDLENLLISQPDTGEQALE 96
Cdd:cd01393     1 GKITEIYGPPGSGKTQLALQLAANALLLGGGVVWIDTEGAFPPSRLVqileaspsselELAEALSRLLYFRPPDTLAHLL 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1025728149  97 ICDTLVRSGA----VDVLVVDSVAALTPRAEIEGEMGD 130
Cdd:cd01393    81 ALDSLPESLFpppnTSLVVVDSVSALFRKAFPRGGDGD 118
archRadB cd01394
archaeal RadB; The archaeal protein RadB shares similarity RadA, the archaeal functional ...
 9-127 1.35e-17

archaeal RadB; The archaeal protein RadB shares similarity RadA, the archaeal functional homologue to the bacterial RecA. The precise function of RadB is unclear.


Pssm-ID: 410882 [Multi-domain]  Cd Length: 216  Bit Score: 75.04  E-value: 1.35e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   9 VPTGSLGLDIALGvGGLPRGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEhALDP-----VYARKLGVDLENL 83
Cdd:cd01394     1 LSTGSKSLDSLLG-GGVERGTITQIYGPPGSGKTNICLQLAVEAAKQGKKVVYIDTE-GLSPerfqqIAGERFESIASNI 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1025728149  84 LISQP-DTGEQALEICDT--LVRSGAVDVLVVDSVAALTpRAEIEGE 127
Cdd:cd01394    79 IVFEPySFDEQGVAIQEAekLLKSDKVDLVVVDSATALY-RLELGDD 124
COG4544 COG4544
Uncharacterized conserved protein [Function unknown];
8-122 5.97e-15

Uncharacterized conserved protein [Function unknown];


Pssm-ID: 443609 [Multi-domain]  Cd Length: 230  Bit Score: 68.42  E-value: 5.97e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   8 TVPTGSLGLDIALGVGGLPRGRIIEIYGPE-SSGKTTLALHTVAEAQKKGGICAFVDAEHALDPVYARKLGVDLENLLIS 86
Cdd:COG4544    28 VLPTGFAALDAALPGGGLPRGALHEILGPApGIGELGLLLPLLARLAQAGGPVLWIAPPYDLYAPGLAAAGLDPERLLLV 107

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1025728149  87 QPDTGEQALEICDTLVRSGAVDVLVVDsVAALTPRA 122
Cdd:COG4544   108 RARRPADALWAAEEALRSGACGAVVAW-LERLDLTA 142
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
9-118 9.20e-14

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


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 64.94  E-value: 9.20e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   9 VPTGSLGLDIALGvGGLPRGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEHALDPV--YARKLGVDLE----- 81
Cdd:COG0467     2 VPTGIPGLDELLG-GGLPRGSSTLLSGPPGTGKTTLALQFLAEGLRRGEKGLYVSFEESPEQLlrRAESLGLDLEeyies 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1025728149  82 -NLLISQPDTGEQALEICDTL------VRSGAVDVLVVDSVAAL 118
Cdd:COG0467    81 gLLRIIDLSPEELGLDLEELLarlreaVEEFGAKRVVIDSLSGL 124
radB PRK09361
DNA repair and recombination protein RadB; Provisional
 5-127 1.48e-12

DNA repair and recombination protein RadB; Provisional


Pssm-ID: 236482 [Multi-domain]  Cd Length: 225  Bit Score: 61.80  E-value: 1.48e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   5 EIETVPTGSLGLDIALGvGGLPRGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEhALDPVYARKLGVD----- 79
Cdd:PRK09361    1 MDERLPTGCKMLDELLG-GGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE-GLSPERFKQIAGEdfeel 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1025728149  80 LENLLISQP-DTGEQALEICDT--LVRSGaVDVLVVDSVAALTpRAEIEGE 127
Cdd:PRK09361   79 LSNIIIFEPsSFEEQSEAIRKAekLAKEN-VGLIVLDSATSLY-RLELEDE 127
recomb_radB TIGR02237
DNA repair and recombination protein RadB; This family consists exclusively of archaeal RadB ...
 16-130 2.51e-12

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


Pssm-ID: 274047 [Multi-domain]  Cd Length: 209  Bit Score: 60.89  E-value: 2.51e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149  16 LDIALGvGGLPRGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEhALDPVYARKLGVD-----LENLLISQP-D 89
Cdd:TIGR02237   1 IDELLG-GGVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTE-GLSPERFKQIAEDrperaLSNFIVFEVfD 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1025728149  90 TGEQALEICDT--LVRSGAVDVLVVDSVAALTpRAEIEGEMGD 130
Cdd:TIGR02237  79 FDEQGVAIQKTskFIDRDSASLVVVDSFTALY-RLELSDDRIS 120
Rad51B cd19493
RAD51B recombinase; RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 17-130 2.58e-11

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: 58.49  E-value: 2.58e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149  17 DIALGvGGLPRGRIIEIYGPESSGKTTLALHTVAEA---QKKGG---ICAFVDAEHAL------------DPVYARK--- 75
Cdd:cd19493     1 DTALA-GGLPLGAITEITGASGSGKTQFALTLASSAampARKGGldgGVLYIDTESKFsaerlaeiaearFPEAFSGfme 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1025728149  76 ----LGVDLENLLISQPDTGEQALEICDTL---VRSGAVDVLVVDSVAALTpRAEIEGEMGD 130
Cdd:cd19493    80 enerAEEMLKRVAVVRVTTLAQLLERLPNLeehILSSGVRLVVIDSIAALV-RREFGGSDGE 140
KaiC-like cd01124
Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most studied in cyanobacteria. ...
 9-118 3.07e-11

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: 58.04  E-value: 3.07e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   9 VPTGSLGLDIALGvGGLPRGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEHALDPVY--ARKLGVDLE----- 81
Cdd:cd01124     1 VKTGIPGLDELLG-GGIPKGSVTLLTGGPGTGKTLFGLQFLYAGAKNGEPGLFFTFEESPERLLrnAKSFGWDFDemede 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1025728149  82 -NLLISQPDTGEQALEICDTL-------VRSGAVDVLVVDSVAAL 118
Cdd:cd01124    80 gKLIIVDAPPTEAGRFSLDELlsrilsiIKSFKAKRVVIDSLSGL 124
DMC1 cd19514
homologous-pairing protein DMC1; DMC1 has a central role in homologous recombination in ...
 9-118 4.26e-09

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: 52.36  E-value: 4.26e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   9 VPTGSLGLDIALGvGGLPRGRIIEIYGPESSGKTTLAlHTVA-------EAQKKGGICAFVDAEHALDP----VYARKLG 77
Cdd:cd19514     1 ISTGSTELDKLLG-GGIESMSITEVFGEFRTGKTQLS-HTLCvtaqlpgSMGGGGGKVAYIDTEGTFRPdrirPIAERFG 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1025728149  78 VD----LENLLISQPDTGEQALEICDTL----VRSGAVDVLVVDSVAAL 118
Cdd:cd19514    79 VDhdavLDNILYARAYTSEHQMELLDYVaakfHEEAVFRLLIIDSIMAL 127
Rad51 pfam08423
Rad51; Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ...
 5-126 8.73e-09

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


Pssm-ID: 462471 [Multi-domain]  Cd Length: 255  Bit Score: 51.92  E-value: 8.73e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   5 EIETVPTGSLGLDIALGvGGLPRGRIIEIYGPESSGKTTLAlHTVA-------EAQKKGGICAFVDAEHALDPV----YA 73
Cdd:pfam08423  15 ELIQITTGSKELDKLLG-GGIETGSITEIFGEFRTGKTQLC-HTLCvtcqlplEMGGGEGKALYIDTEGTFRPErlvaIA 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1025728149  74 RKLGVD----LENLLISQPDTGEQALEIcdtLVRSGA------VDVLVVDSVAALTpRAEIEG 126
Cdd:pfam08423  93 ERYGLDpedvLDNVAYARAYNSEHQMQL---LQQAAAmmsesrFALLIVDSATALY-RTDFSG 151
ATPase pfam06745
KaiC; This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and ...
 9-119 1.10e-08

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


Pssm-ID: 429095 [Multi-domain]  Cd Length: 231  Bit Score: 51.09  E-value: 1.10e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   9 VPTGSLGLDIALGvGGLPRGRIIEIYGPESSGKTTLALH-TVAEAQKKGGICAFVDA-EHALDPVY-ARKLGVDLENLL- 84
Cdd:pfam06745   1 VKTGIPGLDEILK-GGFPEGRVVLITGGPGTGKTIFGLQfLYNGALKYGEPGVFVTLeEPPEDLREnARSFGWDLEKLEe 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1025728149  85 --------ISQPDTGEQALEICDTL----------VRSGAVDVLVVDSVAALT 119
Cdd:pfam06745  80 egklaiidASTSGIGIAEVEDRFDLeelierlreaIREIGAKRVVIDSITTLF 132
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 27-128 1.16e-07

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: 47.37  E-value: 1.16e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   27 RGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEHALDPVYARKLGVDLENLLISqpDTGEQALEICDTLVRSGA 106
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS--GSGELRLRLALALARKLK 78

                           90       100
                   ....*....|....*....|..
gi 1025728149  107 VDVLVVDSVAALTPRAEIEGEM 128
Cdd:smart00382  79 PDVLILDEITSLLDAEQEALLL 100
Rad51_DMC1_archRadA cd01123
recombinase Rad51, DMC1, and archaeal RadA; This group of recombinases includes the eukaryotic ...
 9-118 1.48e-07

recombinase Rad51, DMC1, and archaeal RadA; This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal protein RadA. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .


Pssm-ID: 410868 [Multi-domain]  Cd Length: 234  Bit Score: 48.30  E-value: 1.48e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   9 VPTGSLGLDIALGvGGLPRGRIIEIYGPESSGKTTLAlHTVA-------EAQKKGGICAFVDAEHALDPV----YARKLG 77
Cdd:cd01123     1 ITTGSKELDKLLG-GGIETGSITEMFGEFRTGKTQLC-HTLAvtcqlpiDRGGGEGKAIYIDTEGTFRPErlraIAQRFG 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1025728149  78 VD----LENLLISQPDTGEQALEICD---TLVRSGAVDVLVVDSVAAL 118
Cdd:cd01123    79 LDpddvLDNVAYARAFNSDHQTQLLDqaaAMMVESRFKLLIVDSATAL 126
recomb_DMC1 TIGR02238
meiotic recombinase Dmc1; This model describes DMC1, a subfamily of a larger family of DNA ...
 9-118 8.20e-07

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: 46.31  E-value: 8.20e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   9 VPTGSLGLDIALGvGGLPRGRIIEIYGPESSGKTTLAlHTVA-------EAQKKGGICAFVDAEHALDP----VYARKLG 77
Cdd:TIGR02238  78 ITTGSQALDGILG-GGIESMSITEVFGEFRCGKTQLS-HTLCvtaqlprEMGGGNGKVAYIDTEGTFRPdrirAIAERFG 155

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1025728149  78 VD----LENLLISQPDTGEQALE---ICDTLVRSGAVDVLVVDSVAAL 118
Cdd:TIGR02238 156 VDpdavLDNILYARAYTSEHQMElldYLAAKFSEEPFRLLIVDSIMAL 203
KaiC-like_N cd19488
N-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 11-62 8.30e-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: 46.19  E-value: 8.30e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1025728149  11 TGSLGLDIALGvGGLPRGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFV 62
Cdd:cd19488     3 TGIPGLDDILR-GGLPPRRLYLVEGAPGTGKTTLALQFLLEGAANGETGLYI 53
KaiC_C cd19484
C-terminal domain of Circadian Clock Protein KaiC; KaiC is a circadian clock protein, most ...
 9-119 1.18e-06

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: 45.40  E-value: 1.18e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   9 VPTGSLGLDIALGVGGLPRGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEHALDPVY--ARKLGVDLENLLIS 86
Cdd:cd19484     1 ISTGIPRLDAMLGGGGFFRGSSILVSGATGTGKTLLAASFADAACRRGERCLYFAFEESPAQLIrnAKSIGIDLEQMERK 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1025728149  87 Q---------PDTG-EQALEICDTLVRSGAVDVLVVDSVAALT 119
Cdd:cd19484    81 GllkiicarpELYGlEDHLIIIKSEINEFKPSRVIVDPLSALA 123
XRCC3 cd19491
XRCC3 recombinase; XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells ...
 16-118 1.20e-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: 45.75  E-value: 1.20e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149  16 LDIALGvGGLPRGRIIEIYGPESSGKTTLALHTVAEAQ------KKGGICAFVDAEHAL-------------DPVYARKL 76
Cdd:cd19491     1 LDELLG-GGIPVGGITEIAGESGAGKTQLCLQLALTVQlprelgGLGGGAVYICTESSFpskrlqqlasslpKRYHLEKA 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1025728149  77 GVDLENLLISQ-PDTgeQALEICDT-----LVRSGAVDVLVVDSVAAL 118
Cdd:cd19491    80 KNFLDNIFVEHvADL--ETLEHCLNyqlpaLLERGPIRLVVIDSIAAL 125
PLN03187 PLN03187
meiotic recombination protein DMC1 homolog; Provisional
 11-118 4.15e-06

meiotic recombination protein DMC1 homolog; Provisional


Pssm-ID: 215620 [Multi-domain]  Cd Length: 344  Bit Score: 44.38  E-value: 4.15e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149  11 TGSLGLDIALGvGGLPRGRIIEIYGPESSGKTTLAlHTVAEA----QKKGGIC---AFVDAEHALDP----VYARKLGVD 79
Cdd:PLN03187  110 TGSQALDELLG-GGIETRCITEAFGEFRSGKTQLA-HTLCVTtqlpTEMGGGNgkvAYIDTEGTFRPdrivPIAERFGMD 187

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1025728149  80 ----LENLLISQPDTGEQ---ALEICDTLVRSGAVDVLVVDSVAAL 118
Cdd:PLN03187  188 adavLDNIIYARAYTYEHqynLLLGLAAKMAEEPFRLLIVDSVIAL 233
PLN03186 PLN03186
DNA repair protein RAD51 homolog; Provisional
 5-126 6.05e-06

DNA repair protein RAD51 homolog; Provisional


Pssm-ID: 178728 [Multi-domain]  Cd Length: 342  Bit Score: 43.95  E-value: 6.05e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   5 EIETVPTGSLGLDIALGvGGLPRGRIIEIYGPESSGKTTLAlHTVA-EAQ---KKG---GICAFVDAEHALDP----VYA 73
Cdd:PLN03186  101 EIIQITTGSRELDKILE-GGIETGSITEIYGEFRTGKTQLC-HTLCvTCQlplDQGggeGKAMYIDTEGTFRPqrliQIA 178

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1025728149  74 RKLGVD----LENLLISQPDTGEQALEIcdtLVRSGA------VDVLVVDSVAALTpRAEIEG 126
Cdd:PLN03186  179 ERFGLNgadvLENVAYARAYNTDHQSEL---LLEAASmmaetrFALMIVDSATALY-RTEFSG 237
RadA_SMS_N cd01121
bacterial RadA DNA repair protein; Sms or bacterial RadA is a DNA repair protein that plays a ...
 2-115 6.32e-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: 43.67  E-value: 6.32e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   2 KIVEIETVPTGSLGLDIALGvGGLPRGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEHALDPV--YARKLGVD 79
Cdd:cd01121    57 EAEEEERISTGIGELDRVLG-GGLVPGSVVLIGGDPGIGKSTLLLQVAARLAQRGGKVLYVSGEESLSQIklRAERLGLG 135

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1025728149  80 LENLLIsqpdTGEQALE-ICDTLVRSGAvDVLVVDSV 115
Cdd:cd01121   136 SDNLYL----LAETNLEaILAEIEELKP-SLVVIDSI 167
PTZ00035 PTZ00035
Rad51 protein; Provisional
 11-118 8.58e-06

Rad51 protein; Provisional


Pssm-ID: 185407 [Multi-domain]  Cd Length: 337  Bit Score: 43.45  E-value: 8.58e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149  11 TGSLGLDIALGvGGLPRGRIIEIYGPESSGKTTLAlHTVA-------EAQKKGGICAFVDAEHALDP----VYARKLGVD 79
Cdd:PTZ00035  102 TGSTQLDKLLG-GGIETGSITELFGEFRTGKTQLC-HTLCvtcqlpiEQGGGEGKVLYIDTEGTFRPerivQIAERFGLD 179

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1025728149  80 ----LENLLISQPDTGEQALEIcdtLVRSGAVDV------LVVDSVAAL 118
Cdd:PTZ00035  180 pedvLDNIAYARAYNHEHQMQL---LSQAAAKMAeerfalLIVDSATAL 225
KaiC-like_C cd19487
C-terminal domain of KaiC family protein; uncharacterized subfamily; KaiC is a circadian clock ...
 9-116 1.46e-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: 42.67  E-value: 1.46e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   9 VPTGSLGLDIALGvGGLPRGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEHALDPVYAR--KLGVDLE----- 81
Cdd:cd19487     1 VSSGVPELDELLG-GGLERGTSTLLIGPAGVGKSTLALQFAKAAAARGERSVLFSFDESIGTLFERseALGIDLRamvek 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1025728149  82 -NLLISQPDTGE----QALEICDTLVRSGAVDVLVVDSVA 116
Cdd:cd19487    80 gLLSIEQIDPAElspgEFAQRVRTSVEQEDARVVVIDSLN 119
recomb_RAD51 TIGR02239
DNA repair protein RAD51; This eukaryotic sequence family consists of RAD51, a protein ...
 5-118 2.21e-05

DNA repair protein RAD51; This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).


Pssm-ID: 274048 [Multi-domain]  Cd Length: 316  Bit Score: 42.40  E-value: 2.21e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   5 EIETVPTGSLGLDIALGvGGLPRGRIIEIYGPESSGKTTLAlHTVA-----EAQKKG--GICAFVDAEHALDPV----YA 73
Cdd:TIGR02239  74 EVIQLTTGSKELDKLLG-GGIETGSITEIFGEFRTGKTQLC-HTLAvtcqlPIDQGGgeGKALYIDTEGTFRPErllaIA 151

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1025728149  74 RKLGVD----LENLLISQPDTGEQALEIcdtLVRSGAV------DVLVVDSVAAL 118
Cdd:TIGR02239 152 ERYGLNpedvLDNVAYARAYNTDHQLQL---LQQAAAMmsesrfALLIVDSATAL 203
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 7-119 3.43e-05

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 41.79  E-value: 3.43e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149   7 ETVPTGSLGLDIALGvGGLPRGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEHALDPVY--ARKLGVDLEN-- 82
Cdd:PRK09302  253 ERISSGVPDLDEMLG-GGFFRGSIILVSGATGTGKTLLASKFAEAACRRGERCLLFAFEESRAQLIrnARSWGIDLEKme 331

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1025728149  83 ----LLI--SQPD-TG-EQALEICDTLVRSGAVDVLVVDSVAALT 119
Cdd:PRK09302  332 ekglLKIicARPEsYGlEDHLIIIKREIEEFKPSRVAIDPLSALA 376
Rad51 cd19513
RAD51D recombinase; RAD51 recombinase plays an essential role in DNA repair by homologous ...
 11-118 8.85e-05

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


Pssm-ID: 410921 [Multi-domain]  Cd Length: 235  Bit Score: 40.38  E-value: 8.85e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149  11 TGSLGLDIALGvGGLPRGRIIEIYGPESSGKTTLAlHTVA-------EAQKKGGICAFVDAEHALDPV----YARKLGVD 79
Cdd:cd19513     3 TGSKELDKLLG-GGIETGSITELFGEFRTGKTQLC-HTLAvtcqlpiDQGGGEGKALYIDTEGTFRPErllaIAERYGLN 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1025728149  80 ----LENLLISQPDTGEQALEIcdtLVRSGAV------DVLVVDSVAAL 118
Cdd:cd19513    81 gedvLDNVAYARAYNTDHQMQL---LIQASAMmaesryALLIVDSATAL 126
PRK09302 PRK09302
circadian clock protein KaiC; Reviewed
 5-61 9.42e-05

circadian clock protein KaiC; Reviewed


Pssm-ID: 236461 [Multi-domain]  Cd Length: 509  Bit Score: 40.63  E-value: 9.42e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1025728149   5 EIETVPTGSLGLDIALGvGGLPRGRIIEIYGPESSGKTTLALHTVAEaqkkgGICAF 61
Cdd:PRK09302    9 GIEKLPTGIEGFDDITH-GGLPKGRPTLVSGTAGTGKTLFALQFLVN-----GIKRF 59
AAA_24 pfam13479
AAA domain; This AAA domain is found in a wide variety of presumed phage proteins.
 27-115 2.22e-04

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


Pssm-ID: 433243  Cd Length: 199  Bit Score: 39.23  E-value: 2.22e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149  27 RGRIIEIYGPESSGKTTLAlhtvAEAQKKggicAFVDAEHALDPVYARKLGVdlenllISQPDTGEQALEICDTLVRSGA 106
Cdd:pfam13479   1 KKLKILIYGPSGIGKTTFA----KTLPKP----LFLDTEKGSKALDGDRFPD------IVIRDSWQDFLDAIDELTAAEL 66

                          90
                  ....*....|.
gi 1025728149 107 V--DVLVVDSV 115
Cdd:pfam13479  67 AdyKTIVIDTV 77
archRadA cd19515
archaeal recombinase Rad51/RadA; This group includes the archaeal protein RadA which is a ...
 11-126 2.39e-04

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: 39.27  E-value: 2.39e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149  11 TGSLGLDIALGvGGLPRGRIIEIYGPESSGKTTLAlHTVA----EAQKKGGI---CAFVDAEHALDP----VYARKLGVD 79
Cdd:cd19515     3 TGSKELDKLLG-GGIETQAITEVFGEFGSGKTQLC-HQLAvnvqLPPEEGGLngkAVYIDTENTFRPerimQMAKALGLD 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1025728149  80 LENLL-----ISQPDTGEQAL---EICDTLVRSGAVDVLVVDSVAALTpRAEIEG 126
Cdd:cd19515    81 PDEVLdniyvARAYNSNHQMLlveKAEDLIKEGNNIKLLIVDSLTSHF-RAEYVG 134
XRCC2 cd19490
XRCC2 recombinase; XRCC2 (X-ray repair complementing defective repair in Chinese hamster cells ...
 28-71 3.26e-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: 38.87  E-value: 3.26e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1025728149  28 GRIIEIYGPESSGKTTLALHTVAEA---QKKGGICA--------FVDAEHALDPV 71
Cdd:cd19490     1 GDVIEITGPSGSGKTELLYHLAARCilpSSWGGVPLggleaavvFIDTDGRFDIL 55
Rad51D cd19489
RAD51D recombinase; RAD51D recombinase, a RAD51 paralog, plays an important role in DNA repair ...
 23-53 5.07e-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: 38.00  E-value: 5.07e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1025728149  23 GGLPRGRIIEIYGPESSGKT----TLALHTVAEAQ 53
Cdd:cd19489     2 GGLRTGEITELVGESSSGKTqlclTAAANVASRSG 36
radA PRK04301
DNA repair and recombination protein RadA; Validated
 11-126 5.37e-04

DNA repair and recombination protein RadA; Validated


Pssm-ID: 235273 [Multi-domain]  Cd Length: 317  Bit Score: 38.32  E-value: 5.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149  11 TGSLGLDIALGvGGLPRGRIIEIYGPESSGKTTLAlH----TVAEAQKKGGI---CAFVDAE--------------HALD 69
Cdd:PRK04301   86 TGSKELDELLG-GGIETQSITEFYGEFGSGKTQIC-HqlavNVQLPEEKGGLegkAVYIDTEgtfrperieqmaeaLGLD 163

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1025728149  70 P-------VYARKLGVDLENLLIsqpdtgEQALEICDtlvRSGAVDVLVVDSVAALTpRAEIEG 126
Cdd:PRK04301  164 PdevldniHVARAYNSDHQMLLA------EKAEELIK---EGENIKLVIVDSLTAHF-RAEYVG 217
AAA_22 pfam13401
AAA domain;
29-122 1.45e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 36.17  E-value: 1.45e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149  29 RIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDAEH-----ALDPVYARKLGVDLENllisqPDTGEQALE-ICDTLV 102
Cdd:pfam13401   6 GILVLTGESGTGKTTLLRRLLEQLPEVRDSVVFVDLPSgtspkDLLRALLRALGLPLSG-----RLSKEELLAaLQQLLL 80

                          90       100
                  ....*....|....*....|
gi 1025728149 103 RSGAVDVLVVDSVAALTPRA 122
Cdd:pfam13401  81 ALAVAVVLIIDEAQHLSLEA 100
ATPase_2 pfam01637
ATPase domain predominantly from Archaea; This family contain a conserved P-loop motif that is ...
 30-64 2.24e-03

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: 36.14  E-value: 2.24e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1025728149  30 IIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDA 64
Cdd:pfam01637  22 IYVIYGPEGCGKTALLRESIENLLDLGYYVIYYDP 56
FlaH COG2874
Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];
7-45 2.41e-03

Archaellum biogenesis ATPase ArlH/FlaH [Cell motility];


Pssm-ID: 442121  Cd Length: 230  Bit Score: 36.35  E-value: 2.41e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1025728149   7 ETVPTGSLGLDIALGvGGLPRGRIIEIYGPESSGKTTLA 45
Cdd:COG2874     1 EIISTGNDELDKRLG-GGIPLGSLVLIEGENGTGKSVLS 38
RepA COG3598
RecA-family ATPase [Replication, recombination and repair];
25-129 2.70e-03

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


Pssm-ID: 442817 [Multi-domain]  Cd Length: 313  Bit Score: 36.42  E-value: 2.70e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149  25 LPRGRIIEIYGPESSGKTTLALH---TVAEAQK------KGGICAFVDAE----------HALDPVYARKLGVDLENLLI 85
Cdd:COG3598    10 LPEGGVTLLAGPPGTGKSFLALQlaaAVAAGGPwlgrrvPPGKVLYLAAEddrgelrrrlKALGADLGLPFADLDGRLRL 89

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1025728149  86 SQPDTGEQALEICDTL---VRSGAVDVLVVDSVAALTPRAEIE-GEMG 129
Cdd:COG3598    90 LSLAGDLDDTDDLEALeraIEEEGPDLVVIDPLARVFGGDENDaEEMR 137
NadR3 COG3172
Nicotinamide riboside kinase [Coenzyme transport and metabolism]; Nicotinamide riboside kinase ...
 29-100 3.40e-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: 35.57  E-value: 3.40e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1025728149  29 RIIEIYGPESSGKTTLA------LHT--VAEA-----QKKGGICAFVDaehaLDPVYARKLgvDLENLLISQPDtgeqAL 95
Cdd:COG3172     9 KKIVLLGAESTGKTTLAralaahYNTpwVPEYgreylEEKGRALTYDD----LLAIARGQL--ALEDAAAKRAN----KL 78


                  ....*
gi 1025728149  96 EICDT 100
Cdd:COG3172    79 LFCDT 83
Grc3 COG1341
Polynucleotide 5'-kinase, involved in rRNA processing [Translation, ribosomal structure and ...
 26-64 9.03e-03

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


Pssm-ID: 440952  Cd Length: 353  Bit Score: 34.61  E-value: 9.03e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1025728149  26 PRGRIIEIYGPESSGKTTLALHTVAEAQKKGGICAFVDA 64
Cdd:COG1341    33 SGPGRIMVLGPVDSGKSTLTTLLANKLLAEGLKVAIIDA 71
 
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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